# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 13 17:00:51 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-nitrophenoxy)-3,5-bis(oxidanyl)oxan-4-yl]sulfanyl-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@@H](Oc2ccc(cc2)[N+]([O-])=O)[C@@H](O)[C@@H](S[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[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
 BV6  BV6  (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-nitrophenoxy)-3,5-bis(oxidanyl)oxan-4-yl]sulfanyl-oxane-3,4,5-triol  ligand  57  32  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BV6
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
 BV6  C1   C  CR6    0   0.397  27.8308  31.4836  35.8581
 BV6  C2   C  CR16   0  -0.358  27.5516  32.6994  35.2306
 BV6  C3   C  CR16   0  -0.255  27.7870  33.8834  35.9042
 BV6  C4   C  CR6    0   0.228  28.2844  33.8585  37.1987
 BV6  C5   C  CR16   0  -0.252  28.5539  32.6524  37.8369
 BV6  O5   O  O     -1  -0.384  28.9310  35.0521  39.0326
 BV6  C6   C  CR16   0  -0.341  28.3287  31.4726  37.1644
 BV6  O6   O  O      0  -0.384  28.2918  36.1370  37.3097
 BV6  C1A  C  CH1    0  -0.096  25.4349  26.0831  35.0976
 BV6  C2A  C  CH1    0   0.002  25.0959  25.8682  36.5852
 BV6  C3A  C  CH1    0   0.029  24.1797  24.6660  36.7459
 BV6  C4A  C  CH1    0  -0.037  22.9581  24.9298  35.8789
 BV6  C5A  C  CH1    0  -0.008  23.3698  24.9260  34.4031
 BV6  C6A  C  CH2    0  -0.200  22.4217  25.7150  33.5101
 BV6  O2A  O  OH1    0  -0.659  26.3150  25.7407  37.2674
 BV6  O4A  O  OH1    0  -0.669  21.9978  23.9252  36.1200
 BV6  O5A  O  O2     0  -0.472  24.7344  25.2844  34.1992
 BV6  O6A  O  OH1    0  -0.675  22.2199  27.0505  33.8880
 BV6  C1B  C  CH1    0   0.258  27.3491  30.1816  33.9424
 BV6  C2B  C  CH1    0   0.030  27.6080  28.7333  33.4546
 BV6  C3B  C  CH1    0  -0.472  26.2733  28.0252  33.2263
 BV6  C4B  C  CH1    0   0.051  25.5249  28.7938  32.1456
 BV6  C5B  C  CH1    0  -0.046  25.3895  30.2782  32.5674
 BV6  C6B  C  CH2    0  -0.179  25.9084  31.2053  31.4825
 BV6  O1B  O  O2     0  -0.461  27.6575  30.2763  35.2992
 BV6  O2B  O  OH1    0  -0.643  28.4500  28.0734  34.3491
 BV6  O4B  O  OH1    0  -0.654  24.2924  28.1727  31.9015
 BV6  O5B  O  O2     0  -0.485  25.9979  30.5134  33.8251
 BV6  N4   N  N      1   0.325  28.5184  35.1027  37.8959
 BV6  S1A  S  S2     0  -0.011  25.3121  27.8776  34.7673
 BV6  O3A  O  OH1    0  -0.669  23.8509  24.5731  38.1081
 BV6  H1   H  HCR6   0   0.301  27.1322  32.7486  34.2355
 BV6  H2   H  HCR6   0   0.298  27.5674  34.8190  35.4107
 BV6  H3   H  HCR6   0   0.297  28.9409  32.6257  38.8450
 BV6  H4   H  HCR6   0   0.283  28.5396  30.5261  37.6443
 BV6  H5   H  HCH1   0   0.281  26.4840  25.8141  34.9582
 BV6  H6   H  HCH1   0   0.229  24.5333  26.7347  36.9682
 BV6  H7   H  HCH1   0   0.216  24.6915  23.7527  36.4020
 BV6  H8   H  HCH1   0   0.225  22.5549  25.9136  36.1543
 BV6  H9   H  HCH1   0   0.238  23.3126  23.8838  34.0690
 BV6  H10  H  HCH2   0   0.212  22.7688  25.6300  32.4724
 BV6  H11  H  HCH2   0   0.217  21.4490  25.2167  33.5537
