# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 01:41:09 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-phenyl-1~{H}-imidazol-2-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]cc(n2)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
 9L2  9L2  (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-phenyl-1~{H}-imidazol-2-yl)oxane-3,4-diol  ligand  41  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_9L2
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
 9L2  O6'  O  OH1   0  -0.669   2.9801   3.3819   0.1670
 9L2  C6'  C  CH2   0  -0.161   3.3224   2.3340  -0.7079
 9L2  C5'  C  CH1   0  -0.018   3.0498   1.0129  -0.0220
 9L2  C4'  C  CH1   0   0.001   3.5004  -0.1824  -0.8685
 9L2  O4'  O  OH1   0  -0.675   4.9007  -0.1994  -1.0489
 9L2  C3'  C  CH1   0   0.039   3.1205  -1.4773  -0.1605
 9L2  O3'  O  OH1   0  -0.670   3.4057  -2.6061  -0.9488
 9L2  O5'  O  O2    0  -0.495   1.6586   0.9330   0.2072
 9L2  C1'  C  CH1   0  -0.023   1.2625  -0.2127   0.9235
 9L2  C2'  C  CH1   0  -0.147   1.6338  -1.5011   0.1822
 9L2  N2'  N  NH2   0  -0.788   1.2132  -2.6324   0.9844
 9L2  C1   C  CR5   0   0.491  -0.2145  -0.1217   1.1085
 9L2  N2   N  NR15  0  -0.621  -0.8227  -0.0795   2.3108
 9L2  C3   C  CR15  0  -0.122  -2.1643   0.0111   2.1006
 9L2  C4   C  CR5   0   0.137  -2.3175   0.0270   0.7359
 9L2  N5   N  N     0  -0.462  -1.0894  -0.0589   0.1402
 9L2  C6   C  CR6   0   0.036  -3.5484   0.1204  -0.0479
 9L2  C7   C  CR16  0  -0.311  -3.5019   0.0685  -1.4427
 9L2  C8   C  CR16  0  -0.238  -4.6638   0.1572  -2.1954
 9L2  C9   C  CR16  0  -0.274  -5.8964   0.2997  -1.5722
 9L2  C10  C  CR16  0  -0.235  -5.9543   0.3531  -0.1846
 9L2  C11  C  CR16  0  -0.339  -4.7941   0.2651   0.5687
 9L2  H1   H  HOH1  0   0.457   3.1880   4.2127  -0.2693
 9L2  H2   H  HCH2  0   0.199   2.7441   2.3757  -1.6413
 9L2  H3   H  HCH2  0   0.203   4.3831   2.3714  -0.9818
 9L2  H4   H  HCH1  0   0.216   3.5976   0.9899   0.9351
 9L2  H5   H  HCH1  0   0.223   2.9783  -0.1440  -1.8353
 9L2  H6   H  HOH1  0   0.462   5.1232   0.2911  -1.8447
 9L2  H7   H  HCH1  0   0.196   3.6864  -1.5128   0.7876
 9L2  H8   H  HOH1  0   0.449   4.3443  -2.5878  -1.1635
 9L2  H9   H  HCH1  0   0.234   1.7464  -0.2299   1.9140
 9L2  H10  H  HCH1  0   0.248   1.0591  -1.5187  -0.7501
 9L2  H11  H  HNH2  0   0.356   1.2898  -3.4845   0.4452
 9L2  H12  H  HNH2  0   0.341   1.8350  -2.7453   1.7772
 9L2  H14  H  HNR5  0   0.421  -0.3715  -0.1155   3.2120
 9L2  H15  H  HCR5  0   0.288  -2.8671   0.0524   2.9151
 9L2  H17  H  HCR6  0   0.247  -2.5472  -0.0443  -1.9393
 9L2  H18  H  HCR6  0   0.254  -4.6041   0.1157  -3.2754
 9L2  H19  H  HCR6  0   0.254  -6.8018   0.3705  -2.1609
 9L2  H20  H  HCR6  0   0.255  -6.9079   0.4669   0.3149
 9L2  H21  H  HCR6  0   0.242  -4.8650   0.3117   1.6486

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
 9L2  O3'  C3'  single    1.406  0.020  1.406
 9L2  O4'  C4'  single    1.412  0.020  1.412
 9L2  C3'  C4'  single    1.524  0.020  1.524
 9L2  C3'  C2'  single    1.526  0.020  1.526
 9L2  C4'  C5'  single    1.532  0.020  1.532
 9L2  N2'  C2'  single    1.449  0.020  1.449
 9L2  C2'  C1'  single    1.532  0.020  1.532
 9L2  O6'  C6'  single    1.407  0.020  1.407
