# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:44:15 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: (1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@H](N[C@H]2C=C(CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 VDM  VDM  (1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol  ligand  48  23  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VDM
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
 VDM  O7    O  OH1   0  -0.666   6.1914   2.9270  -2.3311
 VDM  C7    C  CH2   0  -0.229   5.3894   1.9755  -1.6650
 VDM  C5    C  C     0   0.033   4.5212   1.1713  -2.5973
 VDM  C6    C  C1    0  -0.269   3.2160   1.0285  -2.3776
 VDM  C4    C  CH1   0  -0.052   5.2034   0.5606  -3.7970
 VDM  O4    O  OH1   0  -0.663   6.5026   0.0900  -3.4934
 VDM  C3    C  CH1   0   0.004   4.3450  -0.5178  -4.4492
 VDM  O3    O  OH1   0  -0.681   4.8255  -0.8587  -5.7313
 VDM  C2    C  CH1   0   0.049   2.9241   0.0072  -4.6091
 VDM  O2    O  OH1   0  -0.680   2.1130  -0.8627  -5.3582
 VDM  C1    C  CH1   0  -0.157   2.2949   0.2024  -3.2313
 VDM  N1'   N  NH1   0  -0.594   2.0418  -1.1007  -2.6282
 VDM  C1'   C  CH1   0  -0.122   1.5940  -1.0975  -1.2481
 VDM  C2'   C  CH1   0   0.056   1.3604  -2.5222  -0.7494
 VDM  O2'   O  OH1   0  -0.668   2.5162  -3.2922  -0.9568
 VDM  C6'   C  CH2   0  -0.477   0.3213  -0.2908  -0.9692
 VDM  C5'   C  CH1   0  -0.355  -0.9121  -0.8838  -1.6452
 VDM  C7'   C  CH2   0  -0.150  -2.1198  -0.0039  -1.3301
 VDM  O7'   O  OH1   0  -0.667  -3.3259  -0.4308  -1.9442
 VDM  C4'   C  CH1   0   0.075  -1.1216  -2.3332  -1.1931
 VDM  O4'   O  OH1   0  -0.690  -2.1796  -2.9725  -1.8679
 VDM  C3'   C  CH1   0  -0.025   0.1368  -3.1693  -1.4059
 VDM  O3'   O  OH1   0  -0.666  -0.0228  -4.4943  -0.9381
 VDM  H7    H  HOH1  0   0.452   6.9275   2.4602  -2.7388
 VDM  H7C1  H  HCH2  0   0.216   6.0024   1.2965  -1.0604
 VDM  H7C2  H  HCH2  0   0.235   4.7528   2.5209  -0.9659
 VDM  H6    H  H     0   0.256   2.7739   1.5428  -1.5292
 VDM  H4    H  HCH1  0   0.250   5.3571   1.3533  -4.5393
 VDM  H1    H  HCH1  0   0.232   1.3658   0.7796  -3.3674
 VDM  HA    H  HOH1  0   0.449   6.4310  -0.6042  -2.8286
 VDM  H3    H  HCH1  0   0.223   4.3158  -1.3994  -3.7928
 VDM  HB    H  HOH1  0   0.457   5.6190  -1.3929  -5.6313
 VDM  H2    H  HCH1  0   0.210   2.9744   0.9957  -5.0950
 VDM  HC    H  HOH1  0   0.450   2.6205  -1.1588  -6.1220
 VDM  H1'   H  HNH1  0   0.345   1.3938  -1.6016  -3.2224
 VDM  HD    H  HCH1  0   0.250   2.4005  -0.6708  -0.6425
 VDM  H2'   H  HCH1  0   0.201   1.1441  -2.4384   0.3301
 VDM  H6'1  H  HCH2  0   0.252   0.4519   0.7464  -1.2890
 VDM  H6'2  H  HCH2  0   0.237   0.1626  -0.2488   0.1143
 VDM  HE    H  HOH1  0   0.442   2.3137  -4.1935  -0.6831
 VDM  H3'   H  HCH1  0   0.227   0.3107  -3.2722  -2.4837
 VDM  H5'   H  HCH1  0   0.232  -0.7588  -0.8752  -2.7336
 VDM  H7'1  H  HCH2  0   0.227  -1.8929   1.0326  -1.6044
 VDM  H7'2  H  HCH2  0   0.223  -2.3047  -0.0168  -0.2526
 VDM  H4'   H  HCH1  0   0.181  -1.3215  -2.3018  -0.1046
 VDM  H7'   H  HOH1  0   0.458  -3.2678  -0.2408  -2.8866
