# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Nov 25 16:31:07 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: (1S)-1,4-anhydro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-1-(3-methoxynaphthalen-2-yl)-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2ccccc2cc1[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 WCG  WCG  "(1S)-1,4-anhydro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-1-(3-methoxynaphthalen-2-yl)-D-ribitol"  ligand  54  33  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WCG
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
 WCG  C01  C  CH3   0  -0.441  168.5442  -6.3353  49.8608
 WCG  C03  C  CR6   0   0.392  168.6311  -6.8004  52.1842
 WCG  C04  C  CR16  0  -0.474  169.8114  -7.4892  52.0641
 WCG  C05  C  CR66  0   0.107  170.4545  -8.0187  53.2053
 WCG  C06  C  CR16  0  -0.384  171.6769  -8.7283  53.1154
 WCG  C07  C  CR16  0  -0.243  172.2873  -9.2127  54.2452
 WCG  C08  C  CR16  0  -0.255  171.7035  -9.0202  55.5122
 WCG  C09  C  CR16  0  -0.312  170.5160  -8.3453  55.6222
 WCG  C10  C  CR66  0   0.136  169.8701  -7.8294  54.4784
 WCG  C11  C  CR16  0  -0.383  168.6456  -7.1240  54.5632
 WCG  C12  C  CR6   0   0.022  168.0179  -6.6102  53.4637
 WCG  C13  C  CR15  0  -0.047  166.7041  -5.8599  53.5156
 WCG  C15  C  CR15  0   0.022  166.8464  -3.6134  54.1632
 WCG  C16  C  CH2   0  -0.194  168.0742  -2.7325  54.1779
 WCG  C30  C  CR15  0  -0.045  166.7517  -4.4695  55.4272
 WCG  C32  C  CR15  0  -0.023  166.0620  -5.7283  54.8904
 WCG  O02  O  O2    0  -0.457  167.9628  -6.2761  51.1478
 WCG  O14  O  O     0  -0.491  166.8877  -4.5121  53.0768
 WCG  O17  O  O2    0  -0.574  168.0733  -1.7396  53.1427
 WCG  O19  O  O     0  -0.656  167.0289  -2.3875  50.8103
 WCG  O20  O  OH1   0  -0.725  168.8729  -0.5915  51.1860
 WCG  O21  O  O2    0  -0.691  169.4097  -3.0732  51.4541
 WCG  O23  O  OH1   0  -0.720  171.4341  -1.7998  52.3155
 WCG  O24  O  O     0  -0.658  171.3851  -2.6322  49.8320
 WCG  O25  O  O2    0  -0.681  171.4792  -4.2303  51.9008
 WCG  O27  O  OH1   0  -0.721  173.1093  -5.8473  52.8363
 WCG  O28  O  OH1   0  -0.729  173.8854  -3.9820  51.4079
 WCG  O29  O  O     0  -0.667  172.5613  -5.9469  50.2769
 WCG  O31  O  OH1   0  -0.654  166.0252  -3.7908  56.4134
 WCG  O33  O  OH1   0  -0.666  164.6909  -5.4945  54.6970
 WCG  P18  P  P     0   1.486  168.2057  -1.9797  51.5868
 WCG  P22  P  P     0   1.480  170.9875  -2.8590  51.2258
 WCG  P26  P  P     0   1.466  172.7785  -5.1181  51.4711
 WCG  H1   H  HCH3  0   0.262  167.8708  -5.8020  49.1949
 WCG  H2   H  HCH3  0   0.229  169.5234  -5.8507  49.8375
 WCG  H3   H  HCH3  0   0.230  168.6502  -7.3643  49.5079
 WCG  H4   H  HCR6  0   0.281  170.2788  -7.6423  51.1005
 WCG  H5   H  HCR6  0   0.281  172.1164  -8.9011  52.1387
