# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:17:56 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 3-{7-(trifluoromethyl)-5-[2-(trifluoromethyl)phenyl]-1H-benzimidazol-2-yl}-1-oxa-2-azaspiro[4.5]dec-2-ene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc(cc2nc([nH]c12)C3=NOC4(CCCCC4)C3)c5ccccc5C(F)(F)F
#
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
 T14  T14  3-{7-(trifluoromethyl)-5-[2-(trifluoromethyl)phenyl]-1H-benzimidazol-2-yl}-1-oxa-2-azaspiro[4.5]dec-2-ene  ligand  52  33  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T14
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
 T14  C02   C  CT    0   1.062  -4.2115   1.7396  -1.4426
 T14  C03   C  CR6   0  -0.257  -4.7947   1.3744  -0.1099
 T14  C04   C  CR16  0  -0.281  -6.0584   1.8379   0.2378
 T14  C05   C  CR16  0  -0.249  -6.6181   1.4991   1.4605
 T14  C06   C  CR16  0  -0.228  -5.9159   0.6911   2.3395
 T14  C07   C  CR16  0  -0.282  -4.6537   0.2304   1.9938
 T14  C08   C  CR6   0   0.104  -4.0736   0.5646   0.7750
 T14  C09   C  CR6   0  -0.000  -2.7138   0.0397   0.4773
 T14  C10   C  CR16  0  -0.351  -2.5809  -1.2793   0.0137
 T14  C11   C  CR6   0  -0.226  -1.3436  -1.8451  -0.2318
 T14  C12   C  CT    0   1.064  -1.1897  -3.2380  -0.7410
 T14  C16   C  CR56  0   0.363  -0.2216  -1.0499   0.0015
 T14  C18   C  CR5   0   0.473   1.7371  -0.1052   0.2614
 T14  C19   C  CR5   0   0.124   3.1751   0.0444   0.2646
 T14  C22   C  CR5   0   0.201   5.3460   0.8581   0.3189
 T14  C23   C  CH2   0  -0.444   6.3348   1.0021   1.4658
 T14  C24   C  CH2   0  -0.439   7.7476   0.5734   1.0806
 T14  C25   C  CH2   0  -0.435   8.2310   1.3045  -0.1679
 T14  C26   C  CH2   0  -0.437   7.2569   1.1276  -1.3280
 T14  C27   C  CH2   0  -0.431   5.8476   1.5609  -0.9382
 T14  C28   C  CH2   0  -0.561   3.9140   1.2684   0.6808
 T14  C30   C  CR56  0   0.171  -0.3410   0.2692   0.4703
 T14  C31   C  CR16  0  -0.348  -1.5964   0.8209   0.7101
 T14  F01   F  F     0  -0.313  -3.1173   2.5063  -1.3238
 T14  F13   F  F     0  -0.315  -0.4071  -3.9723   0.0655
 T14  F14   F  F     0  -0.295  -2.3511  -3.8792  -0.8576
 T14  F15   F  F     0  -0.314  -0.6019  -3.2544  -1.9478
 T14  F32   F  F     0  -0.311  -3.8503   0.6580  -2.1459
 T14  F33   F  F     0  -0.302  -5.0711   2.4231  -2.2050
 T14  N17   N  NR15  0  -0.718   1.1196  -1.2575  -0.1216
 T14  N20   N  N     0  -0.100   3.9269  -0.9244  -0.0794
 T14  N29   N  N     0  -0.464   0.9004   0.8284   0.6210
 T14  O21   O  O     0  -0.401   5.2230  -0.5693   0.0088
 T14  H041  H  HCR6  0   0.275  -6.6219   2.4652  -0.4380
 T14  H051  H  HCR6  0   0.271  -7.6019   1.8666   1.7183
 T14  H061  H  HCR6  0   0.270  -6.3449   0.4193   3.2948
 T14  H071  H  HCR6  0   0.265  -4.1020  -0.3975   2.6815
