# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 01:15:54 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(5-phenyl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1c2[nH]c(nn2)c3ccccc3
#
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
 9LB  9LB  (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(5-phenyl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4-diol  ligand  40  22  .  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_9LB
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
 9LB  O6'  O  OH1   0  -0.669   3.0450   3.5013   0.0191
 9LB  C6'  C  CH2   0  -0.161   3.7772   2.3748  -0.3991
 9LB  C5'  C  CH1   0  -0.021   3.1760   1.1383   0.2316
 9LB  C4'  C  CH1   0   0.001   3.9794  -0.1266  -0.0865
 9LB  O4'  O  OH1   0  -0.675   5.2763  -0.0761   0.4683
 9LB  C3'  C  CH1   0   0.038   3.2769  -1.3411   0.5103
 9LB  O3'  O  OH1   0  -0.669   3.9092  -2.5414   0.1434
 9LB  O5'  O  O2    0  -0.493   1.8600   1.0011  -0.2682
 9LB  C1'  C  CH1   0  -0.024   1.1497  -0.0603   0.3164
 9LB  C2'  C  CH1   0  -0.145   1.8231  -1.4106   0.0502
 9LB  N2'  N  NH2   0  -0.789   1.0291  -2.4518   0.6683
 9LB  C1   C  CR5   0   0.446  -0.2277  -0.0418  -0.2536
 9LB  N2   N  N     0  -0.320  -0.5376  -0.0750  -1.5186
 9LB  N3   N  N     0  -0.334  -1.8860  -0.0474  -1.6139
 9LB  C4   C  CR5   0   0.433  -2.3793   0.0010  -0.4034
 9LB  N5   N  NR15  0  -0.675  -1.3556   0.0080   0.4840
 9LB  C6   C  CR6   0   0.029  -3.7959   0.0444  -0.0563
 9LB  C7   C  CR16  0  -0.284  -4.7444   0.2038  -1.0681
 9LB  C8   C  CR16  0  -0.238  -6.0938   0.2462  -0.7599
 9LB  C9   C  CR16  0  -0.257  -6.5158   0.1305   0.5593
 9LB  C10  C  CR16  0  -0.238  -5.5775  -0.0301   1.5692
 9LB  C11  C  CR16  0  -0.304  -4.2249  -0.0741   1.2651
 9LB  H1   H  HOH1  0   0.457   3.4382   4.2792  -0.3862
 9LB  H2   H  HCH2  0   0.200   3.7641   2.2609  -1.4919
 9LB  H3   H  HCH2  0   0.205   4.8284   2.4432  -0.0950
 9LB  H4   H  HCH1  0   0.220   3.1510   1.2717   1.3260
 9LB  H5   H  HCH1  0   0.225   4.0210  -0.2496  -1.1785
 9LB  H6   H  HOH1  0   0.463   5.8840   0.2905  -0.1796
 9LB  H7   H  HCH1  0   0.199   3.2805  -1.2198   1.6082
 9LB  H8   H  HOH1  0   0.450   4.8263  -2.4939   0.4334
 9LB  H9   H  HCH1  0   0.246   1.0751   0.0822   1.4076
 9LB  H10  H  HCH1  0   0.252   1.8097  -1.5774  -1.0328
 9LB  H11  H  HNH2  0   0.359   1.3598  -3.3602   0.3724
 9LB  H12  H  HNH2  0   0.343   1.1399  -2.4268   1.6759
 9LB  H15  H  HCR6  0   0.258  -4.4211   0.2989  -2.0962
 9LB  H16  H  HCR6  0   0.264  -6.8193   0.3727  -1.5525
 9LB  H17  H  HCR6  0   0.263  -7.5709   0.1648   0.7968
 9LB  H18  H  HCR6  0   0.265  -5.8957  -0.1249   2.5990
 9LB  H19  H  HCR6  0   0.247  -3.5152  -0.2076   2.0719
 9LB  H13  H  HNR5  0   0.434  -1.4083   0.0602   1.4897

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
 9LB  O3'  C3'  single    1.405  0.020  1.405
 9LB  O4'  C4'  single    1.412  0.020  1.412
 9LB  C3'  C4'  single    1.525  0.020  1.525
 9LB  C3'  C2'  single    1.526  0.020  1.526
 9LB  C4'  C5'  single    1.532  0.020  1.532
 9LB  N2'  C2'  single    1.448  0.020  1.448
 9LB  C2'  C1'  single    1.532  0.020  1.532
