# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 03:14:05 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 5-chloro-N-[(3R,5S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-5-(hydroxymethyl)pyrrolidin-3-yl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1C[C@H](CN1CC(=O)Nc2ccc(cc2F)N3C=CC=CC3=O)NC(=O)c4sc(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
 LZH  LZH  5-chloro-N-[(3R,5S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-5-(hydroxymethyl)pyrrolidin-3-yl]thiophene-2-carboxamide  ligand  56  34  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LZH
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
 LZH  F32   F   F     0  -0.300   9.9402  63.2103  1.8740
 LZH  C17   C   CR6   0   0.553   9.0823  62.6899  2.7564
 LZH  C11   C   CR16  0  -0.426   9.1262  61.3368  3.0068
 LZH  C9    C   CR6   0   0.315   8.2408  60.8125  3.9375
 LZH  N1    N   NR6   0  -0.614   8.2785  59.4198  4.2408
 LZH  C21   C   CR16  0   0.051   8.6177  59.0418  5.5058
 LZH  C29   C   CR16  0  -0.397   8.6525  57.7411  5.8753
 LZH  C30   C   CR16  0  -0.118   8.3255  56.7650  4.9043
 LZH  C23   C   CR16  0  -0.454   7.9810  57.1304  3.6428
 LZH  C8    C   CR6   0   0.553   7.9250  58.5094  3.2379
 LZH  O25   O   O     0  -0.499   7.5889  58.9085  2.1300
 LZH  C26   C   CR16  0  -0.281   7.3379  61.6284  4.5989
 LZH  C28   C   CR16  0  -0.284   7.3233  62.9901  4.3324
 LZH  C16   C   CR6   0   0.160   8.1955  63.5417  3.4070
 LZH  N15   N   NH1   0  -0.716   8.2354  64.9256  3.1734
 LZH  C14   C   C     0   0.489   7.8620  65.5283  2.0237
 LZH  C13   C   CR15  0  -0.077  11.5200  67.1531  3.5071
 LZH  O27   O   O     0  -0.471   7.3111  64.9565  1.1012
 LZH  C24   C   CH2   0  -0.504  10.8174  68.2755  4.3035
 LZH  C22   C   CH2   0  -0.391   8.1766  67.0250  2.0069
 LZH  N4    N   NR5   0  -0.460   9.3157  67.2987  2.8359
 LZH  C20   C   CH2   0  -0.305  10.6079  66.9448  2.2965
 LZH  N7    N   NH1   0  -0.667  11.5830  65.9356  4.3000
 LZH  C5    C   C     0   0.561  12.1983  64.8295  3.8523
 LZH  O24   O   O     0  -0.486  12.9366  64.8140  2.8754
 LZH  C2    C   CR5   0  -0.289  11.9201  63.5753  4.5751
 LZH  C12   C   CR15  0  -0.217  11.1847  63.3012  5.6927
 LZH  C19   C   CR15  0  -0.125  11.1484  61.9219  6.0060
 LZH  S3    S   S2    0   0.315  12.5827  62.1465  3.8805
 LZH  C10   C   CR5   0  -0.246  11.8583  61.1900  5.1027
 LZH  CL1   CL  CL    0  -0.060  12.0447  59.4955  5.0908
 LZH  C15   C   CR15  0  -0.132   9.4915  68.5425  3.5632
 LZH  H11   H   HCR6  0   0.294   9.8433  60.7109  2.4937
 LZH  H26   H   HCR6  0   0.282   6.6432  61.2064  5.3130
 LZH  H21   H   HCR6  0   0.306   8.8600  59.8449  6.1863
 LZH  H29   H   HCR6  0   0.280   8.9327  57.4734  6.8821
 LZH  H30   H   HCR6  0   0.281   8.3509  55.7163  5.1712
