# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 22:52:55 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-({4-[(2,4,6-trimethylphenyl)amino]pyrimidin-2-yl}amino)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(Nc2ccnc(Nc3ccc(cc3)C#N)n2)c(C)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
 TPB  TPB  4-({4-[(2,4,6-trimethylphenyl)amino]pyrimidin-2-yl}amino)benzonitrile  ligand  44  25  .  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_TPB
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
 TPB  C1    C  CR6   0   0.141   0.3036   0.3594   3.5803
 TPB  N7    N  NH1   0  -0.731   0.7524   0.6099   2.2608
 TPB  C2    C  CR6   0   0.132   0.9509  -0.6177   4.3415
 TPB  C21   C  CH3   0  -0.725   2.0953  -1.3989   3.7673
 TPB  C3    C  CR16  0  -0.395   0.5105  -0.8483   5.6395
 TPB  C4    C  CR6   0   0.139  -0.5549  -0.1391   6.1855
 TPB  C5    C  CR16  0  -0.394  -1.1799   0.8241   5.4013
 TPB  C6    C  CR6   0   0.141  -0.7635   1.0947   4.1014
 TPB  C61   C  CH3   0  -0.732  -1.4559   2.1451   3.2845
 TPB  C8    C  CR6   0   0.521   0.1427   0.1634   1.1460
 TPB  N1    N  N     0  -0.523   0.7140   0.4793  -0.0131
 TPB  C9    C  CR6   0   0.607   0.1257   0.0478  -1.1244
 TPB  N5    N  NH1   0  -0.769   0.7921   0.4144  -2.2673
 TPB  N3    N  N     0  -0.493  -0.9845  -0.6673  -1.2076
 TPB  C10   C  CR16  0  -0.005  -1.5436  -0.9822  -0.0355
 TPB  C7    C  CR16  0  -0.432  -1.0385  -0.6063   1.1812
 TPB  C11   C  CR6   0   0.390   0.5371   0.1704  -3.5968
 TPB  C12   C  CR16  0  -0.305  -0.5860  -0.5075  -4.0907
 TPB  C13   C  CR16  0  -0.230  -0.7407  -0.6885  -5.4514
 TPB  C14   C  CR6   0  -0.022   0.2071  -0.2065  -6.3533
 TPB  C15   C  CR16  0  -0.229   1.3292   0.4699  -5.8667
 TPB  C16   C  CR16  0  -0.350   1.4878   0.6528  -4.5130
 TPB  C17   C  CSP   0   0.046   0.0343  -0.4004  -7.7514
 TPB  N6    N  NS    0  -0.265  -0.1074  -0.5547  -8.8860
 TPB  C41   C  CH3   0  -0.723  -1.0001  -0.3873   7.5974
 TPB  HN7   H  HNH1  0   0.394   1.6354   1.0813   2.1260
 TPB  H211  H  HCH3  0   0.246   1.8322  -1.8554   2.8122
 TPB  H212  H  HCH3  0   0.248   2.9645  -0.7635   3.5861
 TPB  H213  H  HCH3  0   0.250   2.4066  -2.1930   4.4444
 TPB  H3    H  HCR6  0   0.242   1.0060  -1.6049   6.2376
 TPB  H5    H  HCR6  0   0.241  -2.0112   1.3865   5.8127
 TPB  H611  H  HCH3  0   0.249  -2.1042   1.6984   2.5270
 TPB  H612  H  HCH3  0   0.251  -2.0772   2.7801   3.9139
 TPB  H613  H  HCH3  0   0.247  -0.7453   2.7809   2.7569
 TPB  HN5   H  HNH1  0   0.411   1.6318   0.9408  -2.0763
 TPB  H10   H  HCR6  0   0.269  -2.4501  -1.5748  -0.0855
 TPB  H7    H  HCR6  0   0.282  -1.5178  -0.8912   2.1058
 TPB  H12   H  HCR6  0   0.298  -1.3310  -0.8896  -3.4134
 TPB  H13   H  HCR6  0   0.278  -1.6145  -1.2123  -5.8155
 TPB  H15   H  HCR6  0   0.280   2.0770   0.8501  -6.5494
 TPB  H16   H  HCR6  0   0.282   2.3648   1.1745  -4.1499
 TPB  H411  H  HCH3  0   0.249  -0.4489   0.2450   8.2967
