# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:17:26 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-hydroxypyrrolidin-3-yl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CN(C[C@@H]1NC(=O)c2sc(Cl)cc2)CC(=O)Nc3ccc(cc3F)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
 H25  H25  5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-hydroxypyrrolidin-3-yl]thiophene-2-carboxamide  ligand  53  33  .  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_H25
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
 H25  F3    F   F     0  -0.299   9.4745  62.2088  1.2933
 H25  C17   C   CR6   0   0.535   8.6029  61.8302  2.2309
 H25  C11   C   CR16  0  -0.430   8.2903  60.4927  2.3431
 H25  C9    C   CR6   0   0.301   7.4329  60.0949  3.3578
 H25  N1    N   NR6   0  -0.613   7.1232  58.7117  3.5162
 H25  C21   C   CR16  0   0.049   7.6619  58.0422  4.5741
 H25  C29   C   CR16  0  -0.399   7.3894  56.7354  4.7979
 H25  C30   C   CR16  0  -0.118   6.5198  56.0734  3.8980
 H25  C23   C   CR16  0  -0.453   5.9770  56.7342  2.8433
 H25  C8    C   CR6   0   0.554   6.2529  58.1238  2.5937
 H25  O25   O   O     0  -0.501   5.7895  58.7863  1.6736
 H25  C26   C   CR16  0  -0.271   6.9009  61.0207  4.2392
 H25  C28   C   CR16  0  -0.294   7.2181  62.3629  4.0942
 H25  C16   C   CR6   0   0.181   8.0698  62.7909  3.0846
 H25  N15   N   NH1   0  -0.720   8.4090  64.1425  2.9556
 H25  C14   C   C     0   0.504   8.1921  64.8720  1.8384
 H25  O27   O   O     0  -0.474   7.6850  64.4288  0.8252
 H25  C22   C   CH2   0  -0.394   8.5851  66.3328  1.9776
 H25  N4    N   NT    0  -0.466   9.5342  66.5562  3.0338
 H25  C31   C   CH2   0  -0.295   9.5836  67.9029  3.5652
 H25  C34   C   CH1   0   0.025  10.7477  67.8126  4.5374
 H25  O33   O   OH1   0  -0.660  11.2375  69.0868  4.8455
 H25  C20   C   CH2   0  -0.280  10.9112  66.2228  2.6951
 H25  C6    C   CH1   0  -0.119  11.7462  66.8879  3.8037
 H25  N7    N   NH1   0  -0.670  12.3710  65.9640  4.7240
 H25  C5    C   C     0   0.569  13.4932  65.2989  4.4160
 H25  O24   O   O     0  -0.491  14.0843  65.4252  3.3498
 H25  C2    C   CR5   0  -0.292  14.0211  64.3801  5.4406
 H25  C12   C   CR15  0  -0.220  13.6148  64.0925  6.7126
 H25  C19   C   CR15  0  -0.119  14.4364  63.1352  7.3535
 H25  S3    S   S2    0   0.321  15.4256  63.4846  5.0023
 H25  C10   C   CR5   0  -0.251  15.4490  62.7264  6.5390
 H25  CL1   CL  CL    0  -0.068  16.6588  61.5870  6.9197
 H25  H11   H   HCR6  0   0.294   8.7349  59.7738  1.6675
 H25  H26   H   HCR6  0   0.281   6.2350  60.7025  5.0302
 H25  H21   H   HCR6  0   0.315   8.3182  58.6194  5.2095
 H25  H29   H   HCR6  0   0.281   7.8329  56.2265  5.6395
 H25  H30   H   HCR6  0   0.282   6.2845  55.0286  4.0547
 H25  H23   H   HCR6  0   0.277   5.3085  56.2362  2.1545
 H25  H28   H   HCR6  0   0.286   6.7945  63.0931  4.7709
 H25  H15   H   HNH1  0   0.413   8.7538  64.6509  3.7613
 H25  H221  H   HCH2  0   0.247   8.9329  66.6874  0.9969
 H25  H222  H   HCH2  0   0.288   7.6638  66.8795  2.2011
 H25  H201  H   HCH2  0   0.251  11.0607  65.1429  2.6434
 H25  H202  H   HCH2  0   0.227  11.1929  66.6419  1.7184
 H25  H311  H   HCH2  0   0.215   9.7962  68.6595  2.7923
 H25  H312  H   HCH2  0   0.258   8.6443  68.1699  4.0517
 H25  H6    H   HCH1  0   0.275  12.5278  67.4981  3.3497
