From 31b940a85f0b0f1f45ad7bd379e8cb680305b321 Mon Sep 17 00:00:00 2001 From: root Date: Thu, 26 Sep 2024 16:36:12 +0800 Subject: [PATCH] remove --- script/S112D/mol.gro | 38 ----- script/S112D/mol.itp | 350 ------------------------------------------ script/S112D/mol.mol2 | 80 ---------- script/S112D/mol.top | 14 -- 4 files changed, 482 deletions(-) delete mode 100644 script/S112D/mol.gro delete mode 100644 script/S112D/mol.itp delete mode 100644 script/S112D/mol.mol2 delete mode 100644 script/S112D/mol.top diff --git a/script/S112D/mol.gro b/script/S112D/mol.gro deleted file mode 100644 index 35af87e..0000000 --- a/script/S112D/mol.gro +++ /dev/null @@ -1,38 +0,0 @@ -Conformer3D_COMPOUND_CID_2733285 - 35 - 1MOL N 1 -0.539 0.212 -0.953 - 1MOL N 2 -1.066 0.319 -0.942 - 1MOL N 3 -1.349 0.194 -1.089 - 1MOL C 4 -0.707 0.366 -0.976 - 1MOL C 5 -0.661 0.237 -0.951 - 1MOL C 6 -0.753 0.135 -0.922 - 1MOL C 7 -0.889 0.163 -0.919 - 1MOL C 8 -0.935 0.292 -0.945 - 1MOL C 9 -0.844 0.394 -0.973 - 1MOL C 10 -1.141 0.309 -1.056 - 1MOL C 11 -1.207 0.178 -1.092 - 1MOL C 12 -1.163 0.136 -1.232 - 1MOL C 13 -1.044 0.042 -1.222 - 1MOL C 14 -0.921 0.109 -1.282 - 1MOL C 15 -1.074 -0.087 -1.298 - 1MOL O 16 -0.454 0.307 -0.982 - 1MOL O 17 -0.496 0.091 -0.927 - 1MOL O 18 -1.154 0.405 -1.129 - 1MOL H01 19 -0.636 0.446 -0.999 - 1MOL H02 20 -0.717 0.034 -0.902 - 1MOL H03 21 -0.960 0.084 -0.897 - 1MOL H04 22 -0.879 0.495 -0.994 - 1MOL H05 23 -1.177 0.101 -1.020 - 1MOL H06 24 -1.135 0.224 -1.290 - 1MOL H07 25 -1.246 0.085 -1.282 - 1MOL H08 26 -1.025 0.018 -1.118 - 1MOL H09 27 -0.837 0.039 -1.280 - 1MOL H10 28 -0.942 0.137 -1.385 - 1MOL H11 29 -0.896 0.198 -1.224 - 1MOL H12 30 -1.162 -0.071 -1.362 - 1MOL H13 31 -0.989 -0.113 -1.361 - 1MOL H14 32 -1.094 -0.167 -1.228 - 1MOL H 33 -1.111 0.347 -0.855 - 1MOL H 34 -1.377 0.233 -0.999 - 1MOL H 35 -1.377 0.264 -1.158 - 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/script/S112D/mol.itp b/script/S112D/mol.itp deleted file mode 100644 index 553c47a..0000000 --- a/script/S112D/mol.itp +++ /dev/null @@ -1,350 +0,0 @@ -; Created by Sobtop (http://sobereva.com/soft/sobtop) Version 1.0(dev5) on 2024-09-19 - -[ atomtypes ] -; name at.num mass charge ptype sigma (nm) epsilon (kJ/mol) -no 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01 -n 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01 -n3 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01 -ca 6 12.010736 0.000000 A 3.399670E-01 3.598240E-01 -c 6 12.010736 0.000000 A 3.399670E-01 3.598240E-01 -c3 6 12.010736 0.000000 A 3.399670E-01 4.577296E-01 -o 8 15.999405 0.000000 A 2.959922E-01 8.786400E-01 -ha 1 1.007941 0.000000 A 2.599642E-01 6.276000E-02 -h1 1 1.007941 0.000000 