 TPB  H412  H  HCH3  0   0.244  -2.0587  -0.1659   7.7278
 TPB  H413  H  HCH3  0   0.244  -0.8318  -1.4219   7.8960

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
 TPB  C1   N7    single    1.416  0.020  1.416
 TPB  C1   C2    aromatic  1.398  0.020  1.398
 TPB  C1   C6    aromatic  1.397  0.020  1.397
 TPB  N7   C8    single    1.347  0.020  1.347
 TPB  N7   HN7   single    0.860  0.020  1.020
 TPB  C2   C21   single    1.500  0.020  1.500
 TPB  C2   C3    aromatic  1.390  0.020  1.390
 TPB  C21  H211  single    0.970  0.020  1.090
 TPB  C21  H212  single    0.970  0.020  1.090
 TPB  C21  H213  single    0.970  0.020  1.090
 TPB  C3   C4    aromatic  1.391  0.020  1.391
 TPB  C3   H3    single    0.930  0.020  1.080
 TPB  C4   C5    aromatic  1.391  0.020  1.391
 TPB  C4   C41   single    1.501  0.020  1.501
 TPB  C5   C6    aromatic  1.391  0.020  1.391
 TPB  C5   H5    single    0.930  0.020  1.080
 TPB  C6   C61   single    1.500  0.020  1.500
 TPB  C61  H611  single    0.970  0.020  1.090
 TPB  C61  H612  single    0.970  0.020  1.090
 TPB  C61  H613  single    0.970  0.020  1.090
 TPB  C8   N1    aromatic  1.330  0.020  1.330
 TPB  C8   C7    aromatic  1.410  0.020  1.410
 TPB  N1   C9    aromatic  1.329  0.020  1.329
 TPB  C9   N5    single    1.373  0.020  1.373
 TPB  C9   N3    aromatic  1.323  0.020  1.323
 TPB  N5   C11   single    1.376  0.020  1.376
 TPB  N5   HN5   single    0.860  0.020  1.020
 TPB  N3   C10   aromatic  1.336  0.020  1.336
 TPB  C10  C7    aromatic  1.370  0.020  1.370
 TPB  C10  H10   single    0.930  0.020  1.080
 TPB  C7   H7    single    0.930  0.020  1.080
 TPB  C11  C12   aromatic  1.402  0.020  1.402
 TPB  C11  C16   aromatic  1.406  0.020  1.406
 TPB  C12  C13   aromatic  1.381  0.020  1.381
 TPB  C12  H12   single    0.930  0.020  1.080
 TPB  C13  C14   aromatic  1.394  0.020  1.394
 TPB  C13  H13   single    0.930  0.020  1.080
 TPB  C14  C15   aromatic  1.398  0.020  1.398
 TPB  C14  C17   single    1.422  0.020  1.422
 TPB  C15  C16   aromatic  1.375  0.020  1.375
 TPB  C15  H15   single    0.930  0.020  1.080
 TPB  C16  H16   single    0.930  0.020  1.080
 TPB  C17  N6    triple    1.154  0.020  1.154
 TPB  C41  H411  single    0.970  0.020  1.090
 TPB  C41  H412  single    0.970  0.020  1.090
 TPB  C41  H413  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
 TPB  C6    C1   C2    121.24  3.000
 TPB  C6    C1   N7    119.78  3.000
 TPB  C2    C1   N7    118.97  3.000
 TPB  HN7   N7   C8    116.11  3.000
 TPB  HN7   N7   C1    118.95  3.000
 TPB  C8    N7   C1    124.69  3.000
 TPB  C3    C2   C21   120.86  3.000
 TPB  C3    C2   C1    118.55  3.000
 TPB  C21   C2   C1    120.60  3.000
 TPB  H213  C21  H212  107.45  3.000
 TPB  H213  C21  H211  107.94  3.000
 TPB  H212  C21  H211  106.87  3.000
 TPB  H213  C21  C2    111.09  3.000
 TPB  H212  C21  C2    111.59  3.000
 TPB  H211  C21  C2    111.67  3.000
