# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:01:36 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 3-iodanyl-2-oxidanyl-5-propylsulfanyl-4-pyrrol-1-yl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCSc1cc(C(O)=O)c(O)c(I)c1n2cccc2
#
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
 9GN  9GN  '3-iodanyl-2-oxidanyl-5-propylsulfanyl-4-pyrrol-1-yl-benzoic acid'  ligand  34  20  .  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_9GN
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
 9GN  C10  C  CR15  0  -0.065  -0.4406  -2.6365  -1.1602
 9GN  C13  C  CR15  0  -0.064  -0.5029  -2.5801   1.0771
 9GN  C01  C  CR6   0  -0.196   0.8107   2.1925  -0.1156
 9GN  C02  C  CR16  0  -0.313   1.7885   1.1987  -0.0538
 9GN  C03  C  CR6   0  -0.116   1.4475  -0.1409  -0.0356
 9GN  C04  C  CR6   0   0.377   0.0882  -0.4837  -0.0778
 9GN  C05  C  CR6   0  -0.379  -0.8909   0.4931  -0.1389
 9GN  C06  C  CR6   0   0.429  -0.5520   1.8515  -0.1594
 9GN  I01  I  I     0   0.124  -2.9114  -0.0354  -0.1975
 9GN  C07  C  CH2   0  -0.578   4.1981  -0.6171   0.1149
 9GN  C08  C  CH2   0  -0.429   5.3060  -1.6614   0.1547
 9GN  N01  N  NR5   0  -0.514  -0.2633  -1.8469  -0.0549
 9GN  O01  O  OH1   0  -0.604  -1.5271   2.7462  -0.2157
 9GN  C09  C  C     0   0.613   1.1755   3.6205  -0.1321
 9GN  O02  O  O     0  -0.477   0.3460   4.5136  -0.1770
 9GN  O03  O  OH1   0  -0.577   2.4685   3.8507  -0.0929
 9GN  C11  C  CR15  0  -0.354  -0.7954  -3.8850  -0.7295
 9GN  C12  C  CR15  0  -0.353  -0.8352  -3.8492   0.6907
 9GN  C14  C  CH3   0  -0.659   6.6745  -0.9999   0.2468
 9GN  H1   H  HCR5  0   0.284  -0.3012  -2.2394  -2.1526
 9GN  H2   H  HCR5  0   0.284  -0.4154  -2.1347   2.0548
 9GN  H3   H  HCR6  0   0.293   2.8261   1.4953  -0.0176
 9GN  H4   H  HCH2  0   0.274   4.3167   0.0248  -0.7600
 9GN  H5   H  HCH2  0   0.275   4.2324   0.0075   1.0098
 9GN  H6   H  HCH2  0   0.238   5.1584  -2.3241   1.0106
 9GN  H7   H  HCH2  0   0.239   5.2542  -2.2858  -0.7404
 9GN  H8   H  HOH1  0   0.487  -1.1206   3.6417  -0.2186
 9GN  H9   H  HOH1  0   0.499   2.6438   4.8046  -0.1021
 9GN  H10  H  HCR5  0   0.247  -1.0056  -4.7328  -1.3623
 9GN  H11  H  HCR5  0   0.246  -1.0795  -4.6644   1.3532
 9GN  H12  H  HCH3  0   0.225   6.8569  -0.3469  -0.6081
 9GN  H13  H  HCH3  0   0.225   6.7597  -0.3956   1.1514
 9GN  H14  H  HCH3  0   0.238   7.4671  -1.7473   0.2699
 9GN  S01  S  S2    0   0.082   2.6004  -1.4693   0.0316

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
 9GN  C14  C08  single    1.523  0.020  1.523
 9GN  C08  C07  single    1.523  0.020  1.523
 9GN  C07  S01  single    1.813  0.020  1.813
 9GN  O02  C09  double    1.220  0.020  1.220
 9GN  S01  C03  single    1.760  0.020  1.760
 9GN  C02  C03  aromatic  1.382  0.020  1.382
 9GN  C02  C01  aromatic  1.396  0.020  1.396
 9GN  C09  O03  single    1.314  0.020  1.314
 9GN  C09  C01  single    1.474  0.020  1.474
