# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 01:05:54 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-{[(1R,2S)-2-aminocyclohexyl]amino}-5-cyano-2-[(3-methylphenyl)amino]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Nc2nc(N[C@@H]3CCCC[C@@H]3N)c(cc2C(N)=O)C#N)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
 9FC  9FC  6-{[(1R,2S)-2-aminocyclohexyl]amino}-5-cyano-2-[(3-methylphenyl)amino]pyridine-3-carboxamide  ligand  51  27  .  2022-07-24  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_9FC
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
 9FC  C7   C  CR6   0  -0.260  -1.1964   2.3570  -0.2121
 9FC  C4   C  CR6   0   0.582   1.1963   0.9479  -0.3896
 9FC  C5   C  CR6   0  -0.166   1.2091   2.3705  -0.4718
 9FC  C6   C  CR16  0  -0.148  -0.0020   3.0354  -0.3669
 9FC  C3   C  CH3   0  -0.724  -5.6432  -3.2602   0.2263
 9FC  C2   C  CSP   0   0.015   2.4221   3.0769  -0.6230
 9FC  C1   C  C     0   0.543  -2.4819   3.0716  -0.0536
 9FC  C8   C  CR6   0   0.556  -1.1099   0.9239  -0.2294
 9FC  N9   N  N     0  -0.533   0.0510   0.2866  -0.2883
 9FC  N10  N  NH1   0  -0.794  -2.2462   0.2020  -0.1796
 9FC  N11  N  NH1   0  -0.662   2.3376   0.2553  -0.4139
 9FC  C12  C  CR6   0   0.394  -2.4781  -1.1729  -0.1682
 9FC  C13  C  CR16  0  -0.428  -3.8132  -1.5538   0.0239
 9FC  C14  C  CR6   0   0.116  -4.2014  -2.8843   0.0432
 9FC  C15  C  CR16  0  -0.317  -3.2259  -3.8677  -0.1276
 9FC  C16  C  CR16  0  -0.237  -1.9055  -3.5002  -0.3202
 9FC  C17  C  CR16  0  -0.333  -1.5157  -2.1666  -0.3454
 9FC  C18  C  CH1   0  -0.084   2.4312  -1.1945  -0.3953
 9FC  C19  C  CH2   0  -0.453   2.0782  -1.7855   0.9709
 9FC  C20  C  CH2   0  -0.430   3.0816  -1.3958   2.0479
 9FC  C21  C  CH2   0  -0.437   4.4920  -1.8109   1.6502
 9FC  C22  C  CH2   0  -0.436   4.8724  -1.2204   0.2983
 9FC  C23  C  CH1   0  -0.111   3.8638  -1.5831  -0.7897
 9FC  N24  N  NH2   0  -0.799   4.2244  -0.9087  -2.0267
 9FC  N25  N  NS    0  -0.263   3.4305   3.6283  -0.7440
 9FC  O26  O  O     0  -0.515  -3.5679   2.4963  -0.1815
 9FC  N27  N  NH2   0  -0.817  -2.4321   4.3812   0.2315
 9FC  H1   H  HCR6  0   0.281   0.0164   4.1153  -0.4254
 9FC  H2   H  HCH3  0   0.249  -6.0767  -3.6100  -0.7125
 9FC  H3   H  HCH3  0   0.245  -5.7546  -4.0676   0.9505
 9FC  H4   H  HCH3  0   0.244  -6.2402  -2.4159   0.5687
 9FC  H5   H  HNH1  0   0.436  -3.0776   0.7926  -0.1666
 9FC  H6   H  HNH1  0   0.396   3.1644   0.7258  -0.7562
 9FC  H7   H  HCR6  0   0.257  -4.5664  -0.7848   0.1607
 9FC  H8   H  HCR6  0   0.245  -3.5025  -4.9150  -0.1084
 9FC  H9   H  HCR6  0   0.251  -1.1506  -4.2646  -0.4552
 9FC  H10  H  HCR6  0   0.300  -0.4830  -1.9100  -0.5021
 9FC  H11  H  HCH1  0   0.256   1.7443  -1.6027  -1.1472
 9FC  H12  H  HCH2  0   0.251   1.0680  -1.4887   1.2523
 9FC  H13  H  HCH2  0   0.226   2.0606  -2.8753   0.8657
 9FC  H14  H  HCH2  0   0.217   3.0488  -0.3144   2.2121
 9FC  H15  H  HCH2  0   0.233   2.7994  -1.8605   2.9952
 9FC  H16  H  HCH2  0   0.233   5.2137  -1.4987   2.4083
 9FC  H17  H  HCH2  0   0.213   4.5470  -2.9037   1.5983
