# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:29:52 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: trans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cc(n1)C(=O)NCc2ccc(F)cc2)c3ncn(C[C@@H]4CC[C@H](CC4)C(O)=O)n3
#
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
 3EK  3EK  'trans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid'  ligand  58  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3EK
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
 3EK  C1    C  CH1    0  -0.249  -5.0780  -0.1896  -0.8612
 3EK  C2    C  CH2    0  -0.426  -5.4767  -0.4613   0.5866
 3EK  C3    C  CH2    0  -0.407  -6.0557   0.7815   1.2550
 3EK  C4    C  CH1    0  -0.383  -7.2438   1.3444   0.4829
 3EK  C5    C  CH2    0  -0.416  -6.8453   1.6154  -0.9679
 3EK  C6    C  CH2    0  -0.419  -6.2632   0.3774  -1.6400
 3EK  C7    C  CH2    0  -0.277  -4.5577  -1.4379  -1.5672
 3EK  N8    N  NR5    0  -0.254  -3.4057  -2.0169  -0.9058
 3EK  N9    N  N      0  -0.274  -2.2243  -1.4092  -0.9124
 3EK  C10   C  CR5    0   0.324  -1.4785  -2.1874  -0.1560
 3EK  N11   N  N      0  -0.469  -2.1325  -3.2614   0.3367
 3EK  C12   C  CR15   0   0.105  -3.3420  -3.1188  -0.1525
 3EK  C13   C  CR6    0   0.156  -0.0718  -1.9047   0.1197
 3EK  C14   C  CR16   0  -0.385   0.6541  -2.7096   0.9839
 3EK  C15   C  CR6    0   0.264   1.9933  -2.4152   1.2412
 3EK  N16   N  N      0  -0.464   2.5926  -1.3765   0.6769
 3EK  C17   C  CR6    0   0.126   1.9011  -0.6041  -0.1572
 3EK  C18   C  CR16   0  -0.356   0.5741  -0.8188  -0.4706
 3EK  C19   C  CH3    0  -0.732   2.8054  -3.2808   2.1538
 3EK  C20   C  C      0   0.545   2.6285   0.5606  -0.7710
 3EK  O21   O  O      0  -0.488   2.0802   1.3056  -1.5724
 3EK  N22   N  NH1    0  -0.645   3.8936   0.6953  -0.3667
 3EK  C23   C  CH2    0  -0.317   4.7580   1.7658  -0.8172
 3EK  C24   C  CR6    0   0.047   6.1932   1.4308  -0.5209
 3EK  C25   C  CR16   0  -0.263   6.8402   0.4183  -1.2272
 3EK  C26   C  CR16   0  -0.396   8.1570   0.0840  -0.9534
 3EK  C27   C  CR6    0   0.516   8.8207   0.7792   0.0410
 3EK  C28   C  CR16   0  -0.397   8.2146   1.7877   0.7617
 3EK  C29   C  CR16   0  -0.281   6.8935   2.1050   0.4728
 3EK  C30   C  C      0   0.428  -7.8901   2.5805   1.1453
 3EK  O31   O  O      0  -0.605  -7.5670   2.8463   2.3207
 3EK  F32   F  F      0  -0.315  10.0970   0.4618   0.3125
 3EK  O33   O  OC    -1  -0.619  -8.7144   3.2152   0.4536
 3EK  H1    H  HCH1   0   0.230  -4.2759   0.5595  -0.8658
 3EK  H2    H  HCH2   0   0.207  -6.2203  -1.2684   0.6098
 3EK  H2A   H  HCH2   0   0.229  -4.6165  -0.8151   1.1625
 3EK  H3    H  HCH2   0   0.219  -6.3483   0.5427   2.2782
 3EK  H3A   H  HCH2   0   0.200  -5.2738   1.5461   1.3297
 3EK  H4    H  HCH1   0   0.211  -8.0229   0.5655   0.4602
 3EK  H5    H  HCH2   0   0.223  -7.7085   1.9689  -1.5322
 3EK  H5A   H  HCH2   0   0.202  -6.1025   2.4222  -0.9972
 3EK  H6    H  HCH2   0   0.229  -5.9581   0.6142  -2.6637
