# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 02:03:52 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-3-yl]-3-methoxy-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)C(=O)N[C@@H]2[C@@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@@H](CO)O[C@H]2NC(C)=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
 8VW  8VW  ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-3-yl]-3-methoxy-benzamide  ligand  68  36  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8VW
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
 8VW  O35  O  O     0  -0.485  -2.7047  -4.0707  -0.9783
 8VW  C33  C  C     0   0.527  -2.9218  -3.6026   0.1260
 8VW  C34  C  CH3   0  -0.785  -4.1186  -4.0020   0.9491
 8VW  N1   N  NH1   0  -0.671  -2.1321  -2.6582   0.6927
 8VW  C1,  C  CH1   0   0.259  -0.9904  -2.0968   0.0576
 8VW  C2,  C  CH1   0  -0.188  -0.8680  -0.6065   0.3806
 8VW  N2   N  NH1   0  -0.674  -2.0164   0.1308  -0.0863
 8VW  C36  C  C     0   0.546  -3.0431   0.5002   0.7123
 8VW  C38  C  CR6   0  -0.021  -4.1601   1.2179   0.0257
 8VW  C39  C  CR16  0  -0.317  -3.9618   1.9726  -1.1317
 8VW  C40  C  CR16  0  -0.227  -5.0406   2.6169  -1.7110
 8VW  C41  C  CR16  0  -0.377  -6.3147   2.5198  -1.1656
 8VW  C42  C  CR6   0   0.409  -6.5100   1.7715  -0.0064
 8VW  O44  O  O2    0  -0.470  -7.6976   1.6125   0.6032
 8VW  C45  C  CH3   0  -0.439  -8.8370   2.2264   0.0321
 8VW  C43  C  CR16  0  -0.370  -5.4239   1.1318   0.5901
 8VW  O37  O  O     0  -0.473  -3.0700   0.2727   1.9116
 8VW  O5,  O  O2    0  -0.482   0.1647  -2.7576   0.5120
 8VW  C5,  C  CH1   0  -0.008   1.3358  -2.3548  -0.1642
 8VW  C6,  C  CH2   0  -0.164   2.4668  -3.2396   0.3173
 8VW  O6,  O  OH1   0  -0.667   2.1891  -4.5666  -0.0576
 8VW  C4,  C  CH1   0   0.017   1.6198  -0.8691   0.1032
 8VW  C3,  C  CH1   0   0.042   0.3999  -0.0261  -0.2549
 8VW  O3,  O  OH1   0  -0.644   0.6063   1.2938   0.1682
 8VW  O1   O  O2    0  -0.512   2.7168  -0.4815  -0.7044
 8VW  C1   C  CH1   0   0.294   3.8142   0.0609  -0.0662
 8VW  C2   C  CH1   0  -0.035   5.0170  -0.0066  -1.0058
 8VW  O2   O  OH1   0  -0.667   5.4020  -1.3342  -1.2726
 8VW  C3   C  CH1   0   0.002   6.2011   0.6899  -0.3387
 8VW  O3   O  OH1   0  -0.673   7.3134   0.7689  -1.1946
 8VW  C4   C  CH1   0   0.010   5.8288   2.1133   0.0806
 8VW  O4   O  OH1   0  -0.671   5.5824   2.9345  -1.0329
 8VW  C5   C  CH1   0  -0.039   4.5727   2.0437   0.9372
 8VW  O5   O  O2    0  -0.489   3.5339   1.3953   0.2343
 8VW  C6   C  CH2   0  -0.165   4.0108   3.3897   1.3632
 8VW  O6   O  OH1   0  -0.672   2.8630   3.2336   2.1644
 8VW  H1   H  HCH3  0   0.270  -4.2648  -5.0787   0.8881
 8VW  H2   H  HCH3  0   0.253  -4.0418  -3.7162   1.9965
 8VW  H3   H  HCH3  0   0.275  -5.0085  -3.5264   0.5337
 8VW  H4   H  HNH1  0   0.400  -2.3611  -2.3324   1.6192
 8VW  H5   H  HCH1  0   0.231  -1.0973  -2.2289  -1.0273
