# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 15:33:23 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1OCc2cccnc2)[C@@H]3Cc4ccccc4B(O)O3
#
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
 LH5  LH5  4-[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide  ligand  48  28  .  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_LH5
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
 LH5  C10  C  CR16  0  -0.333   0.8660   2.2936  -0.3065
 LH5  C13  C  CR16  0  -0.438  -0.2611   0.1737  -0.2568
 LH5  C15  C  CR6   0   0.408  -1.4890   0.8081  -0.1028
 LH5  C17  C  CH2   0  -0.265  -2.6732  -1.2608  -0.1146
 LH5  C20  C  CR6   0   0.003  -4.1019  -1.7001  -0.0412
 LH5  C21  C  CR16  0  -0.166  -5.0629  -1.2029  -0.9154
 LH5  C28  C  CR16  0  -0.100  -4.5128  -2.6315   0.9034
 LH5  N01  N  N     0  -0.633  -3.8512   2.7785  -0.7170
 LH5  N05  N  NH2   0  -0.793  -2.8501   3.9092   1.0091
 LH5  C07  C  CR6   0  -0.145  -1.5468   2.2092  -0.0596
 LH5  C08  C  CR16  0  -0.234  -0.3593   2.9252  -0.1489
 LH5  C12  C  CR6   0   0.108   0.9152   0.9088  -0.3637
 LH5  O16  O  O2    0  -0.461  -2.6548   0.1501   0.0301
 LH5  C23  C  CR16  0  -0.319  -6.3660  -1.6558  -0.8083
 LH5  C25  C  CR16  0  -0.064  -6.6636  -2.5956   0.1698
 LH5  N27  N  N     0  -0.400  -5.7589  -3.0777   1.0113
 LH5  C30  C  CH1   0   0.013   2.2172   0.1589  -0.4705
 LH5  C32  C  CH2   0  -0.535   2.7576  -0.1787   0.9175
 LH5  C35  C  CR6   0   0.055   4.1013  -0.8491   0.8402
 LH5  C36  C  CR16  0  -0.294   4.4881  -1.8148   1.7626
 LH5  C38  C  CR16  0  -0.261   5.7458  -2.3967   1.6778
 LH5  C40  C  CR16  0  -0.243   6.6267  -2.0186   0.6711
 LH5  C42  C  CR16  0  -0.329   6.2417  -1.0548  -0.2490
 LH5  C44  C  CR6   0  -0.112   4.9809  -0.4616  -0.1777
 LH5  B45  B  B     0   0.512   4.4740   0.6197  -1.1764
 LH5  O46  O  OH1   0  -0.615   5.3360   1.2691  -1.9969
 LH5  O48  O  O2    0  -0.471   3.1452   0.9273  -1.2155
 LH5  H1   H  HCR6  0   0.256   1.7653   2.8885  -0.3861
 LH5  H2   H  HCR6  0   0.285  -0.1984  -0.9064  -0.2944
 LH5  H3   H  HCH2  0   0.251  -2.0864  -1.7436   0.6740
 LH5  H4   H  HCH2  0   0.253  -2.2355  -1.5484  -1.0769
 LH5  H5   H  HCR6  0   0.269  -4.7998  -0.4756  -1.6738
 LH5  H6   H  HCR6  0   0.263  -3.7933  -3.0381   1.6078
 LH5  H7   H  H     0   0.329  -3.6540   2.0840  -1.4263
 LH5  H8   H  HNH2  0   0.383  -3.7343   4.3567   1.1927
 LH5  H9   H  HNH2  0   0.392  -2.2662   3.7829   1.8182
 LH5  H10  H  HCR6  0   0.264  -0.3951   4.0065  -0.1129
 LH5  H11  H  HCR6  0   0.275  -7.1400  -1.2948  -1.4712
 LH5  H12  H  HCR6  0   0.268  -7.6749  -2.9724   0.2751
 LH5  H13  H  HCH1  0   0.252   2.0342  -0.7824  -1.0045
 LH5  H14  H  HCH2  0   0.266   2.8299   0.7408   1.5102
 LH5  H15  H  HCH2  0   0.272   2.0366  -0.8179   1.4314
 LH5  H16  H  HCR6  0   0.249   3.8047  -2.1198   2.5464
 LH5  H17  H  HCR6  0   0.259   6.0376  -3.1511   2.3975
 LH5  H18  H  HCR6  0   0.254   7.6059  -2.4751   0.6063
 LH5  H19  H  HCR6  0   0.252   6.9321  -0.7650  -1.0321
