# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 08:10:02 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(5-phenyl-1,2,3,4-tetrazol-2-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)n2nnc(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
 KVN  KVN  (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(5-phenyl-1,2,3,4-tetrazol-2-yl)oxane-3,4,5-triol  ligand  38  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KVN
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
 KVN  C7   C  CR16  0  -0.279  -4.7059   0.0411   0.8673
 KVN  C8   C  CR16  0  -0.239  -6.0066  -0.2875   0.5178
 KVN  N1   N  NR5   0  -0.168  -0.2836   0.5368   0.2853
 KVN  C4   C  CR5   0   0.379  -2.2988   0.1931   0.3291
 KVN  C6   C  CR6   0   0.038  -3.6657  -0.1611  -0.0384
 KVN  C9   C  CR16  0  -0.252  -6.2796  -0.8211  -0.7350
 KVN  C10  C  CR16  0  -0.239  -5.2447  -1.0264  -1.6388
 KVN  C11  C  CR16  0  -0.282  -3.9430  -0.6984  -1.2950
 KVN  O5'  O  O2    0  -0.478   1.6122  -0.6888  -0.0555
 KVN  C5'  C  CH1   0  -0.024   2.9052  -0.8000  -0.6328
 KVN  C4'  C  CH1   0   0.036   3.8759   0.1260   0.1022
 KVN  C3'  C  CH1   0  -0.008   3.3336   1.5525   0.1032
 KVN  C2'  C  CH1   0  -0.043   1.9129   1.5883   0.6588
 KVN  C1'  C  CH1   0   0.254   1.0893   0.5973  -0.1647
 KVN  O2'  O  OH1   0  -0.662   1.4199   2.8942   0.5382
 KVN  O3'  O  OH1   0  -0.667   4.2075   2.3361   0.8734
 KVN  O4'  O  OH1   0  -0.669   5.1155   0.0537  -0.5532
 KVN  N5   N  N     0  -0.267  -1.2596   0.1125  -0.4768
 KVN  N3   N  N     0  -0.325  -1.9337   0.6596   1.5411
 KVN  N2   N  N     0  -0.054  -0.6649   0.8637   1.4881
 KVN  H1   H  HCR6  0   0.262  -4.5003   0.4581   1.8444
 KVN  H2   H  HCR6  0   0.264  -6.8085  -0.1248   1.2255
 KVN  H3   H  HCR6  0   0.265  -7.2955  -1.0749  -1.0075
 KVN  H4   H  HCR6  0   0.265  -5.4523  -1.4438  -2.6152
 KVN  H5   H  HCR6  0   0.262  -3.1429  -0.8615  -2.0053
 KVN  H6   H  HCH1  0   0.239   2.8632  -0.4984  -1.6916
 KVN  H7   H  HCH1  0   0.220   3.9577  -0.2143   1.1471
 KVN  H8   H  HCH1  0   0.225   3.3042   1.9047  -0.9404
 KVN  H9   H  HCH1  0   0.254   1.9382   1.2538   1.7030
 KVN  H10  H  HCH1  0   0.262   1.0509   0.9264  -1.2116
 KVN  H11  H  HOH1  0   0.462   0.7810   3.0550   1.2394
 KVN  H12  H  HOH1  0   0.459   4.0012   3.2643   0.7249
 KVN  H13  H  HOH1  0   0.457   5.7303   0.6415  -0.1018
 KVN  H16  H  HOH1  0   0.458   2.7364  -3.9388  -1.2791
 KVN  C6'  C  CH2   0  -0.156   3.3205  -2.2513  -0.5378
 KVN  O6'  O  OH1   0  -0.669   2.4421  -3.0245  -1.3180
 KVN  H14  H  HCH2  0   0.218   4.3555  -2.3368  -0.8841
 KVN  H15  H  HCH2  0   0.202   3.3077  -2.5543   0.5185

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
 KVN  O3'  C3'  single    1.404  0.020  1.404
 KVN  O4'  C4'  single    1.404  0.020  1.404
 KVN  C3'  C4'  single    1.526  0.020  1.526
 KVN  C3'  C2'  single    1.526  0.020  1.526
 KVN  C4'  C5'  single    1.530  0.020  1.530
 KVN  O2'  C2'  single    1.401  0.020  1.401
 KVN  C2'  C1'  single    1.529  0.020  1.529
