# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:24:42 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  38  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  -0.426   0.6423   1.3635  -0.6227
 3VT  C2   C  CR6   0   0.335   1.4307   0.2658  -0.9045
 3VT  C3   C  CR6   0  -0.010   0.9075  -1.0130  -1.1241
 3VT  C7   C  CH2   0  -0.604  -3.2006  -0.8154   0.7228
 3VT  C8   C  C     0   0.561  -4.6898  -0.7529   0.9394
 3VT  C10  C  CH3   0  -0.747   1.8323  -2.1568  -1.4192
 3VT  C11  C  CR6   0   0.465   3.5953   0.1801  -0.0029
 3VT  C12  C  CR16  0  -0.136   4.9731   0.3569  -0.1911
 3VT  C13  C  CR16  0  -0.123   5.3185  -0.3433   1.9378
 3VT  C14  C  CR16  0  -0.101   3.9587  -0.5118   2.1061
 3VT  O1   O  OH1   0  -0.590  -5.0128  -0.9464   2.2111
 3VT  O2   O  O     0  -0.442  -5.5030  -0.5804   0.0666
 3VT  C6   C  CR15  0   0.003  -2.7610  -0.0447  -0.5123
 3VT  O    O  O     0  -0.480  -3.0788   1.3313  -0.3238
 3VT  B    B  B     0   0.502  -1.9428   2.0996  -0.2779
 3VT  C5   C  CR56  0  -0.037  -1.2652  -0.0940  -0.7172
 3VT  C    C  CR56  0  -0.093  -0.7269   1.1744  -0.5311
 3VT  C4   C  CR6   0   0.061  -0.4813  -1.1991  -1.0394
 3VT  O3   O  O2    0  -0.513   2.7920   0.4693  -1.0387
 3VT  N1   N  N     0  -0.391   3.0938  -0.2473   1.1284
 3VT  N    N  N     0  -0.342   5.8180   0.0938   0.7813
 3VT  H1   H  HCR6  0   0.266   1.0953   2.3377  -0.4836
 3VT  H2   H  HOH1  0   0.494  -2.8105   3.8143   0.0875
 3VT  H3   H  HCH2  0   0.291  -2.6701  -0.4512   1.6055
 3VT  H4   H  HCH2  0   0.305  -2.9342  -1.8717   0.6223
 3VT  H5   H  HCH3  0   0.262  -0.6908  -3.0214  -2.1788
 3VT  H6   H  HCH3  0   0.258  -0.9321  -3.2281  -0.4541
 3VT  H7   H  HCH3  0   0.253  -2.1764  -2.4740  -1.4415
 3VT  H8   H  HCH3  0   0.258   2.1671  -2.6293  -0.4926
 3VT  H9   H  HCH3  0   0.257   1.3500  -2.9291  -2.0136
 3VT  H10  H  HCH3  0   0.255   2.7210  -1.8394  -1.9615
 3VT  H11  H  HCR6  0   0.285   5.3655   0.7122  -1.1370
 3VT  H12  H  HCR6  0   0.277   6.0136  -0.5626   2.7376
 3VT  H13  H  HCR6  0   0.281   3.5512  -0.8665   3.0443
 3VT  H14  H  HOH1  0   0.481  -5.9766  -0.9406   2.3145
 3VT  H15  H  HCR5  0   0.271  -3.3007  -0.4077  -1.3927
 3VT  O4   O  OH1   0  -0.610  -1.9397   3.4300  -0.0601
 3VT  C9   C  CH3   0  -0.775  -1.1012  -2.5445  -1.2889

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   double    1.205  0.020  1.205
 3VT  N    C13  aromatic  1.333  0.020  1.333
 3VT  N    C12  aromatic  1.315  0.020  1.315
 3VT  C8   C7   single    1.506  0.020  1.506
 3VT  C8   O1   single    1.326  0.020  1.326
 3VT  C13  C14  aromatic  1.380  0.020  1.380
 3VT  O4   B    single    1.348  0.020  1.348
 3VT  C7   C6   single    1.521  0.020  1.521
 3VT  C12  C11  aromatic  1.402  0.020  1.402
 3VT  C14  N1   aromatic  1.332  0.020  1.332
 3VT  B    O    single    1.372  0.020  1.372
 3VT  B    C    single    1.549  0.020  1.549
 3VT  C6   O    single    1.425  0.020  1.425
 3VT  C6   C5   single    1.511  0.020  1.511
 3VT  C11  N1   aromatic  1.309  0.020  1.309
 3VT  C11  O3   single    1.342  0.020  1.342
 3VT  C    C5   aromatic  1.390  0.020  1.390
 3VT  C    C1   aromatic  1.385  0.020  1.385
 3VT  C5   C4   aromatic  1.393  0.020  1.393
