# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 17:36:45 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-[[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]methylamino]benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(NC[C@@H]2Cc3ccccc3B(O)O2)cc1
#
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
 LH2  LH2  4-[[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]methylamino]benzenecarboximidamide  ligand  40  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_LH2
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
 LH2  C10  C  CR16  0  -0.306  -3.0116   1.3116  -0.3364
 LH2  C15  C  CH2   0  -0.253   0.1240  -0.6369   0.1948
 LH2  C20  C  CH2   0  -0.514   2.5285  -1.3453   0.2255
 LH2  C24  C  CR16  0  -0.275   4.9177  -1.8700  -0.4090
 LH2  C26  C  CR16  0  -0.244   6.2256  -1.4649  -0.6391
 LH2  C28  C  CR16  0  -0.224   6.5757  -0.1247  -0.5202
 LH2  N01  N  NH2   0  -0.783  -7.1684   0.6494  -0.7172
 LH2  C04  C  C     0   0.325  -6.4528  -0.2222   0.0550
 LH2  N05  N  N     0  -0.639  -7.0664  -1.0671   0.7963
 LH2  C07  C  CR6   0  -0.008  -4.9794  -0.0633  -0.0194
 LH2  C08  C  CR16  0  -0.260  -4.3824   1.1730  -0.2844
 LH2  C12  C  CR6   0   0.401  -2.1630   0.2092  -0.1367
 LH2  N13  N  NH1   0  -0.692  -0.8092   0.3715  -0.2419
 LH2  C18  C  CH1   0   0.025   1.5424  -0.2672  -0.1933
 LH2  C23  C  CR6   0   0.067   3.9479  -0.9373  -0.0583
 LH2  C30  C  CR16  0  -0.305   5.6095   0.8061  -0.1686
 LH2  C32  C  CR6   0  -0.107   4.2907   0.4150   0.0654
 LH2  B33  B  B     0   0.526   3.1550   1.4014   0.4677
 LH2  O34  O  OH1   0  -0.591   3.4430   2.6565   0.8929
 LH2  O36  O  O2    0  -0.472   1.8571   0.9866   0.4065
 LH2  C37  C  CR16  0  -0.308  -2.7596  -1.0310   0.1361
 LH2  C39  C  CR16  0  -0.259  -4.1369  -1.1524   0.1902
 LH2  H1   H  HCR6  0   0.231  -2.5803   2.2855  -0.5366
 LH2  H2   H  HCH2  0   0.222   0.0695  -0.8136   1.2786
 LH2  H3   H  HCH2  0   0.227  -0.1100  -1.5850  -0.2939
 LH2  H5   H  HCH2  0   0.245   2.2819  -2.2717  -0.2973
 LH2  H6   H  HCR6  0   0.222   4.6526  -2.9163  -0.5065
 LH2  H7   H  HCR6  0   0.238   6.9740  -2.1970  -0.9156
 LH2  H8   H  HCR6  0   0.234   7.5956   0.1879  -0.7034
 LH2  H9   H  HNH2  0   0.368  -6.7558   0.9628  -1.5799
 LH2  H10  H  HNH2  0   0.365  -8.1572   0.4652  -0.7818
 LH2  H11  H  H     0   0.314  -6.4104  -1.5603   1.3906
 LH2  H12  H  HCR6  0   0.234  -4.9959   2.0528  -0.4326
 LH2  H13  H  HNH1  0   0.362  -0.4882   1.3221  -0.1377
 LH2  H14  H  HCH1  0   0.229   1.5860  -0.1485  -1.2831
 LH2  H15  H  HCR6  0   0.239   5.8867   1.8498  -0.0794
 LH2  H16  H  HCR6  0   0.239  -2.1542  -1.9116   0.3032
 LH2  H17  H  HCR6  0   0.220  -4.5553  -2.1323   0.3874
 LH2  H18  H  HOH1  0   0.456   2.6664   3.1886   1.0974
 LH2  H4   H  HCH2  0   0.249   2.4098  -1.5519   1.2958

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
 LH2  N05  C04  double    1.281  0.020  1.281
 LH2  C04  N01  single    1.367  0.020  1.367
 LH2  C04  C07  single    1.484  0.020  1.484
 LH2  C08  C07  aromatic  1.398  0.020  1.398
 LH2  C08  C10  aromatic  1.379  0.020  1.379
 LH2  C07  C39  aromatic  1.393  0.020  1.393
 LH2  C10  C12  aromatic  1.405  0.020  1.405
 LH2  C39  C37  aromatic  1.384  0.020  1.384
 LH2  O34  B33  single    1.356  0.020  1.356
 LH2  C12  C37  aromatic  1.403  0.020  1.403