 9L2  C5'  C6'  single    1.513  0.020  1.513
 9L2  C5'  O5'  single    1.412  0.020  1.412
 9L2  C1'  O5'  single    1.408  0.020  1.408
 9L2  C1'  C1   single    1.491  0.020  1.491
 9L2  N2   C1   aromatic  1.348  0.020  1.348
 9L2  N2   C3   aromatic  1.361  0.020  1.361
 9L2  C1   N5   aromatic  1.306  0.020  1.306
 9L2  C3   C4   aromatic  1.373  0.020  1.373
 9L2  N5   C4   aromatic  1.368  0.020  1.368
 9L2  C4   C6   single    1.462  0.020  1.462
 9L2  C6   C7   aromatic  1.397  0.020  1.397
 9L2  C6   C11  aromatic  1.397  0.020  1.397
 9L2  C7   C8   aromatic  1.387  0.020  1.387
 9L2  C11  C10  aromatic  1.386  0.020  1.386
 9L2  C8   C9   aromatic  1.389  0.020  1.389
 9L2  C10  C9   aromatic  1.390  0.020  1.390
 9L2  O6'  H1   single    0.850  0.020  0.980
 9L2  C6'  H2   single    0.970  0.020  1.090
 9L2  C6'  H3   single    0.970  0.020  1.090
 9L2  C5'  H4   single    0.970  0.020  1.090
 9L2  C4'  H5   single    0.970  0.020  1.090
 9L2  O4'  H6   single    0.850  0.020  0.980
 9L2  C3'  H7   single    0.970  0.020  1.090
 9L2  O3'  H8   single    0.850  0.020  0.980
 9L2  C1'  H9   single    0.970  0.020  1.090
 9L2  C2'  H10  single    0.970  0.020  1.090
 9L2  N2'  H11  single    0.890  0.020  1.040
 9L2  N2'  H12  single    0.890  0.020  1.040
 9L2  N2   H14  single    0.860  0.020  1.020
 9L2  C3   H15  single    0.930  0.020  1.080
 9L2  C7   H17  single    0.930  0.020  1.080
 9L2  C8   H18  single    0.930  0.020  1.080
 9L2  C9   H19  single    0.930  0.020  1.080
 9L2  C10  H20  single    0.930  0.020  1.080
 9L2  C11  H21  single    0.930  0.020  1.080

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
 9L2  H1   O6'  C6'  107.98  3.000
 9L2  H3   C6'  H2   107.20  3.000
 9L2  H3   C6'  C5'  108.50  3.000
 9L2  H2   C6'  C5'  108.86  3.000
 9L2  H3   C6'  O6'  111.43  3.000
 9L2  H2   C6'  O6'  111.83  3.000
 9L2  C5'  C6'  O6'  108.93  3.000
 9L2  H4   C5'  O5'  110.33  3.000
 9L2  H4   C5'  C4'  108.48  3.000
 9L2  O5'  C5'  C4'  109.59  3.000
 9L2  H4   C5'  C6'  108.78  3.000
 9L2  O5'  C5'  C6'  107.48  3.000
 9L2  C4'  C5'  C6'  112.18  3.000
 9L2  H5   C4'  C3'  108.65  3.000
 9L2  H5   C4'  O4'  111.04  3.000
 9L2  C3'  C4'  O4'  107.24  3.000
 9L2  H5   C4'  C5'  108.60  3.000
 9L2  C3'  C4'  C5'  109.44  3.000
 9L2  O4'  C4'  C5'  111.82  3.000
 9L2  H6   O4'  C4'  109.23  3.000
 9L2  H7   C3'  C2'  107.81  3.000
 9L2  H7   C3'  O3'  110.58  3.000
 9L2  C2'  C3'  O3'  108.12  3.000
 9L2  H7   C3'  C4'  107.36  3.000
 9L2  C2'  C3'  C4'  111.13  3.000
 9L2  O3'  C3'  C4'  111.78  3.000
 9L2  H8   O3'  C3'  107.90  3.000
 9L2  C1'  O5'  C5'  113.93  3.000
 9L2  H9   C1'  C1   108.92  3.000
 9L2  H9   C1'  C2'  108.37  3.000
 9L2  C1   C1'  C2'  110.57  3.000
 9L2  H9   C1'  O5'  110.26  3.000
 9L2  C1   C1'  O5'  106.98  3.000
 9L2  C2'  C1'  O5'  111.71  3.000
 9L2  H10  C2'  N2'  107.84  3.000
 9L2  H10  C2'  C1'  107.35  3.000
 9L2  N2'  C2'  C1'  108.56  3.000
 9L2  H10  C2'  C3'  108.68  3.000
 9L2  C1'  C2'  C3'  109.37  3.000
 9L2  N2'  C2'  C3'  114.79  3.000
 9L2  H12  N2'  H11  106.06  3.000
 9L2  H12  N2'  C2'  109.98  3.000
 9L2  H11  N2'  C2'  109.91  3.000
 9L2  N5   C1   N2   110.94  3.000
 9L2  N5   C1   C1'  125.04  3.000
 9L2  N2   C1   C1'  124.01  3.000
