# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 19:22:40 2020
#   Inital geometry file: a 146 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-methoxypyrrolidin-3-yl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[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
 LZF  LZF  5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide  ligand  56  34  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LZF
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
 LZF  F32   F   F     0  -0.312  16.8404   5.3533  28.3548
 LZF  C17   C   CR6   0   0.477  16.5534   6.6034  28.7542
 LZF  C11   C   CR16  0  -0.413  16.9467   7.0070  30.0074
 LZF  C9    C   CR6   0   0.280  16.6358   8.2962  30.4129
 LZF  N1    N   NR6   0  -0.612  17.0040   8.7275  31.7226
 LZF  C21   C   CR16  0   0.051  16.1181   8.5473  32.7416
 LZF  C29   C   CR16  0  -0.398  16.4061   8.9356  34.0061
 LZF  C30   C   CR16  0  -0.119  17.6635   9.5406  34.2455
 LZF  C23   C   CR16  0  -0.453  18.5513   9.7240  33.2343
 LZF  C8    C   CR6   0   0.551  18.2602   9.3152  31.8862
 LZF  O25   O   O     0  -0.503  19.0084   9.4446  30.9246
 LZF  C26   C   CR16  0  -0.255  15.9552   9.1484  29.5637
 LZF  C28   C   CR16  0  -0.322  15.5687   8.7240  28.3003
 LZF  C16   C   CR6   0   0.239  15.8603   7.4305  27.8677
 LZF  N15   N   NH1   0  -0.734  15.5105   6.8981  26.6353
 LZF  C14   C   C     0   0.513  14.7964   7.4595  25.6306
 LZF  O27   O   O     0  -0.463  14.3610   8.5952  25.6223
 LZF  C22   C   CH2   0  -0.390  14.6206   6.5220  24.4439
 LZF  N4    N   NT    0  -0.479  14.7555   5.1386  24.8117
 LZF  C20   C   CH2   0  -0.300  15.1665   4.2256  23.7642
 LZF  C13   C   CH1   0   0.037  15.0907   2.8889  24.4995
 LZF  O33   O   O2    0  -0.484  15.0170   1.7478  23.6992
 LZF  C34   C   CH3   0  -0.411  16.2084   1.4737  22.9983
 LZF  C18   C   CH2   0  -0.277  13.5671   4.5474  25.4144
 LZF  C6    C   CH1   0  -0.107  13.8095   3.0292  25.3309
 LZF  N7    N   NH1   0  -0.675  13.9349   2.3679  26.6101
 LZF  C5    C   C     0   0.572  12.8668   2.1350  27.3860
 LZF  O24   O   O     0  -0.490  11.7255   2.4466  27.0666
 LZF  C2    C   CR5   0  -0.290  13.1090   1.4717  28.6787
 LZF  C12   C   CR15  0  -0.222  14.2500   1.0327  29.2877
 LZF  C19   C   CR15  0  -0.118  14.0121   0.4510  30.5553
 LZF  S3    S   S2    0   0.323  11.7156   1.1817  29.6487
 LZF  C10   C   CR5   0  -0.250  12.6859   0.4679  30.8671
 LZF  CL1   CL  CL    0  -0.067  11.9721  -0.1330  32.2939
 LZF  H11   H   HCR6  0   0.296  17.4805   6.3242  30.6556
 LZF  H26   H   HCR6  0   0.277  15.7157  10.1541  29.8826
 LZF  H21   H   HCR6  0   0.314  15.1827   8.0787  32.4716
 LZF  H29   H   HCR6  0   0.280  15.6888   8.7817  34.7973
 LZF  H30   H   HCR6  0   0.282  17.9198   9.8599  35.2475
 LZF  H23   H   HCR6  0   0.276  19.5128  10.1868  33.4111