 3EK  H6A   H  HCH2   0   0.209  -7.0420  -0.3917  -1.7170
 3EK  H7    H  HCH2   0   0.263  -5.3259  -2.2123  -1.5979
 3EK  H7A   H  HCH2   0   0.277  -4.2751  -1.2118  -2.5960
 3EK  H12   H  HCR5   0   0.306  -4.1839  -3.7753   0.0025
 3EK  H14   H  HCR6   0   0.267   0.1876  -3.5608   1.4618
 3EK  H18   H  HCR6   0   0.268   0.0550  -0.1605  -1.1525
 3EK  H19   H  HCH3   0   0.259   3.0495  -4.2266   1.6664
 3EK  H19A  H  HCH3   0   0.254   3.7381  -2.7897   2.4219
 3EK  H19B  H  HCH3   0   0.253   2.2592  -3.5208   3.0657
 3EK  HN22  H  HNH1   0   0.406   4.2273   0.0487   0.3337
 3EK  H23   H  HCH2   0   0.261   4.6160   1.9075  -1.8904
 3EK  H23A  H  HCH2   0   0.258   4.4863   2.7089  -0.3347
 3EK  H25   H  HCR6   0   0.267   6.3119  -0.1174  -2.0066
 3EK  H26   H  HCR6   0   0.281   8.6600  -0.6999  -1.5042
 3EK  H28   H  HCR6   0   0.281   8.7582   2.3147   1.5345
 3EK  H29   H  HCR6   0   0.266   6.4069   2.8929   1.0344

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
 3EK  C7   C1    single    1.526  0.020  1.526
 3EK  C2   C1    single    1.526  0.020  1.526
 3EK  C1   C6    single    1.527  0.020  1.527
 3EK  C1   H1    single    0.970  0.020  1.090
 3EK  C2   C3    single    1.525  0.020  1.525
 3EK  C2   H2    single    0.970  0.020  1.090
 3EK  C2   H2A   single    0.970  0.020  1.090
 3EK  C3   C4    single    1.525  0.020  1.525
 3EK  C3   H3    single    0.970  0.020  1.090
 3EK  C3   H3A   single    0.970  0.020  1.090
 3EK  C4   C5    single    1.529  0.020  1.529
 3EK  C4   C30   single    1.544  0.020  1.544
 3EK  C4   H4    single    0.970  0.020  1.090
 3EK  C6   C5    single    1.524  0.020  1.524
 3EK  C5   H5    single    0.970  0.020  1.090
 3EK  C5   H5A   single    0.970  0.020  1.090
 3EK  C6   H6    single    0.970  0.020  1.090
 3EK  C6   H6A   single    0.970  0.020  1.090
 3EK  C7   N8    single    1.449  0.020  1.449
 3EK  C7   H7    single    0.970  0.020  1.090
 3EK  C7   H7A   single    0.970  0.020  1.090
 3EK  C12  N8    aromatic  1.336  0.020  1.336
 3EK  N8   N9    aromatic  1.329  0.020  1.329
 3EK  C10  N9    aromatic  1.317  0.020  1.317
 3EK  N11  C10   aromatic  1.350  0.020  1.350
 3EK  C10  C13   single    1.461  0.020  1.461
 3EK  C12  N11   aromatic  1.313  0.020  1.313
 3EK  C12  H12   single    0.930  0.020  1.080
 3EK  C18  C13   aromatic  1.395  0.020  1.395
 3EK  C13  C14   aromatic  1.386  0.020  1.386
 3EK  C14  C15   aromatic  1.395  0.020  1.395
 3EK  C14  H14   single    0.930  0.020  1.080
 3EK  C15  N16   aromatic  1.325  0.020  1.325
 3EK  C15  C19   single    1.497  0.020  1.497
 3EK  C17  N16   aromatic  1.331  0.020  1.331
 3EK  C18  C17   aromatic  1.380  0.020  1.380
 3EK  C17  C20   single    1.504  0.020  1.504
 3EK  C18  H18   single    0.930  0.020  1.080
 3EK  C19  H19   single    0.970  0.020  1.090
 3EK  C19  H19A  single    0.970  0.020  1.090
 3EK  C19  H19B  single    0.970  0.020  1.090
 3EK  O21  C20   double    1.224  0.020  1.224
 3EK  C20  N22   single    1.335  0.020  1.335
