# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:29:35 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C(c1ccccc1)c2ccccc2)C(=O)N3CCC[C@H]3C(=O)NCc4ccncc4
#
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
 LXW  LXW  (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide  ligand  60  32  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LXW
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
 LXW  C4   C  CH2   0  -0.329   0.4755  -14.9767  14.0399
 LXW  C5   C  CR6   0   0.166   0.9965  -15.3805  15.3964
 LXW  C6   C  CR16  0  -0.378   0.6978  -14.6920  16.5632
 LXW  N1   N  NR5   0  -0.470  -0.1835  -10.2232  14.6607
 LXW  C7   C  CR16  0  -0.067   1.2186  -15.1527  17.7647
 LXW  C8   C  CR16  0  -0.064   2.2756  -16.8827  16.7543
 LXW  N2   N  NH1   0  -0.642  -0.2610  -13.7426  14.0085
 LXW  C9   C  CR16  0  -0.358   1.8092  -16.5052  15.5069
 LXW  C10  C  CH2   0  -0.480  -0.5221  -10.8270  12.4069
 LXW  C11  C  CH2   0  -0.468  -0.6489   -9.3176  12.5725
 LXW  C12  C  CH2   0  -0.278   0.1294   -9.0515  13.8502
 LXW  N3   N  N     0  -0.412   1.9931  -16.2246  17.8748
 LXW  C13  C  CH1   0  -0.429  -1.2658   -8.6049  17.4506
 LXW  C14  C  CR6   0   0.148  -2.2652   -8.2794  16.3572
 LXW  C15  C  CR16  0  -0.311  -2.2253   -7.0818  15.6464
 LXW  N    N  NH2   0  -0.775   1.0505   -9.5300  17.8524
 LXW  C    C  CH1   0  -0.212   0.0773   -9.1162  16.8618
 LXW  O    O  O     0  -0.480   1.5472  -12.4005  14.1232
 LXW  C1   C  C     0   0.605  -0.2314  -10.3308  15.9935
 LXW  C16  C  CR16  0  -0.236  -3.1182   -6.8387  14.6113
 LXW  C17  C  CR16  0  -0.268  -4.0717   -7.7894  14.2708
 LXW  C18  C  CR16  0  -0.241  -4.1252   -8.9839  14.9754
 LXW  C19  C  CR16  0  -0.296  -3.2301   -9.2226  16.0089
 LXW  C2   C  CR15  0  -0.178  -0.5945  -11.3559  13.8491
 LXW  C20  C  CR6   0   0.168  -1.0722   -7.4589  18.4167
 LXW  C21  C  CR16  0  -0.307  -1.8276   -7.4230  19.5870
 LXW  C22  C  CR16  0  -0.240  -1.7037   -6.3756  20.4889
 LXW  C23  C  CR16  0  -0.269  -0.8123   -5.3411  20.2368
 LXW  C24  C  CR16  0  -0.244  -0.0484   -5.3669  19.0783
 LXW  C25  C  CR16  0  -0.328  -0.1769   -6.4171  18.1785
 LXW  C3   C  C     0   0.566   0.3395  -12.5418  14.0361
 LXW  O1   O  O     0  -0.500  -0.5505  -11.3846  16.5355
 LXW  H1   H  HCH2  0   0.286  -0.1830  -15.7623  13.6678
 LXW  H2   H  HCH2  0   0.268   1.3134  -14.9239  13.3413
 LXW  H3   H  HCR6  0   0.281   0.0782  -13.8059  16.5527
 LXW  H4   H  HCR6  0   0.259   0.9964  -14.6211  18.6839
 LXW  H5   H  HCR6  0   0.261   2.9086  -17.7578  16.8519
 LXW  H6   H  HNH1  0   0.408  -1.2667  -13.7896  14.0042
 LXW  H7   H  HCR6  0   0.264   2.0805  -17.0855  14.6333
 LXW  H8   H  HCH2  0   0.266  -1.2985  -11.2643  11.7815
 LXW  H9   H  HCH2  0   0.251   0.4445  -11.0701  11.9612
 LXW  H10  H  HCH2  0   0.256  -0.2550   -8.7624  11.7223
 LXW  H11  H  HCH2  0   0.247  -1.6926   -9.0289  12.7151
 LXW  H12  H  HCH2  0   0.248   1.2044   -8.9915  13.6589
