# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 22:08:23 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: trans-4-{[4-(1H-indazol-1-yl)pyrimidin-2-yl]amino}cyclohexanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CC[C@H](CC1)Nc2nccc(n2)n3ncc4ccccc34
#
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
 1BJ  1BJ  trans-4-{[4-(1H-indazol-1-yl)pyrimidin-2-yl]amino}cyclohexanol  ligand  42  23  .  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_1BJ
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
 1BJ  N1   N  N     0  -0.479  -1.0814   1.9200   0.4557
 1BJ  C2   C  CR6   0   0.621  -0.6533   0.6678   0.2770
 1BJ  N3   N  N     0  -0.517   0.6301   0.3006   0.1448
 1BJ  C4   C  CR16  0  -0.012  -0.1384   2.8513   0.5058
 1BJ  C5   C  CR16  0  -0.440   1.2114   2.5963   0.3845
 1BJ  C6   C  CR6   0   0.556   1.5363   1.2498   0.2020
 1BJ  N7   N  NR5   0  -0.503   2.8597   0.8482   0.0759
 1BJ  N8   N  NH1   0  -0.670  -1.5591  -0.3227   0.2384
 1BJ  C9   C  CH1   0  -0.038  -2.9922  -0.1353   0.3124
 1BJ  C10  C  CH2   0  -0.461  -3.6477  -1.4277   0.7908
 1BJ  C11  C  CH2   0  -0.463  -5.1608  -1.2703   0.8944
 1BJ  C12  C  CH1   0   0.085  -5.7602  -0.8201  -0.4288
 1BJ  C13  C  CH2   0  -0.483  -5.1066   0.4762  -0.8963
 1BJ  C14  C  CH2   0  -0.443  -3.5959   0.3106  -1.0195
 1BJ  O15  O  OH1   0  -0.678  -7.1556  -0.6831  -0.2506
 1BJ  C16  C  CR15  0  -0.053   4.9674   1.1667  -0.0100
 1BJ  N17  N  N     0  -0.232   3.8329   1.7845   0.1044
 1BJ  C18  C  CR56  0  -0.138   4.7775  -0.2415  -0.1189
 1BJ  C19  C  CR56  0   0.443   3.3866  -0.4192  -0.0600
 1BJ  C20  C  CR16  0  -0.279   2.8153  -1.6932  -0.1342
 1BJ  C21  C  CR16  0  -0.258   3.6825  -2.7595  -0.2658
 1BJ  C22  C  CR16  0  -0.264   5.0763  -2.5917  -0.3254
 1BJ  C23  C  CR16  0  -0.316   5.6358  -1.3349  -0.2529
 1BJ  H1   H  HCR6  0   0.271  -0.4800   3.8704   0.6519
 1BJ  H2   H  HCR6  0   0.281   1.9478   3.3806   0.4304
 1BJ  H3   H  HNH1  0   0.391  -1.2086  -1.2409   0.0151
 1BJ  H4   H  HCH1  0   0.235  -3.1887   0.6437   1.0550
 1BJ  H5   H  HCH2  0   0.225  -3.4094  -2.2353   0.0885
 1BJ  H6   H  HCH2  0   0.249  -3.2343  -1.7171   1.7595
 1BJ  H7   H  HCH2  0   0.242  -5.6114  -2.2151   1.2079
 1BJ  H8   H  HCH2  0   0.221  -5.3983  -0.5290   1.6656
 1BJ  H9   H  HCH1  0   0.186  -5.5447  -1.5968  -1.1806
 1BJ  H10  H  HCH2  0   0.237  -5.5289   0.7839  -1.8573
 1BJ  H11  H  HCH2  0   0.219  -5.3354   1.2707  -0.1769
 1BJ  H12  H  HCH2  0   0.243  -3.1353   1.2471  -1.3381
 1BJ  H13  H  HCH2  0   0.218  -3.3644  -0.4390  -1.7844
 1BJ  H14  H  HOH1  0   0.446  -7.5372  -0.3882  -1.0834
 1BJ  H15  H  HCR5  0   0.284   5.8954   1.7185  -0.0126
 1BJ  H16  H  HCR6  0   0.284   1.7488  -1.8401  -0.0917
 1BJ  H17  H  HCR6  0   0.264   3.2723  -3.7593  -0.3253