A 2.471353E-01 6.568880E-02 -hc 1 1.007941 0.000000 A 2.649533E-01 6.568880E-02 -hn 1 1.007941 0.000000 A 1.069078E-01 6.568880E-02 - -[ moleculetype ] -; name nrexcl -Conformer3D_COMPOUND_CID_2733285 3 - -; Atomic charges are those loaded from .mol2 file -[ atoms ] -; Index type residue resname atom cgnr charge mass - 1 no 1 MOL N 1 0.00000000 14.006703 - 2 n 1 MOL N 2 0.00000000 14.006703 - 3 n3 1 MOL N 3 0.00000000 14.006703 - 4 ca 1 MOL C 4 0.00000000 12.010736 - 5 ca 1 MOL C 5 0.00000000 12.010736 - 6 ca 1 MOL C 6 0.00000000 12.010736 - 7 ca 1 MOL C 7 0.00000000 12.010736 - 8 ca 1 MOL C 8 0.00000000 12.010736 - 9 ca 1 MOL C 9 0.00000000 12.010736 - 10 c 1 MOL C 10 0.00000000 12.010736 - 11 c3 1 MOL C 11 0.00000000 12.010736 - 12 c3 1 MOL C 12 0.00000000 12.010736 - 13 c3 1 MOL C 13 0.00000000 12.010736 - 14 c3 1 MOL C 14 0.00000000 12.010736 - 15 c3 1 MOL C 15 0.00000000 12.010736 - 16 o 1 MOL O 16 0.00000000 15.999405 - 17 o 1 MOL O 17 0.00000000 15.999405 - 18 o 1 MOL O 18 0.00000000 15.999405 - 19 ha 1 MOL H01 19 0.00000000 1.007941 - 20 ha 1 MOL H02 20 0.00000000 1.007941 - 21 ha 1 MOL H03 21 0.00000000 1.007941 - 22 ha 1 MOL H04 22 0.00000000 1.007941 - 23 h1 1 MOL H05 23 0.00000000 1.007941 - 24 hc 1 MOL H06 24 0.00000000 1.007941 - 25 hc 1 MOL H07 25 0.00000000 1.007941 - 26 hc 1 MOL H08 26 0.00000000 1.007941 - 27 hc 1 MOL H09 27 0.00000000 1.007941 - 28 hc 1 MOL H10 28 0.00000000 1.007941 - 29 hc 1 MOL H11 29 0.00000000 1.007941 - 30 hc 1 MOL H12 30 0.00000000 1.007941 - 31 hc 1 MOL H13 31 0.00000000 1.007941 - 32 hc 1 MOL H14 32 0.00000000 1.007941 - 33 hn 1 MOL H 33 0.00000000 1.007941 - 34 hn 1 MOL H 34 0.00000000 1.007941 - 35 hn 1 MOL H 35 0.00000000 1.007941 - -[ bonds ] -; atom_i atom_j functype r0 (nm) k (kJ/mol/nm^2) - 1 5 1 0.146890 2.691986E+05 ; N-C, prebuilt ca-no - 1 16 1 0.122600 6.207382E+05 ; N-O, prebuilt no-o - 1 17 1 0.122600 6.207382E+05 ; N-O, prebuilt no-o - 2 8 1 0.141210 3.214986E+05 ; N-C, prebuilt ca-n - 2 10 1 0.137890 3.578157E+05 ; N-C, prebuilt c-n - 2 33 1 0.101290 3.373978E+05 ; N-H, prebuilt hn-n - 3 11 1 0.146470 2.727131E+05 ; N-C, prebuilt c3-n3 - 3 34 1 0.101900 3.283603E+05 ; N-H, prebuilt hn-n3 - 3 35 1 0.101900 3.283603E+05 ; N-H, prebuilt hn-n3 - 4 5 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 4 9 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 4 19 1 0.108600 2.893654E+05 ; C-H01, prebuilt ca-ha - 5 6 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 6 7 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 6 20 1 0.108600 2.893654E+05 ; C-H02, prebuilt ca-ha - 7 8 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 7 21 1 0.108600 2.893654E+05 ; C-H03, prebuilt