 LXW  H13  H  HCH2  0   0.260  -0.1861   -8.1292  14.3299
 LXW  H14  H  HCH1  0   0.269  -1.6836   -9.4397  18.0217
 LXW  H15  H  HCR6  0   0.258  -1.4944   -6.3223  15.8964
 LXW  H16  H  HNH2  0   0.356   1.2660   -8.7541  18.4662
 LXW  H17  H  HNH2  0   0.346   0.6527  -10.2551  18.4370
 LXW  H19  H  HCH1  0   0.259   0.5341   -8.3227  16.2677
 LXW  H20  H  HCR6  0   0.254  -3.0689   -5.9019  14.0712
 LXW  H21  H  HCR6  0   0.255  -4.7695   -7.5996  13.4654
 LXW  H22  H  HCR6  0   0.254  -4.8666   -9.7317  14.7247
 LXW  H23  H  HCR6  0   0.249  -3.2769  -10.1588  16.5522
 LXW  H24  H  HCR5  0   0.273  -1.6224  -11.6339  14.1021
 LXW  H25  H  HCR6  0   0.251  -2.5224   -8.2282  19.7954
 LXW  H26  H  HCR6  0   0.256  -2.3006   -6.3706  21.3920
 LXW  H27  H  HCR6  0   0.256  -0.7101   -4.5250  20.9402
 LXW  H28  H  HCR6  0   0.257   0.6541   -4.5695  18.8729
 LXW  H29  H  HCR6  0   0.258   0.4341   -6.4134  17.2837

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
 LXW  C10  C11  single    1.524  0.020  1.524
 LXW  C10  C2   single    1.538  0.020  1.538
 LXW  C11  C12  single    1.520  0.020  1.520
 LXW  C2   C3   single    1.521  0.020  1.521
 LXW  C2   N1   single    1.453  0.020  1.453
 LXW  C12  N1   single    1.459  0.020  1.459
 LXW  O    C3   double    1.219  0.020  1.219
 LXW  C3   N2   single    1.343  0.020  1.343
 LXW  N2   C4   single    1.438  0.020  1.438
 LXW  C17  C18  aromatic  1.388  0.020  1.388
 LXW  C17  C16  aromatic  1.389  0.020  1.389
 LXW  C4   C5   single    1.508  0.020  1.508
 LXW  N1   C1   single    1.338  0.020  1.338
 LXW  C18  C19  aromatic  1.388  0.020  1.388
 LXW  C16  C15  aromatic  1.388  0.020  1.388
 LXW  C5   C9   aromatic  1.392  0.020  1.392
 LXW  C5   C6   aromatic  1.387  0.020  1.387
 LXW  C19  C14  aromatic  1.394  0.020  1.394
 LXW  C1   O1   double    1.227  0.020  1.227
 LXW  C1   C    single    1.525  0.020  1.525
 LXW  C15  C14  aromatic  1.393  0.020  1.393
 LXW  C9   C8   aromatic  1.384  0.020  1.384
 LXW  C14  C13  single    1.517  0.020  1.517
 LXW  C6   C7   aromatic  1.388  0.020  1.388
 LXW  C    C13  single    1.553  0.020  1.553
 LXW  C    N    single    1.449  0.020  1.449
 LXW  C13  C20  single    1.511  0.020  1.511
 LXW  C8   N3   aromatic  1.330  0.020  1.330
 LXW  C7   N3   aromatic  1.327  0.020  1.327
 LXW  C25  C20  aromatic  1.394  0.020  1.394
 LXW  C25  C24  aromatic  1.389  0.020  1.389
 LXW  C20  C21  aromatic  1.393  0.020  1.393
 LXW  C24  C23  aromatic  1.388  0.020  1.388
 LXW  C21  C22  aromatic  1.388  0.020  1.388
 LXW  C23  C22  aromatic  1.389  0.020  1.389
 LXW  C4   H1   single    0.970  0.020  1.090
 LXW  C4   H2   single    0.970  0.020  1.090
 LXW  C6   H3   single    0.930  0.020  1.080
 LXW  C7   H4   single    0.930  0.020  1.080
 LXW  C8   H5   single    0.930  0.020  1.080
 LXW  N2   H6   single    0.860  0.020  1.020
 LXW  C9   H7   single    0.930  0.020  1.080
 LXW  C10  H8   single    0.970  0.020  1.090