 LZH  H23   H   HCR6  0   0.276   7.7242  56.3911  2.8963
 LZH  H28   H   HCR6  0   0.283   6.6235  63.6367  4.8444
 LZH  H15   H   HNH1  0   0.403   8.7214  65.5257  3.8294
 LZH  H221  H   HCH2  0   0.245   8.2879  67.3319  0.9608
 LZH  H222  H   HCH2  0   0.280   7.2983  67.5442  2.3989
 LZH  H13   H   HCR5  0   0.273  12.5260  67.4405  3.2048
 LZH  H241  H   HCH2  0   0.265  10.6142  67.9537  5.3258
 LZH  H242  H   HCH2  0   0.263  11.4414  69.1662  4.3763
 LZH  H201  H   HCH2  0   0.229  10.9208  67.5742  1.4503
 LZH  H202  H   HCH2  0   0.258  10.6176  65.9145  1.9401
 LZH  H7    H   HNH1  0   0.407  10.9646  65.8628  5.0916
 LZH  HA    H   HCR5  0   0.253   8.6653  68.6697  4.2714
 LZH  H33   H   HOH1  0   0.448   7.6994  70.1977  2.5638
 LZH  H12   H   HCR5  0   0.284  10.6739  64.0467  6.2870
 LZH  H19   H   HCR5  0   0.295  10.6301  61.5025  6.8550
 LZH  C34   C   CH2   0  -0.154   9.5920  69.8050  2.7077
 LZH  O33   O   OH1   0  -0.660   8.4323  70.0678  1.9538
 LZH  H341  H   HCH2  0   0.220  10.4152  69.7152  1.9947
 LZH  H342  H   HCH2  0   0.210   9.8401  70.6455  3.3703

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
 LZH  F32  C17   single    1.336  0.020  1.336
 LZH  C17  C11   aromatic  1.377  0.020  1.377
 LZH  C17  C16   aromatic  1.391  0.020  1.391
 LZH  C11  C9    aromatic  1.387  0.020  1.387
 LZH  C9   N1    single    1.426  0.020  1.426
 LZH  C9   C26   aromatic  1.385  0.020  1.385
 LZH  N1   C21   single    1.363  0.020  1.363
 LZH  N1   C8    single    1.400  0.020  1.400
 LZH  C21  C29   double    1.353  0.020  1.353
 LZH  C29  C30   single    1.415  0.020  1.415
 LZH  C30  C23   double    1.358  0.020  1.358
 LZH  C23  C8    single    1.438  0.020  1.438
 LZH  C8   O25   double    1.225  0.020  1.225
 LZH  C26  C28   aromatic  1.388  0.020  1.388
 LZH  C28  C16   aromatic  1.386  0.020  1.386
 LZH  C16  N15   single    1.404  0.020  1.404
 LZH  N15  C14   single    1.351  0.020  1.351
 LZH  C14  O27   double    1.217  0.020  1.217
 LZH  C14  C22   single    1.530  0.020  1.530
 LZH  C13  C24   single    1.545  0.020  1.545
 LZH  C13  C20   single    1.530  0.020  1.530
 LZH  C13  N7    single    1.454  0.020  1.454
 LZH  C24  C15   single    1.542  0.020  1.542
 LZH  C22  N4    single    1.435  0.020  1.435
 LZH  N4   C20   single    1.444  0.020  1.444
 LZH  N4   C15   single    1.452  0.020  1.452
 LZH  O33  C34   single    1.408  0.020  1.408
 LZH  C34  C15   single    1.528  0.020  1.528
 LZH  N7   C5    single    1.343  0.020  1.343
 LZH  C5   O24   double    1.225  0.020  1.225
 LZH  C5   C2    single    1.474  0.020  1.474
 LZH  C2   C12   aromatic  1.366  0.020  1.366
 LZH  C2   S3    aromatic  1.721  0.020  1.721
 LZH  C12  C19   aromatic  1.415  0.020  1.415