 TPB  H3    C3   C4    119.28  3.000
 TPB  H3    C3   C2    119.08  3.000
 TPB  C4    C3   C2    121.63  3.000
 TPB  C41   C4   C5    120.78  3.000
 TPB  C41   C4   C3    120.79  3.000
 TPB  C5    C4   C3    118.42  3.000
 TPB  H5    C5   C6    118.87  3.000
 TPB  H5    C5   C4    119.32  3.000
 TPB  C6    C5   C4    121.80  3.000
 TPB  C61   C6   C5    120.45  3.000
 TPB  C61   C6   C1    121.20  3.000
 TPB  C5    C6   C1    118.35  3.000
 TPB  H613  C61  H612  108.16  3.000
 TPB  H613  C61  H611  106.84  3.000
 TPB  H612  C61  H611  107.50  3.000
 TPB  H613  C61  C6    111.79  3.000
 TPB  H612  C61  C6    110.92  3.000
 TPB  H611  C61  C6    111.42  3.000
 TPB  C7    C8   N1    120.74  3.000
 TPB  C7    C8   N7    122.65  3.000
 TPB  N1    C8   N7    116.62  3.000
 TPB  C9    N1   C8    117.47  3.000
 TPB  N3    C9   N5    119.95  3.000
 TPB  N3    C9   N1    126.82  3.000
 TPB  N5    C9   N1    113.23  3.000
 TPB  HN5   N5   C11   115.45  3.000
 TPB  HN5   N5   C9    112.68  3.000
 TPB  C11   N5   C9    131.86  3.000
 TPB  C10   N3   C9    115.04  3.000
 TPB  H10   C10  C7    119.95  3.000
 TPB  H10   C10  N3    115.99  3.000
 TPB  C7    C10  N3    124.06  3.000
 TPB  H7    C7   C10   121.64  3.000
 TPB  H7    C7   C8    122.49  3.000
 TPB  C10   C7   C8    115.87  3.000
 TPB  C16   C11  C12   118.57  3.000
 TPB  C16   C11  N5    116.34  3.000
 TPB  C12   C11  N5    125.09  3.000
 TPB  H12   C12  C13   119.70  3.000
 TPB  H12   C12  C11   120.29  3.000
 TPB  C13   C12  C11   120.01  3.000
 TPB  H13   C13  C14   119.92  3.000
 TPB  H13   C13  C12   119.04  3.000
 TPB  C14   C13  C12   121.04  3.000
 TPB  C17   C14  C15   120.39  3.000
 TPB  C17   C14  C13   120.41  3.000
 TPB  C15   C14  C13   119.20  3.000
 TPB  H15   C15  C16   119.66  3.000
 TPB  H15   C15  C14   120.36  3.000
 TPB  C16   C15  C14   119.98  3.000
 TPB  H16   C16  C15   119.17  3.000
 TPB  H16   C16  C11   119.63  3.000
 TPB  C15   C16  C11   121.20  3.000
 TPB  N6    C17  C14   180.00  3.000
 TPB  H413  C41  H412  108.07  3.000
 TPB  H413  C41  H411  107.23  3.000
 TPB  H412  C41  H411  107.23  3.000
 TPB  H413  C41  C4    111.64  3.000
 TPB  H412  C41  C4    111.54  3.000
 TPB  H411  C41  C4    110.91  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
 TPB  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 TPB  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 TPB  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 TPB  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 TPB  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 TPB  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 TPB  CONST_07  N3    C9   N1   C8      0.00   0.0  0
 TPB  CONST_08  N3    C10  C7   C8      0.00   0.0  0
 TPB  CONST_09  C10   C7   C8   N1      0.00   0.0  0
 TPB  CONST_10  C10   N3   C9   N1      0.00   0.0  0
 TPB  CONST_11  C7    C8   N1   C9      0.00   0.0  0
 TPB  CONST_12  C7    C10  N3   C9      0.00   0.0  0