 BV6  H12  H  HOH1   0   0.454  26.1371  25.7621  38.2133
 BV6  H13  H  HOH1   0   0.460  21.1188  24.3052  36.0388
 BV6  H14  H  HOH1   0   0.454  23.0322  27.5400  33.7003
 BV6  H15  H  HCH1   0   0.246  27.9814  30.8811  33.3765
 BV6  H16  H  HCH1   0   0.248  28.0867  28.8181  32.4674
 BV6  H17  H  HCH1   0   0.315  26.4629  27.0135  32.8578
 BV6  H18  H  HCH1   0   0.243  26.1524  28.7376  31.2426
 BV6  H19  H  HCH1   0   0.269  24.3318  30.4904  32.7412
 BV6  H20  H  HCH2   0   0.209  26.9547  30.9647  31.2459
 BV6  H21  H  HCH2   0   0.222  25.3311  30.9922  30.5719
 BV6  H22  H  HOH1   0   0.459  28.7963  27.2908  33.9080
 BV6  H23  H  HOH1   0   0.460  23.8910  28.5674  31.1198
 BV6  H24  H  HOH1   0   0.459  26.1634  33.1098  31.2461
 BV6  H25  H  HOH1   0   0.450  23.2069  23.8645  38.2123
 BV6  O6B  O  OH1    0  -0.655  25.7624  32.5362  31.9057

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
 BV6  C1   C2   aromatic  1.396  0.020  1.396
 BV6  C1   C6   aromatic  1.398  0.020  1.398
 BV6  C1   O1B  single    1.342  0.020  1.342
 BV6  C2   C3   aromatic  1.382  0.020  1.382
 BV6  C3   C4   aromatic  1.387  0.020  1.387
 BV6  C4   C5   aromatic  1.391  0.020  1.391
 BV6  C4   N4   single    1.445  0.020  1.445
 BV6  C5   C6   aromatic  1.377  0.020  1.377
 BV6  O5   N4   single    1.210  0.020  1.210
 BV6  O6   N4   double    1.210  0.020  1.210
 BV6  C1A  C2A  single    1.541  0.020  1.541
 BV6  C1A  O5A  single    1.391  0.020  1.391
 BV6  C1A  S1A  single    1.829  0.020  1.829
 BV6  C2A  C3A  single    1.520  0.020  1.520
 BV6  C2A  O2A  single    1.403  0.020  1.403
 BV6  C3A  C4A  single    1.521  0.020  1.521
 BV6  C3A  O3A  single    1.404  0.020  1.404
 BV6  C4A  C5A  single    1.532  0.020  1.532
 BV6  C4A  O4A  single    1.411  0.020  1.411
 BV6  C5A  C6A  single    1.523  0.020  1.523
 BV6  C5A  O5A  single    1.426  0.020  1.426
 BV6  C6A  O6A  single    1.402  0.020  1.402
 BV6  C1B  C2B  single    1.550  0.020  1.550
 BV6  C1B  O1B  single    1.395  0.020  1.395
 BV6  C1B  O5B  single    1.396  0.020  1.396
 BV6  C2B  C3B  single    1.528  0.020  1.528
 BV6  C2B  O2B  single    1.394  0.020  1.394
 BV6  C3B  C4B  single    1.523  0.020  1.523
 BV6  C3B  S1A  single    1.822  0.020  1.822
 BV6  C4B  C5B  single    1.549  0.020  1.549
 BV6  C4B  O4B  single    1.402  0.020  1.402
 BV6  C5B  C6B  single    1.518  0.020  1.518
 BV6  C5B  O5B  single    1.417  0.020  1.417
 BV6  C6B  O6B  single    1.404  0.020  1.404
 BV6  C2   H1   single    0.930  0.020  1.080
 BV6  C3   H2   single    0.930  0.020  1.080
 BV6  C5   H3   single    0.930  0.020  1.080
 BV6  C6   H4   single    0.930  0.020  1.080
 BV6  C1A  H5   single    0.970  0.020  1.090
 BV6  C2A  H6   single    0.970  0.020  1.090
 BV6  C3A  H7   single    0.970  0.020  1.090
 BV6  C4A  H8   single    0.970  0.020  1.090
 BV6  C5A  H9   single    0.970  0.020  1.090
 BV6  C6A  H10  single    0.970  0.020  1.090
 BV6  C6A  H11  single    0.970  0.020  1.090
 BV6  O2A  H12  single    0.850  0.020  0.980
