# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 21:59:58 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: ~{N}-[7-methyl-1-[(3~{R})-1-propanoylazepan-3-yl]benzimidazol-2-yl]-3-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCCC[C@H](C1)n2c(NC(=O)c3cccc(c3)C(F)(F)F)nc4cccc(C)c24
#
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
 5X4  5X4  ~{N}-[7-methyl-1-[(3~{R})-1-propanoylazepan-3-yl]benzimidazol-2-yl]-3-(trifluoromethyl)benzamide  ligand  61  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5X4
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
 5X4  C11  C  C     0   0.536  -1.3271  -0.8106  -0.1103
 5X4  C12  C  CR6   0  -0.022  -2.5786  -0.0908   0.2640
 5X4  C13  C  CR16  0  -0.287  -3.1076  -0.1090   1.5504
 5X4  C14  C  CR16  0  -0.224  -4.2849   0.5692   1.8294
 5X4  C15  C  CR16  0  -0.262  -4.9384   1.2702   0.8313
 5X4  C16  C  CR6   0  -0.173  -4.4158   1.2821  -0.4592
 5X4  C17  C  CT    0   1.059  -5.1234   2.0703  -1.5181
 5X4  C21  C  CR16  0  -0.310  -3.2457   0.6001  -0.7449
 5X4  C24  C  CH1   0  -0.112   2.2967   0.1404   0.7595
 5X4  C25  C  CH2   0  -0.438   2.1377   0.6230   2.1987
 5X4  C26  C  CH2   0  -0.440   2.4695   2.0986   2.4172
 5X4  C27  C  CH2   0  -0.480   1.4978   3.0636   1.7355
 5X4  C28  C  CH2   0  -0.294   1.8614   3.4081   0.2927
 5X4  C02  C  CR6   0   0.095   4.1996  -2.4581   0.3142
 5X4  C03  C  CR16  0  -0.338   4.6720  -3.7489   0.1247
 5X4  C04  C  CR16  0  -0.259   3.8399  -4.8759   0.0683
 5X4  C05  C  CR16  0  -0.344   2.4750  -4.7533   0.2047
 5X4  C06  C  CR56  0   0.139   1.9623  -3.4704   0.3959
 5X4  C07  C  CR56  0   0.315   2.8055  -2.3442   0.4445
 5X4  N08  N  NR5   0  -0.561   1.9488  -1.2748   0.6359
 5X4  C09  C  CR5   0   0.635   0.6964  -1.8088   0.7042
 5X4  N10  N  NH1   0  -0.792  -0.4334  -1.0149   0.8979
 5X4  F18  F  F     0  -0.310  -6.4426   1.8423  -1.5069
 5X4  F19  F  F     0  -0.313  -4.9619   3.3891  -1.3355
 5X4  F20  F  F     0  -0.300  -4.6850   1.7893  -2.7473
 5X4  O22  O  O     0  -0.436  -1.0977  -1.1531  -1.2523
 5X4  N23  N  N     0  -0.450   0.6562  -3.0972   0.5666
 5X4  N29  N  NT    0  -0.460   2.2880   2.2501  -0.4791
 5X4  C31  C  CH2   0  -0.596   4.0415   3.5700  -1.5925
 5X4  C32  C  CH3   0  -0.651   5.0919   3.4832  -2.6859
 5X4  O33  O  O     0  -0.500   3.6524   1.2382  -1.9508
 5X4  C34  C  CH2   0  -0.318   1.5706   1.0083  -0.2819
 5X4  H1   H  HCR6  0   0.275  -2.6343  -0.6693   2.3467
 5X4  H2   H  HCR6  0   0.283  -4.6956   0.5460   2.8290
 5X4  H3   H  HCR6  0   0.287  -5.8545   1.7957   1.0671
 5X4  H4   H  HCR6  0   0.281  -2.8332   0.5971  -1.7443
 5X4  H5   H  HCH1  0   0.293   3.3493   0.2013   0.5030
 5X4  H6   H  HCH2  0   0.224   1.1138   0.4538   2.5442
 5X4  H7   H  HCH2  0   0.253   2.7796   0.0097   2.8357
 5X4  H8   H  HCH2  0   0.251   2.4424   2.2760   3.4936
 5X4  H9   H  HCH2  0   0.230   3.4972   2.3095   2.1046
 5X4  H10  H  HCH2  0   0.231   0.4816   2.6627   1.7960