 9LB  O6'  C6'  single    1.407  0.020  1.407
 9LB  C5'  C6'  single    1.513  0.020  1.513
 9LB  C5'  O5'  single    1.414  0.020  1.414
 9LB  C1'  O5'  single    1.405  0.020  1.405
 9LB  C1'  C1   single    1.491  0.020  1.491
 9LB  N2   C1   aromatic  1.303  0.020  1.303
 9LB  N2   N3   aromatic  1.352  0.020  1.352
 9LB  C1   N5   aromatic  1.349  0.020  1.349
 9LB  N3   C4   aromatic  1.308  0.020  1.308
 9LB  N5   C4   aromatic  1.355  0.020  1.355
 9LB  C4   C6   single    1.459  0.020  1.459
 9LB  C6   C7   aromatic  1.396  0.020  1.396
 9LB  C6   C11  aromatic  1.394  0.020  1.394
 9LB  C7   C8   aromatic  1.385  0.020  1.385
 9LB  C11  C10  aromatic  1.387  0.020  1.387
 9LB  C8   C9   aromatic  1.390  0.020  1.390
 9LB  C10  C9   aromatic  1.388  0.020  1.388
 9LB  O6'  H1   single    0.850  0.020  0.980
 9LB  C6'  H2   single    0.970  0.020  1.090
 9LB  C6'  H3   single    0.970  0.020  1.090
 9LB  C5'  H4   single    0.970  0.020  1.090
 9LB  C4'  H5   single    0.970  0.020  1.090
 9LB  O4'  H6   single    0.850  0.020  0.980
 9LB  C3'  H7   single    0.970  0.020  1.090
 9LB  O3'  H8   single    0.850  0.020  0.980
 9LB  C1'  H9   single    0.970  0.020  1.090
 9LB  C2'  H10  single    0.970  0.020  1.090
 9LB  N2'  H11  single    0.890  0.020  1.040
 9LB  N2'  H12  single    0.890  0.020  1.040
 9LB  C7   H15  single    0.930  0.020  1.080
 9LB  C8   H16  single    0.930  0.020  1.080
 9LB  C9   H17  single    0.930  0.020  1.080
 9LB  C10  H18  single    0.930  0.020  1.080
 9LB  C11  H19  single    0.930  0.020  1.080
 9LB  N5   H13  single    0.860  0.020  1.020

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
 9LB  H1   O6'  C6'  108.04  3.000
 9LB  H3   C6'  H2   107.08  3.000
 9LB  H3   C6'  C5'  108.45  3.000
 9LB  H2   C6'  C5'  108.98  3.000
 9LB  H3   C6'  O6'  111.50  3.000
 9LB  H2   C6'  O6'  111.86  3.000
 9LB  C5'  C6'  O6'  108.88  3.000
 9LB  H4   C5'  O5'  109.96  3.000
 9LB  H4   C5'  C4'  108.53  3.000
 9LB  O5'  C5'  C4'  109.54  3.000
 9LB  H4   C5'  C6'  108.90  3.000
 9LB  O5'  C5'  C6'  107.57  3.000
 9LB  C4'  C5'  C6'  112.33  3.000
 9LB  H5   C4'  C3'  108.49  3.000
 9LB  H5   C4'  O4'  111.07  3.000
 9LB  C3'  C4'  O4'  107.34  3.000
 9LB  H5   C4'  C5'  108.57  3.000
 9LB  C3'  C4'  C5'  109.56  3.000
 9LB  O4'  C4'  C5'  111.75  3.000
 9LB  H6   O4'  C4'  109.25  3.000
 9LB  H7   C3'  C2'  107.92  3.000
 9LB  H7   C3'  O3'  110.60  3.000
 9LB  C2'  C3'  O3'  108.11  3.000
 9LB  H7   C3'  C4'  107.47  3.000
 9LB  C2'  C3'  C4'  110.92  3.000
 9LB  O3'  C3'  C4'  111.76  3.000
 9LB  H8   O3'  C3'  107.92  3.000
 9LB  C1'  O5'  C5'  113.38  3.000
 9LB  H9   C1'  C1   108.31  3.000
 9LB  H9   C1'  C2'  108.39  3.000
 9LB  C1   C1'  C2'  110.52  3.000
 9LB  H9   C1'  O5'  110.39  3.000
 9LB  C1   C1'  O5'  107.38  3.000
 9LB  C2'  C1'  O5'  111.80  3.000
 9LB  H10  C2'  N2'  107.80  3.000
 9LB  H10  C2'  C1'  107.48  3.000
 9LB  N2'  C2'  C1'  108.58  3.000
 9LB  H10  C2'  C3'  108.45  3.000
 9LB  C1'  C2'  C3'  109.03  3.000
 9LB  N2'  C2'  C3'  115.24  3.000
 9LB  H12  N2'  H11  106.09  3.000
 9LB  H12  N2'  C2'  110.27  3.000
 9LB  H11  N2'  C2'  109.99  3.000
 9LB  N5   C1   N2   109.45  3.000
