# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:13:26 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2Z,4E)-6-amino-3-[(dioxidosulfanyl)methyl]-2-[(2-formylindolizin-3-yl)amino]-6-oxohexa-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)\C=C\C(C[SH](=O)=O)=C(\Nc1n2ccccc2cc1C=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 DVR  DVR  '(2Z,4E)-6-amino-3-[(dioxidosulfanyl)methyl]-2-[(2-formylindolizin-3-yl)amino]-6-oxohexa-2,4-dienoic acid'  ligand  41  26  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DVR
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 DVR  S1    S  SH1   0   1.065  -0.3898  -2.4008   2.4852
 DVR  C2    C  CH2   0  -0.785  -1.2299  -2.1841   0.9123
 DVR  C3    C  C     0   0.041  -2.2992  -1.1420   1.0293
 DVR  C4    C  C     0   0.316  -3.5510  -1.4918   1.4240
 DVR  N5    N  NH1   0  -0.741  -3.9613  -2.7489   1.7554
 DVR  C6    C  CR5   0   0.432  -5.2260  -3.0040   2.2767
 DVR  C7    C  CR5   0  -0.057  -5.7190  -2.8609   3.5673
 DVR  C8    C  C1    0   0.085  -4.9372  -2.3712   4.6924
 DVR  C9    C  CR15  0  -0.429  -7.0672  -3.2632   3.5693
 DVR  C10   C  C1    0  -0.216  -2.0017   0.2242   0.6643
 DVR  C11   C  C1    0  -0.424  -0.8015   0.7215   0.3349
 DVR  C12   C  C     0   0.522  -0.6589   2.1415  -0.0495
 DVR  N12   N  NH2   0  -0.821   0.6026   2.5180  -0.3219
 DVR  O12   O  O     0  -0.502  -1.6088   2.9159  -0.1197
 DVR  O8    O  O     0  -0.390  -5.3864  -2.2160   5.8067
 DVR  C4A   C  C     0   0.427  -4.6781  -0.4904   1.4534
 DVR  O4A   O  OH1   0  -0.561  -4.6201   0.2705   2.5263
 DVR  O4B   O  O     0  -0.389  -5.5166  -0.4410   0.5957
 DVR  O1A   O  OS    0  -0.663   0.3432  -1.1866   2.8211
 DVR  O1B   O  OS    0  -0.670  -1.3472  -2.9349   3.4518
 DVR  CG    C  CR56  0   0.455  -7.3753  -3.6498   2.2791
 DVR  CD1   C  CR16  0  -0.379  -8.5448  -4.1429   1.6519
 DVR  ND2   N  N     0  -0.557  -6.2329  -3.4850   1.4978
 DVR  CE1   C  CR16  0  -0.162  -8.5296  -4.4287   0.3238
 DVR  CE2   C  CR16  0   0.034  -6.2172  -3.7644   0.1558
 DVR  CZ    C  CR16  0  -0.392  -7.3392  -4.2314  -0.4350
 DVR  HS1   H  HSH1  0   0.246   0.5018  -3.3771   2.1784
 DVR  HC21  H  HCH2  0   0.340  -0.4665  -1.9178   0.1799
 DVR  HC22  H  HCH2  0   0.337  -1.6075  -3.1676   0.6232
 DVR  HN5   H  HNH1  0   0.418  -3.2629  -3.4668   1.8836
 DVR  HC8   H  H     0   0.191  -3.8790  -2.1513   4.4723
 DVR  HC9   H  HCR5  0   0.267  -7.7448  -3.2736   4.4074
 DVR  H10   H  H     0   0.264  -2.8278   0.9270   0.6387
 DVR  H11   H  H     0   0.255   0.0951   0.1144   0.3507
 DVR  H121  H  HNH2  0   0.406   1.3799   1.8892  -0.2194
 DVR  H122  H  HNH2  0   0.399   0.8088   3.4725  -0.5656
 DVR  HXT   H  HOH1  0   0.499  -5.3632   0.8961   2.5468
