# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 08:05:34 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: [3-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1cccc(c1)c2n[nH]nn2
#
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
 RY2  RY2  '[3-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]boronic acid'  ligand  21  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RY2
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
 RY2  C1  C  CR16  0  -0.319  -4.9111  3.2096  18.3719
 RY2  N1  N  NR15  0  -0.227  -0.9544  3.2655  13.5758
 RY2  C2  C  CR16  0  -0.212  -4.9745  2.0895  17.5556
 RY2  N2  N  N     0  -0.055  -1.4531  2.1107  13.2594
 RY2  C3  C  CR16  0  -0.303  -4.1394  1.9812  16.4553
 RY2  C4  C  CR6   0   0.072  -3.2287  2.9973  16.1716
 RY2  C5  C  CR5   0   0.364  -2.3534  2.8910  15.0079
 RY2  C6  C  CR16  0  -0.361  -3.1625  4.1091  17.0088
 RY2  C   C  CR6   0  -0.059  -4.0012  4.2385  18.1149
 RY2  N3  N  N     0  -0.337  -2.3463  1.8488  14.1543
 RY2  N   N  N     0  -0.266  -1.4684  3.8029  14.6475
 RY2  H1  H  HCR6  0   0.255  -5.5777  3.2771  19.2225
 RY2  H2  H  HNR5  0   0.457  -0.2258  3.7082  13.0292
 RY2  H3  H  HCR6  0   0.258  -5.6785  1.2973  17.7746
 RY2  H4  H  HCR6  0   0.260  -4.1986  1.1095  15.8167
 RY2  H5  H  HCR6  0   0.254  -2.4469  4.8908  16.7861
 RY2  O2  O  OH1   0  -0.629  -2.7940  6.2653  18.9676
 RY2  O1  O  OH1   0  -0.628  -4.9702  5.7438  19.8704
 RY2  H6  H  HOH1  0   0.483  -2.7699  7.0464  19.5303
 RY2  H7  H  HOH1  0   0.483  -4.8913  6.5160  20.4401
 RY2  B   B  B     0   0.509  -3.9157  5.5006  19.0471

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
 RY2  N2  N1  aromatic  1.297  0.020  1.297
 RY2  N2  N3  aromatic  1.291  0.020  1.291
 RY2  N1  N   aromatic  1.304  0.020  1.304
 RY2  N3  C5  aromatic  1.347  0.020  1.347
 RY2  N   C5  aromatic  1.321  0.020  1.321
 RY2  C5  C4  single    1.460  0.020  1.460
 RY2  C4  C3  aromatic  1.394  0.020  1.394
 RY2  C4  C6  aromatic  1.393  0.020  1.393
 RY2  C3  C2  aromatic  1.386  0.020  1.386
 RY2  C6  C   aromatic  1.394  0.020  1.394
 RY2  C2  C1  aromatic  1.387  0.020  1.387
 RY2  C   C1  aromatic  1.397  0.020  1.397
 RY2  C   B   single    1.571  0.020  1.571
 RY2  C1  H1  single    0.930  0.020  1.080
 RY2  N1  H2  single    0.860  0.020  1.020
 RY2  C2  H3  single    0.930  0.020  1.080
 RY2  C3  H4  single    0.930  0.020  1.080
 RY2  C6  H5  single    0.930  0.020  1.080
 RY2  B   O2  single    1.360  0.020  1.360
 RY2  B   O1  single    1.360  0.020  1.360
 RY2  O2  H6  single    0.850  0.020  0.980
 RY2  O1  H7  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
 RY2  H1  C1  C   119.96  3.000
 RY2  H1  C1  C2  118.97  3.000
 RY2  C   C1  C2  121.06  3.000
