# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 05:58:07 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-[(3~{R})-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
 RH5  RH5  4-[(3~{R})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide  ligand  48  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RH5
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
 RH5  C10  C  CR16  0  -0.334   0.8742   2.3679  -0.0455
 RH5  C12  C  CR6   0   0.106   0.9357   1.0063   0.2105
 RH5  C13  C  CR16  0  -0.438  -0.2374   0.2585   0.2423
 RH5  C15  C  CR6   0   0.406  -1.4717   0.8542   0.0076
 RH5  C17  C  CH2   0  -0.272  -2.6224  -1.2212   0.2277
 RH5  C20  C  CR6   0   0.007  -4.0329  -1.7021   0.0959
 RH5  C21  C  CR16  0  -0.166  -4.7274  -1.5869  -1.1038
 RH5  C28  C  CR16  0  -0.097  -4.6966  -2.2757   1.1720
 RH5  N01  N  N     0  -0.633  -3.6999   2.5517  -1.3950
 RH5  N05  N  NH2   0  -0.793  -3.0102   4.0709   0.1786
 RH5  C07  C  CR6   0  -0.141  -1.5403   2.2317  -0.2533
 RH5  C08  C  CR16  0  -0.236  -0.3600   2.9643  -0.2613
 RH5  O16  O  O2    0  -0.459  -2.6388   0.1865   0.0466
 RH5  C23  C  CR16  0  -0.319  -6.0300  -2.0483  -1.1717
 RH5  C25  C  CR16  0  -0.063  -6.5932  -2.6119  -0.0341
 RH5  N27  N  N     0  -0.401  -5.9447  -2.7263   1.1173
 RH5  C30  C  CH1   0   0.014   2.2427   0.2833   0.4039
 RH5  C32  C  CH2   0  -0.534   2.7426  -0.2908  -0.9187
 RH5  C35  C  CR6   0   0.056   4.0799  -0.9597  -0.7565
 RH5  C36  C  CR16  0  -0.295   4.4349  -2.0723  -1.5108
 RH5  C38  C  CR16  0  -0.261   5.6875  -2.6502  -1.3542
 RH5  C40  C  CR16  0  -0.243   6.5957  -2.1201  -0.4450
 RH5  C42  C  CR16  0  -0.329   6.2427  -1.0091   0.3064
 RH5  C44  C  CR6   0  -0.111   4.9870  -0.4181   0.1619
 RH5  B45  B  B     0   0.511   4.5177   0.8304   0.9652
 RH5  O46  O  OH1   0  -0.615   5.4079   1.5958   1.6427
 RH5  O48  O  O2    0  -0.471   3.1948   1.1655   0.9726
 RH5  H1   H  HCR6  0   0.256   1.7699   2.9726  -0.0732
 RH5  H2   H  HCR6  0   0.285  -0.1684  -0.7978   0.4692
 RH5  H3   H  HCH2  0   0.251  -2.2190  -1.4830   1.2115
 RH5  H4   H  HCH2  0   0.252  -1.9881  -1.6940  -0.5295
 RH5  H5   H  HCR6  0   0.271  -4.2551  -1.1498  -1.9750
 RH5  H6   H  HCR6  0   0.263  -4.1879  -2.3769   2.1262
 RH5  H7   H  H     0   0.329  -3.3862   1.7234  -1.8842
 RH5  H8   H  HNH2  0   0.382  -3.9202   4.5002   0.1195
 RH5  H9   H  HNH2  0   0.392  -2.5697   4.1477   1.0798
 RH5  H10  H  HCR6  0   0.264  -0.4055   4.0281  -0.4562
 RH5  H11  H  HCR6  0   0.275  -6.6026  -1.9808  -2.0864
 RH5  H12  H  HCR6  0   0.268  -7.6105  -2.9868  -0.0586
 RH5  H13  H  HCH1  0   0.252   2.0785  -0.5480   1.1018
 RH5  H14  H  HCH2  0   0.272   2.0033  -0.9950  -1.3048
 RH5  H15  H  HCH2  0   0.267   2.8165   0.5165  -1.6568
 RH5  H16  H  HCR6  0   0.249   3.7321  -2.4936  -2.2199
 RH5  H17  H  HCR6  0   0.259   5.9547  -3.5204  -1.9404
 RH5  H18  H  HCR6  0   0.254   7.5714  -2.5729  -0.3250
