# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:20:33 2020
#   Inital geometry file: a 163 line input string
#   Ligand name: (3R,4R)-N-(4-chlorophenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-[2-(methylamino)-2-oxoethyl]pyrrolidine-3,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)CN1C[C@@H]([C@H](C1)C(=O)Nc2ccc(cc2F)N3C=CC=CC3=O)C(=O)Nc4ccc(Cl)cc4
#
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
 63C  63C  (3R,4R)-N-(4-chlorophenyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-1-[2-(methylamino)-2-oxoethyl]pyrrolidine-3,4-dicarboxamide  ligand  62  37  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_63C
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
 63C  C2    C   CR15  0  -0.437  -0.6810  -1.2994  -0.0243
 63C  C3    C   CR15  0  -0.429  -1.9610  -0.7938   0.6482
 63C  N4    N   NR5   0  -0.413  -2.1984  -3.0440  -0.0595
 63C  C5    C   C     0   0.579   0.5943  -0.7700   0.5962
 63C  N6    N   NR6   0  -0.613   7.0532   0.5904   0.3480
 63C  C7    C   C     0   0.568  -2.6589   0.2928  -0.1502
 63C  C8    C   CH2   0  -0.265  -2.8521  -2.0537   0.7736
 63C  C9    C   CH2   0  -0.246  -0.7804  -2.8229   0.1161
 63C  C10   C   CR6   0   0.552   7.4638   1.8661  -0.0488
 63C  C11   C   CR6   0   0.289   5.6716   0.2636   0.2153
 63C  N12   N   NH1   0  -0.745   1.6422  -0.7698  -0.2707
 63C  C13   C   CR16  0  -0.413   5.1556  -0.0357  -1.0370
 63C  N14   N   NH1   0  -0.745  -3.5071   1.0381   0.6043
 63C  C15   C   CR6   0   0.231   2.9666  -0.4149  -0.0333
 63C  C16   C   CR6   0   0.478   3.8261  -0.3637  -1.1341
 63C  C19   C   CR16  0   0.049   7.8988  -0.3433   0.8671
 63C  O20   O   O     0  -0.448   0.6760  -0.4277   1.7597
 63C  O21   O   O     0  -0.451  -2.4989   0.4496  -1.3458
 63C  C22   C   CR16  0  -0.453   8.8702   2.1160   0.1224
 63C  O23   O   O     0  -0.502   6.6488   2.6648  -0.4947
 63C  C24   C   CR16  0  -0.259   4.8553   0.2252   1.3299
 63C  C25   C   CR16  0  -0.317   3.5144  -0.1158   1.2130
 63C  C26   C   CR16  0  -0.399   9.2193  -0.0915   1.0278
 63C  C27   C   CR16  0  -0.118   9.7070   1.1792   0.6383
 63C  C28   C   CR6   0   0.385  -4.3898   2.0467   0.2115
 63C  F30   F   F     0  -0.311   3.3192  -0.6609  -2.3422
 63C  C31   C   CR6   0  -0.058  -6.2093   4.0704  -0.3781
 63C  C33   C   CR16  0  -0.352  -5.2486   2.5477   1.1929
 63C  C34   C   CR16  0  -0.318  -4.4571   2.5802  -1.0763
 63C  C35   C   CR16  0  -0.200  -5.3666   3.5879  -1.3639
 63C  C36   C   CR16  0  -0.200  -6.1538   3.5525   0.9065
 63C  C1    C   CH2   0  -0.404  -2.6189  -4.3947   0.1886
 63C  CL    CL  CL    0  -0.134  -7.3407   5.3304  -0.7502
 63C  C40   C   C     0   0.523  -4.0465  -4.6323  -0.2822
 63C  O41   O   O     0  -0.494  -4.5035  -4.0972  -1.2815
 63C  N42   N   NH1   0  -0.622  -4.7414  -5.5035   0.4589
 63C  C43   C   CH3   0  -0.513  -6.0836  -5.9136   0.1204
 63C  H2    H   HCR5  0   0.298  -0.7061  -1.0552  -1.0891
 63C  H3    H   HCR5  0   0.303  -1.7397  -0.4149   1.6481
 63C  H91C  H   HCH2  0   0.261  -0.2002  -3.3524  -0.6414
 63C  H92C  H   HCH2  0   0.215  -0.4188  -3.1442   1.1078
 63C  H81C  H   HCH2  0   0.225  -2.8868  -2.3639   1.8286