 3EK  N22  C23   single    1.448  0.020  1.448
 3EK  N22  HN22  single    0.860  0.020  1.020
 3EK  C23  C24   single    1.503  0.020  1.503
 3EK  C23  H23   single    0.970  0.020  1.090
 3EK  C23  H23A  single    0.970  0.020  1.090
 3EK  C24  C25   aromatic  1.394  0.020  1.394
 3EK  C24  C29   aromatic  1.390  0.020  1.390
 3EK  C25  C26   aromatic  1.386  0.020  1.386
 3EK  C25  H25   single    0.930  0.020  1.080
 3EK  C26  C27   aromatic  1.383  0.020  1.383
 3EK  C26  H26   single    0.930  0.020  1.080
 3EK  C28  C27   aromatic  1.380  0.020  1.380
 3EK  C27  F32   single    1.343  0.020  1.343
 3EK  C29  C28   aromatic  1.389  0.020  1.389
 3EK  C28  H28   single    0.930  0.020  1.080
 3EK  C29  H29   single    0.930  0.020  1.080
 3EK  C30  O31   deloc     1.248  0.020  1.248
 3EK  C30  O33   deloc     1.249  0.020  1.249

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
 3EK  H1    C1   C7    107.89  3.000
 3EK  H1    C1   C6    108.15  3.000
 3EK  C7    C1   C6    109.42  3.000
 3EK  H1    C1   C2    108.44  3.000
 3EK  C6    C1   C2    110.31  3.000
 3EK  C7    C1   C2    112.49  3.000
 3EK  H2A   C2   H2    106.48  3.000
 3EK  H2A   C2   C3    109.35  3.000
 3EK  H2    C2   C3    109.43  3.000
 3EK  H2A   C2   C1    110.59  3.000
 3EK  H2    C2   C1    109.14  3.000
 3EK  C3    C2   C1    111.71  3.000
 3EK  H3A   C3   H3    106.27  3.000
 3EK  H3A   C3   C4    109.44  3.000
 3EK  H3    C3   C4    110.29  3.000
 3EK  H3A   C3   C2    109.11  3.000
 3EK  H3    C3   C2    109.55  3.000
 3EK  C4    C3   C2    112.01  3.000
 3EK  H4    C4   C30   106.19  3.000
 3EK  H4    C4   C5    106.86  3.000
 3EK  C30   C4   C5    111.98  3.000
 3EK  H4    C4   C3    107.48  3.000
 3EK  C30   C4   C3    113.86  3.000
 3EK  C5    C4   C3    110.05  3.000
 3EK  H5A   C5   H5    106.49  3.000
 3EK  H5A   C5   C6    109.08  3.000
 3EK  H5    C5   C6    109.73  3.000
 3EK  H5A   C5   C4    109.40  3.000
 3EK  H5    C5   C4    110.02  3.000
 3EK  C6    C5   C4    111.97  3.000
 3EK  H6A   C6   H6    106.50  3.000
 3EK  H6A   C6   C5    109.21  3.000
 3EK  H6    C6   C5    110.08  3.000
 3EK  H6A   C6   C1    109.04  3.000
 3EK  H6    C6   C1    109.94  3.000
 3EK  C5    C6   C1    111.90  3.000
 3EK  H7A   C7   H7    107.64  3.000
 3EK  H7A   C7   N8    107.90  3.000
 3EK  H7    C7   N8    106.79  3.000
 3EK  H7A   C7   C1    110.81  3.000
 3EK  H7    C7   C1    110.70  3.000
 3EK  N8    C7   C1    112.76  3.000
 3EK  C12   N8   N9    109.73  3.000
 3EK  N9    N8   C7    121.46  3.000
 3EK  C12   N8   C7    128.66  3.000
 3EK  C10   N9   N8    103.32  3.000
 3EK  C13   C10  N11   123.45  3.000
 3EK  C13   C10  N9    122.64  3.000
 3EK  N11   C10  N9    113.91  3.000
 3EK  C12   N11  C10   102.93  3.000
 3EK  H12   C12  N11   126.83  3.000
 3EK  H12   C12  N8    123.07  3.000
 3EK  N11   C12  N8    110.10  3.000
 3EK  C18   C13  C14   118.26  3.000
 3EK  C14   C13  C10   120.63  3.000
 3EK  C18   C13  C10   121.11  3.000
 3EK  H14   C14  C15   119.90  3.000