 LH5  H20  H  HOH1  0   0.489   4.9110   1.8948  -2.5936
 LH5  C04  C  C     0   0.332  -2.8422   2.9426   0.0475

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
 LH5  N01  C04  double    1.276  0.020  1.276
 LH5  C08  C10  aromatic  1.387  0.020  1.387
 LH5  C08  C07  aromatic  1.390  0.020  1.390
 LH5  C04  N05  single    1.363  0.020  1.363
 LH5  C04  C07  single    1.492  0.020  1.492
 LH5  C10  C12  aromatic  1.387  0.020  1.387
 LH5  C07  C15  aromatic  1.403  0.020  1.403
 LH5  O46  B45  single    1.356  0.020  1.356
 LH5  O48  B45  single    1.364  0.020  1.364
 LH5  O48  C30  single    1.417  0.020  1.417
 LH5  C12  C30  single    1.506  0.020  1.506
 LH5  C12  C13  aromatic  1.391  0.020  1.391
 LH5  B45  C44  single    1.557  0.020  1.557
 LH5  C15  C13  aromatic  1.391  0.020  1.391
 LH5  C15  O16  single    1.345  0.020  1.345
 LH5  C30  C32  single    1.527  0.020  1.527
 LH5  O16  C17  single    1.418  0.020  1.418
 LH5  C44  C42  aromatic  1.395  0.020  1.395
 LH5  C44  C35  aromatic  1.400  0.020  1.400
 LH5  C32  C35  single    1.504  0.020  1.504
 LH5  C42  C40  aromatic  1.387  0.020  1.387
 LH5  C35  C36  aromatic  1.390  0.020  1.390
 LH5  C17  C20  single    1.497  0.020  1.497
 LH5  C28  C20  aromatic  1.389  0.020  1.389
 LH5  C28  N27  aromatic  1.328  0.020  1.328
 LH5  C20  C21  aromatic  1.391  0.020  1.391
 LH5  N27  C25  aromatic  1.326  0.020  1.326
 LH5  C40  C38  aromatic  1.390  0.020  1.390
 LH5  C36  C38  aromatic  1.388  0.020  1.388
 LH5  C21  C23  aromatic  1.384  0.020  1.384
 LH5  C25  C23  aromatic  1.389  0.020  1.389
 LH5  C10  H1   single    0.930  0.020  1.080
 LH5  C13  H2   single    0.930  0.020  1.080
 LH5  C17  H3   single    0.970  0.020  1.090
 LH5  C17  H4   single    0.970  0.020  1.090
 LH5  C21  H5   single    0.930  0.020  1.080
 LH5  C28  H6   single    0.930  0.020  1.080
 LH5  N01  H7   single    0.890  0.020  1.040
 LH5  N05  H8   single    0.890  0.020  1.040
 LH5  N05  H9   single    0.890  0.020  1.040
 LH5  C08  H10  single    0.930  0.020  1.080
 LH5  C23  H11  single    0.930  0.020  1.080
 LH5  C25  H12  single    0.930  0.020  1.080
 LH5  C30  H13  single    0.970  0.020  1.090
 LH5  C32  H14  single    0.970  0.020  1.090
 LH5  C32  H15  single    0.970  0.020  1.090
 LH5  C36  H16  single    0.930  0.020  1.080
 LH5  C38  H17  single    0.930  0.020  1.080
 LH5  C40  H18  single    0.930  0.020  1.080
 LH5  C42  H19  single    0.930  0.020  1.080
 LH5  O46  H20  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
 LH5  H1   C10  C12  121.12  3.000
 LH5  H1   C10  C08  119.50  3.000
 LH5  C12  C10  C08  119.38  3.000
 LH5  H2   C13  C12  118.39  3.000
 LH5  H2   C13  C15  120.67  3.000
 LH5  C12  C13  C15  120.93  3.000
 LH5  O16  C15  C07  116.73  3.000
 LH5  O16  C15  C13  123.57  3.000
 LH5  C07  C15  C13  119.69  3.000
 LH5  H4   C17  H3   107.62  3.000
 LH5  H4   C17  O16  110.22  3.000
 LH5  H3   C17  O16  110.99  3.000
 LH5  H4   C17  C20  110.33  3.000
 LH5  H3   C17  C20  110.29  3.000