 1BJ  H18  H  HCR6  0   0.262   5.7115  -3.4609  -0.4298
 1BJ  H19  H  HCR6  0   0.264   6.7080  -1.1947  -0.2970

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
 1BJ  C14  C13  single    1.525  0.020  1.525
 1BJ  C14  C9   single    1.529  0.020  1.529
 1BJ  N8   C9   single    1.447  0.020  1.447
 1BJ  N8   C2   single    1.343  0.020  1.343
 1BJ  C13  C12  single    1.525  0.020  1.525
 1BJ  N1   C2   aromatic  1.335  0.020  1.335
 1BJ  N1   C4   aromatic  1.326  0.020  1.326
 1BJ  C9   C10  single    1.526  0.020  1.526
 1BJ  C2   N3   aromatic  1.341  0.020  1.341
 1BJ  C12  O15  single    1.413  0.020  1.413
 1BJ  C12  C11  single    1.521  0.020  1.521
 1BJ  C4   C5   aromatic  1.379  0.020  1.379
 1BJ  C10  C11  single    1.525  0.020  1.525
 1BJ  N3   C6   aromatic  1.314  0.020  1.314
 1BJ  C5   C6   aromatic  1.397  0.020  1.397
 1BJ  C6   N7   single    1.389  0.020  1.389
 1BJ  N7   C19  aromatic  1.379  0.020  1.379
 1BJ  N7   N17  aromatic  1.351  0.020  1.351
 1BJ  C20  C19  aromatic  1.398  0.020  1.398
 1BJ  C20  C21  aromatic  1.381  0.020  1.381
 1BJ  C19  C18  aromatic  1.403  0.020  1.403
 1BJ  C21  C22  aromatic  1.405  0.020  1.405
 1BJ  N17  C16  aromatic  1.297  0.020  1.297
 1BJ  C18  C16  aromatic  1.425  0.020  1.425
 1BJ  C18  C23  aromatic  1.396  0.020  1.396
 1BJ  C22  C23  aromatic  1.378  0.020  1.378
 1BJ  C4   H1   single    0.930  0.020  1.080
 1BJ  C5   H2   single    0.930  0.020  1.080
 1BJ  N8   H3   single    0.860  0.020  1.020
 1BJ  C9   H4   single    0.970  0.020  1.090
 1BJ  C10  H5   single    0.970  0.020  1.090
 1BJ  C10  H6   single    0.970  0.020  1.090
 1BJ  C11  H7   single    0.970  0.020  1.090
 1BJ  C11  H8   single    0.970  0.020  1.090
 1BJ  C12  H9   single    0.970  0.020  1.090
 1BJ  C13  H10  single    0.970  0.020  1.090
 1BJ  C13  H11  single    0.970  0.020  1.090
 1BJ  C14  H12  single    0.970  0.020  1.090
 1BJ  C14  H13  single    0.970  0.020  1.090
 1BJ  O15  H14  single    0.850  0.020  0.980
 1BJ  C16  H15  single    0.930  0.020  1.080
 1BJ  C20  H16  single    0.930  0.020  1.080
 1BJ  C21  H17  single    0.930  0.020  1.080
 1BJ  C22  H18  single    0.930  0.020  1.080
 1BJ  C23  H19  single    0.930  0.020  1.080

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
 1BJ  C4   N1   C2   115.82  3.000
 1BJ  N8   C2   N3   116.14  3.000
 1BJ  N3   C2   N1   125.21  3.000
 1BJ  N8   C2   N1   118.64  3.000
 1BJ  C6   N3   C2   117.25  3.000
 1BJ  H1   C4   C5   119.59  3.000
 1BJ  H1   C4   N1   116.17  3.000
 1BJ  C5   C4   N1   124.24  3.000
 1BJ  H2   C5   C6   123.26  3.000
 1BJ  H2   C5   C4   122.07  3.000
 1BJ  C6   C5   C4   114.67  3.000
 1BJ  N7   C6   C5   120.81  3.000
 1BJ  N7   C6   N3   116.39  3.000
 1BJ  C5   C6   N3   122.80  3.000
