# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 09:34:53 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(2-sulfanylethyl)-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(COP(O)O)[C@@H](O)C(=O)NCCC(=O)NCCS
#
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
 4S8  4S8  "N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(2-sulfanylethyl)-beta-alaninamide"  ligand  44  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4S8
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
 4S8  P2A  P  P     0   0.881  -18.7306  -48.8416   -5.2300
 4S8  O3A  O  OH1   0  -0.767  -19.4424  -47.6279   -6.0784
 4S8  O4A  O  OH1   0  -0.761  -19.0085  -48.3304   -3.6992
 4S8  O6A  O  O2    0  -0.607  -17.1937  -48.2774   -5.2929
 4S8  CCP  C  CH2   0  -0.108  -16.3449  -48.7367   -6.3370
 4S8  CBP  C  CT    0  -0.163  -15.1068  -47.8294   -6.4238
 4S8  CDP  C  CH3   0  -0.645  -14.4408  -47.7579   -5.0479
 4S8  CEP  C  CH3   0  -0.657  -15.5140  -46.4259   -6.8761
 4S8  CAP  C  CH1   0  -0.031  -14.1501  -48.4982   -7.4440
 4S8  OAP  O  OH1   0  -0.660  -14.8442  -48.6714   -8.6574
 4S8  C9P  C  C     0   0.500  -12.8554  -47.7019   -7.6417
 4S8  O9P  O  O     0  -0.490  -11.9370  -47.7701   -6.8355
 4S8  N8P  N  NH1   0  -0.621  -12.8155  -46.9318   -8.7377
 4S8  C7P  C  CH2   0  -0.277  -11.7028  -46.0667   -9.0515
 4S8  C6P  C  CH2   0  -0.585  -10.5615  -46.7949   -9.7583
 4S8  C5P  C  C     0   0.559   -9.3759  -45.8815   -9.9897
 4S8  O5P  O  O     0  -0.493   -9.0386  -45.0410   -9.1676
 4S8  N4P  N  NH1   0  -0.632   -8.7153  -46.0665  -11.1473
 4S8  C3P  C  CH2   0  -0.281   -7.5281  -45.3254  -11.5004
 4S8  C2P  C  CH2   0  -0.552   -6.2693  -45.9326  -10.8904
 4S8  S1P  S  S2    0  -0.258   -4.8393  -44.9183  -11.3963
 4S8  H1   H  HOH1  0   0.478  -20.1993  -47.9527   -6.5801
 4S8  H2   H  HOH1  0   0.482  -19.4275  -49.0237   -3.1770
 4S8  H3   H  HCH2  0   0.232  -16.8743  -48.7381   -7.2935
 4S8  H4   H  HCH2  0   0.220  -16.0273  -49.7663   -6.1286
 4S8  H5   H  HCH3  0   0.234  -15.1327  -47.3516   -4.3122
 4S8  H6   H  HCH3  0   0.223  -14.1261  -48.7456   -4.7036
 4S8  H7   H  HCH3  0   0.237  -13.5640  -47.1142   -5.0572
 4S8  H8   H  HCH3  0   0.237  -16.2431  -46.0008   -6.1865
 4S8  H9   H  HCH3  0   0.232  -14.6588  -45.7493   -6.8941
 4S8  H10  H  HCH3  0   0.231  -15.9636  -46.4299   -7.8696
 4S8  H11  H  HCH1  0   0.248  -13.8499  -49.4683   -7.0249
 4S8  H12  H  HOH1  0   0.461  -14.3938  -49.3411   -9.1824
 4S8  H13  H  HNH1  0   0.400  -13.5955  -46.9725   -9.3741
 4S8  H14  H  HCH2  0   0.247  -11.3390  -45.6052   -8.1347
 4S8  H15  H  HCH2  0   0.259  -12.0810  -45.2645   -9.6851
 4S8  H16  H  HCH2  0   0.258  -10.9155  -47.2304  -10.6947
 4S8  H17  H  HCH2  0   0.278  -10.2193  -47.6261   -9.1347
 4S8  H18  H  HNH1  0   0.404   -9.0200  -46.7923  -11.7753
 4S8  H19  H  HCH2  0   0.262   -7.4490  -45.3179  -12.5876
