# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:46:57 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-[(3R)-pyrrolidin-3-yl]-2-({[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1nn(CC(=O)Nc2sc3CCCCc3c2C(=O)N[C@@H]4CCNC4)c5CCCCc15
#
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
 O27  O27  N-[(3R)-pyrrolidin-3-yl]-2-({[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide  peptide  62  34  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_O27
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
 O27  F1    F  F     0  -0.306   5.3241   0.0153   2.8598
 O27  C2    C  CT    0   1.065   5.4559  -0.1684   1.5461
 O27  F3    F  F     0  -0.316   6.0042   0.9429   1.0329
 O27  F4    F  F     0  -0.318   6.3601  -1.1464   1.3707
 O27  C5    C  CR5   0  -0.065   4.1659  -0.4865   0.8885
 O27  N6    N  N     0  -0.281   3.0989  -0.7758   1.6073
 O27  N7    N  NR5   0  -0.343   2.1554  -1.0449   0.7181
 O27  C8    C  CR5   0   0.461   2.5885  -0.9196  -0.5570
 O27  C9    C  CR5   0  -0.160   3.9134  -0.5624  -0.4920
 O27  C10   C  CH2   0  -0.508   4.7573  -0.3443  -1.7047
 O27  C11   C  CH2   0  -0.453   4.0664  -0.9645  -2.9216
 O27  C12   C  CH2   0  -0.446   2.5853  -0.5937  -2.9877
 O27  C13   C  CH2   0  -0.526   1.8005  -1.1521  -1.7968
 O27  C14   C  CH2   0  -0.473   0.8070  -1.3130   1.1363
 O27  C15   C  C     0   0.544   0.0023  -0.0246   1.1951
 O27  O16   O  O     0  -0.443   0.4248   0.9590   1.7719
 O27  C22   C  CR5   0  -0.070  -3.3364   1.0268  -0.0148
 O27  O28   O  O     0  -0.472  -4.3436   0.0778  -1.9366
 O27  S19   S  S2    0   0.236  -1.7025   2.5123   1.2994
 O27  C27   C  C     0   0.485  -3.8957  -0.0900  -0.8115
 O27  N17   N  NH1   0  -0.744  -1.1990  -0.0705   0.5776
 O27  C21   C  CR5   0   0.210  -3.9701   2.3043   0.1103
 O27  C20   C  CR5   0  -0.277  -3.2117   3.1908   0.8049
 O27  C18   C  CR5   0   0.054  -2.0964   0.9895   0.5764
 O27  C23   C  CH2   0  -0.493  -5.3274   2.6644  -0.4191
 O27  C24   C  CH2   0  -0.448  -5.8530   3.9381   0.2394
 O27  C25   C  CH2   0  -0.447  -4.7849   5.0250   0.2840
 O27  C26   C  CH2   0  -0.477  -3.5985   4.5942   1.1454
 O27  N29   N  NH1   0  -0.644  -3.8276  -1.2966  -0.2172
 O27  C30   C  CH1   0  -0.098  -3.8426  -2.5514  -0.9487
 O27  C31   C  CH2   0  -0.295  -2.6280  -2.6254  -1.8691
 O27  N32   N  NH1   0  -0.643  -1.5439  -2.7433  -0.8983
 O27  C33   C  CH2   0  -0.289  -1.9971  -3.7208   0.1071
 O27  C34   C  CH2   0  -0.518  -3.5377  -3.6922   0.0221
 O27  H10   H  HCH2  0   0.245   4.9053   0.7271  -1.8711
 O27  H10A  H  HCH2  0   0.248   5.7527  -0.7745  -1.5751
 O27  H11   H  HCH2  0   0.244   4.5697  -0.6372  -3.8328
 O27  H11A  H  HCH2  0   0.230   4.1657  -2.0534  -2.8811
 O27  H12   H  HCH2  0   0.235   2.4833   0.4949  -3.0093
 O27  H12A  H  HCH2  0   0.248   2.1449  -0.9687  -3.9124
 O27  H13   H  HCH2  0   0.263   1.6317  -2.2261  -1.9314
 O27  H13A  H  HCH2  0   0.255   0.8138  -0.6843  -1.7407
 O27  H14   H  HCH2  0   0.294   0.3607  -2.0473   0.4686