ca-ha - 8 9 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 9 22 1 0.108600 2.893654E+05 ; C-H04, prebuilt ca-ha - 10 11 1 0.152410 2.619184E+05 ; C-C, prebuilt c-c3 - 10 18 1 0.121830 5.336274E+05 ; C-O, prebuilt c-o - 11 12 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 11 23 1 0.109690 2.766461E+05 ; C-H05, prebuilt c3-h1 - 12 13 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 12 24 1 0.109690 2.766461E+05 ; C-H06, prebuilt c3-hc - 12 25 1 0.109690 2.766461E+05 ; C-H07, prebuilt c3-hc - 13 14 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 13 15 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 13 26 1 0.109690 2.766461E+05 ; C-H08, prebuilt c3-hc - 14 27 1 0.109690 2.766461E+05 ; C-H09, prebuilt c3-hc - 14 28 1 0.109690 2.766461E+05 ; C-H10, prebuilt c3-hc - 14 29 1 0.109690 2.766461E+05 ; C-H11, prebuilt c3-hc - 15 30 1 0.109690 2.766461E+05 ; C-H12, prebuilt c3-hc - 15 31 1 0.109690 2.766461E+05 ; C-H13, prebuilt c3-hc - 15 32 1 0.109690 2.766461E+05 ; C-H14, prebuilt c3-hc - -[ angles ] -; atom_i atom_j atom_k functype a0 (Deg.) k (kJ/mol/rad^2) - 5 1 16 1 117.760 5.748816E+02 ; C-N-O, prebuilt ca-no-o - 5 1 17 1 117.760 5.748816E+02 ; C-N-O, prebuilt ca-no-o - 16 1 17 1 125.080 6.418256E+02 ; O-N-O, prebuilt o-no-o - 8 2 10 1 123.710 5.338784E+02 ; C-N-C, prebuilt c-n-ca - 8 2 33 1 116.000 3.983168E+02 ; C-N-H, prebuilt ca-n-hn - 10 2 33 1 117.550 4.041744E+02 ; C-N-H, prebuilt c-n-hn - 11 3 34 1 109.290 3.966432E+02 ; C-N-H, prebuilt c3-n3-hn - 11 3 35 1 109.290 3.966432E+02 ; C-N-H, prebuilt c3-n3-hn - 34 3 35 1 106.400 3.464352E+02 ; H-N-H, prebuilt hn-n3-hn - 5 4 9 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 5 4 19 1 119.880 4.033376E+02 ; C-C-H01, prebuilt ca-ca-ha - 9 4 19 1 119.880 4.033376E+02 ; C-C-H01, prebuilt ca-ca-ha - 1 5 4 1 119.010 5.589824E+02 ; N-C-C, prebuilt ca-ca-no - 1 5 6 1 119.010 5.589824E+02 ; N-C-C, prebuilt ca-ca-no - 4 5 6 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 5 6 7 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 5 6 20 1 119.880 4.033376E+02 ; C-C-H02, prebuilt ca-ca-ha - 7 6 20 1 119.880 4.033376E+02 ; C-C-H02, prebuilt ca-ca-ha - 6 7 8 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 6 7 21 1 119.880 4.033376E+02 ; C-C-H03, prebuilt ca-ca-ha - 8 7 21 1 119.880 4.033376E+02 ; C-C-H03, prebuilt ca-ca-ha - 2 8 7 1 120.190 5.681872E+02 ; N-C-C, prebuilt ca-ca-n - 2 8 9 1 120.190 5.681872E+02 ; N-C-C, prebuilt ca-ca-n - 7 8 9 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 4 9 8 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 4 9 22 1 119.880 4.033376E+02 ; C-C-H04, prebuilt ca-ca-ha - 8 9 22 1 119.880 4.033376E+02 ; C-C-H04, prebuilt