# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:55:26 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: [4-({5-carbamoyl-4-[(3-methylphenyl)amino]pyrimidin-2-yl}amino)phenyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Nc2nc(Nc3ccc(CC(O)=O)cc3)ncc2C(N)=O)c1
#
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
 S91  S91  '[4-({5-carbamoyl-4-[(3-methylphenyl)amino]pyrimidin-2-yl}amino)phenyl]acetic acid'  ligand  46  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S91
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
 S91  C1    C  CR6    0   0.164  -5.2447   0.2414   0.4745
 S91  C2    C  CR16   0  -0.293  -4.5105   1.3707   0.8328
 S91  C3    C  CR16   0  -0.338  -3.1292   1.3799   0.7785
 S91  C4    C  CR6    0   0.336  -2.4204   0.2541   0.3478
 S91  C5    C  CR16   0  -0.286  -3.1390  -0.8800  -0.0235
 S91  C6    C  CR16   0  -0.311  -4.5268  -0.8704   0.0500
 S91  C7    C  CH2    0  -0.691  -6.7388   0.2324   0.5262
 S91  C8    C  C      0   0.420  -7.4355   0.9642  -0.6493
 S91  O1    O  OC    -1  -0.623  -8.6586   0.7481  -0.7592
 S91  O2    O  O      0  -0.597  -6.7411   1.7120  -1.3593
 S91  N1    N  N      0  -0.532   1.1815  -0.0671   0.1974
 S91  C9    C  CR6    0   0.577   2.1998  -0.9092   0.1398
 S91  C10   C  CR6    0  -0.296   1.9722  -2.3233   0.1045
 S91  C11   C  CR16   0  -0.009   0.6418  -2.6927   0.1985
 S91  N2    N  N      0  -0.484  -0.3780  -1.8541   0.2693
 S91  C12   C  CR6    0   0.624  -0.0547  -0.5619   0.2447
 S91  O3    O  O      0  -0.515   4.2505  -2.9751   0.1381
 S91  N4    N  NH1    0  -0.760  -1.0286   0.3749   0.2882
 S91  N5    N  NH2    0  -0.818   2.7411  -4.5832  -0.2490
 S91  C14   C  CR16   0  -0.317   5.2207   3.3620  -0.0151
 S91  C15   C  CR16   0  -0.232   3.8437   3.2668   0.0868
 S91  C16   C  CR16   0  -0.331   3.1977   2.0370   0.1340
 S91  C17   C  CR6    0   0.392   3.9577   0.8685   0.0768
 S91  C18   C  CR16   0  -0.428   5.3514   0.9738  -0.0251
 S91  C19   C  CR6    0   0.117   5.9934   2.2014  -0.0702
 S91  C20   C  CH3    0  -0.724   7.4894   2.2804  -0.1637
 S91  H2    H  HCR6   0   0.242  -5.0238   2.2596   1.1790
 S91  H3    H  HCR6   0   0.261  -2.5880   2.2710   1.0763
 S91  H5    H  HCR6   0   0.270  -2.6297  -1.7672  -0.3629
 S91  H6    H  HCR6   0   0.242  -5.0615  -1.7669  -0.2430
 S91  H71   H  HCH2   0   0.238  -7.1079  -0.7951   0.5749
 S91  H72   H  HCH2   0   0.247  -7.0812   0.7142   1.4489
 S91  H11   H  HCR6   0   0.264   0.3643  -3.7408   0.2373
 S91  HN3   H  HNH1   0   0.434   4.1537  -1.1780   0.1101
 S91  HN4   H  HNH1   0   0.410  -0.6748   1.3184   0.3413
 S91  HN51  H  HNH2   0   0.415   1.8182  -4.8809  -0.5092
 S91  HN52  H  HNH2   0   0.409   3.4785  -5.2613  -0.3511
 S91  H15   H  HCR6   0   0.253   3.2451   4.1681   0.1302
 S91  H16   H  HCR6   0   0.284   2.1251   1.9940   0.2105
 S91  H18   H  HCR6   0   0.256   5.9478   0.0686  -0.0765
 S91  H201  H  HCH3   0   0.249   7.9254   2.5845   0.7898
 S91  H202  H  HCH3   0   0.244   7.9277   1.3206  -0.4343
 S91  H203  H  HCH3   0   0.245   7.8017   3.0149  -0.9065
 S91  C13   C  C      0   0.545   3.0688  -3.3075  -0.0013