 LXW  C10  H9   single    0.970  0.020  1.090
 LXW  C11  H10  single    0.970  0.020  1.090
 LXW  C11  H11  single    0.970  0.020  1.090
 LXW  C12  H12  single    0.970  0.020  1.090
 LXW  C12  H13  single    0.970  0.020  1.090
 LXW  C13  H14  single    0.970  0.020  1.090
 LXW  C15  H15  single    0.930  0.020  1.080
 LXW  N    H16  single    0.890  0.020  1.040
 LXW  N    H17  single    0.890  0.020  1.040
 LXW  C    H19  single    0.970  0.020  1.090
 LXW  C16  H20  single    0.930  0.020  1.080
 LXW  C17  H21  single    0.930  0.020  1.080
 LXW  C18  H22  single    0.930  0.020  1.080
 LXW  C19  H23  single    0.930  0.020  1.080
 LXW  C2   H24  single    0.970  0.020  1.090
 LXW  C21  H25  single    0.930  0.020  1.080
 LXW  C22  H26  single    0.930  0.020  1.080
 LXW  C23  H27  single    0.930  0.020  1.080
 LXW  C24  H28  single    0.930  0.020  1.080
 LXW  C25  H29  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
 LXW  H2   C4   H1   106.25  3.000
 LXW  H2   C4   N2   109.73  3.000
 LXW  H1   C4   N2   107.55  3.000
 LXW  H2   C4   C5   108.86  3.000
 LXW  H1   C4   C5   108.82  3.000
 LXW  N2   C4   C5   115.25  3.000
 LXW  C9   C5   C6   117.38  3.000
 LXW  C6   C5   C4   123.31  3.000
 LXW  C9   C5   C4   119.31  3.000
 LXW  H3   C6   C7   119.69  3.000
 LXW  H3   C6   C5   121.46  3.000
 LXW  C7   C6   C5   118.84  3.000
 LXW  C2   N1   C1   118.93  3.000
 LXW  C1   N1   C12  128.74  3.000
 LXW  C2   N1   C12  112.12  3.000
 LXW  H4   C7   N3   116.43  3.000
 LXW  H4   C7   C6   119.60  3.000
 LXW  N3   C7   C6   123.97  3.000
 LXW  H5   C8   N3   116.58  3.000
 LXW  H5   C8   C9   119.86  3.000
 LXW  N3   C8   C9   123.56  3.000
 LXW  H6   N2   C3   119.24  3.000
 LXW  H6   N2   C4   118.15  3.000
 LXW  C3   N2   C4   122.56  3.000
 LXW  H7   C9   C8   119.75  3.000
 LXW  H7   C9   C5   121.00  3.000
 LXW  C8   C9   C5   119.25  3.000
 LXW  H9   C10  H8   107.91  3.000
 LXW  H9   C10  C2   110.36  3.000
 LXW  H8   C10  C2   111.54  3.000
 LXW  H9   C10  C11  109.79  3.000
 LXW  H8   C10  C11  113.64  3.000
 LXW  C2   C10  C11  103.58  3.000
 LXW  H11  C11  H10  108.22  3.000
 LXW  H11  C11  C12  109.47  3.000
 LXW  H10  C11  C12  112.45  3.000
 LXW  H11  C11  C10  110.82  3.000
 LXW  H10  C11  C10  112.96  3.000
 LXW  C12  C11  C10  102.84  3.000
 LXW  H13  C12  H12  108.43  3.000
 LXW  H13  C12  C11  111.79  3.000
 LXW  H12  C12  C11  111.47  3.000
 LXW  H13  C12  N1   111.98  3.000
 LXW  H12  C12  N1   110.62  3.000
 LXW  C11  C12  N1   102.52  3.000
 LXW  C8   N3   C7   116.99  3.000
 LXW  H14  C13  C20  107.08  3.000
 LXW  H14  C13  C    106.07  3.000
 LXW  C20  C13  C    112.41  3.000
 LXW  H14  C13  C14  106.76  3.000
 LXW  C20  C13  C14  112.49  3.000
 LXW  C    C13  C14  111.54  3.000
 LXW  C19  C14  C15  118.30  3.000
 LXW  C15  C14  C13  122.24  3.000
 LXW  C19  C14  C13  119.42  3.000
 LXW  H15  C15  C16  118.90  3.000
 LXW  H15  C15  C14  120.28  3.000
 LXW  C16  C15  C14  120.82  3.000