 8VW  H6   H  HCH1  0   0.286  -0.7998  -0.4866   1.4648
 8VW  H7   H  HNH1  0   0.409  -2.1569   0.1686  -1.0852
 8VW  H8   H  HCR6  0   0.253  -2.9789   2.0889  -1.5693
 8VW  H9   H  HCR6  0   0.270  -4.8950   3.2125  -2.6023
 8VW  H10  H  HCR6  0   0.288  -7.1328   3.0335  -1.6514
 8VW  H11  H  HCH3  0   0.262  -9.6797   1.9620   0.6656
 8VW  H12  H  HCH3  0   0.231  -8.7438   3.3151   0.0056
 8VW  H13  H  HCH3  0   0.231  -9.0298   1.8638  -0.9807
 8VW  H14  H  HCR6  0   0.268  -5.5810   0.5551   1.4927
 8VW  H15  H  HCH1  0   0.229   1.2075  -2.4910  -1.2508
 8VW  H16  H  HCH2  0   0.206   3.4045  -2.8861  -0.1230
 8VW  H17  H  HCH2  0   0.201   2.5603  -3.1320   1.4072
 8VW  H18  H  HOH1  0   0.457   2.9251  -5.1147   0.2286
 8VW  H19  H  HCH1  0   0.246   1.8476  -0.7339   1.1702
 8VW  H20  H  HCH1  0   0.220   0.2824  -0.0751  -1.3504
 8VW  H21  H  HOH1  0   0.451  -0.1370   1.8265  -0.1340
 8VW  H22  H  HCH1  0   0.189   4.0489  -0.4904   0.8650
 8VW  H23  H  HCH1  0   0.232   4.7606   0.5284  -1.9299
 8VW  H24  H  HOH1  0   0.463   4.8334  -1.6895  -1.9625
 8VW  H25  H  HCH1  0   0.213   6.4528   0.1301   0.5768
 8VW  H26  H  HOH1  0   0.455   7.4653  -0.1016  -1.5784
 8VW  H27  H  HCH1  0   0.234   6.6434   2.5159   0.7013
 8VW  H28  H  HOH1  0   0.453   6.3469   2.8803  -1.6162
 8VW  H29  H  HCH1  0   0.228   4.8302   1.4732   1.8445
 8VW  H30  H  HCH2  0   0.227   4.7578   3.9164   1.9602
 8VW  H31  H  HCH2  0   0.206   3.8036   4.0049   0.4800
 8VW  H32  H  HOH1  0   0.442   2.2287   2.7040   1.6665

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
 8VW  O6,  C6,  single    1.407  0.020  1.407
 8VW  C6,  C5,  single    1.514  0.020  1.514
 8VW  O5,  C5,  single    1.411  0.020  1.411
 8VW  O5,  C1,  single    1.406  0.020  1.406
 8VW  O35  C33  double    1.219  0.020  1.219
 8VW  O2   C2   single    1.408  0.020  1.408
 8VW  C5,  C4,  single    1.536  0.020  1.536
 8VW  C34  C33  single    1.506  0.020  1.506
 8VW  C33  N1   single    1.355  0.020  1.355
 8VW  C3   O3   single    1.406  0.020  1.406
 8VW  C3   C2   single    1.527  0.020  1.527
 8VW  C3   C4   single    1.530  0.020  1.530
 8VW  N1   C1,  single    1.422  0.020  1.422
 8VW  C1   C2   single    1.528  0.020  1.528
 8VW  C1   O1   single    1.380  0.020  1.380
 8VW  C1   O5   single    1.396  0.020  1.396
 8VW  C1,  C2,  single    1.530  0.020  1.530
 8VW  C4,  O1   single    1.416  0.020  1.416
 8VW  C4,  C3,  single    1.526  0.020  1.526
 8VW  C5   C4   single    1.522  0.020  1.522
 8VW  C5   O5   single    1.412  0.020  1.412
 8VW  C5   C6   single    1.520  0.020  1.520
 8VW  C4   O4   single    1.405  0.020  1.405
 8VW  O6   C6   single    1.408  0.020  1.408
 8VW  C2,  C3,  single    1.532  0.020  1.532
 8VW  C2,  N2   single    1.442  0.020  1.442
 8VW  C3,  O3,  single    1.401  0.020  1.401
 8VW  O37  C36  double    1.221  0.020  1.221
 8VW  N2   C36  single    1.352  0.020  1.352
