# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:06:35 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (3R,4R)-N-(4-chlorophenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-(2,2,2-trifluoroethyl)pyrrolidine-3,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(ccc1NC(=O)[C@H]2CN(C[C@@H]2C(=O)Nc3ccc(Cl)cc3)CC(F)(F)F)N4C=CC=CC4=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
 IVK  IVK  (3R,4R)-N-(4-chlorophenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-(2,2,2-trifluoroethyl)pyrrolidine-3,4-dicarboxamide  ligand  58  37  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IVK
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
 IVK  C1    C   CH1   0  -0.425    1.7691  -0.7703  -0.6801
 IVK  C2    C   CH1   0  -0.431    0.5243  -1.1526   0.1305
 IVK  C3    C   CH2   0  -0.260    0.5282  -2.6885   0.1334
 IVK  N4    N   NT    0  -0.432    1.9413  -3.0038   0.0574
 IVK  C5    C   CH2   0  -0.277    2.4662  -2.1170  -0.9652
 IVK  C6    C   C     0   0.570    2.7043   0.1402   0.0956
 IVK  C7    C   C     0   0.569   -0.7737  -0.6276  -0.4453
 IVK  N8    N   NH1   0  -0.739   -1.7861  -0.6173   0.4638
 IVK  O9    O   O     0  -0.446   -0.9107  -0.2977  -1.6062
 IVK  O10   O   O     0  -0.451    2.7892   0.1243   1.3089
 IVK  N11   N   NH1   0  -0.746    3.4651   0.9301  -0.7056
 IVK  C12   C   CR6   0   0.385    4.4749   1.8295  -0.3560
 IVK  C14   C   CR6   0  -0.058    6.5052   3.6672   0.1479
 IVK  C15   C   CR16  0  -0.200    6.0287   2.8644   1.1693
 IVK  C16   C   CR16  0  -0.200    5.9789   3.5620  -1.1300
 IVK  C17   C   CR16  0  -0.316    5.0174   1.9466   0.9243
 IVK  CL1   CL  CL    0  -0.134    7.7683   4.8111   0.4674
 IVK  C19   C   CR6   0   0.220   -3.1091  -0.2372   0.2371
 IVK  C20   C   CR16  0  -0.299   -3.7788  -0.4175  -0.9719
 IVK  C21   C   CR6   0   0.285   -5.7816   0.5236  -0.0389
 IVK  C22   C   CR16  0  -0.417   -5.1449   0.7055   1.1780
 IVK  C23   C   CR16  0  -0.260   -5.1035  -0.0346  -1.1086
 IVK  C24   C   CR6   0   0.491   -3.8264   0.3259   1.2899
 IVK  N25   N   NR6   0  -0.612   -7.1523   0.8955  -0.1743
 IVK  C26   C   CR16  0   0.050   -8.1104   0.0376   0.2750
 IVK  C27   C   CR16  0  -0.118   -9.7882   1.5704  -0.4120
 IVK  C28   C   CR16  0  -0.453   -8.8384   2.4309  -0.8608
 IVK  C29   C   CR16  0  -0.398   -9.4275   0.3341   0.1762
 IVK  C30   C   CR6   0   0.552   -7.4349   2.1321  -0.7596
 IVK  O31   O   O     0  -0.502   -6.5225   2.8592  -1.1338
 IVK  F32   F   F     0  -0.306   -3.1991   0.4986   2.4626
 IVK  C33   C   CH2   0  -0.477    2.2025  -4.4070  -0.1331
 IVK  C34   C   CT    0   0.994    3.5434  -4.8156   0.4297
 IVK  F35   F   F     0  -0.307    3.6557  -4.5300   1.7317
 IVK  F36   F   F     0  -0.313    3.7302  -6.1380   0.2971
 IVK  F30   F   F     0  -0.311    4.5766  -4.2186  -0.1848
 IVK  C35   C   CR16  0  -0.351    4.9706   2.6480  -1.3740
 IVK  H1    H   HCH1  0   0.301    1.4919  -0.2978  -1.6238