 O27  H14A  H  HCH2  0   0.330   0.8353  -1.7509   2.1346
 O27  HN17  H  HNH1  0   0.444  -1.4210  -0.9190   0.0321
 O27  H23   H  HCH2  0   0.241  -5.2703   2.8025  -1.5027
 O27  H23A  H  HCH2  0   0.243  -6.0299   1.8432  -0.2587
 O27  H24   H  HCH2  0   0.238  -6.7318   4.2907  -0.3036
 O27  H24A  H  HCH2  0   0.223  -6.1844   3.7145   1.2583
 O27  H25   H  HCH2  0   0.226  -4.4395   5.2392  -0.7317
 O27  H25A  H  HCH2  0   0.240  -5.1997   5.9546   0.6776
 O27  H26   H  HCH2  0   0.247  -3.8645   4.6623   2.2053
 O27  H26A  H  HCH2  0   0.253  -2.7576   5.2765   0.9987
 O27  HN29  H  HNH1  0   0.404  -3.5991  -1.3272   0.7643
 O27  H30   H  HCH1  0   0.270  -4.7865  -2.6846  -1.4775
 O27  H31   H  HCH2  0   0.236  -2.7221  -3.5055  -2.5175
 O27  H31A  H  HCH2  0   0.256  -2.4988  -1.7520  -2.5074
 O27  HN32  H  HNH1  0   0.374  -0.6872  -3.0458  -1.3434
 O27  H33   H  HCH2  0   0.243  -1.6208  -4.7249  -0.1019
 O27  H33A  H  HCH2  0   0.233  -1.6349  -3.4393   1.0981
 O27  H34   H  HCH2  0   0.265  -4.0159  -3.5584   0.9932
 O27  H34A  H  HCH2  0   0.269  -3.9155  -4.6242  -0.3957

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
 O27  C2   F1    single    1.333  0.020  1.333
 O27  C5   C2    single    1.482  0.020  1.482
 O27  F3   C2    single    1.341  0.020  1.341
 O27  C2   F4    single    1.343  0.020  1.343
 O27  C9   C5    aromatic  1.405  0.020  1.405
 O27  N6   C5    aromatic  1.319  0.020  1.319
 O27  N7   N6    aromatic  1.324  0.020  1.324
 O27  C14  N7    single    1.437  0.020  1.437
 O27  C8   N7    aromatic  1.352  0.020  1.352
 O27  C13  C8    single    1.487  0.020  1.487
 O27  C8   C9    aromatic  1.374  0.020  1.374
 O27  C9   C10   single    1.493  0.020  1.493
 O27  C11  C10   single    1.531  0.020  1.531
 O27  C10  H10   single    0.970  0.020  1.090
 O27  C10  H10A  single    0.970  0.020  1.090
 O27  C12  C11   single    1.528  0.020  1.528
 O27  C11  H11   single    0.970  0.020  1.090
 O27  C11  H11A  single    0.970  0.020  1.090
 O27  C12  C13   single    1.532  0.020  1.532
 O27  C12  H12   single    0.970  0.020  1.090
 O27  C12  H12A  single    0.970  0.020  1.090
 O27  C13  H13   single    0.970  0.020  1.090
 O27  C13  H13A  single    0.970  0.020  1.090
 O27  C14  C15   single    1.520  0.020  1.520
 O27  C14  H14   single    0.970  0.020  1.090
 O27  C14  H14A  single    0.970  0.020  1.090
 O27  N17  C15   single    1.351  0.020  1.351
 O27  C15  O16   double    1.216  0.020  1.216
 O27  N17  C18   single    1.389  0.020  1.389
 O27  N17  HN17  single    0.860  0.020  1.020
 O27  C18  C22   aromatic  1.374  0.020  1.374
 O27  C18  S19   aromatic  1.731  0.020  1.731
 O27  S19  C20   aromatic  1.727  0.020  1.727
 O27  C21  C20   aromatic  1.358  0.020  1.358
 O27  C20  C26   single    1.495  0.020  1.495
 O27  C22  C21   aromatic  1.431  0.020  1.431
 O27  C21  C23   single    1.501  0.020  1.501
 O27  C27  C22   single    1.482  0.020  1.482
 O27  C23  C24   single    1.527  0.020  1.527
