# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:33:22 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-thiophen-2-yl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)c1ccc(cc1)c2sccc2)C(=O)N3C[C@H](F)[C@H]4OC[C@H](O)[C@@H]34
#
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
 HKH  HKH  ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-thiophen-2-yl-benzamide  ligand  58  31  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HKH
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
 HKH  C2   C  CR15  0   0.173   5.4150  -1.6275   0.8035
 HKH  C3   C  C     0  -0.065   5.7620  -0.2539   1.3423
 HKH  O4   O  O     0  -0.496   6.5960   0.3999   0.4146
 HKH  C8   C  CH2   0  -0.208   6.3543   1.7834   0.5626
 HKH  C9   C  CH2   0  -0.356   4.3237  -1.3399  -0.2014
 HKH  C13  C  CH1   0  -0.199   1.4555  -0.8251  -0.6243
 HKH  C14  C  CH2   0  -0.433   1.7851  -0.6191  -2.1168
 HKH  C15  C  CH1   0  -0.231   1.3339   0.6921  -2.7629
 HKH  C22  C  CR6   0  -0.045  -2.3001  -1.0220  -0.3121
 HKH  C24  C  CR16  0  -0.308  -3.9929   0.6543   0.0728
 HKH  C27  C  CR16  0  -0.248  -3.2732  -2.0070  -0.1536
 HKH  C30  C  CR15  0  -0.170  -8.6760  -0.0931   0.6973
 HKH  C31  C  CR15  0  -0.466  -8.4526   1.1354   1.2411
 HKH  F1   F  F     0  -0.373   4.8878  -2.3712   1.8549
 HKH  C6   C  CR15  0   0.014   4.8396   1.9250   0.7967
 HKH  O7   O  OH1   0  -0.665   4.5123   2.9089   1.7408
 HKH  C5   C  C     0  -0.093   4.4455   0.5324   1.3223
 HKH  N10  N  NR5   0  -0.493   3.6005  -0.2333   0.4095
 HKH  C17  C  CH3   0  -0.675   2.1154   1.9107  -2.2809
 HKH  C18  C  CH3   0  -0.652   1.4536   0.5614  -4.2796
 HKH  N19  N  NH1   0  -0.668   0.0661  -0.5727  -0.3339
 HKH  O21  O  O     0  -0.488  -0.6812  -2.5401  -1.1423
 HKH  C26  C  CR16  0  -0.311  -4.5808  -1.6689   0.1377
 HKH  C25  C  CR6   0   0.157  -4.9669  -0.3299   0.2522
 HKH  C23  C  CR16  0  -0.276  -2.6792   0.3132  -0.1988
 HKH  C28  C  CR5   0  -0.215  -6.3576   0.0114   0.5371
 HKH  S32  S  S2    0   0.220  -6.7851   1.5167   1.2702
 HKH  C29  C  CR15  0  -0.243  -7.4785  -0.7368   0.2959
 HKH  H1   H  HCR5  0   0.260   6.2624  -2.1695   0.3824
 HKH  H2   H  H     0   0.274   6.2168  -0.2903   2.3395
 HKH  H3   H  HCH2  0   0.217   6.8909   2.1869   1.4315
 HKH  H4   H  HCH2  0   0.249   6.7066   2.2931  -0.3342
 HKH  H5   H  HCH2  0   0.269   4.7710  -1.0548  -1.1564
 HKH  H6   H  HCH2  0   0.289   3.6936  -2.2107  -0.3755
 HKH  H7   H  HCH1  0   0.289   1.6613  -1.8759  -0.3954
 HKH  H8   H  HCH2  0   0.246   2.8591  -0.7484  -2.2758
 HKH  H9   H  HCH2  0   0.251   1.3110  -1.4482  -2.6470
 HKH  H10  H  HCH1  0   0.222   0.2762   0.8474  -2.5252
 HKH  H11  H  HCR6  0   0.261  -4.2576   1.7034   0.1232