 8VW  C36  C38  single    1.495  0.020  1.495
 8VW  C38  C39  aromatic  1.396  0.020  1.396
 8VW  C38  C43  aromatic  1.387  0.020  1.387
 8VW  C39  C40  aromatic  1.384  0.020  1.384
 8VW  C43  C42  aromatic  1.395  0.020  1.395
 8VW  C40  C41  aromatic  1.389  0.020  1.389
 8VW  C42  C41  aromatic  1.394  0.020  1.394
 8VW  C42  O44  single    1.344  0.020  1.344
 8VW  C45  O44  single    1.415  0.020  1.415
 8VW  C34  H1   single    0.970  0.020  1.090
 8VW  C34  H2   single    0.970  0.020  1.090
 8VW  C34  H3   single    0.970  0.020  1.090
 8VW  N1   H4   single    0.860  0.020  1.020
 8VW  C1,  H5   single    0.970  0.020  1.090
 8VW  C2,  H6   single    0.970  0.020  1.090
 8VW  N2   H7   single    0.860  0.020  1.020
 8VW  C39  H8   single    0.930  0.020  1.080
 8VW  C40  H9   single    0.930  0.020  1.080
 8VW  C41  H10  single    0.930  0.020  1.080
 8VW  C45  H11  single    0.970  0.020  1.090
 8VW  C45  H12  single    0.970  0.020  1.090
 8VW  C45  H13  single    0.970  0.020  1.090
 8VW  C43  H14  single    0.930  0.020  1.080
 8VW  C5,  H15  single    0.970  0.020  1.090
 8VW  C6,  H16  single    0.970  0.020  1.090
 8VW  C6,  H17  single    0.970  0.020  1.090
 8VW  O6,  H18  single    0.850  0.020  0.980
 8VW  C4,  H19  single    0.970  0.020  1.090
 8VW  C3,  H20  single    0.970  0.020  1.090
 8VW  O3,  H21  single    0.850  0.020  0.980
 8VW  C1   H22  single    0.970  0.020  1.090
 8VW  C2   H23  single    0.970  0.020  1.090
 8VW  O2   H24  single    0.850  0.020  0.980
 8VW  C3   H25  single    0.970  0.020  1.090
 8VW  O3   H26  single    0.850  0.020  0.980
 8VW  C4   H27  single    0.970  0.020  1.090
 8VW  O4   H28  single    0.850  0.020  0.980
 8VW  C5   H29  single    0.970  0.020  1.090
 8VW  C6   H30  single    0.970  0.020  1.090
 8VW  C6   H31  single    0.970  0.020  1.090
 8VW  O6   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
 8VW  N1   C33  C34  114.79  3.000
 8VW  N1   C33  O35  122.86  3.000
 8VW  C34  C33  O35  122.32  3.000
 8VW  H3   C34  H2   108.03  3.000
 8VW  H3   C34  H1   107.47  3.000
 8VW  H2   C34  H1   108.85  3.000
 8VW  H3   C34  C33  108.93  3.000
 8VW  H2   C34  C33  113.59  3.000
 8VW  H1   C34  C33  109.78  3.000
 8VW  H4   N1   C1,  117.72  3.000
 8VW  H4   N1   C33  118.48  3.000
 8VW  C1,  N1   C33  123.79  3.000
 8VW  H5   C1,  O5,  110.04  3.000
 8VW  H5   C1,  C2,  109.48  3.000
 8VW  O5,  C1,  C2,  108.89  3.000
 8VW  H5   C1,  N1   108.40  3.000
 8VW  C2,  C1,  N1   110.77  3.000
 8VW  O5,  C1,  N1   109.25  3.000
 8VW  H6   C2,  C3,  108.56  3.000
 8VW  H6   C2,  N2   108.34  3.000
 8VW  C3,  C2,  N2   109.33  3.000
 8VW  H6   C2,  C1,  108.74  3.000
 8VW  N2   C2,  C1,  111.46  3.000
 8VW  C3,  C2,  C1,  110.34  3.000
 8VW  H7   N2   C36  117.94  3.000
 8VW  H7   N2   C2,  116.76  3.000
 8VW  C36  N2   C2,  123.58  3.000
 8VW  O37  C36  C38  121.61  3.000
