# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:57:31 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 6-{[3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl]amino}-2-(cyclohexylamino)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2ccc(Nc3ccc(C#N)c(NC4CCCCC4)n3)cc2OCC#N
#
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
 O38  O38  6-{[3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl]amino}-2-(cyclohexylamino)pyridine-3-carbonitrile  ligand  57  32  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_O38
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
 O38  N6   N  NS    0  -0.242  -6.3009   4.2997   0.8111
 O38  C23  C  CSP   0   0.110  -5.2080   3.9773   0.6675
 O38  C22  C  CH2   0  -0.251  -3.8115   3.5928   0.4807
 O38  O    O  O2    0  -0.466  -3.7892   2.1934   0.3850
 O38  C21  C  CR6   0   0.359  -2.5932   1.5713   0.2542
 O38  C4   C  CR6   0  -0.025  -2.6369   0.1685   0.2142
 O38  C2   C  CR5   0  -0.130  -3.8836  -0.5908   0.3071
 O38  C1   C  CR15  0   0.021  -4.1353  -1.8148  -0.2874
 O38  C3   C  CR15  0  -0.090  -5.0684  -0.3321   1.0295
 O38  N1   N  N     0  -0.283  -5.9459  -1.3072   0.8877
 O38  N    N  NR5   0  -0.266  -5.3657  -2.1947   0.0876
 O38  C    C  CH3   0  -0.507  -6.0723  -3.3907  -0.3025
 O38  C20  C  CR16  0  -0.514  -1.3949   2.2569   0.1555
 O38  C7   C  CR6   0   0.395  -0.1824   1.5702   0.0040
 O38  C6   C  CR16  0  -0.329  -0.2060   0.1784  -0.0500
 O38  C5   C  CR16  0  -0.319  -1.4189  -0.4832   0.0615
 O38  N2   N  NH1   0  -0.784   0.9569   2.3602  -0.0909
 O38  C8   C  CR6   0   0.573   2.2767   2.0310  -0.1429
 O38  N5   N  N     0  -0.536   2.6290   0.7589  -0.0784
 O38  C13  C  CR6   0   0.587   3.9146   0.4155  -0.1224
 O38  C11  C  CR6   0  -0.193   4.9298   1.3989  -0.2487
 O38  C12  C  CSP   0   0.012   6.2909   1.0320  -0.2998
 O38  N3   N  NS    0  -0.271   7.4006   0.7094  -0.3409
 O38  C10  C  CR16  0  -0.115   4.5376   2.7405  -0.3176
 O38  C9   C  CR16  0  -0.460   3.2132   3.0813  -0.2649
 O38  N4   N  NH1   0  -0.682   4.2121  -0.8900  -0.0221
 O38  C14  C  CH1   0  -0.062   3.2226  -1.9523  -0.0019
 O38  C19  C  CH2   0  -0.444   3.8140  -3.1906   0.6630
 O38  C18  C  CH2   0  -0.438   2.7900  -4.3214   0.7064
 O38  C17  C  CH2   0  -0.431   2.2527  -4.6510  -0.6828
 O38  C16  C  CH2   0  -0.443   1.6777  -3.4094  -1.3560
 O38  C15  C  CH2   0  -0.439   2.7064  -2.2838  -1.4026
 O38  H1   H  HCH2  0   0.301  -3.4379   4.0849  -0.4237
 O38  H2   H  HCH2  0   0.302  -3.2344   3.9659   1.3332
 O38  H3   H  HCR5  0   0.290  -3.5343  -2.4166  -0.9506
 O38  H4   H  HCR5  0   0.252  -5.3036   0.5142   1.6549
 O38  H5   H  HCH3  0   0.261  -6.3824  -3.9481   0.5791
 O38  H6   H  HCH3  0   0.260  -6.9512  -3.1395  -0.8934
 O38  H7   H  HCH3  0   0.258  -5.4117  -4.0129  -0.8988
 O38  H8   H  HCR6  0   0.302  -1.3723   3.3391   0.1904