 HKH  H12  H  HCR6  0   0.263  -3.0028  -3.0505  -0.2441
 HKH  H14  H  HCR5  0   0.300  -9.1773   1.8354   1.6275
 HKH  H15  H  HCR5  0   0.237   4.3332   2.1099  -0.1577
 HKH  H16  H  HOH1  0   0.457   4.7267   3.7703   1.3697
 HKH  H17  H  H     0   0.288   3.9756   0.6064   2.3041
 HKH  H18  H  HCH3  0   0.213   3.1897   1.7693  -2.4274
 HKH  H19  H  HCH3  0   0.233   1.8218   2.7993  -2.8427
 HKH  H20  H  HCH3  0   0.234   1.9426   2.1284  -1.2286
 HKH  H21  H  HCH3  0   0.226   0.8535  -0.2679  -4.6581
 HKH  H22  H  HCH3  0   0.228   1.1184   1.4712  -4.7801
 HKH  H23  H  HCH3  0   0.215   2.4901   0.3845  -4.5780
 HKH  H24  H  HNH1  0   0.405  -0.1396   0.2613   0.1955
 HKH  H25  H  HCR6  0   0.261  -5.3081  -2.4560   0.2884
 HKH  H26  H  HCR6  0   0.260  -1.9670   1.1135  -0.3542
 HKH  H27  H  HCR5  0   0.268  -7.4524  -1.7102  -0.1742
 HKH  C11  C  C     0   0.572   2.2861   0.0277   0.3322
 HKH  C20  C  C     0   0.547  -0.9057  -1.4483  -0.6351
 HKH  O12  O  O     0  -0.490   1.7693   0.9121   1.0032
 HKH  H13  H  HCR5  0   0.271  -9.6600  -0.5233   0.5801

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
 HKH  C18  C15  single    1.527  0.020  1.527
 HKH  C17  C15  single    1.526  0.020  1.526
 HKH  C15  C14  single    1.530  0.020  1.530
 HKH  C14  C13  single    1.542  0.020  1.542
 HKH  C13  N19  single    1.442  0.020  1.442
 HKH  C13  C11  single    1.527  0.020  1.527
 HKH  N19  C20  single    1.342  0.020  1.342
 HKH  C8   C6   single    1.539  0.020  1.539
 HKH  C8   O4   single    1.412  0.020  1.412
 HKH  C11  O12  double    1.225  0.020  1.225
 HKH  C11  N10  single    1.342  0.020  1.342
 HKH  C6   O7   single    1.402  0.020  1.402
 HKH  C6   C5   single    1.540  0.020  1.540
 HKH  C23  C24  aromatic  1.384  0.020  1.384
 HKH  C23  C22  aromatic  1.393  0.020  1.393
 HKH  N10  C9   single    1.456  0.020  1.456
 HKH  N10  C5   single    1.461  0.020  1.461
 HKH  C9   C2   single    1.511  0.020  1.511
 HKH  C20  C22  single    1.494  0.020  1.494
 HKH  C20  O21  double    1.225  0.020  1.225
 HKH  C24  C25  aromatic  1.396  0.020  1.396
 HKH  O4   C3   single    1.408  0.020  1.408
 HKH  C5   C3   single    1.534  0.020  1.534
 HKH  C22  C27  aromatic  1.394  0.020  1.394
 HKH  C3   C2   single    1.516  0.020  1.516
 HKH  C2   F1   single    1.392  0.020  1.392
 HKH  C29  C28  aromatic  1.369  0.020  1.369
 HKH  C29  C30  aromatic  1.418  0.020  1.418
 HKH  C25  C28  single    1.460  0.020  1.460
 HKH  C25  C26  aromatic  1.398  0.020  1.398
 HKH  C27  C26  aromatic  1.382  0.020  1.382
 HKH  C28  S32  aromatic  1.728  0.020  1.728
 HKH  C30  C31  aromatic  1.362  0.020  1.362
 HKH  C31  S32  aromatic  1.711  0.020  1.711
 HKH  C2   H1   single    0.970  0.020  1.090