 LZF  H28   H   HCR6  0   0.298  15.0359   9.4043  27.6573
 LZF  H15   H   HNH1  0   0.413  15.7759   5.9379  26.4371
 LZF  H221  H   HCH2  0   0.253  13.6581   6.7546  23.9697
 LZF  H222  H   HCH2  0   0.293  15.4008   6.7810  23.7217
 LZF  H201  H   HCH2  0   0.220  14.4815   4.2222  22.9012
 LZF  H202  H   HCH2  0   0.260  16.1679   4.4714  23.4082
 LZF  H181  H   HCH2  0   0.252  13.4273   4.8899  26.4414
 LZF  H182  H   HCH2  0   0.234  12.6605   4.8145  24.8542
 LZF  H13   H   HCH1  0   0.223  15.9637   2.8325  25.1700
 LZF  H6    H   HCH1  0   0.280  12.9882   2.5655  24.7814
 LZF  H341  H   HCH3  0   0.241  16.0884   0.5088  22.5079
 LZF  H342  H   HCH3  0   0.215  16.4235   2.2238  22.2306
 LZF  H343  H   HCH3  0   0.211  17.0726   1.4161  23.6701
 LZF  H7    H   HNH1  0   0.406  14.8562   2.1240  26.9358
 LZF  H12   H   HCR5  0   0.281  15.2409   1.1121  28.8622
 LZF  H19   H   HCR5  0   0.297  14.7798   0.0459  31.1974

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
 LZF  F32  C17   single    1.343  0.020  1.343
 LZF  C17  C11   aromatic  1.374  0.020  1.374
 LZF  C17  C16   aromatic  1.397  0.020  1.397
 LZF  C11  C9    aromatic  1.387  0.020  1.387
 LZF  C9   N1    single    1.427  0.020  1.427
 LZF  C9   C26   aromatic  1.382  0.020  1.382
 LZF  N1   C21   single    1.362  0.020  1.362
 LZF  N1   C8    single    1.396  0.020  1.396
 LZF  C21  C29   double    1.354  0.020  1.354
 LZF  C29  C30   single    1.416  0.020  1.416
 LZF  C30  C23   double    1.358  0.020  1.358
 LZF  C23  C8    single    1.439  0.020  1.439
 LZF  C8   O25   double    1.225  0.020  1.225
 LZF  C26  C28   aromatic  1.388  0.020  1.388
 LZF  C28  C16   aromatic  1.395  0.020  1.395
 LZF  C16  N15   single    1.387  0.020  1.387
 LZF  N15  C14   single    1.354  0.020  1.354
 LZF  C14  O27   double    1.216  0.020  1.216
 LZF  C14  C22   single    1.522  0.020  1.522
 LZF  C22  N4    single    1.438  0.020  1.438
 LZF  N4   C20   single    1.449  0.020  1.449
 LZF  N4   C18   single    1.458  0.020  1.458
 LZF  C20  C13   single    1.528  0.020  1.528
 LZF  C13  O33   single    1.396  0.020  1.396
 LZF  C13  C6    single    1.534  0.020  1.534
 LZF  O33  C34   single    1.409  0.020  1.409
 LZF  C18  C6    single    1.540  0.020  1.540
 LZF  C6   N7    single    1.446  0.020  1.446
 LZF  N7   C5    single    1.341  0.020  1.341
 LZF  C5   O24   double    1.225  0.020  1.225
 LZF  C5   C2    single    1.473  0.020  1.473
 LZF  C2   C12   aromatic  1.366  0.020  1.366
 LZF  C2   S3    aromatic  1.722  0.020  1.722
 LZF  C12  C19   aromatic  1.415  0.020  1.415
 LZF  C19  C10   aromatic  1.362  0.020  1.362
 LZF  S3   C10   aromatic  1.713  0.020  1.713
 LZF  C10  CL1   single    1.705  0.020  1.705
 LZF  C11  H11   single    0.930  0.020  1.080
 LZF  C26  H26   single    0.930  0.020  1.080
