# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:50:13 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{S},6~{R})-2-[5-(4-aminophenyl)-4~{H}-1,2,4-triazol-3-yl]-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1)c2[nH]c(nn2)[C@@H]3O[C@H](CO)[C@@H](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
 B1W  B1W  (2~{S},3~{R},4~{R},5~{S},6~{R})-2-[5-(4-aminophenyl)-4~{H}-1,2,4-triazol-3-yl]-6-(hydroxymethyl)oxane-3,4,5-triol  ligand  41  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B1W
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
 B1W  C1   C  CR5   0   0.427   0.1340  -0.0771  -0.3602
 B1W  C4   C  CR5   0   0.436  -2.0194  -0.0004  -0.5176
 B1W  C6   C  CR6   0  -0.007  -3.4300   0.0803  -0.1720
 B1W  C10  C  CR16  0  -0.311  -5.2114   0.1789   1.4639
 B1W  C11  C  CR16  0  -0.298  -3.8675   0.1093   1.1527
 B1W  O4'  O  OH1   0  -0.673   5.6023   0.0208   0.5994
 B1W  C4'  C  CH1   0   0.037   4.3545  -0.1446  -0.0256
 B1W  C5'  C  CH1   0  -0.017   3.5243   1.1151   0.2276
 B1W  C6'  C  CH2   0  -0.157   4.1537   2.3439  -0.3926
 B1W  O6'  O  OH1   0  -0.670   3.3811   3.4701  -0.0516
 B1W  C3'  C  CH1   0  -0.020   3.6158  -1.3619   0.5196
 B1W  O3'  O  OH1   0  -0.675   4.3723  -2.5059   0.1907
 B1W  C2'  C  CH1   0   0.015   2.2057  -1.4259  -0.0570
 B1W  O2'  O  OH1   0  -0.670   1.4359  -2.4419   0.5363
 B1W  C1'  C  CH1   0  -0.059   1.5046  -0.0976   0.2237
 B1W  O5'  O  O2    0  -0.492   2.2355   0.9640  -0.3366
 B1W  N5   N  NR15  0  -0.680  -0.9967   0.0319   0.3712
 B1W  N3   N  N     0  -0.344  -1.5219  -0.1194  -1.7237
 B1W  N2   N  N     0  -0.321  -0.1726  -0.1691  -1.6212
 B1W  C7   C  CR16  0  -0.279  -4.3963   0.1219  -1.1803
 B1W  C8   C  CR16  0  -0.312  -5.7405   0.1913  -0.8801
 B1W  C9   C  CR6   0   0.315  -6.1807   0.2225   0.4523
 B1W  N12  N  NH2   0  -0.855  -7.5111   0.3402   0.7517
 B1W  H1   H  HCR6  0   0.263  -5.5171   0.1978   2.5029
 B1W  H2   H  HCR6  0   0.244  -3.1608   0.0705   1.9728
 B1W  H3   H  HOH1  0   0.454   6.1082  -0.7887   0.4714
 B1W  H4   H  HCH1  0   0.213   4.4702  -0.2680  -1.1150
 B1W  H5   H  HCH1  0   0.224   3.4394   1.2647   1.3166
 B1W  H6   H  HCH2  0   0.215   5.1805   2.4305  -0.0232
 B1W  H7   H  HCH2  0   0.197   4.2124   2.2035  -1.4811
 B1W  H8   H  HOH1  0   0.457   3.8381   4.2514  -0.3748
 B1W  H9   H  HCH1  0   0.220   3.5347  -1.2505   1.6118
 B1W  H10  H  HOH1  0   0.460   4.1755  -3.2034   0.8228
 B1W  H11  H  HCH1  0   0.230   2.2669  -1.5558  -1.1460
 B1W  H12  H  HOH1  0   0.461   1.6276  -3.2742   0.0949
 B1W  H13  H  HCH1  0   0.251   1.4171   0.0257   1.3155
 B1W  H14  H  HNR5  0   0.434  -1.0513   0.1256   1.3737
 B1W  H15  H  HCR6  0   0.253  -4.0889   0.0982  -2.2179
 B1W  H16  H  HCR6  0   0.263  -6.4665   0.2233  -1.6833
 B1W  H17  H  HNH2  0   0.386  -7.7972   0.0606   1.6756
 B1W  H18  H  HNH2  0   0.386  -8.1638   0.0581   0.0390

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
 B1W  O3'  C3'  single    1.410  0.020  1.410
 B1W  O4'  C4'  single    1.405  0.020  1.405
 B1W  C3'  C4'  single    1.525  0.020  1.525
 B1W  C3'  C2'  single    1.525  0.020  1.525
 B1W  C4'  C5'  single    1.530  0.020  1.530
 B1W  O2'  C2'  single    1.406  0.020  1.406
 B1W  C2'  C1'  single    1.528  0.020  1.528
 B1W  O6'  C6'  single    1.408  0.020  1.408