 9FC  H18  H  HCH2  0   0.214   4.9541  -0.1310   0.3796
 9FC  H19  H  HCH2  0   0.238   5.8611  -1.5756  -0.0057
 9FC  H20  H  HCH1  0   0.226   3.8581  -2.6794  -0.8857
 9FC  H21  H  HNH2  0   0.352   5.1813  -1.1312  -2.2719
 9FC  H22  H  HNH2  0   0.349   3.6512  -1.2497  -2.7894
 9FC  H24  H  HNH2  0   0.416  -1.5953   4.8511   0.5282
 9FC  H25  H  HNH2  0   0.409  -3.2973   4.8736   0.3835

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
 9FC  C3   C14  single    1.501  0.020  1.501
 9FC  C15  C14  aromatic  1.396  0.020  1.396
 9FC  C15  C16  aromatic  1.384  0.020  1.384
 9FC  C14  C13  aromatic  1.386  0.020  1.386
 9FC  C16  C17  aromatic  1.390  0.020  1.390
 9FC  C22  C21  single    1.523  0.020  1.523
 9FC  C22  C23  single    1.527  0.020  1.527
 9FC  C21  C20  single    1.523  0.020  1.523
 9FC  C13  C12  aromatic  1.402  0.020  1.402
 9FC  C17  C12  aromatic  1.395  0.020  1.395
 9FC  C12  N10  single    1.394  0.020  1.394
 9FC  C20  C19  single    1.523  0.020  1.523
 9FC  C23  N24  single    1.454  0.020  1.454
 9FC  C23  C18  single    1.536  0.020  1.536
 9FC  N10  C8   single    1.347  0.020  1.347
 9FC  C18  C19  single    1.530  0.020  1.530
 9FC  C18  N11  single    1.453  0.020  1.453
 9FC  N9   C8   aromatic  1.326  0.020  1.326
 9FC  N9   C4   aromatic  1.326  0.020  1.326
 9FC  C8   C7   aromatic  1.436  0.020  1.436
 9FC  O26  C1   double    1.236  0.020  1.236
 9FC  N11  C4   single    1.335  0.020  1.335
 9FC  C4   C5   aromatic  1.425  0.020  1.425
 9FC  C7   C1   single    1.479  0.020  1.479
 9FC  C7   C6   aromatic  1.382  0.020  1.382
 9FC  C1   N27  single    1.341  0.020  1.341
 9FC  C5   C6   aromatic  1.386  0.020  1.386
 9FC  C5   C2   single    1.412  0.020  1.412
 9FC  C2   N25  triple    1.156  0.020  1.156
 9FC  C6   H1   single    0.930  0.020  1.080
 9FC  C3   H2   single    0.970  0.020  1.090
 9FC  C3   H3   single    0.970  0.020  1.090
 9FC  C3   H4   single    0.970  0.020  1.090
 9FC  N10  H5   single    0.860  0.020  1.020
 9FC  N11  H6   single    0.890  0.020  1.040
 9FC  C13  H7   single    0.930  0.020  1.080
 9FC  C15  H8   single    0.930  0.020  1.080
 9FC  C16  H9   single    0.930  0.020  1.080
 9FC  C17  H10  single    0.930  0.020  1.080
 9FC  C18  H11  single    0.970  0.020  1.090
 9FC  C19  H12  single    0.970  0.020  1.090
 9FC  C19  H13  single    0.970  0.020  1.090
 9FC  C20  H14  single    0.970  0.020  1.090
 9FC  C20  H15  single    0.970  0.020  1.090
 9FC  C21  H16  single    0.970  0.020  1.090
 9FC  C21  H17  single    0.970  0.020  1.090
 9FC  C22  H18  single    0.970  0.020  1.090
 9FC  C22  H19  single    0.970  0.020  1.090
 9FC  C23  H20  single    0.970  0.020  1.090
 9FC  N24  H21  single    0.890  0.020  1.040
 9FC  N24  H22  single    0.890  0.020  1.040
 9FC  N27  H24  single    0.860  0.020  1.020
 9FC  N27  H25  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
 9FC  C8   C7   C1   122.39  3.000
 9FC  C1   C7   C6   121.72  3.000
 9FC  C8   C7   C6   115.88  3.000
 9FC  N11  C4   N9   118.74  3.000
 9FC  N11  C4   C5   120.61  3.000
 9FC  N9   C4   C5   120.66  3.000
 9FC  C2   C5   C6   121.27  3.000