 O38  H9   H  HCR6  0   0.305   0.7030  -0.3851  -0.1650
 O38  H10  H  HCR6  0   0.250  -1.4078  -1.5663   0.0429
 O38  H11  H  HNH1  0   0.421   0.7782   3.3526  -0.1057
 O38  H12  H  HCR6  0   0.283   5.2924   3.5095  -0.4132
 O38  H13  H  HCR6  0   0.277   2.8957   4.1132  -0.3190
 O38  H14  H  HNH1  0   0.398   5.1712  -1.1705  -0.1584
 O38  H15  H  HCH1  0   0.237   2.3842  -1.6078   0.6108
 O38  H16  H  HCH2  0   0.221   4.6981  -3.5153   0.1016
 O38  H17  H  HCH2  0   0.243   4.1507  -2.9431   1.6725
 O38  H18  H  HCH2  0   0.235   3.2381  -5.2067   1.1622
 O38  H19  H  HCH2  0   0.215   1.9582  -4.0263   1.3551
 O38  H20  H  HCH2  0   0.213   3.0629  -5.0540  -1.2997
 O38  H21  H  HCH2  0   0.232   1.4930  -5.4331  -0.6155
 O38  H22  H  HCH2  0   0.235   1.3370  -3.6451  -2.3665
 O38  H23  H  HCH2  0   0.211   0.7914  -3.0746  -0.8038
 O38  H24  H  HCH2  0   0.238   2.2776  -1.3902  -1.8621
 O38  H25  H  HCH2  0   0.220   3.5550  -2.5880  -2.0255

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
 O38  N3   C12  triple    1.156  0.020  1.156
 O38  C12  C11  single    1.411  0.020  1.411
 O38  C15  C16  single    1.526  0.020  1.526
 O38  C15  C14  single    1.529  0.020  1.529
 O38  C17  C16  single    1.525  0.020  1.525
 O38  C17  C18  single    1.526  0.020  1.526
 O38  N4   C14  single    1.452  0.020  1.452
 O38  N4   C13  single    1.343  0.020  1.343
 O38  C11  C13  aromatic  1.419  0.020  1.419
 O38  C11  C10  aromatic  1.399  0.020  1.399
 O38  C14  C19  single    1.525  0.020  1.525
 O38  C19  C18  single    1.526  0.020  1.526
 O38  C13  N5   aromatic  1.331  0.020  1.331
 O38  C10  C9   aromatic  1.368  0.020  1.368
 O38  N5   C8   aromatic  1.322  0.020  1.322
 O38  C9   C8   aromatic  1.412  0.020  1.412
 O38  C8   N2   single    1.361  0.020  1.361
 O38  N2   C7   single    1.390  0.020  1.390
 O38  C6   C7   aromatic  1.393  0.020  1.393
 O38  C6   C5   aromatic  1.386  0.020  1.386
 O38  C7   C20  aromatic  1.402  0.020  1.402
 O38  C5   C4   aromatic  1.390  0.020  1.390
 O38  C20  C21  aromatic  1.384  0.020  1.384
 O38  C4   C21  aromatic  1.404  0.020  1.404
 O38  C4   C2   single    1.463  0.020  1.463
 O38  C1   C2   aromatic  1.384  0.020  1.384
 O38  C1   N    aromatic  1.341  0.020  1.341
 O38  C21  O    single    1.354  0.020  1.354
 O38  C2   C3   aromatic  1.412  0.020  1.412
 O38  N    C    single    1.443  0.020  1.443
 O38  N    N1   aromatic  1.328  0.020  1.328
 O38  O    C22  single    1.403  0.020  1.403
 O38  C3   N1   aromatic  1.319  0.020  1.319
 O38  C22  C23  single    1.460  0.020  1.460
 O38  C23  N6   triple    1.148  0.020  1.148
 O38  C22  H1   single    0.970  0.020  1.090
 O38  C22  H2   single    0.970  0.020  1.090
 O38  C1   H3   single    0.930  0.020  1.080
 O38  C3   H4   single    0.930  0.020  1.080
 O38  C    H5   single    0.970  0.020  1.090
