# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 09:12:58 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-naphthalen-2-yl-1~{H}-imidazol-4-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)c2c[nH]c(n2)c3ccc4ccccc4c3
#
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
 KV5  KV5  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-naphthalen-2-yl-1~{H}-imidazol-4-yl)oxane-3,4,5-triol  ligand  46  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KV5
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
 KV5  C4   C  CR5   0   0.467  -1.1479   1.3898  -0.0450
 KV5  C6   C  CR6   0   0.042  -2.5329   0.9298  -0.0757
 KV5  C8   C  CR66  0   0.152  -4.1294  -0.8998  -0.0813
 KV5  N3   N  NR15  0  -0.645  -0.7750   2.6877  -0.1511
 KV5  C2   C  CR15  0  -0.123   0.5831   2.7406  -0.0901
 KV5  O5'  O  O2    0  -0.497   2.6467   0.1047  -0.9325
 KV5  C5'  C  CH1   0  -0.011   3.9790  -0.3572  -0.9990
 KV5  C4'  C  CH1   0   0.037   4.2898  -1.2115   0.2307
 KV5  C3'  C  CH1   0  -0.033   4.0211  -0.3946   1.4887
 KV5  C2'  C  CH1   0   0.033   2.5940   0.1385   1.4707
 KV5  C1'  C  CH1   0  -0.065   2.3803   0.9321   0.1817
 KV5  C1   C  CR5   0   0.157   0.9896   1.4436   0.0578
 KV5  N5   N  N     0  -0.465  -0.0929   0.6185   0.0855
 KV5  O2'  O  OH1   0  -0.672   2.3364   0.9987   2.5515
 KV5  O3'  O  OH1   0  -0.679   4.2439  -1.2165   2.6184
 KV5  O4'  O  OH1   0  -0.674   5.6322  -1.6242   0.1637
 KV5  C11  C  CR16  0  -0.302  -3.6126   1.8474  -0.1258
 KV5  C10  C  CR16  0  -0.297  -4.9043   1.4070  -0.1541
 KV5  C9   C  CR66  0   0.103  -5.2041   0.0254  -0.1334
 KV5  C7   C  CR16  0  -0.386  -2.8041  -0.4185  -0.0534
 KV5  C15  C  CR16  0  -0.307  -6.5318  -0.4582  -0.1627
 KV5  C14  C  CR16  0  -0.258  -6.7829  -1.8035  -0.1415
 KV5  C13  C  CR16  0  -0.255  -5.7154  -2.7258  -0.0904
 KV5  C12  C  CR16  0  -0.316  -4.4206  -2.2855  -0.0609
 KV5  H1   H  HNR5  0   0.425  -1.3773   3.4865  -0.2713
 KV5  H2   H  HCR5  0   0.292   1.1300   3.6661  -0.1542
 KV5  H3   H  HCH1  0   0.216   4.6737   0.4998  -1.0108
 KV5  H4   H  HCH1  0   0.208   3.6088  -2.0787   0.2268
 KV5  H5   H  HCH1  0   0.224   4.7102   0.4626   1.4925
 KV5  H6   H  HCH1  0   0.211   1.8977  -0.7135   1.4656
 KV5  H7   H  HCH1  0   0.227   3.0702   1.7924   0.1881
 KV5  H9   H  HOH1  0   0.452   2.3860   0.4847   3.3637
 KV5  H10  H  HOH1  0   0.463   4.7557  -0.7266   3.2669
 KV5  H11  H  HOH1  0   0.451   5.8241  -2.1233   0.9649
 KV5  H14  H  HOH1  0   0.456   4.0437  -0.7875  -4.1825
 KV5  H15  H  HCR6  0   0.244  -3.4328   2.9147  -0.1376
 KV5  H16  H  HCR6  0   0.261  -5.7162   2.1225  -0.1906
 KV5  H17  H  HCR6  0   0.252  -1.9885  -1.1303  -0.0167
 KV5  H18  H  HCR6  0   0.258  -7.3487   0.2523  -0.2022
 KV5  H19  H  HCR6  0   0.260  -7.8024  -2.1659  -0.1642
 KV5  H20  H  HCR6  0   0.260  -5.9261  -3.7871  -0.0746