 WCG  H6   H  HCR6  0   0.263  173.2217  -9.7526  54.1627
 WCG  H7   H  HCR6  0   0.258  172.1931  -9.4099  56.3948
 WCG  H8   H  HCR6  0   0.257  170.0586  -8.1977  56.5936
 WCG  H9   H  HCR6  0   0.255  168.2148  -7.0083  55.5496
 WCG  H10  H  HCR5  0   0.260  166.0001  -6.3435  52.8313
 WCG  H11  H  HCR5  0   0.242  165.9508  -2.9820  54.0907
 WCG  H12  H  HCH2  0   0.249  168.9830  -3.3373  54.1209
 WCG  H13  H  HCH2  0   0.266  168.1007  -2.1659  55.1083
 WCG  H14  H  HCR5  0   0.245  167.7566  -4.7309  55.7843
 WCG  H15  H  HCR5  0   0.247  166.2212  -6.6032  55.5314
 WCG  H16  H  HOH1  0   0.507  168.6523  -0.2937  50.2917
 WCG  H17  H  HOH1  0   0.511  171.6885  -0.9337  51.9657
 WCG  H18  H  HOH1  0   0.514  172.7371  -6.7387  52.9455
 WCG  H19  H  HOH1  0   0.510  174.6080  -4.1533  50.7871
 WCG  H20  H  HOH1  0   0.464  166.2369  -4.1698  57.2726
 WCG  H21  H  HOH1  0   0.446  164.3544  -5.0482  55.4833

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
 WCG  O29  P26  double    1.470  0.020  1.470
 WCG  O24  P22  double    1.467  0.020  1.467
 WCG  O19  P18  double    1.468  0.020  1.468
 WCG  O20  P18  single    1.592  0.020  1.592
 WCG  P26  O25  single    1.631  0.020  1.631
 WCG  P26  O27  single    1.583  0.020  1.583
 WCG  P26  O28  single    1.587  0.020  1.587
 WCG  O25  P22  single    1.606  0.020  1.606
 WCG  O21  P18  single    1.632  0.020  1.632
 WCG  O21  P22  single    1.609  0.020  1.609
 WCG  P18  O17  single    1.580  0.020  1.580
 WCG  P22  O23  single    1.584  0.020  1.584
 WCG  C01  O02  single    1.413  0.020  1.413
 WCG  O02  C03  single    1.340  0.020  1.340
 WCG  O17  C16  single    1.434  0.020  1.434
 WCG  C03  C04  aromatic  1.372  0.020  1.372
 WCG  C03  C12  aromatic  1.432  0.020  1.432
 WCG  C04  C05  aromatic  1.413  0.020  1.413
 WCG  O14  C13  single    1.429  0.020  1.429
 WCG  O14  C15  single    1.410  0.020  1.410
 WCG  C16  C15  single    1.511  0.020  1.511
 WCG  C12  C13  single    1.514  0.020  1.514
 WCG  C12  C11  aromatic  1.366  0.020  1.366
 WCG  C13  C32  single    1.523  0.020  1.523
 WCG  C05  C06  aromatic  1.416  0.020  1.416
 WCG  C05  C10  aromatic  1.414  0.020  1.414
 WCG  C06  C07  aromatic  1.373  0.020  1.373
 WCG  C15  C30  single    1.530  0.020  1.530
 WCG  C11  C10  aromatic  1.416  0.020  1.416
 WCG  C10  C09  aromatic  1.411  0.020  1.411
 WCG  C07  C08  aromatic  1.408  0.020  1.408
 WCG  C30  C32  single    1.532  0.020  1.532
 WCG  C30  O31  single    1.400  0.020  1.400
 WCG  C32  O33  single    1.404  0.020  1.404
 WCG  C09  C08  aromatic  1.370  0.020  1.370
 WCG  C01  H1   single    0.970  0.020  1.090
 WCG  C01  H2   single    0.970  0.020  1.090
 WCG  C01  H3   single    0.970  0.020  1.090
 WCG  C04  H4   single    0.930  0.020  1.080