 5X4  H11  H  HCH2  0   0.260   1.4677   4.0081   2.2825
 5X4  H12  H  HCH2  0   0.250   1.0123   3.8981  -0.1938
 5X4  H13  H  HCH2  0   0.260   2.6722   4.1318   0.3174
 5X4  H14  H  HCH3  0   0.256   5.0045  -0.5938  -0.4351
 5X4  H15  H  HCH3  0   0.247   5.1262  -0.7773   1.3148
 5X4  H16  H  HCH3  0   0.268   6.1888  -1.6894   0.2593
 5X4  H17  H  HCR6  0   0.250   5.7409  -3.8889   0.0171
 5X4  H18  H  HCR6  0   0.253   4.2843  -5.8508  -0.0833
 5X4  H19  H  HCR6  0   0.255   1.8159  -5.6108   0.1685
 5X4  H20  H  HNH1  0   0.432  -0.6409  -0.7032   1.8348
 5X4  H21  H  HCH2  0   0.266   3.3124   4.3481  -1.8325
 5X4  H22  H  HCH2  0   0.266   4.5100   3.8863  -0.6551
 5X4  H23  H  HCH3  0   0.228   5.8661   2.7556  -2.4467
 5X4  H24  H  HCH3  0   0.227   4.6552   3.2068  -3.6449
 5X4  H25  H  HCH3  0   0.232   5.5740   4.4527  -2.8083
 5X4  H26  H  HCH2  0   0.279   1.5006   0.4673  -1.2248
 5X4  H27  H  HCH2  0   0.250   0.5557   1.2486   0.0300
 5X4  C30  C  C     0   0.578   3.3195   2.2577  -1.3599
 5X4  C01  C  CH3   0  -0.775   5.1719  -1.3154   0.3659

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
 5X4  F20  C17  single    1.335  0.020  1.335
 5X4  F18  C17  single    1.339  0.020  1.339
 5X4  C17  C16  single    1.498  0.020  1.498
 5X4  C17  F19  single    1.341  0.020  1.341
 5X4  C15  C14  aromatic  1.384  0.020  1.384
 5X4  C15  C16  aromatic  1.392  0.020  1.392
 5X4  C14  C13  aromatic  1.387  0.020  1.387
 5X4  C16  C21  aromatic  1.384  0.020  1.384
 5X4  C13  C12  aromatic  1.391  0.020  1.391
 5X4  C21  C12  aromatic  1.393  0.020  1.393
 5X4  C12  C11  single    1.491  0.020  1.491
 5X4  C27  C28  single    1.527  0.020  1.527
 5X4  C27  C26  single    1.530  0.020  1.530
 5X4  C11  O22  double    1.214  0.020  1.214
 5X4  C11  N10  single    1.363  0.020  1.363
 5X4  C28  N29  single    1.455  0.020  1.455
 5X4  C26  C25  single    1.528  0.020  1.528
 5X4  N10  C09  single    1.394  0.020  1.394
 5X4  C25  C24  single    1.526  0.020  1.526
 5X4  N29  C34  single    1.448  0.020  1.448
 5X4  N29  C30  single    1.356  0.020  1.356
 5X4  C34  C24  single    1.538  0.020  1.538
 5X4  C09  N08  aromatic  1.363  0.020  1.363
 5X4  C09  N23  aromatic  1.296  0.020  1.296
 5X4  C32  C31  single    1.519  0.020  1.519
 5X4  C24  N08  single    1.463  0.020  1.463
 5X4  C31  C30  single    1.516  0.020  1.516
 5X4  C30  O33  double    1.225  0.020  1.225
 5X4  N08  C07  aromatic  1.384  0.020  1.384
 5X4  N23  C06  aromatic  1.369  0.020  1.369
 5X4  C07  C06  aromatic  1.408  0.020  1.408
 5X4  C07  C02  aromatic  1.405  0.020  1.405
 5X4  C06  C05  aromatic  1.395  0.020  1.395
 5X4  C01  C02  single    1.501  0.020  1.501
 5X4  C02  C03  aromatic  1.387  0.020  1.387
 5X4  C05  C04  aromatic  1.377  0.020  1.377
 5X4  C03  C04  aromatic  1.402  0.020  1.402
 5X4  C13  H1   single    0.930  0.020  1.080
 5X4  C14  H2   single    0.930  0.020  1.080
 5X4  C15  H3   single    0.930  0.020  1.080