 IVK  H2    H   HCH1  0   0.303    0.6361  -0.8079   1.1612
 IVK  H51C  H   HCH2  0   0.232    2.1946  -2.4559  -1.9765
 IVK  H52C  H   HCH2  0   0.260    3.5528  -2.0442  -0.9286
 IVK  H31C  H   HCH2  0   0.265    0.0787  -3.1045   1.0360
 IVK  H32C  H   HCH2  0   0.224   -0.0307  -3.0792  -0.7327
 IVK  H331  H   HCH2  0   0.291    1.4476  -4.9874   0.4021
 IVK  H332  H   HCH2  0   0.256    2.1541  -4.7206  -1.1866
 IVK  H11   H   HNH1  0   0.420    3.2544   0.8938  -1.6916
 IVK  H8    H   HNH1  0   0.420   -1.5316  -0.8058   1.4214
 IVK  H17   H   HCR6  0   0.289    4.6672   1.3322   1.7367
 IVK  H35   H   HCR6  0   0.282    4.5623   2.5736  -2.3747
 IVK  H15   H   HCR6  0   0.281    6.4404   2.9437   2.1663
 IVK  H16   H   HCR6  0   0.283    6.3439   4.1869  -1.9335
 IVK  H20   H   HCR6  0   0.290   -3.2753  -0.8704  -1.8107
 IVK  H23   H   HCR6  0   0.277   -5.6094  -0.1883  -2.0522
 IVK  H22   H   HCR6  0   0.297   -5.6591   1.1437   2.0235
 IVK  H26   H   HCR6  0   0.314   -7.7494  -0.8850   0.7064
 IVK  H29   H   HCR6  0   0.280  -10.1684  -0.3630   0.5364
 IVK  H27   H   HCR6  0   0.282  -10.8345   1.8321  -0.5046
 IVK  H28   H   HCR6  0   0.276   -9.1079   3.3774  -1.3089

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
 IVK  C1   C2    single    1.534  0.020  1.534
 IVK  C1   C5    single    1.543  0.020  1.543
 IVK  C1   C6    single    1.518  0.020  1.518
 IVK  C2   C3    single    1.536  0.020  1.536
 IVK  C2   C7    single    1.514  0.020  1.514
 IVK  C3   N4    single    1.450  0.020  1.450
 IVK  N4   C5    single    1.452  0.020  1.452
 IVK  N4   C33   single    1.440  0.020  1.440
 IVK  C6   O10   double    1.216  0.020  1.216
 IVK  C6   N11   single    1.358  0.020  1.358
 IVK  C7   N8    single    1.361  0.020  1.361
 IVK  C7   O9    double    1.215  0.020  1.215
 IVK  N8   C19   single    1.395  0.020  1.395
 IVK  N11  C12   single    1.397  0.020  1.397
 IVK  C12  C17   aromatic  1.395  0.020  1.395
 IVK  C12  C35   aromatic  1.397  0.020  1.397
 IVK  C14  C15   aromatic  1.384  0.020  1.384
 IVK  C14  C16   aromatic  1.386  0.020  1.386
 IVK  C14  CL1   single    1.734  0.020  1.734
 IVK  C15  C17   aromatic  1.387  0.020  1.387
 IVK  C16  C35   aromatic  1.383  0.020  1.383
 IVK  C19  C20   aromatic  1.394  0.020  1.394
 IVK  C19  C24   aromatic  1.393  0.020  1.393
 IVK  C20  C23   aromatic  1.386  0.020  1.386
 IVK  C21  C22   aromatic  1.385  0.020  1.385
 IVK  C21  C23   aromatic  1.384  0.020  1.384
 IVK  C21  N25   single    1.427  0.020  1.427
 IVK  C22  C24   aromatic  1.377  0.020  1.377
 IVK  C24  F32   single    1.341  0.020  1.341
 IVK  N25  C26   single    1.362  0.020  1.362
 IVK  N25  C30   single    1.397  0.020  1.397
 IVK  C26  C29   double    1.354  0.020  1.354
 IVK  C27  C28   double    1.358  0.020  1.358
 IVK  C27  C29   single    1.416  0.020  1.416
 IVK  C28  C30   single    1.439  0.020  1.439
 IVK  C30  O31   double    1.225  0.020  1.225
 IVK  C33  C34   single    1.511  0.020  1.511