 WCG  C06  H5   single    0.930  0.020  1.080
 WCG  C07  H6   single    0.930  0.020  1.080
 WCG  C08  H7   single    0.930  0.020  1.080
 WCG  C09  H8   single    0.930  0.020  1.080
 WCG  C11  H9   single    0.930  0.020  1.080
 WCG  C13  H10  single    0.970  0.020  1.090
 WCG  C15  H11  single    0.970  0.020  1.090
 WCG  C16  H12  single    0.970  0.020  1.090
 WCG  C16  H13  single    0.970  0.020  1.090
 WCG  C30  H14  single    0.970  0.020  1.090
 WCG  C32  H15  single    0.970  0.020  1.090
 WCG  O20  H16  single    0.850  0.020  0.980
 WCG  O23  H17  single    0.850  0.020  0.980
 WCG  O27  H18  single    0.850  0.020  0.980
 WCG  O28  H19  single    0.850  0.020  0.980
 WCG  O31  H20  single    0.850  0.020  0.980
 WCG  O33  H21  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
 WCG  H3   C01  H2   108.88  3.000
 WCG  H3   C01  H1   108.92  3.000
 WCG  H2   C01  H1   108.94  3.000
 WCG  H3   C01  O02  111.92  3.000
 WCG  H2   C01  O02  111.68  3.000
 WCG  H1   C01  O02  106.41  3.000
 WCG  O02  C03  C12  115.19  3.000
 WCG  C12  C03  C04  120.90  3.000
 WCG  O02  C03  C04  123.91  3.000
 WCG  H4   C04  C05  118.02  3.000
 WCG  H4   C04  C03  121.38  3.000
 WCG  C05  C04  C03  120.60  3.000
 WCG  C10  C05  C06  118.76  3.000
 WCG  C10  C05  C04  119.28  3.000
 WCG  C06  C05  C04  121.96  3.000
 WCG  H5   C06  C07  120.31  3.000
 WCG  H5   C06  C05  119.12  3.000
 WCG  C07  C06  C05  120.56  3.000
 WCG  H6   C07  C08  119.65  3.000
 WCG  H6   C07  C06  119.82  3.000
 WCG  C08  C07  C06  120.53  3.000
 WCG  H7   C08  C09  120.27  3.000
 WCG  H7   C08  C07  119.81  3.000
 WCG  C09  C08  C07  119.92  3.000
 WCG  H8   C09  C10  118.91  3.000
 WCG  H8   C09  C08  120.32  3.000
 WCG  C10  C09  C08  120.77  3.000
 WCG  C11  C10  C09  121.97  3.000
 WCG  C09  C10  C05  119.46  3.000
 WCG  C11  C10  C05  118.57  3.000
 WCG  H9   C11  C12  120.67  3.000
 WCG  H9   C11  C10  116.87  3.000
 WCG  C12  C11  C10  122.45  3.000
 WCG  C13  C12  C11  123.89  3.000
 WCG  C11  C12  C03  118.19  3.000
 WCG  C13  C12  C03  117.92  3.000
 WCG  H10  C13  O14  107.90  3.000
 WCG  H10  C13  C32  109.35  3.000
 WCG  O14  C13  C32  104.46  3.000
 WCG  H10  C13  C12  108.53  3.000
 WCG  C32  C13  C12  116.08  3.000
 WCG  O14  C13  C12  110.21  3.000
 WCG  H11  C15  O14  109.84  3.000
 WCG  H11  C15  C30  109.01  3.000
 WCG  O14  C15  C30  106.36  3.000
 WCG  H11  C15  C16  109.15  3.000
 WCG  C30  C15  C16  111.62  3.000
 WCG  O14  C15  C16  110.80  3.000
 WCG  H13  C16  H12  108.18  3.000
 WCG  H13  C16  O17  104.85  3.000
 WCG  H12  C16  O17  110.23  3.000
 WCG  H13  C16  C15  109.34  3.000
 WCG  H12  C16  C15  110.64  3.000
 WCG  O17  C16  C15  113.33  3.000
 WCG  H14  C30  O31  111.17  3.000
 WCG  H14  C30  C32  109.28  3.000