 B1W  C5'  C6'  single    1.514  0.020  1.514
 B1W  C5'  O5'  single    1.415  0.020  1.415
 B1W  C1'  O5'  single    1.405  0.020  1.405
 B1W  C1'  C1   single    1.490  0.020  1.490
 B1W  N2   C1   aromatic  1.301  0.020  1.301
 B1W  N2   N3   aromatic  1.354  0.020  1.354
 B1W  C1   N5   aromatic  1.351  0.020  1.351
 B1W  N3   C4   aromatic  1.310  0.020  1.310
 B1W  N5   C4   aromatic  1.355  0.020  1.355
 B1W  C4   C6   single    1.455  0.020  1.455
 B1W  C6   C7   aromatic  1.397  0.020  1.397
 B1W  C6   C11  aromatic  1.395  0.020  1.395
 B1W  C7   C8   aromatic  1.379  0.020  1.379
 B1W  C11  C10  aromatic  1.381  0.020  1.381
 B1W  C8   C9   aromatic  1.404  0.020  1.404
 B1W  C10  C9   aromatic  1.402  0.020  1.402
 B1W  C9   N12  single    1.369  0.020  1.369
 B1W  C10  H1   single    0.930  0.020  1.080
 B1W  C11  H2   single    0.930  0.020  1.080
 B1W  O4'  H3   single    0.850  0.020  0.980
 B1W  C4'  H4   single    0.970  0.020  1.090
 B1W  C5'  H5   single    0.970  0.020  1.090
 B1W  C6'  H6   single    0.970  0.020  1.090
 B1W  C6'  H7   single    0.970  0.020  1.090
 B1W  O6'  H8   single    0.850  0.020  0.980
 B1W  C3'  H9   single    0.970  0.020  1.090
 B1W  O3'  H10  single    0.850  0.020  0.980
 B1W  C2'  H11  single    0.970  0.020  1.090
 B1W  O2'  H12  single    0.850  0.020  0.980
 B1W  C1'  H13  single    0.970  0.020  1.090
 B1W  N5   H14  single    0.860  0.020  1.020
 B1W  C7   H15  single    0.930  0.020  1.080
 B1W  C8   H16  single    0.930  0.020  1.080
 B1W  N12  H17  single    0.890  0.020  1.040
 B1W  N12  H18  single    0.890  0.020  1.040

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
 B1W  N2   C1   N5   109.46  3.000
 B1W  N5   C1   C1'  123.97  3.000
 B1W  N2   C1   C1'  126.56  3.000
 B1W  N3   C4   N5   108.62  3.000
 B1W  N5   C4   C6   125.08  3.000
 B1W  N3   C4   C6   126.30  3.000
 B1W  C7   C6   C11  117.88  3.000
 B1W  C11  C6   C4   122.06  3.000
 B1W  C7   C6   C4   120.06  3.000
 B1W  H1   C10  C9   119.77  3.000
 B1W  H1   C10  C11  119.45  3.000
 B1W  C9   C10  C11  120.78  3.000
 B1W  H2   C11  C10  117.77  3.000
 B1W  H2   C11  C6   120.90  3.000
 B1W  C10  C11  C6   121.33  3.000
 B1W  H3   O4'  C4'  107.97  3.000
 B1W  H4   C4'  C3'  108.35  3.000
 B1W  H4   C4'  C5'  108.22  3.000
 B1W  C3'  C4'  C5'  109.59  3.000
 B1W  H4   C4'  O4'  111.07  3.000
 B1W  C5'  C4'  O4'  108.14  3.000
 B1W  C3'  C4'  O4'  111.41  3.000
 B1W  H5   C5'  O5'  109.77  3.000
 B1W  H5   C5'  C6'  109.06  3.000
 B1W  O5'  C5'  C6'  107.58  3.000
 B1W  H5   C5'  C4'  108.48  3.000
 B1W  O5'  C5'  C4'  109.90  3.000
 B1W  C6'  C5'  C4'  112.02  3.000
 B1W  H7   C6'  H6   107.11  3.000
 B1W  H7   C6'  O6'  111.80  3.000
 B1W  H6   C6'  O6'  111.71  3.000
 B1W  H7   C6'  C5'  108.93  3.000
 B1W  H6   C6'  C5'  108.42  3.000
 B1W  O6'  C6'  C5'  108.79  3.000
 B1W  H8   O6'  C6'  107.94  3.000
 B1W  H9   C3'  C2'  108.13  3.000
 B1W  H9   C3'  O3'  110.67  3.000
 B1W  C2'  C3'  O3'  111.95  3.000
 B1W  H9   C3'  C4'  108.04  3.000
 B1W  C2'  C3'  C4'  110.27  3.000
 B1W  O3'  C3'  C4'  107.72  3.000
 B1W  H10  O3'  C3'  108.99  3.000
 B1W  H11  C2'  C1'  108.09  3.000
 B1W  H11  C2'  O2'  111.30  3.000
 B1W  C1'  C2'  O2'  107.42  3.000
 B1W  H11  C2'  C3'  109.17  3.000
 B1W  C1'  C2'  C3'  108.57  3.000