 5X4  C21  H4   single    0.930  0.020  1.080
 5X4  C24  H5   single    0.970  0.020  1.090
 5X4  C25  H6   single    0.970  0.020  1.090
 5X4  C25  H7   single    0.970  0.020  1.090
 5X4  C26  H8   single    0.970  0.020  1.090
 5X4  C26  H9   single    0.970  0.020  1.090
 5X4  C27  H10  single    0.970  0.020  1.090
 5X4  C27  H11  single    0.970  0.020  1.090
 5X4  C28  H12  single    0.970  0.020  1.090
 5X4  C28  H13  single    0.970  0.020  1.090
 5X4  C01  H14  single    0.970  0.020  1.090
 5X4  C01  H15  single    0.970  0.020  1.090
 5X4  C01  H16  single    0.970  0.020  1.090
 5X4  C03  H17  single    0.930  0.020  1.080
 5X4  C04  H18  single    0.930  0.020  1.080
 5X4  C05  H19  single    0.930  0.020  1.080
 5X4  N10  H20  single    0.860  0.020  1.020
 5X4  C31  H21  single    0.970  0.020  1.090
 5X4  C31  H22  single    0.970  0.020  1.090
 5X4  C32  H23  single    0.970  0.020  1.090
 5X4  C32  H24  single    0.970  0.020  1.090
 5X4  C32  H25  single    0.970  0.020  1.090
 5X4  C34  H26  single    0.970  0.020  1.090
 5X4  C34  H27  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
 5X4  O22  C11  N10  121.99  3.000
 5X4  N10  C11  C12  115.91  3.000
 5X4  O22  C11  C12  122.05  3.000
 5X4  C21  C12  C13  119.61  3.000
 5X4  C21  C12  C11  117.35  3.000
 5X4  C13  C12  C11  123.02  3.000
 5X4  H1   C13  C14  118.44  3.000
 5X4  H1   C13  C12  121.38  3.000
 5X4  C14  C13  C12  120.16  3.000
 5X4  H2   C14  C15  119.90  3.000
 5X4  H2   C14  C13  119.87  3.000
 5X4  C15  C14  C13  120.23  3.000
 5X4  H3   C15  C16  121.03  3.000
 5X4  H3   C15  C14  119.25  3.000
 5X4  C16  C15  C14  119.71  3.000
 5X4  C21  C16  C17  120.85  3.000
 5X4  C21  C16  C15  120.29  3.000
 5X4  C17  C16  C15  118.85  3.000
 5X4  F20  C17  F19  107.03  3.000
 5X4  F19  C17  F18  106.55  3.000
 5X4  F20  C17  F18  107.18  3.000
 5X4  F19  C17  C16  111.37  3.000
 5X4  F18  C17  C16  111.72  3.000
 5X4  F20  C17  C16  112.65  3.000
 5X4  H4   C21  C16  120.98  3.000
 5X4  H4   C21  C12  119.04  3.000
 5X4  C16  C21  C12  119.98  3.000
 5X4  H5   C24  C34  105.44  3.000
 5X4  H5   C24  N08  105.37  3.000
 5X4  C34  C24  N08  112.12  3.000
 5X4  H5   C24  C25  107.84  3.000
 5X4  N08  C24  C25  111.16  3.000
 5X4  C34  C24  C25  114.26  3.000
 5X4  H7   C25  H6   106.19  3.000
 5X4  H7   C25  C26  109.33  3.000
 5X4  H6   C25  C26  107.91  3.000
 5X4  H7   C25  C24  108.12  3.000
 5X4  H6   C25  C24  110.27  3.000
 5X4  C26  C25  C24  114.68  3.000
 5X4  H9   C26  H8   105.88  3.000
 5X4  H9   C26  C27  110.34  3.000
 5X4  H8   C26  C27  108.74  3.000
 5X4  H9   C26  C25  110.43  3.000
 5X4  H8   C26  C25  107.01  3.000
 5X4  C27  C26  C25  114.04  3.000
 5X4  H11  C27  H10  105.28  3.000
 5X4  H11  C27  C28  106.54  3.000
 5X4  H10  C27  C28  110.86  3.000
 5X4  H11  C27  C26  109.87  3.000
 5X4  H10  C27  C26  109.52  3.000
 5X4  C28  C27  C26  114.34  3.000
 5X4  H13  C28  H12  106.90  3.000
 5X4  H13  C28  N29  108.85  3.000
 5X4  H12  C28  N29  110.36  3.000