 KV5  H21  H  HCR6  0   0.257  -3.6022  -2.9938  -0.0223
 KV5  C6'  C  CH2   0  -0.157   4.1331  -1.1413  -2.2844
 KV5  O6'  O  OH1   0  -0.671   3.9135  -0.2803  -3.3764
 KV5  H12  H  HCH2  0   0.211   5.1380  -1.5755  -2.3067
 KV5  H13  H  HCH2  0   0.195   3.4208  -1.9783  -2.2758

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
 KV5  O3'  C3'  single    1.415  0.020  1.415
 KV5  O4'  C4'  single    1.406  0.020  1.406
 KV5  C3'  C4'  single    1.524  0.020  1.524
 KV5  C3'  C2'  single    1.524  0.020  1.524
 KV5  C4'  C5'  single    1.529  0.020  1.529
 KV5  O2'  C2'  single    1.405  0.020  1.405
 KV5  C2'  C1'  single    1.529  0.020  1.529
 KV5  O6'  C6'  single    1.408  0.020  1.408
 KV5  C5'  C6'  single    1.514  0.020  1.514
 KV5  C5'  O5'  single    1.412  0.020  1.412
 KV5  C1'  O5'  single    1.413  0.020  1.413
 KV5  C1'  C1   single    1.487  0.020  1.487
 KV5  C2   C1   aromatic  1.367  0.020  1.367
 KV5  C2   N3   aromatic  1.361  0.020  1.361
 KV5  C1   N5   aromatic  1.361  0.020  1.361
 KV5  N3   C4   aromatic  1.355  0.020  1.355
 KV5  N5   C4   aromatic  1.313  0.020  1.313
 KV5  C4   C6   single    1.460  0.020  1.460
 KV5  C6   C7   aromatic  1.376  0.020  1.376
 KV5  C6   C11  aromatic  1.418  0.020  1.418
 KV5  C7   C8   aromatic  1.410  0.020  1.410
 KV5  C11  C10  aromatic  1.365  0.020  1.365
 KV5  C8   C12  aromatic  1.416  0.020  1.416
 KV5  C8   C9   aromatic  1.419  0.020  1.419
 KV5  C12  C13  aromatic  1.368  0.020  1.368
 KV5  C10  C9   aromatic  1.414  0.020  1.414
 KV5  C9   C15  aromatic  1.413  0.020  1.413
 KV5  C13  C14  aromatic  1.412  0.020  1.412
 KV5  C15  C14  aromatic  1.369  0.020  1.369
 KV5  N3   H1   single    0.860  0.020  1.020
 KV5  C2   H2   single    0.930  0.020  1.080
 KV5  C5'  H3   single    0.970  0.020  1.090
 KV5  C4'  H4   single    0.970  0.020  1.090
 KV5  C3'  H5   single    0.970  0.020  1.090
 KV5  C2'  H6   single    0.970  0.020  1.090
 KV5  C1'  H7   single    0.970  0.020  1.090
 KV5  O2'  H9   single    0.850  0.020  0.980
 KV5  O3'  H10  single    0.850  0.020  0.980
 KV5  O4'  H11  single    0.850  0.020  0.980
 KV5  C6'  H12  single    0.970  0.020  1.090
 KV5  C6'  H13  single    0.970  0.020  1.090
 KV5  O6'  H14  single    0.850  0.020  0.980
 KV5  C11  H15  single    0.930  0.020  1.080
 KV5  C10  H16  single    0.930  0.020  1.080
 KV5  C7   H17  single    0.930  0.020  1.080
 KV5  C15  H18  single    0.930  0.020  1.080
 KV5  C14  H19  single    0.930  0.020  1.080
 KV5  C13  H20  single    0.930  0.020  1.080
 KV5  C12  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
 KV5  N5   C4   N3   110.45  3.000
 KV5  N5   C4   C6   125.39  3.000
 KV5  N3   C4   C6   124.15  3.000
 KV5  C7   C6   C11  119.00  3.000
 KV5  C11  C6   C4   121.29  3.000
 KV5  C7   C6   C4   119.71  3.000
 KV5  C12  C8   C7   121.80  3.000
 KV5  C12  C8   C9   118.87  3.000
 KV5  C7   C8   C9   119.34  3.000