 LZF  C21  H21   single    0.930  0.020  1.080
 LZF  C29  H29   single    0.930  0.020  1.080
 LZF  C30  H30   single    0.930  0.020  1.080
 LZF  C23  H23   single    0.930  0.020  1.080
 LZF  C28  H28   single    0.930  0.020  1.080
 LZF  N15  H15   single    0.860  0.020  1.020
 LZF  C22  H221  single    0.970  0.020  1.090
 LZF  C22  H222  single    0.970  0.020  1.090
 LZF  C20  H201  single    0.970  0.020  1.090
 LZF  C20  H202  single    0.970  0.020  1.090
 LZF  C18  H181  single    0.970  0.020  1.090
 LZF  C18  H182  single    0.970  0.020  1.090
 LZF  C13  H13   single    0.970  0.020  1.090
 LZF  C6   H6    single    0.970  0.020  1.090
 LZF  C34  H341  single    0.970  0.020  1.090
 LZF  C34  H342  single    0.970  0.020  1.090
 LZF  C34  H343  single    0.970  0.020  1.090
 LZF  N7   H7    single    0.860  0.020  1.020
 LZF  C12  H12   single    0.930  0.020  1.080
 LZF  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
 LZF  C16   C17  C11   123.16  3.000
 LZF  C16   C17  F32   117.93  3.000
 LZF  C11   C17  F32   118.91  3.000
 LZF  H11   C11  C9    121.46  3.000
 LZF  H11   C11  C17   120.14  3.000
 LZF  C9    C11  C17   118.40  3.000
 LZF  C26   C9   N1    120.29  3.000
 LZF  C26   C9   C11   120.26  3.000
 LZF  N1    C9   C11   119.44  3.000
 LZF  C8    N1   C21   123.58  3.000
 LZF  C8    N1   C9    117.82  3.000
 LZF  C21   N1   C9    118.60  3.000
 LZF  H21   C21  C29   122.82  3.000
 LZF  H21   C21  N1    115.69  3.000
 LZF  C29   C21  N1    121.49  3.000
 LZF  H29   C29  C30   121.83  3.000
 LZF  H29   C29  C21   120.17  3.000
 LZF  C30   C29  C21   118.00  3.000
 LZF  H30   C30  C23   119.65  3.000
 LZF  H30   C30  C29   119.53  3.000
 LZF  C23   C30  C29   120.83  3.000
 LZF  H23   C23  C8    117.04  3.000
 LZF  H23   C23  C30   121.15  3.000
 LZF  C8    C23  C30   121.81  3.000
 LZF  O25   C8   C23   125.58  3.000
 LZF  O25   C8   N1    120.13  3.000
 LZF  C23   C8   N1    114.29  3.000
 LZF  H26   C26  C28   119.41  3.000
 LZF  H26   C26  C9    120.07  3.000
 LZF  C28   C26  C9    120.52  3.000
 LZF  H28   C28  C16   120.26  3.000
 LZF  H28   C28  C26   119.22  3.000
 LZF  C16   C28  C26   120.52  3.000
 LZF  N15   C16  C28   125.36  3.000
 LZF  N15   C16  C17   117.50  3.000
 LZF  C28   C16  C17   117.13  3.000
 LZF  H15   N15  C14   112.63  3.000
 LZF  H15   N15  C16   118.05  3.000
 LZF  C14   N15  C16   129.26  3.000
 LZF  C22   C14  O27   121.90  3.000
 LZF  C22   C14  N15   112.57  3.000
 LZF  O27   C14  N15   125.50  3.000
 LZF  H222  C22  H221  106.85  3.000
 LZF  H222  C22  N4    109.24  3.000
 LZF  H221  C22  N4    113.36  3.000
 LZF  H222  C22  C14   106.64  3.000
 LZF  H221  C22  C14   107.91  3.000
 LZF  N4    C22  C14   112.48  3.000
 LZF  C18   N4   C20   105.94  3.000
 LZF  C18   N4   C22   114.80  3.000