ca-ca-ha - 2 10 11 1 115.180 5.589824E+02 ; N-C-C, prebuilt c3-c-n - 2 10 18 1 123.050 6.209056E+02 ; N-C-O, prebuilt n-c-o - 11 10 18 1 123.200 5.640032E+02 ; C-C-O, prebuilt c3-c-o - 3 11 10 1 111.140 5.547984E+02 ; N-C-C, prebuilt c-c3-n3 - 3 11 12 1 111.040 5.522880E+02 ; N-C-C, prebuilt c3-c3-n3 - 3 11 23 1 109.880 4.142160E+02 ; N-C-H05, prebuilt h1-c3-n3 - 10 11 12 1 111.040 5.296944E+02 ; C-C-C, prebuilt c-c3-c3 - 10 11 23 1 108.220 3.932960E+02 ; C-C-H05, prebuilt c-c3-h1 - 12 11 23 1 109.560 3.882752E+02 ; C-C-H05, prebuilt c3-c3-h1 - 11 12 13 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 11 12 24 1 109.800 3.874384E+02 ; C-C-H06, prebuilt c3-c3-hc - 11 12 25 1 109.800 3.874384E+02 ; C-C-H07, prebuilt c3-c3-hc - 13 12 24 1 109.800 3.874384E+02 ; C-C-H06, prebuilt c3-c3-hc - 13 12 25 1 109.800 3.874384E+02 ; C-C-H07, prebuilt c3-c3-hc - 24 12 25 1 107.580 3.296992E+02 ; H06-C-H07, prebuilt hc-c3-hc - 12 13 14 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 12 13 15 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 12 13 26 1 109.800 3.874384E+02 ; C-C-H08, prebuilt c3-c3-hc - 14 13 15 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 14 13 26 1 109.800 3.874384E+02 ; C-C-H08, prebuilt c3-c3-hc - 15 13 26 1 109.800 3.874384E+02 ; C-C-H08, prebuilt c3-c3-hc - 13 14 27 1 109.800 3.874384E+02 ; C-C-H09, prebuilt c3-c3-hc - 13 14 28 1 109.800 3.874384E+02 ; C-C-H10, prebuilt c3-c3-hc - 13 14 29 1 109.800 3.874384E+02 ; C-C-H11, prebuilt c3-c3-hc - 27 14 28 1 107.580 3.296992E+02 ; H09-C-H10, prebuilt hc-c3-hc - 27 14 29 1 107.580 3.296992E+02 ; H09-C-H11, prebuilt hc-c3-hc - 28 14 29 1 107.580 3.296992E+02 ; H10-C-H11, prebuilt hc-c3-hc - 13 15 30 1 109.800 3.874384E+02 ; C-C-H12, prebuilt c3-c3-hc - 13 15 31 1 109.800 3.874384E+02 ; C-C-H13, prebuilt c3-c3-hc - 13 15 32 1 109.800 3.874384E+02 ; C-C-H14, prebuilt c3-c3-hc - 30 15 31 1 107.580 3.296992E+02 ; H12-C-H13, prebuilt hc-c3-hc - 30 15 32 1 107.580 3.296992E+02 ; H12-C-H14, prebuilt hc-c3-hc - 31 15 32 1 107.580 3.296992E+02 ; H13-C-H14, prebuilt hc-c3-hc - -[ dihedrals ] ; propers -; atom_i atom_j atom_k atom_l functype d0 (Deg.) k (kJ/mol/rad^2) ; Case of functype=2 -; atom_i atom_j atom_k atom_l functype phase (Deg.) kd (kJ/mol) pn ; Case of functype=9 - 1 5 4 9 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 1 5 4 19 9 180.000 15.16700 2 ; N-C-C-H01, prebuilt X-ca-ca-X - 1 5 6 7 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 1 5 6 20 9 180.000 15.16700 2 ; N-C-C-H02, prebuilt X-ca-ca-X - 2 8 7 6 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 2 8 7 21 9 180.000 15.16700 2 ; N-C-C-H03, prebuilt X-ca-ca-X - 2 8 9 4 