 9L2  H14  N2   C3   125.55  3.000
 9L2  H14  N2   C1   126.44  3.000
 9L2  C3   N2   C1   108.00  3.000
 9L2  H15  C3   C4   132.72  3.000
 9L2  H15  C3   N2   121.95  3.000
 9L2  C4   C3   N2   105.32  3.000
 9L2  C6   C4   N5   121.76  3.000
 9L2  C6   C4   C3   128.85  3.000
 9L2  N5   C4   C3   109.38  3.000
 9L2  C4   N5   C1   106.35  3.000
 9L2  C11  C6   C7   118.31  3.000
 9L2  C11  C6   C4   121.36  3.000
 9L2  C7   C6   C4   120.33  3.000
 9L2  H17  C7   C8   119.77  3.000
 9L2  H17  C7   C6   119.46  3.000
 9L2  C8   C7   C6   120.77  3.000
 9L2  H18  C8   C9   120.05  3.000
 9L2  H18  C8   C7   119.52  3.000
 9L2  C9   C8   C7   120.43  3.000
 9L2  H19  C9   C10  120.38  3.000
 9L2  H19  C9   C8   120.35  3.000
 9L2  C10  C9   C8   119.27  3.000
 9L2  H20  C10  C11  119.56  3.000
 9L2  H20  C10  C9   120.09  3.000
 9L2  C11  C10  C9   120.35  3.000
 9L2  H21  C11  C10  118.96  3.000
 9L2  H21  C11  C6   120.18  3.000
 9L2  C10  C11  C6   120.86  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
 9L2  CONST_01  C4   C3   N2   C1     0.00  0.0  0
 9L2  CONST_02  C3   C4   N5   C1     0.00  0.0  0
 9L2  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 9L2  CONST_04  C4   N5   C1   N2     0.00  0.0  0
 9L2  CONST_05  N5   C4   C3   N2     0.00  0.0  0
 9L2  CONST_06  C6   C4   C3   N2   180.00  0.0  0
 9L2  CONST_07  N5   C1   N2   C3     0.00  0.0  0
 9L2  CONST_08  C7   C6   C4   C3   180.00  0.0  0
 9L2  CONST_09  C11  C6   C4   C3     0.00  0.0  0
 9L2  CONST_10  C8   C7   C6   C4   180.00  0.0  0
 9L2  CONST_11  C10  C11  C6   C4   180.00  0.0  0
 9L2  CONST_12  C7   C6   C4   N5     0.00  0.0  0
 9L2  CONST_13  C11  C6   C4   N5   180.00  0.0  0
 9L2  CONST_14  C9   C8   C7   C6     0.00  0.0  0
 9L2  CONST_15  C9   C10  C11  C6     0.00  0.0  0
 9L2  CONST_16  C10  C11  C6   C7     0.00  0.0  0
 9L2  CONST_17  C10  C9   C8   C7     0.00  0.0  0
 9L2  CONST_18  C11  C6   C7   C8     0.00  0.0  0
 9L2  CONST_19  C11  C10  C9   C8     0.00  0.0  0
 9L2  CONST_20  C3   N2   C1   C1'  180.00  0.0  0
 9L2  CONST_21  C4   N5   C1   C1'  180.00  0.0  0
 9L2  CONST_22  H14  N2   C1   C1'    0.00  0.0  0
 9L2  CONST_23  H15  C3   N2   C1   180.00  0.0  0
 9L2  CONST_24  H17  C7   C6   C4     0.00  0.0  0
 9L2  CONST_25  H21  C11  C6   C4     0.00  0.0  0
 9L2  CONST_26  H18  C8   C7   C6   180.00  0.0  0
 9L2  CONST_27  H20  C10  C11  C6   180.00  0.0  0
 9L2  CONST_28  H19  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
 9L2  chir_01  C5'  C4'  C6'  O5'  negativ
 9L2  chir_02  C4'  O4'  C5'  C3'  positiv
 9L2  chir_03  C3'  O3'  C4'  C2'  negativ
 9L2  chir_04  C1'  O5'  C1   C2'  negativ
 9L2  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
 9L2  plan-1  C1'  0.020
 9L2  plan-1  C1   0.020
 9L2  plan-1  N2   0.020
 9L2  plan-1  C3   0.020
 9L2  plan-1  C4   0.020
 9L2  plan-1  N5   0.020
 9L2  plan-1  C6   0.020
 9L2  plan-1  H14  0.020
 9L2  plan-1  H15  0.020
 9L2  plan-2  C4   0.020
 9L2  plan-2  C6   0.020
 9L2  plan-2  C7   0.020
 9L2  plan-2  C8   0.020
 9L2  plan-2  C9   0.020
 9L2  plan-2  C10  0.020
 9L2  plan-2  C11  0.020
 9L2  plan-2  H17  0.020
 9L2  plan-2  H18  0.020
 9L2  plan-2  H19  0.020
 9L2  plan-2  H20  0.020
 9L2  plan-2  H21  0.020

