# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:15:59 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)c2cnc(N)c(n2)c3ccc(cc3)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
 T3M  T3M  '4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]benzoic acid'  ligand  46  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T3M
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
 T3M  O26   O  OC    -1  -0.591   7.1518   1.2507  -1.4930
 T3M  C24   C  C      0   0.396   6.2872   1.7369  -0.7394
 T3M  O25   O  O      0  -0.591   6.3346   2.8376  -0.1584
 T3M  C23   C  CR6    0  -0.103   5.0375   0.8967  -0.5056
 T3M  C22   C  CR16   0  -0.276   4.0060   1.3575   0.3102
 T3M  C21   C  CR16   0  -0.275   2.8673   0.5979   0.5203
 T3M  C27   C  CR16   0  -0.272   4.8922  -0.3496  -1.1070
 T3M  C28   C  CR16   0  -0.297   3.7601  -1.1213  -0.8925
 T3M  C20   C  CR6    0   0.042   2.7320  -0.6594  -0.0699
 T3M  C19   C  C      0   0.119   1.4930  -1.4349   0.1439
 T3M  N14   N  N      0  -0.393   0.3576  -0.7741   0.0924
 T3M  C17   C  C      0   0.402   1.4873  -2.8287   0.4301
 T3M  N18   N  NH2    0  -0.831   2.6222  -3.5652   0.5273
 T3M  N16   N  N      0  -0.408   0.3339  -3.4622   0.6050
 T3M  C15   C  C1     0  -0.115  -0.7907  -2.7709   0.5162
 T3M  C13   C  C      0   0.165  -0.8050  -1.4052   0.2646
 T3M  C12   C  CR6    0   0.106  -2.0410  -0.6037   0.1990
 T3M  C4    C  CR16   0  -0.518  -3.2748  -1.2108  -0.0260
 T3M  C11   C  CR16   0  -0.477  -1.9644   0.7767   0.3674
 T3M  C8    C  CR6    0   0.363  -3.1200   1.5492   0.3212
 T3M  O9    O  O2     0  -0.464  -3.1455   2.8840   0.4768
 T3M  C10   C  CH3    0  -0.440  -1.9236   3.5594   0.7004
 T3M  C5    C  CR6    0   0.165  -4.3623   0.9440   0.1121
 T3M  O6    O  O2     0  -0.480  -5.4948   1.6938   0.1000
 T3M  C7    C  CH3    0  -0.408  -5.8594   2.1829  -1.1841
 T3M  C3    C  CR6    0   0.370  -4.4325  -0.4393  -0.0711
 T3M  O2    O  O2     0  -0.466  -5.6635  -0.9341  -0.2863
 T3M  C1    C  CH3    0  -0.441  -5.8083  -2.3297  -0.4617
 T3M  H22   H  HCR6   0   0.245   4.0972   2.3246   0.7863
 T3M  H27   H  HCR6   0   0.246   5.6730  -0.7218  -1.7566
 T3M  H21   H  HCR6   0   0.247   2.0759   0.9770   1.1546
 T3M  H28   H  HCR6   0   0.260   3.6708  -2.0770  -1.3939
 T3M  H181  H  HNH2   0   0.401   3.4886  -3.0958   0.7331
 T3M  H182  H  HNH2   0   0.393   2.5248  -4.4703   0.9597
 T3M  H15   H  H      0   0.263  -1.7048  -3.3292   0.6810
 T3M  H4    H  HCR6   0   0.272  -3.3316  -2.2770  -0.1917
 T3M  H11   H  HCR6   0   0.272  -0.9975   1.2277   0.5390
 T3M  H101  H  HCH3   0   0.229  -1.2222   3.4223  -0.1264
 T3M  H102  H  HCH3   0   0.262  -2.1670   4.6158   0.7818
 T3M  H103  H  HCH3   0   0.229  -1.4423   3.2369   1.6273
 T3M  H71C  H  HCH3   0   0.237  -6.7680   2.7692  -1.0585
 T3M  H72C  H  HCH3   0   0.222  -5.0841   2.8255  -1.6080
 T3M  H73C  H  HCH3   0   0.221  -6.0637   1.3698  -1.8850
 T3M  H11C  H  HCH3   0   0.230  -5.2619  -2.6906  -1.3367
 T3M  H12C  H  HCH3   0   0.229  -5.4756  -2.8876   0.4175