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 2 8 9 22 9 180.000 15.16700 2 ; N-C-C-H04, prebuilt X-ca-ca-X - 2 10 11 3 9 180.000 0.00000 2 ; N-C-C-N, prebuilt X-c-c3-X - 2 10 11 12 9 0.000 0.41840 4 ; N-C-C-C, prebuilt c3-c3-c-n - 2 10 11 12 9 0.000 0.29288 2 ; N-C-C-C, prebuilt c3-c3-c-n - 2 10 11 23 9 180.000 0.00000 2 ; N-C-C-H05, prebuilt X-c-c3-X - 3 11 10 18 9 180.000 0.00000 2 ; N-C-C-O, prebuilt X-c-c3-X - 3 11 12 13 9 0.000 0.65084 3 ; N-C-C-C, prebuilt X-c3-c3-X - 3 11 12 24 9 0.000 0.65084 3 ; N-C-C-H06, prebuilt X-c3-c3-X - 3 11 12 25 9 0.000 0.65084 3 ; N-C-C-H07, prebuilt X-c3-c3-X - 4 5 1 16 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X - 4 5 1 17 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X - 4 5 6 7 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 4 5 6 20 9 180.000 15.16700 2 ; C-C-C-H02, prebuilt X-ca-ca-X - 4 9 8 7 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 5 4 9 8 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 5 4 9 22 9 180.000 15.16700 2 ; C-C-C-H04, prebuilt X-ca-ca-X - 5 6 7 8 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 5 6 7 21 9 180.000 15.16700 2 ; C-C-C-H03, prebuilt X-ca-ca-X - 6 5 1 16 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X - 6 5 1 17 9 180.000 2.51040 2 ; C-C-N-O, prebuilt X-ca-no-X - 6 5 4 9 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 6 5 4 19 9 180.000 15.16700 2 ; C-C-C-H01, prebuilt X-ca-ca-X - 6 7 8 9 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 7 8 2 10 9 180.000 1.88280 2 ; C-C-N-C, prebuilt X-ca-n-X - 7 8 2 33 9 180.000 1.88280 2 ; C-C-N-H, prebuilt X-ca-n-X - 7 8 9 22 9 180.000 15.16700 2 ; C-C-C-H04, prebuilt X-ca-ca-X - 8 2 10 11 9 180.000 10.46000 2 ; C-N-C-C, prebuilt X-c-n-X - 8 2 10 18 9 180.000 10.46000 2 ; C-N-C-O, prebuilt X-c-n-X - 8 7 6 20 9 180.000 15.16700 2 ; C-C-C-H02, prebuilt X-ca-ca-X - 8 9 4 19 9 180.000 15.16700 2 ; C-C-C-H01, prebuilt X-ca-ca-X - 9 8 2 10 9 180.000 1.88280 2 ; C-C-N-C, prebuilt X-ca-n-X - 9 8 2 33 9 180.000 1.88280 2 ; C-C-N-H, prebuilt X-ca-n-X - 9 8 7 21 9 180.000 15.16700 2 ; C-C-C-H03, prebuilt X-ca-ca-X - 10 11 3 34 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 10 11 3 35 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 10 11 12 13 9 0.000 0.65084 3 ; C-C-C-C, prebuilt X-c3-c3-X - 10 11 12 24 9 0.000 0.65084 3 ; C-C-C-H06, prebuilt X-c3-c3-X - 10 11 12 25 9 0.000 0.65084 3 ; C-C-C-H07, prebuilt X-c3-c3-X - 11 10 2 33 9 180.000 10.46000 2 ; C-C-N-H, prebuilt X-c-n-X - 11 12 13 14 9 0.000 0.75312 3 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 11 12 13 14 9 180.000 1.04600 2 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 11 12 13 14 9 180.000 0.83680 1 