 O27  C23  H23   single    0.970  0.020  1.090
 O27  C23  H23A  single    0.970  0.020  1.090
 O27  C24  C25   single    1.525  0.020  1.525
 O27  C24  H24   single    0.970  0.020  1.090
 O27  C24  H24A  single    0.970  0.020  1.090
 O27  C25  C26   single    1.528  0.020  1.528
 O27  C25  H25   single    0.970  0.020  1.090
 O27  C25  H25A  single    0.970  0.020  1.090
 O27  C26  H26   single    0.970  0.020  1.090
 O27  C26  H26A  single    0.970  0.020  1.090
 O27  O28  C27   double    1.223  0.020  1.223
 O27  C27  N29   single    1.347  0.020  1.347
 O27  C30  N29   single    1.453  0.020  1.453
 O27  N29  HN29  single    0.860  0.020  1.020
 O27  C34  C30   single    1.529  0.020  1.529
 O27  C30  C31   single    1.526  0.020  1.526
 O27  C30  H30   single    0.970  0.020  1.090
 O27  N32  C31   single    1.460  0.020  1.460
 O27  C31  H31   single    0.970  0.020  1.090
 O27  C31  H31A  single    0.970  0.020  1.090
 O27  C33  N32   single    1.474  0.020  1.474
 O27  N32  HN32  single    0.890  0.020  1.040
 O27  C33  C34   single    1.543  0.020  1.543
 O27  C33  H33   single    0.970  0.020  1.090
 O27  C33  H33A  single    0.970  0.020  1.090
 O27  C34  H34   single    0.970  0.020  1.090
 O27  C34  H34A  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
 O27  C5    C2   F4   111.81  3.000
 O27  F4    C2   F3   106.15  3.000
 O27  C5    C2   F3   111.33  3.000
 O27  F4    C2   F1   107.19  3.000
 O27  F3    C2   F1   107.66  3.000
 O27  C5    C2   F1   112.38  3.000
 O27  C9    C5   N6   112.22  3.000
 O27  N6    C5   C2   120.62  3.000
 O27  C9    C5   C2   127.13  3.000
 O27  N7    N6   C5   104.78  3.000
 O27  C14   N7   C8   126.31  3.000
 O27  C8    N7   N6   112.71  3.000
 O27  C14   N7   N6   120.74  3.000
 O27  C13   C8   C9   126.23  3.000
 O27  C9    C8   N7   106.76  3.000
 O27  C13   C8   N7   126.99  3.000
 O27  C10   C9   C8   123.00  3.000
 O27  C10   C9   C5   133.48  3.000
 O27  C8    C9   C5   103.52  3.000
 O27  H10A  C10  H10  106.29  3.000
 O27  H10A  C10  C11  110.25  3.000
 O27  H10   C10  C11  109.68  3.000
 O27  H10A  C10  C9   111.17  3.000
 O27  H10   C10  C9   110.06  3.000
 O27  C11   C10  C9   109.34  3.000
 O27  H11A  C11  H11  106.72  3.000
 O27  H11A  C11  C12  109.33  3.000
 O27  H11   C11  C12  109.76  3.000
 O27  H11A  C11  C10  109.44  3.000
 O27  H11   C11  C10  109.52  3.000
 O27  C12   C11  C10  111.94  3.000
 O27  H12A  C12  H12  106.73  3.000
 O27  H12A  C12  C13  109.09  3.000
 O27  H12   C12  C13  109.30  3.000
 O27  H12A  C12  C11  110.16  3.000
 O27  H12   C12  C11  109.44  3.000
 O27  C13   C12  C11  111.99  3.000
 O27  H13A  C13  H13  106.66  3.000
 O27  H13A  C13  C12  110.26  3.000
 O27  H13   C13  C12  109.93  3.000
 O27  H13A  C13  C8   111.62  3.000
 O27  H13   C13  C8   109.71  3.000
 O27  C12   C13  C8   108.64  3.000
 O27  H14A  C14  H14  107.54  3.000
 O27  H14A  C14  C15  108.59  3.000
 O27  H14   C14  C15  112.24  3.000
 O27  H14A  C14  N7   108.48  3.000