 S91  N3    N  NH1    0  -0.795   3.4588  -0.4332   0.1092
 S91  H14   H  HCR6   0   0.244   5.6982   4.3336  -0.0552

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
 S91  C1   C2    aromatic  1.394  0.020  1.394
 S91  C1   C6    aromatic  1.390  0.020  1.390
 S91  C1   C7    single    1.495  0.020  1.495
 S91  C2   C3    aromatic  1.382  0.020  1.382
 S91  C2   H2    single    0.930  0.020  1.080
 S91  C3   C4    aromatic  1.398  0.020  1.398
 S91  C3   H3    single    0.930  0.020  1.080
 S91  C4   C5    aromatic  1.393  0.020  1.393
 S91  C4   N4    single    1.398  0.020  1.398
 S91  C5   C6    aromatic  1.390  0.020  1.390
 S91  C5   H5    single    0.930  0.020  1.080
 S91  C6   H6    single    0.930  0.020  1.080
 S91  C7   C8    single    1.550  0.020  1.550
 S91  C7   H71   single    0.970  0.020  1.090
 S91  C7   H72   single    0.970  0.020  1.090
 S91  C8   O1    deloc     1.247  0.020  1.247
 S91  C8   O2    deloc     1.243  0.020  1.243
 S91  N1   C9    aromatic  1.323  0.020  1.323
 S91  N1   C12   aromatic  1.332  0.020  1.332
 S91  C9   C10   aromatic  1.433  0.020  1.433
 S91  C9   N3    single    1.346  0.020  1.346
 S91  C10  C11   aromatic  1.384  0.020  1.384
 S91  C10  C13   single    1.477  0.020  1.477
 S91  C11  N2    aromatic  1.322  0.020  1.322
 S91  C11  H11   single    0.930  0.020  1.080
 S91  N2   C12   aromatic  1.332  0.020  1.332
 S91  C12  N4    single    1.352  0.020  1.352
 S91  C13  O3    double    1.235  0.020  1.235
 S91  C13  N5    single    1.340  0.020  1.340
 S91  N3   C17   single    1.394  0.020  1.394
 S91  N3   HN3   single    0.860  0.020  1.020
 S91  N4   HN4   single    0.860  0.020  1.020
 S91  N5   HN51  single    0.860  0.020  1.020
 S91  N5   HN52  single    0.860  0.020  1.020
 S91  C14  C15   aromatic  1.384  0.020  1.384
 S91  C14  C19   aromatic  1.395  0.020  1.395
 S91  C14  H14   single    0.930  0.020  1.080
 S91  C15  C16   aromatic  1.390  0.020  1.390
 S91  C15  H15   single    0.930  0.020  1.080
 S91  C16  C17   aromatic  1.395  0.020  1.395
 S91  C16  H16   single    0.930  0.020  1.080
 S91  C17  C18   aromatic  1.401  0.020  1.401
 S91  C18  C19   aromatic  1.386  0.020  1.386
 S91  C18  H18   single    0.930  0.020  1.080
 S91  C19  C20   single    1.501  0.020  1.501
 S91  C20  H201  single    0.970  0.020  1.090
 S91  C20  H202  single    0.970  0.020  1.090
 S91  C20  H203  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
 S91  C7    C1   C6    121.46  3.000
 S91  C7    C1   C2    121.49  3.000
 S91  C6    C1   C2    117.04  3.000
 S91  H2    C2   C3    118.72  3.000
 S91  H2    C2   C1    119.83  3.000
 S91  C3    C2   C1    121.44  3.000
 S91  H3    C3   C4    119.55  3.000
 S91  H3    C3   C2    119.56  3.000
 S91  C4    C3   C2    120.88  3.000
 S91  N4    C4   C5    124.92  3.000
 S91  N4    C4   C3    116.63  3.000
 S91  C5    C4   C3    118.42  3.000
 S91  H5    C5   C6    119.62  3.000
 S91  H5    C5   C4    120.68  3.000
 S91  C6    C5   C4    119.70  3.000
 S91  H6    C6   C5    118.20  3.000
 S91  H6    C6   C1    119.29  3.000