 BV6  O4A  H13  single    0.850  0.020  0.980
 BV6  O6A  H14  single    0.850  0.020  0.980
 BV6  C1B  H15  single    0.970  0.020  1.090
 BV6  C2B  H16  single    0.970  0.020  1.090
 BV6  C3B  H17  single    0.970  0.020  1.090
 BV6  C4B  H18  single    0.970  0.020  1.090
 BV6  C5B  H19  single    0.970  0.020  1.090
 BV6  C6B  H20  single    0.970  0.020  1.090
 BV6  C6B  H21  single    0.970  0.020  1.090
 BV6  O2B  H22  single    0.850  0.020  0.980
 BV6  O4B  H23  single    0.850  0.020  0.980
 BV6  O6B  H24  single    0.850  0.020  0.980
 BV6  O3A  H25  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
 BV6  O1B  C1   C6   115.36  3.000
 BV6  O1B  C1   C2   124.78  3.000
 BV6  C6   C1   C2   119.86  3.000
 BV6  H1   C2   C3   118.40  3.000
 BV6  H1   C2   C1   122.06  3.000
 BV6  C3   C2   C1   119.52  3.000
 BV6  H2   C3   C4   120.98  3.000
 BV6  H2   C3   C2   118.98  3.000
 BV6  C4   C3   C2   120.03  3.000
 BV6  N4   C4   C5   119.59  3.000
 BV6  N4   C4   C3   119.53  3.000
 BV6  C5   C4   C3   120.88  3.000
 BV6  H3   C5   C6   119.56  3.000
 BV6  H3   C5   C4   121.27  3.000
 BV6  C6   C5   C4   119.16  3.000
 BV6  H4   C6   C5   120.07  3.000
 BV6  H4   C6   C1   119.39  3.000
 BV6  C5   C6   C1   120.53  3.000
 BV6  H5   C1A  S1A  106.45  3.000
 BV6  H5   C1A  O5A  105.06  3.000
 BV6  S1A  C1A  O5A  114.39  3.000
 BV6  H5   C1A  C2A  107.47  3.000
 BV6  S1A  C1A  C2A  107.24  3.000
 BV6  O5A  C1A  C2A  115.63  3.000
 BV6  H6   C2A  O2A  110.25  3.000
 BV6  H6   C2A  C3A  106.11  3.000
 BV6  O2A  C2A  C3A  113.60  3.000
 BV6  H6   C2A  C1A  109.77  3.000
 BV6  O2A  C2A  C1A  106.92  3.000
 BV6  C3A  C2A  C1A  110.18  3.000
 BV6  H7   C3A  O3A  110.90  3.000
 BV6  H7   C3A  C4A  109.81  3.000
 BV6  O3A  C3A  C4A  112.10  3.000
 BV6  H7   C3A  C2A  110.04  3.000
 BV6  O3A  C3A  C2A  107.22  3.000
 BV6  C4A  C3A  C2A  106.65  3.000
 BV6  H8   C4A  O4A  110.20  3.000
 BV6  H8   C4A  C5A  110.03  3.000
 BV6  O4A  C4A  C5A  110.23  3.000
 BV6  H8   C4A  C3A  107.89  3.000
 BV6  O4A  C4A  C3A  109.01  3.000
 BV6  C5A  C4A  C3A  109.44  3.000
 BV6  H9   C5A  O5A  104.21  3.000
 BV6  H9   C5A  C6A  106.35  3.000
 BV6  O5A  C5A  C6A  112.45  3.000
 BV6  H9   C5A  C4A  106.38  3.000
 BV6  O5A  C5A  C4A  113.23  3.000
 BV6  C6A  C5A  C4A  113.34  3.000
 BV6  H11  C6A  H10  106.48  3.000
 BV6  H11  C6A  O6A  107.16  3.000
 BV6  H10  C6A  O6A  111.97  3.000
 BV6  H11  C6A  C5A  107.11  3.000
 BV6  H10  C6A  C5A  108.51  3.000
 BV6  O6A  C6A  C5A  115.14  3.000
 BV6  H12  O2A  C2A  108.37  3.000
 BV6  H13  O4A  C4A  109.06  3.000
 BV6  C5A  O5A  C1A  122.27  3.000
 BV6  H14  O6A  C6A  107.99  3.000
 BV6  H15  C1B  O5B  111.22  3.000
 BV6  H15  C1B  O1B  109.29  3.000
 BV6  O5B  C1B  O1B  106.24  3.000
 BV6  H15  C1B  C2B  109.65  3.000
 BV6  O5B  C1B  C2B  110.93  3.000
 BV6  O1B  C1B  C2B  109.43  3.000
 BV6  H16  C2B  O2B  110.44  3.000
 BV6  H16  C2B  C3B  106.36  3.000
 BV6  O2B  C2B  C3B  113.82  3.000
 BV6  H16  C2B  C1B  106.44  3.000
 BV6  O2B  C2B  C1B  109.95  3.000
 BV6  C3B  C2B  C1B  109.52  3.000
