# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 05:50:49 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-[4-(trifluoromethyl)phenyl]-4~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2[nH]c(nn2)c3ccc(cc3)C(F)(F)F
#
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
 B0Z  B0Z  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-[4-(trifluoromethyl)phenyl]-4~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol  ligand  42  26  .  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_B0Z
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
 B0Z  C1   C  CR5   0   0.436   1.3043   0.1275   0.4026
 B0Z  C4   C  CR5   0   0.448  -0.8370   0.0905   0.6386
 B0Z  C6   C  CR6   0   0.035  -2.2660   0.0318   0.3562
 B0Z  C11  C  CR16  0  -0.290  -2.7477  -0.0838  -0.9451
 B0Z  F13  F  F     0  -0.313  -6.9873   1.1489  -0.3928
 B0Z  F14  F  F     0  -0.308  -7.1466  -0.7700   0.5611
 B0Z  F15  F  F     0  -0.303  -6.7961  -0.6480  -1.5590
 B0Z  C9   C  CR6   0  -0.203  -5.0070  -0.0830  -0.1329
 B0Z  C8   C  CR16  0  -0.254  -4.5344   0.0373   1.1707
 B0Z  C7   C  CR16  0  -0.270  -3.1754   0.0925   1.4128
 B0Z  C10  C  CR16  0  -0.258  -4.1099  -0.1399  -1.1902
 B0Z  N5   N  NR15  0  -0.676   0.1497   0.0319  -0.2865
 B0Z  N3   N  N     0  -0.326  -0.2975   0.2115   1.8246
 B0Z  N2   N  N     0  -0.314   1.0429   0.2372   1.6756
 B0Z  C1'  C  CH1   0  -0.060   2.6559   0.1181  -0.2244
 B0Z  C2'  C  CH1   0   0.014   3.3904   1.4330   0.0317
 B0Z  O2'  O  OH1   0  -0.670   2.6242   2.4645  -0.5393
 B0Z  O5'  O  O2    0  -0.492   3.3801  -0.9556   0.3193
 B0Z  C5'  C  CH1   0  -0.017   4.6467  -1.1373  -0.2855
 B0Z  C6'  C  CH2   0  -0.157   5.2694  -2.3750   0.3235
 B0Z  O6'  O  OH1   0  -0.670   4.4666  -3.4873   0.0082
 B0Z  C4'  C  CH1   0   0.038   5.5112   0.1064  -0.0677
 B0Z  O4'  O  OH1   0  -0.672   6.7311  -0.0880  -0.7373
 B0Z  C3'  C  CH1   0  -0.020   4.7797   1.3387  -0.5898
 B0Z  O3'  O  OH1   0  -0.674   5.5705   2.4657  -0.2863
 B0Z  H1   H  HCR6  0   0.259  -2.0740  -0.1304  -1.7905
 B0Z  H2   H  HCR6  0   0.282  -5.2171   0.0856   2.0084
 B0Z  H3   H  HCR6  0   0.270  -2.8170   0.1830   2.4289
 B0Z  H4   H  HCR6  0   0.281  -4.4520  -0.2310  -2.2118
 B0Z  H5   H  HNR5  0   0.441   0.0600  -0.0664  -1.2868
 B0Z  H6   H  HCH1  0   0.255   2.5318  -0.0069  -1.3120
 B0Z  H7   H  HCH1  0   0.233   3.4894   1.5633   1.1177
 B0Z  H8   H  HOH1  0   0.463   2.8100   3.2843  -0.0728
 B0Z  H9   H  HCH1  0   0.225   4.5224  -1.2918  -1.3699