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 11 12 13 15 9 0.000 0.75312 3 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 11 12 13 15 9 180.000 1.04600 2 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 11 12 13 15 9 180.000 0.83680 1 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 11 12 13 26 9 0.000 0.66944 3 ; C-C-C-H08, prebuilt hc-c3-c3-c3 - 12 11 3 34 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 12 11 3 35 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 12 11 10 18 9 180.000 0.00000 2 ; C-C-C-O, prebuilt X-c-c3-X - 12 13 14 27 9 0.000 0.66944 3 ; C-C-C-H09, prebuilt hc-c3-c3-c3 - 12 13 14 28 9 0.000 0.66944 3 ; C-C-C-H10, prebuilt hc-c3-c3-c3 - 12 13 14 29 9 0.000 0.66944 3 ; C-C-C-H11, prebuilt hc-c3-c3-c3 - 12 13 15 30 9 0.000 0.66944 3 ; C-C-C-H12, prebuilt hc-c3-c3-c3 - 12 13 15 31 9 0.000 0.66944 3 ; C-C-C-H13, prebuilt hc-c3-c3-c3 - 12 13 15 32 9 0.000 0.66944 3 ; C-C-C-H14, prebuilt hc-c3-c3-c3 - 13 12 11 23 9 0.000 0.65084 3 ; C-C-C-H05, prebuilt X-c3-c3-X - 14 13 12 24 9 0.000 0.66944 3 ; C-C-C-H06, prebuilt hc-c3-c3-c3 - 14 13 12 25 9 0.000 0.66944 3 ; C-C-C-H07, prebuilt hc-c3-c3-c3 - 14 13 15 30 9 0.000 0.66944 3 ; C-C-C-H12, prebuilt hc-c3-c3-c3 - 14 13 15 31 9 0.000 0.66944 3 ; C-C-C-H13, prebuilt hc-c3-c3-c3 - 14 13 15 32 9 0.000 0.66944 3 ; C-C-C-H14, prebuilt hc-c3-c3-c3 - 15 13 12 24 9 0.000 0.66944 3 ; C-C-C-H06, prebuilt hc-c3-c3-c3 - 15 13 12 25 9 0.000 0.66944 3 ; C-C-C-H07, prebuilt hc-c3-c3-c3 - 15 13 14 27 9 0.000 0.66944 3 ; C-C-C-H09, prebuilt hc-c3-c3-c3 - 15 13 14 28 9 0.000 0.66944 3 ; C-C-C-H10, prebuilt hc-c3-c3-c3 - 15 13 14 29 9 0.000 0.66944 3 ; C-C-C-H11, prebuilt hc-c3-c3-c3 - 18 10 2 33 9 180.000 10.46000 2 ; O-C-N-H, prebuilt hn-n-c-o - 18 10 2 33 9 0.000 8.36800 1 ; O-C-N-H, prebuilt hn-n-c-o - 18 10 11 23 9 0.000 3.34720 1 ; O-C-C-H05, prebuilt h1-c3-c-o - 18 10 11 23 9 0.000 0.00000 2 ; O-C-C-H05, prebuilt h1-c3-c-o - 18 10 11 23 9 180.000 0.33472 3 ; O-C-C-H05, prebuilt h1-c3-c-o - 19 4 9 22 9 180.000 15.16700 2 ; H01-C-C-H04, prebuilt X-ca-ca-X - 20 6 7 21 9 180.000 15.16700 2 ; H02-C-C-H03, prebuilt X-ca-ca-X - 23 11 3 34 9 0.000 1.25520 3 ; H05-C-N-H, prebuilt X-c3-n3-X - 23 11 3 35 9 0.000 1.25520 3 ; H05-C-N-H, prebuilt X-c3-n3-X - 23 11 12 24 9 0.000 0.65084 3 ; H05-C-C-H06, prebuilt X-c3-c3-X - 23 11 12 25 9 0.000 0.65084 3 ; H05-C-C-H07, prebuilt X-c3-c3-X - 24 12 13 26 9 0.000 0.62760 3 ; H06-C-C-H08, prebuilt hc-c3-c3-hc - 25 12 13 26 9 0.000 0.62760 3 ; H07-C-C-H08, prebuilt hc-c3-c3-hc - 26 13 14 27 9 0.000 0.62760 3 ; H08-C-C-H09, prebuilt hc-c3-c3-hc - 26 13 14 28 9 0.000 0.62760 3 ; H08-C-C-H10, prebuilt hc-c3-c3-hc - 26 13 14 29 9 0.000 0.62760 