 LXW  H17  N    H16  106.39  3.000
 LXW  H17  N    C    109.59  3.000
 LXW  H16  N    C    109.79  3.000
 LXW  H19  C    C1   110.72  3.000
 LXW  H19  C    N    107.37  3.000
 LXW  C1   C    N    107.33  3.000
 LXW  H19  C    C13  109.21  3.000
 LXW  N    C    C13  114.56  3.000
 LXW  C1   C    C13  107.65  3.000
 LXW  O1   C1   C    119.02  3.000
 LXW  C    C1   N1   119.74  3.000
 LXW  O1   C1   N1   121.22  3.000
 LXW  H20  C16  C17  120.09  3.000
 LXW  H20  C16  C15  119.62  3.000
 LXW  C17  C16  C15  120.30  3.000
 LXW  H21  C17  C18  120.25  3.000
 LXW  H21  C17  C16  120.33  3.000
 LXW  C18  C17  C16  119.41  3.000
 LXW  H22  C18  C19  119.69  3.000
 LXW  H22  C18  C17  120.23  3.000
 LXW  C19  C18  C17  120.08  3.000
 LXW  H23  C19  C18  119.62  3.000
 LXW  H23  C19  C14  119.30  3.000
 LXW  C18  C19  C14  121.08  3.000
 LXW  H24  C2   C3   110.50  3.000
 LXW  H24  C2   C10  110.39  3.000
 LXW  C3   C2   C10  110.76  3.000
 LXW  H24  C2   N1   109.55  3.000
 LXW  C3   C2   N1   111.44  3.000
 LXW  C10  C2   N1   104.04  3.000
 LXW  C25  C20  C21  118.19  3.000
 LXW  C21  C20  C13  119.14  3.000
 LXW  C25  C20  C13  122.66  3.000
 LXW  H25  C21  C22  119.54  3.000
 LXW  H25  C21  C20  119.34  3.000
 LXW  C22  C21  C20  121.13  3.000
 LXW  H26  C22  C23  120.13  3.000
 LXW  H26  C22  C21  119.76  3.000
 LXW  C23  C22  C21  120.10  3.000
 LXW  H27  C23  C24  120.31  3.000
 LXW  H27  C23  C22  120.29  3.000
 LXW  C24  C23  C22  119.41  3.000
 LXW  H28  C24  C25  119.61  3.000
 LXW  H28  C24  C23  120.13  3.000
 LXW  C25  C24  C23  120.26  3.000
 LXW  H29  C25  C24  118.70  3.000
 LXW  H29  C25  C20  120.38  3.000
 LXW  C24  C25  C20  120.91  3.000
 LXW  C2   C3   O    121.78  3.000
 LXW  O    C3   N2   123.24  3.000
 LXW  C2   C3   N2   114.84  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
 LXW  CONST_01  N3   C8   C9   C5     0.00   0.0  0
 LXW  CONST_02  N3   C7   C6   C5     0.00   0.0  0
 LXW  CONST_03  C8   C9   C5   C6     0.00   0.0  0
 LXW  CONST_04  C8   N3   C7   C6     0.00   0.0  0
 LXW  CONST_05  C9   C5   C6   C7     0.00   0.0  0
 LXW  CONST_06  C9   C8   N3   C7     0.00   0.0  0
 LXW  CONST_07  C17  C18  C19  C14    0.00   0.0  0
 LXW  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 LXW  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 LXW  CONST_10  C18  C19  C14  C15    0.00   0.0  0
 LXW  CONST_11  C19  C18  C17  C16    0.00   0.0  0
 LXW  CONST_12  C19  C14  C15  C16    0.00   0.0  0
 LXW  CONST_13  C23  C24  C25  C20    0.00   0.0  0
 LXW  CONST_14  C23  C22  C21  C20    0.00   0.0  0
 LXW  CONST_15  C24  C25  C20  C21    0.00   0.0  0
 LXW  CONST_16  C24  C23  C22  C21    0.00   0.0  0
 LXW  CONST_17  C25  C20  C21  C22    0.00   0.0  0
 LXW  CONST_18  C25  C24  C23  C22    0.00   0.0  0
 LXW  CONST_19  C8   C9   C5   C4   180.00   0.0  0
 LXW  CONST_20  C7   C6   C5   C4   180.00   0.0  0
 LXW  CONST_21  C18  C19  C14  C13  180.00   0.0  0
