# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:01:24 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methoxyphenyl)-1~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2[nH]nc(n2)[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
 B1K  B1K  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methoxyphenyl)-1~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol  ligand  43  24  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B1K
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
 B1K  C1   C  CR5   0   0.316   0.5094  -0.7445  -0.1288
 B1K  C4   C  CR5   0   0.536  -1.5851  -0.6569   0.0795
 B1K  C6   C  CR6   0  -0.009  -2.9813  -0.2483   0.0466
 B1K  C7   C  CR16  0  -0.273  -3.9808  -0.9729   0.6884
 B1K  N3   N  NR15  0  -0.508  -1.1143  -1.7990   0.5906
 B1K  N2   N  N     0  -0.256   0.2160  -1.8712   0.4686
 B1K  C13  C  CH3   0  -0.440  -7.9495   0.3799   0.5030
 B1K  C9   C  CR6   0   0.390  -5.6515   0.5937  -0.0473
 B1K  C10  C  CR16  0  -0.327  -4.6527   1.3281  -0.6951
 B1K  C11  C  CR16  0  -0.270  -3.3407   0.9115  -0.6464
 B1K  C8   C  CR16  0  -0.369  -5.3048  -0.5646   0.6469
 B1K  N5   N  N     0  -0.545  -0.5624   0.0351  -0.3903
 B1K  C1'  C  CH1   0  -0.041   1.8921  -0.3235  -0.5124
 B1K  O5'  O  O2    0  -0.490   2.7991  -1.0993   0.2203
 B1K  C5'  C  CH1   0  -0.014   4.1483  -0.8588  -0.1231
 B1K  C6'  C  CH2   0  -0.158   5.0034  -1.8351   0.6558
 B1K  O6'  O  OH1   0  -0.670   4.6692  -3.1455   0.2649
 B1K  C4'  C  CH1   0   0.038   4.5055   0.5934   0.1958
 B1K  O4'  O  OH1   0  -0.673   5.8405   0.8129  -0.1869
 B1K  C3'  C  CH1   0  -0.008   3.5569   1.5240  -0.5491
 B1K  O3'  O  OH1   0  -0.673   3.8776   2.8427  -0.1736
 B1K  C2'  C  CH1   0   0.009   2.1079   1.1763  -0.2387
 B1K  O2'  O  OH1   0  -0.687   1.2886   1.9819  -1.0448
 B1K  H1   H  HCR6  0   0.254  -3.7490  -1.8732   1.2438
 B1K  H2   H  HNR5  0   0.434  -1.6181  -2.5595   1.0199
 B1K  H3   H  HCH3  0   0.233  -7.7975   0.3302   1.5840
 B1K  H4   H  HCH3  0   0.263  -8.8578   0.9415   0.3013
 B1K  H5   H  HCH3  0   0.233  -8.0675  -0.6344   0.1140
 B1K  H6   H  HCR6  0   0.272  -4.9184   2.2280  -1.2350
 B1K  H7   H  HCR6  0   0.263  -2.5822   1.4908  -1.1557
 B1K  H8   H  HCR6  0   0.289  -6.0464  -1.1573   1.1640
 B1K  H9   H  HCH1  0   0.245   2.0207  -0.4907  -1.5957
 B1K  H10  H  HCH1  0   0.221   4.2979  -1.0286  -1.2022
 B1K  H11  H  HCH2  0   0.215   6.0549  -1.6092   0.4540
 B1K  H12  H  HCH2  0   0.196   4.8390  -1.6742   1.7309
 B1K  H13  H  HOH1  0   0.457   5.3013  -3.7447   0.6712
 B1K  H14  H  HCH1  0   0.212   4.3740   0.7494   1.2789
 B1K  H15  H  HOH1  0   0.454   6.0562   1.7325   0.0001
 B1K  H16  H  HCH1  0   0.213   3.7167   1.3763  -1.6296
 B1K  H17  H  HOH1  0   0.457   3.4526   3.4493  -0.7875
 B1K  H18  H  HCH1  0   0.212   1.9224   1.3543   0.8327
 B1K  H19  H  HOH1  0   0.460   0.3720   1.6955  -0.8986
 B1K  O12  O  O2    0  -0.462  -6.8984   1.0735  -0.1444

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
 B1K  O3'  C3'  single    1.408  0.020  1.408
 B1K  O4'  C4'  single    1.406  0.020  1.406
 B1K  C3'  C4'  single    1.523  0.020  1.523
 B1K  C3'  C2'  single    1.522  0.020  1.522
 B1K  C4'  C5'  single    1.529  0.020  1.529
 B1K  O2'  C2'  single    1.404  0.020  1.404
 B1K  C2'  C1'  single    1.540  0.020  1.540
 B1K  O6'  C6'  single    1.408  0.020  1.408