 LZF  C20   N4   C22   116.61  3.000
 LZF  H202  C20  H201  108.41  3.000
 LZF  H202  C20  C13   113.57  3.000
 LZF  H201  C20  C13   110.09  3.000
 LZF  H202  C20  N4    110.76  3.000
 LZF  H201  C20  N4    113.07  3.000
 LZF  C13   C20  N4    100.91  3.000
 LZF  H13   C13  C6    109.67  3.000
 LZF  H13   C13  O33   110.41  3.000
 LZF  C6    C13  O33   109.97  3.000
 LZF  H13   C13  C20   107.35  3.000
 LZF  C6    C13  C20   102.85  3.000
 LZF  O33   C13  C20   116.23  3.000
 LZF  C34   O33  C13   113.56  3.000
 LZF  H343  C34  H342  108.12  3.000
 LZF  H343  C34  H341  108.45  3.000
 LZF  H342  C34  H341  108.23  3.000
 LZF  H343  C34  O33   111.84  3.000
 LZF  H342  C34  O33   112.43  3.000
 LZF  H341  C34  O33   107.65  3.000
 LZF  H182  C18  H181  107.32  3.000
 LZF  H182  C18  C6    110.00  3.000
 LZF  H181  C18  C6    112.37  3.000
 LZF  H182  C18  N4    111.31  3.000
 LZF  H181  C18  N4    111.48  3.000
 LZF  C6    C18  N4    104.42  3.000
 LZF  H6    C6   N7    108.45  3.000
 LZF  H6    C6   C18   109.13  3.000
 LZF  N7    C6   C18   114.63  3.000
 LZF  H6    C6   C13   108.47  3.000
 LZF  N7    C6   C13   111.43  3.000
 LZF  C18   C6   C13   104.54  3.000
 LZF  H7    N7   C5    119.97  3.000
 LZF  H7    N7   C6    118.45  3.000
 LZF  C5    N7   C6    121.50  3.000
 LZF  C2    C5   O24   119.76  3.000
 LZF  C2    C5   N7    117.07  3.000
 LZF  O24   C5   N7    123.17  3.000
 LZF  S3    C2   C12   111.75  3.000
 LZF  S3    C2   C5    115.91  3.000
 LZF  C12   C2   C5    132.33  3.000
 LZF  H12   C12  C19   122.47  3.000
 LZF  H12   C12  C2    124.50  3.000
 LZF  C19   C12  C2    113.03  3.000
 LZF  H19   C19  C10   124.11  3.000
 LZF  H19   C19  C12   124.57  3.000
 LZF  C10   C19  C12   111.32  3.000
 LZF  C10   S3   C2     90.72  3.000
 LZF  CL1   C10  S3    120.33  3.000
 LZF  CL1   C10  C19   126.49  3.000
 LZF  S3    C10  C19   113.18  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
 LZF  CONST_01  C26   C9   C11  C17     0.00   0.0  0
 LZF  CONST_02  C26   C28  C16  C17     0.00   0.0  0
 LZF  CONST_03  C28   C16  C17  C11     0.00   0.0  0
 LZF  CONST_04  C28   C26  C9   C11     0.00   0.0  0
 LZF  CONST_05  C16   C17  C11  C9      0.00   0.0  0
 LZF  CONST_06  C16   C28  C26  C9      0.00   0.0  0
 LZF  CONST_07  C10   C19  C12  C2      0.00   0.0  0
 LZF  CONST_08  C19   C10  S3   C2      0.00   0.0  0
 LZF  CONST_09  C10   S3   C2   C12     0.00   0.0  0
 LZF  CONST_10  S3    C10  C19  C12     0.00   0.0  0
 LZF  CONST_11  S3    C2   C12  C19     0.00   0.0  0
 LZF  CONST_12  N1    C9   C11  C17   180.00   0.0  0
 LZF  CONST_13  C28   C26  C9   N1    180.00   0.0  0
 LZF  CONST_14  C23   C8   N1   C9    180.00   0.0  0
 LZF  CONST_15  C23   C8   N1   C21     0.00   0.0  0
 LZF  CONST_16  C9    C11  C17  F32   180.00   0.0  0
 LZF  CONST_17  C28   C16  C17  F32   180.00   0.0  0