 DVR  HD1   H  HCR6  0   0.278  -9.4331  -4.2795   2.2532
 DVR  HE1   H  HCR6  0   0.273  -9.4166  -4.8060  -0.1651
 DVR  HE2   H  HCR6  0   0.306  -5.2857  -3.5950  -0.3623
 DVR  HCZ   H  HCR6  0   0.281  -7.3193  -4.4509  -1.4923

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 DVR  S1   C2    single    1.796  0.020  1.796
 DVR  S1   O1A   double    1.458  0.020  1.458
 DVR  S1   O1B   double    1.462  0.020  1.462
 DVR  S1   HS1   single    1.200  0.020  1.300
 DVR  C2   C3    single    1.498  0.020  1.498
 DVR  C2   HC21  single    0.970  0.020  1.090
 DVR  C2   HC22  single    0.970  0.020  1.090
 DVR  C3   C4    double    1.358  0.020  1.358
 DVR  C3   C10   single    1.445  0.020  1.445
 DVR  C4   N5    single    1.363  0.020  1.363
 DVR  C4   C4A   single    1.508  0.020  1.508
 DVR  N5   C6    single    1.392  0.020  1.392
 DVR  N5   HN5   single    0.860  0.020  1.020
 DVR  C6   C7    aromatic  1.389  0.020  1.389
 DVR  C6   ND2   aromatic  1.361  0.020  1.361
 DVR  C7   C8    single    1.455  0.020  1.455
 DVR  C7   C9    aromatic  1.407  0.020  1.407
 DVR  C8   O8    double    1.211  0.020  1.211
 DVR  C8   HC8   single    0.930  0.020  1.080
 DVR  C9   CG    aromatic  1.382  0.020  1.382
 DVR  C9   HC9   single    0.930  0.020  1.080
 DVR  C10  C11   double    1.340  0.020  1.340
 DVR  C10  H10   single    0.930  0.020  1.080
 DVR  C11  C12   single    1.478  0.020  1.478
 DVR  C11  H11   single    0.930  0.020  1.080
 DVR  C12  N12   single    1.344  0.020  1.344
 DVR  C12  O12   double    1.228  0.020  1.228
 DVR  N12  H121  single    0.860  0.020  1.020
 DVR  N12  H122  single    0.860  0.020  1.020
 DVR  C4A  O4A   single    1.317  0.020  1.317
 DVR  C4A  O4B   double    1.200  0.020  1.200
 DVR  O4A  HXT   single    0.850  0.020  0.980
 DVR  CG   CD1   aromatic  1.416  0.020  1.416
 DVR  CG   ND2   aromatic  1.394  0.020  1.394
 DVR  CD1  CE1   aromatic  1.359  0.020  1.359
 DVR  CD1  HD1   single    0.930  0.020  1.080
 DVR  ND2  CE2   aromatic  1.371  0.020  1.371
 DVR  CE1  CZ    aromatic  1.425  0.020  1.425
 DVR  CE1  HE1   single    0.930  0.020  1.080
 DVR  CE2  CZ    aromatic  1.351  0.020  1.351
 DVR  CE2  HE2   single    0.930  0.020  1.080
 DVR  CZ   HCZ   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 DVR  HS1   S1   O1B   108.47  3.000
 DVR  HS1   S1   O1A   108.72  3.000
 DVR  O1B   S1   O1A   118.78  3.000
 DVR  HS1   S1   C2    101.31  3.000
 DVR  O1B   S1   C2    108.47  3.000
 DVR  O1A   S1   C2    109.66  3.000
 DVR  HC22  C2   HC21  106.50  3.000
 DVR  HC22  C2   C3    113.59  3.000
 DVR  HC21  C2   C3    112.47  3.000
 DVR  HC22  C2   S1    106.55  3.000
 DVR  HC21  C2   S1    106.86  3.000
 DVR  C3    C2   S1    110.46  3.000