 4S8  H20  H  HCH2  0   0.252   -7.6402  -44.2900  -11.1766
 4S8  H21  H  HCH2  0   0.273   -6.3432  -45.9423   -9.8039
 4S8  H22  H  HCH2  0   0.270   -6.1358  -46.9554  -11.2415
 4S8  H23  H  HSH1  0   0.227   -3.8956  -45.6232  -10.7638

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
 4S8  C3P  N4P  single  1.443  0.020  1.443
 4S8  C3P  C2P  single  1.525  0.020  1.525
 4S8  S1P  C2P  single  1.825  0.020  1.825
 4S8  N4P  C5P  single  1.346  0.020  1.346
 4S8  C5P  O5P  double  1.223  0.020  1.223
 4S8  C5P  C6P  single  1.514  0.020  1.514
 4S8  C6P  C7P  single  1.527  0.020  1.527
 4S8  C7P  N8P  single  1.444  0.020  1.444
 4S8  N8P  C9P  single  1.340  0.020  1.340
 4S8  OAP  CAP  single  1.409  0.020  1.409
 4S8  C9P  CAP  single  1.533  0.020  1.533
 4S8  C9P  O9P  double  1.224  0.020  1.224
 4S8  CAP  CBP  single  1.550  0.020  1.550
 4S8  CEP  CBP  single  1.530  0.020  1.530
 4S8  CBP  CCP  single  1.537  0.020  1.537
 4S8  CBP  CDP  single  1.530  0.020  1.530
 4S8  CCP  O6A  single  1.422  0.020  1.422
 4S8  O3A  P2A  single  1.643  0.020  1.643
 4S8  O6A  P2A  single  1.638  0.020  1.638
 4S8  P2A  O4A  single  1.638  0.020  1.638
 4S8  O3A  H1   single  0.850  0.020  0.980
 4S8  O4A  H2   single  0.850  0.020  0.980
 4S8  CCP  H3   single  0.970  0.020  1.090
 4S8  CCP  H4   single  0.970  0.020  1.090
 4S8  CDP  H5   single  0.970  0.020  1.090
 4S8  CDP  H6   single  0.970  0.020  1.090
 4S8  CDP  H7   single  0.970  0.020  1.090
 4S8  CEP  H8   single  0.970  0.020  1.090
 4S8  CEP  H9   single  0.970  0.020  1.090
 4S8  CEP  H10  single  0.970  0.020  1.090
 4S8  CAP  H11  single  0.970  0.020  1.090
 4S8  OAP  H12  single  0.850  0.020  0.980
 4S8  N8P  H13  single  0.860  0.020  1.020
 4S8  C7P  H14  single  0.970  0.020  1.090
 4S8  C7P  H15  single  0.970  0.020  1.090
 4S8  C6P  H16  single  0.970  0.020  1.090
 4S8  C6P  H17  single  0.970  0.020  1.090
 4S8  N4P  H18  single  0.860  0.020  1.020
 4S8  C3P  H19  single  0.970  0.020  1.090
 4S8  C3P  H20  single  0.970  0.020  1.090
 4S8  C2P  H21  single  0.970  0.020  1.090
 4S8  C2P  H22  single  0.970  0.020  1.090
 4S8  S1P  H23  single  1.200  0.020  1.300

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
 4S8  O6A  P2A  O4A   95.02  3.000
 4S8  O4A  P2A  O3A  100.29  3.000
 4S8  O6A  P2A  O3A   97.60  3.000
 4S8  H1   O3A  P2A  111.09  3.000
 4S8  H2   O4A  P2A  110.83  3.000
 4S8  CCP  O6A  P2A  118.49  3.000
 4S8  H4   CCP  H3   107.76  3.000
 4S8  H4   CCP  CBP  109.35  3.000
 4S8  H3   CCP  CBP  109.96  3.000
 4S8  H4   CCP  O6A  109.66  3.000
 4S8  H3   CCP  O6A  110.72  3.000
 4S8  CBP  CCP  O6A  109.37  3.000
 4S8  CAP  CBP  CEP  111.44  3.000
 4S8  CEP  CBP  CDP  109.80  3.000
 4S8  CAP  CBP  CDP  110.08  3.000
 4S8  CDP  CBP  CCP  109.10  3.000
 4S8  CEP  CBP  CCP  110.11  3.000
 4S8  CAP  CBP  CCP  106.23  3.000
 4S8  H7   CDP  H6   107.79  3.000
