# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 09:38:21 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 4-{2-[(1S)-1-({[trans-4-(aminomethyl)cyclohexyl]carbonyl}amino)-2-phenylethyl]-1H-imidazol-4-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CC[C@H](CC1)C(=O)N[C@@H](Cc2ccccc2)c3[nH]cc(n3)c4ccc(cc4)C(N)=O
#
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
 39D  39D  4-{2-[(1S)-1-({[trans-4-(aminomethyl)cyclohexyl]carbonyl}amino)-2-phenylethyl]-1H-imidazol-4-yl}benzamide  ligand  64  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_39D
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
 39D  C18  C  CH2   0  -0.411    4.7664  -1.1601   1.7991
 39D  C17  C  CH1   0  -0.406    3.7173  -1.0959   0.6950
 39D  C15  C  C     0   0.605    2.5639  -0.1791   1.0674
 39D  C19  C  CH2   0  -0.427    5.9235  -2.0722   1.4092
 39D  C20  C  CH1   0  -0.227    6.5827  -1.6508   0.0976
 39D  C21  C  CH2   0  -0.427    5.5290  -1.5718  -1.0045
 39D  C22  C  CH2   0  -0.425    4.3655  -0.6615  -0.6278
 39D  C23  C  CH2   0  -0.266    7.7218  -2.6004  -0.2545
 39D  C11  C  CR5   0   0.510   -0.9239  -0.2121   0.4105
 39D  C12  C  CH1   0  -0.169    0.3385   0.5947   0.3341
 39D  C27  C  CR16  0  -0.247   -6.6539  -1.6062   0.3593
 39D  C1   C  CR6   0   0.148    1.4797   2.5104  -0.8174
 39D  C2   C  CR16  0  -0.312    2.5639   2.2815  -1.6583
 39D  C3   C  CR16  0  -0.237    3.6845   3.1021  -1.6166
 39D  C4   C  CR16  0  -0.275    3.7336   4.1678  -0.7293
 39D  C5   C  CR16  0  -0.241    2.6545   4.4088   0.1128
 39D  C6   C  CR16  0  -0.297    1.5396   3.5854   0.0676
 39D  N7   N  N     0  -0.474   -2.1267   0.2263   0.1536
 39D  C8   C  CR5   0   0.145   -2.9790  -0.8148   0.4118
 39D  C9   C  CR15  0  -0.107   -2.2558  -1.9031   0.8319
 39D  N10  N  NR15  0  -0.619   -0.9578  -1.4982   0.8222
 39D  N13  N  NH1   0  -0.662    1.4858  -0.2752   0.2505
 39D  C14  C  CH2   0  -0.523    0.2856   1.6007  -0.8246
 39D  O16  O  O     0  -0.474    2.5930   0.5709   2.0275
 39D  N24  N  NH2   0  -0.807    8.4526  -2.1750  -1.4404
 39D  C25  C  CR6   0   0.036   -4.4216  -0.6840   0.2469
 39D  C26  C  CR16  0  -0.329   -5.2878  -1.7501   0.5048
 39D  C28  C  CR6   0  -0.060   -7.2093  -0.3954  -0.0544
 39D  C29  C  CR16  0  -0.264   -6.3468   0.6688  -0.3119
 39D  C30  C  CR16  0  -0.292   -4.9780   0.5281  -0.1652
 39D  C31  C  C     0   0.498   -8.6967  -0.3124  -0.1787
 39D  O32  O  O     0  -0.485   -9.4098  -1.2397   0.1855
 39D  N33  N  NH2   0  -0.825   -9.2069   0.8149  -0.6971
 39D  H46  H  HCH2  0   0.218    5.1479  -0.1547   1.9984
 39D  H47  H  HCH2  0   0.233    4.3166  -1.5134   2.7297
 39D  H45  H  HCH1  0   0.255    3.3030  -2.1023   0.5465
 39D  H49  H  HCH2  0   0.229    6.6657  -2.0812   2.2123
 39D  H48  H  HCH2  0   0.208    5.5600  -3.1027   1.3140
 39D  H50  H  HCH1  0   0.208    7.0085  -0.6476   0.2339
 39D  H51  H  HCH2  0   0.232    5.9690  -1.2062  -1.9358
 39D  H52  H  HCH2  0   0.210    5.1496  -2.5801  -1.2120
 39D  H53  H  HCH2  0   0.233    3.6330  -0.6573  -1.4385
 39D  H54  H  HCH2  0   0.230    4.7205   0.3696  -0.5297