 LH5  O16  C17  C20  107.42  3.000
 LH5  C28  C20  C21  117.57  3.000
 LH5  C21  C20  C17  121.59  3.000
 LH5  C28  C20  C17  120.84  3.000
 LH5  H5   C21  C23  120.18  3.000
 LH5  H5   C21  C20  120.82  3.000
 LH5  C23  C21  C20  119.00  3.000
 LH5  H6   C28  N27  116.31  3.000
 LH5  H6   C28  C20  119.75  3.000
 LH5  N27  C28  C20  123.93  3.000
 LH5  H7   N01  C04  110.73  3.000
 LH5  H9   N05  H8   114.74  3.000
 LH5  H9   N05  C04  118.36  3.000
 LH5  H8   N05  C04  116.64  3.000
 LH5  C08  C07  C04  119.55  3.000
 LH5  C04  C07  C15  121.92  3.000
 LH5  C08  C07  C15  118.52  3.000
 LH5  H10  C08  C07  118.97  3.000
 LH5  H10  C08  C10  119.19  3.000
 LH5  C07  C08  C10  121.83  3.000
 LH5  C30  C12  C13  118.24  3.000
 LH5  C13  C12  C10  119.63  3.000
 LH5  C30  C12  C10  122.05  3.000
 LH5  C17  O16  C15  119.19  3.000
 LH5  H11  C23  C25  120.29  3.000
 LH5  H11  C23  C21  121.15  3.000
 LH5  C25  C23  C21  118.55  3.000
 LH5  H12  C25  N27  116.63  3.000
 LH5  H12  C25  C23  120.23  3.000
 LH5  N27  C25  C23  123.14  3.000
 LH5  C25  N27  C28  117.80  3.000
 LH5  H13  C30  O48  108.58  3.000
 LH5  H13  C30  C32  108.16  3.000
 LH5  O48  C30  C32  111.47  3.000
 LH5  H13  C30  C12  108.50  3.000
 LH5  C32  C30  C12  110.58  3.000
 LH5  O48  C30  C12  109.48  3.000
 LH5  H15  C32  H14  106.26  3.000
 LH5  H15  C32  C35  110.69  3.000
 LH5  H14  C32  C35  110.05  3.000
 LH5  H15  C32  C30  108.87  3.000
 LH5  H14  C32  C30  109.22  3.000
 LH5  C35  C32  C30  111.59  3.000
 LH5  C44  C35  C36  119.99  3.000
 LH5  C36  C35  C32  121.61  3.000
 LH5  C44  C35  C32  118.39  3.000
 LH5  H16  C36  C38  119.83  3.000
 LH5  H16  C36  C35  119.99  3.000
 LH5  C38  C36  C35  120.17  3.000
 LH5  H17  C38  C40  120.00  3.000
 LH5  H17  C38  C36  119.71  3.000
 LH5  C40  C38  C36  120.29  3.000
 LH5  H18  C40  C42  120.30  3.000
 LH5  H18  C40  C38  120.13  3.000
 LH5  C42  C40  C38  119.57  3.000
 LH5  H19  C42  C44  119.93  3.000
 LH5  H19  C42  C40  119.24  3.000
 LH5  C44  C42  C40  120.82  3.000
 LH5  B45  C44  C42  123.84  3.000
 LH5  C42  C44  C35  119.16  3.000
 LH5  B45  C44  C35  117.01  3.000
 LH5  O48  B45  O46  119.60  3.000
 LH5  O48  B45  C44  119.48  3.000
 LH5  O46  B45  C44  120.92  3.000
 LH5  H20  O46  B45  113.92  3.000
 LH5  B45  O48  C30  120.04  3.000
 LH5  C07  C04  N05  113.83  3.000
 LH5  C07  C04  N01  125.45  3.000
 LH5  N05  C04  N01  120.59  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
 LH5  CONST_01  C15  C07  C08  C10     0.00   0.0  0
 LH5  CONST_02  C15  C13  C12  C10     0.00   0.0  0
 LH5  CONST_03  C08  C10  C12  C13     0.00   0.0  0
 LH5  CONST_04  C08  C07  C15  C13     0.00   0.0  0
 LH5  CONST_05  C25  N27  C28  C20     0.00   0.0  0
 LH5  CONST_06  C25  C23  C21  C20     0.00   0.0  0
 LH5  CONST_07  N27  C28  C20  C21     0.00   0.0  0
 LH5  CONST_08  N27  C25  C23  C21     0.00   0.0  0
 LH5  CONST_09  C23  C21  C20  C28     0.00   0.0  0
 LH5  CONST_10  C23  C25  N27  C28     0.00   0.0  0
 LH5  CONST_11  C12  C10  C08  C07     0.00   0.0  0
