# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 12:21:10 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: [(3R)-1-hydroxy-4,5-dimethyl-6-(pyrazin-2-yloxy)-1,3-dihydro-2,1-benzoxaborol-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(C)c2[C@@H](CC(O)=O)OB(O)c2cc1Oc3cnccn3
#
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
 3VT  3VT  '[(3R)-1-hydroxy-4,5-dimethyl-6-(pyrazin-2-yloxy)-1,3-dihydro-2,1-benzoxaborol-3-yl]acetic acid'  ligand  37  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3VT
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
 3VT  C1   C  CR16   0  -0.427   0.6732   1.3738  -0.6340
 3VT  C2   C  CR6    0   0.330   1.4413   0.2585  -0.9002
 3VT  C3   C  CR6    0  -0.010   0.8939  -1.0145  -1.0930
 3VT  C7   C  CH2    0  -0.603  -3.2025  -0.7211   0.7942
 3VT  C8   C  C      0   0.422  -4.7252  -0.7050   1.0327
 3VT  C10  C  CH3    0  -0.746   1.7975  -2.1793  -1.3745
 3VT  C11  C  CR6    0   0.466   3.6080   0.1586  -0.0051
 3VT  C12  C  CR16   0  -0.137   4.9880   0.3114  -0.2007
 3VT  C13  C  CR16   0  -0.124   5.3304  -0.3427   1.9430
 3VT  C14  C  CR16   0  -0.102   3.9691  -0.4886   2.1187
 3VT  O1   O  OC    -1  -0.618  -5.0962  -0.8328   2.2161
 3VT  O2   O  O      0  -0.607  -5.4570  -0.6099   0.0286
 3VT  C6   C  CR15   0   0.007  -2.7537   0.0183  -0.4534
 3VT  O    O  O      0  -0.480  -3.0442   1.4110  -0.2991
 3VT  B    B  B      0   0.488  -1.8987   2.1574  -0.2839
 3VT  C5   C  CR56   0  -0.027  -1.2629  -0.0529  -0.6823
 3VT  C    C  CR56   0  -0.097  -0.6984   1.2091  -0.5272
 3VT  C4   C  CR6    0   0.052  -0.4967  -1.1750  -0.9938
 3VT  O3   O  O2     0  -0.514   2.8066   0.4351  -1.0449
 3VT  N1   N  N      0  -0.391   3.1046  -0.2355   1.1376
 3VT  N    N  N      0  -0.343   5.8324   0.0599   0.7751
 3VT  H1   H  HCR6   0   0.263   1.1439   2.3428  -0.5171
 3VT  H2   H  HOH1   0   0.491  -2.7329   3.8944   0.0480
 3VT  H3   H  HCH2   0   0.231  -2.6716  -0.3234   1.6643
 3VT  H4   H  HCH2   0   0.249  -2.8964  -1.7693   0.7140
 3VT  H5   H  HCH3   0   0.256  -0.7448  -3.0081  -2.1079
 3VT  H6   H  HCH3   0   0.254  -0.9686  -3.1912  -0.3779
 3VT  H7   H  HCH3   0   0.253  -2.2142  -2.4306  -1.3565
 3VT  H8   H  HCH3   0   0.256   2.1259  -2.6458  -0.4425
 3VT  H9   H  HCH3   0   0.255   1.3000  -2.9504  -1.9580
 3VT  H10  H  HCH3   0   0.253   2.6907  -1.8853  -1.9224
 3VT  H11  H  HCR6   0   0.285   5.3823   0.6390  -1.1558
 3VT  H12  H  HCR6   0   0.277   6.0249  -0.5523   2.7461
 3VT  H13  H  HCR6   0   0.280   3.5598  -0.8155   3.0662
 3VT  H15  H  HCR5   0   0.244  -3.3130  -0.3507  -1.3185
 3VT  O4   O  OH1    0  -0.616  -1.8685   3.4959  -0.0986
 3VT  C9   C  CH3    0  -0.771  -1.1382  -2.5151  -1.2187

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
 3VT  O2   C8   deloc     1.246  0.020  1.246
 3VT  N    C13  aromatic  1.334  0.020  1.334
 3VT  N    C12  aromatic  1.315  0.020  1.315
 3VT  C8   C7   single    1.541  0.020  1.541
 3VT  C8   O1   deloc     1.247  0.020  1.247
 3VT  C13  C14  aromatic  1.380  0.020  1.380
 3VT  O4   B    single    1.352  0.020  1.352
 3VT  C7   C6   single    1.518  0.020  1.518