 H25  H34   H   HCH1  0   0.227  10.3927  67.2968  5.4405
 H25  H33   H   HOH1  0   0.457  11.8732  69.0078  5.5631
 H25  H7    H   HNH1  0   0.409  11.8909  65.7504  5.5840
 H25  H12   H   HCR5  0   0.281  12.7607  64.5427  7.1992
 H25  H19   H   HCR5  0   0.297  14.2847  62.7739  8.3594

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
 H25  F3   C17   single    1.335  0.020  1.335
 H25  C17  C11   aromatic  1.378  0.020  1.378
 H25  C17  C16   aromatic  1.391  0.020  1.391
 H25  C11  C9    aromatic  1.387  0.020  1.387
 H25  C9   N1    single    1.426  0.020  1.426
 H25  C9   C26   aromatic  1.385  0.020  1.385
 H25  N1   C21   single    1.363  0.020  1.363
 H25  N1   C8    single    1.398  0.020  1.398
 H25  C21  C29   double    1.353  0.020  1.353
 H25  C29  C30   single    1.416  0.020  1.416
 H25  C30  C23   double    1.358  0.020  1.358
 H25  C23  C8    single    1.439  0.020  1.439
 H25  C8   O25   double    1.225  0.020  1.225
 H25  C26  C28   aromatic  1.387  0.020  1.387
 H25  C28  C16   aromatic  1.388  0.020  1.388
 H25  C16  N15   single    1.399  0.020  1.399
 H25  N15  C14   single    1.352  0.020  1.352
 H25  C14  O27   double    1.217  0.020  1.217
 H25  C14  C22   single    1.519  0.020  1.519
 H25  C22  N4    single    1.437  0.020  1.437
 H25  N4   C20   single    1.457  0.020  1.457
 H25  N4   C31   single    1.449  0.020  1.449
 H25  C20  C6    single    1.539  0.020  1.539
 H25  C34  C31   single    1.519  0.020  1.519
 H25  C34  O33   single    1.399  0.020  1.399
 H25  C34  C6    single    1.546  0.020  1.546
 H25  N7   C5    single    1.340  0.020  1.340
 H25  N7   C6    single    1.446  0.020  1.446
 H25  C5   O24   double    1.226  0.020  1.226
 H25  C5   C2    single    1.474  0.020  1.474
 H25  C2   C12   aromatic  1.366  0.020  1.366
 H25  C2   S3    aromatic  1.722  0.020  1.722
 H25  C12  C19   aromatic  1.415  0.020  1.415
 H25  C19  C10   aromatic  1.362  0.020  1.362
 H25  S3   C10   aromatic  1.714  0.020  1.714
 H25  C10  CL1   single    1.705  0.020  1.705
 H25  C11  H11   single    0.930  0.020  1.080
 H25  C26  H26   single    0.930  0.020  1.080
 H25  C21  H21   single    0.930  0.020  1.080
 H25  C29  H29   single    0.930  0.020  1.080
 H25  C30  H30   single    0.930  0.020  1.080
 H25  C23  H23   single    0.930  0.020  1.080
 H25  C28  H28   single    0.930  0.020  1.080
 H25  N15  H15   single    0.860  0.020  1.020
 H25  C22  H221  single    0.970  0.020  1.090
 H25  C22  H222  single    0.970  0.020  1.090
 H25  C20  H201  single    0.970  0.020  1.090
 H25  C20  H202  single    0.970  0.020  1.090
 H25  C31  H311  single    0.970  0.020  1.090
 H25  C31  H312  single    0.970  0.020  1.090
 H25  C6   H6    single    0.970  0.020  1.090
 H25  C34  H34   single    0.970  0.020  1.090
 H25  O33  H33   single    0.850  0.020  0.980
 H25  N7   H7    single    0.860  0.020  1.020
 H25  C12  H12   single    0.930  0.020  1.080
 H25  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
 H25  C16   C17  C11   122.23  3.000
 H25  C16   C17  F3    119.03  3.000
 H25  C11   C17  F3    118.72  3.000
 H25  H11   C11  C9    121.36  3.000
 H25  H11   C11  C17   120.05  3.000
 H25  C9    C11  C17   118.57  3.000
 H25  C26   C9   N1    119.62  3.000
 H25  C26   C9   C11   120.77  3.000
 H25  N1    C9   C11   119.58  3.000