 1BJ  C19  N7   N17  111.33  3.000
 1BJ  N17  N7   C6   118.96  3.000
 1BJ  C19  N7   C6   129.70  3.000
 1BJ  H3   N8   C9   118.27  3.000
 1BJ  H3   N8   C2   116.35  3.000
 1BJ  C9   N8   C2   124.82  3.000
 1BJ  H4   C9   C14  108.23  3.000
 1BJ  H4   C9   C10  108.25  3.000
 1BJ  C14  C9   C10  110.52  3.000
 1BJ  H4   C9   N8   107.74  3.000
 1BJ  C10  C9   N8   109.37  3.000
 1BJ  C14  C9   N8   112.60  3.000
 1BJ  H6   C10  H5   106.90  3.000
 1BJ  H6   C10  C11  110.04  3.000
 1BJ  H5   C10  C11  109.59  3.000
 1BJ  H6   C10  C9   109.87  3.000
 1BJ  H5   C10  C9   109.25  3.000
 1BJ  C11  C10  C9   111.10  3.000
 1BJ  H8   C11  H7   107.08  3.000
 1BJ  H8   C11  C12  109.07  3.000
 1BJ  H7   C11  C12  110.06  3.000
 1BJ  H8   C11  C10  109.43  3.000
 1BJ  H7   C11  C10  109.84  3.000
 1BJ  C12  C11  C10  111.26  3.000
 1BJ  H9   C12  O15  110.32  3.000
 1BJ  H9   C12  C13  107.82  3.000
 1BJ  O15  C12  C13  112.29  3.000
 1BJ  H9   C12  C11  107.93  3.000
 1BJ  O15  C12  C11  107.95  3.000
 1BJ  C13  C12  C11  110.45  3.000
 1BJ  H11  C13  H10  106.99  3.000
 1BJ  H11  C13  C14  109.79  3.000
 1BJ  H10  C13  C14  110.00  3.000
 1BJ  H11  C13  C12  109.00  3.000
 1BJ  H10  C13  C12  110.06  3.000
 1BJ  C14  C13  C12  110.92  3.000
 1BJ  H13  C14  H12  107.11  3.000
 1BJ  H13  C14  C13  109.88  3.000
 1BJ  H12  C14  C13  110.40  3.000
 1BJ  H13  C14  C9   108.98  3.000
 1BJ  H12  C14  C9   109.75  3.000
 1BJ  C13  C14  C9   110.64  3.000
 1BJ  H14  O15  C12  108.19  3.000
 1BJ  H15  C16  C18  128.27  3.000
 1BJ  H15  C16  N17  120.57  3.000
 1BJ  C18  C16  N17  111.16  3.000
 1BJ  C16  N17  N7   107.34  3.000
 1BJ  C23  C18  C19  120.93  3.000
 1BJ  C23  C18  C16  134.35  3.000
 1BJ  C19  C18  C16  104.71  3.000
 1BJ  C20  C19  C18  121.20  3.000
 1BJ  C18  C19  N7   105.45  3.000
 1BJ  C20  C19  N7   133.34  3.000
 1BJ  H16  C20  C21  121.35  3.000
 1BJ  H16  C20  C19  121.78  3.000
 1BJ  C21  C20  C19  116.88  3.000
 1BJ  H17  C21  C22  118.94  3.000
 1BJ  H17  C21  C20  118.72  3.000
 1BJ  C22  C21  C20  122.33  3.000
 1BJ  H18  C22  C23  119.98  3.000
 1BJ  H18  C22  C21  119.38  3.000
 1BJ  C23  C22  C21  120.64  3.000
 1BJ  H19  C23  C22  121.23  3.000
 1BJ  H19  C23  C18  120.76  3.000
 1BJ  C22  C23  C18  118.01  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
 1BJ  CONST_01  C6   N3   C2   N1     0.00   0.0  0
 1BJ  CONST_02  C6   C5   C4   N1     0.00   0.0  0
 1BJ  CONST_03  C5   C4   N1   C2     0.00   0.0  0
 1BJ  CONST_04  C5   C6   N3   C2     0.00   0.0  0
 1BJ  CONST_05  N7   C6   N3   C2   180.00   0.0  0
 1BJ  CONST_06  C4   N1   C2   N3     0.00   0.0  0
 1BJ  CONST_07  C4   C5   C6   N3     0.00   0.0  0
 1BJ  CONST_08  C19  N7   C6   N3     0.00   0.0  0
 1BJ  CONST_09  N17  N7   C6   N3   180.00   0.0  0
 1BJ  CONST_10  N7   C6   C5   C4   180.00   0.0  0