 IVK  C34  F35   single    1.338  0.020  1.338
 IVK  C34  F36   single    1.342  0.020  1.342
 IVK  C34  F30   single    1.342  0.020  1.342
 IVK  C1   H1    single    0.970  0.020  1.090
 IVK  C2   H2    single    0.970  0.020  1.090
 IVK  C5   H51C  single    0.970  0.020  1.090
 IVK  C5   H52C  single    0.970  0.020  1.090
 IVK  C3   H31C  single    0.970  0.020  1.090
 IVK  C3   H32C  single    0.970  0.020  1.090
 IVK  C33  H331  single    0.970  0.020  1.090
 IVK  C33  H332  single    0.970  0.020  1.090
 IVK  N11  H11   single    0.860  0.020  1.020
 IVK  N8   H8    single    0.860  0.020  1.020
 IVK  C17  H17   single    0.930  0.020  1.080
 IVK  C35  H35   single    0.930  0.020  1.080
 IVK  C15  H15   single    0.930  0.020  1.080
 IVK  C16  H16   single    0.930  0.020  1.080
 IVK  C20  H20   single    0.930  0.020  1.080
 IVK  C23  H23   single    0.930  0.020  1.080
 IVK  C22  H22   single    0.930  0.020  1.080
 IVK  C26  H26   single    0.930  0.020  1.080
 IVK  C29  H29   single    0.930  0.020  1.080
 IVK  C27  H27   single    0.930  0.020  1.080
 IVK  C28  H28   single    0.930  0.020  1.080

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
 IVK  H1    C1   C6    109.79  3.000
 IVK  H1    C1   C5    109.45  3.000
 IVK  C6    C1   C5    109.85  3.000
 IVK  H1    C1   C2    111.03  3.000
 IVK  C6    C1   C2    112.29  3.000
 IVK  C5    C1   C2    104.29  3.000
 IVK  H2    C2   C7    109.71  3.000
 IVK  H2    C2   C3    108.27  3.000
 IVK  C7    C2   C3    110.47  3.000
 IVK  H2    C2   C1    109.68  3.000
 IVK  C7    C2   C1    114.10  3.000
 IVK  C3    C2   C1    104.37  3.000
 IVK  H32C  C3   H31C  107.82  3.000
 IVK  H32C  C3   N4    112.08  3.000
 IVK  H31C  C3   N4    111.23  3.000
 IVK  H32C  C3   C2    110.59  3.000
 IVK  H31C  C3   C2    112.45  3.000
 IVK  N4    C3   C2    102.70  3.000
 IVK  C33   N4   C5    115.88  3.000
 IVK  C33   N4   C3    113.31  3.000
 IVK  C5    N4   C3    104.86  3.000
 IVK  H52C  C5   H51C  107.30  3.000
 IVK  H52C  C5   N4    112.20  3.000
 IVK  H51C  C5   N4    111.71  3.000
 IVK  H52C  C5   C1    112.71  3.000
 IVK  H51C  C5   C1    109.09  3.000
 IVK  N4    C5   C1    103.86  3.000
 IVK  N11   C6   O10   123.84  3.000
 IVK  N11   C6   C1    113.11  3.000
 IVK  O10   C6   C1    123.01  3.000
 IVK  O9    C7   N8    123.55  3.000
 IVK  O9    C7   C2    123.67  3.000
 IVK  N8    C7   C2    112.73  3.000
 IVK  H8    N8   C19   116.40  3.000
 IVK  H8    N8   C7    116.43  3.000
 IVK  C19   N8   C7    126.80  3.000
 IVK  H11   N11  C12   114.75  3.000
 IVK  H11   N11  C6    116.01  3.000
 IVK  C12   N11  C6    129.19  3.000
 IVK  C35   C12  C17   118.78  3.000
 IVK  C35   C12  N11   116.83  3.000
 IVK  C17   C12  N11   124.38  3.000
 IVK  CL1   C14  C16   119.78  3.000
 IVK  CL1   C14  C15   119.85  3.000
 IVK  C16   C14  C15   120.38  3.000
 IVK  H15   C15  C17   119.26  3.000
 IVK  H15   C15  C14   120.45  3.000
 IVK  C17   C15  C14   120.29  3.000