 LZF  CONST_18  N15   C16  C17  C11   180.00   0.0  0
 LZF  CONST_19  N15   C16  C28  C26   180.00   0.0  0
 LZF  CONST_20  C19   C12  C2   C5    180.00   0.0  0
 LZF  CONST_21  C10   S3   C2   C5    180.00   0.0  0
 LZF  CONST_22  CL1   C10  S3   C2    180.00   0.0  0
 LZF  CONST_23  CL1   C10  C19  C12   180.00   0.0  0
 LZF  CONST_24  O25   C8   N1   C9      0.00   0.0  0
 LZF  CONST_25  O25   C8   N1   C21   180.00   0.0  0
 LZF  CONST_26  H28   C28  C16  C17   180.00   0.0  0
 LZF  CONST_27  H26   C26  C9   C11   180.00   0.0  0
 LZF  CONST_28  H11   C11  C9   N1      0.00   0.0  0
 LZF  CONST_29  H19   C19  C12  C2    180.00   0.0  0
 LZF  CONST_30  H12   C12  C2   S3    180.00   0.0  0
 LZF  CONST_31  C2    C5   N7   C6    180.00   0.0  0
 LZF  CONST_32  C14   N15  C16  C17   180.00   0.0  0
 LZF  CONST_33  C14   N15  C16  C28     0.00   0.0  0
 LZF  CONST_34  H15   N15  C16  C17     0.00   0.0  0
 LZF  CONST_35  O27   C14  N15  C16     0.00   0.0  0
 LZF  CONST_36  C22   C14  N15  C16   180.00   0.0  0
 LZF  CONST_37  O24   C5   N7   C6      0.00   0.0  0
 LZF  CONST_38  H7    N7   C5   C2      0.00   0.0  0
 LZF  Var_01    C21   N1   C9   C11   -90.47  30.0  2
 LZF  Var_02    C6    C18  N4   C20    33.84  30.0  1
 LZF  Var_03    C18   N4   C20  C13   -46.80  30.0  1
 LZF  Var_04    C20   N4   C22  C14  -154.78  30.0  3
 LZF  Var_05    C12   C2   C5   N7      0.68  30.0  2
 LZF  Var_06    N4    C22  C14  N15    23.12  30.0  3
 LZF  Var_07    H341  C34  O33  C13   173.14  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
 LZF  chir_01  C13  C20  O33  C6   positiv
 LZF  chir_02  C6   N7   C13  C18  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
 LZF  plan-1  C5   0.020
 LZF  plan-1  C2   0.020
 LZF  plan-1  C12  0.020
 LZF  plan-1  C19  0.020
 LZF  plan-1  S3   0.020
 LZF  plan-1  C10  0.020
 LZF  plan-1  CL1  0.020
 LZF  plan-1  H12  0.020
 LZF  plan-1  H19  0.020
 LZF  plan-2  F32  0.020
 LZF  plan-2  C17  0.020
 LZF  plan-2  C11  0.020
 LZF  plan-2  C9   0.020
 LZF  plan-2  N1   0.020
 LZF  plan-2  C26  0.020
 LZF  plan-2  C28  0.020
 LZF  plan-2  C16  0.020
 LZF  plan-2  N15  0.020
 LZF  plan-2  H11  0.020
 LZF  plan-2  H26  0.020
 LZF  plan-2  H28  0.020
 LZF  plan-3  C9   0.020
 LZF  plan-3  N1   0.020
 LZF  plan-3  C21  0.020
 LZF  plan-3  C29  0.020
 LZF  plan-3  C30  0.020
 LZF  plan-3  C23  0.020
 LZF  plan-3  C8   0.020
 LZF  plan-3  O25  0.020
 LZF  plan-3  H21  0.020
 LZF  plan-3  H29  0.020
 LZF  plan-3  H30  0.020
 LZF  plan-3  H23  0.020
 LZF  plan-4  C6   0.020
 LZF  plan-4  N7   0.020
 LZF  plan-4  C5   0.020
 LZF  plan-4  O24  0.020
 LZF  plan-4  C2   0.020
 LZF  plan-4  H7   0.020
 LZF  plan-5  C16  0.020
 LZF  plan-5  N15  0.020
 LZF  plan-5  C14  0.020
 LZF  plan-5  O27  0.020
 LZF  plan-5  C22  0.020
 LZF  plan-5  H15  0.020