 B1K  C5'  C6'  single    1.514  0.020  1.514
 B1K  C5'  O5'  single    1.413  0.020  1.413
 B1K  C1'  O5'  single    1.401  0.020  1.401
 B1K  C1'  C1   single    1.495  0.020  1.495
 B1K  N2   C1   aromatic  1.309  0.020  1.309
 B1K  N2   N3   aromatic  1.338  0.020  1.338
 B1K  C1   N5   aromatic  1.351  0.020  1.351
 B1K  N3   C4   aromatic  1.337  0.020  1.337
 B1K  N5   C4   aromatic  1.321  0.020  1.321
 B1K  C4   C6   single    1.455  0.020  1.455
 B1K  C6   C7   aromatic  1.391  0.020  1.391
 B1K  C6   C11  aromatic  1.398  0.020  1.398
 B1K  C7   C8   aromatic  1.386  0.020  1.386
 B1K  C11  C10  aromatic  1.377  0.020  1.377
 B1K  C8   C9   aromatic  1.394  0.020  1.394
 B1K  C10  C9   aromatic  1.399  0.020  1.399
 B1K  C9   O12  single    1.340  0.020  1.340
 B1K  O12  C13  single    1.416  0.020  1.416
 B1K  C7   H1   single    0.930  0.020  1.080
 B1K  N3   H2   single    0.860  0.020  1.020
 B1K  C13  H3   single    0.970  0.020  1.090
 B1K  C13  H4   single    0.970  0.020  1.090
 B1K  C13  H5   single    0.970  0.020  1.090
 B1K  C10  H6   single    0.930  0.020  1.080
 B1K  C11  H7   single    0.930  0.020  1.080
 B1K  C8   H8   single    0.930  0.020  1.080
 B1K  C1'  H9   single    0.970  0.020  1.090
 B1K  C5'  H10  single    0.970  0.020  1.090
 B1K  C6'  H11  single    0.970  0.020  1.090
 B1K  C6'  H12  single    0.970  0.020  1.090
 B1K  O6'  H13  single    0.850  0.020  0.980
 B1K  C4'  H14  single    0.970  0.020  1.090
 B1K  O4'  H15  single    0.850  0.020  0.980
 B1K  C3'  H16  single    0.970  0.020  1.090
 B1K  O3'  H17  single    0.850  0.020  0.980
 B1K  C2'  H18  single    0.970  0.020  1.090
 B1K  O2'  H19  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
 B1K  C1'  C1   N5   121.43  3.000
 B1K  N5   C1   N2   114.04  3.000
 B1K  C1'  C1   N2   124.53  3.000
 B1K  N5   C4   N3   108.10  3.000
 B1K  N5   C4   C6   125.99  3.000
 B1K  N3   C4   C6   125.91  3.000
 B1K  C11  C6   C7   118.43  3.000
 B1K  C11  C6   C4   119.39  3.000
 B1K  C7   C6   C4   122.18  3.000
 B1K  H1   C7   C8   117.69  3.000
 B1K  H1   C7   C6   121.05  3.000
 B1K  C8   C7   C6   121.26  3.000
 B1K  H2   N3   N2   119.67  3.000
 B1K  H2   N3   C4   129.14  3.000
 B1K  N2   N3   C4   111.19  3.000
 B1K  N3   N2   C1   102.60  3.000
 B1K  H5   C13  H4   108.86  3.000
 B1K  H5   C13  H3   108.96  3.000
 B1K  H4   C13  H3   108.86  3.000
 B1K  H5   C13  O12  111.85  3.000
 B1K  H4   C13  O12  106.41  3.000
 B1K  H3   C13  O12  111.80  3.000
 B1K  C8   C9   C10  119.29  3.000
 B1K  C10  C9   O12  116.30  3.000
 B1K  C8   C9   O12  124.41  3.000
 B1K  H6   C10  C11  120.18  3.000
 B1K  H6   C10  C9   119.49  3.000
 B1K  C11  C10  C9   120.33  3.000
 B1K  H7   C11  C10  119.29  3.000
 B1K  H7   C11  C6   119.83  3.000
 B1K  C10  C11  C6   120.88  3.000
 B1K  H8   C8   C9   121.54  3.000
 B1K  H8   C8   C7   118.65  3.000
 B1K  C9   C8   C7   119.81  3.000
 B1K  C4   N5   C1   104.07  3.000
 B1K  H9   C1'  C2'  107.80  3.000
 B1K  H9   C1'  O5'  110.74  3.000
 B1K  C2'  C1'  O5'  110.84  3.000
 B1K  H9   C1'  C1   108.47  3.000
 B1K  O5'  C1'  C1   107.98  3.000
 B1K  C2'  C1'  C1   110.99  3.000
 B1K  C5'  O5'  C1'  113.39  3.000
 B1K  H10  C5'  C4'  108.58  3.000
 B1K  H10  C5'  C6'  109.13  3.000
 B1K  C4'  C5'  C6'  111.92  3.000
 B1K  H10  C5'  O5'  109.95  3.000
 B1K  C6'  C5'  O5'  107.73  3.000
 B1K  C4'  C5'  O5'  109.52  3.000
 B1K  H12  C6'  H11  107.09  3.000