 O27  H14   C14  N7   109.40  3.000
 O27  C15   C14  N7   110.48  3.000
 O27  N17   C15  O16  123.57  3.000
 O27  O16   C15  C14  121.33  3.000
 O27  N17   C15  C14  115.09  3.000
 O27  C18   C22  C21  112.72  3.000
 O27  C21   C22  C27  123.54  3.000
 O27  C18   C22  C27  123.47  3.000
 O27  C18   S19  C20   91.56  3.000
 O27  N29   C27  O28  123.20  3.000
 O27  N29   C27  C22  114.77  3.000
 O27  O28   C27  C22  121.99  3.000
 O27  HN17  N17  C18  119.18  3.000
 O27  HN17  N17  C15  117.40  3.000
 O27  C18   N17  C15  123.29  3.000
 O27  C23   C21  C20  121.94  3.000
 O27  C23   C21  C22  125.71  3.000
 O27  C20   C21  C22  112.34  3.000
 O27  C26   C20  C21  125.79  3.000
 O27  C26   C20  S19  121.98  3.000
 O27  C21   C20  S19  112.22  3.000
 O27  N17   C18  S19  121.60  3.000
 O27  S19   C18  C22  111.16  3.000
 O27  N17   C18  C22  127.17  3.000
 O27  H23A  C23  H23  105.89  3.000
 O27  H23A  C23  C24  110.01  3.000
 O27  H23   C23  C24  109.86  3.000
 O27  H23A  C23  C21  110.45  3.000
 O27  H23   C23  C21  109.43  3.000
 O27  C24   C23  C21  111.06  3.000
 O27  H24A  C24  H24  106.58  3.000
 O27  H24A  C24  C25  109.30  3.000
 O27  H24   C24  C25  110.38  3.000
 O27  H24A  C24  C23  109.58  3.000
 O27  H24   C24  C23  109.39  3.000
 O27  C25   C24  C23  111.48  3.000
 O27  H25A  C25  H25  106.75  3.000
 O27  H25A  C25  C26  109.39  3.000
 O27  H25   C25  C26  109.48  3.000
 O27  H25A  C25  C24  110.58  3.000
 O27  H25   C25  C24  109.48  3.000
 O27  C26   C25  C24  111.07  3.000
 O27  H26A  C26  H26  106.15  3.000
 O27  H26A  C26  C25  110.23  3.000
 O27  H26   C26  C25  109.85  3.000
 O27  H26A  C26  C20  110.88  3.000
 O27  H26   C26  C20  109.98  3.000
 O27  C25   C26  C20  109.70  3.000
 O27  HN29  N29  C30  117.80  3.000
 O27  HN29  N29  C27  117.92  3.000
 O27  C30   N29  C27  123.45  3.000
 O27  H30   C30  C34  112.93  3.000
 O27  H30   C30  C31  113.00  3.000
 O27  C34   C30  C31  100.84  3.000
 O27  H30   C30  N29  111.03  3.000
 O27  C31   C30  N29  109.72  3.000
 O27  C34   C30  N29  108.83  3.000
 O27  H31A  C31  H31  107.88  3.000
 O27  H31A  C31  N32  111.48  3.000
 O27  H31   C31  N32  113.07  3.000
 O27  H31A  C31  C30  114.14  3.000
 O27  H31   C31  C30  109.10  3.000
 O27  N32   C31  C30  101.18  3.000
 O27  HN32  N32  C33  111.23  3.000
 O27  HN32  N32  C31  111.12  3.000
 O27  C33   N32  C31  106.19  3.000
 O27  H33A  C33  H33  107.23  3.000
 O27  H33A  C33  C34  112.10  3.000
 O27  H33   C33  C34  110.51  3.000
 O27  H33A  C33  N32  110.25  3.000
 O27  H33   C33  N32  111.92  3.000
 O27  C34   C33  N32  104.90  3.000
 O27  H34A  C34  H34  107.12  3.000
 O27  H34A  C34  C33  110.58  3.000
 O27  H34   C34  C33  113.01  3.000
 O27  H34A  C34  C30  109.02  3.000
 O27  H34   C34  C30  112.74  3.000
 O27  C33   C34  C30  104.36  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
 O27  CONST_01  N7    C8   C9   C5     0.00   0.0  0
 O27  CONST_02  C8    N7   N6   C5     0.00   0.0  0
 O27  CONST_03  C8    C9   C5   N6     0.00   0.0  0