 5X4  H13  C28  C27  107.83  3.000
 5X4  H12  C28  C27  109.65  3.000
 5X4  N29  C28  C27  113.03  3.000
 5X4  C07  C02  C03  115.21  3.000
 5X4  C03  C02  C01  119.49  3.000
 5X4  C07  C02  C01  125.30  3.000
 5X4  H17  C03  C04  118.53  3.000
 5X4  H17  C03  C02  118.01  3.000
 5X4  C04  C03  C02  123.45  3.000
 5X4  H18  C04  C05  120.07  3.000
 5X4  H18  C04  C03  119.08  3.000
 5X4  C05  C04  C03  120.84  3.000
 5X4  H19  C05  C06  120.63  3.000
 5X4  H19  C05  C04  121.99  3.000
 5X4  C06  C05  C04  117.37  3.000
 5X4  N23  C06  C07  110.43  3.000
 5X4  C07  C06  C05  121.36  3.000
 5X4  N23  C06  C05  128.21  3.000
 5X4  N08  C07  C06  104.61  3.000
 5X4  C06  C07  C02  121.76  3.000
 5X4  N08  C07  C02  133.63  3.000
 5X4  C09  N08  C07  105.85  3.000
 5X4  C07  N08  C24  127.76  3.000
 5X4  C09  N08  C24  126.39  3.000
 5X4  N23  C09  N10  123.75  3.000
 5X4  N23  C09  N08  114.36  3.000
 5X4  N10  C09  N08  121.89  3.000
 5X4  H20  N10  C09  118.13  3.000
 5X4  H20  N10  C11  120.39  3.000
 5X4  C09  N10  C11  120.93  3.000
 5X4  C09  N23  C06  104.75  3.000
 5X4  C34  N29  C30  118.04  3.000
 5X4  C30  N29  C28  124.25  3.000
 5X4  C34  N29  C28  117.71  3.000
 5X4  H22  C31  H21  105.54  3.000
 5X4  H22  C31  C32  109.70  3.000
 5X4  H21  C31  C32  110.12  3.000
 5X4  H22  C31  C30  108.82  3.000
 5X4  H21  C31  C30  109.40  3.000
 5X4  C32  C31  C30  112.98  3.000
 5X4  H25  C32  H24  107.71  3.000
 5X4  H25  C32  H23  107.73  3.000
 5X4  H24  C32  H23  107.98  3.000
 5X4  H25  C32  C31  109.64  3.000
 5X4  H24  C32  C31  111.78  3.000
 5X4  H23  C32  C31  111.83  3.000
 5X4  H27  C34  H26  107.32  3.000
 5X4  H27  C34  N29  108.16  3.000
 5X4  H26  C34  N29  109.87  3.000
 5X4  H27  C34  C24  111.76  3.000
 5X4  H26  C34  C24  109.65  3.000
 5X4  N29  C34  C24  110.02  3.000
 5X4  O33  C30  C31  121.15  3.000
 5X4  O33  C30  N29  121.03  3.000
 5X4  C31  C30  N29  117.82  3.000
 5X4  H16  C01  H15  107.07  3.000
 5X4  H16  C01  H14  107.38  3.000
 5X4  H15  C01  H14  107.80  3.000
 5X4  H16  C01  C02  109.88  3.000
 5X4  H15  C01  C02  112.21  3.000
 5X4  H14  C01  C02  112.26  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
 5X4  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 5X4  CONST_02  C15  C16  C21  C12     0.00   0.0  0
 5X4  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 5X4  CONST_04  C16  C21  C12  C13     0.00   0.0  0
 5X4  CONST_05  C21  C16  C15  C14     0.00   0.0  0
 5X4  CONST_06  C21  C12  C13  C14     0.00   0.0  0
 5X4  CONST_07  C09  N08  C07  C02   180.00   0.0  0
 5X4  CONST_08  N23  C06  C07  C02   180.00   0.0  0
 5X4  CONST_09  C05  C06  C07  C02     0.00   0.0  0
 5X4  CONST_10  C05  C04  C03  C02     0.00   0.0  0
 5X4  CONST_11  N08  C07  C02  C03   180.00   0.0  0
 5X4  CONST_12  C06  C07  C02  C03     0.00   0.0  0
 5X4  CONST_13  C06  C05  C04  C03     0.00   0.0  0
 5X4  CONST_14  N23  C06  C05  C04   180.00   0.0  0
 5X4  CONST_15  C07  C06  C05  C04     0.00   0.0  0