 3VT  C1   C2   aromatic  1.381  0.020  1.381
 3VT  C4   C9   single    1.502  0.020  1.502
 3VT  C4   C3   aromatic  1.404  0.020  1.404
 3VT  C2   C3   aromatic  1.399  0.020  1.399
 3VT  C2   O3   single    1.383  0.020  1.383
 3VT  C3   C10  single    1.500  0.020  1.500
 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  O1   H14  single    0.850  0.020  0.980
 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    121.85  3.000
 3VT  H1   C1   C2   120.16  3.000
 3VT  C    C1   C2   117.99  3.000
 3VT  O3   C2   C3   119.17  3.000
 3VT  O3   C2   C1   117.71  3.000
 3VT  C3   C2   C1   123.04  3.000
 3VT  C4   C3   C10  121.38  3.000
 3VT  C10  C3   C2   119.82  3.000
 3VT  C4   C3   C2   118.80  3.000
 3VT  H4   C7   H3   106.13  3.000
 3VT  H4   C7   C6   110.14  3.000
 3VT  H3   C7   C6   110.30  3.000
 3VT  H4   C7   C8   107.10  3.000
 3VT  H3   C7   C8   110.50  3.000
 3VT  C6   C7   C8   112.43  3.000
 3VT  O2   C8   O1   123.43  3.000
 3VT  O1   C8   C7   111.88  3.000
 3VT  O2   C8   C7   124.67  3.000
 3VT  H10  C10  H9   107.28  3.000
 3VT  H10  C10  H8   107.36  3.000
 3VT  H9   C10  H8   107.00  3.000
 3VT  H10  C10  C3   112.27  3.000
 3VT  H9   C10  C3   112.06  3.000
 3VT  H8   C10  C3   110.59  3.000
 3VT  N1   C11  O3   120.52  3.000
 3VT  O3   C11  C12  117.22  3.000
 3VT  N1   C11  C12  122.26  3.000
 3VT  H11  C12  N    118.58  3.000
 3VT  H11  C12  C11  120.95  3.000
 3VT  N    C12  C11  120.47  3.000
 3VT  H12  C13  N    117.82  3.000
 3VT  H12  C13  C14  121.20  3.000
 3VT  N    C13  C14  120.98  3.000
 3VT  H13  C14  N1   117.18  3.000
 3VT  H13  C14  C13  121.09  3.000
 3VT  N1   C14  C13  121.73  3.000
 3VT  H14  O1   C8   110.09  3.000
 3VT  H15  C6   C5   111.61  3.000
 3VT  H15  C6   O    108.47  3.000
 3VT  C5   C6   O    105.68  3.000
 3VT  H15  C6   C7   110.04  3.000
 3VT  C5   C6   C7   112.32  3.000
 3VT  O    C6   C7   108.51  3.000
 3VT  B    O    C6   111.14  3.000
 3VT  C    B    O    108.06  3.000
 3VT  C    B    O4   127.89  3.000
 3VT  O    B    O4   124.05  3.000
 3VT  C4   C5   C    122.47  3.000
 3VT  C4   C5   C6   127.93  3.000
 3VT  C    C5   C6   109.60  3.000
 3VT  C5   C    B    105.24  3.000
 3VT  C5   C    C1   119.90  3.000
 3VT  B    C    C1   134.85  3.000
 3VT  C5   C4   C9   121.12  3.000
 3VT  C9   C4   C3   121.13  3.000
 3VT  C5   C4   C3   117.75  3.000
 3VT  C11  O3   C2   118.85  3.000
 3VT  C14  N1   C11  116.77  3.000
 3VT  C13  N    C12  117.79  3.000
 3VT  H2   O4   B    114.60  3.000
 3VT  H7   C9   H6   107.50  3.000
 3VT  H7   C9   H5   106.61  3.000
 3VT  H6   C9   H5   106.98  3.000
 3VT  H7   C9   C4   111.90  3.000
 3VT  H6   C9   C4   111.70  3.000
 3VT  H5   C9   C4   111.84  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  CONST_26  H14  O1   C8   C7    180.00   0.0  0
 3VT  Var_01    O    B    C    C1    178.89  30.0  1
 3VT  Var_02    C    B    O    C6      3.14  30.0  1
 3VT  Var_03    C12  C11  O3   C2    177.92  30.0  1
 3VT  Var_04    H8   C10  C3   C2     88.07  30.0  2
 3VT  Var_05    H5   C9   C4   C3    -45.58  30.0  2
 3VT  Var_06    C6   C7   C8   O1   -155.56  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
 3VT  plan-3  H14  0.020