 RH5  H19  H  HCR6  0   0.252   6.9532  -0.5999   1.0145
 RH5  H20  H  HOH1  0   0.489   5.0104   2.3319   2.1206
 RH5  C04  C  C     0   0.331  -2.8356   2.9189  -0.5303

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
 RH5  N01  C04  double    1.277  0.020  1.277
 RH5  C08  C10  aromatic  1.388  0.020  1.388
 RH5  C08  C07  aromatic  1.389  0.020  1.389
 RH5  C04  N05  single    1.364  0.020  1.364
 RH5  C04  C07  single    1.492  0.020  1.492
 RH5  C10  C12  aromatic  1.387  0.020  1.387
 RH5  C07  C15  aromatic  1.404  0.020  1.404
 RH5  O46  B45  single    1.355  0.020  1.355
 RH5  O48  B45  single    1.365  0.020  1.365
 RH5  O48  C30  single    1.417  0.020  1.417
 RH5  C12  C30  single    1.506  0.020  1.506
 RH5  C12  C13  aromatic  1.392  0.020  1.392
 RH5  B45  C44  single    1.557  0.020  1.557
 RH5  C15  C13  aromatic  1.390  0.020  1.390
 RH5  C15  O16  single    1.345  0.020  1.345
 RH5  C30  C32  single    1.526  0.020  1.526
 RH5  O16  C17  single    1.419  0.020  1.419
 RH5  C44  C42  aromatic  1.395  0.020  1.395
 RH5  C44  C35  aromatic  1.400  0.020  1.400
 RH5  C32  C35  single    1.504  0.020  1.504
 RH5  C42  C40  aromatic  1.387  0.020  1.387
 RH5  C28  N27  aromatic  1.328  0.020  1.328
 RH5  C28  C20  aromatic  1.388  0.020  1.388
 RH5  C35  C36  aromatic  1.390  0.020  1.390
 RH5  C17  C20  single    1.496  0.020  1.496
 RH5  N27  C25  aromatic  1.326  0.020  1.326
 RH5  C20  C21  aromatic  1.391  0.020  1.391
 RH5  C40  C38  aromatic  1.390  0.020  1.390
 RH5  C25  C23  aromatic  1.389  0.020  1.389
 RH5  C36  C38  aromatic  1.388  0.020  1.388
 RH5  C21  C23  aromatic  1.384  0.020  1.384
 RH5  C10  H1   single    0.930  0.020  1.080
 RH5  C13  H2   single    0.930  0.020  1.080
 RH5  C17  H3   single    0.970  0.020  1.090
 RH5  C17  H4   single    0.970  0.020  1.090
 RH5  C21  H5   single    0.930  0.020  1.080
 RH5  C28  H6   single    0.930  0.020  1.080
 RH5  N01  H7   single    0.890  0.020  1.040
 RH5  N05  H8   single    0.890  0.020  1.040
 RH5  N05  H9   single    0.890  0.020  1.040
 RH5  C08  H10  single    0.930  0.020  1.080
 RH5  C23  H11  single    0.930  0.020  1.080
 RH5  C25  H12  single    0.930  0.020  1.080
 RH5  C30  H13  single    0.970  0.020  1.090
 RH5  C32  H14  single    0.970  0.020  1.090
 RH5  C32  H15  single    0.970  0.020  1.090
 RH5  C36  H16  single    0.930  0.020  1.080
 RH5  C38  H17  single    0.930  0.020  1.080
 RH5  C40  H18  single    0.930  0.020  1.080
 RH5  C42  H19  single    0.930  0.020  1.080
 RH5  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
 RH5  H1   C10  C08  119.50  3.000
 RH5  H1   C10  C12  121.15  3.000
 RH5  C08  C10  C12  119.35  3.000
 RH5  C30  C12  C13  118.07  3.000
 RH5  C13  C12  C10  119.64  3.000
 RH5  C30  C12  C10  122.24  3.000
 RH5  H2   C13  C15  120.66  3.000
 RH5  H2   C13  C12  118.39  3.000
 RH5  C15  C13  C12  120.94  3.000
 RH5  O16  C15  C07  116.75  3.000