 HKH  C3   H2   single    0.970  0.020  1.090
 HKH  C8   H3   single    0.970  0.020  1.090
 HKH  C8   H4   single    0.970  0.020  1.090
 HKH  C9   H5   single    0.970  0.020  1.090
 HKH  C9   H6   single    0.970  0.020  1.090
 HKH  C13  H7   single    0.970  0.020  1.090
 HKH  C14  H8   single    0.970  0.020  1.090
 HKH  C14  H9   single    0.970  0.020  1.090
 HKH  C15  H10  single    0.970  0.020  1.090
 HKH  C24  H11  single    0.930  0.020  1.080
 HKH  C27  H12  single    0.930  0.020  1.080
 HKH  C30  H13  single    0.930  0.020  1.080
 HKH  C31  H14  single    0.930  0.020  1.080
 HKH  C6   H15  single    0.970  0.020  1.090
 HKH  O7   H16  single    0.850  0.020  0.980
 HKH  C5   H17  single    0.970  0.020  1.090
 HKH  C17  H18  single    0.970  0.020  1.090
 HKH  C17  H19  single    0.970  0.020  1.090
 HKH  C17  H20  single    0.970  0.020  1.090
 HKH  C18  H21  single    0.970  0.020  1.090
 HKH  C18  H22  single    0.970  0.020  1.090
 HKH  C18  H23  single    0.970  0.020  1.090
 HKH  N19  H24  single    0.860  0.020  1.020
 HKH  C26  H25  single    0.930  0.020  1.080
 HKH  C23  H26  single    0.930  0.020  1.080
 HKH  C29  H27  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
 HKH  H1   C2   F1   108.70  3.000
 HKH  H1   C2   C9   113.51  3.000
 HKH  F1   C2   C9   109.30  3.000
 HKH  H1   C2   C3   114.20  3.000
 HKH  F1   C2   C3   107.61  3.000
 HKH  C9   C2   C3   103.25  3.000
 HKH  H2   C3   C5   112.64  3.000
 HKH  H2   C3   O4   111.64  3.000
 HKH  C5   C3   O4   105.17  3.000
 HKH  H2   C3   C2   112.84  3.000
 HKH  C5   C3   C2   105.28  3.000
 HKH  O4   C3   C2   108.79  3.000
 HKH  C8   O4   C3   106.52  3.000
 HKH  H4   C8   H3   108.74  3.000
 HKH  H4   C8   C6   113.59  3.000
 HKH  H3   C8   C6   109.07  3.000
 HKH  H4   C8   O4   108.46  3.000
 HKH  H3   C8   O4   111.05  3.000
 HKH  C6   C8   O4   105.94  3.000
 HKH  H6   C9   H5   107.82  3.000
 HKH  H6   C9   N10  112.79  3.000
 HKH  H5   C9   N10  111.82  3.000
 HKH  H6   C9   C2   111.84  3.000
 HKH  H5   C9   C2   109.59  3.000
 HKH  N10  C9   C2   102.96  3.000
 HKH  H7   C13  N19  107.88  3.000
 HKH  H7   C13  C14  106.88  3.000
 HKH  N19  C13  C14  112.18  3.000
 HKH  H7   C13  C11  107.62  3.000
 HKH  N19  C13  C11  107.48  3.000
 HKH  C14  C13  C11  114.54  3.000
 HKH  H9   C14  H8   105.42  3.000
 HKH  H9   C14  C15  108.52  3.000
 HKH  H8   C14  C15  109.25  3.000
 HKH  H9   C14  C13  106.00  3.000
 HKH  H8   C14  C13  109.56  3.000
 HKH  C15  C14  C13  117.40  3.000
 HKH  H10  C15  C18  107.66  3.000
 HKH  H10  C15  C17  108.23  3.000
 HKH  C18  C15  C17  110.00  3.000
 HKH  H10  C15  C14  108.34  3.000
 HKH  C17  C15  C14  113.58  3.000
 HKH  C18  C15  C14  108.84  3.000
 HKH  C23  C22  C27  118.58  3.000