 B1W  O2'  C2'  C3'  112.16  3.000
 B1W  H12  O2'  C2'  108.83  3.000
 B1W  H13  C1'  O5'  110.59  3.000
 B1W  H13  C1'  C2'  108.40  3.000
 B1W  O5'  C1'  C2'  110.17  3.000
 B1W  H13  C1'  C1   108.28  3.000
 B1W  O5'  C1'  C1   108.17  3.000
 B1W  C2'  C1'  C1   111.23  3.000
 B1W  C1'  O5'  C5'  113.29  3.000
 B1W  H14  N5   C4   127.83  3.000
 B1W  H14  N5   C1   126.23  3.000
 B1W  C4   N5   C1   105.94  3.000
 B1W  N2   N3   C4   108.18  3.000
 B1W  N3   N2   C1   107.80  3.000
 B1W  H15  C7   C8   119.12  3.000
 B1W  H15  C7   C6   119.65  3.000
 B1W  C8   C7   C6   121.23  3.000
 B1W  H16  C8   C9   119.55  3.000
 B1W  H16  C8   C7   119.56  3.000
 B1W  C9   C8   C7   120.89  3.000
 B1W  N12  C9   C8   120.96  3.000
 B1W  N12  C9   C10  121.13  3.000
 B1W  C8   C9   C10  117.88  3.000
 B1W  H18  N12  H17  112.80  3.000
 B1W  H18  N12  C9   116.82  3.000
 B1W  H17  N12  C9   116.94  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
 B1W  CONST_01  C4   N3   N2   C1     0.00  0.0  0
 B1W  CONST_02  N3   C4   N5   C1     0.00  0.0  0
 B1W  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 B1W  CONST_04  N2   C1   N5   C4     0.00  0.0  0
 B1W  CONST_05  C8   C7   C6   C4   180.00  0.0  0
 B1W  CONST_06  C10  C11  C6   C4   180.00  0.0  0
 B1W  CONST_07  N2   N3   C4   C6   180.00  0.0  0
 B1W  CONST_08  C9   C8   C7   C6     0.00  0.0  0
 B1W  CONST_09  C9   C10  C11  C6     0.00  0.0  0
 B1W  CONST_10  C7   C6   C11  C10    0.00  0.0  0
 B1W  CONST_11  C7   C8   C9   C10    0.00  0.0  0
 B1W  CONST_12  N3   C4   C6   C11  180.00  0.0  0
 B1W  CONST_13  N5   C4   C6   C11    0.00  0.0  0
 B1W  CONST_14  C8   C7   C6   C11    0.00  0.0  0
 B1W  CONST_15  C8   C9   C10  C11    0.00  0.0  0
 B1W  CONST_16  N3   N2   C1   N5     0.00  0.0  0
 B1W  CONST_17  N2   N3   C4   N5     0.00  0.0  0
 B1W  CONST_18  C7   C6   C4   N5   180.00  0.0  0
 B1W  CONST_19  C7   C6   C4   N3     0.00  0.0  0
 B1W  CONST_20  C1'  C1   N5   C4   180.00  0.0  0
 B1W  CONST_21  N3   N2   C1   C1'  180.00  0.0  0
 B1W  CONST_22  N12  C9   C10  C11  180.00  0.0  0
 B1W  CONST_23  N12  C9   C8   C7   180.00  0.0  0
 B1W  CONST_24  H15  C7   C6   C4     0.00  0.0  0
 B1W  CONST_25  H2   C11  C6   C4     0.00  0.0  0
 B1W  CONST_26  H14  N5   C4   C6     0.00  0.0  0
 B1W  CONST_27  H16  C8   C7   C6   180.00  0.0  0
 B1W  CONST_28  H1   C10  C11  C6   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
 B1W  chir_01  C4'  O4'  C3'  C5'  negativ
 B1W  chir_02  C5'  O5'  C4'  C6'  negativ
 B1W  chir_03  C3'  O3'  C4'  C2'  negativ
 B1W  chir_04  C2'  O2'  C3'  C1'  positiv
 B1W  chir_05  C1'  O5'  C2'  C1   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
 B1W  plan-1  C1   0.020
 B1W  plan-1  C4   0.020
 B1W  plan-1  C6   0.020
 B1W  plan-1  C1'  0.020
 B1W  plan-1  N5   0.020
 B1W  plan-1  N3   0.020
 B1W  plan-1  N2   0.020
 B1W  plan-1  H14  0.020
 B1W  plan-2  C4   0.020
 B1W  plan-2  C6   0.020
 B1W  plan-2  C10  0.020
 B1W  plan-2  C11  0.020
 B1W  plan-2  C7   0.020
 B1W  plan-2  C8   0.020
 B1W  plan-2  C9   0.020
 B1W  plan-2  N12  0.020
 B1W  plan-2  H1   0.020
 B1W  plan-2  H2   0.020
 B1W  plan-2  H15  0.020
 B1W  plan-2  H16  0.020
 B1W  plan-3  C9   0.020
 B1W  plan-3  N12  0.020
 B1W  plan-3  H17  0.020
 B1W  plan-3  H18  0.020