 T3M  H13C  H  HCH3   0   0.263  -6.8693  -2.5122  -0.6120

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
 T3M  O26  C24   deloc     1.246  0.020  1.246
 T3M  C24  O25   deloc     1.246  0.020  1.246
 T3M  C24  C23   single    1.524  0.020  1.524
 T3M  C23  C22   aromatic  1.393  0.020  1.393
 T3M  C23  C27   aromatic  1.391  0.020  1.391
 T3M  C22  C21   aromatic  1.385  0.020  1.385
 T3M  C21  C20   aromatic  1.396  0.020  1.396
 T3M  C27  C28   aromatic  1.387  0.020  1.387
 T3M  C28  C20   aromatic  1.395  0.020  1.395
 T3M  C20  C19   single    1.477  0.020  1.477
 T3M  C19  N14   aromatic  1.315  0.020  1.315
 T3M  C19  C17   aromatic  1.423  0.020  1.423
 T3M  N14  C13   aromatic  1.334  0.020  1.334
 T3M  C17  N18   single    1.356  0.020  1.356
 T3M  C17  N16   aromatic  1.327  0.020  1.327
 T3M  N16  C15   aromatic  1.323  0.020  1.323
 T3M  C15  C13   aromatic  1.389  0.020  1.389
 T3M  C13  C12   single    1.475  0.020  1.475
 T3M  C12  C4    aromatic  1.393  0.020  1.393
 T3M  C12  C11   aromatic  1.393  0.020  1.393
 T3M  C4   C3    aromatic  1.392  0.020  1.392
 T3M  C11  C8    aromatic  1.391  0.020  1.391
 T3M  C8   O9    single    1.344  0.020  1.344
 T3M  C8   C5    aromatic  1.398  0.020  1.398
 T3M  O9   C10   single    1.414  0.020  1.414
 T3M  C5   O6    single    1.358  0.020  1.358
 T3M  C5   C3    aromatic  1.397  0.020  1.397
 T3M  O6   C7    single    1.422  0.020  1.422
 T3M  C3   O2    single    1.344  0.020  1.344
 T3M  O2   C1    single    1.414  0.020  1.414
 T3M  C22  H22   single    0.930  0.020  1.080
 T3M  C27  H27   single    0.930  0.020  1.080
 T3M  C21  H21   single    0.930  0.020  1.080
 T3M  C28  H28   single    0.930  0.020  1.080
 T3M  N18  H181  single    0.890  0.020  1.040
 T3M  N18  H182  single    0.890  0.020  1.040
 T3M  C15  H15   single    0.930  0.020  1.080
 T3M  C4   H4    single    0.930  0.020  1.080
 T3M  C11  H11   single    0.930  0.020  1.080
 T3M  C10  H101  single    0.970  0.020  1.090
 T3M  C10  H102  single    0.970  0.020  1.090
 T3M  C10  H103  single    0.970  0.020  1.090
 T3M  C7   H71C  single    0.970  0.020  1.090
 T3M  C7   H72C  single    0.970  0.020  1.090
 T3M  C7   H73C  single    0.970  0.020  1.090
 T3M  C1   H11C  single    0.970  0.020  1.090
 T3M  C1   H12C  single    0.970  0.020  1.090
 T3M  C1   H13C  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
 T3M  C23   C24  O25   116.54  3.000
 T3M  C23   C24  O26   116.54  3.000
 T3M  O25   C24  O26   126.92  3.000
 T3M  C27   C23  C22   118.16  3.000
 T3M  C27   C23  C24   120.87  3.000
 T3M  C22   C23  C24   120.97  3.000
 T3M  H22   C22  C21   119.53  3.000
 T3M  H22   C22  C23   119.39  3.000
 T3M  C21   C22  C23   121.07  3.000
 T3M  H21   C21  C20   119.50  3.000
 T3M  H21   C21  C22   119.86  3.000
 T3M  C20   C21  C22   120.64  3.000
 T3M  H27   C27  C28   119.38  3.000
 T3M  H27   C27  C23   119.50  3.000
 T3M  C28   C27  C23   121.12  3.000
 T3M  H28   C28  C20   120.29  3.000
 T3M  H28   C28  C27   119.13  3.000