 DVR  C10   C3   C4    120.43  3.000
 DVR  C10   C3   C2    119.41  3.000
 DVR  C4    C3   C2    120.10  3.000
 DVR  C4A   C4   N5    112.50  3.000
 DVR  C4A   C4   C3    121.57  3.000
 DVR  N5    C4   C3    125.83  3.000
 DVR  HN5   N5   C6    116.79  3.000
 DVR  HN5   N5   C4    118.58  3.000
 DVR  C6    N5   C4    122.25  3.000
 DVR  ND2   C6   C7    107.80  3.000
 DVR  ND2   C6   N5    121.52  3.000
 DVR  C7    C6   N5    130.68  3.000
 DVR  C9    C7   C8    127.59  3.000
 DVR  C9    C7   C6    108.18  3.000
 DVR  C8    C7   C6    124.23  3.000
 DVR  HC8   C8   O8    120.92  3.000
 DVR  HC8   C8   C7    115.36  3.000
 DVR  O8    C8   C7    123.72  3.000
 DVR  HC9   C9   CG    125.68  3.000
 DVR  HC9   C9   C7    127.32  3.000
 DVR  CG    C9   C7    107.00  3.000
 DVR  H10   C10  C11   115.83  3.000
 DVR  H10   C10  C3    117.49  3.000
 DVR  C11   C10  C3    126.67  3.000
 DVR  H11   C11  C12   117.55  3.000
 DVR  H11   C11  C10   121.99  3.000
 DVR  C12   C11  C10   120.45  3.000
 DVR  O12   C12  N12   122.53  3.000
 DVR  O12   C12  C11   123.12  3.000
 DVR  N12   C12  C11   114.35  3.000
 DVR  H122  N12  H121  117.36  3.000
 DVR  H122  N12  C12   120.46  3.000
 DVR  H121  N12  C12   121.99  3.000
 DVR  O4B   C4A  O4A   126.10  3.000
 DVR  O4B   C4A  C4    122.38  3.000
 DVR  O4A   C4A  C4    111.51  3.000
 DVR  HXT   O4A  C4A   110.83  3.000
 DVR  ND2   CG   CD1   118.03  3.000
 DVR  ND2   CG   C9    107.91  3.000
 DVR  CD1   CG   C9    134.06  3.000
 DVR  HD1   CD1  CE1   121.75  3.000
 DVR  HD1   CD1  CG    118.44  3.000
 DVR  CE1   CD1  CG    119.81  3.000
 DVR  CE2   ND2  CG    122.28  3.000
 DVR  CE2   ND2  C6    128.60  3.000
 DVR  CG    ND2  C6    109.11  3.000
 DVR  HE1   CE1  CZ    119.54  3.000
 DVR  HE1   CE1  CD1   120.42  3.000
 DVR  CZ    CE1  CD1   120.04  3.000
 DVR  HE2   CE2  CZ    124.13  3.000
 DVR  HE2   CE2  ND2   116.60  3.000
 DVR  CZ    CE2  ND2   119.27  3.000
 DVR  HCZ   CZ   CE2   118.88  3.000
 DVR  HCZ   CZ   CE1   120.55  3.000
 DVR  CE2   CZ   CE1   120.57  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DVR  CONST_01  CG    C9   C7   C6     0.00   0.0  0
 DVR  CONST_02  C9    CG   ND2  C6     0.00   0.0  0
 DVR  CONST_03  CD1   CG   ND2  C6   180.00   0.0  0
 DVR  CONST_04  CZ    CE2  ND2  C6   180.00   0.0  0
 DVR  CONST_05  CG    ND2  C6   C7     0.00   0.0  0
 DVR  CONST_06  CE2   ND2  C6   C7   180.00   0.0  0
 DVR  CONST_07  CD1   CG   C9   C7   180.00   0.0  0
 DVR  CONST_08  ND2   CG   C9   C7     0.00   0.0  0
 DVR  CONST_09  ND2   C6   C7   C9     0.00   0.0  0
 DVR  CONST_10  CE1   CD1  CG   C9   180.00   0.0  0
 DVR  CONST_11  CE2   ND2  CG   C9   180.00   0.0  0
 DVR  CONST_12  CZ    CE1  CD1  CG     0.00   0.0  0