 4S8  H7   CDP  H5   107.29  3.000
 4S8  H6   CDP  H5   107.92  3.000
 4S8  H7   CDP  CBP  111.76  3.000
 4S8  H6   CDP  CBP  111.50  3.000
 4S8  H5   CDP  CBP  110.39  3.000
 4S8  H10  CEP  H9   108.09  3.000
 4S8  H10  CEP  H8   107.58  3.000
 4S8  H9   CEP  H8   107.04  3.000
 4S8  H10  CEP  CBP  112.07  3.000
 4S8  H9   CEP  CBP  111.43  3.000
 4S8  H8   CEP  CBP  110.42  3.000
 4S8  H11  CAP  C9P  106.09  3.000
 4S8  H11  CAP  OAP  110.78  3.000
 4S8  C9P  CAP  OAP  111.66  3.000
 4S8  H11  CAP  CBP  107.36  3.000
 4S8  C9P  CAP  CBP  112.46  3.000
 4S8  OAP  CAP  CBP  108.41  3.000
 4S8  H12  OAP  CAP  108.95  3.000
 4S8  N8P  C9P  O9P  123.26  3.000
 4S8  O9P  C9P  CAP  121.32  3.000
 4S8  N8P  C9P  CAP  115.41  3.000
 4S8  H13  N8P  C7P  118.92  3.000
 4S8  H13  N8P  C9P  118.06  3.000
 4S8  C7P  N8P  C9P  123.02  3.000
 4S8  H15  C7P  H14  107.06  3.000
 4S8  H15  C7P  C6P  109.95  3.000
 4S8  H14  C7P  C6P  110.00  3.000
 4S8  H15  C7P  N8P  107.45  3.000
 4S8  H14  C7P  N8P  109.17  3.000
 4S8  C6P  C7P  N8P  113.00  3.000
 4S8  H17  C6P  H16  106.69  3.000
 4S8  H17  C6P  C5P  107.49  3.000
 4S8  H16  C6P  C5P  111.31  3.000
 4S8  H17  C6P  C7P  109.40  3.000
 4S8  H16  C6P  C7P  110.17  3.000
 4S8  C5P  C6P  C7P  111.60  3.000
 4S8  N4P  C5P  O5P  122.50  3.000
 4S8  O5P  C5P  C6P  121.85  3.000
 4S8  N4P  C5P  C6P  115.65  3.000
 4S8  H18  N4P  C3P  117.81  3.000
 4S8  H18  N4P  C5P  119.15  3.000
 4S8  C3P  N4P  C5P  122.93  3.000
 4S8  H20  C3P  H19  107.28  3.000
 4S8  H20  C3P  C2P  110.13  3.000
 4S8  H19  C3P  C2P  109.98  3.000
 4S8  H20  C3P  N4P  109.29  3.000
 4S8  H19  C3P  N4P  107.89  3.000
 4S8  C2P  C3P  N4P  112.13  3.000
 4S8  H22  C2P  H21  108.75  3.000
 4S8  H22  C2P  S1P  109.66  3.000
 4S8  H21  C2P  S1P  109.55  3.000
 4S8  H22  C2P  C3P  110.25  3.000
 4S8  H21  C2P  C3P  110.28  3.000
 4S8  S1P  C2P  C3P  108.34  3.000
 4S8  H23  S1P  C2P   97.41  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
 4S8  CONST_01  C7P  N8P  C9P  CAP   180.00   0.0  0
 4S8  CONST_02  C7P  N8P  C9P  O9P     0.00   0.0  0
 4S8  CONST_03  C3P  N4P  C5P  C6P   180.00   0.0  0
 4S8  CONST_04  C3P  N4P  C5P  O5P     0.00   0.0  0
 4S8  CONST_05  H13  N8P  C9P  CAP     0.00   0.0  0
 4S8  CONST_06  H13  N8P  C9P  O9P   180.00   0.0  0
 4S8  CONST_07  H18  N4P  C5P  C6P     0.00   0.0  0
 4S8  CONST_08  H18  N4P  C5P  O5P   180.00   0.0  0
 4S8  Var_01    CBP  CCP  O6A  P2A   165.47  30.0  1
 4S8  Var_02    CCP  O6A  P2A  O3A   -93.62  30.0  1
 4S8  Var_03    CCP  O6A  P2A  O4A   165.28  30.0  1
 4S8  Var_04    CAP  CBP  CCP  O6A   172.63  30.0  1
 4S8  Var_05    CEP  CBP  CCP  O6A   -66.58  30.0  1
 4S8  Var_06    CDP  CBP  CCP  O6A    53.99  30.0  1
 4S8  Var_07    C6P  C7P  N8P  C9P    83.59  30.0  1
 4S8  Var_08    C5P  C6P  C7P  N8P  -176.21  30.0  1
 4S8  Var_09    N4P  C5P  C6P  C7P  -143.21  30.0  2