 39D  H55  H  HCH2  0   0.218    8.4266  -2.6204   0.5815
 39D  H56  H  HCH2  0   0.182    7.3126  -3.6202  -0.3345
 39D  H41  H  HCH1  0   0.292    0.4373   1.1547   1.2678
 39D  H34  H  HCR6  0   0.245    2.5325   1.4524  -2.3548
 39D  H35  H  HCR6  0   0.252    4.5180   2.9078  -2.2796
 39D  H36  H  HCR6  0   0.252    4.6042   4.8100  -0.6953
 39D  H37  H  HCR6  0   0.252    2.6823   5.2403   0.8056
 39D  H38  H  HCR6  0   0.244    0.7040   3.7804   0.7307
 39D  H39  H  HCR5  0   0.292   -2.5382  -2.9005   1.1216
 39D  H40  H  HNR5  0   0.419   -0.1604  -2.0615   1.0752
 39D  H42  H  HNH1  0   0.400    1.5620  -0.8591  -0.5689
 39D  H43  H  HCH2  0   0.258    0.2225   1.0559  -1.7699
 39D  H44  H  HCH2  0   0.267   -0.6354   2.1784  -0.7302
 39D  H57  H  HNH2  0   0.347    9.2539  -2.7790  -1.5709
 39D  H58  H  HNH2  0   0.342    7.8799  -2.3133  -2.2635
 39D  H59  H  HCR6  0   0.247   -4.8962  -2.7063   0.8285
 39D  H61  H  HCR6  0   0.248   -6.7171   1.6373  -0.6220
 39D  H62  H  HCR6  0   0.257   -4.3309   1.3707  -0.3681
 39D  H64  H  HNH2  0   0.413   -8.6470   1.5591  -1.0711
 39D  H63  H  HNH2  0   0.405  -10.2042   0.9027  -0.8019
 39D  H60  H  HCR6  0   0.261   -7.3001  -2.4478   0.5687

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
 39D  C19  C18  single    1.524  0.020  1.524
 39D  C19  C20  single    1.527  0.020  1.527
 39D  N24  C23  single    1.457  0.020  1.457
 39D  N10  C9   aromatic  1.360  0.020  1.360
 39D  N10  C11  aromatic  1.351  0.020  1.351
 39D  C6   C5   aromatic  1.387  0.020  1.387
 39D  C6   C1   aromatic  1.394  0.020  1.394
 39D  C18  C17  single    1.524  0.020  1.524
 39D  C23  C20  single    1.524  0.020  1.524
 39D  C14  C1   single    1.501  0.020  1.501
 39D  C14  C12  single    1.535  0.020  1.535
 39D  C9   C8   aromatic  1.373  0.020  1.373
 39D  C5   C4   aromatic  1.390  0.020  1.390
 39D  N13  C12  single    1.442  0.020  1.442
 39D  N13  C15  single    1.356  0.020  1.356
 39D  C20  C21  single    1.527  0.020  1.527
 39D  C17  C15  single    1.520  0.020  1.520
 39D  C17  C22  single    1.536  0.020  1.536
 39D  C1   C2   aromatic  1.391  0.020  1.391
 39D  C12  C11  single    1.500  0.020  1.500
 39D  C11  N7   aromatic  1.306  0.020  1.306
 39D  C21  C22  single    1.525  0.020  1.525
 39D  C15  O16  double    1.219  0.020  1.219
 39D  C8   N7   aromatic  1.370  0.020  1.370
 39D  C8   C25  single    1.458  0.020  1.458
 39D  C4   C3   aromatic  1.388  0.020  1.388
 39D  C2   C3   aromatic  1.389  0.020  1.389
 39D  C26  C25  aromatic  1.398  0.020  1.398
 39D  C26  C27  aromatic  1.381  0.020  1.381
 39D  C25  C30  aromatic  1.396  0.020  1.396
 39D  C27  C28  aromatic  1.395  0.020  1.395
 39D  C30  C29  aromatic  1.384  0.020  1.384
 39D  C28  C29  aromatic  1.394  0.020  1.394
 39D  C28  C31  single    1.495  0.020  1.495
 39D  O32  C31  double    1.225  0.020  1.225
 39D  C31  N33  single    1.342  0.020  1.342
 39D  C18  H46  single    0.970  0.020  1.090
 39D  C18  H47  single    0.970  0.020  1.090
 39D  C17  H45  single    0.970  0.020  1.090
 39D  C19  H49  single    0.970  0.020  1.090
 39D  C19  H48  single    0.970  0.020  1.090