 KVN  O6'  C6'  single    1.407  0.020  1.407
 KVN  C5'  C6'  single    1.513  0.020  1.513
 KVN  C5'  O5'  single    1.420  0.020  1.420
 KVN  C1'  O5'  single    1.393  0.020  1.393
 KVN  C1'  N1   single    1.446  0.020  1.446
 KVN  N2   N1   aromatic  1.304  0.020  1.304
 KVN  N2   N3   aromatic  1.286  0.020  1.286
 KVN  N1   N5   aromatic  1.309  0.020  1.309
 KVN  N3   C4   aromatic  1.349  0.020  1.349
 KVN  N5   C4   aromatic  1.318  0.020  1.318
 KVN  C4   C6   single    1.459  0.020  1.459
 KVN  C6   C7   aromatic  1.394  0.020  1.394
 KVN  C6   C11  aromatic  1.394  0.020  1.394
 KVN  C7   C8   aromatic  1.386  0.020  1.386
 KVN  C11  C10  aromatic  1.386  0.020  1.386
 KVN  C8   C9   aromatic  1.389  0.020  1.389
 KVN  C10  C9   aromatic  1.389  0.020  1.389
 KVN  C7   H1   single    0.930  0.020  1.080
 KVN  C8   H2   single    0.930  0.020  1.080
 KVN  C9   H3   single    0.930  0.020  1.080
 KVN  C10  H4   single    0.930  0.020  1.080
 KVN  C11  H5   single    0.930  0.020  1.080
 KVN  C5'  H6   single    0.970  0.020  1.090
 KVN  C4'  H7   single    0.970  0.020  1.090
 KVN  C3'  H8   single    0.970  0.020  1.090
 KVN  C2'  H9   single    0.970  0.020  1.090
 KVN  C1'  H10  single    0.970  0.020  1.090
 KVN  O2'  H11  single    0.850  0.020  0.980
 KVN  O3'  H12  single    0.850  0.020  0.980
 KVN  O4'  H13  single    0.850  0.020  0.980
 KVN  C6'  H14  single    0.970  0.020  1.090
 KVN  C6'  H15  single    0.970  0.020  1.090
 KVN  O6'  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
 KVN  H1   C7   C6   120.05  3.000
 KVN  H1   C7   C8   119.82  3.000
 KVN  C6   C7   C8   120.12  3.000
 KVN  H2   C8   C9   120.14  3.000
 KVN  H2   C8   C7   119.66  3.000
 KVN  C9   C8   C7   120.20  3.000
 KVN  N2   N1   N5   113.60  3.000
 KVN  N5   N1   C1'  122.71  3.000
 KVN  N2   N1   C1'  123.67  3.000
 KVN  N3   C4   N5   110.93  3.000
 KVN  N5   C4   C6   124.75  3.000
 KVN  N3   C4   C6   124.32  3.000
 KVN  C11  C6   C4   120.45  3.000
 KVN  C11  C6   C7   119.54  3.000
 KVN  C4   C6   C7   120.01  3.000
 KVN  H3   C9   C10  120.06  3.000
 KVN  H3   C9   C8   120.13  3.000
 KVN  C10  C9   C8   119.81  3.000
 KVN  H4   C10  C11  119.70  3.000
 KVN  H4   C10  C9   120.08  3.000
 KVN  C11  C10  C9   120.22  3.000
 KVN  H5   C11  C10  119.73  3.000
 KVN  H5   C11  C6   120.16  3.000
 KVN  C10  C11  C6   120.10  3.000
 KVN  C1'  O5'  C5'  112.47  3.000
 KVN  H6   C5'  C6'  109.48  3.000
 KVN  H6   C5'  C4'  108.68  3.000
 KVN  C6'  C5'  C4'  112.11  3.000
 KVN  H6   C5'  O5'  109.55  3.000
 KVN  C6'  C5'  O5'  107.43  3.000
 KVN  C4'  C5'  O5'  109.58  3.000
 KVN  H7   C4'  O4'  111.18  3.000
 KVN  H7   C4'  C3'  108.32  3.000
 KVN  O4'  C4'  C3'  111.23  3.000
 KVN  H7   C4'  C5'  108.41  3.000
 KVN  C3'  C4'  C5'  109.91  3.000
 KVN  O4'  C4'  C5'  107.74  3.000
 KVN  H8   C3'  O3'  110.96  3.000
 KVN  H8   C3'  C2'  108.21  3.000
 KVN  O3'  C3'  C2'  111.51  3.000
 KVN  H8   C3'  C4'  107.92  3.000
 KVN  C2'  C3'  C4'  110.67  3.000
 KVN  O3'  C3'  C4'  107.51  3.000
