# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:06:29 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N-(4-{[3-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-methoxybenzoyl]amino}phenyl)pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(c1)C2=CNC(=O)NC2=O)C(=O)Nc3ccc(NC(=O)c4ccccn4)cc3
#
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
 1SG  1SG  N-(4-{[3-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-methoxybenzoyl]amino}phenyl)pyridine-2-carboxamide  ligand  53  34  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1SG
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
 1SG  C1   C  CH3   0  -0.444  -2.9763  -4.7857   0.1298
 1SG  O2   O  O2    0  -0.470  -4.0468  -3.8629   0.0649
 1SG  C3   C  CR6   0   0.433  -3.7741  -2.5487   0.1240
 1SG  C4   C  CR16  0  -0.386  -4.8726  -1.6934   0.0436
 1SG  C5   C  CR6   0   0.145  -4.7031  -0.3172   0.1185
 1SG  C6   C  CR16  0  -0.368  -3.4178   0.2057   0.2654
 1SG  C7   C  CR6   0   0.013  -2.3223  -0.6412   0.3360
 1SG  C8   C  CR16  0  -0.453  -2.4942  -2.0236   0.2724
 1SG  C9   C  C     0   0.524  -0.9739  -0.0147   0.5059
 1SG  O10  O  O     0  -0.461  -0.8470   1.0588   1.0701
 1SG  N11  N  NH1   0  -0.757   0.0554  -0.7187  -0.0225
 1SG  C12  C  CR6   0   0.369   1.4271  -0.4430   0.0158
 1SG  C13  C  CR16  0  -0.304   1.9981   0.7087   0.5519
 1SG  C14  C  CR16  0  -0.308   3.3750   0.8907   0.5402
 1SG  C15  C  CR6   0   0.372   4.2188  -0.0715  -0.0096
 1SG  C16  C  CR16  0  -0.339   3.6425  -1.2246  -0.5475
 1SG  C17  C  CR16  0  -0.342   2.2762  -1.4061  -0.5339
 1SG  N18  N  NH1   0  -0.757   5.6097   0.0253  -0.0645
 1SG  C19  C  C     0   0.532   6.4142   1.0260   0.3444
 1SG  O20  O  O     0  -0.460   6.0454   2.0676   0.8609
 1SG  C21  C  CR6   0   0.125   7.8719   0.7519   0.1037
 1SG  C22  C  CR16  0  -0.296   8.8178   1.6978   0.4715
 1SG  C23  C  CR16  0  -0.145  10.1543   1.4135   0.2330
 1SG  C24  C  CR16  0  -0.318  10.4879   0.2055  -0.3576
 1SG  C25  C  CR16  0  -0.057   9.4654  -0.6745  -0.6889
 1SG  N26  N  N     0  -0.444   8.1891  -0.4071  -0.4635
 1SG  C27  C  CR6   0  -0.235  -5.8592   0.5937   0.0808
 1SG  C28  C  CR16  0   0.074  -5.9615   1.6246   0.9476
 1SG  N29  N  NR16  0  -0.671  -6.9930   2.5031   0.9305
 1SG  C30  C  CR6   0   0.686  -8.0296   2.4293   0.0388
 1SG  O31  O  O     0  -0.472  -8.9530   3.2146   0.0253
 1SG  N32  N  NR16  0  -0.719  -7.9203   1.3796  -0.8364
 1SG  C33  C  CR6   0   0.567  -6.9116   0.4318  -0.9110
 1SG  O34  O  O     0  -0.444  -6.9509  -0.4339  -1.7641
 1SG  H1   H  HCH3  0   0.265  -3.4162  -5.7744   0.0301
 1SG  H2   H  HCH3  0   0.232  -2.2584  -4.6350  -0.6804
 1SG  H3   H  HCH3  0   0.233  -2.4483  -4.7326   1.0856
 1SG  H4   H  HCR6  0   0.266  -5.8600  -2.1243  -0.0537
 1SG  H5   H  HCR6  0   0.260  -3.2724   1.2773   0.2984
 1SG  H6   H  HCR6  0   0.284  -1.6440  -2.6849   0.3717
