# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 04:22:13 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 2-{[(4R)-4-hydroxyhexyl]oxy}ethyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](O)CCCOCCOC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
#
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
 V4J  V4J  "2-{[(4R)-4-hydroxyhexyl]oxy}ethyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate"  ligand  58  26  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V4J
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
 V4J  C16  C  CH2   0  -0.442   3.2552  12.7496   8.6306
 V4J  C3   C  CH2   0  -0.440  -1.6393  16.1347   7.9241
 V4J  C20  C  C     0  -0.040   5.1960  16.7155   7.2061
 V4J  C21  C  CR5   0   0.638   6.0809  15.2858   5.5715
 V4J  C22  C  CH2   0  -0.469  -2.5512  12.9265   8.8423
 V4J  C23  C  C     0  -0.076   4.8488  15.2398   7.5653
 V4J  S1   S  S2    0  -0.013   2.6629  16.2568   6.4490
 V4J  C15  C  CH2   0  -0.494  -1.8983  14.1331   9.5137
 V4J  C14  C  CH3   0  -0.676  -2.8189  15.7685   7.0366
 V4J  O14  O  O2    0  -0.461  -0.8302  10.2223   9.3888
 V4J  C13  C  C     0   0.606   0.3271  10.2005   8.7338
 V4J  C12  C  CH2   0  -0.197  -1.8417   9.2756   9.0398
 V4J  C10  C  CH2   0  -0.211  -3.1198   9.6510   9.7590
 V4J  C9   C  CH2   0  -0.429   2.5767  11.3825   8.5392
 V4J  C7   C  CH2   0  -0.135  -3.2598  12.0489   9.8638
 V4J  C1   C  CH1   0   0.079  -0.9668  14.9489   8.6024
 V4J  C17  C  CH2   0  -0.438   2.7664  13.7162   7.5531
 V4J  C18  C  CR15  0  -0.371   3.3269  15.1183   7.7091
 V4J  C19  C  CH2   0  -0.572   3.8958  17.4871   6.9450
 V4J  N4   N  NR15  0  -0.659   6.0216  16.5606   6.0372
 V4J  N5   N  NR15  0  -0.659   5.3655  14.5098   6.4347
 V4J  O15  O  O     0  -0.442   0.6368   9.3303   7.9604
 V4J  O5   O  OH1   0  -0.677   0.1229  15.4878   9.3354
 V4J  O8   O  O2    0  -0.491  -3.7244  10.8339   9.3033
 V4J  H1   H  HCH2  0   0.241   4.3358  12.6128   8.5402
 V4J  H2   H  HCH2  0   0.224   3.0856  13.1817   9.6226
 V4J  H4   H  HCH2  0   0.221  -0.8850  16.6539   7.3255
 V4J  H5   H  H     0   0.276   5.7485  17.2062   8.0104
 V4J  H6   H  HCH2  0   0.233  -3.2603  13.2378   8.0724
 V4J  H7   H  HCH2  0   0.225  -1.7814  12.3412   8.3356
 V4J  H8   H  H     0   0.284   5.3349  14.9301   8.4947
 V4J  H9   H  HCH2  0   0.230  -1.3039  13.7571  10.3538
 V4J  H10  H  HCH2  0   0.228  -2.6586  14.7868   9.9553
 V4J  H11  H  HCH3  0   0.235  -3.1800  16.6462   6.5003
 V4J  H12  H  HCH3  0   0.219  -2.5459  15.0190   6.2914
 V4J  H13  H  HCH3  0   0.225  -3.6574  15.3750   7.6118
 V4J  H14  H  HCH2  0   0.237  -1.9971   9.2687   7.9583
 V4J  H15  H  HCH2  0   0.239  -1.5418   8.2698   9.3464
 V4J  H18  H  HCH2  0   0.215  -2.9391   9.6830  10.8414
 V4J  H19  H  HCH2  0   0.241  -3.8305   8.8392   9.5816
