# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:50:20 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (3R,4R)-N-(5-chloropyridin-2-yl)-1-(2,2-difluoroethyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]pyrrolidine-3,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)CN1C[C@@H]([C@H](C1)C(=O)Nc2ccc(cc2F)N3C=CC=CC3=O)C(=O)Nc4ccc(Cl)cn4
#
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
 XBV  XBV  (3R,4R)-N-(5-chloropyridin-2-yl)-1-(2,2-difluoroethyl)-N'-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]pyrrolidine-3,4-dicarboxamide  ligand  57  36  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XBV
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
 XBV  C1    C   CH1   0  -0.442    1.8714   1.2321   0.5348
 XBV  C2    C   CH1   0  -0.435    0.5961   1.5385  -0.2501
 XBV  C3    C   CH2   0  -0.245    0.5685   3.0676  -0.2836
 XBV  N4    N   NT    0  -0.431    1.9697   3.3914  -0.4617
 XBV  C5    C   CH2   0  -0.263    2.6922   2.5451   0.4753
 XBV  C6    C   C     0   0.564    2.6590   0.0672  -0.0394
 XBV  C7    C   C     0   0.579   -0.6601   0.9733   0.3781
 XBV  N8    N   NH1   0  -0.744   -1.6512   0.7424  -0.5235
 XBV  O9    O   O     0  -0.448   -0.7755   0.7874   1.5740
 XBV  O10   O   O     0  -0.426    2.5510  -0.3108  -1.1848
 XBV  N11   N   NH1   0  -0.728    3.5255  -0.4673   0.8737
 XBV  C12   C   CR6   0   0.538    4.4735  -1.4698   0.7142
 XBV  N13   N   N     0  -0.421    4.6844  -1.9931  -0.4794
 XBV  C14   C   CR6   0  -0.129    6.3445  -3.4129   0.4599
 XBV  C15   C   CR16  0  -0.086    6.1329  -2.8649   1.7183
 XBV  C16   C   CR16  0  -0.031    5.5985  -2.9459  -0.6057
 XBV  C17   C   CR16  0  -0.405    5.1815  -1.8783   1.8512
 XBV  CL1   CL  CL    0  -0.118    7.5189  -4.6552   0.2216
 XBV  C19   C   CR6   0   0.228   -2.9456   0.2875  -0.2863
 XBV  C20   C   CR16  0  -0.313   -3.5511   0.1890   0.9649
 XBV  C21   C   CR6   0   0.295   -5.5830  -0.6235  -0.0392
 XBV  C22   C   CR16  0  -0.415   -5.0078  -0.5309  -1.2984
 XBV  C23   C   CR16  0  -0.262   -4.8560  -0.2701   1.0823
 XBV  C24   C   CR6   0   0.479   -3.7123  -0.0861  -1.3933
 XBV  N25   N   NR6   0  -0.613   -6.9350  -1.0543   0.0947
 XBV  C26   C   CR16  0   0.048   -7.8713  -0.1446   0.4869
 XBV  C27   C   CR16  0  -0.118   -9.5352  -1.8376   0.4242
 XBV  C28   C   CR16  0  -0.452   -8.6091  -2.7508   0.0347
 XBV  C29   C   CR16  0  -0.400   -9.1681  -0.4911   0.6614
 XBV  C30   C   CR6   0   0.552   -7.2266  -2.4001  -0.1512
 XBV  O31   O   O     0  -0.502   -6.3381  -3.1731  -0.4883
 XBV  F32   F   F     0  -0.311   -3.1486   0.0074  -2.6089
 XBV  C33   C   CH2   0  -0.391    2.2414   4.8041  -0.3581
 XBV  C34   C   CH1   0   0.524    3.5322   5.2302  -1.0085
 XBV  F35   F   F     0  -0.349    4.6168   4.6793  -0.3835
 XBV  F36   F   F     0  -0.345    3.5858   4.8067  -2.3016
 XBV  H1    H   HCH1  0   0.303    1.6247   1.0161   1.5761