 8VW  C38  C36  N2   115.30  3.000
 8VW  O37  C36  N2   123.09  3.000
 8VW  C43  C38  C39  120.04  3.000
 8VW  C43  C38  C36  117.66  3.000
 8VW  C39  C38  C36  122.30  3.000
 8VW  H8   C39  C40  119.26  3.000
 8VW  H8   C39  C38  121.50  3.000
 8VW  C40  C39  C38  119.22  3.000
 8VW  H9   C40  C41  119.04  3.000
 8VW  H9   C40  C39  119.76  3.000
 8VW  C41  C40  C39  121.21  3.000
 8VW  H10  C41  C42  121.52  3.000
 8VW  H10  C41  C40  118.97  3.000
 8VW  C42  C41  C40  119.51  3.000
 8VW  C43  C42  O44  116.09  3.000
 8VW  O44  C42  C41  124.37  3.000
 8VW  C43  C42  C41  119.54  3.000
 8VW  C45  O44  C42  118.50  3.000
 8VW  H13  C45  H12  108.86  3.000
 8VW  H13  C45  H11  108.82  3.000
 8VW  H12  C45  H11  108.82  3.000
 8VW  H13  C45  O44  111.85  3.000
 8VW  H12  C45  O44  111.92  3.000
 8VW  H11  C45  O44  106.47  3.000
 8VW  H14  C43  C42  119.20  3.000
 8VW  H14  C43  C38  120.31  3.000
 8VW  C42  C43  C38  120.48  3.000
 8VW  C5,  O5,  C1,  113.13  3.000
 8VW  H15  C5,  C4,  108.21  3.000
 8VW  H15  C5,  C6,  109.15  3.000
 8VW  C4,  C5,  C6,  111.82  3.000
 8VW  H15  C5,  O5,  109.91  3.000
 8VW  C4,  C5,  O5,  110.25  3.000
 8VW  C6,  C5,  O5,  107.50  3.000
 8VW  H17  C6,  H16  107.12  3.000
 8VW  H17  C6,  O6,  111.92  3.000
 8VW  H16  C6,  O6,  111.51  3.000
 8VW  H17  C6,  C5,  108.76  3.000
 8VW  H16  C6,  C5,  108.86  3.000
 8VW  O6,  C6,  C5,  108.60  3.000
 8VW  H18  O6,  C6,  107.91  3.000
 8VW  H19  C4,  O1   111.06  3.000
 8VW  H19  C4,  C3,  109.00  3.000
 8VW  O1   C4,  C3,  109.53  3.000
 8VW  H19  C4,  C5,  109.04  3.000
 8VW  C3,  C4,  C5,  110.23  3.000
 8VW  O1   C4,  C5,  107.98  3.000
 8VW  H20  C3,  O3,  110.94  3.000
 8VW  H20  C3,  C4,  107.08  3.000
 8VW  O3,  C3,  C4,  109.38  3.000
 8VW  H20  C3,  C2,  107.88  3.000
 8VW  O3,  C3,  C2,  110.69  3.000
 8VW  C4,  C3,  C2,  110.80  3.000
 8VW  H21  O3,  C3,  108.22  3.000
 8VW  C1   O1   C4,  117.36  3.000
 8VW  H22  C1   O5   109.72  3.000
 8VW  H22  C1   C2   109.17  3.000
 8VW  O5   C1   C2   109.43  3.000
 8VW  H22  C1   O1   111.20  3.000
 8VW  O5   C1   O1   108.39  3.000
 8VW  C2   C1   O1   108.91  3.000
 8VW  H23  C2   C3   109.05  3.000
 8VW  H23  C2   O2   111.33  3.000
 8VW  C3   C2   O2   107.51  3.000
 8VW  H23  C2   C1   108.19  3.000
 8VW  C3   C2   C1   108.76  3.000
 8VW  O2   C2   C1   111.93  3.000
 8VW  H24  O2   C2   108.82  3.000
 8VW  H25  C3   C4   107.48  3.000
 8VW  H25  C3   O3   110.71  3.000
 8VW  C4   C3   O3   107.89  3.000
 8VW  H25  C3   C2   107.95  3.000
 8VW  C4   C3   C2   110.82  3.000
 8VW  O3   C3   C2   111.91  3.000
 8VW  H26  O3   C3   108.45  3.000
 8VW  H27  C4   C5   108.07  3.000
 8VW  H27  C4   O4   111.28  3.000
 8VW  C5   C4   O4   109.14  3.000
 8VW  H27  C4   C3   108.35  3.000
 8VW  O4   C4   C3   111.67  3.000
 8VW  C5   C4   C3   108.21  3.000
 8VW  H28  O4   C4   107.92  3.000
 8VW  H29  C5   C6   108.30  3.000