 V4J  H20  H  HCH2  0   0.241   3.1479  10.6503   9.1137
 V4J  H21  H  HCH2  0   0.229   2.5963  11.0434   7.5008
 V4J  H22  H  HCH2  0   0.201  -2.5923  11.8566  10.7113
 V4J  H23  H  HCH2  0   0.211  -4.1245  12.5890  10.2656
 V4J  H24  H  HCH1  0   0.189  -0.5872  14.2783   7.8142
 V4J  H25  H  HCH2  0   0.254   1.6763  13.7828   7.5790
 V4J  H26  H  HCH2  0   0.235   3.0226  13.3237   6.5652
 V4J  H27  H  HCR5  0   0.274   3.0475  15.5131   8.6916
 V4J  H28  H  HCH2  0   0.289   4.0179  18.2387   6.1657
 V4J  H29  H  HCH2  0   0.274   3.5658  17.9902   7.8550
 V4J  H30  H  HNR5  0   0.397   6.2951  17.3410   5.4633
 V4J  H31  H  HNR5  0   0.398   5.5405  13.5196   6.4803
 V4J  H32  H  HOH1  0   0.446   0.6070  14.7581   9.7353
 V4J  O22  O  O     0  -0.515   6.6702  14.9042   4.5740
 V4J  C11  C  CH2   0  -0.592   1.1472  11.4200   9.0562
 V4J  H3   H  HCH2  0   0.217  -1.9675  16.8388   8.6953
 V4J  H16  H  HCH2  0   0.272   1.1339  11.5883  10.1364
 V4J  H17  H  HCH2  0   0.278   0.6042  12.2695   8.6281

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
 V4J  O22  C21  double  1.220  0.020  1.220
 V4J  C21  N4   single  1.358  0.020  1.358
 V4J  C21  N5   single  1.364  0.020  1.364
 V4J  S1   C19  single  1.811  0.020  1.811
 V4J  S1   C18  single  1.823  0.020  1.823
 V4J  N4   C20  single  1.439  0.020  1.439
 V4J  N5   C23  single  1.442  0.020  1.442
 V4J  C19  C20  single  1.534  0.020  1.534
 V4J  C17  C18  single  1.518  0.020  1.518
 V4J  C17  C16  single  1.528  0.020  1.528
 V4J  C20  C23  single  1.558  0.020  1.558
 V4J  C18  C23  single  1.534  0.020  1.534
 V4J  C1   O5   single  1.419  0.020  1.419
 V4J  C1   C3   single  1.523  0.020  1.523
 V4J  C1   C15  single  1.537  0.020  1.537
 V4J  C11  C9   single  1.521  0.020  1.521
 V4J  C11  C13  single  1.505  0.020  1.505
 V4J  C9   C16  single  1.529  0.020  1.529
 V4J  C14  C3   single  1.521  0.020  1.521
 V4J  C22  C15  single  1.527  0.020  1.527
 V4J  C22  C7   single  1.522  0.020  1.522
 V4J  O15  C13  double  1.205  0.020  1.205
 V4J  C13  O14  single  1.330  0.020  1.330
 V4J  O8   C7   single  1.416  0.020  1.416
 V4J  O8   C10  single  1.405  0.020  1.405
 V4J  O14  C12  single  1.429  0.020  1.429
 V4J  C12  C10  single  1.514  0.020  1.514
 V4J  C16  H1   single  0.970  0.020  1.090
 V4J  C16  H2   single  0.970  0.020  1.090
 V4J  C3   H3   single  0.970  0.020  1.090
 V4J  C3   H4   single  0.970  0.020  1.090
 V4J  C20  H5   single  0.970  0.020  1.090
 V4J  C22  H6   single  0.970  0.020  1.090
 V4J  C22  H7   single  0.970  0.020  1.090
 V4J  C23  H8   single  0.970  0.020  1.090
 V4J  C15  H9   single  0.970  0.020  1.090
 V4J  C15  H10  single  0.970  0.020  1.090
 V4J  C14  H11  single  0.970  0.020  1.090
 V4J  C14  H12  single  0.970  0.020  1.090
 V4J  C14  H13  single  0.970  0.020  1.090