 LH2  C12  N13  single    1.367  0.020  1.367
 LH2  B33  O36  single    1.364  0.020  1.364
 LH2  B33  C32  single    1.557  0.020  1.557
 LH2  N13  C15  single    1.442  0.020  1.442
 LH2  O36  C18  single    1.425  0.020  1.425
 LH2  C15  C18  single    1.516  0.020  1.516
 LH2  C32  C30  aromatic  1.395  0.020  1.395
 LH2  C32  C23  aromatic  1.400  0.020  1.400
 LH2  C30  C28  aromatic  1.387  0.020  1.387
 LH2  C18  C20  single    1.520  0.020  1.520
 LH2  C28  C26  aromatic  1.390  0.020  1.390
 LH2  C23  C20  single    1.504  0.020  1.504
 LH2  C23  C24  aromatic  1.390  0.020  1.390
 LH2  C26  C24  aromatic  1.388  0.020  1.388
 LH2  C10  H1   single    0.930  0.020  1.080
 LH2  C15  H2   single    0.970  0.020  1.090
 LH2  C15  H3   single    0.970  0.020  1.090
 LH2  C20  H4   single    0.970  0.020  1.090
 LH2  C20  H5   single    0.970  0.020  1.090
 LH2  C24  H6   single    0.930  0.020  1.080
 LH2  C26  H7   single    0.930  0.020  1.080
 LH2  C28  H8   single    0.930  0.020  1.080
 LH2  N01  H9   single    0.890  0.020  1.040
 LH2  N01  H10  single    0.890  0.020  1.040
 LH2  N05  H11  single    0.890  0.020  1.040
 LH2  C08  H12  single    0.930  0.020  1.080
 LH2  N13  H13  single    0.890  0.020  1.040
 LH2  C18  H14  single    0.970  0.020  1.090
 LH2  C30  H15  single    0.930  0.020  1.080
 LH2  C37  H16  single    0.930  0.020  1.080
 LH2  C39  H17  single    0.930  0.020  1.080
 LH2  O34  H18  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
 LH2  H1   C10  C12  119.40  3.000
 LH2  H1   C10  C08  119.53  3.000
 LH2  C12  C10  C08  121.07  3.000
 LH2  H3   C15  H2   106.92  3.000
 LH2  H3   C15  C18  107.31  3.000
 LH2  H2   C15  C18  109.75  3.000
 LH2  H3   C15  N13  109.45  3.000
 LH2  H2   C15  N13  112.27  3.000
 LH2  C18  C15  N13  110.94  3.000
 LH2  H5   C20  H4   106.45  3.000
 LH2  H5   C20  C23  110.67  3.000
 LH2  H4   C20  C23  109.72  3.000
 LH2  H5   C20  C18  108.87  3.000
 LH2  H4   C20  C18  109.42  3.000
 LH2  C23  C20  C18  111.58  3.000
 LH2  H6   C24  C23  119.98  3.000
 LH2  H6   C24  C26  119.81  3.000
 LH2  C23  C24  C26  120.20  3.000
 LH2  H7   C26  C28  119.97  3.000
 LH2  H7   C26  C24  119.74  3.000
 LH2  C28  C26  C24  120.29  3.000
 LH2  H8   C28  C30  120.37  3.000
 LH2  H8   C28  C26  120.08  3.000
 LH2  C30  C28  C26  119.55  3.000
 LH2  H10  N01  H9   113.84  3.000
 LH2  H10  N01  C04  115.68  3.000
 LH2  H9   N01  C04  117.92  3.000
 LH2  C07  C04  N05  125.14  3.000
 LH2  C07  C04  N01  115.04  3.000
 LH2  N05  C04  N01  119.80  3.000
 LH2  H11  N05  C04  110.51  3.000
 LH2  C39  C07  C08  117.50  3.000
 LH2  C39  C07  C04  120.62  3.000
 LH2  C08  C07  C04  121.88  3.000
 LH2  H12  C08  C07  120.16  3.000
 LH2  H12  C08  C10  118.45  3.000
 LH2  C07  C08  C10  121.37  3.000
 LH2  C37  C12  N13  122.74  3.000
 LH2  N13  C12  C10  119.58  3.000
 LH2  C37  C12  C10  117.66  3.000
 LH2  H13  N13  C12  114.77  3.000
 LH2  H13  N13  C15  114.95  3.000
 LH2  C12  N13  C15  122.31  3.000
 LH2  H14  C18  O36  108.31  3.000
 LH2  H14  C18  C20  108.95  3.000
 LH2  O36  C18  C20  111.40  3.000
 LH2  H14  C18  C15  108.53  3.000
 LH2  C20  C18  C15  111.30  3.000
 LH2  O36  C18  C15  108.26  3.000
 LH2  C32  C23  C24  119.95  3.000
 LH2  C24  C23  C20  121.59  3.000
 LH2  C32  C23  C20  118.45  3.000
 LH2  H15  C30  C32  119.86  3.000