 BV6  H17  C3B  S1A  107.55  3.000
 BV6  H17  C3B  C4B  108.25  3.000
 BV6  S1A  C3B  C4B  112.45  3.000
 BV6  H17  C3B  C2B  109.13  3.000
 BV6  S1A  C3B  C2B  111.83  3.000
 BV6  C4B  C3B  C2B  107.54  3.000
 BV6  H18  C4B  O4B  109.62  3.000
 BV6  H18  C4B  C5B  108.79  3.000
 BV6  O4B  C4B  C5B  113.28  3.000
 BV6  H18  C4B  C3B  106.03  3.000
 BV6  O4B  C4B  C3B  109.40  3.000
 BV6  C5B  C4B  C3B  109.47  3.000
 BV6  H19  C5B  O5B  104.02  3.000
 BV6  H19  C5B  C6B  109.02  3.000
 BV6  O5B  C5B  C6B  112.72  3.000
 BV6  H19  C5B  C4B  108.30  3.000
 BV6  O5B  C5B  C4B  111.30  3.000
 BV6  C6B  C5B  C4B  111.14  3.000
 BV6  H21  C6B  H20  106.21  3.000
 BV6  H21  C6B  O6B  112.27  3.000
 BV6  H20  C6B  O6B  111.79  3.000
 BV6  H21  C6B  C5B  107.10  3.000
 BV6  H20  C6B  C5B  110.21  3.000
 BV6  O6B  C6B  C5B  109.14  3.000
 BV6  C1B  O1B  C1   119.67  3.000
 BV6  H22  O2B  C2B  107.94  3.000
 BV6  H23  O4B  C4B  109.03  3.000
 BV6  C5B  O5B  C1B  116.79  3.000
 BV6  O6   N4   O5   123.68  3.000
 BV6  O6   N4   C4   118.14  3.000
 BV6  O5   N4   C4   118.18  3.000
 BV6  C3B  S1A  C1A  101.35  3.000
 BV6  H25  O3A  C3A  108.07  3.000
 BV6  H24  O6B  C6B  108.37  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
 BV6  CONST_01  C4   C3  C2  C1    0.00  0.0  0
 BV6  CONST_02  C4   C5  C6  C1    0.00  0.0  0
 BV6  CONST_03  C5   C6  C1  C2    0.00  0.0  0
 BV6  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 BV6  CONST_05  C6   C1  C2  C3    0.00  0.0  0
 BV6  CONST_06  C6   C5  C4  C3    0.00  0.0  0
 BV6  CONST_07  N4   C4  C3  C2  180.00  0.0  0
 BV6  CONST_08  O1B  C1  C2  C3  180.00  0.0  0
 BV6  CONST_09  O1B  C1  C6  C5  180.00  0.0  0
 BV6  CONST_10  N4   C4  C5  C6  180.00  0.0  0
 BV6  CONST_11  H2   C3  C2  C1  180.00  0.0  0
 BV6  CONST_12  H3   C5  C6  C1  180.00  0.0  0
 BV6  CONST_13  H4   C6  C1  C2  180.00  0.0  0
 BV6  CONST_14  H1   C2  C3  C4  180.00  0.0  0
 BV6  CONST_15  O5   N4  C4  C3  180.00  0.0  0
 BV6  CONST_16  O6   N4  C4  C3    0.00  0.0  0
 BV6  CONST_17  O5   N4  C4  C5    0.00  0.0  0
 BV6  CONST_18  O6   N4  C4  C5  180.00  0.0  0

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
 BV6  chir_01  C1A  C2A  O5A  S1A  negativ
 BV6  chir_02  C2A  O2A  C1A  C3A  negativ
 BV6  chir_03  C3A  O3A  C2A  C4A  positiv
 BV6  chir_04  C4A  O4A  C5A  C3A  positiv
 BV6  chir_05  C5A  O5A  C4A  C6A  negativ
 BV6  chir_06  C1B  O1B  O5B  C2B  positiv
 BV6  chir_07  C2B  O2B  C1B  C3B  positiv
 BV6  chir_08  C3B  S1A  C4B  C2B  negativ
 BV6  chir_09  C4B  O4B  C5B  C3B  negativ
 BV6  chir_10  C5B  O5B  C4B  C6B  positiv

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
 BV6  plan-1  C1   0.020
 BV6  plan-1  C2   0.020
 BV6  plan-1  C3   0.020
 BV6  plan-1  C4   0.020
 BV6  plan-1  C5   0.020
 BV6  plan-1  C6   0.020
 BV6  plan-1  O1B  0.020
 BV6  plan-1  N4   0.020
 BV6  plan-1  H1   0.020
 BV6  plan-1  H2   0.020
 BV6  plan-1  H3   0.020
 BV6  plan-1  H4   0.020
 BV6  plan-2  C4   0.020
 BV6  plan-2  O5   0.020
 BV6  plan-2  O6   0.020
 BV6  plan-2  N4   0.020