 1SG  H7   H  HNH1  0   0.420  -0.1842  -1.5474  -0.5442
 1SG  H8   H  HCR6  0   0.283   1.3870   1.4831   0.9839
 1SG  H9   H  HCR6  0   0.283   3.7721   1.7972   0.9659
 1SG  H10  H  HCR6  0   0.276   4.2704  -1.9931  -0.9824
 1SG  H11  H  HCR6  0   0.276   1.8643  -2.3148  -0.9564
 1SG  H12  H  HNH1  0   0.420   6.0994  -0.7605  -0.4760
 1SG  H13  H  HCR6  0   0.279   8.5173   2.6286   0.9304
 1SG  H14  H  HCR6  0   0.283  10.9221   2.1254   0.5047
 1SG  H15  H  HCR6  0   0.282  11.5166  -0.0573  -0.5600
 1SG  H16  H  HCR6  0   0.275   9.6885  -1.6278  -1.1529
 1SG  H17  H  HCR6  0   0.325  -5.2245   1.8028   1.7179
 1SG  H18  H  HNR6  0   0.442  -7.0190   3.2495   1.6097
 1SG  H19  H  HNR6  0   0.429  -8.6675   1.2942  -1.5151

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
 1SG  C24  C23  aromatic  1.385  0.020  1.385
 1SG  C24  C25  aromatic  1.389  0.020  1.389
 1SG  C23  C22  aromatic  1.387  0.020  1.387
 1SG  C25  N26  aromatic  1.323  0.020  1.323
 1SG  C22  C21  aromatic  1.387  0.020  1.387
 1SG  C21  N26  aromatic  1.329  0.020  1.329
 1SG  C21  C19  single    1.503  0.020  1.503
 1SG  C19  N18  single    1.348  0.020  1.348
 1SG  C19  O20  double    1.220  0.020  1.220
 1SG  N18  C15  single    1.395  0.020  1.395
 1SG  C16  C15  aromatic  1.397  0.020  1.397
 1SG  C16  C17  aromatic  1.378  0.020  1.378
 1SG  C15  C14  aromatic  1.393  0.020  1.393
 1SG  C17  C12  aromatic  1.397  0.020  1.397
 1SG  O10  C9   double    1.219  0.020  1.219
 1SG  C14  C13  aromatic  1.389  0.020  1.389
 1SG  C12  C13  aromatic  1.393  0.020  1.393
 1SG  C12  N11  single    1.400  0.020  1.400
 1SG  N29  C28  single    1.355  0.020  1.355
 1SG  N29  C30  single    1.369  0.020  1.369
 1SG  O31  C30  double    1.212  0.020  1.212
 1SG  C9   N11  single    1.354  0.020  1.354
 1SG  C9   C7   single    1.497  0.020  1.497
 1SG  C28  C27  double    1.351  0.020  1.351
 1SG  C30  N32  single    1.371  0.020  1.371
 1SG  C6   C7   aromatic  1.386  0.020  1.386
 1SG  C6   C5   aromatic  1.395  0.020  1.395
 1SG  C7   C8   aromatic  1.394  0.020  1.394
 1SG  C27  C5   single    1.472  0.020  1.472
 1SG  C27  C33  single    1.455  0.020  1.455
 1SG  N32  C33  single    1.386  0.020  1.386
 1SG  C5   C4   aromatic  1.389  0.020  1.389
 1SG  C33  O34  double    1.216  0.020  1.216
 1SG  C8   C3   aromatic  1.391  0.020  1.391
 1SG  C4   C3   aromatic  1.395  0.020  1.395
 1SG  C3   O2   single    1.343  0.020  1.343
 1SG  O2   C1   single    1.415  0.020  1.415
 1SG  C1   H1   single    0.970  0.020  1.090
 1SG  C1   H2   single    0.970  0.020  1.090
 1SG  C1   H3   single    0.970  0.020  1.090
 1SG  C4   H4   single    0.930  0.020  1.080
 1SG  C6   H5   single    0.930  0.020  1.080
 1SG  C8   H6   single    0.930  0.020  1.080
 1SG  N11  H7   single    0.860  0.020  1.020
 1SG  C13  H8   single    0.930  0.020  1.080