 3EK  H14   C14  C13   120.43  3.000
 3EK  C15   C14  C13   119.68  3.000
 3EK  C19   C15  N16   117.86  3.000
 3EK  C19   C15  C14   120.74  3.000
 3EK  N16   C15  C14   121.39  3.000
 3EK  C17   N16  C15   119.14  3.000
 3EK  C20   C17  C18   119.52  3.000
 3EK  C20   C17  N16   117.00  3.000
 3EK  C18   C17  N16   123.48  3.000
 3EK  H18   C18  C17   120.68  3.000
 3EK  H18   C18  C13   121.27  3.000
 3EK  C17   C18  C13   118.05  3.000
 3EK  H19B  C19  H19A  108.85  3.000
 3EK  H19B  C19  H19   107.15  3.000
 3EK  H19A  C19  H19   108.02  3.000
 3EK  H19B  C19  C15   111.45  3.000
 3EK  H19A  C19  C15   110.76  3.000
 3EK  H19   C19  C15   110.49  3.000
 3EK  N22   C20  O21   124.16  3.000
 3EK  N22   C20  C17   114.38  3.000
 3EK  O21   C20  C17   121.46  3.000
 3EK  HN22  N22  C23   119.47  3.000
 3EK  HN22  N22  C20   117.29  3.000
 3EK  C23   N22  C20   123.10  3.000
 3EK  H23A  C23  H23   106.83  3.000
 3EK  H23A  C23  C24   110.02  3.000
 3EK  H23   C23  C24   110.29  3.000
 3EK  H23A  C23  N22   110.61  3.000
 3EK  H23   C23  N22   108.92  3.000
 3EK  C24   C23  N22   110.11  3.000
 3EK  C29   C24  C25   118.74  3.000
 3EK  C29   C24  C23   120.91  3.000
 3EK  C25   C24  C23   120.34  3.000
 3EK  H25   C25  C26   119.09  3.000
 3EK  H25   C25  C24   119.83  3.000
 3EK  C26   C25  C24   121.07  3.000
 3EK  H26   C26  C27   120.46  3.000
 3EK  H26   C26  C25   121.06  3.000
 3EK  C27   C26  C25   118.48  3.000
 3EK  F32   C27  C28   118.99  3.000
 3EK  F32   C27  C26   118.86  3.000
 3EK  C28   C27  C26   122.15  3.000
 3EK  H28   C28  C29   121.01  3.000
 3EK  H28   C28  C27   120.55  3.000
 3EK  C29   C28  C27   118.43  3.000
 3EK  H29   C29  C28   119.05  3.000
 3EK  H29   C29  C24   119.82  3.000
 3EK  C28   C29  C24   121.13  3.000
 3EK  O33   C30  O31   125.75  3.000
 3EK  O33   C30  C4    116.44  3.000
 3EK  O31   C30  C4    117.80  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
 3EK  CONST_01  C10   N11  C12  N8      0.00   0.0  0
 3EK  CONST_02  N11   C10  N9   N8      0.00   0.0  0
 3EK  CONST_03  C13   C10  N9   N8    180.00   0.0  0
 3EK  CONST_04  N11   C12  N8   N9      0.00   0.0  0
 3EK  CONST_05  C12   N11  C10  N9      0.00   0.0  0
 3EK  CONST_06  C18   C13  C10  N9      0.00   0.0  0
 3EK  CONST_07  C14   C13  C10  N9    180.00   0.0  0
 3EK  CONST_08  C12   N8   N9   C10     0.00   0.0  0
 3EK  CONST_09  C17   C18  C13  C10   180.00   0.0  0
 3EK  CONST_10  C15   C14  C13  C10   180.00   0.0  0
 3EK  CONST_11  C18   C13  C10  N11   180.00   0.0  0
 3EK  CONST_12  C14   C13  C10  N11     0.00   0.0  0
 3EK  CONST_13  C13   C10  N11  C12   180.00   0.0  0
 3EK  CONST_14  N16   C17  C18  C13     0.00   0.0  0
 3EK  CONST_15  N16   C15  C14  C13     0.00   0.0  0
 3EK  CONST_16  C17   C18  C13  C14     0.00   0.0  0
 3EK  CONST_17  C17   N16  C15  C14     0.00   0.0  0
 3EK  CONST_18  C18   C13  C14  C15     0.00   0.0  0
 3EK  CONST_19  C18   C17  N16  C15     0.00   0.0  0