 O38  C    H6   single    0.970  0.020  1.090
 O38  C    H7   single    0.970  0.020  1.090
 O38  C20  H8   single    0.930  0.020  1.080
 O38  C6   H9   single    0.930  0.020  1.080
 O38  C5   H10  single    0.930  0.020  1.080
 O38  N2   H11  single    0.860  0.020  1.020
 O38  C10  H12  single    0.930  0.020  1.080
 O38  C9   H13  single    0.930  0.020  1.080
 O38  N4   H14  single    0.860  0.020  1.020
 O38  C14  H15  single    0.970  0.020  1.090
 O38  C19  H16  single    0.970  0.020  1.090
 O38  C19  H17  single    0.970  0.020  1.090
 O38  C18  H18  single    0.970  0.020  1.090
 O38  C18  H19  single    0.970  0.020  1.090
 O38  C17  H20  single    0.970  0.020  1.090
 O38  C17  H21  single    0.970  0.020  1.090
 O38  C16  H22  single    0.970  0.020  1.090
 O38  C16  H23  single    0.970  0.020  1.090
 O38  C15  H24  single    0.970  0.020  1.090
 O38  C15  H25  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
 O38  C22  C23  N6   180.00  3.000
 O38  H2   C22  H1   108.06  3.000
 O38  H2   C22  O    112.62  3.000
 O38  H1   C22  O    112.74  3.000
 O38  H2   C22  C23  108.34  3.000
 O38  H1   C22  C23  108.27  3.000
 O38  O    C22  C23  106.65  3.000
 O38  C21  O    C22  118.60  3.000
 O38  C20  C21  C4   121.32  3.000
 O38  C4   C21  O    115.73  3.000
 O38  C20  C21  O    122.95  3.000
 O38  C5   C4   C2   120.70  3.000
 O38  C2   C4   C21  122.91  3.000
 O38  C5   C4   C21  116.38  3.000
 O38  C3   C2   C1   103.25  3.000
 O38  C3   C2   C4   130.76  3.000
 O38  C1   C2   C4   125.94  3.000
 O38  H3   C1   N    121.67  3.000
 O38  H3   C1   C2   131.03  3.000
 O38  N    C1   C2   107.30  3.000
 O38  H4   C3   N1   119.82  3.000
 O38  H4   C3   C2   128.58  3.000
 O38  N1   C3   C2   111.58  3.000
 O38  N    N1   C3   105.55  3.000
 O38  C    N    N1   120.18  3.000
 O38  N1   N    C1   112.32  3.000
 O38  C    N    C1   127.48  3.000
 O38  H7   C    H6   108.99  3.000
 O38  H7   C    H5   108.95  3.000
 O38  H6   C    H5   109.14  3.000
 O38  H7   C    N    109.00  3.000
 O38  H6   C    N    110.55  3.000
 O38  H5   C    N    110.19  3.000
 O38  H8   C20  C7   118.36  3.000
 O38  H8   C20  C21  120.71  3.000
 O38  C7   C20  C21  120.93  3.000
 O38  N2   C7   C6   125.40  3.000
 O38  C6   C7   C20  118.62  3.000
 O38  N2   C7   C20  115.98  3.000
 O38  H9   C6   C5   119.87  3.000
 O38  H9   C6   C7   120.88  3.000
 O38  C5   C6   C7   119.25  3.000
 O38  H10  C5   C6   117.83  3.000
 O38  H10  C5   C4   118.67  3.000
 O38  C6   C5   C4   123.49  3.000
 O38  H11  N2   C8   114.16  3.000
 O38  H11  N2   C7   114.53  3.000
 O38  C8   N2   C7   131.30  3.000
 O38  C9   C8   N5   122.90  3.000
 O38  C9   C8   N2   117.80  3.000
 O38  N5   C8   N2   119.30  3.000
 O38  C13  N5   C8   120.28  3.000
 O38  N4   C13  C11  121.46  3.000
 O38  C11  C13  N5   120.99  3.000