 63C  H82C  H   HCH2  0   0.254  -3.8818  -1.8862   0.4513
 63C  H11C  H   HCH2  0   0.284  -1.9798  -5.0736  -0.3851
 63C  H12C  H   HCH2  0   0.226  -2.5075  -4.6838   1.2471
 63C  H12   H   HNH1  0   0.424   1.4247  -1.0364  -1.2186
 63C  H19   H   HCR6  0   0.314   7.4487  -1.2890   1.1336
 63C  H14   H   HNH1  0   0.421  -3.5406   0.8084   1.5862
 63C  H22   H   HCR6  0   0.276   9.2337   3.0898  -0.1761
 63C  H13   H   HCR6  0   0.296   5.7767  -0.0210  -1.9228
 63C  H24   H   HCR6  0   0.279   5.2575   0.4626   2.3057
 63C  H25   H   HCR6  0   0.299   2.9015  -0.1431   2.0980
 63C  H26   H   HCR6  0   0.280   9.8686  -0.8501   1.4370
 63C  H27   H   HCR6  0   0.281  10.7594   1.4050   0.7536
 63C  H33   H   HCR6  0   0.282  -5.2126   2.1468   2.1988
 63C  H34   H   HCR6  0   0.290  -3.8097   2.2264  -1.8609
 63C  H35   H   HCR6  0   0.282  -5.4067   3.9929  -2.3661
 63C  H36   H   HCR6  0   0.283  -6.8094   3.9226   1.6827
 63C  H42   H   HNH1  0   0.404  -4.3269  -5.8736   1.2972
 63C  H50   H   HCH3  0   0.251  -6.4005  -6.6743   0.8278
 63C  H51   H   HCH3  0   0.238  -6.7868  -5.0816   0.1733
 63C  H52   H   HCH3  0   0.239  -6.1304  -6.3374  -0.8829

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
 63C  C2   C3    single    1.532  0.020  1.532
 63C  C2   C5    single    1.514  0.020  1.514
 63C  C2   C9    single    1.533  0.020  1.533
 63C  C3   C7    single    1.518  0.020  1.518
 63C  C3   C8    single    1.548  0.020  1.548
 63C  N4   C8    single    1.450  0.020  1.450
 63C  N4   C9    single    1.446  0.020  1.446
 63C  N4   C1    single    1.436  0.020  1.436
 63C  C5   N12   single    1.360  0.020  1.360
 63C  C5   O20   double    1.216  0.020  1.216
 63C  N6   C10   single    1.398  0.020  1.398
 63C  N6   C11   single    1.426  0.020  1.426
 63C  N6   C19   single    1.362  0.020  1.362
 63C  C7   N14   single    1.358  0.020  1.358
 63C  C7   O21   double    1.216  0.020  1.216
 63C  C10  C22   single    1.439  0.020  1.439
 63C  C10  O23   double    1.225  0.020  1.225
 63C  C11  C13   aromatic  1.387  0.020  1.387
 63C  C11  C24   aromatic  1.382  0.020  1.382
 63C  N12  C15   single    1.391  0.020  1.391
 63C  C13  C16   aromatic  1.373  0.020  1.373
 63C  N14  C28   single    1.397  0.020  1.397
 63C  C15  C16   aromatic  1.398  0.020  1.398
 63C  C15  C25   aromatic  1.394  0.020  1.394
 63C  C16  F30   single    1.343  0.020  1.343
 63C  C19  C26   double    1.354  0.020  1.354
 63C  C22  C27   double    1.358  0.020  1.358
 63C  C24  C25   aromatic  1.388  0.020  1.388
 63C  C26  C27   single    1.416  0.020  1.416
 63C  C28  C33   aromatic  1.397  0.020  1.397
 63C  C28  C34   aromatic  1.395  0.020  1.395
 63C  C31  C35   aromatic  1.384  0.020  1.384
 63C  C31  C36   aromatic  1.386  0.020  1.386
 63C  C31  CL    single    1.734  0.020  1.734
 63C  C33  C36   aromatic  1.382  0.020  1.382
 63C  C34  C35   aromatic  1.388  0.020  1.388
 63C  C1   C40   single    1.522  0.020  1.522
 63C  C40  O41   double    1.222  0.020  1.222
 63C  C40  N42   single    1.338  0.020  1.338
 63C  N42  C43   single    1.444  0.020  1.444
 63C  C2   H2    single    0.970  0.020  1.090