3 ; H08-C-C-H11, prebuilt hc-c3-c3-hc - 26 13 15 30 9 0.000 0.62760 3 ; H08-C-C-H12, prebuilt hc-c3-c3-hc - 26 13 15 31 9 0.000 0.62760 3 ; H08-C-C-H13, prebuilt hc-c3-c3-hc - 26 13 15 32 9 0.000 0.62760 3 ; H08-C-C-H14, prebuilt hc-c3-c3-hc - -[ pairs ] ; Yielded based on rotatable dihedrals -; atom_i atom_j functype - 1 9 1 ; N-C-C-C - 1 19 1 ; N-C-C-H01 - 1 7 1 ; N-C-C-C - 1 20 1 ; N-C-C-H02 - 2 6 1 ; N-C-C-C - 2 21 1 ; N-C-C-H03 - 2 4 1 ; N-C-C-C - 2 22 1 ; N-C-C-H04 - 2 3 1 ; N-C-C-N - 2 12 1 ; N-C-C-C - 2 23 1 ; N-C-C-H05 - 3 18 1 ; N-C-C-O - 3 13 1 ; N-C-C-C - 3 24 1 ; N-C-C-H06 - 3 25 1 ; N-C-C-H07 - 4 16 1 ; C-C-N-O - 4 17 1 ; C-C-N-O - 4 7 1 ; C-C-C-C - 4 20 1 ; C-C-C-H02 - 5 8 1 ; C-C-C-C - 5 22 1 ; C-C-C-H04 - 5 21 1 ; C-C-C-H03 - 6 16 1 ; C-C-N-O - 6 17 1 ; C-C-N-O - 6 9 1 ; C-C-C-C - 6 19 1 ; C-C-C-H01 - 7 10 1 ; C-C-N-C - 7 33 1 ; C-C-N-H - 7 22 1 ; C-C-C-H04 - 8 11 1 ; C-N-C-C - 8 18 1 ; C-N-C-O - 8 20 1 ; C-C-C-H02 - 8 19 1 ; C-C-C-H01 - 9 10 1 ; C-C-N-C - 9 33 1 ; C-C-N-H - 9 21 1 ; C-C-C-H03 - 10 34 1 ; C-C-N-H - 10 35 1 ; C-C-N-H - 10 13 1 ; C-C-C-C - 10 24 1 ; C-C-C-H06 - 10 25 1 ; C-C-C-H07 - 11 33 1 ; C-C-N-H - 11 14 1 ; C-C-C-C - 11 15 1 ; C-C-C-C - 11 26 1 ; C-C-C-H08 - 12 34 1 ; C-C-N-H - 12 35 1 ; C-C-N-H - 12 18 1 ; C-C-C-O - 12 27 1 ; C-C-C-H09 - 12 28 1 ; C-C-C-H10 - 12 29 1 ; C-C-C-H11 - 12 30 1 ; C-C-C-H12 - 12 31 1 ; C-C-C-H13 - 12 32 1 ; C-C-C-H14 - 13 23 1 ; C-C-C-H05 - 14 24 1 ; C-C-C-H06 - 14 25 1 ; C-C-C-H07 - 14 30 1 ; C-C-C-H12 - 14 31 1 ; C-C-C-H13 - 14 32 1 ; C-C-C-H14 - 15 24 1 ; C-C-C-H06 - 15 25 1 ; C-C-C-H07 - 15 27 1 ; C-C-C-H09 - 15 28 1 ; C-C-C-H10 - 15 29 1 ; C-C-C-H11 - 18 33 1 ; O-C-N-H - 18 23 1 ; O-C-C-H05 - 19 22 1 ; H01-C-C-H04 - 20 21 1 ; H02-C-C-H03 - 23 34 1 ; H05-C-N-H - 23 35 1 ; H05-C-N-H - 23 24 1 ; H05-C-C-H06 - 23 25 1 ; H05-C-C-H07 - 24 26 1 ; H06-C-C-H08 - 25 26 1 ; H07-C-C-H08 - 26 27 1 ; H08-C-C-H09 - 26 28 1 ; H08-C-C-H10 - 26 29 1 ; H08-C-C-H11 - 26 30 1 ; H08-C-C-H12 - 26 31 1 ; H08-C-C-H13 - 26 32 1 ; H08-C-C-H14 - -[ dihedrals ] ; impropers -; atom_i atom_j atom_k atom_l functype phase (Deg.) kd (kJ/mol) pn - 8 10 2 33 4 180.000 4.60240 2 ; C-C-N-H, prebuilt X-X-n-hn - 5 9 4 19 4 180.000 4.60240 2 ; C-C-C-H01, prebuilt X-X-ca-ha - 1 4 5 6 4 180.000 4.60240 2 ; N-C-C-C, guess (same as GAFF X -X -ca-ha) - 5 7 6 20 4 180.000 4.60240 2 ; C-C-C-H02, prebuilt X-X-ca-ha - 6 8 7 21 4 180.000 4.60240 2 ; C-C-C-H03, prebuilt X-X-ca-ha - 2 7 8 9 4 180.000 4.60240 2 ; N-C-C-C, guess (same as GAFF X -X -ca-ha) - 4 8 9 22 4 180.000 4.60240 2 ; C-C-C-H04, prebuilt X-X-ca-ha - 2 11 10 18 4 180.000 43.93200 2 ; N-C-C-O, prebuilt X-X-c-o diff --git a/script/S112D/mol.mol2 b/script/S112D/mol.mol2 