 VDM  HF    H  HOH1  0   0.443  -2.9027  -2.3323  -1.9264
 VDM  HG    H  HOH1  0   0.445  -0.2921  -4.4618  -0.0127

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
 VDM  O7   C7    single  1.411  0.020  1.411
 VDM  O7   H7    single  0.850  0.020  0.980
 VDM  C7   C5    single  1.507  0.020  1.507
 VDM  C7   H7C1  single  0.970  0.020  1.090
 VDM  C7   H7C2  single  0.970  0.020  1.090
 VDM  C5   C6    double  1.331  0.020  1.331
 VDM  C5   C4    single  1.509  0.020  1.509
 VDM  C6   C1    single  1.503  0.020  1.503
 VDM  C6   H6    single  0.930  0.020  1.080
 VDM  C4   O4    single  1.415  0.020  1.415
 VDM  C4   C3    single  1.525  0.020  1.525
 VDM  C4   H4    single  0.970  0.020  1.090
 VDM  O4   HA    single  0.850  0.020  0.980
 VDM  C3   O3    single  1.411  0.020  1.411
 VDM  C3   C2    single  1.523  0.020  1.523
 VDM  C3   H3    single  0.970  0.020  1.090
 VDM  O3   HB    single  0.850  0.020  0.980
 VDM  C2   O2    single  1.406  0.020  1.406
 VDM  C2   C1    single  1.527  0.020  1.527
 VDM  C2   H2    single  0.970  0.020  1.090
 VDM  O2   HC    single  0.850  0.020  0.980
 VDM  C1   N1'   single  1.458  0.020  1.458
 VDM  C1   H1    single  0.970  0.020  1.090
 VDM  N1'  C1'   single  1.451  0.020  1.451
 VDM  N1'  H1'   single  0.890  0.020  1.040
 VDM  C1'  HD    single  0.970  0.020  1.090
 VDM  C1'  C2'   single  1.527  0.020  1.527
 VDM  C1'  C6'   single  1.532  0.020  1.532
 VDM  C2'  H2'   single  0.970  0.020  1.090
 VDM  C2'  O2'   single  1.404  0.020  1.404
 VDM  C2'  C3'   single  1.532  0.020  1.532
 VDM  O2'  HE    single  0.850  0.020  0.980
 VDM  C6'  H6'1  single  0.970  0.020  1.090
 VDM  C6'  H6'2  single  0.970  0.020  1.090
 VDM  C6'  C5'   single  1.526  0.020  1.526
 VDM  C5'  H5'   single  0.970  0.020  1.090
 VDM  C5'  C7'   single  1.527  0.020  1.527
 VDM  C5'  C4'   single  1.533  0.020  1.533
 VDM  C7'  H7'1  single  0.970  0.020  1.090
 VDM  C7'  H7'2  single  0.970  0.020  1.090
 VDM  C7'  O7'   single  1.419  0.020  1.419
 VDM  O7'  H7'   single  0.850  0.020  0.980
 VDM  C4'  H4'   single  0.970  0.020  1.090
 VDM  C4'  O4'   single  1.408  0.020  1.408
 VDM  C4'  C3'   single  1.526  0.020  1.526
 VDM  O4'  HF    single  0.850  0.020  0.980
 VDM  C3'  H3'   single  0.970  0.020  1.090
 VDM  C3'  O3'   single  1.414  0.020  1.414
 VDM  O3'  HG    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
 VDM  H7    O7   C7    107.91  3.000
 VDM  H7C2  C7   H7C1  106.40  3.000
 VDM  H7C2  C7   C5    109.08  3.000
 VDM  H7C1  C7   C5    109.43  3.000
 VDM  H7C2  C7   O7    107.27  3.000
 VDM  H7C1  C7   O7    111.11  3.000
 VDM  C5    C7   O7    113.28  3.000
 VDM  C4    C5   C6    122.07  3.000
 VDM  C4    C5   C7    116.58  3.000
 VDM  C6    C5   C7    121.34  3.000
 VDM  H6    C6   C1    117.03  3.000
 VDM  H6    C6   C5    118.50  3.000
 VDM  C1    C6   C5    124.47  3.000
 VDM  H4    C4   C3    107.49  3.000
 VDM  H4    C4   O4    104.88  3.000
 VDM  C3    C4   O4    111.94  3.000
 VDM  H4    C4   C5    107.99  3.000
 VDM  C3    C4   C5    111.82  3.000
 VDM  O4    C4   C5    112.28  3.000
 VDM  HA    O4   C4    108.62  3.000