 LZH  C19  C10   aromatic  1.362  0.020  1.362
 LZH  S3   C10   aromatic  1.713  0.020  1.713
 LZH  C10  CL1   single    1.705  0.020  1.705
 LZH  C11  H11   single    0.930  0.020  1.080
 LZH  C26  H26   single    0.930  0.020  1.080
 LZH  C21  H21   single    0.930  0.020  1.080
 LZH  C29  H29   single    0.930  0.020  1.080
 LZH  C30  H30   single    0.930  0.020  1.080
 LZH  C23  H23   single    0.930  0.020  1.080
 LZH  C28  H28   single    0.930  0.020  1.080
 LZH  N15  H15   single    0.860  0.020  1.020
 LZH  C22  H221  single    0.970  0.020  1.090
 LZH  C22  H222  single    0.970  0.020  1.090
 LZH  C13  H13   single    0.970  0.020  1.090
 LZH  C24  H241  single    0.970  0.020  1.090
 LZH  C24  H242  single    0.970  0.020  1.090
 LZH  C20  H201  single    0.970  0.020  1.090
 LZH  C20  H202  single    0.970  0.020  1.090
 LZH  N7   H7    single    0.860  0.020  1.020
 LZH  C15  HA    single    0.970  0.020  1.090
 LZH  O33  H33   single    0.850  0.020  0.980
 LZH  C34  H341  single    0.970  0.020  1.090
 LZH  C34  H342  single    0.970  0.020  1.090
 LZH  C12  H12   single    0.930  0.020  1.080
 LZH  C19  H19   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
 LZH  C16   C17  C11   122.48  3.000
 LZH  C16   C17  F32   118.66  3.000
 LZH  C11   C17  F32   118.84  3.000
 LZH  H11   C11  C9    121.52  3.000
 LZH  H11   C11  C17   120.24  3.000
 LZH  C9    C11  C17   118.23  3.000
 LZH  C26   C9   N1    119.41  3.000
 LZH  C26   C9   C11   120.91  3.000
 LZH  N1    C9   C11   119.67  3.000
 LZH  C8    N1   C21   123.18  3.000
 LZH  C8    N1   C9    118.44  3.000
 LZH  C21   N1   C9    118.35  3.000
 LZH  H21   C21  C29   122.48  3.000
 LZH  H21   C21  N1    115.74  3.000
 LZH  C29   C21  N1    121.78  3.000
 LZH  H29   C29  C30   121.96  3.000
 LZH  H29   C29  C21   120.01  3.000
 LZH  C30   C29  C21   118.02  3.000
 LZH  H30   C30  C23   119.72  3.000
 LZH  H30   C30  C29   119.58  3.000
 LZH  C23   C30  C29   120.70  3.000
 LZH  H23   C23  C8    116.86  3.000
 LZH  H23   C23  C30   121.17  3.000
 LZH  C8    C23  C30   121.97  3.000
 LZH  O25   C8   C23   125.29  3.000
 LZH  O25   C8   N1    120.37  3.000
 LZH  C23   C8   N1    114.34  3.000
 LZH  H26   C26  C28   120.19  3.000
 LZH  H26   C26  C9    120.26  3.000
 LZH  C28   C26  C9    119.55  3.000
 LZH  H28   C28  C16   119.02  3.000
 LZH  H28   C28  C26   120.17  3.000
 LZH  C16   C28  C26   120.81  3.000
 LZH  N15   C16  C28   121.41  3.000
 LZH  N15   C16  C17   120.51  3.000
 LZH  C28   C16  C17   118.01  3.000
 LZH  H15   N15  C14   114.80  3.000
 LZH  H15   N15  C16   119.32  3.000
 LZH  C14   N15  C16   125.00  3.000
 LZH  C22   C14  O27   122.99  3.000
 LZH  C22   C14  N15   112.90  3.000
 LZH  O27   C14  N15   124.10  3.000
 LZH  H13   C13  N7    109.41  3.000