 WCG  O31  C30  C32  114.29  3.000
 WCG  H14  C30  C15  110.20  3.000
 WCG  O31  C30  C15  110.05  3.000
 WCG  C32  C30  C15  101.43  3.000
 WCG  H15  C32  O33  110.81  3.000
 WCG  H15  C32  C30  112.67  3.000
 WCG  O33  C32  C30  110.54  3.000
 WCG  H15  C32  C13  113.43  3.000
 WCG  O33  C32  C13  107.56  3.000
 WCG  C30  C32  C13  101.39  3.000
 WCG  C03  O02  C01  118.86  3.000
 WCG  C15  O14  C13  111.14  3.000
 WCG  P18  O17  C16  127.26  3.000
 WCG  H16  O20  P18  113.91  3.000
 WCG  P22  O21  P18  130.24  3.000
 WCG  H17  O23  P22  115.08  3.000
 WCG  P26  O25  P22  126.73  3.000
 WCG  H18  O27  P26  116.06  3.000
 WCG  H19  O28  P26  114.80  3.000
 WCG  H20  O31  C30  108.89  3.000
 WCG  H21  O33  C32  107.78  3.000
 WCG  O21  P18  O20  104.76  3.000
 WCG  O21  P18  O19  111.25  3.000
 WCG  O20  P18  O19  116.44  3.000
 WCG  O21  P18  O17  104.11  3.000
 WCG  O20  P18  O17   98.66  3.000
 WCG  O19  P18  O17  119.74  3.000
 WCG  O25  P22  O24  116.64  3.000
 WCG  O25  P22  O23  101.28  3.000
 WCG  O24  P22  O23  118.28  3.000
 WCG  O23  P22  O21  105.54  3.000
 WCG  O25  P22  O21   97.29  3.000
 WCG  O24  P22  O21  114.91  3.000
 WCG  O29  P26  O28  118.31  3.000
 WCG  O28  P26  O27  102.61  3.000
 WCG  O29  P26  O27  118.16  3.000
 WCG  O28  P26  O25  100.16  3.000
 WCG  O27  P26  O25  100.95  3.000
 WCG  O29  P26  O25  113.78  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
 WCG  CONST_01  C06  C05  C04  C03   180.00   0.0  0
 WCG  CONST_02  C10  C05  C04  C03     0.00   0.0  0
 WCG  CONST_03  C10  C11  C12  C03     0.00   0.0  0
 WCG  CONST_04  C11  C12  C03  C04     0.00   0.0  0
 WCG  CONST_05  C07  C06  C05  C04   180.00   0.0  0
 WCG  CONST_06  C11  C10  C05  C04     0.00   0.0  0
 WCG  CONST_07  C09  C10  C05  C04   180.00   0.0  0
 WCG  CONST_08  C12  C03  C04  C05     0.00   0.0  0
 WCG  CONST_09  C08  C07  C06  C05     0.00   0.0  0
 WCG  CONST_10  C12  C11  C10  C05     0.00   0.0  0
 WCG  CONST_11  C08  C09  C10  C05     0.00   0.0  0
 WCG  CONST_12  C11  C10  C05  C06   180.00   0.0  0
 WCG  CONST_13  C09  C10  C05  C06     0.00   0.0  0
 WCG  CONST_14  C09  C08  C07  C06     0.00   0.0  0
 WCG  CONST_15  C10  C05  C06  C07     0.00   0.0  0
 WCG  CONST_16  C10  C09  C08  C07     0.00   0.0  0
 WCG  CONST_17  C11  C10  C09  C08   180.00   0.0  0
 WCG  CONST_18  C12  C11  C10  C09   180.00   0.0  0
 WCG  CONST_19  C13  C12  C03  C04   180.00   0.0  0
 WCG  CONST_20  C13  C12  C11  C10   180.00   0.0  0
 WCG  CONST_21  O02  C03  C04  C05   180.00   0.0  0
 WCG  CONST_22  O02  C03  C12  C11   180.00   0.0  0
 WCG  CONST_23  O02  C03  C12  C13     0.00   0.0  0
 WCG  CONST_24  H9   C11  C12  C03   180.00   0.0  0
 WCG  CONST_25  H5   C06  C05  C04     0.00   0.0  0
 WCG  CONST_26  H6   C07  C06  C05   180.00   0.0  0