 LH2  H15  C30  C28  119.29  3.000
 LH2  C32  C30  C28  120.85  3.000
 LH2  B33  C32  C30  123.72  3.000
 LH2  C30  C32  C23  119.16  3.000
 LH2  B33  C32  C23  117.13  3.000
 LH2  O36  B33  O34  119.84  3.000
 LH2  O36  B33  C32  119.33  3.000
 LH2  O34  B33  C32  120.83  3.000
 LH2  H18  O34  B33  113.99  3.000
 LH2  B33  O36  C18  119.77  3.000
 LH2  H16  C37  C39  118.66  3.000
 LH2  H16  C37  C12  120.78  3.000
 LH2  C39  C37  C12  120.56  3.000
 LH2  H17  C39  C37  118.08  3.000
 LH2  H17  C39  C07  120.07  3.000
 LH2  C37  C39  C07  121.84  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
 LH2  CONST_01  C39  C07  C08  C10     0.00   0.0  0
 LH2  CONST_02  C39  C37  C12  C10     0.00   0.0  0
 LH2  CONST_03  C30  C32  C23  C24     0.00   0.0  0
 LH2  CONST_04  C30  C28  C26  C24     0.00   0.0  0
 LH2  CONST_05  C32  C30  C28  C26     0.00   0.0  0
 LH2  CONST_06  C32  C23  C24  C26     0.00   0.0  0
 LH2  CONST_07  C23  C32  C30  C28     0.00   0.0  0
 LH2  CONST_08  C23  C24  C26  C28     0.00   0.0  0
 LH2  CONST_09  C12  C10  C08  C07     0.00   0.0  0
 LH2  CONST_10  C12  C37  C39  C07     0.00   0.0  0
 LH2  CONST_11  C37  C39  C07  C08     0.00   0.0  0
 LH2  CONST_12  C37  C12  C10  C08     0.00   0.0  0
 LH2  CONST_13  C04  C07  C08  C10   180.00   0.0  0
 LH2  CONST_14  C37  C39  C07  C04   180.00   0.0  0
 LH2  CONST_15  N13  C12  C10  C08   180.00   0.0  0
 LH2  CONST_16  C39  C37  C12  N13   180.00   0.0  0
 LH2  CONST_17  H16  C37  C12  C10   180.00   0.0  0
 LH2  CONST_18  H6   C24  C23  C20     0.00   0.0  0
 LH2  CONST_19  H8   C28  C26  C24   180.00   0.0  0
 LH2  CONST_20  H15  C30  C28  C26   180.00   0.0  0
 LH2  CONST_21  H1   C10  C08  C07   180.00   0.0  0
 LH2  CONST_22  H17  C39  C07  C08   180.00   0.0  0
 LH2  CONST_23  H12  C08  C10  C12   180.00   0.0  0
 LH2  CONST_24  H7   C26  C24  C23   180.00   0.0  0
 LH2  CONST_25  C15  N13  C12  C10   180.00   0.0  0
 LH2  CONST_26  C37  C12  N13  C15     0.00   0.0  0
 LH2  CONST_28  H11  N05  C04  C07     0.00   0.0  0
 LH2  CONST_30  H10  N01  C04  C07   180.00   0.0  0
 LH2  Var_01    C18  C20  C23  C24  -147.24  30.0  1
 LH2  Var_02    C32  B33  O36  C18    -8.60  30.0  1
 LH2  Var_03    O36  B33  C32  C23   -13.71  30.0  1
 LH2  Var_04    C08  C07  C04  N01    29.29  30.0  2
 LH2  Var_05    C18  C15  N13  C12   173.09  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
 LH2  chir_01  C18  O36  C15  C20  positiv

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
 LH2  plan-1  C10  0.020
 LH2  plan-1  C04  0.020
 LH2  plan-1  C07  0.020
 LH2  plan-1  C08  0.020
 LH2  plan-1  C12  0.020
 LH2  plan-1  N13  0.020
 LH2  plan-1  C37  0.020
 LH2  plan-1  C39  0.020
 LH2  plan-1  H1   0.020
 LH2  plan-1  H12  0.020
 LH2  plan-1  H16  0.020
 LH2  plan-1  H17  0.020
 LH2  plan-2  C20  0.020
 LH2  plan-2  C24  0.020
 LH2  plan-2  C26  0.020
 LH2  plan-2  C28  0.020
 LH2  plan-2  C23  0.020
 LH2  plan-2  C30  0.020
 LH2  plan-2  C32  0.020
 LH2  plan-2  B33  0.020
 LH2  plan-2  H6   0.020
 LH2  plan-2  H7   0.020
 LH2  plan-2  H8   0.020
 LH2  plan-2  H15  0.020
 LH2  plan-3  C15  0.020
 LH2  plan-3  C12  0.020
 LH2  plan-3  N13  0.020
 LH2  plan-3  H13  0.020
 LH2  plan-4  N01  0.020
 LH2  plan-4  C04  0.020
 LH2  plan-4  N05  0.020
 LH2  plan-4  C07  0.020
 LH2  plan-4  H9   0.020
 LH2  plan-4  H10  0.020
 LH2  plan-4  H11  0.020