 HKH  C27  C22  C20  118.34  3.000
 HKH  C23  C22  C20  123.05  3.000
 HKH  H11  C24  C23  118.67  3.000
 HKH  H11  C24  C25  120.42  3.000
 HKH  C23  C24  C25  120.90  3.000
 HKH  H12  C27  C26  119.35  3.000
 HKH  H12  C27  C22  119.86  3.000
 HKH  C26  C27  C22  120.79  3.000
 HKH  H13  C30  C29  123.91  3.000
 HKH  H13  C30  C31  123.50  3.000
 HKH  C29  C30  C31  112.59  3.000
 HKH  H14  C31  S32  120.26  3.000
 HKH  H14  C31  C30  128.16  3.000
 HKH  S32  C31  C30  111.58  3.000
 HKH  H15  C6   C5   109.36  3.000
 HKH  H15  C6   O7   111.10  3.000
 HKH  C5   C6   O7   110.18  3.000
 HKH  H15  C6   C8   109.74  3.000
 HKH  C5   C6   C8   102.74  3.000
 HKH  O7   C6   C8   113.37  3.000
 HKH  H16  O7   C6   108.45  3.000
 HKH  H17  C5   N10  110.42  3.000
 HKH  H17  C5   C6   110.86  3.000
 HKH  N10  C5   C6   114.13  3.000
 HKH  H17  C5   C3   113.13  3.000
 HKH  N10  C5   C3   103.65  3.000
 HKH  C6   C5   C3   104.38  3.000
 HKH  C5   N10  C11  120.03  3.000
 HKH  C5   N10  C9   111.91  3.000
 HKH  C11  N10  C9   127.58  3.000
 HKH  H20  C17  H19  106.99  3.000
 HKH  H20  C17  H18  108.14  3.000
 HKH  H19  C17  H18  107.49  3.000
 HKH  H20  C17  C15  112.58  3.000
 HKH  H19  C17  C15  110.48  3.000
 HKH  H18  C17  C15  110.96  3.000
 HKH  H23  C18  H22  107.52  3.000
 HKH  H23  C18  H21  107.68  3.000
 HKH  H22  C18  H21  107.79  3.000
 HKH  H23  C18  C15  111.06  3.000
 HKH  H22  C18  C15  111.11  3.000
 HKH  H21  C18  C15  111.50  3.000
 HKH  H24  N19  C20  120.61  3.000
 HKH  H24  N19  C13  116.54  3.000
 HKH  C20  N19  C13  122.57  3.000
 HKH  H25  C26  C25  119.97  3.000
 HKH  H25  C26  C27  119.17  3.000
 HKH  C25  C26  C27  120.86  3.000
 HKH  C28  C25  C26  120.19  3.000
 HKH  C26  C25  C24  118.16  3.000
 HKH  C28  C25  C24  121.64  3.000
 HKH  H26  C23  C24  118.06  3.000
 HKH  H26  C23  C22  121.21  3.000
 HKH  C24  C23  C22  120.70  3.000
 HKH  C29  C28  S32  110.38  3.000
 HKH  S32  C28  C25  121.48  3.000
 HKH  C29  C28  C25  128.15  3.000
 HKH  C28  S32  C31   92.28  3.000
 HKH  H27  C29  C28  123.28  3.000
 HKH  H27  C29  C30  123.53  3.000
 HKH  C28  C29  C30  113.18  3.000
 HKH  O12  C11  N10  121.48  3.000
 HKH  N10  C11  C13  117.39  3.000
 HKH  O12  C11  C13  121.13  3.000
 HKH  O21  C20  N19  122.81  3.000
 HKH  O21  C20  C22  121.01  3.000
 HKH  N19  C20  C22  116.18  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
 HKH  CONST_01  C25  C24  C23  C22     0.00   0.0  0
 HKH  CONST_02  C25  C26  C27  C22     0.00   0.0  0
 HKH  CONST_03  C27  C22  C23  C24     0.00   0.0  0
 HKH  CONST_06  C27  C26  C25  C24     0.00   0.0  0
 HKH  CONST_07  C28  C25  C26  C27   180.00   0.0  0
 HKH  CONST_08  C25  C28  C29  C30   180.00   0.0  0
 HKH  CONST_09  S32  C28  C29  C30     0.00   0.0  0