 1SG  C14  H9   single    0.930  0.020  1.080
 1SG  C16  H10  single    0.930  0.020  1.080
 1SG  C17  H11  single    0.930  0.020  1.080
 1SG  N18  H12  single    0.860  0.020  1.020
 1SG  C22  H13  single    0.930  0.020  1.080
 1SG  C23  H14  single    0.930  0.020  1.080
 1SG  C24  H15  single    0.930  0.020  1.080
 1SG  C25  H16  single    0.930  0.020  1.080
 1SG  C28  H17  single    0.930  0.020  1.080
 1SG  N29  H18  single    0.860  0.020  1.020
 1SG  N32  H19  single    0.860  0.020  1.020

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
 1SG  H3   C1   H2   108.92  3.000
 1SG  H3   C1   H1   108.66  3.000
 1SG  H2   C1   H1   108.86  3.000
 1SG  H3   C1   O2   111.95  3.000
 1SG  H2   C1   O2   111.91  3.000
 1SG  H1   C1   O2   106.43  3.000
 1SG  C3   O2   C1   118.84  3.000
 1SG  C8   C3   C4   119.95  3.000
 1SG  C4   C3   O2   115.95  3.000
 1SG  C8   C3   O2   124.10  3.000
 1SG  H4   C4   C5   120.73  3.000
 1SG  H4   C4   C3   118.68  3.000
 1SG  C5   C4   C3   120.57  3.000
 1SG  C27  C5   C6   119.61  3.000
 1SG  C27  C5   C4   121.06  3.000
 1SG  C6   C5   C4   119.31  3.000
 1SG  H5   C6   C7   119.83  3.000
 1SG  H5   C6   C5   119.88  3.000
 1SG  C7   C6   C5   120.28  3.000
 1SG  C9   C7   C8   122.09  3.000
 1SG  C8   C7   C6   120.39  3.000
 1SG  C9   C7   C6   117.51  3.000
 1SG  H6   C8   C7   120.33  3.000
 1SG  H6   C8   C3   120.14  3.000
 1SG  C7   C8   C3   119.49  3.000
 1SG  N11  C9   O10  123.99  3.000
 1SG  N11  C9   C7   115.01  3.000
 1SG  O10  C9   C7   120.99  3.000
 1SG  H7   N11  C12  114.15  3.000
 1SG  H7   N11  C9   116.65  3.000
 1SG  C12  N11  C9   129.18  3.000
 1SG  C17  C12  C13  118.20  3.000
 1SG  C13  C12  N11  125.11  3.000
 1SG  C17  C12  N11  116.69  3.000
 1SG  H8   C13  C14  118.14  3.000
 1SG  H8   C13  C12  121.09  3.000
 1SG  C14  C13  C12  120.77  3.000
 1SG  H9   C14  C15  120.93  3.000
 1SG  H9   C14  C13  118.19  3.000
 1SG  C15  C14  C13  120.89  3.000
 1SG  N18  C15  C16  116.96  3.000
 1SG  C16  C15  C14  118.19  3.000
 1SG  N18  C15  C14  124.85  3.000
 1SG  H10  C16  C17  119.01  3.000
 1SG  H10  C16  C15  120.07  3.000
 1SG  C17  C16  C15  120.92  3.000
 1SG  H11  C17  C16  118.91  3.000
 1SG  H11  C17  C12  120.04  3.000
 1SG  C16  C17  C12  121.04  3.000
 1SG  H12  N18  C19  114.25  3.000
 1SG  H12  N18  C15  116.35  3.000
 1SG  C19  N18  C15  129.40  3.000
 1SG  C21  C19  O20  121.13  3.000
 1SG  O20  C19  N18  125.60  3.000
 1SG  C21  C19  N18  113.27  3.000
 1SG  N26  C21  C22  123.03  3.000
 1SG  N26  C21  C19  117.33  3.000
 1SG  C22  C21  C19  119.64  3.000
 1SG  H13  C22  C23  121.17  3.000
 1SG  H13  C22  C21  120.69  3.000
 1SG  C23  C22  C21  118.14  3.000
 1SG  H14  C23  C24  120.66  3.000
 1SG  H14  C23  C22  120.39  3.000
 1SG  C24  C23  C22  118.95  3.000
 1SG  H15  C24  C25  120.12  3.000
 1SG  H15  C24  C23  121.40  3.000
 1SG  C25  C24  C23  118.48  3.000