 LH5  CONST_12  C12  C13  C15  C07     0.00   0.0  0
 LH5  CONST_13  C40  C42  C44  C35     0.00   0.0  0
 LH5  CONST_14  C40  C38  C36  C35     0.00   0.0  0
 LH5  CONST_15  C42  C44  C35  C36     0.00   0.0  0
 LH5  CONST_16  C42  C40  C38  C36     0.00   0.0  0
 LH5  CONST_17  C44  C42  C40  C38     0.00   0.0  0
 LH5  CONST_18  C44  C35  C36  C38     0.00   0.0  0
 LH5  CONST_19  C30  C12  C13  C15   180.00   0.0  0
 LH5  CONST_20  C30  C12  C10  C08   180.00   0.0  0
 LH5  CONST_21  C04  C07  C08  C10   180.00   0.0  0
 LH5  CONST_22  C04  C07  C15  C13   180.00   0.0  0
 LH5  CONST_23  N27  C28  C20  C17   180.00   0.0  0
 LH5  CONST_24  C23  C21  C20  C17   180.00   0.0  0
 LH5  CONST_25  O16  C15  C07  C08   180.00   0.0  0
 LH5  CONST_26  O16  C15  C13  C12   180.00   0.0  0
 LH5  CONST_27  H2   C13  C12  C10   180.00   0.0  0
 LH5  CONST_28  H1   C10  C12  C13   180.00   0.0  0
 LH5  CONST_29  H10  C08  C07  C15   180.00   0.0  0
 LH5  CONST_30  H11  C23  C21  C20   180.00   0.0  0
 LH5  CONST_31  H6   C28  C20  C21   180.00   0.0  0
 LH5  CONST_32  H12  C25  C23  C21   180.00   0.0  0
 LH5  CONST_33  H5   C21  C20  C28   180.00   0.0  0
 LH5  CONST_34  H16  C36  C35  C32     0.00   0.0  0
 LH5  CONST_35  H19  C42  C44  C35   180.00   0.0  0
 LH5  CONST_36  H17  C38  C36  C35   180.00   0.0  0
 LH5  CONST_37  H18  C40  C38  C36   180.00   0.0  0
 LH5  CONST_38  H7   N01  C04  C07     0.00   0.0  0
 LH5  CONST_39  H8   N05  C04  C07   180.00   0.0  0
 LH5  Var_01    C44  B45  O48  C30    -7.51  30.0  1
 LH5  Var_02    C44  C35  C32  C30    34.44  30.0  1
 LH5  Var_03    O48  B45  C44  C35   -14.16  30.0  1
 LH5  Var_04    N01  C04  C07  C15   -52.51  30.0  2
 LH5  Var_05    C20  C17  O16  C15  -174.96  30.0  3
 LH5  Var_06    C07  C15  O16  C17   174.90  30.0  2
 LH5  Var_07    O16  C17  C20  C21    57.28  30.0  2

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
 LH5  chir_01  C30  O48  C12  C32  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
 LH5  plan-1  C17  0.020
 LH5  plan-1  C20  0.020
 LH5  plan-1  C21  0.020
 LH5  plan-1  C28  0.020
 LH5  plan-1  C23  0.020
 LH5  plan-1  C25  0.020
 LH5  plan-1  N27  0.020
 LH5  plan-1  H5   0.020
 LH5  plan-1  H6   0.020
 LH5  plan-1  H11  0.020
 LH5  plan-1  H12  0.020
 LH5  plan-2  C10  0.020
 LH5  plan-2  C13  0.020
 LH5  plan-2  C15  0.020
 LH5  plan-2  C07  0.020
 LH5  plan-2  C08  0.020
 LH5  plan-2  C12  0.020
 LH5  plan-2  O16  0.020
 LH5  plan-2  C30  0.020
 LH5  plan-2  H1   0.020
 LH5  plan-2  H2   0.020
 LH5  plan-2  H10  0.020
 LH5  plan-2  C04  0.020
 LH5  plan-3  C32  0.020
 LH5  plan-3  C35  0.020
 LH5  plan-3  C36  0.020
 LH5  plan-3  C38  0.020
 LH5  plan-3  C40  0.020
 LH5  plan-3  C42  0.020
 LH5  plan-3  C44  0.020
 LH5  plan-3  B45  0.020
 LH5  plan-3  H16  0.020
 LH5  plan-3  H17  0.020
 LH5  plan-3  H18  0.020
 LH5  plan-3  H19  0.020
 LH5  plan-4  N01  0.020
 LH5  plan-4  N05  0.020
 LH5  plan-4  C07  0.020
 LH5  plan-4  H7   0.020
 LH5  plan-4  H8   0.020
 LH5  plan-4  H9   0.020
 LH5  plan-4  C04  0.020