 3VT  C12  C11  aromatic  1.402  0.020  1.402
 3VT  C14  N1   aromatic  1.332  0.020  1.332
 3VT  B    O    single    1.367  0.020  1.367
 3VT  B    C    single    1.549  0.020  1.549
 3VT  C6   O    single    1.431  0.020  1.431
 3VT  C6   C5   single    1.510  0.020  1.510
 3VT  C11  N1   aromatic  1.309  0.020  1.309
 3VT  C11  O3   single    1.342  0.020  1.342
 3VT  C    C5   aromatic  1.391  0.020  1.391
 3VT  C    C1   aromatic  1.386  0.020  1.386
 3VT  C5   C4   aromatic  1.394  0.020  1.394
 3VT  C1   C2   aromatic  1.380  0.020  1.380
 3VT  C4   C9   single    1.503  0.020  1.503
 3VT  C4   C3   aromatic  1.403  0.020  1.403
 3VT  C2   C3   aromatic  1.399  0.020  1.399
 3VT  C2   O3   single    1.384  0.020  1.384
 3VT  C3   C10  single    1.501  0.020  1.501
 3VT  C1   H1   single    0.930  0.020  1.080
 3VT  O4   H2   single    0.850  0.020  0.980
 3VT  C7   H3   single    0.970  0.020  1.090
 3VT  C7   H4   single    0.970  0.020  1.090
 3VT  C9   H5   single    0.970  0.020  1.090
 3VT  C9   H6   single    0.970  0.020  1.090
 3VT  C9   H7   single    0.970  0.020  1.090
 3VT  C10  H8   single    0.970  0.020  1.090
 3VT  C10  H9   single    0.970  0.020  1.090
 3VT  C10  H10  single    0.970  0.020  1.090
 3VT  C12  H11  single    0.930  0.020  1.080
 3VT  C13  H12  single    0.930  0.020  1.080
 3VT  C14  H13  single    0.930  0.020  1.080
 3VT  C6   H15  single    0.970  0.020  1.090

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
 3VT  H1   C1   C    121.87  3.000
 3VT  H1   C1   C2   120.12  3.000
 3VT  C    C1   C2   118.01  3.000
 3VT  O3   C2   C3   119.18  3.000
 3VT  O3   C2   C1   117.77  3.000
 3VT  C3   C2   C1   122.97  3.000
 3VT  C4   C3   C10  121.41  3.000
 3VT  C10  C3   C2   119.77  3.000
 3VT  C4   C3   C2   118.81  3.000
 3VT  H4   C7   H3   105.70  3.000
 3VT  H4   C7   C6   108.87  3.000
 3VT  H3   C7   C6   109.46  3.000
 3VT  H4   C7   C8   107.30  3.000
 3VT  H3   C7   C8   110.64  3.000
 3VT  C6   C7   C8   114.46  3.000
 3VT  O2   C8   O1   126.72  3.000
 3VT  O1   C8   C7   116.09  3.000
 3VT  O2   C8   C7   117.15  3.000
 3VT  H10  C10  H9   107.27  3.000
 3VT  H10  C10  H8   107.34  3.000
 3VT  H9   C10  H8   107.00  3.000
 3VT  H10  C10  C3   112.26  3.000
 3VT  H9   C10  C3   112.06  3.000
 3VT  H8   C10  C3   110.63  3.000
 3VT  N1   C11  O3   120.58  3.000
 3VT  O3   C11  C12  117.22  3.000
 3VT  N1   C11  C12  122.20  3.000
 3VT  H11  C12  N    118.56  3.000
 3VT  H11  C12  C11  120.92  3.000
 3VT  N    C12  C11  120.52  3.000
 3VT  H12  C13  N    117.83  3.000
 3VT  H12  C13  C14  121.20  3.000
 3VT  N    C13  C14  120.97  3.000
 3VT  H13  C14  N1   117.17  3.000
 3VT  H13  C14  C13  121.08  3.000
 3VT  N1   C14  C13  121.76  3.000
 3VT  H15  C6   C5   111.65  3.000
 3VT  H15  C6   O    108.04  3.000
 3VT  C5   C6   O    105.22  3.000
 3VT  H15  C6   C7   109.53  3.000
 3VT  C5   C6   C7   113.17  3.000
 3VT  O    C6   C7   108.99  3.000
 3VT  B    O    C6   111.25  3.000
 3VT  C    B    O    108.26  3.000
 3VT  C    B    O4   127.62  3.000
 3VT  O    B    O4   124.11  3.000
 3VT  C4   C5   C    122.15  3.000