 T14  H101  H  HCR6  0   0.273  -3.4807  -1.8568  -0.1490
 T14  H231  H  HCH2  0   0.236   6.3412   2.0555   1.7639
 T14  H232  H  HCH2  0   0.245   5.9766   0.4386   2.3316
 T14  H241  H  HCH2  0   0.235   8.4231   0.7656   1.9170
 T14  H242  H  HCH2  0   0.221   7.7751  -0.5066   0.9079
 T14  H251  H  HCH2  0   0.212   8.3368   2.3716   0.0557
 T14  H252  H  HCH2  0   0.232   9.2237   0.9478  -0.4512
 T14  H261  H  HCH2  0   0.235   7.5877   1.7076  -2.1923
 T14  H262  H  HCH2  0   0.221   7.2495   0.0814  -1.6469
 T14  H272  H  HCH2  0   0.244   5.1440   1.3942  -1.7594
 T14  H271  H  HCH2  0   0.232   5.8364   2.6372  -0.7379
 T14  H281  H  HCH2  0   0.289   3.5822   2.1586   0.1443
 T14  H282  H  HCH2  0   0.290   3.7778   1.4610   1.7487
 T14  H311  H  HCR6  0   0.270  -1.6874   1.8332   1.0817
 T14  H171  H  HNR5  0   0.424   1.5947  -2.0896  -0.4367

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
 T14  C06  C05   aromatic  1.385  0.020  1.385
 T14  C06  C07   aromatic  1.387  0.020  1.387
 T14  C05  C04   aromatic  1.387  0.020  1.387
 T14  C07  C08   aromatic  1.391  0.020  1.391
 T14  C04  C03   aromatic  1.390  0.020  1.390
 T14  C08  C03   aromatic  1.400  0.020  1.400
 T14  C08  C09   single    1.488  0.020  1.488
 T14  C03  C02   single    1.500  0.020  1.500
 T14  F01  C02   single    1.341  0.020  1.341
 T14  C09  C10   aromatic  1.404  0.020  1.404
 T14  C09  C31   aromatic  1.383  0.020  1.383
 T14  C10  C11   aromatic  1.382  0.020  1.382
 T14  C02  F33   single    1.337  0.020  1.337
 T14  C02  F32   single    1.340  0.020  1.340
 T14  F15  C12   single    1.342  0.020  1.342
 T14  F13  C12   single    1.343  0.020  1.343
 T14  C31  C30   aromatic  1.392  0.020  1.392
 T14  C11  C12   single    1.491  0.020  1.491
 T14  C11  C16   aromatic  1.395  0.020  1.395
 T14  C12  F14   single    1.332  0.020  1.332
 T14  C30  C16   aromatic  1.405  0.020  1.405
 T14  C30  N29   aromatic  1.370  0.020  1.370
 T14  C16  N17   aromatic  1.363  0.020  1.363
 T14  N29  C18   aromatic  1.304  0.020  1.304
 T14  N17  C18   aromatic  1.362  0.020  1.362
 T14  C18  C19   single    1.446  0.020  1.446
 T14  C19  C28   single    1.489  0.020  1.489
 T14  C19  N20   double    1.274  0.020  1.274
 T14  C28  C22   single    1.533  0.020  1.533
 T14  N20  O21   single    1.347  0.020  1.347
 T14  C22  O21   single    1.466  0.020  1.466
 T14  C22  C27   single    1.525  0.020  1.525
 T14  C22  C23   single    1.521  0.020  1.521
 T14  C27  C26   single    1.525  0.020  1.525
 T14  C23  C24   single    1.526  0.020  1.526
 T14  C26  C25   single    1.525  0.020  1.525
 T14  C24  C25   single    1.525  0.020  1.525
 T14  C04  H041  single    0.930  0.020  1.080
 T14  C05  H051  single    0.930  0.020  1.080