 O38  N4   C13  N5   117.54  3.000
 O38  C10  C11  C12  121.20  3.000
 O38  C10  C11  C13  117.92  3.000
 O38  C12  C11  C13  120.88  3.000
 O38  N3   C12  C11  180.00  3.000
 O38  H12  C10  C9   120.10  3.000
 O38  H12  C10  C11  119.36  3.000
 O38  C9   C10  C11  120.53  3.000
 O38  H13  C9   C10  121.34  3.000
 O38  H13  C9   C8   121.29  3.000
 O38  C10  C9   C8   117.38  3.000
 O38  H14  N4   C14  116.52  3.000
 O38  H14  N4   C13  118.10  3.000
 O38  C14  N4   C13  124.15  3.000
 O38  H15  C14  C15  108.82  3.000
 O38  H15  C14  C19  107.98  3.000
 O38  C15  C14  C19  110.75  3.000
 O38  H15  C14  N4   107.44  3.000
 O38  C19  C14  N4   109.63  3.000
 O38  C15  C14  N4   112.09  3.000
 O38  H17  C19  H16  106.96  3.000
 O38  H17  C19  C18  110.39  3.000
 O38  H16  C19  C18  109.64  3.000
 O38  H17  C19  C14  109.78  3.000
 O38  H16  C19  C14  109.26  3.000
 O38  C18  C19  C14  110.73  3.000
 O38  H19  C18  H18  106.43  3.000
 O38  H19  C18  C17  109.27  3.000
 O38  H18  C18  C17  110.46  3.000
 O38  H19  C18  C19  109.07  3.000
 O38  H18  C18  C19  109.71  3.000
 O38  C17  C18  C19  111.75  3.000
 O38  H21  C17  H20  106.60  3.000
 O38  H21  C17  C16  110.36  3.000
 O38  H20  C17  C16  109.26  3.000
 O38  H21  C17  C18  110.10  3.000
 O38  H20  C17  C18  109.38  3.000
 O38  C16  C17  C18  111.03  3.000
 O38  H23  C16  H22  106.24  3.000
 O38  H23  C16  C15  109.58  3.000
 O38  H22  C16  C15  109.96  3.000
 O38  H23  C16  C17  109.33  3.000
 O38  H22  C16  C17  110.51  3.000
 O38  C15  C16  C17  111.10  3.000
 O38  H25  C15  H24  106.97  3.000
 O38  H25  C15  C16  109.56  3.000
 O38  H24  C15  C16  110.59  3.000
 O38  H25  C15  C14  108.63  3.000
 O38  H24  C15  C14  109.90  3.000
 O38  C16  C15  C14  111.08  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
 O38  CONST_01  C6   C7   C20  C21     0.00   0.0  0
 O38  CONST_02  C6   C5   C4   C21     0.00   0.0  0
 O38  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 O38  CONST_06  C7   C20  C21  C4      0.00   0.0  0
 O38  CONST_07  N    C1   C2   C4    180.00   0.0  0
 O38  CONST_08  N1   C3   C2   C4    180.00   0.0  0
 O38  CONST_09  C6   C5   C4   C2    180.00   0.0  0
 O38  CONST_10  C20  C21  C4   C2    180.00   0.0  0
 O38  CONST_11  N1   N    C1   C2      0.00   0.0  0
 O38  CONST_12  N    N1   C3   C2      0.00   0.0  0
 O38  CONST_14  N1   C3   C2   C1      0.00   0.0  0
 O38  CONST_15  C3   N1   N    C1      0.00   0.0  0
 O38  CONST_17  N    C1   C2   C3      0.00   0.0  0
 O38  CONST_18  C5   C6   C7   C20     0.00   0.0  0
 O38  CONST_19  C5   C4   C21  C20     0.00   0.0  0
 O38  CONST_20  C11  C13  N5   C8      0.00   0.0  0
 O38  CONST_21  C11  C10  C9   C8      0.00   0.0  0
 O38  CONST_22  C10  C11  C13  N5      0.00   0.0  0
 O38  CONST_23  C10  C9   C8   N5      0.00   0.0  0
 O38  CONST_24  C9   C10  C11  C13     0.00   0.0  0