 KVN  H9   C2'  O2'  111.98  3.000
 KVN  H9   C2'  C1'  109.12  3.000
 KVN  O2'  C2'  C1'  111.60  3.000
 KVN  H9   C2'  C3'  108.54  3.000
 KVN  C1'  C2'  C3'  106.87  3.000
 KVN  O2'  C2'  C3'  108.55  3.000
 KVN  H10  C1'  C2'  109.76  3.000
 KVN  H10  C1'  O5'  111.38  3.000
 KVN  C2'  C1'  O5'  110.73  3.000
 KVN  H10  C1'  N1   106.02  3.000
 KVN  O5'  C1'  N1   107.06  3.000
 KVN  C2'  C1'  N1   111.77  3.000
 KVN  H11  O2'  C2'  109.06  3.000
 KVN  H12  O3'  C3'  108.68  3.000
 KVN  H13  O4'  C4'  108.26  3.000
 KVN  C4   N5   N1   102.25  3.000
 KVN  N2   N3   C4   106.55  3.000
 KVN  N3   N2   N1   106.67  3.000
 KVN  H15  C6'  H14  107.07  3.000
 KVN  H15  C6'  O6'  111.99  3.000
 KVN  H14  C6'  O6'  111.84  3.000
 KVN  H15  C6'  C5'  108.77  3.000
 KVN  H14  C6'  C5'  108.34  3.000
 KVN  O6'  C6'  C5'  108.73  3.000
 KVN  H16  O6'  C6'  108.01  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
 KVN  CONST_01  N3   C4   C6   C7     0.00  0.0  0
 KVN  CONST_02  N5   C4   C6   C7   180.00  0.0  0
 KVN  CONST_03  C10  C11  C6   C7     0.00  0.0  0
 KVN  CONST_04  C10  C9   C8   C7     0.00  0.0  0
 KVN  CONST_05  C4   C6   C7   C8   180.00  0.0  0
 KVN  CONST_06  C11  C6   C7   C8     0.00  0.0  0
 KVN  CONST_07  C11  C10  C9   C8     0.00  0.0  0
 KVN  CONST_08  C4   N3   N2   N1     0.00  0.0  0
 KVN  CONST_09  N3   C4   N5   N1     0.00  0.0  0
 KVN  CONST_10  C6   C4   N5   N1   180.00  0.0  0
 KVN  CONST_11  N2   N1   N5   C4     0.00  0.0  0
 KVN  CONST_12  C10  C11  C6   C4   180.00  0.0  0
 KVN  CONST_13  N2   N3   C4   C6   180.00  0.0  0
 KVN  CONST_14  C9   C8   C7   C6     0.00  0.0  0
 KVN  CONST_15  C9   C10  C11  C6     0.00  0.0  0
 KVN  CONST_16  N3   C4   C6   C11  180.00  0.0  0
 KVN  CONST_17  N5   C4   C6   C11    0.00  0.0  0
 KVN  CONST_18  N3   N2   N1   N5     0.00  0.0  0
 KVN  CONST_19  N2   N3   C4   N5     0.00  0.0  0
 KVN  CONST_20  C1'  N1   N5   C4   180.00  0.0  0
 KVN  CONST_21  N3   N2   N1   C1'  180.00  0.0  0
 KVN  CONST_22  H5   C11  C6   C7   180.00  0.0  0
 KVN  CONST_23  H3   C9   C8   C7   180.00  0.0  0
 KVN  CONST_24  H4   C10  C9   C8   180.00  0.0  0
 KVN  CONST_25  H1   C7   C6   C4     0.00  0.0  0
 KVN  CONST_26  H2   C8   C7   C6   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
 KVN  chir_01  C5'  C4'  C6'  O5'  negativ
 KVN  chir_02  C4'  O4'  C5'  C3'  positiv
 KVN  chir_03  C3'  O3'  C4'  C2'  negativ
 KVN  chir_04  C2'  O2'  C3'  C1'  positiv
 KVN  chir_05  C1'  O5'  N1   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
 KVN  plan-1  N1   0.020
 KVN  plan-1  C4   0.020
 KVN  plan-1  C6   0.020
 KVN  plan-1  C1'  0.020
 KVN  plan-1  N5   0.020
 KVN  plan-1  N3   0.020
 KVN  plan-1  N2   0.020
 KVN  plan-2  C7   0.020
 KVN  plan-2  C8   0.020
 KVN  plan-2  C4   0.020
 KVN  plan-2  C6   0.020
 KVN  plan-2  C9   0.020
 KVN  plan-2  C10  0.020
 KVN  plan-2  C11  0.020
 KVN  plan-2  H1   0.020
 KVN  plan-2  H2   0.020
 KVN  plan-2  H3   0.020
 KVN  plan-2  H4   0.020
 KVN  plan-2  H5   0.020