 B0Z  H10  H  HCH2  0   0.215   6.2845  -2.4828  -0.0722
 B0Z  H11  H  HCH2  0   0.198   5.3592  -2.2306   1.4093
 B0Z  H12  H  HOH1  0   0.457   4.8995  -4.2729   0.3537
 B0Z  H13  H  HCH1  0   0.213   5.6689   0.2308   1.0162
 B0Z  H14  H  HOH1  0   0.454   7.2574   0.7125  -0.6370
 B0Z  H15  H  HCH1  0   0.220   4.6605   1.2288  -1.6789
 B0Z  H16  H  HOH1  0   0.460   5.3536   3.1743  -0.8995
 B0Z  C12  C  CT    0   1.054  -6.4822  -0.0945  -0.3840

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
 B0Z  O3'  C3'  single    1.410  0.020  1.410
 B0Z  O4'  C4'  single    1.405  0.020  1.405
 B0Z  C3'  C4'  single    1.525  0.020  1.525
 B0Z  C3'  C2'  single    1.525  0.020  1.525
 B0Z  C4'  C5'  single    1.530  0.020  1.530
 B0Z  O2'  C2'  single    1.406  0.020  1.406
 B0Z  C2'  C1'  single    1.528  0.020  1.528
 B0Z  O6'  C6'  single    1.407  0.020  1.407
 B0Z  C5'  C6'  single    1.513  0.020  1.513
 B0Z  C5'  O5'  single    1.415  0.020  1.415
 B0Z  C1'  O5'  single    1.405  0.020  1.405
 B0Z  C1'  C1   single    1.490  0.020  1.490
 B0Z  N2   C1   aromatic  1.304  0.020  1.304
 B0Z  N2   N3   aromatic  1.349  0.020  1.349
 B0Z  C1   N5   aromatic  1.348  0.020  1.348
 B0Z  N3   C4   aromatic  1.308  0.020  1.308
 B0Z  N5   C4   aromatic  1.354  0.020  1.354
 B0Z  C4   C6   single    1.458  0.020  1.458
 B0Z  C6   C7   aromatic  1.395  0.020  1.395
 B0Z  C6   C11  aromatic  1.392  0.020  1.392
 B0Z  C7   C8   aromatic  1.382  0.020  1.382
 B0Z  C11  C10  aromatic  1.385  0.020  1.385
 B0Z  C8   C9   aromatic  1.392  0.020  1.392
 B0Z  C10  C9   aromatic  1.388  0.020  1.388
 B0Z  C9   C12  single    1.496  0.020  1.496
 B0Z  F14  C12  single    1.338  0.020  1.338
 B0Z  C12  F13  single    1.342  0.020  1.342
 B0Z  C12  F15  single    1.336  0.020  1.336
 B0Z  C11  H1   single    0.930  0.020  1.080
 B0Z  C8   H2   single    0.930  0.020  1.080
 B0Z  C7   H3   single    0.930  0.020  1.080
 B0Z  C10  H4   single    0.930  0.020  1.080
 B0Z  N5   H5   single    0.860  0.020  1.020
 B0Z  C1'  H6   single    0.970  0.020  1.090
 B0Z  C2'  H7   single    0.970  0.020  1.090
 B0Z  O2'  H8   single    0.850  0.020  0.980
 B0Z  C5'  H9   single    0.970  0.020  1.090
 B0Z  C6'  H10  single    0.970  0.020  1.090
 B0Z  C6'  H11  single    0.970  0.020  1.090
 B0Z  O6'  H12  single    0.850  0.020  0.980
 B0Z  C4'  H13  single    0.970  0.020  1.090
 B0Z  O4'  H14  single    0.850  0.020  0.980
 B0Z  C3'  H15  single    0.970  0.020  1.090
 B0Z  O3'  H16  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