 9GN  C03  C04  aromatic  1.403  0.020  1.403
 9GN  C01  C06  aromatic  1.405  0.020  1.405
 9GN  C04  N01  single    1.408  0.020  1.408
 9GN  C04  C05  aromatic  1.384  0.020  1.384
 9GN  C06  C05  aromatic  1.400  0.020  1.400
 9GN  C06  O01  single    1.325  0.020  1.325
 9GN  N01  C13  aromatic  1.370  0.020  1.370
 9GN  N01  C10  aromatic  1.370  0.020  1.370
 9GN  C05  I01  single    2.089  0.020  2.089
 9GN  C13  C12  aromatic  1.368  0.020  1.368
 9GN  C10  C11  aromatic  1.368  0.020  1.368
 9GN  C12  C11  aromatic  1.421  0.020  1.421
 9GN  C10  H1   single    0.930  0.020  1.080
 9GN  C13  H2   single    0.930  0.020  1.080
 9GN  C02  H3   single    0.930  0.020  1.080
 9GN  C07  H4   single    0.970  0.020  1.090
 9GN  C07  H5   single    0.970  0.020  1.090
 9GN  C08  H6   single    0.970  0.020  1.090
 9GN  C08  H7   single    0.970  0.020  1.090
 9GN  O01  H8   single    0.850  0.020  0.980
 9GN  O03  H9   single    0.850  0.020  0.980
 9GN  C11  H10  single    0.930  0.020  1.080
 9GN  C12  H11  single    0.930  0.020  1.080
 9GN  C14  H12  single    0.970  0.020  1.090
 9GN  C14  H13  single    0.970  0.020  1.090
 9GN  C14  H14  single    0.970  0.020  1.090

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
 9GN  H1   C10  C11  131.29  3.000
 9GN  H1   C10  N01  120.92  3.000
 9GN  C11  C10  N01  107.80  3.000
 9GN  H2   C13  C12  131.26  3.000
 9GN  H2   C13  N01  120.94  3.000
 9GN  C12  C13  N01  107.80  3.000
 9GN  C09  C01  C06  118.34  3.000
 9GN  C06  C01  C02  120.53  3.000
 9GN  C09  C01  C02  121.13  3.000
 9GN  H3   C02  C03  120.18  3.000
 9GN  H3   C02  C01  118.64  3.000
 9GN  C03  C02  C01  121.18  3.000
 9GN  S01  C03  C04  116.84  3.000
 9GN  C04  C03  C02  118.39  3.000
 9GN  S01  C03  C02  124.77  3.000
 9GN  N01  C04  C05  120.48  3.000
 9GN  C05  C04  C03  120.96  3.000
 9GN  N01  C04  C03  118.56  3.000
 9GN  I01  C05  C06  118.62  3.000
 9GN  I01  C05  C04  120.45  3.000
 9GN  C06  C05  C04  120.93  3.000
 9GN  O01  C06  C05  118.54  3.000
 9GN  O01  C06  C01  123.45  3.000
 9GN  C05  C06  C01  118.01  3.000
 9GN  H5   C07  H4   108.49  3.000
 9GN  H5   C07  C08  110.36  3.000
 9GN  H4   C07  C08  110.19  3.000
 9GN  H5   C07  S01  109.53  3.000
 9GN  H4   C07  S01  109.60  3.000
 9GN  C08  C07  S01  108.66  3.000
 9GN  H7   C08  H6   106.78  3.000
 9GN  H7   C08  C14  109.90  3.000
 9GN  H6   C08  C14  109.72  3.000
 9GN  H7   C08  C07  109.64  3.000
 9GN  H6   C08  C07  109.77  3.000
 9GN  C14  C08  C07  110.94  3.000
 9GN  C04  N01  C13  125.12  3.000
 9GN  C13  N01  C10  109.61  3.000
 9GN  C04  N01  C10  125.25  3.000
 9GN  H8   O01  C06  108.11  3.000
 9GN  O03  C09  O02  122.83  3.000
 9GN  O03  C09  C01  114.39  3.000
 9GN  O02  C09  C01  122.78  3.000
 9GN  H9   O03  C09  110.48  3.000
 9GN  H10  C11  C12  126.92  3.000
 9GN  H10  C11  C10  125.69  3.000
 9GN  C12  C11  C10  107.40  3.000
 9GN  H11  C12  C11  126.95  3.000
 9GN  H11  C12  C13  125.66  3.000