 HKH  CONST_10  C28  S32  C31  C30     0.00   0.0  0
 HKH  CONST_11  C28  C29  C30  C31     0.00   0.0  0
 HKH  CONST_12  C29  C28  S32  C31     0.00   0.0  0
 HKH  CONST_13  C25  C28  S32  C31   180.00   0.0  0
 HKH  CONST_14  C23  C24  C25  C26     0.00   0.0  0
 HKH  CONST_17  C23  C22  C27  C26     0.00   0.0  0
 HKH  CONST_18  C28  C25  C24  C23   180.00   0.0  0
 HKH  CONST_19  C29  C30  C31  S32     0.00   0.0  0
 HKH  CONST_20  C24  C23  C22  C20   180.00   0.0  0
 HKH  CONST_21  C26  C27  C22  C20   180.00   0.0  0
 HKH  CONST_22  H11  C24  C23  C22   180.00   0.0  0
 HKH  CONST_23  H25  C26  C27  C22   180.00   0.0  0
 HKH  CONST_24  H26  C23  C22  C27   180.00   0.0  0
 HKH  CONST_25  H27  C29  C30  C31   180.00   0.0  0
 HKH  CONST_26  H12  C27  C26  C25   180.00   0.0  0
 HKH  CONST_27  H13  C30  C29  C28   180.00   0.0  0
 HKH  CONST_28  H14  C31  S32  C28   180.00   0.0  0
 HKH  CONST_29  C13  C11  N10  C9      0.00   0.0  0
 HKH  CONST_30  O12  C11  N10  C9    180.00   0.0  0
 HKH  CONST_31  C5   N10  C11  C13   180.00   0.0  0
 HKH  CONST_32  O12  C11  N10  C5      0.00   0.0  0
 HKH  CONST_33  C22  C20  N19  C13   180.00   0.0  0
 HKH  CONST_34  H24  N19  C20  C22     0.00   0.0  0
 HKH  CONST_35  O21  C20  N19  C13     0.00   0.0  0
 HKH  Var_01    C5   N10  C9   C2     25.31  30.0  1
 HKH  Var_02    C6   C8   O4   C3    -38.82  30.0  1
 HKH  Var_03    N19  C20  C22  C27  -157.86  30.0  2
 HKH  Var_04    C18  C15  C14  C13  -166.75  30.0  2
 HKH  Var_05    H21  C18  C15  C14    58.43  30.0  3
 HKH  Var_06    H18  C17  C15  C14    55.31  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
 HKH  chir_01  C2   C9   C3   F1   negativ
 HKH  chir_02  C3   O4   C5   C2   negativ
 HKH  chir_03  C13  N19  C11  C14  positiv
 HKH  chir_04  C6   O7   C8   C5   negativ
 HKH  chir_05  C5   N10  C3   C6   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
 HKH  plan-1  C30  0.020
 HKH  plan-1  C31  0.020
 HKH  plan-1  C25  0.020
 HKH  plan-1  C28  0.020
 HKH  plan-1  S32  0.020
 HKH  plan-1  C29  0.020
 HKH  plan-1  H14  0.020
 HKH  plan-1  H27  0.020
 HKH  plan-1  H13  0.020
 HKH  plan-2  C22  0.020
 HKH  plan-2  C24  0.020
 HKH  plan-2  C27  0.020
 HKH  plan-2  C26  0.020
 HKH  plan-2  C25  0.020
 HKH  plan-2  C23  0.020
 HKH  plan-2  C28  0.020
 HKH  plan-2  H11  0.020
 HKH  plan-2  H12  0.020
 HKH  plan-2  H25  0.020
 HKH  plan-2  H26  0.020
 HKH  plan-2  C20  0.020
 HKH  plan-3  C9   0.020
 HKH  plan-3  C13  0.020
 HKH  plan-3  C5   0.020
 HKH  plan-3  N10  0.020
 HKH  plan-3  C11  0.020
 HKH  plan-3  O12  0.020
 HKH  plan-4  C13  0.020
 HKH  plan-4  C22  0.020
 HKH  plan-4  N19  0.020
 HKH  plan-4  O21  0.020
 HKH  plan-4  H24  0.020
 HKH  plan-4  C20  0.020