 B0Z  C1'  C1   N2   126.38  3.000
 B0Z  N2   C1   N5   109.47  3.000
 B0Z  C1'  C1   N5   124.15  3.000
 B0Z  N3   C4   N5   108.84  3.000
 B0Z  N5   C4   C6   125.47  3.000
 B0Z  N3   C4   C6   125.70  3.000
 B0Z  C7   C6   C11  119.06  3.000
 B0Z  C11  C6   C4   121.57  3.000
 B0Z  C7   C6   C4   119.36  3.000
 B0Z  H1   C11  C10  118.18  3.000
 B0Z  H1   C11  C6   121.22  3.000
 B0Z  C10  C11  C6   120.60  3.000
 B0Z  C10  C9   C8   119.84  3.000
 B0Z  C10  C9   C12  120.60  3.000
 B0Z  C8   C9   C12  119.51  3.000
 B0Z  H2   C8   C7   118.91  3.000
 B0Z  H2   C8   C9   120.98  3.000
 B0Z  C7   C8   C9   120.11  3.000
 B0Z  H3   C7   C8   119.61  3.000
 B0Z  H3   C7   C6   119.95  3.000
 B0Z  C8   C7   C6   120.44  3.000
 B0Z  H4   C10  C9   121.25  3.000
 B0Z  H4   C10  C11  118.80  3.000
 B0Z  C9   C10  C11  119.95  3.000
 B0Z  H5   N5   C4   128.09  3.000
 B0Z  H5   N5   C1   126.14  3.000
 B0Z  C4   N5   C1   105.77  3.000
 B0Z  N2   N3   C4   108.14  3.000
 B0Z  N3   N2   C1   107.78  3.000
 B0Z  H6   C1'  O5'  110.70  3.000
 B0Z  H6   C1'  C2'  108.50  3.000
 B0Z  O5'  C1'  C2'  110.19  3.000
 B0Z  H6   C1'  C1   108.30  3.000
 B0Z  O5'  C1'  C1   108.04  3.000
 B0Z  C2'  C1'  C1   111.11  3.000
 B0Z  H7   C2'  C3'  109.16  3.000
 B0Z  H7   C2'  O2'  111.32  3.000
 B0Z  C3'  C2'  O2'  112.10  3.000
 B0Z  H7   C2'  C1'  108.13  3.000
 B0Z  O2'  C2'  C1'  107.54  3.000
 B0Z  C3'  C2'  C1'  108.45  3.000
 B0Z  H8   O2'  C2'  108.86  3.000
 B0Z  C5'  O5'  C1'  113.21  3.000
 B0Z  H9   C5'  C4'  108.52  3.000
 B0Z  H9   C5'  C6'  109.12  3.000
 B0Z  C4'  C5'  C6'  112.02  3.000
 B0Z  H9   C5'  O5'  109.72  3.000
 B0Z  C6'  C5'  O5'  107.53  3.000
 B0Z  C4'  C5'  O5'  109.90  3.000
 B0Z  H11  C6'  H10  107.11  3.000
 B0Z  H11  C6'  O6'  111.82  3.000
 B0Z  H10  C6'  O6'  111.72  3.000
 B0Z  H11  C6'  C5'  108.89  3.000
 B0Z  H10  C6'  C5'  108.46  3.000
 B0Z  O6'  C6'  C5'  108.75  3.000
 B0Z  H12  O6'  C6'  107.97  3.000
 B0Z  H13  C4'  C3'  108.30  3.000
 B0Z  H13  C4'  O4'  111.09  3.000
 B0Z  C3'  C4'  O4'  111.41  3.000
 B0Z  H13  C4'  C5'  108.21  3.000
 B0Z  C3'  C4'  C5'  109.69  3.000
 B0Z  O4'  C4'  C5'  108.08  3.000
 B0Z  H14  O4'  C4'  108.04  3.000
 B0Z  H15  C3'  O3'  110.69  3.000
 B0Z  H15  C3'  C4'  108.05  3.000
 B0Z  O3'  C3'  C4'  107.65  3.000
 B0Z  H15  C3'  C2'  108.10  3.000
 B0Z  C4'  C3'  C2'  110.33  3.000
 B0Z  O3'  C3'  C2'  111.96  3.000
 B0Z  H16  O3'  C3'  108.98  3.000
 B0Z  C9   C12  F15  112.48  3.000
 B0Z  F15  C12  F14  107.17  3.000