 9GN  C11  C12  C13  107.39  3.000
 9GN  H14  C14  H13  107.79  3.000
 9GN  H14  C14  H12  107.79  3.000
 9GN  H13  C14  H12  107.76  3.000
 9GN  H14  C14  C08  110.92  3.000
 9GN  H13  C14  C08  111.15  3.000
 9GN  H12  C14  C08  111.27  3.000
 9GN  C07  S01  C03  102.96  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
 9GN  CONST_03  C12  C13  N01  C10     0.00   0.0  0
 9GN  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 9GN  CONST_07  C11  C10  N01  C13     0.00   0.0  0
 9GN  CONST_08  C04  C03  C02  C01     0.00   0.0  0
 9GN  CONST_09  C04  C05  C06  C01     0.00   0.0  0
 9GN  CONST_10  N01  C04  C03  C02   180.00   0.0  0
 9GN  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 9GN  CONST_12  C05  C06  C01  C02     0.00   0.0  0
 9GN  CONST_13  C06  C01  C02  C03     0.00   0.0  0
 9GN  CONST_14  C06  C05  C04  C03     0.00   0.0  0
 9GN  CONST_15  C12  C13  N01  C04   180.00   0.0  0
 9GN  CONST_16  C11  C10  N01  C04   180.00   0.0  0
 9GN  CONST_17  N01  C04  C05  C06   180.00   0.0  0
 9GN  CONST_18  C11  C12  C13  N01     0.00   0.0  0
 9GN  CONST_19  C12  C11  C10  N01     0.00   0.0  0
 9GN  CONST_20  S01  C03  C02  C01   180.00   0.0  0
 9GN  CONST_21  I01  C05  C06  C01   180.00   0.0  0
 9GN  CONST_22  O01  C06  C01  C02   180.00   0.0  0
 9GN  CONST_23  C09  C01  C02  C03   180.00   0.0  0
 9GN  CONST_24  I01  C05  C04  C03   180.00   0.0  0
 9GN  CONST_25  O01  C06  C05  C04   180.00   0.0  0
 9GN  CONST_26  S01  C03  C04  C05   180.00   0.0  0
 9GN  CONST_27  C09  C01  C06  C05   180.00   0.0  0
 9GN  CONST_28  N01  C04  C05  I01     0.00   0.0  0
 9GN  CONST_29  N01  C04  C03  S01     0.00   0.0  0
 9GN  CONST_30  H2   C13  N01  C10   180.00   0.0  0
 9GN  CONST_31  H11  C12  C11  C10   180.00   0.0  0
 9GN  CONST_32  H1   C10  N01  C13   180.00   0.0  0
 9GN  CONST_33  H10  C11  C12  C13   180.00   0.0  0
 9GN  CONST_34  H3   C02  C03  C04   180.00   0.0  0
 9GN  CONST_35  H9   O03  C09  C01   180.00   0.0  0
 9GN  Var_01    O02  C09  C01  C02  -179.52  30.0  3
 9GN  Var_02    C08  C07  S01  C03  -179.05  30.0  1
 9GN  Var_03    C14  C08  C07  S01  -179.13  30.0  1
 9GN  Var_04    H12  C14  C08  C07   -59.71  30.0  3

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
 9GN  plan-1  C10  0.020
 9GN  plan-1  C13  0.020
 9GN  plan-1  C04  0.020
 9GN  plan-1  N01  0.020
 9GN  plan-1  C11  0.020
 9GN  plan-1  C12  0.020
 9GN  plan-1  H1   0.020
 9GN  plan-1  H2   0.020
 9GN  plan-1  H10  0.020
 9GN  plan-1  H11  0.020
 9GN  plan-2  C01  0.020
 9GN  plan-2  C02  0.020
 9GN  plan-2  C03  0.020
 9GN  plan-2  C04  0.020
 9GN  plan-2  C05  0.020
 9GN  plan-2  C06  0.020
 9GN  plan-2  I01  0.020
 9GN  plan-2  N01  0.020
 9GN  plan-2  O01  0.020
 9GN  plan-2  C09  0.020
 9GN  plan-2  H3   0.020
 9GN  plan-2  S01  0.020
 9GN  plan-3  C01  0.020
 9GN  plan-3  C09  0.020
 9GN  plan-3  O02  0.020
 9GN  plan-3  O03  0.020
 9GN  plan-3  H9   0.020