 TPB  CONST_13  C14   C13  C12  C11     0.00   0.0  0
 TPB  CONST_14  C14   C15  C16  C11     0.00   0.0  0
 TPB  CONST_15  C15   C16  C11  C12     0.00   0.0  0
 TPB  CONST_16  C15   C14  C13  C12     0.00   0.0  0
 TPB  CONST_17  C16   C11  C12  C13     0.00   0.0  0
 TPB  CONST_18  C16   C15  C14  C13     0.00   0.0  0
 TPB  CONST_19  C3    C2   C1   N7    180.00   0.0  0
 TPB  CONST_20  C5    C6   C1   N7    180.00   0.0  0
 TPB  CONST_21  C9    N1   C8   N7    180.00   0.0  0
 TPB  CONST_22  C10   C7   C8   N7    180.00   0.0  0
 TPB  CONST_23  C61   C6   C1   C2    180.00   0.0  0
 TPB  CONST_24  C41   C4   C3   C2    180.00   0.0  0
 TPB  CONST_25  C6    C1   C2   C21   180.00   0.0  0
 TPB  CONST_26  C4    C3   C2   C21   180.00   0.0  0
 TPB  CONST_27  C61   C6   C5   C4    180.00   0.0  0
 TPB  CONST_28  C41   C4   C5   C6    180.00   0.0  0
 TPB  CONST_29  N5    C9   N1   C8    180.00   0.0  0
 TPB  CONST_30  C10   N3   C9   N5    180.00   0.0  0
 TPB  CONST_31  C13   C12  C11  N5    180.00   0.0  0
 TPB  CONST_32  C15   C16  C11  N5    180.00   0.0  0
 TPB  CONST_33  C17   C14  C13  C12   180.00   0.0  0
 TPB  CONST_34  C17   C14  C15  C16   180.00   0.0  0
 TPB  CONST_35  H3    C3   C2   C1    180.00   0.0  0
 TPB  CONST_36  H5    C5   C6   C1    180.00   0.0  0
 TPB  CONST_37  H10   C10  C7   C8    180.00   0.0  0
 TPB  CONST_38  H7    C7   C8   N1    180.00   0.0  0
 TPB  CONST_39  H13   C13  C12  C11   180.00   0.0  0
 TPB  CONST_40  H15   C15  C16  C11   180.00   0.0  0
 TPB  CONST_41  H16   C16  C11  C12   180.00   0.0  0
 TPB  CONST_42  H12   C12  C13  C14   180.00   0.0  0
 TPB  Var_01    N1    C8   N7   C1   -179.12  30.0  2
 TPB  Var_02    C8    N7   C1   C2    102.29  30.0  2
 TPB  Var_03    C11   N5   C9   N1    179.35  30.0  2
 TPB  Var_04    C12   C11  N5   C9      3.43  30.0  2
 TPB  Var_05    H211  C21  C2   C1    -52.78  30.0  2
 TPB  Var_06    H611  C61  C6   C1     74.72  30.0  2
 TPB  Var_07    H411  C41  C4   C3     88.37  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
 TPB  plan-1  C1   0.020
 TPB  plan-1  N7   0.020
 TPB  plan-1  C2   0.020
 TPB  plan-1  C21  0.020
 TPB  plan-1  C3   0.020
 TPB  plan-1  C4   0.020
 TPB  plan-1  C5   0.020
 TPB  plan-1  C6   0.020
 TPB  plan-1  C61  0.020
 TPB  plan-1  C41  0.020
 TPB  plan-1  H3   0.020
 TPB  plan-1  H5   0.020
 TPB  plan-2  N7   0.020
 TPB  plan-2  C8   0.020
 TPB  plan-2  N1   0.020
 TPB  plan-2  C9   0.020
 TPB  plan-2  N5   0.020
 TPB  plan-2  N3   0.020
 TPB  plan-2  C10  0.020
 TPB  plan-2  C7   0.020
 TPB  plan-2  H10  0.020
 TPB  plan-2  H7   0.020
 TPB  plan-3  N5   0.020
 TPB  plan-3  C11  0.020
 TPB  plan-3  C12  0.020
 TPB  plan-3  C13  0.020
 TPB  plan-3  C14  0.020
 TPB  plan-3  C15  0.020
 TPB  plan-3  C16  0.020
 TPB  plan-3  C17  0.020
 TPB  plan-3  N6   0.020
 TPB  plan-3  H12  0.020
 TPB  plan-3  H13  0.020
 TPB  plan-3  H15  0.020
 TPB  plan-3  H16  0.020