 4S8  Var_10    O5P  C5P  C6P  C7P    37.45  30.0  2
 4S8  Var_11    C2P  C3P  N4P  C5P    83.44  30.0  2
 4S8  Var_12    S1P  C2P  C3P  N4P  -179.86  30.0  3
 4S8  Var_13    H3   CCP  O6A  P2A    44.15  30.0  1
 4S8  Var_14    H4   CCP  O6A  P2A   -74.64  30.0  1
 4S8  Var_15    H8   CEP  CBP  CCP    58.16  30.0  3
 4S8  Var_16    H9   CEP  CBP  CCP   176.98  30.0  3
 4S8  Var_17    H10  CEP  CBP  CCP   -61.75  30.0  3
 4S8  Var_18    H5   CDP  CBP  CCP   -59.93  30.0  3
 4S8  Var_19    H6   CDP  CBP  CCP    60.02  30.0  3
 4S8  Var_20    H7   CDP  CBP  CCP  -179.26  30.0  3
 4S8  Var_21    H8   CEP  CBP  CDP   -61.99  30.0  3
 4S8  Var_22    H9   CEP  CBP  CDP    56.83  30.0  3
 4S8  Var_23    H10  CEP  CBP  CDP   178.10  30.0  3
 4S8  Var_24    H3   CCP  CBP  CDP   175.77  30.0  3
 4S8  Var_25    H4   CCP  CBP  CDP   -66.10  30.0  3
 4S8  Var_26    H3   CCP  CBP  CEP    55.20  30.0  3
 4S8  Var_27    H4   CCP  CBP  CEP   173.33  30.0  3
 4S8  Var_28    H5   CDP  CBP  CEP    60.83  30.0  3
 4S8  Var_29    H6   CDP  CBP  CEP  -179.23  30.0  3
 4S8  Var_30    H7   CDP  CBP  CEP   -58.50  30.0  3
 4S8  Var_31    H8   CEP  CBP  CAP   175.78  30.0  3
 4S8  Var_32    H9   CEP  CBP  CAP   -65.40  30.0  3
 4S8  Var_33    H10  CEP  CBP  CAP    55.86  30.0  3
 4S8  Var_34    H3   CCP  CBP  CAP   -65.59  30.0  3
 4S8  Var_35    H4   CCP  CBP  CAP    52.54  30.0  3
 4S8  Var_36    H5   CDP  CBP  CAP  -176.13  30.0  3
 4S8  Var_37    H6   CDP  CBP  CAP   -56.19  30.0  3
 4S8  Var_38    H7   CDP  CBP  CAP    64.54  30.0  3
 4S8  Var_39    H14  C7P  N8P  C9P   -39.16  30.0  1
 4S8  Var_40    H15  C7P  N8P  C9P  -154.94  30.0  1
 4S8  Var_41    H16  C6P  C7P  N8P    59.60  30.0  1
 4S8  Var_42    H17  C6P  C7P  N8P   -57.39  30.0  1
 4S8  Var_43    H13  N8P  C7P  C6P   -95.56  30.0  3
 4S8  Var_44    H19  C3P  N4P  C5P  -155.30  30.0  2
 4S8  Var_45    H20  C3P  N4P  C5P   -38.97  30.0  2
 4S8  Var_46    H14  C7P  C6P  C5P   -53.93  30.0  3
 4S8  Var_47    H15  C7P  C6P  C5P    63.74  30.0  3
 4S8  Var_48    H16  C6P  C5P  O5P   161.00  30.0  3
 4S8  Var_49    H17  C6P  C5P  O5P   -82.50  30.0  3
 4S8  Var_50    H21  C2P  C3P  N4P   -59.97  30.0  3
 4S8  Var_51    H22  C2P  C3P  N4P    60.14  30.0  3
 4S8  Var_52    H16  C6P  C5P  N4P   -19.66  30.0  3
 4S8  Var_53    H17  C6P  C5P  N4P    96.84  30.0  3
 4S8  Var_54    H18  N4P  C3P  C2P   -92.56  30.0  3
 4S8  Var_55    H19  C3P  C2P  S1P    60.10  30.0  1
 4S8  Var_56    H20  C3P  C2P  S1P   -57.93  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
 4S8  chir_01  CAP  OAP  C9P  CBP  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
 4S8  plan-1  CAP  0.020
 4S8  plan-1  C9P  0.020
 4S8  plan-1  O9P  0.020
 4S8  plan-1  N8P  0.020
 4S8  plan-1  C7P  0.020
 4S8  plan-1  H13  0.020
 4S8  plan-2  C6P  0.020
 4S8  plan-2  C5P  0.020
 4S8  plan-2  O5P  0.020
 4S8  plan-2  N4P  0.020
 4S8  plan-2  C3P  0.020
 4S8  plan-2  H18  0.020