 IVK  H16   C16  C35   119.81  3.000
 IVK  H16   C16  C14   120.86  3.000
 IVK  C35   C16  C14   119.32  3.000
 IVK  H17   C17  C15   118.76  3.000
 IVK  H17   C17  C12   121.18  3.000
 IVK  C15   C17  C12   120.06  3.000
 IVK  C24   C19  C20   117.42  3.000
 IVK  C24   C19  N8    118.40  3.000
 IVK  C20   C19  N8    124.15  3.000
 IVK  H20   C20  C23   119.07  3.000
 IVK  H20   C20  C19   120.32  3.000
 IVK  C23   C20  C19   120.61  3.000
 IVK  N25   C21  C23   120.16  3.000
 IVK  N25   C21  C22   119.39  3.000
 IVK  C23   C21  C22   120.44  3.000
 IVK  H22   C22  C24   120.21  3.000
 IVK  H22   C22  C21   121.40  3.000
 IVK  C24   C22  C21   118.38  3.000
 IVK  H23   C23  C21   120.16  3.000
 IVK  H23   C23  C20   119.60  3.000
 IVK  C21   C23  C20   120.24  3.000
 IVK  F32   C24  C22   118.92  3.000
 IVK  F32   C24  C19   118.17  3.000
 IVK  C22   C24  C19   122.91  3.000
 IVK  C30   N25  C26   123.60  3.000
 IVK  C30   N25  C21   117.70  3.000
 IVK  C26   N25  C21   118.70  3.000
 IVK  H26   C26  C29   122.76  3.000
 IVK  H26   C26  N25   115.75  3.000
 IVK  C29   C26  N25   121.49  3.000
 IVK  H27   C27  C29   119.53  3.000
 IVK  H27   C27  C28   119.64  3.000
 IVK  C29   C27  C28   120.83  3.000
 IVK  H28   C28  C30   117.01  3.000
 IVK  H28   C28  C27   121.15  3.000
 IVK  C30   C28  C27   121.84  3.000
 IVK  H29   C29  C27   121.86  3.000
 IVK  H29   C29  C26   120.14  3.000
 IVK  C27   C29  C26   118.00  3.000
 IVK  O31   C30  C28   125.57  3.000
 IVK  O31   C30  N25   120.18  3.000
 IVK  C28   C30  N25   114.25  3.000
 IVK  H332  C33  H331  106.70  3.000
 IVK  H332  C33  C34   108.58  3.000
 IVK  H331  C33  C34   106.69  3.000
 IVK  H332  C33  N4    113.35  3.000
 IVK  H331  C33  N4    109.12  3.000
 IVK  C34   C33  N4    112.05  3.000
 IVK  F30   C34  F36   106.61  3.000
 IVK  F30   C34  F35   106.62  3.000
 IVK  F36   C34  F35   107.15  3.000
 IVK  F30   C34  C33   113.11  3.000
 IVK  F36   C34  C33   110.69  3.000
 IVK  F35   C34  C33   112.30  3.000
 IVK  H35   C35  C16   118.89  3.000
 IVK  H35   C35  C12   119.95  3.000
 IVK  C16   C35  C12   121.16  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
 IVK  CONST_01  C14  C15  C17  C12     0.00   0.0  0
 IVK  CONST_02  C14  C16  C35  C12     0.00   0.0  0
 IVK  CONST_03  C35  C16  C14  C15     0.00   0.0  0
 IVK  CONST_04  C35  C12  C17  C15     0.00   0.0  0
 IVK  CONST_05  C17  C15  C14  C16     0.00   0.0  0
 IVK  CONST_06  C17  C12  C35  C16     0.00   0.0  0
 IVK  CONST_07  C21  C23  C20  C19     0.00   0.0  0
 IVK  CONST_08  C21  C22  C24  C19     0.00   0.0  0
 IVK  CONST_09  C22  C24  C19  C20     0.00   0.0  0
 IVK  CONST_10  C22  C21  C23  C20     0.00   0.0  0
 IVK  CONST_11  C24  C19  C20  C23     0.00   0.0  0
 IVK  CONST_12  C24  C22  C21  C23     0.00   0.0  0
 IVK  CONST_13  N25  C21  C23  C20   180.00   0.0  0
 IVK  CONST_14  N25  C21  C22  C24   180.00   0.0  0
 IVK  CONST_15  C28  C30  N25  C21   180.00   0.0  0