 5X4  CONST_16  C07  C02  C03  C04     0.00   0.0  0
 5X4  CONST_17  C09  N23  C06  C05   180.00   0.0  0
 5X4  CONST_18  N08  C07  C06  C05   180.00   0.0  0
 5X4  CONST_19  N08  C09  N23  C06     0.00   0.0  0
 5X4  CONST_20  C09  N08  C07  C06     0.00   0.0  0
 5X4  CONST_21  N23  C09  N08  C07     0.00   0.0  0
 5X4  CONST_22  C09  N23  C06  C07     0.00   0.0  0
 5X4  CONST_23  N23  C06  C07  N08     0.00   0.0  0
 5X4  CONST_24  N23  C09  N08  C24   180.00   0.0  0
 5X4  CONST_25  C06  C07  N08  C24   180.00   0.0  0
 5X4  CONST_26  C02  C07  N08  C24     0.00   0.0  0
 5X4  CONST_27  C14  C13  C12  C11   180.00   0.0  0
 5X4  CONST_28  C16  C21  C12  C11   180.00   0.0  0
 5X4  CONST_29  C17  C16  C21  C12   180.00   0.0  0
 5X4  CONST_30  C17  C16  C15  C14   180.00   0.0  0
 5X4  CONST_31  N10  C09  N08  C24     0.00   0.0  0
 5X4  CONST_32  N08  C07  C02  C01     0.00   0.0  0
 5X4  CONST_33  C06  C07  C02  C01   180.00   0.0  0
 5X4  CONST_34  C04  C03  C02  C01   180.00   0.0  0
 5X4  CONST_35  N10  C09  N23  C06   180.00   0.0  0
 5X4  CONST_36  N10  C09  N08  C07   180.00   0.0  0
 5X4  CONST_37  H2   C14  C13  C12   180.00   0.0  0
 5X4  CONST_38  H3   C15  C14  C13   180.00   0.0  0
 5X4  CONST_39  H4   C21  C12  C13   180.00   0.0  0
 5X4  CONST_40  H1   C13  C14  C15   180.00   0.0  0
 5X4  CONST_41  H18  C04  C03  C02   180.00   0.0  0
 5X4  CONST_42  H19  C05  C04  C03   180.00   0.0  0
 5X4  CONST_43  H17  C03  C04  C05   180.00   0.0  0
 5X4  CONST_44  C09  N10  C11  C12   180.00   0.0  0
 5X4  CONST_48  O22  C11  N10  C09     0.00   0.0  0
 5X4  Var_01    O22  C11  C12  C13   155.92  30.0  2
 5X4  Var_02    F20  C17  C16  C15  -167.47  30.0  2
 5X4  Var_03    H14  C01  C02  C03   118.21  30.0  2
 5X4  Var_04    C32  C31  C30  N29  -174.87  30.0  1
 5X4  Var_05    H23  C32  C31  C30   -60.67  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
 5X4  chir_01  C24  C25  C34  N08  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
 5X4  plan-1  C11  0.020
 5X4  plan-1  C12  0.020
 5X4  plan-1  C13  0.020
 5X4  plan-1  C14  0.020
 5X4  plan-1  C15  0.020
 5X4  plan-1  C16  0.020
 5X4  plan-1  C17  0.020
 5X4  plan-1  C21  0.020
 5X4  plan-1  H1   0.020
 5X4  plan-1  H2   0.020
 5X4  plan-1  H3   0.020
 5X4  plan-1  H4   0.020
 5X4  plan-2  C24  0.020
 5X4  plan-2  C02  0.020
 5X4  plan-2  C03  0.020
 5X4  plan-2  C04  0.020
 5X4  plan-2  C05  0.020
 5X4  plan-2  C06  0.020
 5X4  plan-2  C07  0.020
 5X4  plan-2  N08  0.020
 5X4  plan-2  C09  0.020
 5X4  plan-2  N10  0.020
 5X4  plan-2  N23  0.020
 5X4  plan-2  H17  0.020
 5X4  plan-2  H18  0.020
 5X4  plan-2  H19  0.020
 5X4  plan-2  C01  0.020
 5X4  plan-3  C28  0.020
 5X4  plan-3  N29  0.020
 5X4  plan-3  C31  0.020
 5X4  plan-3  O33  0.020
 5X4  plan-3  C34  0.020
 5X4  plan-3  C30  0.020
 5X4  plan-4  C11  0.020
 5X4  plan-4  C12  0.020
 5X4  plan-4  C09  0.020
 5X4  plan-4  N10  0.020
 5X4  plan-4  O22  0.020
 5X4  plan-4  H20  0.020