 XBV  H2    H   HCH1  0   0.297    0.7008   1.1776  -1.2757
 XBV  H51C  H   HCH2  0   0.226    2.7340   2.9904   1.4796
 XBV  H52C  H   HCH2  0   0.253    3.7203   2.3795   0.1528
 XBV  H31C  H   HCH2  0   0.263   -0.0319   3.4586  -1.1064
 XBV  H32C  H   HCH2  0   0.217    0.1573   3.4679   0.6582
 XBV  H331  H   HCH2  0   0.272    1.4445   5.3547  -0.8636
 XBV  H332  H   HCH2  0   0.231    2.2508   5.1639   0.6834
 XBV  H11   H   HNH1  0   0.426    3.4712  -0.0856   1.8060
 XBV  H8    H   HNH1  0   0.424   -1.4103   0.8947  -1.4911
 XBV  H17   H   HCR6  0   0.293    4.9908  -1.4308   2.8179
 XBV  H16   H   HCR6  0   0.285    5.7442  -3.3532  -1.5997
 XBV  H15   H   HCR6  0   0.299    6.6984  -3.2001   2.5771
 XBV  H20   H   HCR6  0   0.298   -3.0136   0.4637   1.8564
 XBV  H23   H   HCR6  0   0.280   -5.3023  -0.3476   2.0650
 XBV  H22   H   HCR6  0   0.296   -5.5554  -0.7911  -2.1944
 XBV  H26   H   HCR6  0   0.314   -7.5111   0.8627   0.6404
 XBV  H29   H   HCR6  0   0.280   -9.8898   0.2506   0.9675
 XBV  H27   H   HCR6  0   0.281  -10.5662  -2.1403   0.5555
 XBV  H28   H   HCR6  0   0.276   -8.8793  -3.7823  -0.1455
 XBV  H34   H   HCH1  0   0.205    3.6526   6.3146  -0.9917

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
 XBV  C1   C2    single    1.528  0.020  1.528
 XBV  C1   C5    single    1.550  0.020  1.550
 XBV  C1   C6    single    1.519  0.020  1.519
 XBV  C2   C3    single    1.530  0.020  1.530
 XBV  C2   C7    single    1.514  0.020  1.514
 XBV  C3   N4    single    1.449  0.020  1.449
 XBV  N4   C5    single    1.455  0.020  1.455
 XBV  N4   C33   single    1.442  0.020  1.442
 XBV  C6   O10   double    1.211  0.020  1.211
 XBV  C6   N11   single    1.368  0.020  1.368
 XBV  C7   N8    single    1.360  0.020  1.360
 XBV  C7   O9    double    1.216  0.020  1.216
 XBV  N8   C19   single    1.392  0.020  1.392
 XBV  N11  C12   single    1.389  0.020  1.389
 XBV  C12  N13   aromatic  1.320  0.020  1.320
 XBV  C12  C17   aromatic  1.400  0.020  1.400
 XBV  N13  C16   aromatic  1.326  0.020  1.326
 XBV  C14  C15   aromatic  1.389  0.020  1.389
 XBV  C14  C16   aromatic  1.382  0.020  1.382
 XBV  C14  CL1   single    1.726  0.020  1.726
 XBV  C15  C17   aromatic  1.377  0.020  1.377
 XBV  C19  C20   aromatic  1.393  0.020  1.393
 XBV  C19  C24   aromatic  1.397  0.020  1.397
 XBV  C20  C23   aromatic  1.388  0.020  1.388
 XBV  C21  C22   aromatic  1.387  0.020  1.387
 XBV  C21  C23   aromatic  1.382  0.020  1.382
 XBV  C21  N25   single    1.425  0.020  1.425
 XBV  C22  C24   aromatic  1.373  0.020  1.373
 XBV  C24  F32   single    1.343  0.020  1.343
 XBV  N25  C26   single    1.363  0.020  1.363
 XBV  N25  C30   single    1.399  0.020  1.399
 XBV  C26  C29   double    1.354  0.020  1.354
 XBV  C27  C28   double    1.358  0.020  1.358
 XBV  C27  C29   single    1.416  0.020  1.416
 XBV  C28  C30   single    1.438  0.020  1.438
 XBV  C30  O31   double    1.225  0.020  1.225