 LXW  CONST_22  C16  C15  C14  C13  180.00   0.0  0
 LXW  CONST_23  C24  C25  C20  C13  180.00   0.0  0
 LXW  CONST_24  C22  C21  C20  C13  180.00   0.0  0
 LXW  CONST_25  H5   C8   C9   C5   180.00   0.0  0
 LXW  CONST_26  H4   C7   C6   C5   180.00   0.0  0
 LXW  CONST_27  H7   C9   C5   C6   180.00   0.0  0
 LXW  CONST_28  H3   C6   C5   C9   180.00   0.0  0
 LXW  CONST_29  H22  C18  C19  C14  180.00   0.0  0
 LXW  CONST_30  H20  C16  C15  C14  180.00   0.0  0
 LXW  CONST_31  H21  C17  C16  C15  180.00   0.0  0
 LXW  CONST_32  H23  C19  C14  C15  180.00   0.0  0
 LXW  CONST_33  H15  C15  C16  C17  180.00   0.0  0
 LXW  CONST_34  H28  C24  C25  C20  180.00   0.0  0
 LXW  CONST_35  H26  C22  C21  C20  180.00   0.0  0
 LXW  CONST_36  H29  C25  C20  C21  180.00   0.0  0
 LXW  CONST_37  H27  C23  C22  C21  180.00   0.0  0
 LXW  CONST_38  H25  C21  C22  C23  180.00   0.0  0
 LXW  CONST_39  O1   C1   N1   C12  180.00   0.0  0
 LXW  CONST_40  C    C1   N1   C12    0.00   0.0  0
 LXW  CONST_41  C2   N1   C1   C    180.00   0.0  0
 LXW  CONST_42  O1   C1   N1   C2     0.00   0.0  0
 LXW  CONST_43  C2   C3   N2   C4   180.00   0.0  0
 LXW  CONST_44  H6   N2   C3   C2     0.00   0.0  0
 LXW  CONST_45  O    C3   N2   C4     0.00   0.0  0
 LXW  Var_01    C10  C11  C12  N1   -36.45  30.0  1
 LXW  Var_02    C2   N1   C12  C11   22.96  30.0  1
 LXW  Var_03    C2   C10  C11  C12   37.05  30.0  1
 LXW  Var_04    C25  C20  C13  C14  -85.06  30.0  2
 LXW  Var_05    C20  C13  C14  C15   46.96  30.0  2
 LXW  Var_06    N2   C4   C5   C6     5.62  30.0  2
 LXW  Var_07    C3   N2   C4   C5    77.65  30.0  1

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
 LXW  chir_01  C   C1  C13  N   negativ
 LXW  chir_02  C2  N1  C10  C3  negativ

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
 LXW  plan-1  C4   0.020
 LXW  plan-1  C5   0.020
 LXW  plan-1  C6   0.020
 LXW  plan-1  C7   0.020
 LXW  plan-1  C8   0.020
 LXW  plan-1  C9   0.020
 LXW  plan-1  N3   0.020
 LXW  plan-1  H3   0.020
 LXW  plan-1  H4   0.020
 LXW  plan-1  H5   0.020
 LXW  plan-1  H7   0.020
 LXW  plan-2  C13  0.020
 LXW  plan-2  C14  0.020
 LXW  plan-2  C15  0.020
 LXW  plan-2  C16  0.020
 LXW  plan-2  C17  0.020
 LXW  plan-2  C18  0.020
 LXW  plan-2  C19  0.020
 LXW  plan-2  H15  0.020
 LXW  plan-2  H20  0.020
 LXW  plan-2  H21  0.020
 LXW  plan-2  H22  0.020
 LXW  plan-2  H23  0.020
 LXW  plan-3  C13  0.020
 LXW  plan-3  C20  0.020
 LXW  plan-3  C21  0.020
 LXW  plan-3  C22  0.020
 LXW  plan-3  C23  0.020
 LXW  plan-3  C24  0.020
 LXW  plan-3  C25  0.020
 LXW  plan-3  H25  0.020
 LXW  plan-3  H26  0.020
 LXW  plan-3  H27  0.020
 LXW  plan-3  H28  0.020
 LXW  plan-3  H29  0.020
 LXW  plan-4  C4   0.020
 LXW  plan-4  N2   0.020
 LXW  plan-4  O    0.020
 LXW  plan-4  C2   0.020
 LXW  plan-4  C3   0.020
 LXW  plan-4  H6   0.020
 LXW  plan-5  N1   0.020
 LXW  plan-5  C12  0.020
 LXW  plan-5  C    0.020
 LXW  plan-5  C1   0.020
 LXW  plan-5  C2   0.020
 LXW  plan-5  O1   0.020