 H25  C8    N1   C21   123.48  3.000
 H25  C8    N1   C9    118.02  3.000
 H25  C21   N1   C9    118.48  3.000
 H25  H21   C21  C29   122.74  3.000
 H25  H21   C21  N1    115.73  3.000
 H25  C29   C21  N1    121.54  3.000
 H25  H29   C29  C30   121.85  3.000
 H25  H29   C29  C21   120.11  3.000
 H25  C30   C29  C21   118.04  3.000
 H25  H30   C30  C23   119.69  3.000
 H25  H30   C30  C29   119.53  3.000
 H25  C23   C30  C29   120.78  3.000
 H25  H23   C23  C8    116.93  3.000
 H25  H23   C23  C30   121.19  3.000
 H25  C8    C23  C30   121.89  3.000
 H25  O25   C8   C23   125.47  3.000
 H25  O25   C8   N1    120.25  3.000
 H25  C23   C8   N1    114.28  3.000
 H25  H26   C26  C28   120.13  3.000
 H25  H26   C26  C9    120.35  3.000
 H25  C28   C26  C9    119.52  3.000
 H25  H28   C28  C16   119.13  3.000
 H25  H28   C28  C26   119.89  3.000
 H25  C16   C28  C26   120.98  3.000
 H25  N15   C16  C28   120.90  3.000
 H25  N15   C16  C17   121.16  3.000
 H25  C28   C16  C17   117.92  3.000
 H25  H15   N15  C14   116.16  3.000
 H25  H15   N15  C16   119.60  3.000
 H25  C14   N15  C16   123.95  3.000
 H25  C22   C14  O27   122.31  3.000
 H25  C22   C14  N15   113.68  3.000
 H25  O27   C14  N15   123.96  3.000
 H25  H222  C22  H221  106.70  3.000
 H25  H222  C22  N4    109.16  3.000
 H25  H221  C22  N4    113.36  3.000
 H25  H222  C22  C14   106.34  3.000
 H25  H221  C22  C14   108.07  3.000
 H25  N4    C22  C14   112.80  3.000
 H25  C20   N4   C31   105.42  3.000
 H25  C31   N4   C22   115.88  3.000
 H25  C20   N4   C22   114.69  3.000
 H25  H312  C31  H311  108.11  3.000
 H25  H312  C31  C34   112.88  3.000
 H25  H311  C31  C34   109.98  3.000
 H25  H312  C31  N4    111.21  3.000
 H25  H311  C31  N4    112.80  3.000
 H25  C34   C31  N4    101.86  3.000
 H25  H34   C34  C6    108.53  3.000
 H25  H34   C34  O33   111.07  3.000
 H25  C6    C34  O33   115.03  3.000
 H25  H34   C34  C31   107.83  3.000
 H25  C6    C34  C31   103.10  3.000
 H25  O33   C34  C31   110.79  3.000
 H25  H33   O33  C34   108.71  3.000
 H25  H202  C20  H201  107.46  3.000
 H25  H202  C20  C6    109.64  3.000
 H25  H201  C20  C6    112.79  3.000
 H25  H202  C20  N4    111.19  3.000
 H25  H201  C20  N4    111.53  3.000
 H25  C6    C20  N4    104.27  3.000
 H25  H6    C6   N7    108.23  3.000
 H25  H6    C6   C20   109.32  3.000
 H25  N7    C6   C20   114.63  3.000
 H25  H6    C6   C34   109.01  3.000
 H25  N7    C6   C34   111.05  3.000
 H25  C20   C6   C34   104.47  3.000
 H25  H7    N7   C5    119.33  3.000
 H25  H7    N7   C6    118.20  3.000
 H25  C5    N7   C6    122.18  3.000
 H25  C2    C5   O24   119.75  3.000
 H25  C2    C5   N7    116.71  3.000
 H25  O24   C5   N7    123.54  3.000
 H25  S3    C2   C12   111.71  3.000
 H25  S3    C2   C5    116.06  3.000
 H25  C12   C2   C5    132.23  3.000
 H25  H12   C12  C19   122.45  3.000
 H25  H12   C12  C2    124.50  3.000
 H25  C19   C12  C2    113.05  3.000
 H25  H19   C19  C10   124.14  3.000
 H25  H19   C19  C12   124.53  3.000
 H25  C10   C19  C12   111.33  3.000
 H25  C10   S3   C2     90.74  3.000
 H25  CL1   C10  S3    120.37  3.000
 H25  CL1   C10  C19   126.47  3.000
 H25  S3    C10  C19   113.16  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
 H25  CONST_01  C26  C9   C11  C17    0.00   0.0  0