 B0Z  C9   C12  F14  112.01  3.000
 B0Z  F15  C12  F13  106.83  3.000
 B0Z  F14  C12  F13  106.59  3.000
 B0Z  C9   C12  F13  111.41  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
 B0Z  CONST_01  C4   N3   N2   C1     0.00   0.0  0
 B0Z  CONST_02  N3   C4   N5   C1     0.00   0.0  0
 B0Z  CONST_03  C6   C4   N5   C1   180.00   0.0  0
 B0Z  CONST_04  N2   C1   N5   C4     0.00   0.0  0
 B0Z  CONST_05  C8   C7   C6   C4   180.00   0.0  0
 B0Z  CONST_06  C10  C11  C6   C4   180.00   0.0  0
 B0Z  CONST_07  N2   N3   C4   C6   180.00   0.0  0
 B0Z  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 B0Z  CONST_09  C9   C10  C11  C6     0.00   0.0  0
 B0Z  CONST_10  N3   C4   C6   C11  180.00   0.0  0
 B0Z  CONST_11  N5   C4   C6   C11    0.00   0.0  0
 B0Z  CONST_12  C8   C7   C6   C11    0.00   0.0  0
 B0Z  CONST_13  C8   C9   C10  C11    0.00   0.0  0
 B0Z  CONST_14  N3   C4   C6   C7     0.00   0.0  0
 B0Z  CONST_15  N5   C4   C6   C7   180.00   0.0  0
 B0Z  CONST_16  C10  C11  C6   C7     0.00   0.0  0
 B0Z  CONST_17  C10  C9   C8   C7     0.00   0.0  0
 B0Z  CONST_18  N3   N2   C1   N5     0.00   0.0  0
 B0Z  CONST_19  N2   N3   C4   N5     0.00   0.0  0
 B0Z  CONST_20  C1'  C1   N5   C4   180.00   0.0  0
 B0Z  CONST_21  C1'  C1   N2   N3   180.00   0.0  0
 B0Z  CONST_22  C12  C9   C10  C11  180.00   0.0  0
 B0Z  CONST_23  C7   C8   C9   C12  180.00   0.0  0
 B0Z  CONST_24  H3   C7   C6   C4     0.00   0.0  0
 B0Z  CONST_25  H1   C11  C6   C4     0.00   0.0  0
 B0Z  CONST_26  H5   N5   C4   C6     0.00   0.0  0
 B0Z  CONST_27  H2   C8   C7   C6   180.00   0.0  0
 B0Z  CONST_28  H4   C10  C11  C6   180.00   0.0  0
 B0Z  Var_01    C8   C9   C12  F13   81.06  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
 B0Z  chir_01  C1'  C2'  O5'  C1   negativ
 B0Z  chir_02  C2'  O2'  C1'  C3'  negativ
 B0Z  chir_03  C5'  O5'  C4'  C6'  negativ
 B0Z  chir_04  C4'  O4'  C5'  C3'  positiv
 B0Z  chir_05  C3'  O3'  C4'  C2'  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
 B0Z  plan-1  C1   0.020
 B0Z  plan-1  C4   0.020
 B0Z  plan-1  C6   0.020
 B0Z  plan-1  N5   0.020
 B0Z  plan-1  N3   0.020
 B0Z  plan-1  N2   0.020
 B0Z  plan-1  C1'  0.020
 B0Z  plan-1  H5   0.020
 B0Z  plan-2  C4   0.020
 B0Z  plan-2  C6   0.020
 B0Z  plan-2  C11  0.020
 B0Z  plan-2  C9   0.020
 B0Z  plan-2  C8   0.020
 B0Z  plan-2  C7   0.020
 B0Z  plan-2  C10  0.020
 B0Z  plan-2  H1   0.020
 B0Z  plan-2  H2   0.020
 B0Z  plan-2  H3   0.020
 B0Z  plan-2  H4   0.020
 B0Z  plan-2  C12  0.020