 V4J  C12  H14  single  0.970  0.020  1.090
 V4J  C12  H15  single  0.970  0.020  1.090
 V4J  C11  H16  single  0.970  0.020  1.090
 V4J  C11  H17  single  0.970  0.020  1.090
 V4J  C10  H18  single  0.970  0.020  1.090
 V4J  C10  H19  single  0.970  0.020  1.090
 V4J  C9   H20  single  0.970  0.020  1.090
 V4J  C9   H21  single  0.970  0.020  1.090
 V4J  C7   H22  single  0.970  0.020  1.090
 V4J  C7   H23  single  0.970  0.020  1.090
 V4J  C1   H24  single  0.970  0.020  1.090
 V4J  C17  H25  single  0.970  0.020  1.090
 V4J  C17  H26  single  0.970  0.020  1.090
 V4J  C18  H27  single  0.970  0.020  1.090
 V4J  C19  H28  single  0.970  0.020  1.090
 V4J  C19  H29  single  0.970  0.020  1.090
 V4J  N4   H30  single  0.860  0.020  1.020
 V4J  N5   H31  single  0.890  0.020  1.040
 V4J  O5   H32  single  0.850  0.020  0.980

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
 V4J  H2   C16  H1   106.10  3.000
 V4J  H2   C16  C17  109.85  3.000
 V4J  H1   C16  C17  109.70  3.000
 V4J  H2   C16  C9   109.77  3.000
 V4J  H1   C16  C9   108.78  3.000
 V4J  C17  C16  C9   112.43  3.000
 V4J  H4   C3   H3   106.67  3.000
 V4J  H4   C3   C1   107.98  3.000
 V4J  H3   C3   C1   108.63  3.000
 V4J  H4   C3   C14  109.26  3.000
 V4J  H3   C3   C14  109.48  3.000
 V4J  C1   C3   C14  114.52  3.000
 V4J  H5   C20  N4   110.87  3.000
 V4J  H5   C20  C19  109.15  3.000
 V4J  N4   C20  C19  113.71  3.000
 V4J  H5   C20  C23  111.62  3.000
 V4J  C19  C20  C23  109.07  3.000
 V4J  N4   C20  C23  102.31  3.000
 V4J  O22  C21  N5   126.38  3.000
 V4J  N5   C21  N4   107.10  3.000
 V4J  O22  C21  N4   126.52  3.000
 V4J  H7   C22  H6   106.47  3.000
 V4J  H7   C22  C7   109.31  3.000
 V4J  H6   C22  C7   109.59  3.000
 V4J  H7   C22  C15  109.03  3.000
 V4J  H6   C22  C15  111.24  3.000
 V4J  C7   C22  C15  111.07  3.000
 V4J  H8   C23  N5   111.33  3.000
 V4J  H8   C23  C18  109.82  3.000
 V4J  N5   C23  C18  112.90  3.000
 V4J  H8   C23  C20  111.42  3.000
 V4J  C18  C23  C20  108.53  3.000
 V4J  N5   C23  C20  102.64  3.000
 V4J  C19  S1   C18   89.25  3.000
 V4J  H10  C15  H9   105.79  3.000
 V4J  H10  C15  C1   110.05  3.000
 V4J  H9   C15  C1   107.93  3.000
 V4J  H10  C15  C22  110.60  3.000
 V4J  H9   C15  C22  107.32  3.000
 V4J  C1   C15  C22  114.68  3.000
 V4J  H13  C14  H12  107.74  3.000
 V4J  H13  C14  H11  107.18  3.000
 V4J  H12  C14  H11  107.45  3.000
 V4J  H13  C14  C3   112.06  3.000
 V4J  H12  C14  C3   111.70  3.000
 V4J  H11  C14  C3   110.49  3.000
 V4J  C12  O14  C13  119.01  3.000
 V4J  O15  C13  C11  125.65  3.000
 V4J  O15  C13  O14  123.49  3.000
 V4J  C11  C13  O14  110.82  3.000
 V4J  H15  C12  H14  108.10  3.000
 V4J  H15  C12  C10  109.05  3.000
 V4J  H14  C12  C10  110.60  3.000
 V4J  H15  C12  O14  110.29  3.000
 V4J  H14  C12  O14  110.28  3.000
 V4J  C10  C12  O14  108.50  3.000