 H25  CONST_02  C26  C28  C16  C17    0.00   0.0  0
 H25  CONST_03  C28  C16  C17  C11    0.00   0.0  0
 H25  CONST_04  C28  C26  C9   C11    0.00   0.0  0
 H25  CONST_05  C16  C17  C11  C9     0.00   0.0  0
 H25  CONST_06  C16  C28  C26  C9     0.00   0.0  0
 H25  CONST_07  C10  C19  C12  C2     0.00   0.0  0
 H25  CONST_08  C19  C10  S3   C2     0.00   0.0  0
 H25  CONST_09  C10  S3   C2   C12    0.00   0.0  0
 H25  CONST_10  S3   C10  C19  C12    0.00   0.0  0
 H25  CONST_11  S3   C2   C12  C19    0.00   0.0  0
 H25  CONST_12  N1   C9   C11  C17  180.00   0.0  0
 H25  CONST_13  C28  C26  C9   N1   180.00   0.0  0
 H25  CONST_14  C23  C8   N1   C9   180.00   0.0  0
 H25  CONST_15  C23  C8   N1   C21    0.00   0.0  0
 H25  CONST_16  C9   C11  C17  F3   180.00   0.0  0
 H25  CONST_17  C28  C16  C17  F3   180.00   0.0  0
 H25  CONST_18  N15  C16  C17  C11  180.00   0.0  0
 H25  CONST_19  N15  C16  C28  C26  180.00   0.0  0
 H25  CONST_20  C19  C12  C2   C5   180.00   0.0  0
 H25  CONST_21  C10  S3   C2   C5   180.00   0.0  0
 H25  CONST_22  CL1  C10  S3   C2   180.00   0.0  0
 H25  CONST_23  CL1  C10  C19  C12  180.00   0.0  0
 H25  CONST_24  O25  C8   N1   C9     0.00   0.0  0
 H25  CONST_25  O25  C8   N1   C21  180.00   0.0  0
 H25  CONST_26  H28  C28  C16  C17  180.00   0.0  0
 H25  CONST_27  H26  C26  C9   C11  180.00   0.0  0
 H25  CONST_28  H11  C11  C9   N1     0.00   0.0  0
 H25  CONST_29  H19  C19  C12  C2   180.00   0.0  0
 H25  CONST_30  H12  C12  C2   S3   180.00   0.0  0
 H25  CONST_31  C2   C5   N7   C6   180.00   0.0  0
 H25  CONST_35  O27  C14  N15  C16    0.00   0.0  0
 H25  CONST_36  C22  C14  N15  C16  180.00   0.0  0
 H25  CONST_37  O24  C5   N7   C6     0.00   0.0  0
 H25  CONST_38  H7   N7   C5   C2     0.00   0.0  0
 H25  Var_01    C21  N1   C9   C11  107.44  30.0  2
 H25  Var_02    C6   C20  N4   C31   36.60  30.0  1
 H25  Var_03    C20  N4   C31  C34  -46.97  30.0  1
 H25  Var_04    C12  C2   C5   N7    -3.06  30.0  2
 H25  Var_05    N4   C22  C14  N15   21.58  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
 H25  chir_01  C34  C31  O33  C6   positiv
 H25  chir_02  C6   N7   C34  C20  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
 H25  plan-1  C5   0.020
 H25  plan-1  C2   0.020
 H25  plan-1  C12  0.020
 H25  plan-1  C19  0.020
 H25  plan-1  S3   0.020
 H25  plan-1  C10  0.020
 H25  plan-1  CL1  0.020
 H25  plan-1  H12  0.020
 H25  plan-1  H19  0.020
 H25  plan-2  F3   0.020
 H25  plan-2  C17  0.020
 H25  plan-2  C11  0.020
 H25  plan-2  C9   0.020
 H25  plan-2  N1   0.020
 H25  plan-2  C26  0.020
 H25  plan-2  C28  0.020
 H25  plan-2  C16  0.020
 H25  plan-2  N15  0.020
 H25  plan-2  H11  0.020
 H25  plan-2  H26  0.020
 H25  plan-2  H28  0.020
 H25  plan-3  C9   0.020
 H25  plan-3  N1   0.020
 H25  plan-3  C21  0.020
 H25  plan-3  C29  0.020
 H25  plan-3  C30  0.020
 H25  plan-3  C23  0.020
 H25  plan-3  C8   0.020
 H25  plan-3  O25  0.020
 H25  plan-3  H21  0.020
 H25  plan-3  H29  0.020
 H25  plan-3  H30  0.020
 H25  plan-3  H23  0.020
 H25  plan-4  C6   0.020
 H25  plan-4  N7   0.020
 H25  plan-4  C5   0.020
 H25  plan-4  O24  0.020
 H25  plan-4  C2   0.020
 H25  plan-4  H7   0.020
 H25  plan-5  C16  0.020
 H25  plan-5  N15  0.020
 H25  plan-5  C14  0.020
 H25  plan-5  O27  0.020
 H25  plan-5  C22  0.020
 H25  plan-5  H15  0.020