 XBV  C33  C34   single    1.507  0.020  1.507
 XBV  C34  F35   single    1.368  0.020  1.368
 XBV  C34  F36   single    1.362  0.020  1.362
 XBV  C1   H1    single    0.970  0.020  1.090
 XBV  C2   H2    single    0.970  0.020  1.090
 XBV  C5   H51C  single    0.970  0.020  1.090
 XBV  C5   H52C  single    0.970  0.020  1.090
 XBV  C3   H31C  single    0.970  0.020  1.090
 XBV  C3   H32C  single    0.970  0.020  1.090
 XBV  C33  H331  single    0.970  0.020  1.090
 XBV  C33  H332  single    0.970  0.020  1.090
 XBV  N11  H11   single    0.860  0.020  1.020
 XBV  N8   H8    single    0.860  0.020  1.020
 XBV  C17  H17   single    0.930  0.020  1.080
 XBV  C16  H16   single    0.930  0.020  1.080
 XBV  C15  H15   single    0.930  0.020  1.080
 XBV  C20  H20   single    0.930  0.020  1.080
 XBV  C23  H23   single    0.930  0.020  1.080
 XBV  C22  H22   single    0.930  0.020  1.080
 XBV  C26  H26   single    0.930  0.020  1.080
 XBV  C29  H29   single    0.930  0.020  1.080
 XBV  C27  H27   single    0.930  0.020  1.080
 XBV  C28  H28   single    0.930  0.020  1.080
 XBV  C34  H34   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
 XBV  H1    C1   C6    109.03  3.000
 XBV  H1    C1   C5    108.90  3.000
 XBV  C6    C1   C5    111.14  3.000
 XBV  H1    C1   C2    109.93  3.000
 XBV  C6    C1   C2    113.10  3.000
 XBV  C5    C1   C2    104.62  3.000
 XBV  H2    C2   C7    110.23  3.000
 XBV  H2    C2   C3    108.14  3.000
 XBV  C7    C2   C3    111.55  3.000
 XBV  H2    C2   C1    109.63  3.000
 XBV  C7    C2   C1    113.86  3.000
 XBV  C3    C2   C1    103.10  3.000
 XBV  H32C  C3   H31C  107.99  3.000
 XBV  H32C  C3   N4    112.60  3.000
 XBV  H31C  C3   N4    111.06  3.000
 XBV  H32C  C3   C2    110.54  3.000
 XBV  H31C  C3   C2    112.62  3.000
 XBV  N4    C3   C2    102.04  3.000
 XBV  C33   N4   C5    115.47  3.000
 XBV  C33   N4   C3    113.08  3.000
 XBV  C5    N4   C3    105.73  3.000
 XBV  H52C  C5   H51C  107.21  3.000
 XBV  H52C  C5   N4    111.48  3.000
 XBV  H51C  C5   N4    111.81  3.000
 XBV  H52C  C5   C1    112.47  3.000
 XBV  H51C  C5   C1    109.16  3.000
 XBV  N4    C5   C1    104.75  3.000
 XBV  N11   C6   O10   124.48  3.000
 XBV  N11   C6   C1    112.08  3.000
 XBV  O10   C6   C1    123.41  3.000
 XBV  O9    C7   N8    123.86  3.000
 XBV  O9    C7   C2    122.96  3.000
 XBV  N8    C7   C2    113.15  3.000
 XBV  H8    N8   C19   115.78  3.000
 XBV  H8    N8   C7    115.87  3.000
 XBV  C19   N8   C7    128.33  3.000
 XBV  H11   N11  C12   114.57  3.000
 XBV  H11   N11  C6    115.79  3.000
 XBV  C12   N11  C6    129.63  3.000
 XBV  C17   C12  N13   122.53  3.000
 XBV  C17   C12  N11   117.54  3.000
 XBV  N13   C12  N11   119.93  3.000
 XBV  C16   N13  C12   118.74  3.000
 XBV  CL1   C14  C16   120.26  3.000
 XBV  CL1   C14  C15   120.85  3.000
 XBV  C16   C14  C15   118.89  3.000
 XBV  H15   C15  C17   120.44  3.000
 XBV  H15   C15  C14   121.17  3.000
 XBV  C17   C15  C14   118.39  3.000