 KV5  H1   N3   C2   124.84  3.000
 KV5  H1   N3   C4   127.19  3.000
 KV5  C2   N3   C4   107.97  3.000
 KV5  H2   C2   C1   132.12  3.000
 KV5  H2   C2   N3   122.52  3.000
 KV5  C1   C2   N3   105.35  3.000
 KV5  C1'  O5'  C5'  113.99  3.000
 KV5  H3   C5'  C6'  109.23  3.000
 KV5  H3   C5'  C4'  108.34  3.000
 KV5  C6'  C5'  C4'  111.89  3.000
 KV5  H3   C5'  O5'  109.91  3.000
 KV5  C6'  C5'  O5'  107.79  3.000
 KV5  C4'  C5'  O5'  109.68  3.000
 KV5  H4   C4'  O4'  111.02  3.000
 KV5  H4   C4'  C3'  108.39  3.000
 KV5  O4'  C4'  C3'  111.41  3.000
 KV5  H4   C4'  C5'  108.12  3.000
 KV5  C3'  C4'  C5'  109.18  3.000
 KV5  O4'  C4'  C5'  108.65  3.000
 KV5  H5   C3'  O3'  110.57  3.000
 KV5  H5   C3'  C2'  108.31  3.000
 KV5  O3'  C3'  C2'  111.11  3.000
 KV5  H5   C3'  C4'  108.07  3.000
 KV5  C2'  C3'  C4'  110.06  3.000
 KV5  O3'  C3'  C4'  108.67  3.000
 KV5  H6   C2'  O2'  111.20  3.000
 KV5  H6   C2'  C1'  108.04  3.000
 KV5  O2'  C2'  C1'  107.76  3.000
 KV5  H6   C2'  C3'  108.78  3.000
 KV5  C1'  C2'  C3'  108.82  3.000
 KV5  O2'  C2'  C3'  112.14  3.000
 KV5  H7   C1'  C1   108.49  3.000
 KV5  H7   C1'  C2'  108.22  3.000
 KV5  C1   C1'  C2'  112.31  3.000
 KV5  H7   C1'  O5'  110.09  3.000
 KV5  C1   C1'  O5'  108.18  3.000
 KV5  C2'  C1'  O5'  109.55  3.000
 KV5  N5   C1   C1'  122.24  3.000
 KV5  N5   C1   C2   109.92  3.000
 KV5  C1'  C1   C2   127.84  3.000
 KV5  C1   N5   C4   106.30  3.000
 KV5  H9   O2'  C2'  108.22  3.000
 KV5  H10  O3'  C3'  109.07  3.000
 KV5  H11  O4'  C4'  107.62  3.000
 KV5  H15  C11  C10  118.37  3.000
 KV5  H15  C11  C6   120.80  3.000
 KV5  C10  C11  C6   120.83  3.000
 KV5  H16  C10  C9   119.16  3.000
 KV5  H16  C10  C11  119.80  3.000
 KV5  C9   C10  C11  121.04  3.000
 KV5  C15  C9   C10  122.22  3.000
 KV5  C15  C9   C8   119.28  3.000
 KV5  C10  C9   C8   118.49  3.000
 KV5  H17  C7   C8   118.95  3.000
 KV5  H17  C7   C6   119.75  3.000
 KV5  C8   C7   C6   121.30  3.000
 KV5  H18  C15  C14  120.46  3.000
 KV5  H18  C15  C9   118.99  3.000
 KV5  C14  C15  C9   120.55  3.000
 KV5  H19  C14  C13  119.63  3.000
 KV5  H19  C14  C15  120.11  3.000
 KV5  C13  C14  C15  120.26  3.000
 KV5  H20  C13  C12  119.98  3.000
 KV5  H20  C13  C14  119.60  3.000
 KV5  C12  C13  C14  120.42  3.000
 KV5  H21  C12  C13  120.37  3.000
 KV5  H21  C12  C8   119.01  3.000
 KV5  C13  C12  C8   120.62  3.000
 KV5  H13  C6'  H12  107.04  3.000
 KV5  H13  C6'  O6'  111.76  3.000
 KV5  H12  C6'  O6'  111.70  3.000
 KV5  H13  C6'  C5'  108.78  3.000
 KV5  H12  C6'  C5'  108.43  3.000
 KV5  O6'  C6'  C5'  109.02  3.000
 KV5  H14  O6'  C6'  107.86  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
 KV5  CONST_01  C1   C2   N3   C4     0.00  0.0  0
 KV5  CONST_02  C2   C1   N5   C4     0.00  0.0  0
 KV5  CONST_03  C8   C7   C6   C4   180.00  0.0  0
 KV5  CONST_04  C10  C11  C6   C4   180.00  0.0  0