 T14  C06  H061  single    0.930  0.020  1.080
 T14  C07  H071  single    0.930  0.020  1.080
 T14  C10  H101  single    0.930  0.020  1.080
 T14  C23  H231  single    0.970  0.020  1.090
 T14  C23  H232  single    0.970  0.020  1.090
 T14  C24  H241  single    0.970  0.020  1.090
 T14  C24  H242  single    0.970  0.020  1.090
 T14  C25  H251  single    0.970  0.020  1.090
 T14  C25  H252  single    0.970  0.020  1.090
 T14  C26  H261  single    0.970  0.020  1.090
 T14  C26  H262  single    0.970  0.020  1.090
 T14  C27  H272  single    0.970  0.020  1.090
 T14  C27  H271  single    0.970  0.020  1.090
 T14  C28  H281  single    0.970  0.020  1.090
 T14  C28  H282  single    0.970  0.020  1.090
 T14  C31  H311  single    0.930  0.020  1.080
 T14  N17  H171  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
 T14  F33   C02  F32   106.66  3.000
 T14  F32   C02  F01   106.74  3.000
 T14  F33   C02  F01   106.43  3.000
 T14  F32   C02  C03   112.00  3.000
 T14  F33   C02  C03   112.41  3.000
 T14  F01   C02  C03   112.19  3.000
 T14  C08   C03  C04   120.21  3.000
 T14  C08   C03  C02   120.16  3.000
 T14  C04   C03  C02   119.63  3.000
 T14  H041  C04  C05   118.87  3.000
 T14  H041  C04  C03   120.74  3.000
 T14  C05   C04  C03   120.39  3.000
 T14  H051  C05  C06   120.54  3.000
 T14  H051  C05  C04   119.63  3.000
 T14  C06   C05  C04   119.83  3.000
 T14  H061  C06  C07   119.82  3.000
 T14  H061  C06  C05   120.39  3.000
 T14  C07   C06  C05   119.79  3.000
 T14  H071  C07  C08   118.93  3.000
 T14  H071  C07  C06   119.87  3.000
 T14  C08   C07  C06   121.20  3.000
 T14  C09   C08  C07   118.16  3.000
 T14  C09   C08  C03   123.27  3.000
 T14  C07   C08  C03   118.57  3.000
 T14  C31   C09  C10   120.63  3.000
 T14  C31   C09  C08   120.36  3.000
 T14  C10   C09  C08   118.94  3.000
 T14  H101  C10  C11   119.96  3.000
 T14  H101  C10  C09   118.19  3.000
 T14  C11   C10  C09   121.85  3.000
 T14  C16   C11  C12   120.44  3.000
 T14  C16   C11  C10   117.19  3.000
 T14  C12   C11  C10   122.37  3.000
 T14  F15   C12  F14   107.29  3.000
 T14  F14   C12  F13   107.32  3.000
 T14  F15   C12  F13   106.15  3.000
 T14  F14   C12  C11   112.93  3.000
 T14  F13   C12  C11   111.47  3.000
 T14  F15   C12  C11   111.32  3.000
 T14  N17   C16  C30   104.88  3.000
 T14  N17   C16  C11   133.61  3.000
 T14  C30   C16  C11   121.51  3.000
 T14  N29   C18  N17   113.09  3.000
 T14  N17   C18  C19   122.61  3.000
 T14  N29   C18  C19   124.29  3.000
 T14  N20   C19  C28   114.07  3.000
 T14  N20   C19  C18   120.52  3.000
 T14  C28   C19  C18   125.39  3.000
 T14  O21   C22  C28   103.42  3.000
 T14  O21   C22  C27   107.57  3.000
 T14  C28   C22  C27   112.24  3.000
 T14  C27   C22  C23   111.35  3.000