 XBV  H16   C16  C14   120.50  3.000
 XBV  H16   C16  N13   116.73  3.000
 XBV  C14   C16  N13   122.77  3.000
 XBV  H17   C17  C15   120.28  3.000
 XBV  H17   C17  C12   121.04  3.000
 XBV  C15   C17  C12   118.68  3.000
 XBV  C24   C19  C20   117.00  3.000
 XBV  C24   C19  N8    117.54  3.000
 XBV  C20   C19  N8    125.45  3.000
 XBV  H20   C20  C23   118.92  3.000
 XBV  H20   C20  C19   120.57  3.000
 XBV  C23   C20  C19   120.51  3.000
 XBV  N25   C21  C23   119.99  3.000
 XBV  N25   C21  C22   119.91  3.000
 XBV  C23   C21  C22   120.08  3.000
 XBV  H22   C22  C24   119.89  3.000
 XBV  H22   C22  C21   121.72  3.000
 XBV  C24   C22  C21   118.39  3.000
 XBV  H23   C23  C21   120.10  3.000
 XBV  H23   C23  C20   119.22  3.000
 XBV  C21   C23  C20   120.68  3.000
 XBV  F32   C24  C22   118.76  3.000
 XBV  F32   C24  C19   117.91  3.000
 XBV  C22   C24  C19   123.33  3.000
 XBV  C30   N25  C26   123.33  3.000
 XBV  C30   N25  C21   118.17  3.000
 XBV  C26   N25  C21   118.48  3.000
 XBV  H26   C26  C29   122.65  3.000
 XBV  H26   C26  N25   115.73  3.000
 XBV  C29   C26  N25   121.62  3.000
 XBV  H27   C27  C29   119.51  3.000
 XBV  H27   C27  C28   119.76  3.000
 XBV  C29   C27  C28   120.73  3.000
 XBV  H28   C28  C30   116.82  3.000
 XBV  H28   C28  C27   121.26  3.000
 XBV  C30   C28  C27   121.92  3.000
 XBV  H29   C29  C27   121.86  3.000
 XBV  H29   C29  C26   120.09  3.000
 XBV  C27   C29  C26   118.05  3.000
 XBV  O31   C30  C28   125.37  3.000
 XBV  O31   C30  N25   120.29  3.000
 XBV  C28   C30  N25   114.34  3.000
 XBV  H332  C33  H331  106.20  3.000
 XBV  H332  C33  C34   107.95  3.000
 XBV  H331  C33  C34   106.41  3.000
 XBV  H332  C33  N4    112.91  3.000
 XBV  H331  C33  N4    108.85  3.000
 XBV  C34   C33  N4    114.03  3.000
 XBV  H34   C34  F36   108.62  3.000
 XBV  H34   C34  F35   107.81  3.000
 XBV  F36   C34  F35   106.11  3.000
 XBV  H34   C34  C33   111.64  3.000
 XBV  F36   C34  C33   110.83  3.000
 XBV  F35   C34  C33   111.60  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
 XBV  CONST_01  C14  C16  N13  C12     0.00   0.0  0
 XBV  CONST_02  C14  C15  C17  C12     0.00   0.0  0
 XBV  CONST_03  C15  C17  C12  N13     0.00   0.0  0
 XBV  CONST_04  C15  C14  C16  N13     0.00   0.0  0
 XBV  CONST_05  C17  C12  N13  C16     0.00   0.0  0
 XBV  CONST_06  C17  C15  C14  C16     0.00   0.0  0
 XBV  CONST_07  C21  C23  C20  C19     0.00   0.0  0
 XBV  CONST_08  C21  C22  C24  C19     0.00   0.0  0
 XBV  CONST_09  C22  C24  C19  C20     0.00   0.0  0
 XBV  CONST_10  C22  C21  C23  C20     0.00   0.0  0
 XBV  CONST_11  C24  C19  C20  C23     0.00   0.0  0
 XBV  CONST_12  C24  C22  C21  C23     0.00   0.0  0
 XBV  CONST_13  N25  C21  C23  C20   180.00   0.0  0
 XBV  CONST_14  N25  C21  C22  C24   180.00   0.0  0
 XBV  CONST_15  C28  C30  N25  C21   180.00   0.0  0
 XBV  CONST_16  C28  C30  N25  C26     0.00   0.0  0
 XBV  CONST_17  C23  C20  C19  N8    180.00   0.0  0