 63C  C3   H3    single    0.970  0.020  1.090
 63C  C9   H91C  single    0.970  0.020  1.090
 63C  C9   H92C  single    0.970  0.020  1.090
 63C  C8   H81C  single    0.970  0.020  1.090
 63C  C8   H82C  single    0.970  0.020  1.090
 63C  C1   H11C  single    0.970  0.020  1.090
 63C  C1   H12C  single    0.970  0.020  1.090
 63C  N12  H12   single    0.860  0.020  1.020
 63C  C19  H19   single    0.930  0.020  1.080
 63C  N14  H14   single    0.860  0.020  1.020
 63C  C22  H22   single    0.930  0.020  1.080
 63C  C13  H13   single    0.930  0.020  1.080
 63C  C24  H24   single    0.930  0.020  1.080
 63C  C25  H25   single    0.930  0.020  1.080
 63C  C26  H26   single    0.930  0.020  1.080
 63C  C27  H27   single    0.930  0.020  1.080
 63C  C33  H33   single    0.930  0.020  1.080
 63C  C34  H34   single    0.930  0.020  1.080
 63C  C35  H35   single    0.930  0.020  1.080
 63C  C36  H36   single    0.930  0.020  1.080
 63C  N42  H42   single    0.860  0.020  1.020
 63C  C43  H50   single    0.970  0.020  1.090
 63C  C43  H51   single    0.970  0.020  1.090
 63C  C43  H52   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
 63C  H2    C2   C9    108.05  3.000
 63C  H2    C2   C5    109.91  3.000
 63C  C9    C2   C5    111.38  3.000
 63C  H2    C2   C3    109.57  3.000
 63C  C9    C2   C3    103.51  3.000
 63C  C5    C2   C3    114.11  3.000
 63C  H3    C3   C8    108.96  3.000
 63C  H3    C3   C7    109.05  3.000
 63C  C8    C3   C7    111.13  3.000
 63C  H3    C3   C2    110.32  3.000
 63C  C8    C3   C2    104.35  3.000
 63C  C7    C3   C2    112.92  3.000
 63C  C1    N4   C9    114.20  3.000
 63C  C1    N4   C8    114.27  3.000
 63C  C9    N4   C8    105.54  3.000
 63C  O20   C5   N12   123.93  3.000
 63C  O20   C5   C2    123.19  3.000
 63C  N12   C5   C2    112.82  3.000
 63C  C19   N6   C11   118.67  3.000
 63C  C19   N6   C10   123.46  3.000
 63C  C11   N6   C10   117.87  3.000
 63C  O21   C7   N14   123.88  3.000
 63C  O21   C7   C3    123.28  3.000
 63C  N14   C7   C3    112.81  3.000
 63C  H82C  C8   H81C  107.25  3.000
 63C  H82C  C8   N4    111.12  3.000
 63C  H81C  C8   N4    111.88  3.000
 63C  H82C  C8   C3    113.21  3.000
 63C  H81C  C8   C3    108.98  3.000
 63C  N4    C8   C3    104.47  3.000
 63C  H92C  C9   H91C  107.96  3.000
 63C  H92C  C9   N4    112.71  3.000
 63C  H91C  C9   N4    111.28  3.000
 63C  H92C  C9   C2    110.52  3.000
 63C  H91C  C9   C2    112.59  3.000
 63C  N4    C9   C2    101.80  3.000
 63C  O23   C10  C22   125.48  3.000
 63C  O23   C10  N6    120.19  3.000
 63C  C22   C10  N6    114.33  3.000
 63C  C24   C11  C13   120.16  3.000
 63C  C24   C11  N6    120.24  3.000
 63C  C13   C11  N6    119.60  3.000
 63C  H12   N12  C15   115.66  3.000
 63C  H12   N12  C5    115.65  3.000
 63C  C15   N12  C5    128.66  3.000
 63C  H13   C13  C16   120.09  3.000
 63C  H13   C13  C11   121.51  3.000
 63C  C16   C13  C11   118.40  3.000
 63C  H14   N14  C28   114.65  3.000
 63C  H14   N14  C7    115.88  3.000
 63C  C28   N14  C7    129.41  3.000
 63C  C25   C15  C16   117.04  3.000
 63C  C25   C15  N12   125.55  3.000
 63C  C16   C15  N12   117.41  3.000
 63C  F30   C16  C15   117.92  3.000