 39D  C20  H50  single    0.970  0.020  1.090
 39D  C21  H51  single    0.970  0.020  1.090
 39D  C21  H52  single    0.970  0.020  1.090
 39D  C22  H53  single    0.970  0.020  1.090
 39D  C22  H54  single    0.970  0.020  1.090
 39D  C23  H55  single    0.970  0.020  1.090
 39D  C23  H56  single    0.970  0.020  1.090
 39D  C12  H41  single    0.970  0.020  1.090
 39D  C27  H60  single    0.930  0.020  1.080
 39D  C2   H34  single    0.930  0.020  1.080
 39D  C3   H35  single    0.930  0.020  1.080
 39D  C4   H36  single    0.930  0.020  1.080
 39D  C5   H37  single    0.930  0.020  1.080
 39D  C6   H38  single    0.930  0.020  1.080
 39D  C9   H39  single    0.930  0.020  1.080
 39D  N10  H40  single    0.860  0.020  1.020
 39D  N13  H42  single    0.860  0.020  1.020
 39D  C14  H43  single    0.970  0.020  1.090
 39D  C14  H44  single    0.970  0.020  1.090
 39D  N24  H57  single    0.890  0.020  1.040
 39D  N24  H58  single    0.890  0.020  1.040
 39D  C26  H59  single    0.930  0.020  1.080
 39D  C29  H61  single    0.930  0.020  1.080
 39D  C30  H62  single    0.930  0.020  1.080
 39D  N33  H64  single    0.860  0.020  1.020
 39D  N33  H63  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
 39D  H47  C18  H46  106.60  3.000
 39D  H47  C18  C19  109.70  3.000
 39D  H46  C18  C19  109.39  3.000
 39D  H47  C18  C17  110.32  3.000
 39D  H46  C18  C17  109.47  3.000
 39D  C19  C18  C17  111.25  3.000
 39D  H45  C17  C22  107.58  3.000
 39D  H45  C17  C15  107.43  3.000
 39D  C22  C17  C15  111.15  3.000
 39D  H45  C17  C18  108.59  3.000
 39D  C22  C17  C18  110.20  3.000
 39D  C15  C17  C18  111.73  3.000
 39D  O16  C15  N13  122.49  3.000
 39D  O16  C15  C17  123.11  3.000
 39D  N13  C15  C17  114.40  3.000
 39D  H48  C19  H49  106.31  3.000
 39D  H48  C19  C20  109.13  3.000
 39D  H49  C19  C20  109.88  3.000
 39D  H48  C19  C18  109.44  3.000
 39D  H49  C19  C18  109.41  3.000
 39D  C20  C19  C18  112.48  3.000
 39D  H50  C20  C23  107.93  3.000
 39D  H50  C20  C21  108.05  3.000
 39D  C23  C20  C21  112.42  3.000
 39D  H50  C20  C19  108.22  3.000
 39D  C21  C20  C19  109.65  3.000
 39D  C23  C20  C19  110.43  3.000
 39D  H52  C21  H51  106.59  3.000
 39D  H52  C21  C22  109.37  3.000
 39D  H51  C21  C22  108.55  3.000
 39D  H52  C21  C20  109.12  3.000
 39D  H51  C21  C20  110.76  3.000
 39D  C22  C21  C20  112.29  3.000
 39D  H54  C22  H53  106.27  3.000
 39D  H54  C22  C21  109.70  3.000
 39D  H53  C22  C21  109.31  3.000
 39D  H54  C22  C17  109.03  3.000
 39D  H53  C22  C17  110.93  3.000
 39D  C21  C22  C17  111.47  3.000
 39D  H56  C23  H55  106.14  3.000
 39D  H56  C23  N24  113.43  3.000
 39D  H55  C23  N24  107.72  3.000
 39D  H56  C23  C20  108.41  3.000
 39D  H55  C23  C20  108.45  3.000
 39D  N24  C23  C20  112.40  3.000
 39D  N10  C11  N7   110.89  3.000
 39D  N7   C11  C12  125.77  3.000
 39D  N10  C11  C12  123.28  3.000
 39D  H41  C12  C14  108.18  3.000
 39D  H41  C12  N13  106.66  3.000
 39D  C14  C12  N13  112.27  3.000
 39D  H41  C12  C11  107.94  3.000
 39D  N13  C12  C11  110.36  3.000
 39D  C14  C12  C11  111.21  3.000
 39D  H60  C27  C28  119.67  3.000
 39D  H60  C27  C26  119.31  3.000