 3EK  CONST_20  C27   C26  C25  C24     0.00   0.0  0
 3EK  CONST_21  C27   C28  C29  C24     0.00   0.0  0
 3EK  CONST_22  C28   C29  C24  C25     0.00   0.0  0
 3EK  CONST_23  C28   C27  C26  C25     0.00   0.0  0
 3EK  CONST_24  C29   C24  C25  C26     0.00   0.0  0
 3EK  CONST_25  C29   C28  C27  C26     0.00   0.0  0
 3EK  CONST_26  N11   C12  N8   C7    180.00   0.0  0
 3EK  CONST_27  C10   N9   N8   C7    180.00   0.0  0
 3EK  CONST_28  C20   C17  C18  C13   180.00   0.0  0
 3EK  CONST_29  C19   C15  C14  C13   180.00   0.0  0
 3EK  CONST_30  C20   C17  N16  C15   180.00   0.0  0
 3EK  CONST_31  C19   C15  N16  C17   180.00   0.0  0
 3EK  CONST_32  C26   C25  C24  C23   180.00   0.0  0
 3EK  CONST_33  C28   C29  C24  C23   180.00   0.0  0
 3EK  CONST_34  F32   C27  C26  C25   180.00   0.0  0
 3EK  CONST_35  F32   C27  C28  C29   180.00   0.0  0
 3EK  CONST_36  H12   C12  N8   N9    180.00   0.0  0
 3EK  CONST_37  H18   C18  C13  C10     0.00   0.0  0
 3EK  CONST_38  H14   C14  C13  C10     0.00   0.0  0
 3EK  CONST_39  H26   C26  C25  C24   180.00   0.0  0
 3EK  CONST_40  H28   C28  C29  C24   180.00   0.0  0
 3EK  CONST_41  H29   C29  C24  C25   180.00   0.0  0
 3EK  CONST_42  H25   C25  C26  C27   180.00   0.0  0
 3EK  CONST_43  C23   N22  C20  C17   180.00   0.0  0
 3EK  CONST_44  HN22  N22  C20  C17     0.00   0.0  0
 3EK  CONST_45  C23   N22  C20  O21     0.00   0.0  0
 3EK  Var_01    C4    C3   C2   C1     56.04  30.0  1
 3EK  Var_02    C4    C5   C6   C1    -55.53  30.0  1
 3EK  Var_03    C12   N8   C7   C1    105.17  30.0  2
 3EK  Var_04    O21   C20  C17  N16   178.31  30.0  2
 3EK  Var_05    C25   C24  C23  N22    70.08  30.0  2
 3EK  Var_06    H19   C19  C15  C14    73.45  30.0  2
 3EK  Var_07    C24   C23  N22  C20  -163.48  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
 3EK  chir_01  C1  C7  C2  C6   positiv
 3EK  chir_02  C4  C3  C5  C30  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
 3EK  plan-1  C7    0.020
 3EK  plan-1  N8    0.020
 3EK  plan-1  N9    0.020
 3EK  plan-1  C10   0.020
 3EK  plan-1  N11   0.020
 3EK  plan-1  C12   0.020
 3EK  plan-1  C13   0.020
 3EK  plan-1  H12   0.020
 3EK  plan-2  C10   0.020
 3EK  plan-2  C13   0.020
 3EK  plan-2  C14   0.020
 3EK  plan-2  C15   0.020
 3EK  plan-2  N16   0.020
 3EK  plan-2  C17   0.020
 3EK  plan-2  C18   0.020
 3EK  plan-2  C19   0.020
 3EK  plan-2  C20   0.020
 3EK  plan-2  H14   0.020
 3EK  plan-2  H18   0.020
 3EK  plan-3  C23   0.020
 3EK  plan-3  C24   0.020
 3EK  plan-3  C25   0.020
 3EK  plan-3  C26   0.020
 3EK  plan-3  C27   0.020
 3EK  plan-3  C28   0.020
 3EK  plan-3  C29   0.020
 3EK  plan-3  F32   0.020
 3EK  plan-3  H25   0.020
 3EK  plan-3  H26   0.020
 3EK  plan-3  H28   0.020
 3EK  plan-3  H29   0.020
 3EK  plan-4  C17   0.020
 3EK  plan-4  C20   0.020
 3EK  plan-4  O21   0.020
 3EK  plan-4  N22   0.020
 3EK  plan-4  C23   0.020
 3EK  plan-4  HN22  0.020
 3EK  plan-5  C4    0.020
 3EK  plan-5  C30   0.020
 3EK  plan-5  O31   0.020
 3EK  plan-5  O33   0.020