 T3M  C20   C28  C27   120.56  3.000
 T3M  C19   C20  C28   121.97  3.000
 T3M  C19   C20  C21   119.54  3.000
 T3M  C28   C20  C21   118.44  3.000
 T3M  C17   C19  N14   119.79  3.000
 T3M  C17   C19  C20   123.14  3.000
 T3M  N14   C19  C20   117.05  3.000
 T3M  C13   N14  C19   120.65  3.000
 T3M  N16   C17  N18   117.28  3.000
 T3M  N16   C17  C19   119.83  3.000
 T3M  N18   C17  C19   122.88  3.000
 T3M  H182  N18  H181  114.47  3.000
 T3M  H182  N18  C17   115.95  3.000
 T3M  H181  N18  C17   118.78  3.000
 T3M  C15   N16  C17   118.71  3.000
 T3M  H15   C15  C13   121.70  3.000
 T3M  H15   C15  N16   115.95  3.000
 T3M  C13   C15  N16   122.33  3.000
 T3M  C12   C13  C15   123.45  3.000
 T3M  C12   C13  N14   117.88  3.000
 T3M  C15   C13  N14   118.66  3.000
 T3M  C11   C12  C4    120.00  3.000
 T3M  C11   C12  C13   119.16  3.000
 T3M  C4    C12  C13   120.83  3.000
 T3M  H4    C4   C3    119.88  3.000
 T3M  H4    C4   C12   120.09  3.000
 T3M  C3    C4   C12   120.01  3.000
 T3M  H11   C11  C8    121.13  3.000
 T3M  H11   C11  C12   118.81  3.000
 T3M  C8    C11  C12   120.06  3.000
 T3M  C5    C8   O9    115.50  3.000
 T3M  C5    C8   C11   120.20  3.000
 T3M  O9    C8   C11   124.30  3.000
 T3M  C10   O9   C8    118.44  3.000
 T3M  H103  C10  H102  108.77  3.000
 T3M  H103  C10  H101  108.78  3.000
 T3M  H102  C10  H101  108.80  3.000
 T3M  H103  C10  O9    111.94  3.000
 T3M  H102  C10  O9    106.41  3.000
 T3M  H101  C10  O9    112.03  3.000
 T3M  C3    C5   O6    120.24  3.000
 T3M  C3    C5   C8    119.53  3.000
 T3M  O6    C5   C8    120.23  3.000
 T3M  C7    O6   C5    114.32  3.000
 T3M  H73C  C7   H72C  108.75  3.000
 T3M  H73C  C7   H71C  108.59  3.000
 T3M  H72C  C7   H71C  108.67  3.000
 T3M  H73C  C7   O6    111.80  3.000
 T3M  H72C  C7   O6    111.76  3.000
 T3M  H71C  C7   O6    107.16  3.000
 T3M  O2    C3   C5    115.56  3.000
 T3M  O2    C3   C4    124.26  3.000
 T3M  C5    C3   C4    120.19  3.000
 T3M  C1    O2   C3    118.49  3.000
 T3M  H13C  C1   H12C  108.82  3.000
 T3M  H13C  C1   H11C  108.78  3.000
 T3M  H12C  C1   H11C  108.86  3.000
 T3M  H13C  C1   O2    106.43  3.000
 T3M  H12C  C1   O2    111.88  3.000
 T3M  H11C  C1   O2    111.96  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
 T3M  CONST_01  C20   C21  C22  C23     0.00   0.0  0
 T3M  CONST_02  C20   C28  C27  C23     0.00   0.0  0
 T3M  CONST_03  C28   C27  C23  C22     0.00   0.0  0
 T3M  CONST_04  C28   C20  C21  C22     0.00   0.0  0
 T3M  CONST_05  C19   C20  C21  C22   180.00   0.0  0
 T3M  CONST_06  C27   C23  C22  C21     0.00   0.0  0
 T3M  CONST_07  C27   C28  C20  C21     0.00   0.0  0
 T3M  CONST_10  C19   C20  C28  C27   180.00   0.0  0
 T3M  CONST_13  C13   N14  C19  C20   180.00   0.0  0
 T3M  CONST_14  N16   C17  C19  C20   180.00   0.0  0
 T3M  CONST_15  C15   C13  N14  C19     0.00   0.0  0
 T3M  CONST_16  C12   C13  N14  C19   180.00   0.0  0
 T3M  CONST_17  C15   N16  C17  C19     0.00   0.0  0
 T3M  CONST_18  N16   C17  C19  N14     0.00   0.0  0
 T3M  CONST_19  N16   C15  C13  N14     0.00   0.0  0