 39D  C28  C27  C26  121.02  3.000
 39D  C14  C1   C6   120.31  3.000
 39D  C14  C1   C2   121.16  3.000
 39D  C6   C1   C2   118.51  3.000
 39D  H34  C2   C3   119.65  3.000
 39D  H34  C2   C1   119.47  3.000
 39D  C3   C2   C1   120.88  3.000
 39D  H35  C3   C4   120.14  3.000
 39D  H35  C3   C2   119.77  3.000
 39D  C4   C3   C2   120.08  3.000
 39D  H36  C4   C5   120.17  3.000
 39D  H36  C4   C3   120.28  3.000
 39D  C5   C4   C3   119.55  3.000
 39D  H37  C5   C6   119.84  3.000
 39D  H37  C5   C4   120.06  3.000
 39D  C6   C5   C4   120.09  3.000
 39D  H38  C6   C5   119.52  3.000
 39D  H38  C6   C1   119.60  3.000
 39D  C5   C6   C1   120.88  3.000
 39D  C8   N7   C11  106.31  3.000
 39D  C25  C8   C9   128.83  3.000
 39D  C25  C8   N7   121.75  3.000
 39D  C9   C8   N7   109.42  3.000
 39D  H39  C9   N10  121.89  3.000
 39D  H39  C9   C8   132.76  3.000
 39D  N10  C9   C8   105.34  3.000
 39D  H40  N10  C9   125.92  3.000
 39D  H40  N10  C11  126.04  3.000
 39D  C9   N10  C11  108.04  3.000
 39D  H42  N13  C12  117.14  3.000
 39D  H42  N13  C15  118.04  3.000
 39D  C12  N13  C15  123.70  3.000
 39D  H44  C14  H43  106.86  3.000
 39D  H44  C14  C1   110.49  3.000
 39D  H43  C14  C1   110.62  3.000
 39D  H44  C14  C12  108.10  3.000
 39D  H43  C14  C12  109.15  3.000
 39D  C1   C14  C12  111.47  3.000
 39D  H58  N24  H57  105.17  3.000
 39D  H58  N24  C23  109.77  3.000
 39D  H57  N24  C23  109.15  3.000
 39D  C30  C25  C26  118.02  3.000
 39D  C30  C25  C8   120.38  3.000
 39D  C26  C25  C8   121.60  3.000
 39D  H59  C26  C25  120.30  3.000
 39D  H59  C26  C27  118.76  3.000
 39D  C25  C26  C27  120.93  3.000
 39D  C31  C28  C29  123.91  3.000
 39D  C31  C28  C27  117.97  3.000
 39D  C29  C28  C27  118.11  3.000
 39D  H61  C29  C30  117.37  3.000
 39D  H61  C29  C28  121.63  3.000
 39D  C30  C29  C28  120.99  3.000
 39D  H62  C30  C29  119.52  3.000
 39D  H62  C30  C25  119.56  3.000
 39D  C29  C30  C25  120.92  3.000
 39D  N33  C31  O32  121.97  3.000
 39D  N33  C31  C28  117.20  3.000
 39D  O32  C31  C28  120.82  3.000
 39D  H63  N33  H64  116.69  3.000
 39D  H63  N33  C31  119.36  3.000
 39D  H64  N33  C31  123.71  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
 39D  CONST_01  C8   C9   N10  C11    0.00   0.0  0
 39D  CONST_02  C9   C8   N7   C11    0.00   0.0  0
 39D  CONST_03  C25  C8   N7   C11  180.00   0.0  0
 39D  CONST_04  C8   C25  C26  C27  180.00   0.0  0
 39D  CONST_05  C30  C25  C26  C27    0.00   0.0  0
 39D  CONST_06  C30  C29  C28  C27    0.00   0.0  0
 39D  CONST_07  C4   C5   C6   C1     0.00   0.0  0
 39D  CONST_08  C4   C3   C2   C1     0.00   0.0  0
 39D  CONST_09  C5   C6   C1   C2     0.00   0.0  0
 39D  CONST_10  C5   C4   C3   C2     0.00   0.0  0
 39D  CONST_11  C6   C5   C4   C3     0.00   0.0  0
 39D  CONST_12  C6   C1   C2   C3     0.00   0.0  0
 39D  CONST_13  C9   N10  C11  N7     0.00   0.0  0
 39D  CONST_14  N10  C9   C8   N7     0.00   0.0  0
 39D  CONST_15  C26  C25  C8   N7   180.00   0.0  0
 39D  CONST_16  C30  C25  C8   N7     0.00   0.0  0
 39D  CONST_17  N10  C11  N7   C8     0.00   0.0  0
 39D  CONST_18  C29  C30  C25  C8   180.00   0.0  0