 1BJ  CONST_11  C19  N7   C6   C5   180.00   0.0  0
 1BJ  CONST_12  N17  N7   C6   C5     0.00   0.0  0
 1BJ  CONST_13  C20  C19  N7   C6     0.00   0.0  0
 1BJ  CONST_14  C18  C19  N7   C6   180.00   0.0  0
 1BJ  CONST_15  C16  N17  N7   C6   180.00   0.0  0
 1BJ  CONST_16  C21  C20  C19  N7   180.00   0.0  0
 1BJ  CONST_17  C16  C18  C19  N7     0.00   0.0  0
 1BJ  CONST_18  C23  C18  C19  N7   180.00   0.0  0
 1BJ  CONST_19  C18  C16  N17  N7     0.00   0.0  0
 1BJ  CONST_20  C19  N7   N17  C16    0.00   0.0  0
 1BJ  CONST_21  C20  C19  C18  C16  180.00   0.0  0
 1BJ  CONST_22  C22  C23  C18  C16  180.00   0.0  0
 1BJ  CONST_23  C20  C19  N7   N17  180.00   0.0  0
 1BJ  CONST_24  C18  C19  N7   N17    0.00   0.0  0
 1BJ  CONST_25  C19  C18  C16  N17    0.00   0.0  0
 1BJ  CONST_26  C23  C18  C16  N17  180.00   0.0  0
 1BJ  CONST_27  C21  C20  C19  C18    0.00   0.0  0
 1BJ  CONST_28  C21  C22  C23  C18    0.00   0.0  0
 1BJ  CONST_29  C22  C21  C20  C19    0.00   0.0  0
 1BJ  CONST_30  C22  C23  C18  C19    0.00   0.0  0
 1BJ  CONST_31  C23  C18  C19  C20    0.00   0.0  0
 1BJ  CONST_32  C23  C22  C21  C20    0.00   0.0  0
 1BJ  CONST_33  N8   C2   N1   C4   180.00   0.0  0
 1BJ  CONST_34  N8   C2   N3   C6   180.00   0.0  0
 1BJ  CONST_35  C9   N8   C2   N1     0.00   0.0  0
 1BJ  CONST_36  C9   N8   C2   N3   180.00   0.0  0
 1BJ  CONST_37  H2   C5   C4   N1   180.00   0.0  0
 1BJ  CONST_38  H1   C4   N1   C2   180.00   0.0  0
 1BJ  CONST_39  H16  C20  C19  N7     0.00   0.0  0
 1BJ  CONST_40  H15  C16  N17  N7   180.00   0.0  0
 1BJ  CONST_41  H19  C23  C18  C16    0.00   0.0  0
 1BJ  CONST_42  H18  C22  C23  C18  180.00   0.0  0
 1BJ  CONST_43  H17  C21  C20  C19  180.00   0.0  0
 1BJ  CONST_44  H3   N8   C2   N1   180.00   0.0  0
 1BJ  Var_01    C12  C13  C14  C9   -57.35  30.0  1
 1BJ  Var_02    C12  C11  C10  C9    56.12  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 1BJ  chir_01  C9   C14  N8   C10  positiv
 1BJ  chir_02  C12  O15  C11  C13  positiv

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
 1BJ  plan-1  N1   0.020
 1BJ  plan-1  C2   0.020
 1BJ  plan-1  N3   0.020
 1BJ  plan-1  C4   0.020
 1BJ  plan-1  C5   0.020
 1BJ  plan-1  C6   0.020
 1BJ  plan-1  N7   0.020
 1BJ  plan-1  N8   0.020
 1BJ  plan-1  H1   0.020
 1BJ  plan-1  H2   0.020
 1BJ  plan-2  C6   0.020
 1BJ  plan-2  N7   0.020
 1BJ  plan-2  C16  0.020
 1BJ  plan-2  N17  0.020
 1BJ  plan-2  C18  0.020
 1BJ  plan-2  C19  0.020
 1BJ  plan-2  C20  0.020
 1BJ  plan-2  C21  0.020
 1BJ  plan-2  C22  0.020
 1BJ  plan-2  C23  0.020
 1BJ  plan-2  H15  0.020
 1BJ  plan-2  H16  0.020
 1BJ  plan-2  H17  0.020
 1BJ  plan-2  H18  0.020
 1BJ  plan-2  H19  0.020
 1BJ  plan-3  C2   0.020
 1BJ  plan-3  N8   0.020
 1BJ  plan-3  C9   0.020
 1BJ  plan-3  H3   0.020