 T3M  CONST_22  C13   N14  C19  C17     0.00   0.0  0
 T3M  CONST_23  C13   C15  N16  C17     0.00   0.0  0
 T3M  CONST_24  C12   C13  C15  N16   180.00   0.0  0
 T3M  CONST_27  C3    C4   C12  C13   180.00   0.0  0
 T3M  CONST_28  C8    C11  C12  C13   180.00   0.0  0
 T3M  CONST_29  C5    C3   C4   C12     0.00   0.0  0
 T3M  CONST_30  C5    C8   C11  C12     0.00   0.0  0
 T3M  CONST_31  C8    C11  C12  C4      0.00   0.0  0
 T3M  CONST_32  C8    C5   C3   C4      0.00   0.0  0
 T3M  CONST_33  C3    C4   C12  C11     0.00   0.0  0
 T3M  CONST_34  C3    C5   C8   C11     0.00   0.0  0
 T3M  CONST_35  C21   C22  C23  C24   180.00   0.0  0
 T3M  CONST_36  C28   C27  C23  C24   180.00   0.0  0
 T3M  CONST_37  N18   C17  C19  C20     0.00   0.0  0
 T3M  CONST_38  N18   C17  C19  N14   180.00   0.0  0
 T3M  CONST_39  C15   N16  C17  N18   180.00   0.0  0
 T3M  CONST_40  O2    C3   C4   C12   180.00   0.0  0
 T3M  CONST_41  O9    C8   C11  C12   180.00   0.0  0
 T3M  CONST_42  O6    C5   C3   C4    180.00   0.0  0
 T3M  CONST_43  O6    C5   C8   C11   180.00   0.0  0
 T3M  CONST_44  O2    C3   C5   C8    180.00   0.0  0
 T3M  CONST_45  C3    C5   C8   O9    180.00   0.0  0
 T3M  CONST_46  H21   C21  C22  C23   180.00   0.0  0
 T3M  CONST_47  H28   C28  C27  C23   180.00   0.0  0
 T3M  CONST_48  H27   C27  C23  C22   180.00   0.0  0
 T3M  CONST_49  H22   C22  C23  C27   180.00   0.0  0
 T3M  CONST_50  H15   C15  C13  N14   180.00   0.0  0
 T3M  CONST_51  H4    C4   C12  C13     0.00   0.0  0
 T3M  CONST_52  H11   C11  C12  C13     0.00   0.0  0
 T3M  Var_01    C22   C23  C24  O26  -179.35  30.0  2
 T3M  Var_02    C5    C8   O9   C10   179.62  30.0  2
 T3M  Var_03    C3    C5   O6   C7    -90.14  30.0  2
 T3M  Var_04    H101  C10  O9   C8     60.37  30.0  3
 T3M  Var_05    H71C  C7   O6   C5   -179.50  30.0  3
 T3M  Var_06    H11C  C1   O2   C3    -61.69  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
 T3M  plan-1  C24   0.020
 T3M  plan-1  C23   0.020
 T3M  plan-1  C22   0.020
 T3M  plan-1  C21   0.020
 T3M  plan-1  C27   0.020
 T3M  plan-1  C28   0.020
 T3M  plan-1  C20   0.020
 T3M  plan-1  C19   0.020
 T3M  plan-1  H22   0.020
 T3M  plan-1  H27   0.020
 T3M  plan-1  H21   0.020
 T3M  plan-1  H28   0.020
 T3M  plan-2  C20   0.020
 T3M  plan-2  C19   0.020
 T3M  plan-2  N14   0.020
 T3M  plan-2  C17   0.020
 T3M  plan-2  N18   0.020
 T3M  plan-2  N16   0.020
 T3M  plan-2  C15   0.020
 T3M  plan-2  C13   0.020
 T3M  plan-2  C12   0.020
 T3M  plan-2  H15   0.020
 T3M  plan-3  C13   0.020
 T3M  plan-3  C12   0.020
 T3M  plan-3  C4    0.020
 T3M  plan-3  C11   0.020
 T3M  plan-3  C8    0.020
 T3M  plan-3  O9    0.020
 T3M  plan-3  C5    0.020
 T3M  plan-3  O6    0.020
 T3M  plan-3  C3    0.020
 T3M  plan-3  O2    0.020
 T3M  plan-3  H4    0.020
 T3M  plan-3  H11   0.020
 T3M  plan-4  C17   0.020
 T3M  plan-4  N18   0.020
 T3M  plan-4  H181  0.020
 T3M  plan-4  H182  0.020
 T3M  plan-5  O26   0.020
 T3M  plan-5  C24   0.020
 T3M  plan-5  O25   0.020
 T3M  plan-5  C23   0.020