 T14  O21   C22  C23   107.83  3.000
 T14  C28   C22  C23   113.83  3.000
 T14  H232  C23  H231  106.39  3.000
 T14  H232  C23  C24   111.00  3.000
 T14  H231  C23  C24   109.50  3.000
 T14  H232  C23  C22   109.59  3.000
 T14  H231  C23  C22   107.47  3.000
 T14  C24   C23  C22   112.64  3.000
 T14  H242  C24  H241  106.21  3.000
 T14  H242  C24  C25   109.63  3.000
 T14  H241  C24  C25   110.27  3.000
 T14  H242  C24  C23   109.91  3.000
 T14  H241  C24  C23   109.26  3.000
 T14  C25   C24  C23   111.43  3.000
 T14  H252  C25  H251  106.46  3.000
 T14  H252  C25  C26   110.20  3.000
 T14  H251  C25  C26   109.27  3.000
 T14  H252  C25  C24   110.10  3.000
 T14  H251  C25  C24   109.30  3.000
 T14  C26   C25  C24   111.38  3.000
 T14  H262  C26  H261  106.22  3.000
 T14  H262  C26  C27   109.88  3.000
 T14  H261  C26  C27   109.35  3.000
 T14  H262  C26  C25   109.70  3.000
 T14  H261  C26  C25   110.29  3.000
 T14  C27   C26  C25   111.27  3.000
 T14  H271  C27  H272  106.29  3.000
 T14  H271  C27  C26   109.61  3.000
 T14  H272  C27  C26   111.04  3.000
 T14  H271  C27  C22   107.39  3.000
 T14  H272  C27  C22   109.69  3.000
 T14  C26   C27  C22   112.56  3.000
 T14  H282  C28  H281  107.37  3.000
 T14  H282  C28  C22   113.20  3.000
 T14  H281  C28  C22   112.73  3.000
 T14  H282  C28  C19   110.85  3.000
 T14  H281  C28  C19   112.48  3.000
 T14  C22   C28  C19   100.23  3.000
 T14  N29   C30  C31   129.53  3.000
 T14  N29   C30  C16   110.06  3.000
 T14  C31   C30  C16   120.41  3.000
 T14  H311  C31  C30   120.38  3.000
 T14  H311  C31  C09   121.21  3.000
 T14  C30   C31  C09   118.41  3.000
 T14  H171  N17  C18   124.90  3.000
 T14  H171  N17  C16   128.13  3.000
 T14  C18   N17  C16   106.97  3.000
 T14  O21   N20  C19   110.48  3.000
 T14  C30   N29  C18   105.00  3.000
 T14  N20   O21  C22   110.57  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
 T14  CONST_01  C06   C05  C04  C03     0.00   0.0  0
 T14  CONST_02  C06   C07  C08  C03     0.00   0.0  0
 T14  CONST_05  C07   C06  C05  C04     0.00   0.0  0
 T14  CONST_06  C07   C08  C03  C04     0.00   0.0  0
 T14  CONST_07  C09   C08  C03  C04   180.00   0.0  0
 T14  CONST_08  C08   C07  C06  C05     0.00   0.0  0
 T14  CONST_09  C08   C03  C04  C05     0.00   0.0  0
 T14  CONST_10  C09   C08  C07  C06   180.00   0.0  0
 T14  CONST_13  C11   C10  C09  C08   180.00   0.0  0
 T14  CONST_14  C30   C31  C09  C08   180.00   0.0  0
 T14  CONST_15  C16   C11  C10  C09     0.00   0.0  0
 T14  CONST_16  C16   C30  C31  C09     0.00   0.0  0
 T14  CONST_17  N29   C30  C31  C09   180.00   0.0  0
 T14  CONST_18  C30   C31  C09  C10     0.00   0.0  0
 T14  CONST_19  C30   C16  C11  C10     0.00   0.0  0
 T14  CONST_20  N17   C16  C11  C10   180.00   0.0  0