 V4J  H19  C10  H18  106.78  3.000
 V4J  H19  C10  O8   107.03  3.000
 V4J  H18  C10  O8   111.48  3.000
 V4J  H19  C10  C12  106.71  3.000
 V4J  H18  C10  C12  109.68  3.000
 V4J  O8   C10  C12  114.72  3.000
 V4J  H21  C9   H20  106.41  3.000
 V4J  H21  C9   C11  110.35  3.000
 V4J  H20  C9   C11  109.23  3.000
 V4J  H21  C9   C16  109.05  3.000
 V4J  H20  C9   C16  109.63  3.000
 V4J  C11  C9   C16  112.01  3.000
 V4J  H23  C7   H22  106.48  3.000
 V4J  H23  C7   O8   108.00  3.000
 V4J  H22  C7   O8   110.81  3.000
 V4J  H23  C7   C22  109.23  3.000
 V4J  H22  C7   C22  109.68  3.000
 V4J  O8   C7   C22  112.44  3.000
 V4J  H24  C1   O5   109.63  3.000
 V4J  H24  C1   C15  108.04  3.000
 V4J  O5   C1   C15  111.13  3.000
 V4J  H24  C1   C3   107.90  3.000
 V4J  C15  C1   C3   114.18  3.000
 V4J  O5   C1   C3   105.87  3.000
 V4J  H26  C17  H25  106.09  3.000
 V4J  H26  C17  C18  109.75  3.000
 V4J  H25  C17  C18  108.03  3.000
 V4J  H26  C17  C16  109.58  3.000
 V4J  H25  C17  C16  109.94  3.000
 V4J  C18  C17  C16  113.19  3.000
 V4J  H27  C18  C17  109.33  3.000
 V4J  H27  C18  S1   107.58  3.000
 V4J  C17  C18  S1   111.79  3.000
 V4J  H27  C18  C23  107.98  3.000
 V4J  C17  C18  C23  115.46  3.000
 V4J  S1   C18  C23  104.31  3.000
 V4J  H29  C19  H28  108.20  3.000
 V4J  H29  C19  S1   109.62  3.000
 V4J  H28  C19  S1   110.43  3.000
 V4J  H29  C19  C20  110.26  3.000
 V4J  H28  C19  C20  111.94  3.000
 V4J  S1   C19  C20  106.38  3.000
 V4J  H30  N4   C21  121.34  3.000
 V4J  H30  N4   C20  122.37  3.000
 V4J  C21  N4   C20  113.86  3.000
 V4J  H31  N5   C23  121.66  3.000
 V4J  H31  N5   C21  119.83  3.000
 V4J  C23  N5   C21  113.35  3.000
 V4J  H32  O5   C1   108.23  3.000
 V4J  C7   O8   C10  116.93  3.000
 V4J  H17  C11  H16  105.12  3.000
 V4J  H17  C11  C9   110.63  3.000
 V4J  H16  C11  C9   110.56  3.000
 V4J  H17  C11  C13  105.94  3.000
 V4J  H16  C11  C13  109.26  3.000
 V4J  C9   C11  C13  114.81  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
 V4J  CONST_01  N5   C21  N4   C20     0.00   0.0  0
 V4J  CONST_02  N4   C21  N5   C23     0.00   0.0  0
 V4J  CONST_03  O22  C21  N4   C20   180.00   0.0  0
 V4J  CONST_04  O22  C21  N5   C23   180.00   0.0  0
 V4J  CONST_06  H30  N4   C21  N5    180.00   0.0  0
 V4J  CONST_07  H30  N4   C21  O22     0.00   0.0  0
 V4J  Var_01    C18  S1   C19  C20    39.86  30.0  1
 V4J  Var_02    H28  C19  S1   C18   161.52  30.0  1
 V4J  Var_03    H29  C19  S1   C18   -79.36  30.0  1
 V4J  Var_04    C18  C17  C16  C9    174.40  30.0  2
 V4J  Var_05    H1   C16  C17  C18   -64.42  30.0  3
 V4J  Var_06    H2   C16  C17  C18    51.84  30.0  3
 V4J  Var_07    C13  C11  C9   C16   167.68  30.0  2
 V4J  Var_08    C10  O8   C7   C22   113.62  30.0  1
 V4J  Var_09    O8   C7   C22  C15  -172.23  30.0  3
 V4J  Var_10    C9   C11  C13  O14   170.48  30.0  2