 LZH  H13   C13  C20   111.53  3.000
 LZH  N7    C13  C20   110.07  3.000
 LZH  H13   C13  C24   111.81  3.000
 LZH  N7    C13  C24   110.29  3.000
 LZH  C20   C13  C24   103.63  3.000
 LZH  H242  C24  H241  106.56  3.000
 LZH  H242  C24  C15   112.51  3.000
 LZH  H241  C24  C15   109.93  3.000
 LZH  H242  C24  C13   111.57  3.000
 LZH  H241  C24  C13   110.70  3.000
 LZH  C15   C24  C13   105.63  3.000
 LZH  H222  C22  H221  106.92  3.000
 LZH  H222  C22  N4    109.88  3.000
 LZH  H221  C22  N4    114.66  3.000
 LZH  H222  C22  C14   107.19  3.000
 LZH  H221  C22  C14   107.79  3.000
 LZH  N4    C22  C14   110.09  3.000
 LZH  C15   N4   C20   106.78  3.000
 LZH  C15   N4   C22   123.30  3.000
 LZH  C20   N4   C22   116.60  3.000
 LZH  H202  C20  H201  106.66  3.000
 LZH  H202  C20  N4    111.20  3.000
 LZH  H201  C20  N4    113.67  3.000
 LZH  H202  C20  C13   112.46  3.000
 LZH  H201  C20  C13   111.17  3.000
 LZH  N4    C20  C13   101.80  3.000
 LZH  H7    N7   C5    118.95  3.000
 LZH  H7    N7   C13   117.55  3.000
 LZH  C5    N7   C13   121.85  3.000
 LZH  C2    C5   O24   119.61  3.000
 LZH  C2    C5   N7    116.80  3.000
 LZH  O24   C5   N7    123.56  3.000
 LZH  S3    C2   C12   111.77  3.000
 LZH  S3    C2   C5    115.83  3.000
 LZH  C12   C2   C5    132.35  3.000
 LZH  H12   C12  C19   122.56  3.000
 LZH  H12   C12  C2    124.44  3.000
 LZH  C19   C12  C2    113.00  3.000
 LZH  H19   C19  C10   124.26  3.000
 LZH  H19   C19  C12   124.42  3.000
 LZH  C10   C19  C12   111.32  3.000
 LZH  C10   S3   C2     90.73  3.000
 LZH  CL1   C10  S3    120.25  3.000
 LZH  CL1   C10  C19   126.56  3.000
 LZH  S3    C10  C19   113.18  3.000
 LZH  HA    C15  C34   108.39  3.000
 LZH  HA    C15  N4    109.39  3.000
 LZH  C34   C15  N4    115.81  3.000
 LZH  HA    C15  C24   110.99  3.000
 LZH  C34   C15  C24   110.81  3.000
 LZH  N4    C15  C24   101.32  3.000
 LZH  H342  C34  H341  106.64  3.000
 LZH  H342  C34  C15   108.01  3.000
 LZH  H341  C34  C15   110.30  3.000
 LZH  H342  C34  O33   111.48  3.000
 LZH  H341  C34  O33   106.64  3.000
 LZH  C15   C34  O33   113.57  3.000
 LZH  H33   O33  C34   108.24  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
 LZH  CONST_01  C26  C9   C11  C17    0.00   0.0  0
 LZH  CONST_02  C26  C28  C16  C17    0.00   0.0  0
 LZH  CONST_03  C28  C16  C17  C11    0.00   0.0  0
 LZH  CONST_04  C28  C26  C9   C11    0.00   0.0  0
 LZH  CONST_05  C16  C17  C11  C9     0.00   0.0  0
 LZH  CONST_06  C16  C28  C26  C9     0.00   0.0  0
 LZH  CONST_07  C10  C19  C12  C2     0.00   0.0  0
 LZH  CONST_08  C19  C10  S3   C2     0.00   0.0  0
 LZH  CONST_09  C10  S3   C2   C12    0.00   0.0  0
 LZH  CONST_10  S3   C10  C19  C12    0.00   0.0  0
 LZH  CONST_11  S3   C2   C12  C19    0.00   0.0  0
 LZH  CONST_12  N1   C9   C11  C17  180.00   0.0  0