 S91  C5    C6   C1    122.51  3.000
 S91  H72   C7   H71   105.69  3.000
 S91  H72   C7   C8    106.90  3.000
 S91  H71   C7   C8    109.02  3.000
 S91  H72   C7   C1    109.80  3.000
 S91  H71   C7   C1    110.16  3.000
 S91  C8    C7   C1    114.84  3.000
 S91  O2    C8   O1    127.00  3.000
 S91  O2    C8   C7    117.77  3.000
 S91  O1    C8   C7    115.21  3.000
 S91  C12   N1   C9    118.65  3.000
 S91  N3    C9   C10   119.80  3.000
 S91  N3    C9   N1    119.73  3.000
 S91  C10   C9   N1    120.47  3.000
 S91  C13   C10  C11   122.73  3.000
 S91  C13   C10  C9    122.77  3.000
 S91  C11   C10  C9    114.49  3.000
 S91  H11   C11  N2    114.42  3.000
 S91  H11   C11  C10   120.41  3.000
 S91  N2    C11  C10   125.16  3.000
 S91  C12   N2   C11   115.28  3.000
 S91  N4    C12  N2    119.78  3.000
 S91  N4    C12  N1    114.34  3.000
 S91  N2    C12  N1    125.87  3.000
 S91  HN4   N4   C12   113.39  3.000
 S91  HN4   N4   C4    115.31  3.000
 S91  C12   N4   C4    131.19  3.000
 S91  HN52  N5   HN51  116.56  3.000
 S91  HN52  N5   C13   118.73  3.000
 S91  HN51  N5   C13   123.70  3.000
 S91  H14   C14  C19   120.03  3.000
 S91  H14   C14  C15   120.19  3.000
 S91  C19   C14  C15   119.78  3.000
 S91  H15   C15  C16   118.57  3.000
 S91  H15   C15  C14   119.72  3.000
 S91  C16   C15  C14   121.71  3.000
 S91  H16   C16  C17   120.82  3.000
 S91  H16   C16  C15   120.06  3.000
 S91  C17   C16  C15   119.11  3.000
 S91  C18   C17  C16   118.81  3.000
 S91  C18   C17  N3    115.32  3.000
 S91  C16   C17  N3    125.88  3.000
 S91  H18   C18  C19   118.86  3.000
 S91  H18   C18  C17   119.16  3.000
 S91  C19   C18  C17   121.98  3.000
 S91  C20   C19  C18   120.68  3.000
 S91  C20   C19  C14   120.70  3.000
 S91  C18   C19  C14   118.61  3.000
 S91  H203  C20  H202  108.01  3.000
 S91  H203  C20  H201  107.04  3.000
 S91  H202  C20  H201  107.56  3.000
 S91  H203  C20  C19   111.30  3.000
 S91  H202  C20  C19   111.72  3.000
 S91  H201  C20  C19   110.99  3.000
 S91  N5    C13  O3    120.72  3.000
 S91  N5    C13  C10   117.77  3.000
 S91  O3    C13  C10   121.52  3.000
 S91  HN3   N3   C17   116.01  3.000
 S91  HN3   N3   C9    112.30  3.000
 S91  C17   N3   C9    131.69  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
 S91  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 S91  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 S91  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 S91  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 S91  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 S91  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 S91  CONST_07  C11   C10  C9   N1      0.00   0.0  0
 S91  CONST_08  C11   N2   C12  N1      0.00   0.0  0
 S91  CONST_09  N2    C12  N1   C9      0.00   0.0  0
 S91  CONST_10  N2    C11  C10  C9      0.00   0.0  0
 S91  CONST_11  C12   N1   C9   C10     0.00   0.0  0
 S91  CONST_12  C12   N2   C11  C10     0.00   0.0  0
 S91  CONST_13  C17   C16  C15  C14     0.00   0.0  0
 S91  CONST_14  C17   C18  C19  C14     0.00   0.0  0
 S91  CONST_15  C18   C19  C14  C15     0.00   0.0  0