 V4J  Var_11    O8   C10  C12  O14    69.14  30.0  3
 V4J  Var_12    C10  C12  O14  C13  -170.85  30.0  3
 V4J  Var_13    C11  C13  O14  C12   169.20  30.0  1
 V4J  Var_14    O15  C13  O14  C12    -8.72  30.0  1
 V4J  Var_15    C7   O8   C10  C12   -85.36  30.0  1
 V4J  Var_16    C17  C16  C9   C11   -75.15  30.0  3
 V4J  Var_17    O15  C13  C11  C9    -11.66  30.0  3
 V4J  Var_18    C1   C15  C22  C7    170.35  30.0  3
 V4J  Var_19    H16  C11  C9   C16   -68.16  30.0  2
 V4J  Var_20    H17  C11  C9   C16    47.86  30.0  2
 V4J  Var_21    H22  C7   C22  C15   -48.45  30.0  3
 V4J  Var_22    H23  C7   C22  C15    67.89  30.0  3
 V4J  Var_23    H16  C11  C13  O14    45.64  30.0  2
 V4J  Var_24    H17  C11  C13  O14   -67.13  30.0  2
 V4J  Var_25    H18  C10  C12  O14   -57.21  30.0  3
 V4J  Var_26    H19  C10  C12  O14  -172.51  30.0  3
 V4J  Var_27    H20  C9   C11  C13   -70.66  30.0  3
 V4J  Var_28    H21  C9   C11  C13    45.99  30.0  3
 V4J  Var_29    H14  C12  O14  C13   -49.58  30.0  3
 V4J  Var_30    H15  C12  O14  C13    69.76  30.0  3
 V4J  Var_31    H1   C16  C9   C11   163.14  30.0  3
 V4J  Var_32    H2   C16  C9   C11    47.45  30.0  3
 V4J  Var_33    H22  C7   O8   C10    -9.53  30.0  3
 V4J  Var_34    H23  C7   O8   C10  -125.80  30.0  3
 V4J  Var_35    H25  C17  C16  C9     53.49  30.0  2
 V4J  Var_36    H26  C17  C16  C9    -62.74  30.0  2
 V4J  Var_37    H9   C15  C22  C7     50.46  30.0  3
 V4J  Var_38    H10  C15  C22  C7    -64.49  30.0  3
 V4J  Var_39    H18  C10  O8   C7     40.06  30.0  3
 V4J  Var_40    H19  C10  O8   C7    156.48  30.0  3
 V4J  Var_41    H11  C14  C3   C1   -173.75  30.0  3
 V4J  Var_42    H12  C14  C3   C1    -54.20  30.0  3
 V4J  Var_43    H13  C14  C3   C1     66.80  30.0  3
 V4J  Var_44    H6   C22  C15  C1    -67.29  30.0  1
 V4J  Var_45    H7   C22  C15  C1     49.83  30.0  1
 V4J  Var_46    H20  C9   C16  C17   163.42  30.0  2
 V4J  Var_47    H21  C9   C16  C17    47.28  30.0  2
 V4J  Var_48    H16  C11  C13  O15  -136.49  30.0  2
 V4J  Var_49    H17  C11  C13  O15   110.73  30.0  2
 V4J  Var_50    H6   C22  C7   O8     64.46  30.0  1
 V4J  Var_51    H7   C22  C7   O8    -51.88  30.0  1
 V4J  Var_52    H14  C12  C10  O8    -51.94  30.0  1
 V4J  Var_53    H15  C12  C10  O8   -170.69  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
 V4J  chir_01  C20  N4  C19  C23  negativ
 V4J  chir_02  C23  N5  C18  C20  positiv
 V4J  chir_03  C1   O5  C3   C15  positiv
 V4J  chir_04  C18  S1  C17  C23  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
 V4J  plan-1  C20  0.020
 V4J  plan-1  C21  0.020
 V4J  plan-1  C23  0.020
 V4J  plan-1  N4   0.020
 V4J  plan-1  N5   0.020
 V4J  plan-1  H30  0.020
 V4J  plan-1  H31  0.020
 V4J  plan-1  O22  0.020
 V4J  plan-2  O14  0.020
 V4J  plan-2  C13  0.020
 V4J  plan-2  O15  0.020
 V4J  plan-2  C11  0.020