 9FC  C2   C5   C4   120.89  3.000
 9FC  C6   C5   C4   117.83  3.000
 9FC  H1   C6   C5   117.39  3.000
 9FC  H1   C6   C7   120.72  3.000
 9FC  C5   C6   C7   121.89  3.000
 9FC  H4   C3   H3   108.01  3.000
 9FC  H4   C3   H2   107.52  3.000
 9FC  H3   C3   H2   107.06  3.000
 9FC  H4   C3   C14  111.75  3.000
 9FC  H3   C3   C14  111.38  3.000
 9FC  H2   C3   C14  110.90  3.000
 9FC  N25  C2   C5   180.00  3.000
 9FC  N27  C1   O26  120.62  3.000
 9FC  N27  C1   C7   117.52  3.000
 9FC  O26  C1   C7   121.86  3.000
 9FC  N10  C8   N9   118.86  3.000
 9FC  N9   C8   C7   122.22  3.000
 9FC  N10  C8   C7   118.92  3.000
 9FC  C8   N9   C4   121.32  3.000
 9FC  H5   N10  C12  115.80  3.000
 9FC  H5   N10  C8   112.20  3.000
 9FC  C12  N10  C8   131.99  3.000
 9FC  H6   N11  C18  114.58  3.000
 9FC  H6   N11  C4   117.63  3.000
 9FC  C18  N11  C4   124.92  3.000
 9FC  C17  C12  C13  118.76  3.000
 9FC  C17  C12  N10  125.93  3.000
 9FC  C13  C12  N10  115.31  3.000
 9FC  H7   C13  C14  118.96  3.000
 9FC  H7   C13  C12  119.07  3.000
 9FC  C14  C13  C12  121.97  3.000
 9FC  C15  C14  C13  118.62  3.000
 9FC  C13  C14  C3   120.73  3.000
 9FC  C15  C14  C3   120.65  3.000
 9FC  H8   C15  C16  120.18  3.000
 9FC  H8   C15  C14  120.04  3.000
 9FC  C16  C15  C14  119.79  3.000
 9FC  H9   C16  C17  118.66  3.000
 9FC  H9   C16  C15  119.68  3.000
 9FC  C17  C16  C15  121.66  3.000
 9FC  H10  C17  C16  120.06  3.000
 9FC  H10  C17  C12  120.74  3.000
 9FC  C16  C17  C12  119.20  3.000
 9FC  H11  C18  C23  108.29  3.000
 9FC  H11  C18  C19  108.89  3.000
 9FC  C23  C18  C19  110.29  3.000
 9FC  H11  C18  N11  108.79  3.000
 9FC  C19  C18  N11  112.46  3.000
 9FC  C23  C18  N11  108.01  3.000
 9FC  H13  C19  H12  106.32  3.000
 9FC  H13  C19  C20  109.47  3.000
 9FC  H12  C19  C20  111.01  3.000
 9FC  H13  C19  C18  107.60  3.000
 9FC  H12  C19  C18  109.83  3.000
 9FC  C20  C19  C18  112.38  3.000
 9FC  H15  C20  H14  106.41  3.000
 9FC  H15  C20  C21  110.47  3.000
 9FC  H14  C20  C21  109.65  3.000
 9FC  H15  C20  C19  109.53  3.000
 9FC  H14  C20  C19  109.83  3.000
 9FC  C21  C20  C19  110.84  3.000
 9FC  H17  C21  H16  106.55  3.000
 9FC  H17  C21  C22  109.40  3.000
 9FC  H16  C21  C22  109.89  3.000
 9FC  H17  C21  C20  109.32  3.000
 9FC  H16  C21  C20  110.65  3.000
 9FC  C22  C21  C20  110.93  3.000
 9FC  H19  C22  H18  106.03  3.000
 9FC  H19  C22  C23  108.77  3.000
 9FC  H18  C22  C23  109.77  3.000
 9FC  H19  C22  C21  110.27  3.000
 9FC  H18  C22  C21  109.77  3.000
 9FC  C23  C22  C21  112.04  3.000
 9FC  H20  C23  N24  112.90  3.000
 9FC  H20  C23  C22  107.58  3.000
 9FC  N24  C23  C22  109.40  3.000
 9FC  H20  C23  C18  105.64  3.000
 9FC  N24  C23  C18  109.41  3.000
 9FC  C22  C23  C18  111.90  3.000
 9FC  H22  N24  H21  106.17  3.000
 9FC  H22  N24  C23  110.12  3.000
 9FC  H21  N24  C23  109.78  3.000
 9FC  H25  N27  H24  116.26  3.000
 9FC  H25  N27  C1   118.52  3.000
 9FC  H24  N27  C1   123.41  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
 9FC  CONST_01  C4   N9   C8   C7      0.00   0.0  0