 S91  CONST_16  C18   C17  C16  C15     0.00   0.0  0
 S91  CONST_17  C19   C14  C15  C16     0.00   0.0  0
 S91  CONST_18  C19   C18  C17  C16     0.00   0.0  0
 S91  CONST_19  N4    C4   C3   C2    180.00   0.0  0
 S91  CONST_20  C7    C1   C2   C3    180.00   0.0  0
 S91  CONST_21  C7    C1   C6   C5    180.00   0.0  0
 S91  CONST_22  N4    C4   C5   C6    180.00   0.0  0
 S91  CONST_23  C13   C10  C9   N1    180.00   0.0  0
 S91  CONST_24  N4    C12  N1   C9    180.00   0.0  0
 S91  CONST_25  N3    C9   C10  C11   180.00   0.0  0
 S91  CONST_26  N4    C12  N2   C11   180.00   0.0  0
 S91  CONST_27  C13   C10  C11  N2    180.00   0.0  0
 S91  CONST_28  N3    C9   N1   C12   180.00   0.0  0
 S91  CONST_29  C15   C16  C17  N3    180.00   0.0  0
 S91  CONST_30  C19   C18  C17  N3    180.00   0.0  0
 S91  CONST_31  C20   C19  C14  C15   180.00   0.0  0
 S91  CONST_32  C20   C19  C18  C17   180.00   0.0  0
 S91  CONST_33  H3    C3   C2   C1    180.00   0.0  0
 S91  CONST_34  H5    C5   C6   C1    180.00   0.0  0
 S91  CONST_35  H6    C6   C1   C2    180.00   0.0  0
 S91  CONST_36  H2    C2   C3   C4    180.00   0.0  0
 S91  CONST_37  H11   C11  C10  C9    180.00   0.0  0
 S91  CONST_38  H16   C16  C15  C14   180.00   0.0  0
 S91  CONST_39  H18   C18  C19  C14   180.00   0.0  0
 S91  CONST_40  H14   C14  C15  C16   180.00   0.0  0
 S91  CONST_41  H15   C15  C16  C17   180.00   0.0  0
 S91  CONST_42  HN51  N5   C13  C10     0.00   0.0  0
 S91  CONST_43  HN52  N5   C13  C10   180.00   0.0  0
 S91  Var_01    C12   N4   C4   C3    161.44  30.0  2
 S91  Var_02    N1    C12  N4   C4   -179.76  30.0  3
 S91  Var_03    C17   N3   C9   N1     -2.75  30.0  2
 S91  Var_04    C16   C17  N3   C9      3.31  30.0  2
 S91  Var_05    C8    C7   C1   C2     77.29  30.0  2
 S91  Var_06    O3    C13  C10  C9     11.15  30.0  2
 S91  Var_07    H201  C20  C19  C14    73.50  30.0  2
 S91  Var_08    O1    C8   C7   C1    166.81  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
 S91  plan-1  C1    0.020
 S91  plan-1  C2    0.020
 S91  plan-1  C3    0.020
 S91  plan-1  C4    0.020
 S91  plan-1  C5    0.020
 S91  plan-1  C6    0.020
 S91  plan-1  C7    0.020
 S91  plan-1  N4    0.020
 S91  plan-1  H2    0.020
 S91  plan-1  H3    0.020
 S91  plan-1  H5    0.020
 S91  plan-1  H6    0.020
 S91  plan-2  N1    0.020
 S91  plan-2  C9    0.020
 S91  plan-2  C10   0.020
 S91  plan-2  C11   0.020
 S91  plan-2  N2    0.020
 S91  plan-2  C12   0.020
 S91  plan-2  N4    0.020
 S91  plan-2  H11   0.020
 S91  plan-2  C13   0.020
 S91  plan-2  N3    0.020
 S91  plan-3  C14   0.020
 S91  plan-3  C15   0.020
 S91  plan-3  C16   0.020
 S91  plan-3  C17   0.020
 S91  plan-3  C18   0.020
 S91  plan-3  C19   0.020
 S91  plan-3  C20   0.020
 S91  plan-3  H15   0.020
 S91  plan-3  H16   0.020
 S91  plan-3  H18   0.020
 S91  plan-3  N3    0.020
 S91  plan-3  H14   0.020
 S91  plan-4  C10   0.020
 S91  plan-4  O3    0.020
 S91  plan-4  N5    0.020
 S91  plan-4  HN51  0.020
 S91  plan-4  HN52  0.020
 S91  plan-4  C13   0.020
 S91  plan-5  C7    0.020
 S91  plan-5  C8    0.020
 S91  plan-5  O1    0.020
 S91  plan-5  O2    0.020