 B1K  H12  C6'  O6'  111.86  3.000
 B1K  H11  C6'  O6'  111.65  3.000
 B1K  H12  C6'  C5'  108.93  3.000
 B1K  H11  C6'  C5'  108.35  3.000
 B1K  O6'  C6'  C5'  108.87  3.000
 B1K  H13  O6'  C6'  107.87  3.000
 B1K  H14  C4'  C3'  108.64  3.000
 B1K  H14  C4'  O4'  111.02  3.000
 B1K  C3'  C4'  O4'  111.27  3.000
 B1K  H14  C4'  C5'  108.15  3.000
 B1K  C3'  C4'  C5'  109.43  3.000
 B1K  O4'  C4'  C5'  108.26  3.000
 B1K  H15  O4'  C4'  107.99  3.000
 B1K  H16  C3'  C2'  107.90  3.000
 B1K  H16  C3'  O3'  110.72  3.000
 B1K  C2'  C3'  O3'  112.11  3.000
 B1K  H16  C3'  C4'  107.89  3.000
 B1K  C2'  C3'  C4'  110.71  3.000
 B1K  O3'  C3'  C4'  107.45  3.000
 B1K  H17  O3'  C3'  108.65  3.000
 B1K  H18  C2'  O2'  111.56  3.000
 B1K  H18  C2'  C3'  108.77  3.000
 B1K  O2'  C2'  C3'  107.90  3.000
 B1K  H18  C2'  C1'  107.86  3.000
 B1K  O2'  C2'  C1'  112.03  3.000
 B1K  C3'  C2'  C1'  108.64  3.000
 B1K  H19  O2'  C2'  107.16  3.000
 B1K  C9   O12  C13  118.84  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
 B1K  CONST_01  C4   N3   N2   C1     0.00   0.0  0
 B1K  CONST_02  N3   C4   N5   C1     0.00   0.0  0
 B1K  CONST_03  C6   C4   N5   C1   180.00   0.0  0
 B1K  CONST_04  N2   C1   N5   C4     0.00   0.0  0
 B1K  CONST_05  C8   C7   C6   C4   180.00   0.0  0
 B1K  CONST_06  C10  C11  C6   C4   180.00   0.0  0
 B1K  CONST_07  N2   N3   C4   C6   180.00   0.0  0
 B1K  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 B1K  CONST_09  C9   C10  C11  C6     0.00   0.0  0
 B1K  CONST_10  N3   C4   C6   C7     0.00   0.0  0
 B1K  CONST_11  N5   C4   C6   C7   180.00   0.0  0
 B1K  CONST_12  C10  C11  C6   C7     0.00   0.0  0
 B1K  CONST_13  C10  C9   C8   C7     0.00   0.0  0
 B1K  CONST_14  N5   C1   N2   N3     0.00   0.0  0
 B1K  CONST_15  C11  C6   C4   N3   180.00   0.0  0
 B1K  CONST_16  N5   C4   N3   N2     0.00   0.0  0
 B1K  CONST_17  N5   C4   C6   C11    0.00   0.0  0
 B1K  CONST_18  C8   C7   C6   C11    0.00   0.0  0
 B1K  CONST_19  C8   C9   C10  C11    0.00   0.0  0
 B1K  CONST_20  C1'  C1   N5   C4   180.00   0.0  0
 B1K  CONST_21  C1'  C1   N2   N3   180.00   0.0  0
 B1K  CONST_22  O12  C9   C8   C7   180.00   0.0  0
 B1K  CONST_23  C11  C10  C9   O12  180.00   0.0  0
 B1K  CONST_24  H2   N3   N2   C1   180.00   0.0  0
 B1K  CONST_25  H1   C7   C6   C4     0.00   0.0  0
 B1K  CONST_26  H7   C11  C6   C4     0.00   0.0  0
 B1K  CONST_27  H8   C8   C7   C6   180.00   0.0  0
 B1K  CONST_28  H6   C10  C11  C6   180.00   0.0  0
 B1K  Var_01    C8   C9   O12  C13    0.55  30.0  3
 B1K  Var_02    H3   C13  O12  C9    60.82  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
 B1K  chir_01  C1'  C2'  O5'  C1   negativ
 B1K  chir_02  C5'  O5'  C6'  C4'  positiv
 B1K  chir_03  C4'  O4'  C5'  C3'  positiv
 B1K  chir_04  C3'  O3'  C4'  C2'  negativ
 B1K  chir_05  C2'  O2'  C3'  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
 B1K  plan-1  C1   0.020
 B1K  plan-1  C4   0.020
 B1K  plan-1  C6   0.020
 B1K  plan-1  N3   0.020
 B1K  plan-1  N2   0.020
 B1K  plan-1  N5   0.020
 B1K  plan-1  C1'  0.020
 B1K  plan-1  H2   0.020
 B1K  plan-2  C4   0.020
 B1K  plan-2  C6   0.020
 B1K  plan-2  C7   0.020
 B1K  plan-2  C9   0.020
 B1K  plan-2  C10  0.020
 B1K  plan-2  C11  0.020
 B1K  plan-2  C8   0.020
 B1K  plan-2  H1   0.020
 B1K  plan-2  H6   0.020
 B1K  plan-2  H7   0.020
 B1K  plan-2  H8   0.020
 B1K  plan-2  O12  0.020