 XBV  CONST_18  C22  C24  C19  N8    180.00   0.0  0
 XBV  CONST_19  C16  N13  C12  N11   180.00   0.0  0
 XBV  CONST_20  C15  C17  C12  N11   180.00   0.0  0
 XBV  CONST_21  CL1  C14  C16  N13   180.00   0.0  0
 XBV  CONST_22  CL1  C14  C15  C17   180.00   0.0  0
 XBV  CONST_23  F32  C24  C19  C20   180.00   0.0  0
 XBV  CONST_24  F32  C24  C22  C21   180.00   0.0  0
 XBV  CONST_25  O31  C30  N25  C21     0.00   0.0  0
 XBV  CONST_26  O31  C30  N25  C26   180.00   0.0  0
 XBV  CONST_27  H16  C16  N13  C12   180.00   0.0  0
 XBV  CONST_28  H15  C15  C17  C12   180.00   0.0  0
 XBV  CONST_29  H17  C17  C12  N13   180.00   0.0  0
 XBV  CONST_30  H23  C23  C20  C19   180.00   0.0  0
 XBV  CONST_31  H22  C22  C24  C19   180.00   0.0  0
 XBV  CONST_32  H20  C20  C23  C21   180.00   0.0  0
 XBV  CONST_33  C12  N11  C6   C1    180.00   0.0  0
 XBV  CONST_34  C19  N8   C7   C2    180.00   0.0  0
 XBV  CONST_35  N13  C12  N11  C6      0.00   0.0  0
 XBV  CONST_36  C17  C12  N11  C6    180.00   0.0  0
 XBV  CONST_37  C20  C19  N8   C7      0.00   0.0  0
 XBV  CONST_38  C24  C19  N8   C7    180.00   0.0  0
 XBV  CONST_39  H11  N11  C12  N13   180.00   0.0  0
 XBV  CONST_40  H8   N8   C19  C20   180.00   0.0  0
 XBV  CONST_41  C19  N8   C7   O9      0.00   0.0  0
 XBV  CONST_42  C12  N11  C6   O10     0.00   0.0  0
 XBV  Var_01    C3   N4   C5   C1     33.61  30.0  1
 XBV  Var_02    C5   N4   C3   C2    -45.38  30.0  1
 XBV  Var_03    C26  N25  C21  C22  -110.23  30.0  2
 XBV  Var_04    C34  C33  N4   C3   -159.08  30.0  3
 XBV  Var_05    F35  C34  C33  N4    -64.74  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
 XBV  chir_01  C1  C2  C5  C6  positiv
 XBV  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
 XBV  plan-1  N11  0.020
 XBV  plan-1  C12  0.020
 XBV  plan-1  N13  0.020
 XBV  plan-1  C14  0.020
 XBV  plan-1  C15  0.020
 XBV  plan-1  C16  0.020
 XBV  plan-1  C17  0.020
 XBV  plan-1  CL1  0.020
 XBV  plan-1  H17  0.020
 XBV  plan-1  H16  0.020
 XBV  plan-1  H15  0.020
 XBV  plan-2  N8   0.020
 XBV  plan-2  C19  0.020
 XBV  plan-2  C20  0.020
 XBV  plan-2  C21  0.020
 XBV  plan-2  C22  0.020
 XBV  plan-2  C23  0.020
 XBV  plan-2  C24  0.020
 XBV  plan-2  N25  0.020
 XBV  plan-2  F32  0.020
 XBV  plan-2  H20  0.020
 XBV  plan-2  H23  0.020
 XBV  plan-2  H22  0.020
 XBV  plan-3  C21  0.020
 XBV  plan-3  N25  0.020
 XBV  plan-3  C26  0.020
 XBV  plan-3  C27  0.020
 XBV  plan-3  C28  0.020
 XBV  plan-3  C29  0.020
 XBV  plan-3  C30  0.020
 XBV  plan-3  O31  0.020
 XBV  plan-3  H26  0.020
 XBV  plan-3  H29  0.020
 XBV  plan-3  H27  0.020
 XBV  plan-3  H28  0.020
 XBV  plan-4  C2   0.020
 XBV  plan-4  C7   0.020
 XBV  plan-4  N8   0.020
 XBV  plan-4  O9   0.020
 XBV  plan-4  C19  0.020
 XBV  plan-4  H8   0.020
 XBV  plan-5  C1   0.020
 XBV  plan-5  C6   0.020
 XBV  plan-5  O10  0.020
 XBV  plan-5  N11  0.020
 XBV  plan-5  C12  0.020
 XBV  plan-5  H11  0.020