 RY2  H2  N1  N   123.15  3.000
 RY2  H2  N1  N2  122.29  3.000
 RY2  N   N1  N2  114.56  3.000
 RY2  H3  C2  C3  119.71  3.000
 RY2  H3  C2  C1  120.11  3.000
 RY2  C3  C2  C1  120.19  3.000
 RY2  N3  N2  N1  106.11  3.000
 RY2  H4  C3  C4  120.20  3.000
 RY2  H4  C3  C2  119.91  3.000
 RY2  C4  C3  C2  119.90  3.000
 RY2  C6  C4  C5  120.57  3.000
 RY2  C6  C4  C3  119.38  3.000
 RY2  C5  C4  C3  120.06  3.000
 RY2  N   C5  N3  110.95  3.000
 RY2  N   C5  C4  124.68  3.000
 RY2  N3  C5  C4  124.37  3.000
 RY2  H5  C6  C   119.58  3.000
 RY2  H5  C6  C4  118.94  3.000
 RY2  C   C6  C4  121.48  3.000
 RY2  B   C   C6  120.83  3.000
 RY2  B   C   C1  121.18  3.000
 RY2  C6  C   C1  117.99  3.000
 RY2  C5  N3  N2  106.61  3.000
 RY2  C5  N   N1  101.76  3.000
 RY2  H6  O2  B   116.27  3.000
 RY2  H7  O1  B   115.99  3.000
 RY2  O1  B   O2  125.06  3.000
 RY2  O1  B   C   117.43  3.000
 RY2  O2  B   C   117.50  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
 RY2  CONST_01  C4  C3  C2  C1    0.00   0.0  0
 RY2  CONST_02  C4  C6  C   C1    0.00   0.0  0
 RY2  CONST_03  C5  N3  N2  N1    0.00   0.0  0
 RY2  CONST_04  N3  C5  N   N1    0.00   0.0  0
 RY2  CONST_05  C4  C5  N   N1  180.00   0.0  0
 RY2  CONST_06  C5  C4  C3  C2  180.00   0.0  0
 RY2  CONST_07  C6  C4  C3  C2    0.00   0.0  0
 RY2  CONST_08  C6  C   C1  C2    0.00   0.0  0
 RY2  CONST_09  C5  N   N1  N2    0.00   0.0  0
 RY2  CONST_10  N   C5  N3  N2    0.00   0.0  0
 RY2  CONST_11  C4  C5  N3  N2  180.00   0.0  0
 RY2  CONST_12  N3  C5  C4  C3    0.00   0.0  0
 RY2  CONST_13  N   C5  C4  C3  180.00   0.0  0
 RY2  CONST_14  C   C6  C4  C3    0.00   0.0  0
 RY2  CONST_15  C   C1  C2  C3    0.00   0.0  0
 RY2  CONST_16  C   C6  C4  C5  180.00   0.0  0
 RY2  CONST_17  N3  C5  C4  C6  180.00   0.0  0
 RY2  CONST_18  N   C5  C4  C6    0.00   0.0  0
 RY2  CONST_19  N   N1  N2  N3    0.00   0.0  0
 RY2  CONST_20  B   C   C1  C2  180.00   0.0  0
 RY2  CONST_21  B   C   C6  C4  180.00   0.0  0
 RY2  CONST_22  H4  C3  C2  C1  180.00   0.0  0
 RY2  CONST_23  H5  C6  C   C1  180.00   0.0  0
 RY2  CONST_24  H1  C1  C2  C3  180.00   0.0  0
 RY2  CONST_25  H3  C2  C3  C4  180.00   0.0  0
 RY2  CONST_26  H2  N1  N   C5  180.00   0.0  0
 RY2  Var_01    O2  B   C   C1  162.27  30.0  2

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
 RY2  plan-1  N1  0.020
 RY2  plan-1  N2  0.020
 RY2  plan-1  C4  0.020
 RY2  plan-1  C5  0.020
 RY2  plan-1  N3  0.020
 RY2  plan-1  N   0.020
 RY2  plan-1  H2  0.020
 RY2  plan-2  C1  0.020
 RY2  plan-2  C2  0.020
 RY2  plan-2  C3  0.020
 RY2  plan-2  C4  0.020
 RY2  plan-2  C5  0.020
 RY2  plan-2  C6  0.020
 RY2  plan-2  C   0.020
 RY2  plan-2  H1  0.020
 RY2  plan-2  H3  0.020
 RY2  plan-2  H4  0.020
 RY2  plan-2  H5  0.020
 RY2  plan-2  B   0.020