 VDM  H3    C3   C2    108.31  3.000
 VDM  H3    C3   O3    110.96  3.000
 VDM  C2    C3   O3    107.79  3.000
 VDM  H3    C3   C4    109.07  3.000
 VDM  C2    C3   C4    109.04  3.000
 VDM  O3    C3   C4    111.58  3.000
 VDM  HB    O3   C3    108.70  3.000
 VDM  H2    C2   C1    107.57  3.000
 VDM  H2    C2   O2    110.26  3.000
 VDM  C1    C2   O2    108.80  3.000
 VDM  H2    C2   C3    108.22  3.000
 VDM  C1    C2   C3    109.49  3.000
 VDM  O2    C2   C3    112.39  3.000
 VDM  HC    O2   C2    107.98  3.000
 VDM  H1    C1   N1'   111.88  3.000
 VDM  H1    C1   C2    107.63  3.000
 VDM  N1'   C1   C2    109.30  3.000
 VDM  H1    C1   C6    107.39  3.000
 VDM  N1'   C1   C6    111.26  3.000
 VDM  C2    C1   C6    109.28  3.000
 VDM  H1'   N1'  C1'   111.22  3.000
 VDM  H1'   N1'  C1    108.10  3.000
 VDM  C1'   N1'  C1    116.43  3.000
 VDM  HD    C1'  C6'   107.81  3.000
 VDM  C6'   C1'  C2'   107.73  3.000
 VDM  HD    C1'  C2'   107.19  3.000
 VDM  C6'   C1'  N1'   115.51  3.000
 VDM  C2'   C1'  N1'   110.84  3.000
 VDM  HD    C1'  N1'   107.43  3.000
 VDM  H2'   C2'  C3'   107.13  3.000
 VDM  C3'   C2'  O2'   111.25  3.000
 VDM  H2'   C2'  O2'   110.31  3.000
 VDM  C3'   C2'  C1'   112.10  3.000
 VDM  O2'   C2'  C1'   109.72  3.000
 VDM  H2'   C2'  C1'   106.17  3.000
 VDM  HE    O2'  C2'   107.34  3.000
 VDM  H6'2  C6'  H6'1  105.67  3.000
 VDM  H6'2  C6'  C5'   109.62  3.000
 VDM  H6'1  C6'  C5'   109.61  3.000
 VDM  C5'   C6'  C1'   112.70  3.000
 VDM  H6'2  C6'  C1'   108.69  3.000
 VDM  H6'1  C6'  C1'   110.30  3.000
 VDM  H5'   C5'  C4'   108.58  3.000
 VDM  C4'   C5'  C7'   112.08  3.000
 VDM  H5'   C5'  C7'   108.06  3.000
 VDM  C4'   C5'  C6'   110.32  3.000
 VDM  C7'   C5'  C6'   108.89  3.000
 VDM  H5'   C5'  C6'   108.83  3.000
 VDM  H7'2  C7'  H7'1  107.03  3.000
 VDM  H7'2  C7'  O7'   106.22  3.000
 VDM  H7'1  C7'  O7'   110.62  3.000
 VDM  O7'   C7'  C5'   114.17  3.000
 VDM  H7'2  C7'  C5'   109.28  3.000
 VDM  H7'1  C7'  C5'   109.24  3.000
 VDM  H7'   O7'  C7'   108.23  3.000
 VDM  H4'   C4'  C3'   107.55  3.000
 VDM  C3'   C4'  O4'   107.70  3.000
 VDM  H4'   C4'  O4'   110.38  3.000
 VDM  C3'   C4'  C5'   111.37  3.000
 VDM  O4'   C4'  C5'   112.99  3.000
 VDM  H4'   C4'  C5'   106.73  3.000
 VDM  HF    O4'  C4'   106.86  3.000
 VDM  H3'   C3'  O3'   104.78  3.000
 VDM  O3'   C3'  C4'   111.97  3.000
 VDM  H3'   C3'  C4'   108.62  3.000
 VDM  O3'   C3'  C2'   110.13  3.000
 VDM  H3'   C3'  C2'   109.52  3.000
 VDM  C4'   C3'  C2'   111.56  3.000
 VDM  HG    O3'  C3'   108.50  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
 VDM  Var_01  C1  C6  C5  C4     3.38  30.0  1
 VDM  Var_02  C6  C5  C7  O7  -129.75  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
 VDM  chir_01  C4   C5   O4   C3   negativ
 VDM  chir_02  C3   O3   C4   C2   negativ
 VDM  chir_03  C2   O2   C3   C1   positiv
 VDM  chir_04  C1   N1'  C6   C2   negativ
 VDM  chir_05  C1'  N1'  C6'  C2'  negativ
 VDM  chir_06  C2'  O2'  C1'  C3'  negativ
 VDM  chir_07  C5'  C6'  C7'  C4'  positiv
 VDM  chir_08  C4'  O4'  C5'  C3'  positiv
 VDM  chir_09  C3'  O3'  C4'  C2'  negativ