 IVK  CONST_16  C28  C30  N25  C26     0.00   0.0  0
 IVK  CONST_17  C23  C20  C19  N8    180.00   0.0  0
 IVK  CONST_18  C22  C24  C19  N8    180.00   0.0  0
 IVK  CONST_19  C15  C17  C12  N11   180.00   0.0  0
 IVK  CONST_20  C16  C35  C12  N11   180.00   0.0  0
 IVK  CONST_21  CL1  C14  C15  C17   180.00   0.0  0
 IVK  CONST_22  C35  C16  C14  CL1   180.00   0.0  0
 IVK  CONST_23  F32  C24  C19  C20   180.00   0.0  0
 IVK  CONST_24  F32  C24  C22  C21   180.00   0.0  0
 IVK  CONST_25  O31  C30  N25  C21     0.00   0.0  0
 IVK  CONST_26  O31  C30  N25  C26   180.00   0.0  0
 IVK  CONST_27  H15  C15  C17  C12   180.00   0.0  0
 IVK  CONST_28  H16  C16  C35  C12   180.00   0.0  0
 IVK  CONST_29  H17  C17  C15  C14   180.00   0.0  0
 IVK  CONST_30  H35  C35  C16  C14   180.00   0.0  0
 IVK  CONST_31  H23  C23  C20  C19   180.00   0.0  0
 IVK  CONST_32  H22  C22  C24  C19   180.00   0.0  0
 IVK  CONST_33  H20  C20  C23  C21   180.00   0.0  0
 IVK  CONST_34  C12  N11  C6   C1    180.00   0.0  0
 IVK  CONST_35  C19  N8   C7   C2    180.00   0.0  0
 IVK  CONST_36  C17  C12  N11  C6      0.00   0.0  0
 IVK  CONST_37  C35  C12  N11  C6    180.00   0.0  0
 IVK  CONST_40  H11  N11  C12  C17   180.00   0.0  0
 IVK  CONST_42  C19  N8   C7   O9      0.00   0.0  0
 IVK  CONST_43  C12  N11  C6   O10     0.00   0.0  0
 IVK  Var_01    C3   N4   C5   C1     41.64  30.0  1
 IVK  Var_02    C5   N4   C3   C2    -44.93  30.0  1
 IVK  Var_03    C26  N25  C21  C22   -81.01  30.0  2
 IVK  Var_04    C34  C33  N4   C3   -152.64  30.0  3
 IVK  Var_05    F35  C34  C33  N4     57.24  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
 IVK  chir_01  C1  C2  C5  C6  positiv
 IVK  chir_02  C2  C1  C3  C7  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
 IVK  plan-1  N11  0.020
 IVK  plan-1  C12  0.020
 IVK  plan-1  C14  0.020
 IVK  plan-1  C15  0.020
 IVK  plan-1  C16  0.020
 IVK  plan-1  C17  0.020
 IVK  plan-1  CL1  0.020
 IVK  plan-1  C35  0.020
 IVK  plan-1  H17  0.020
 IVK  plan-1  H35  0.020
 IVK  plan-1  H15  0.020
 IVK  plan-1  H16  0.020
 IVK  plan-2  N8   0.020
 IVK  plan-2  C19  0.020
 IVK  plan-2  C20  0.020
 IVK  plan-2  C21  0.020
 IVK  plan-2  C22  0.020
 IVK  plan-2  C23  0.020
 IVK  plan-2  C24  0.020
 IVK  plan-2  N25  0.020
 IVK  plan-2  F32  0.020
 IVK  plan-2  H20  0.020
 IVK  plan-2  H23  0.020
 IVK  plan-2  H22  0.020
 IVK  plan-3  C21  0.020
 IVK  plan-3  N25  0.020
 IVK  plan-3  C26  0.020
 IVK  plan-3  C27  0.020
 IVK  plan-3  C28  0.020
 IVK  plan-3  C29  0.020
 IVK  plan-3  C30  0.020
 IVK  plan-3  O31  0.020
 IVK  plan-3  H26  0.020
 IVK  plan-3  H29  0.020
 IVK  plan-3  H27  0.020
 IVK  plan-3  H28  0.020
 IVK  plan-4  C2   0.020
 IVK  plan-4  C7   0.020
 IVK  plan-4  N8   0.020
 IVK  plan-4  O9   0.020
 IVK  plan-4  C19  0.020
 IVK  plan-4  H8   0.020
 IVK  plan-5  C1   0.020
 IVK  plan-5  C6   0.020
 IVK  plan-5  O10  0.020
 IVK  plan-5  N11  0.020
 IVK  plan-5  C12  0.020
 IVK  plan-5  H11  0.020