 9LB  N5   C1   C1'  124.33  3.000
 9LB  N2   C1   C1'  126.21  3.000
 9LB  N3   N2   C1   107.77  3.000
 9LB  C4   N3   N2   108.16  3.000
 9LB  C6   C4   N5   125.28  3.000
 9LB  C6   C4   N3   125.97  3.000
 9LB  N5   C4   N3   108.74  3.000
 9LB  H13  N5   C4   127.88  3.000
 9LB  H13  N5   C1   126.24  3.000
 9LB  C4   N5   C1   105.87  3.000
 9LB  C11  C6   C7   119.18  3.000
 9LB  C11  C6   C4   121.44  3.000
 9LB  C7   C6   C4   119.38  3.000
 9LB  H15  C7   C8   120.00  3.000
 9LB  H15  C7   C6   119.72  3.000
 9LB  C8   C7   C6   120.28  3.000
 9LB  H16  C8   C9   120.09  3.000
 9LB  H16  C8   C7   119.60  3.000
 9LB  C9   C8   C7   120.30  3.000
 9LB  H17  C9   C10  120.21  3.000
 9LB  H17  C9   C8   120.11  3.000
 9LB  C10  C9   C8   119.67  3.000
 9LB  H18  C10  C11  119.52  3.000
 9LB  H18  C10  C9   120.26  3.000
 9LB  C11  C10  C9   120.23  3.000
 9LB  H19  C11  C10  118.67  3.000
 9LB  H19  C11  C6   120.99  3.000
 9LB  C10  C11  C6   120.34  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
 9LB  CONST_01  C4   N3   N2   C1     0.00  0.0  0
 9LB  CONST_02  N3   C4   N5   C1     0.00  0.0  0
 9LB  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 9LB  CONST_04  C4   N5   C1   N2     0.00  0.0  0
 9LB  CONST_05  N5   C4   N3   N2     0.00  0.0  0
 9LB  CONST_06  C6   C4   N3   N2   180.00  0.0  0
 9LB  CONST_07  N5   C1   N2   N3     0.00  0.0  0
 9LB  CONST_08  C7   C6   C4   N3     0.00  0.0  0
 9LB  CONST_09  C11  C6   C4   N3   180.00  0.0  0
 9LB  CONST_10  C8   C7   C6   C4   180.00  0.0  0
 9LB  CONST_11  C10  C11  C6   C4   180.00  0.0  0
 9LB  CONST_12  C7   C6   C4   N5   180.00  0.0  0
 9LB  CONST_13  C11  C6   C4   N5     0.00  0.0  0
 9LB  CONST_14  C9   C8   C7   C6     0.00  0.0  0
 9LB  CONST_15  C9   C10  C11  C6     0.00  0.0  0
 9LB  CONST_16  C10  C11  C6   C7     0.00  0.0  0
 9LB  CONST_17  C10  C9   C8   C7     0.00  0.0  0
 9LB  CONST_18  C11  C6   C7   C8     0.00  0.0  0
 9LB  CONST_19  C11  C10  C9   C8     0.00  0.0  0
 9LB  CONST_20  N3   N2   C1   C1'  180.00  0.0  0
 9LB  CONST_21  C4   N5   C1   C1'  180.00  0.0  0
 9LB  CONST_22  H13  N5   C1   C1'    0.00  0.0  0
 9LB  CONST_23  H15  C7   C6   C4     0.00  0.0  0
 9LB  CONST_24  H19  C11  C6   C4     0.00  0.0  0
 9LB  CONST_25  H16  C8   C7   C6   180.00  0.0  0
 9LB  CONST_26  H18  C10  C11  C6   180.00  0.0  0
 9LB  CONST_27  H17  C9   C8   C7   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
 9LB  chir_01  C5'  C4'  C6'  O5'  negativ
 9LB  chir_02  C4'  O4'  C5'  C3'  positiv
 9LB  chir_03  C3'  O3'  C4'  C2'  negativ
 9LB  chir_04  C1'  O5'  C2'  C1   positiv
 9LB  chir_05  C2'  N2'  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
 9LB  plan-1  C1'  0.020
 9LB  plan-1  C1   0.020
 9LB  plan-1  N2   0.020
 9LB  plan-1  N3   0.020
 9LB  plan-1  C4   0.020
 9LB  plan-1  N5   0.020
 9LB  plan-1  C6   0.020
 9LB  plan-1  H13  0.020
 9LB  plan-2  C4   0.020
 9LB  plan-2  C6   0.020
 9LB  plan-2  C7   0.020
 9LB  plan-2  C8   0.020
 9LB  plan-2  C9   0.020
 9LB  plan-2  C10  0.020
 9LB  plan-2  C11  0.020
 9LB  plan-2  H15  0.020
 9LB  plan-2  H16  0.020
 9LB  plan-2  H17  0.020
 9LB  plan-2  H18  0.020
 9LB  plan-2  H19  0.020