 KV5  CONST_05  C2   N3   C4   C6   180.00  0.0  0
 KV5  CONST_06  C1   N5   C4   C6   180.00  0.0  0
 KV5  CONST_07  C12  C8   C7   C6   180.00  0.0  0
 KV5  CONST_08  C9   C8   C7   C6     0.00  0.0  0
 KV5  CONST_09  C9   C10  C11  C6     0.00  0.0  0
 KV5  CONST_10  C11  C6   C7   C8     0.00  0.0  0
 KV5  CONST_11  C14  C13  C12  C8     0.00  0.0  0
 KV5  CONST_12  C11  C10  C9   C8     0.00  0.0  0
 KV5  CONST_13  C14  C15  C9   C8     0.00  0.0  0
 KV5  CONST_14  N5   C1   C2   N3     0.00  0.0  0
 KV5  CONST_15  C1   N5   C4   N3     0.00  0.0  0
 KV5  CONST_16  C7   C6   C4   N3   180.00  0.0  0
 KV5  CONST_17  C11  C6   C4   N3     0.00  0.0  0
 KV5  CONST_18  N5   C4   N3   C2     0.00  0.0  0
 KV5  CONST_19  C7   C6   C4   N5     0.00  0.0  0
 KV5  CONST_20  C11  C6   C4   N5   180.00  0.0  0
 KV5  CONST_21  C15  C9   C10  C11  180.00  0.0  0
 KV5  CONST_22  C7   C6   C11  C10    0.00  0.0  0
 KV5  CONST_23  C7   C8   C9   C10    0.00  0.0  0
 KV5  CONST_24  C12  C8   C9   C10  180.00  0.0  0
 KV5  CONST_25  C14  C15  C9   C10  180.00  0.0  0
 KV5  CONST_26  C13  C12  C8   C9     0.00  0.0  0
 KV5  CONST_27  C13  C14  C15  C9     0.00  0.0  0
 KV5  CONST_28  C13  C12  C8   C7   180.00  0.0  0
 KV5  CONST_29  C15  C9   C8   C7   180.00  0.0  0
 KV5  CONST_30  C12  C8   C9   C15    0.00  0.0  0
 KV5  CONST_31  C12  C13  C14  C15    0.00  0.0  0
 KV5  CONST_32  C1'  C1   N5   C4   180.00  0.0  0
 KV5  CONST_33  C1'  C1   C2   N3   180.00  0.0  0
 KV5  CONST_34  H2   C2   N3   C4   180.00  0.0  0
 KV5  CONST_35  H17  C7   C6   C4     0.00  0.0  0
 KV5  CONST_36  H15  C11  C6   C4     0.00  0.0  0
 KV5  CONST_37  H1   N3   C4   C6     0.00  0.0  0
 KV5  CONST_38  H16  C10  C11  C6   180.00  0.0  0
 KV5  CONST_39  H20  C13  C12  C8   180.00  0.0  0
 KV5  CONST_40  H18  C15  C9   C8   180.00  0.0  0
 KV5  CONST_41  H21  C12  C8   C9   180.00  0.0  0
 KV5  CONST_42  H19  C14  C15  C9   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
 KV5  chir_01  C5'  C4'  C6'  O5'  negativ
 KV5  chir_02  C4'  O4'  C5'  C3'  positiv
 KV5  chir_03  C3'  O3'  C4'  C2'  negativ
 KV5  chir_04  C2'  O2'  C3'  C1'  positiv
 KV5  chir_05  C1'  O5'  C1   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
 KV5  plan-1  C4   0.020
 KV5  plan-1  C6   0.020
 KV5  plan-1  N3   0.020
 KV5  plan-1  C2   0.020
 KV5  plan-1  C1'  0.020
 KV5  plan-1  C1   0.020
 KV5  plan-1  N5   0.020
 KV5  plan-1  H1   0.020
 KV5  plan-1  H2   0.020
 KV5  plan-2  C4   0.020
 KV5  plan-2  C6   0.020
 KV5  plan-2  C8   0.020
 KV5  plan-2  C11  0.020
 KV5  plan-2  C10  0.020
 KV5  plan-2  C9   0.020
 KV5  plan-2  C7   0.020
 KV5  plan-2  C15  0.020
 KV5  plan-2  C14  0.020
 KV5  plan-2  C13  0.020
 KV5  plan-2  C12  0.020
 KV5  plan-2  H15  0.020
 KV5  plan-2  H16  0.020
 KV5  plan-2  H17  0.020
 KV5  plan-2  H18  0.020
 KV5  plan-2  H19  0.020
 KV5  plan-2  H20  0.020
 KV5  plan-2  H21  0.020