 1SG  H16  C25  N26  116.70  3.000
 1SG  H16  C25  C24  120.53  3.000
 1SG  N26  C25  C24  122.77  3.000
 1SG  C25  N26  C21  118.64  3.000
 1SG  C33  C27  C28  117.87  3.000
 1SG  C33  C27  C5   121.10  3.000
 1SG  C28  C27  C5   121.02  3.000
 1SG  H17  C28  N29  114.91  3.000
 1SG  H17  C28  C27  122.10  3.000
 1SG  N29  C28  C27  122.99  3.000
 1SG  H18  N29  C30  117.29  3.000
 1SG  H18  N29  C28  119.37  3.000
 1SG  C30  N29  C28  123.34  3.000
 1SG  N32  C30  O31  123.34  3.000
 1SG  N32  C30  N29  113.37  3.000
 1SG  O31  C30  N29  123.30  3.000
 1SG  H19  N32  C33  116.31  3.000
 1SG  H19  N32  C30  115.68  3.000
 1SG  C33  N32  C30  128.01  3.000
 1SG  O34  C33  N32  120.06  3.000
 1SG  O34  C33  C27  125.50  3.000
 1SG  N32  C33  C27  114.43  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
 1SG  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 1SG  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 1SG  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 1SG  CONST_04  C7   C8   C3   C4      0.00   0.0  0
 1SG  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 1SG  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 1SG  CONST_07  C15  C16  C17  C12     0.00   0.0  0
 1SG  CONST_08  C15  C14  C13  C12     0.00   0.0  0
 1SG  CONST_09  C16  C15  C14  C13     0.00   0.0  0
 1SG  CONST_10  C16  C17  C12  C13     0.00   0.0  0
 1SG  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 1SG  CONST_12  C17  C12  C13  C14     0.00   0.0  0
 1SG  CONST_13  C24  C23  C22  C21     0.00   0.0  0
 1SG  CONST_14  C24  C25  N26  C21     0.00   0.0  0
 1SG  CONST_15  C25  C24  C23  C22     0.00   0.0  0
 1SG  CONST_16  C25  N26  C21  C22     0.00   0.0  0
 1SG  CONST_17  N26  C25  C24  C23     0.00   0.0  0
 1SG  CONST_18  N26  C21  C22  C23     0.00   0.0  0
 1SG  CONST_19  C27  C5   C4   C3    180.00   0.0  0
 1SG  CONST_20  C27  C5   C6   C7    180.00   0.0  0
 1SG  CONST_21  C30  N32  C33  C27     0.00   0.0  0
 1SG  CONST_22  N32  C30  N29  C28     0.00   0.0  0
 1SG  CONST_23  C33  N32  C30  N29     0.00   0.0  0
 1SG  CONST_24  C7   C8   C3   O2    180.00   0.0  0
 1SG  CONST_25  C5   C4   C3   O2    180.00   0.0  0
 1SG  CONST_26  C9   C7   C8   C3    180.00   0.0  0
 1SG  CONST_27  C9   C7   C6   C5    180.00   0.0  0
 1SG  CONST_28  C16  C17  C12  N11   180.00   0.0  0
 1SG  CONST_29  C14  C13  C12  N11   180.00   0.0  0
 1SG  CONST_30  N18  C15  C14  C13   180.00   0.0  0
 1SG  CONST_31  N18  C15  C16  C17   180.00   0.0  0
 1SG  CONST_32  C23  C22  C21  C19   180.00   0.0  0
 1SG  CONST_33  C25  N26  C21  C19   180.00   0.0  0
 1SG  CONST_34  O31  C30  N29  C28   180.00   0.0  0
 1SG  CONST_35  O34  C33  N32  C30   180.00   0.0  0
 1SG  CONST_36  C33  N32  C30  O31   180.00   0.0  0
 1SG  CONST_37  H5   C6   C5   C4    180.00   0.0  0
 1SG  CONST_38  H6   C8   C3   C4    180.00   0.0  0