 O38  CONST_25  C9   C8   N5   C13     0.00   0.0  0
 O38  CONST_26  C7   C20  C21  O     180.00   0.0  0
 O38  CONST_27  C5   C4   C21  O     180.00   0.0  0
 O38  CONST_28  C2   C4   C21  O       0.00   0.0  0
 O38  CONST_29  N2   C7   C20  C21   180.00   0.0  0
 O38  CONST_30  C    N    C1   C2    180.00   0.0  0
 O38  CONST_31  C    N    N1   C3    180.00   0.0  0
 O38  CONST_32  N2   C7   C6   C5    180.00   0.0  0
 O38  CONST_33  C13  N5   C8   N2    180.00   0.0  0
 O38  CONST_34  C10  C9   C8   N2    180.00   0.0  0
 O38  CONST_35  N4   C13  N5   C8    180.00   0.0  0
 O38  CONST_36  C12  C11  C13  N5    180.00   0.0  0
 O38  CONST_37  C9   C10  C11  C12   180.00   0.0  0
 O38  CONST_38  N4   C13  C11  C10   180.00   0.0  0
 O38  CONST_39  C14  N4   C13  N5      0.00   0.0  0
 O38  CONST_40  C14  N4   C13  C11   180.00   0.0  0
 O38  CONST_41  H10  C5   C4   C21   180.00   0.0  0
 O38  CONST_42  H9   C6   C5   C4    180.00   0.0  0
 O38  CONST_43  H8   C20  C21  C4    180.00   0.0  0
 O38  CONST_44  H3   C1   C2   C4      0.00   0.0  0
 O38  CONST_45  H4   C3   C2   C4      0.00   0.0  0
 O38  CONST_46  H12  C10  C9   C8    180.00   0.0  0
 O38  CONST_47  H13  C9   C8   N5    180.00   0.0  0
 O38  CONST_48  H14  N4   C13  N5    180.00   0.0  0
 O38  Var_01    C17  C16  C15  C14   -56.17  30.0  1
 O38  Var_02    C17  C18  C19  C14    55.71  30.0  1
 O38  Var_03    C16  C17  C18  C19   -55.11  30.0  1
 O38  Var_04    C15  C16  C17  C18    55.09  30.0  1
 O38  Var_05    C8   N2   C7   C20   174.47  30.0  2
 O38  Var_06    N5   C8   N2   C7     -1.15  30.0  2
 O38  Var_07    C20  C21  O    C22    -2.73  30.0  1
 O38  Var_08    H5   C    N    C1    124.61  30.0  2
 O38  Var_09    H1   C22  O    C21    63.63  30.0  3
 O38  Var_10    O    C22  C23  N6   -169.22  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
 O38  chir_01  C14  C15  N4  C19  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
 O38  plan-1  C4   0.020
 O38  plan-1  C2   0.020
 O38  plan-1  C1   0.020
 O38  plan-1  C3   0.020
 O38  plan-1  N1   0.020
 O38  plan-1  N    0.020
 O38  plan-1  C    0.020
 O38  plan-1  H3   0.020
 O38  plan-1  H4   0.020
 O38  plan-2  O    0.020
 O38  plan-2  C21  0.020
 O38  plan-2  C4   0.020
 O38  plan-2  C2   0.020
 O38  plan-2  C20  0.020
 O38  plan-2  C7   0.020
 O38  plan-2  C6   0.020
 O38  plan-2  C5   0.020
 O38  plan-2  N2   0.020
 O38  plan-2  H8   0.020
 O38  plan-2  H9   0.020
 O38  plan-2  H10  0.020
 O38  plan-3  N2   0.020
 O38  plan-3  C8   0.020
 O38  plan-3  N5   0.020
 O38  plan-3  C13  0.020
 O38  plan-3  C11  0.020
 O38  plan-3  C12  0.020
 O38  plan-3  N3   0.020
 O38  plan-3  C10  0.020
 O38  plan-3  C9   0.020
 O38  plan-3  N4   0.020
 O38  plan-3  H12  0.020
 O38  plan-3  H13  0.020
 O38  plan-4  C13  0.020
 O38  plan-4  N4   0.020
 O38  plan-4  C14  0.020
 O38  plan-4  H14  0.020