 O27  CONST_04  C9    C8   N7   N6     0.00   0.0  0
 O27  CONST_05  C9    C5   N6   N7     0.00   0.0  0
 O27  CONST_06  C20   S19  C18  C22    0.00   0.0  0
 O27  CONST_07  S19   C20  C21  C22    0.00   0.0  0
 O27  CONST_08  C21   C22  C18  S19    0.00   0.0  0
 O27  CONST_09  C18   S19  C20  C21    0.00   0.0  0
 O27  CONST_10  C18   C22  C21  C20    0.00   0.0  0
 O27  CONST_11  C8    C9   C5   C2   180.00   0.0  0
 O27  CONST_12  C10   C9   C5   C2     0.00   0.0  0
 O27  CONST_13  N7    N6   C5   C2   180.00   0.0  0
 O27  CONST_14  C14   N7   N6   C5   180.00   0.0  0
 O27  CONST_15  C14   N7   C8   C9   180.00   0.0  0
 O27  CONST_16  C14   N7   C8   C13    0.00   0.0  0
 O27  CONST_17  C27   C22  C18  S19  180.00   0.0  0
 O27  CONST_18  C20   C21  C22  C27  180.00   0.0  0
 O27  CONST_19  C23   C21  C22  C27    0.00   0.0  0
 O27  CONST_20  C21   C22  C18  N17  180.00   0.0  0
 O27  CONST_21  C20   S19  C18  N17  180.00   0.0  0
 O27  CONST_24  C22   C18  N17  C15  180.00   0.0  0
 O27  CONST_25  S19   C18  N17  C15    0.00   0.0  0
 O27  CONST_26  HN17  N17  C18  C22    0.00   0.0  0
 O27  CONST_27  C18   N17  C15  C14  180.00   0.0  0
 O27  CONST_28  C18   N17  C15  O16    0.00   0.0  0
 O27  CONST_30  HN29  N29  C27  C22    0.00   0.0  0
 O27  Var_01    C11   C10  C9   C5   163.36  30.0  1
 O27  Var_02    C12   C13  C8   N7   167.40  30.0  1
 O27  Var_03    C11   C12  C13  C8    44.06  30.0  1
 O27  Var_04    C12   C11  C10  C9    46.65  30.0  1
 O27  Var_05    C13   C12  C11  C10  -63.85  30.0  1
 O27  Var_06    C24   C23  C21  C22  163.00  30.0  1
 O27  Var_07    C25   C26  C20  S19  165.20  30.0  1
 O27  Var_08    C25   C24  C23  C21   45.89  30.0  1
 O27  Var_09    C24   C25  C26  C20   45.49  30.0  1
 O27  Var_10    C26   C25  C24  C23  -63.24  30.0  1
 O27  Var_11    N32   C33  C34  C30   -6.22  30.0  1
 O27  Var_12    C33   N32  C31  C30   43.95  30.0  1
 O27  Var_13    C34   C33  N32  C31  -23.50  30.0  1
 O27  Var_14    C9    C5   C2   F1   170.87  30.0  2
 O27  Var_15    C15   C14  N7   N6    90.01  30.0  1
 O27  Var_16    N17   C15  C14  N7   131.22  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
 O27  chir_01  C30  N29  C34  C31  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
 O27  plan-1  C2    0.020
 O27  plan-1  C5    0.020
 O27  plan-1  N6    0.020
 O27  plan-1  N7    0.020
 O27  plan-1  C8    0.020
 O27  plan-1  C9    0.020
 O27  plan-1  C10   0.020
 O27  plan-1  C13   0.020
 O27  plan-1  C14   0.020
 O27  plan-2  C14   0.020
 O27  plan-2  C15   0.020
 O27  plan-2  O16   0.020
 O27  plan-2  N17   0.020
 O27  plan-2  C18   0.020
 O27  plan-2  HN17  0.020
 O27  plan-3  C22   0.020
 O27  plan-3  O28   0.020
 O27  plan-3  S19   0.020
 O27  plan-3  C27   0.020
 O27  plan-3  N17   0.020
 O27  plan-3  C21   0.020
 O27  plan-3  C20   0.020
 O27  plan-3  C18   0.020
 O27  plan-3  C23   0.020
 O27  plan-3  C26   0.020
 O27  plan-3  N29   0.020
 O27  plan-3  C30   0.020
 O27  plan-3  HN29  0.020