 WCG  CONST_27  H9   C11  C10  C05   180.00   0.0  0
 WCG  CONST_28  H8   C09  C10  C05   180.00   0.0  0
 WCG  CONST_29  H4   C04  C05  C06     0.00   0.0  0
 WCG  CONST_30  H7   C08  C07  C06   180.00   0.0  0
 WCG  CONST_31  H8   C09  C08  C07   180.00   0.0  0
 WCG  CONST_32  H5   C06  C07  C08   180.00   0.0  0
 WCG  CONST_33  H9   C11  C10  C09     0.00   0.0  0
 WCG  CONST_34  H6   C07  C08  C09   180.00   0.0  0
 WCG  CONST_35  H4   C04  C05  C10   180.00   0.0  0
 WCG  CONST_36  H5   C06  C05  C10   180.00   0.0  0
 WCG  CONST_37  H7   C08  C09  C10   180.00   0.0  0
 WCG  CONST_38  H8   C09  C10  C11     0.00   0.0  0
 WCG  CONST_39  H4   C04  C03  C12   180.00   0.0  0
 WCG  CONST_40  H9   C11  C12  C13     0.00   0.0  0
 WCG  Var_01    C04  C03  O02  C01    -5.18  30.0  2
 WCG  Var_02    C12  C03  O02  C01   175.57  30.0  2
 WCG  Var_03    P18  O17  C16  C15   -68.33  30.0  1
 WCG  Var_04    H1   C01  O02  C03  -176.43  30.0  3
 WCG  Var_05    H2   C01  O02  C03   -57.67  30.0  3
 WCG  Var_06    H3   C01  O02  C03    64.70  30.0  3
 WCG  Var_07    O19  P18  O17  C16    80.81  30.0  1
 WCG  Var_08    O20  P18  O17  C16  -151.91  30.0  1
 WCG  Var_09    O21  P18  O17  C16   -44.22  30.0  1
 WCG  Var_10    P22  O21  P18  O17   -93.43  30.0  1
 WCG  Var_11    P22  O21  P18  O19   136.29  30.0  1
 WCG  Var_12    P22  O21  P18  O20     9.67  30.0  1
 WCG  Var_13    P26  O25  P22  O21   147.47  30.0  1
 WCG  Var_14    P26  O25  P22  O23  -105.02  30.0  1
 WCG  Var_15    P18  O21  P22  O23    50.37  30.0  1
 WCG  Var_16    P26  O25  P22  O24    24.82  30.0  1
 WCG  Var_17    P18  O21  P22  O24   -81.82  30.0  1
 WCG  Var_18    P18  O21  P22  O25   154.27  30.0  1
 WCG  Var_19    P22  O25  P26  O27   153.88  30.0  3
 WCG  Var_20    P22  O25  P26  O28    48.77  30.0  3
 WCG  Var_21    P22  O25  P26  O29   -78.49  30.0  3
 WCG  Var_22    H12  C16  O17  P18    56.28  30.0  3
 WCG  Var_23    H13  C16  O17  P18   172.50  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
 WCG  chir_01  C13  O14  C12  C32  negativ
 WCG  chir_02  C15  O14  C16  C30  positiv
 WCG  chir_03  C30  O31  C15  C32  positiv
 WCG  chir_04  C32  O33  C30  C13  positiv
 WCG  chir_05  P18  O20  O21  O17  both
 WCG  chir_06  P22  O25  O21  O23  both

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
 WCG  plan-1  C03  0.020
 WCG  plan-1  C04  0.020
 WCG  plan-1  C05  0.020
 WCG  plan-1  C06  0.020
 WCG  plan-1  C07  0.020
 WCG  plan-1  C08  0.020
 WCG  plan-1  C09  0.020
 WCG  plan-1  C10  0.020
 WCG  plan-1  C11  0.020
 WCG  plan-1  C12  0.020
 WCG  plan-1  C13  0.020
 WCG  plan-1  O02  0.020
 WCG  plan-1  H4   0.020
 WCG  plan-1  H5   0.020
 WCG  plan-1  H6   0.020
 WCG  plan-1  H7   0.020
 WCG  plan-1  H8   0.020
 WCG  plan-1  H9   0.020