 63C  F30   C16  C13   118.81  3.000
 63C  C15   C16  C13   123.27  3.000
 63C  H19   C19  C26   122.66  3.000
 63C  H19   C19  N6    115.79  3.000
 63C  C26   C19  N6    121.54  3.000
 63C  H22   C22  C27   121.26  3.000
 63C  H22   C22  C10   116.88  3.000
 63C  C27   C22  C10   121.86  3.000
 63C  H24   C24  C25   119.27  3.000
 63C  H24   C24  C11   120.12  3.000
 63C  C25   C24  C11   120.62  3.000
 63C  H25   C25  C24   119.12  3.000
 63C  H25   C25  C15   120.37  3.000
 63C  C24   C25  C15   120.50  3.000
 63C  H26   C26  C27   121.87  3.000
 63C  H26   C26  C19   120.07  3.000
 63C  C27   C26  C19   118.05  3.000
 63C  H27   C27  C26   119.52  3.000
 63C  H27   C27  C22   119.72  3.000
 63C  C26   C27  C22   120.76  3.000
 63C  C34   C28  C33   118.79  3.000
 63C  C34   C28  N14   124.48  3.000
 63C  C33   C28  N14   116.74  3.000
 63C  CL    C31  C36   119.77  3.000
 63C  CL    C31  C35   119.86  3.000
 63C  C36   C31  C35   120.37  3.000
 63C  H33   C33  C36   118.89  3.000
 63C  H33   C33  C28   119.94  3.000
 63C  C36   C33  C28   121.17  3.000
 63C  H34   C34  C35   118.79  3.000
 63C  H34   C34  C28   121.18  3.000
 63C  C35   C34  C28   120.03  3.000
 63C  H35   C35  C34   119.23  3.000
 63C  H35   C35  C31   120.46  3.000
 63C  C34   C35  C31   120.31  3.000
 63C  H36   C36  C33   119.80  3.000
 63C  H36   C36  C31   120.87  3.000
 63C  C33   C36  C31   119.32  3.000
 63C  H12C  C1   H11C  106.34  3.000
 63C  H12C  C1   C40   110.53  3.000
 63C  H11C  C1   C40   106.78  3.000
 63C  H12C  C1   N4    112.50  3.000
 63C  H11C  C1   N4    108.77  3.000
 63C  C40   C1   N4    111.59  3.000
 63C  N42   C40  O41   122.93  3.000
 63C  N42   C40  C1    114.67  3.000
 63C  O41   C40  C1    122.37  3.000
 63C  H42   N42  C43   118.30  3.000
 63C  H42   N42  C40   119.15  3.000
 63C  C43   N42  C40   122.53  3.000
 63C  H52   C43  H51   108.27  3.000
 63C  H52   C43  H50   108.33  3.000
 63C  H51   C43  H50   108.34  3.000
 63C  H52   C43  N42   111.48  3.000
 63C  H51   C43  N42   111.80  3.000
 63C  H50   C43  N42   108.51  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
 63C  CONST_01  C15  C16  C13  C11    0.00   0.0  0
 63C  CONST_02  C15  C25  C24  C11    0.00   0.0  0
 63C  CONST_03  C25  C24  C11  C13    0.00   0.0  0
 63C  CONST_04  C25  C15  C16  C13    0.00   0.0  0
 63C  CONST_05  C24  C11  C13  C16    0.00   0.0  0
 63C  CONST_06  C24  C25  C15  C16    0.00   0.0  0
 63C  CONST_07  C31  C36  C33  C28    0.00   0.0  0
 63C  CONST_08  C31  C35  C34  C28    0.00   0.0  0
 63C  CONST_09  C35  C34  C28  C33    0.00   0.0  0
 63C  CONST_10  C35  C31  C36  C33    0.00   0.0  0
 63C  CONST_11  C36  C33  C28  C34    0.00   0.0  0
 63C  CONST_12  C36  C31  C35  C34    0.00   0.0  0
 63C  CONST_13  C16  C13  C11  N6   180.00   0.0  0
 63C  CONST_14  C25  C24  C11  N6   180.00   0.0  0
 63C  CONST_15  C22  C10  N6   C11  180.00   0.0  0
 63C  CONST_16  C22  C10  N6   C19    0.00   0.0  0
 63C  CONST_17  F30  C16  C13  C11  180.00   0.0  0
 63C  CONST_18  C13  C16  C15  N12  180.00   0.0  0
 63C  CONST_19  C24  C25  C15  N12  180.00   0.0  0
 63C  CONST_20  C36  C33  C28  N14  180.00   0.0  0