 LZH  CONST_13  C28  C26  C9   N1   180.00   0.0  0
 LZH  CONST_14  C23  C8   N1   C9   180.00   0.0  0
 LZH  CONST_15  C23  C8   N1   C21    0.00   0.0  0
 LZH  CONST_16  C9   C11  C17  F32  180.00   0.0  0
 LZH  CONST_17  C28  C16  C17  F32  180.00   0.0  0
 LZH  CONST_18  N15  C16  C17  C11  180.00   0.0  0
 LZH  CONST_19  N15  C16  C28  C26  180.00   0.0  0
 LZH  CONST_20  C19  C12  C2   C5   180.00   0.0  0
 LZH  CONST_21  C10  S3   C2   C5   180.00   0.0  0
 LZH  CONST_22  CL1  C10  S3   C2   180.00   0.0  0
 LZH  CONST_23  CL1  C10  C19  C12  180.00   0.0  0
 LZH  CONST_24  O25  C8   N1   C9     0.00   0.0  0
 LZH  CONST_25  O25  C8   N1   C21  180.00   0.0  0
 LZH  CONST_26  H28  C28  C16  C17  180.00   0.0  0
 LZH  CONST_27  H26  C26  C9   C11  180.00   0.0  0
 LZH  CONST_28  H11  C11  C9   N1     0.00   0.0  0
 LZH  CONST_29  H19  C19  C12  C2   180.00   0.0  0
 LZH  CONST_30  H12  C12  C2   S3   180.00   0.0  0
 LZH  CONST_31  C2   C5   N7   C13  180.00   0.0  0
 LZH  CONST_35  O27  C14  N15  C16    0.00   0.0  0
 LZH  CONST_36  C22  C14  N15  C16  180.00   0.0  0
 LZH  CONST_37  O24  C5   N7   C13    0.00   0.0  0
 LZH  CONST_38  H7   N7   C5   C2     0.00   0.0  0
 LZH  Var_01    C21  N1   C9   C11  115.85  30.0  2
 LZH  Var_02    C15  N4   C20  C13   46.56  30.0  1
 LZH  Var_03    C20  N4   C22  C14   75.84  30.0  3
 LZH  Var_04    C12  C2   C5   N7    -3.78  30.0  2
 LZH  Var_05    N4   C22  C14  N15   28.59  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
 LZH  chir_01  C13  C24  C20  N7   positiv
 LZH  chir_02  C15  N4   C24  C34  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
 LZH  plan-1  C5   0.020
 LZH  plan-1  C2   0.020
 LZH  plan-1  C12  0.020
 LZH  plan-1  C19  0.020
 LZH  plan-1  S3   0.020
 LZH  plan-1  C10  0.020
 LZH  plan-1  CL1  0.020
 LZH  plan-1  H12  0.020
 LZH  plan-1  H19  0.020
 LZH  plan-2  F32  0.020
 LZH  plan-2  C17  0.020
 LZH  plan-2  C11  0.020
 LZH  plan-2  C9   0.020
 LZH  plan-2  N1   0.020
 LZH  plan-2  C26  0.020
 LZH  plan-2  C28  0.020
 LZH  plan-2  C16  0.020
 LZH  plan-2  N15  0.020
 LZH  plan-2  H11  0.020
 LZH  plan-2  H26  0.020
 LZH  plan-2  H28  0.020
 LZH  plan-3  C9   0.020
 LZH  plan-3  N1   0.020
 LZH  plan-3  C21  0.020
 LZH  plan-3  C29  0.020
 LZH  plan-3  C30  0.020
 LZH  plan-3  C23  0.020
 LZH  plan-3  C8   0.020
 LZH  plan-3  O25  0.020
 LZH  plan-3  H21  0.020
 LZH  plan-3  H29  0.020
 LZH  plan-3  H30  0.020
 LZH  plan-3  H23  0.020
 LZH  plan-4  C13  0.020
 LZH  plan-4  N7   0.020
 LZH  plan-4  C5   0.020
 LZH  plan-4  O24  0.020
 LZH  plan-4  C2   0.020
 LZH  plan-4  H7   0.020
 LZH  plan-5  C16  0.020
 LZH  plan-5  N15  0.020
 LZH  plan-5  C14  0.020
 LZH  plan-5  O27  0.020
 LZH  plan-5  C22  0.020
 LZH  plan-5  H15  0.020