 1SG  CONST_39  H4   C4   C5   C6    180.00   0.0  0
 1SG  CONST_40  H10  C16  C17  C12   180.00   0.0  0
 1SG  CONST_41  H9   C14  C13  C12   180.00   0.0  0
 1SG  CONST_42  H11  C17  C12  C13   180.00   0.0  0
 1SG  CONST_43  H8   C13  C14  C15   180.00   0.0  0
 1SG  CONST_44  H14  C23  C22  C21   180.00   0.0  0
 1SG  CONST_45  H16  C25  N26  C21   180.00   0.0  0
 1SG  CONST_46  H15  C24  C23  C22   180.00   0.0  0
 1SG  CONST_47  H13  C22  C23  C24   180.00   0.0  0
 1SG  CONST_48  H19  N32  C33  C27   180.00   0.0  0
 1SG  CONST_49  H18  N29  C30  N32   180.00   0.0  0
 1SG  CONST_50  C12  N11  C9   C7    180.00   0.0  0
 1SG  CONST_51  C21  C19  N18  C15   180.00   0.0  0
 1SG  CONST_52  C17  C12  N11  C9    180.00   0.0  0
 1SG  CONST_53  C13  C12  N11  C9      0.00   0.0  0
 1SG  CONST_54  C19  N18  C15  C14     0.00   0.0  0
 1SG  CONST_55  C19  N18  C15  C16   180.00   0.0  0
 1SG  CONST_56  H7   N11  C12  C13   180.00   0.0  0
 1SG  CONST_57  H12  N18  C15  C14   180.00   0.0  0
 1SG  CONST_58  C12  N11  C9   O10     0.00   0.0  0
 1SG  CONST_59  O20  C19  N18  C15     0.00   0.0  0
 1SG  Var_01    C28  C27  C5   C4    134.64  30.0  2
 1SG  Var_02    C8   C3   O2   C1     -1.28  30.0  3
 1SG  Var_03    O10  C9   C7   C6     28.23  30.0  2
 1SG  Var_04    C22  C21  C19  N18   179.81  30.0  2
 1SG  Var_05    H1   C1   O2   C3   -178.06  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
 1SG  plan-1  O2   0.020
 1SG  plan-1  C3   0.020
 1SG  plan-1  C4   0.020
 1SG  plan-1  C5   0.020
 1SG  plan-1  C6   0.020
 1SG  plan-1  C7   0.020
 1SG  plan-1  C8   0.020
 1SG  plan-1  C9   0.020
 1SG  plan-1  C27  0.020
 1SG  plan-1  H4   0.020
 1SG  plan-1  H5   0.020
 1SG  plan-1  H6   0.020
 1SG  plan-2  N11  0.020
 1SG  plan-2  C12  0.020
 1SG  plan-2  C13  0.020
 1SG  plan-2  C14  0.020
 1SG  plan-2  C15  0.020
 1SG  plan-2  C16  0.020
 1SG  plan-2  C17  0.020
 1SG  plan-2  N18  0.020
 1SG  plan-2  H8   0.020
 1SG  plan-2  H9   0.020
 1SG  plan-2  H10  0.020
 1SG  plan-2  H11  0.020
 1SG  plan-3  C19  0.020
 1SG  plan-3  C21  0.020
 1SG  plan-3  C22  0.020
 1SG  plan-3  C23  0.020
 1SG  plan-3  C24  0.020
 1SG  plan-3  C25  0.020
 1SG  plan-3  N26  0.020
 1SG  plan-3  H13  0.020
 1SG  plan-3  H14  0.020
 1SG  plan-3  H15  0.020
 1SG  plan-3  H16  0.020
 1SG  plan-4  C5   0.020
 1SG  plan-4  C27  0.020
 1SG  plan-4  C28  0.020
 1SG  plan-4  N29  0.020
 1SG  plan-4  C30  0.020
 1SG  plan-4  O31  0.020
 1SG  plan-4  N32  0.020
 1SG  plan-4  C33  0.020
 1SG  plan-4  O34  0.020
 1SG  plan-4  H17  0.020
 1SG  plan-4  H18  0.020
 1SG  plan-4  H19  0.020
 1SG  plan-5  C7   0.020
 1SG  plan-5  C9   0.020
 1SG  plan-5  O10  0.020
 1SG  plan-5  N11  0.020
 1SG  plan-5  C12  0.020
 1SG  plan-5  H7   0.020
 1SG  plan-6  C15  0.020
 1SG  plan-6  N18  0.020
 1SG  plan-6  C19  0.020
 1SG  plan-6  O20  0.020
 1SG  plan-6  C21  0.020
 1SG  plan-6  H12  0.020