 63C  CONST_21  C35  C34  C28  N14  180.00   0.0  0
 63C  CONST_22  F30  C16  C15  C25  180.00   0.0  0
 63C  CONST_23  CL   C31  C36  C33  180.00   0.0  0
 63C  CONST_24  CL   C31  C35  C34  180.00   0.0  0
 63C  CONST_25  O23  C10  N6   C11    0.00   0.0  0
 63C  CONST_26  O23  C10  N6   C19  180.00   0.0  0
 63C  CONST_27  H13  C13  C11  N6     0.00   0.0  0
 63C  CONST_28  H24  C24  C11  N6     0.00   0.0  0
 63C  CONST_29  H25  C25  C24  C11  180.00   0.0  0
 63C  CONST_30  H36  C36  C33  C28  180.00   0.0  0
 63C  CONST_31  H35  C35  C34  C28  180.00   0.0  0
 63C  CONST_32  H34  C34  C35  C31  180.00   0.0  0
 63C  CONST_33  H33  C33  C36  C31  180.00   0.0  0
 63C  CONST_34  C15  N12  C5   C2   180.00   0.0  0
 63C  CONST_35  C28  N14  C7   C3   180.00   0.0  0
 63C  CONST_36  C16  C15  N12  C5   180.00   0.0  0
 63C  CONST_37  C25  C15  N12  C5     0.00   0.0  0
 63C  CONST_38  C33  C28  N14  C7   180.00   0.0  0
 63C  CONST_39  C34  C28  N14  C7     0.00   0.0  0
 63C  CONST_40  H12  N12  C15  C16    0.00   0.0  0
 63C  CONST_41  H14  N14  C28  C33    0.00   0.0  0
 63C  CONST_42  O20  C5   N12  C15    0.00   0.0  0
 63C  CONST_43  C28  N14  C7   O21    0.00   0.0  0
 63C  CONST_44  C43  N42  C40  C1   180.00   0.0  0
 63C  CONST_45  C43  N42  C40  O41    0.00   0.0  0
 63C  CONST_46  H42  N42  C40  C1     0.00   0.0  0
 63C  Var_01    C8   N4   C9   C2   -46.30  30.0  1
 63C  Var_02    C9   N4   C8   C3    36.90  30.0  1
 63C  Var_03    C13  C11  N6   C10   76.39  30.0  2
 63C  Var_04    C40  C1   N4   C8    70.01  30.0  3
 63C  Var_05    O41  C40  C1   N4    35.36  30.0  3
 63C  Var_06    H50  C43  N42  C40  175.89  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
 63C  chir_01  C2  C3  C5  C9  negativ
 63C  chir_02  C3  C8  C7  C2  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
 63C  plan-1  N6   0.020
 63C  plan-1  C10  0.020
 63C  plan-1  C11  0.020
 63C  plan-1  C19  0.020
 63C  plan-1  C22  0.020
 63C  plan-1  O23  0.020
 63C  plan-1  C26  0.020
 63C  plan-1  C27  0.020
 63C  plan-1  H19  0.020
 63C  plan-1  H22  0.020
 63C  plan-1  H26  0.020
 63C  plan-1  H27  0.020
 63C  plan-2  N6   0.020
 63C  plan-2  C11  0.020
 63C  plan-2  N12  0.020
 63C  plan-2  C13  0.020
 63C  plan-2  C15  0.020
 63C  plan-2  C16  0.020
 63C  plan-2  C24  0.020
 63C  plan-2  C25  0.020
 63C  plan-2  F30  0.020
 63C  plan-2  H13  0.020
 63C  plan-2  H24  0.020
 63C  plan-2  H25  0.020
 63C  plan-3  N14  0.020
 63C  plan-3  C28  0.020
 63C  plan-3  C31  0.020
 63C  plan-3  C33  0.020
 63C  plan-3  C34  0.020
 63C  plan-3  C35  0.020
 63C  plan-3  C36  0.020
 63C  plan-3  CL   0.020
 63C  plan-3  H33  0.020
 63C  plan-3  H34  0.020
 63C  plan-3  H35  0.020
 63C  plan-3  H36  0.020
 63C  plan-4  C3   0.020
 63C  plan-4  C7   0.020
 63C  plan-4  N14  0.020
 63C  plan-4  O21  0.020
 63C  plan-4  C28  0.020
 63C  plan-4  H14  0.020
 63C  plan-5  C1   0.020
 63C  plan-5  C40  0.020
 63C  plan-5  O41  0.020
 63C  plan-5  N42  0.020
 63C  plan-5  C43  0.020
 63C  plan-5  H42  0.020
 63C  plan-6  C2   0.020
 63C  plan-6  C5   0.020
 63C  plan-6  N12  0.020
 63C  plan-6  C15  0.020
 63C  plan-6  O20  0.020
 63C  plan-6  H12  0.020