 T14  CONST_21  C31   C09  C10  C11     0.00   0.0  0
 T14  CONST_22  C31   C30  C16  C11     0.00   0.0  0
 T14  CONST_23  N29   C30  C16  C11   180.00   0.0  0
 T14  CONST_24  C18   N17  C16  C11   180.00   0.0  0
 T14  CONST_25  C18   N29  C30  C16     0.00   0.0  0
 T14  CONST_26  N29   C18  N17  C16     0.00   0.0  0
 T14  CONST_27  C31   C30  N29  C18   180.00   0.0  0
 T14  CONST_28  C30   C16  N17  C18     0.00   0.0  0
 T14  CONST_29  N17   C18  N29  C30     0.00   0.0  0
 T14  CONST_30  N17   C16  C30  C31   180.00   0.0  0
 T14  CONST_31  N29   C30  C16  N17     0.00   0.0  0
 T14  CONST_32  C19   C18  N17  C16   180.00   0.0  0
 T14  CONST_33  C30   N29  C18  C19   180.00   0.0  0
 T14  CONST_34  C05   C04  C03  C02   180.00   0.0  0
 T14  CONST_35  C07   C08  C03  C02   180.00   0.0  0
 T14  CONST_36  C09   C08  C03  C02     0.00   0.0  0
 T14  CONST_37  C12   C11  C10  C09   180.00   0.0  0
 T14  CONST_38  C30   C16  C11  C12   180.00   0.0  0
 T14  CONST_39  N17   C16  C11  C12     0.00   0.0  0
 T14  CONST_40  H051  C05  C04  C03   180.00   0.0  0
 T14  CONST_41  H071  C07  C08  C03   180.00   0.0  0
 T14  CONST_42  H061  C06  C05  C04   180.00   0.0  0
 T14  CONST_43  H041  C04  C05  C06   180.00   0.0  0
 T14  CONST_44  H101  C10  C09  C08     0.00   0.0  0
 T14  CONST_45  H311  C31  C09  C08     0.00   0.0  0
 T14  CONST_46  H171  N17  C16  C11     0.00   0.0  0
 T14  Var_01    C22   C28  C19  C18  -174.17  30.0  1
 T14  Var_02    O21   C22  C28  C19   -10.09  30.0  3
 T14  Var_03    C25   C26  C27  C22   -54.26  30.0  1
 T14  Var_04    C25   C24  C23  C22    53.89  30.0  1
 T14  Var_05    C26   C27  C22  C23    52.73  30.0  1
 T14  Var_06    C26   C25  C24  C23   -54.78  30.0  1
 T14  Var_07    C28   C22  C23  C24   179.41  30.0  1
 T14  Var_08    C27   C26  C25  C24    54.97  30.0  1
 T14  Var_09    N29   C18  C19  C28     0.37  30.0  2
 T14  Var_10    F01   C02  C03  C04   115.15  30.0  2
 T14  Var_11    F15   C12  C11  C10   117.38  30.0  2

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
 T14  plan-1  C02   0.020
 T14  plan-1  C03   0.020
 T14  plan-1  C04   0.020
 T14  plan-1  C05   0.020
 T14  plan-1  C06   0.020
 T14  plan-1  C07   0.020
 T14  plan-1  C08   0.020
 T14  plan-1  C09   0.020
 T14  plan-1  H041  0.020
 T14  plan-1  H051  0.020
 T14  plan-1  H061  0.020
 T14  plan-1  H071  0.020
 T14  plan-2  C08   0.020
 T14  plan-2  C09   0.020
 T14  plan-2  C10   0.020
 T14  plan-2  C11   0.020
 T14  plan-2  C12   0.020
 T14  plan-2  C16   0.020
 T14  plan-2  C18   0.020
 T14  plan-2  C19   0.020
 T14  plan-2  C30   0.020
 T14  plan-2  C31   0.020
 T14  plan-2  N17   0.020
 T14  plan-2  N29   0.020
 T14  plan-2  H101  0.020
 T14  plan-2  H311  0.020
 T14  plan-2  H171  0.020