 9FC  CONST_02  C4   C5   C6   C7      0.00   0.0  0
 9FC  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 9FC  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 9FC  CONST_05  N9   C8   C7   C6      0.00   0.0  0
 9FC  CONST_06  N9   C4   C5   C6      0.00   0.0  0
 9FC  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 9FC  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 9FC  CONST_09  C16  C15  C14  C13     0.00   0.0  0
 9FC  CONST_10  C16  C17  C12  C13     0.00   0.0  0
 9FC  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 9FC  CONST_12  C17  C12  C13  C14     0.00   0.0  0
 9FC  CONST_13  C2   C5   C6   C7    180.00   0.0  0
 9FC  CONST_14  N10  C8   N9   C4    180.00   0.0  0
 9FC  CONST_15  C1   C7   C6   C5    180.00   0.0  0
 9FC  CONST_16  N10  C8   C7   C6    180.00   0.0  0
 9FC  CONST_17  N11  C4   C5   C6    180.00   0.0  0
 9FC  CONST_18  C16  C15  C14  C3    180.00   0.0  0
 9FC  CONST_19  C12  C13  C14  C3    180.00   0.0  0
 9FC  CONST_20  N9   C4   C5   C2    180.00   0.0  0
 9FC  CONST_21  N9   C8   C7   C1    180.00   0.0  0
 9FC  CONST_22  N11  C4   N9   C8    180.00   0.0  0
 9FC  CONST_23  C14  C13  C12  N10   180.00   0.0  0
 9FC  CONST_24  C16  C17  C12  N10   180.00   0.0  0
 9FC  CONST_25  C18  N11  C4   C5    180.00   0.0  0
 9FC  CONST_26  C18  N11  C4   N9      0.00   0.0  0
 9FC  CONST_27  H1   C6   C5   C4    180.00   0.0  0
 9FC  CONST_28  H9   C16  C17  C12   180.00   0.0  0
 9FC  CONST_29  H8   C15  C14  C13   180.00   0.0  0
 9FC  CONST_30  H10  C17  C12  C13   180.00   0.0  0
 9FC  CONST_31  H7   C13  C14  C15   180.00   0.0  0
 9FC  CONST_33  H24  N27  C1   C7      0.00   0.0  0
 9FC  CONST_34  H25  N27  C1   C7    180.00   0.0  0
 9FC  Var_01    C21  C20  C19  C18   -56.50  30.0  1
 9FC  Var_02    C22  C21  C20  C19    55.77  30.0  1
 9FC  Var_03    C23  C22  C21  C20   -55.14  30.0  1
 9FC  Var_04    C12  N10  C8   C7   -179.32  30.0  3
 9FC  Var_05    C13  C12  N10  C8    173.93  30.0  3
 9FC  Var_06    O26  C1   C7   C6    165.30  30.0  2
 9FC  Var_07    H2   C3   C14  C13   106.23  30.0  2

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
 9FC  chir_01  C18  C23  C19  N11  negativ
 9FC  chir_02  C23  N24  C22  C18  negativ

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
 9FC  plan-1  C7   0.020
 9FC  plan-1  C4   0.020
 9FC  plan-1  C5   0.020
 9FC  plan-1  C6   0.020
 9FC  plan-1  C2   0.020
 9FC  plan-1  C1   0.020
 9FC  plan-1  C8   0.020
 9FC  plan-1  N9   0.020
 9FC  plan-1  N10  0.020
 9FC  plan-1  N11  0.020
 9FC  plan-1  N25  0.020
 9FC  plan-1  H1   0.020
 9FC  plan-2  C3   0.020
 9FC  plan-2  N10  0.020
 9FC  plan-2  C12  0.020
 9FC  plan-2  C13  0.020
 9FC  plan-2  C14  0.020
 9FC  plan-2  C15  0.020
 9FC  plan-2  C16  0.020
 9FC  plan-2  C17  0.020
 9FC  plan-2  H7   0.020
 9FC  plan-2  H8   0.020
 9FC  plan-2  H9   0.020
 9FC  plan-2  H10  0.020
 9FC  plan-3  C7   0.020
 9FC  plan-3  C1   0.020
 9FC  plan-3  O26  0.020
 9FC  plan-3  N27  0.020
 9FC  plan-3  H24  0.020
 9FC  plan-3  H25  0.020
 9FC  plan-4  C4   0.020
 9FC  plan-4  N11  0.020
 9FC  plan-4  C18  0.020
 9FC  plan-4  H6   0.020