 3VT  C4   C5   C6   127.91  3.000
 3VT  C    C5   C6   109.94  3.000
 3VT  C5   C    B    104.97  3.000
 3VT  C5   C    C1   120.06  3.000
 3VT  B    C    C1   134.95  3.000
 3VT  C5   C4   C9   121.11  3.000
 3VT  C9   C4   C3   120.96  3.000
 3VT  C5   C4   C3   117.93  3.000
 3VT  C11  O3   C2   118.81  3.000
 3VT  C14  N1   C11  116.77  3.000
 3VT  C13  N    C12  117.78  3.000
 3VT  H2   O4   B    114.24  3.000
 3VT  H7   C9   H6   107.41  3.000
 3VT  H7   C9   H5   106.78  3.000
 3VT  H6   C9   H5   106.97  3.000
 3VT  H7   C9   C4   111.84  3.000
 3VT  H6   C9   C4   111.75  3.000
 3VT  H5   C9   C4   111.80  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
 3VT  CONST_01  C4   C5   C    C1      0.00   0.0  0
 3VT  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 3VT  CONST_03  C5   C    C1   C2      0.00   0.0  0
 3VT  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 3VT  CONST_05  C    C5   C4   C3      0.00   0.0  0
 3VT  CONST_06  C    C1   C2   C3      0.00   0.0  0
 3VT  CONST_07  C13  N    C12  C11     0.00   0.0  0
 3VT  CONST_08  C13  C14  N1   C11     0.00   0.0  0
 3VT  CONST_09  C14  C13  N    C12     0.00   0.0  0
 3VT  CONST_10  C14  N1   C11  C12     0.00   0.0  0
 3VT  CONST_11  N    C13  C14  N1      0.00   0.0  0
 3VT  CONST_12  N    C12  C11  N1      0.00   0.0  0
 3VT  CONST_13  C10  C3   C2   C1    180.00   0.0  0
 3VT  CONST_14  C9   C4   C3   C2    180.00   0.0  0
 3VT  CONST_15  C6   C5   C4   C9      0.00   0.0  0
 3VT  CONST_16  C    C5   C4   C9    180.00   0.0  0
 3VT  CONST_17  C5   C4   C3   C10   180.00   0.0  0
 3VT  CONST_18  O3   C11  N1   C14   180.00   0.0  0
 3VT  CONST_19  O3   C2   C1   C     180.00   0.0  0
 3VT  CONST_20  O3   C2   C3   C4    180.00   0.0  0
 3VT  CONST_21  N    C12  C11  O3    180.00   0.0  0
 3VT  CONST_22  H1   C1   C2   C3    180.00   0.0  0
 3VT  CONST_23  H13  C14  N1   C11   180.00   0.0  0
 3VT  CONST_24  H12  C13  N    C12   180.00   0.0  0
 3VT  CONST_25  H11  C12  N    C13   180.00   0.0  0
 3VT  Var_01    O    B    C    C1    179.09  30.0  1
 3VT  Var_02    C    B    O    C6      3.34  30.0  1
 3VT  Var_03    C12  C11  O3   C2    178.16  30.0  1
 3VT  Var_04    H8   C10  C3   C2     88.48  30.0  2
 3VT  Var_05    H5   C9   C4   C3    -45.85  30.0  2
 3VT  Var_06    C6   C7   C8   O1   -154.18  30.0  3

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
 3VT  chir_01  C6  C7  O  C5  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
 3VT  plan-1  C11  0.020
 3VT  plan-1  C12  0.020
 3VT  plan-1  C13  0.020
 3VT  plan-1  C14  0.020
 3VT  plan-1  O3   0.020
 3VT  plan-1  N1   0.020
 3VT  plan-1  N    0.020
 3VT  plan-1  H11  0.020
 3VT  plan-1  H12  0.020
 3VT  plan-1  H13  0.020
 3VT  plan-2  C1   0.020
 3VT  plan-2  C2   0.020
 3VT  plan-2  C3   0.020
 3VT  plan-2  C10  0.020
 3VT  plan-2  C6   0.020
 3VT  plan-2  B    0.020
 3VT  plan-2  C5   0.020
 3VT  plan-2  C    0.020
 3VT  plan-2  C4   0.020
 3VT  plan-2  O3   0.020
 3VT  plan-2  H1   0.020
 3VT  plan-2  C9   0.020
 3VT  plan-3  C7   0.020
 3VT  plan-3  C8   0.020
 3VT  plan-3  O1   0.020
 3VT  plan-3  O2   0.020