 8VW  H29  C5   O5   110.13  3.000
 8VW  C6   C5   O5   105.92  3.000
 8VW  H29  C5   C4   107.10  3.000
 8VW  C6   C5   C4   114.99  3.000
 8VW  O5   C5   C4   110.37  3.000
 8VW  C5   O5   C1   113.48  3.000
 8VW  H31  C6   H30  107.41  3.000
 8VW  H31  C6   O6   111.50  3.000
 8VW  H30  C6   O6   107.46  3.000
 8VW  H31  C6   C5   109.95  3.000
 8VW  H30  C6   C5   109.13  3.000
 8VW  O6   C6   C5   111.26  3.000
 8VW  H32  O6   C6   107.64  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
 8VW  CONST_01  C41  C40  C39  C38     0.00   0.0  0
 8VW  CONST_02  C41  C42  C43  C38     0.00   0.0  0
 8VW  CONST_03  C42  C43  C38  C39     0.00   0.0  0
 8VW  CONST_04  C42  C41  C40  C39     0.00   0.0  0
 8VW  CONST_05  C43  C38  C39  C40     0.00   0.0  0
 8VW  CONST_06  C43  C42  C41  C40     0.00   0.0  0
 8VW  CONST_07  C40  C39  C38  C36   180.00   0.0  0
 8VW  CONST_08  C42  C43  C38  C36   180.00   0.0  0
 8VW  CONST_09  O44  C42  C43  C38   180.00   0.0  0
 8VW  CONST_10  O44  C42  C41  C40   180.00   0.0  0
 8VW  CONST_11  H9   C40  C39  C38   180.00   0.0  0
 8VW  CONST_12  H14  C43  C38  C39   180.00   0.0  0
 8VW  CONST_13  H10  C41  C40  C39   180.00   0.0  0
 8VW  CONST_14  H8   C39  C40  C41   180.00   0.0  0
 8VW  CONST_15  C38  C36  N2   C2,   180.00   0.0  0
 8VW  CONST_16  C1,  N1   C33  O35     0.00   0.0  0
 8VW  CONST_17  C1,  N1   C33  C34   180.00   0.0  0
 8VW  CONST_18  O37  C36  N2   C2,     0.00   0.0  0
 8VW  CONST_19  H7   N2   C36  C38     0.00   0.0  0
 8VW  CONST_20  H4   N1   C33  O35   180.00   0.0  0
 8VW  Var_01    C39  C38  C36  N2    -27.45  30.0  2
 8VW  Var_02    C43  C42  O44  C45  -179.25  30.0  2
 8VW  Var_03    H11  C45  O44  C42   179.17  30.0  3
 8VW  Var_04    H1   C34  C33  O35    42.35  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
 8VW  chir_01  C1,  O5,  N1   C2,  negativ
 8VW  chir_02  C2,  N2   C3,  C1,  positiv
 8VW  chir_03  C5,  O5,  C4,  C6,  negativ
 8VW  chir_04  C4,  O1   C3,  C5,  negativ
 8VW  chir_05  C3,  O3,  C4,  C2,  negativ
 8VW  chir_06  C1   O5   O1   C2   negativ
 8VW  chir_07  C2   O2   C1   C3   negativ
 8VW  chir_08  C3   O3   C2   C4   positiv
 8VW  chir_09  C4   O4   C5   C3   negativ
 8VW  chir_10  C5   O5   C4   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
 8VW  plan-1  C36  0.020
 8VW  plan-1  C38  0.020
 8VW  plan-1  C39  0.020
 8VW  plan-1  C40  0.020
 8VW  plan-1  C41  0.020
 8VW  plan-1  C42  0.020
 8VW  plan-1  O44  0.020
 8VW  plan-1  C43  0.020
 8VW  plan-1  H8   0.020
 8VW  plan-1  H9   0.020
 8VW  plan-1  H10  0.020
 8VW  plan-1  H14  0.020
 8VW  plan-2  O35  0.020
 8VW  plan-2  C33  0.020
 8VW  plan-2  C34  0.020
 8VW  plan-2  N1   0.020
 8VW  plan-2  C1,  0.020
 8VW  plan-2  H4   0.020
 8VW  plan-3  C2,  0.020
 8VW  plan-3  N2   0.020
 8VW  plan-3  C36  0.020
 8VW  plan-3  C38  0.020
 8VW  plan-3  O37  0.020
 8VW  plan-3  H7   0.020