 DVR  CONST_13  CZ    CE2  ND2  CG     0.00   0.0  0
 DVR  CONST_14  CE2   ND2  CG   CD1    0.00   0.0  0
 DVR  CONST_15  CE2   CZ   CE1  CD1    0.00   0.0  0
 DVR  CONST_16  CE1   CD1  CG   ND2    0.00   0.0  0
 DVR  CONST_17  CE1   CZ   CE2  ND2    0.00   0.0  0
 DVR  CONST_18  C9    C7   C6   N5   180.00   0.0  0
 DVR  CONST_19  CG    ND2  C6   N5   180.00   0.0  0
 DVR  CONST_20  CE2   ND2  C6   N5     0.00   0.0  0
 DVR  CONST_21  ND2   C6   C7   C8   180.00   0.0  0
 DVR  CONST_22  CG    C9   C7   C8   180.00   0.0  0
 DVR  CONST_23  HC9   C9   C7   C6   180.00   0.0  0
 DVR  CONST_24  HE2   CE2  ND2  C6     0.00   0.0  0
 DVR  CONST_25  HD1   CD1  CG   C9     0.00   0.0  0
 DVR  CONST_26  HE1   CE1  CD1  CG   180.00   0.0  0
 DVR  CONST_27  HCZ   CZ   CE1  CD1  180.00   0.0  0
 DVR  CONST_31  C6    N5   C4   C3   180.00   0.0  0
 DVR  CONST_32  C4A   C4   N5   C6     0.00   0.0  0
 DVR  CONST_33  H121  N12  C12  C11    0.00   0.0  0
 DVR  CONST_34  H122  N12  C12  C11  180.00   0.0  0
 DVR  CONST_35  HXT   O4A  C4A  C4   180.00   0.0  0
 DVR  Var_01    O8    C8   C7   C6   177.94  30.0  2
 DVR  Var_02    N5    C4   C3   C2     0.71   0.0  2
 DVR  Var_03    C12   C11  C10  C3   178.48   0.0  2
 DVR  Var_04    C4    C3   C2   S1   -87.89  30.0  3
 DVR  Var_05    C11   C10  C3   C2    -6.84  30.0  2
 DVR  Var_06    O1A   S1   C2   C3   -66.19  30.0  3
 DVR  Var_07    O4A   C4A  C4   C3   -79.49  30.0  2
 DVR  Var_08    N12   C12  C11  C10  178.36  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 DVR  plan-1  N5    0.020
 DVR  plan-1  C6    0.020
 DVR  plan-1  C7    0.020
 DVR  plan-1  C8    0.020
 DVR  plan-1  C9    0.020
 DVR  plan-1  CG    0.020
 DVR  plan-1  CD1   0.020
 DVR  plan-1  ND2   0.020
 DVR  plan-1  CE1   0.020
 DVR  plan-1  CE2   0.020
 DVR  plan-1  CZ    0.020
 DVR  plan-1  HC9   0.020
 DVR  plan-1  HD1   0.020
 DVR  plan-1  HE1   0.020
 DVR  plan-1  HE2   0.020
 DVR  plan-1  HCZ   0.020
 DVR  plan-2  C11   0.020
 DVR  plan-2  C12   0.020
 DVR  plan-2  N12   0.020
 DVR  plan-2  O12   0.020
 DVR  plan-2  H121  0.020
 DVR  plan-2  H122  0.020
 DVR  plan-3  C4    0.020
 DVR  plan-3  N5    0.020
 DVR  plan-3  C6    0.020
 DVR  plan-3  HN5   0.020
 DVR  plan-4  C4    0.020
 DVR  plan-4  C4A   0.020
 DVR  plan-4  O4A   0.020
 DVR  plan-4  O4B   0.020
 DVR  plan-4  HXT   0.020
 DVR  plan-5  C2    0.020
 DVR  plan-5  C3    0.020
 DVR  plan-5  C4    0.020
 DVR  plan-5  N5    0.020
 DVR  plan-5  C10   0.020
 DVR  plan-5  C4A   0.020
 DVR  plan-6  C7    0.020
 DVR  plan-6  C8    0.020
 DVR  plan-6  O8    0.020
 DVR  plan-6  HC8   0.020
 DVR  plan-7  C3    0.020
 DVR  plan-7  C10   0.020
 DVR  plan-7  C11   0.020
 DVR  plan-7  C12   0.020
 DVR  plan-7  H10   0.020
 DVR  plan-7  H11   0.020