deleted file mode 100644 index 8d873fa..0000000 --- a/script/S112D/mol.mol2 +++ /dev/null @@ -1,80 +0,0 @@ -# created with PyMOL 3.0.0 -@MOLECULE -complex-S112D -35 35 1 -SMALL -USER_CHARGES -@ATOM -1 N -5.390 2.121 -9.532 N.2 1 UNK1 0.000 -2 N -10.664 3.190 -9.419 N.pl3 1 UNK1 0.000 -3 N -13.495 1.939 -10.893 N.3 1 UNK1 0.000 -4 C -7.068 3.662 -9.763 C.2 1 UNK1 0.000 -5 C -6.613 2.369 -9.506 C.2 1 UNK1 0.000 -6 C -7.525 1.353 -9.220 C.2 1 UNK1 0.000 -7 C -8.891 1.630 -9.190 C.2 1 UNK1 0.000 -8 C -9.347 2.923 -9.447 C.2 1 UNK1 0.000 -9 C -8.435 3.939 -9.734 C.2 1 UNK1 0.000 -10 C -11.408 3.089 -10.564 C.2 1 UNK1 0.000 -11 C -12.066 1.780 -10.923 C.3 1 UNK1 0.000 -12 C -11.633 1.360 -12.322 C.3 1 UNK1 0.000 -13 C -10.441 0.417 -12.222 C.3 1 UNK1 0.000 -14 C -9.212 1.086 -12.822 C.3 1 UNK1 0.000 -15 C -10.744 -0.866 -12.985 C.3 1 UNK1 0.000 -16 O -4.535 3.072 -9.817 O.2 1 UNK1 0.000 -17 O -4.961 0.910 -9.274 O.2 1 UNK1 0.000 -18 O -11.537 4.049 -11.287 O.2 1 UNK1 0.000 -19 H01 -6.356 4.456 -9.987 H 1 UNK1 0.000 -20 H02 -7.170 0.342 -9.020 H 1 UNK1 0.000 -21 H03 -9.603 0.836 -8.966 H 1 UNK1 0.000 -22 H04 -8.791 4.949 -9.936 H 1 UNK1 0.000 -23 H05 -11.769 1.015 -10.205 H 1 UNK1 0.000 -24 H06 -11.351 2.243 -12.896 H 1 UNK1 0.000 -25 H07 -12.458 0.852 -12.822 H 1 UNK1 0.000 -26 H08 -10.251 0.181 -11.175 H 1 UNK1 0.000 -27 H09 -8.372 0.391 -12.797 H 1 UNK1 0.000 -28 H10 -9.419 1.369 -13.854 H 1 UNK1 0.000 -29 H11 -8.963 1.976 -12.244 H 1 UNK1 0.000 -30 H12 -11.619 -0.714 -13.617 H 1 UNK1 0.000 -31 H13 -9.889 -1.130 -13.607 H 1 UNK1 0.000 -32 H14 -10.942 -1.672 -12.278 H 1 UNK1 0.000 -33 H -11.107 3.466 -8.551 H 1 UNK1 0.000 -34 H -13.775 2.330 -9.994 H 1 UNK1 0.000 -35 H -13.774 2.642 -11.577 H 1 UNK1 0.000 -@BOND -1 1 5 1 -2 1 16 ar -3 1 17 ar -4 2 8 1 -5 2 10 1 -6 2 33 1 -7 3 11 1 -8 3 34 1 -9 3 35 1 -10 4 5 ar -11 4 9 ar -12 4 19 1 -13 5 6 ar -14 6 7 ar -15 6 20 1 -16 7 8 ar -17 7 21 1 -18 8 9 ar -19 9 22 1 -20 10 11 1 -21 10 18 2 -22 11 12 1 -23 11 23 1 -24 12 13 1 -25 12 24 1 -26 12 25 1 -27 13 14 1 -28 13 15 1 -29 13 26 1 -30 14 27 1 -31 14 28 1 -32 14 29 1 -33 15 30 1 -34 15 31 1 -35 15 32 1 -@SUBSTRUCTURE -1 UNK1 1 GROUP 1 L_Le UNK diff --git a/script/S112D/mol.top b/script/S112D/mol.top deleted file mode 100644 index b1702b3..0000000 --- a/script/S112D/mol.top +++ /dev/null @@ -1,14 +0,0 @@ -; Created by Sobtop (http://sobereva.com/soft/sobtop) Version 1.0(dev5) on 2024-09-19 - -[ defaults ] -; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ - 1 2 yes 0.5 0.8333 - -#include "Conformer3D_COMPOUND_CID_2733285.itp" - -[ system ] -Conformer3D_COMPOUND_CID_2733285 - -[ molecules ] -; Molecule nmols -Conformer3D_COMPOUND_CID_2733285 1