 39D  CONST_19  C26  C25  C8   C9     0.00   0.0  0
 39D  CONST_20  C30  C25  C8   C9   180.00   0.0  0
 39D  CONST_21  C25  C8   C9   N10  180.00   0.0  0
 39D  CONST_22  C28  C27  C26  C25    0.00   0.0  0
 39D  CONST_23  C28  C29  C30  C25    0.00   0.0  0
 39D  CONST_24  C29  C30  C25  C26    0.00   0.0  0
 39D  CONST_25  C29  C28  C27  C26    0.00   0.0  0
 39D  CONST_26  C9   N10  C11  C12  180.00   0.0  0
 39D  CONST_27  C8   N7   C11  C12  180.00   0.0  0
 39D  CONST_28  C14  C1   C2   C3   180.00   0.0  0
 39D  CONST_29  C14  C1   C6   C5   180.00   0.0  0
 39D  CONST_30  C31  C28  C27  C26  180.00   0.0  0
 39D  CONST_31  C31  C28  C29  C30  180.00   0.0  0
 39D  CONST_32  H39  C9   N10  C11  180.00   0.0  0
 39D  CONST_33  H61  C29  C28  C27  180.00   0.0  0
 39D  CONST_34  H37  C5   C6   C1   180.00   0.0  0
 39D  CONST_35  H35  C3   C2   C1   180.00   0.0  0
 39D  CONST_36  H38  C6   C1   C2   180.00   0.0  0
 39D  CONST_37  H36  C4   C3   C2   180.00   0.0  0
 39D  CONST_38  H34  C2   C3   C4   180.00   0.0  0
 39D  CONST_39  H40  N10  C11  N7   180.00   0.0  0
 39D  CONST_40  H59  C26  C25  C8     0.00   0.0  0
 39D  CONST_41  H62  C30  C25  C8     0.00   0.0  0
 39D  CONST_42  H60  C27  C26  C25  180.00   0.0  0
 39D  CONST_43  C12  N13  C15  C17  180.00   0.0  0
 39D  CONST_44  H42  N13  C15  C17    0.00   0.0  0
 39D  CONST_45  H64  N33  C31  C28    0.00   0.0  0
 39D  CONST_46  H63  N33  C31  C28  180.00   0.0  0
 39D  CONST_47  O16  C15  N13  C12    0.00   0.0  0
 39D  Var_01    C20  C19  C18  C17   56.51  30.0  1
 39D  Var_02    C20  C21  C22  C17  -55.81  30.0  1
 39D  Var_03    C6   C1   C14  C12  -78.51  30.0  2
 39D  Var_04    O32  C31  C28  C27    6.39  30.0  2
 39D  Var_05    H57  N24  C23  C20  173.92  30.0  3

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
 39D  chir_01  C17  C18  C15  C22  negativ
 39D  chir_02  C20  C21  C23  C19  positiv
 39D  chir_03  C12  N13  C14  C11  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
 39D  plan-1  C11  0.020
 39D  plan-1  C12  0.020
 39D  plan-1  N7   0.020
 39D  plan-1  C8   0.020
 39D  plan-1  C9   0.020
 39D  plan-1  N10  0.020
 39D  plan-1  C25  0.020
 39D  plan-1  H39  0.020
 39D  plan-1  H40  0.020
 39D  plan-2  C1   0.020
 39D  plan-2  C2   0.020
 39D  plan-2  C3   0.020
 39D  plan-2  C4   0.020
 39D  plan-2  C5   0.020
 39D  plan-2  C6   0.020
 39D  plan-2  C14  0.020
 39D  plan-2  H34  0.020
 39D  plan-2  H35  0.020
 39D  plan-2  H36  0.020
 39D  plan-2  H37  0.020
 39D  plan-2  H38  0.020
 39D  plan-3  C27  0.020
 39D  plan-3  C8   0.020
 39D  plan-3  C25  0.020
 39D  plan-3  C26  0.020
 39D  plan-3  C28  0.020
 39D  plan-3  C29  0.020
 39D  plan-3  C30  0.020
 39D  plan-3  C31  0.020
 39D  plan-3  H59  0.020
 39D  plan-3  H61  0.020
 39D  plan-3  H62  0.020
 39D  plan-3  H60  0.020
 39D  plan-4  C28  0.020
 39D  plan-4  C31  0.020
 39D  plan-4  O32  0.020
 39D  plan-4  N33  0.020
 39D  plan-4  H64  0.020
 39D  plan-4  H63  0.020
 39D  plan-5  C17  0.020
 39D  plan-5  C15  0.020
 39D  plan-5  C12  0.020
 39D  plan-5  N13  0.020
 39D  plan-5  O16  0.020
 39D  plan-5  H42  0.020