 RH5  O16  C15  C13  123.55  3.000
 RH5  C07  C15  C13  119.68  3.000
 RH5  H4   C17  H3   107.73  3.000
 RH5  H4   C17  O16  110.28  3.000
 RH5  H3   C17  O16  110.85  3.000
 RH5  H4   C17  C20  110.27  3.000
 RH5  H3   C17  C20  110.47  3.000
 RH5  O16  C17  C20  107.26  3.000
 RH5  C28  C20  C21  117.64  3.000
 RH5  C21  C20  C17  121.34  3.000
 RH5  C28  C20  C17  121.02  3.000
 RH5  H5   C21  C23  120.37  3.000
 RH5  H5   C21  C20  120.63  3.000
 RH5  C23  C21  C20  119.00  3.000
 RH5  H6   C28  N27  116.41  3.000
 RH5  H6   C28  C20  119.70  3.000
 RH5  N27  C28  C20  123.89  3.000
 RH5  H7   N01  C04  110.67  3.000
 RH5  H9   N05  H8   114.55  3.000
 RH5  H9   N05  C04  118.30  3.000
 RH5  H8   N05  C04  116.41  3.000
 RH5  C08  C07  C04  119.57  3.000
 RH5  C04  C07  C15  121.93  3.000
 RH5  C08  C07  C15  118.50  3.000
 RH5  H10  C08  C07  118.92  3.000
 RH5  H10  C08  C10  119.20  3.000
 RH5  C07  C08  C10  121.87  3.000
 RH5  C17  O16  C15  119.08  3.000
 RH5  H11  C23  C25  120.24  3.000
 RH5  H11  C23  C21  121.28  3.000
 RH5  C25  C23  C21  118.48  3.000
 RH5  H12  C25  N27  116.64  3.000
 RH5  H12  C25  C23  120.14  3.000
 RH5  N27  C25  C23  123.22  3.000
 RH5  C25  N27  C28  117.77  3.000
 RH5  H13  C30  O48  108.47  3.000
 RH5  H13  C30  C32  108.37  3.000
 RH5  O48  C30  C32  111.22  3.000
 RH5  H13  C30  C12  108.38  3.000
 RH5  C32  C30  C12  110.71  3.000
 RH5  O48  C30  C12  109.61  3.000
 RH5  H15  C32  H14  106.41  3.000
 RH5  H15  C32  C35  109.89  3.000
 RH5  H14  C32  C35  110.70  3.000
 RH5  H15  C32  C30  109.18  3.000
 RH5  H14  C32  C30  109.10  3.000
 RH5  C35  C32  C30  111.42  3.000
 RH5  C44  C35  C36  120.00  3.000
 RH5  C36  C35  C32  121.63  3.000
 RH5  C44  C35  C32  118.35  3.000
 RH5  H16  C36  C38  119.81  3.000
 RH5  H16  C36  C35  120.04  3.000
 RH5  C38  C36  C35  120.16  3.000
 RH5  H17  C38  C40  119.96  3.000
 RH5  H17  C38  C36  119.75  3.000
 RH5  C40  C38  C36  120.29  3.000
 RH5  H18  C40  C42  120.30  3.000
 RH5  H18  C40  C38  120.13  3.000
 RH5  C42  C40  C38  119.57  3.000
 RH5  H19  C42  C44  119.87  3.000
 RH5  H19  C42  C40  119.32  3.000
 RH5  C44  C42  C40  120.81  3.000
 RH5  B45  C44  C42  123.88  3.000
 RH5  C42  C44  C35  119.16  3.000
 RH5  B45  C44  C35  116.96  3.000
 RH5  O48  B45  O46  119.69  3.000
 RH5  O48  B45  C44  119.46  3.000
 RH5  O46  B45  C44  120.84  3.000
 RH5  H20  O46  B45  114.10  3.000
 RH5  B45  O48  C30  119.75  3.000
 RH5  C07  C04  N05  113.80  3.000
 RH5  C07  C04  N01  125.52  3.000
 RH5  N05  C04  N01  120.56  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
 RH5  CONST_01  C15  C07  C08  C10     0.00   0.0  0
 RH5  CONST_02  C15  C13  C12  C10     0.00   0.0  0
 RH5  CONST_03  C07  C08  C10  C12     0.00   0.0  0
 RH5  CONST_04  C07  C15  C13  C12     0.00   0.0  0
 RH5  CONST_05  C08  C10  C12  C13     0.00   0.0  0
 RH5  CONST_06  C08  C07  C15  C13     0.00   0.0  0
 RH5  CONST_07  C25  N27  C28  C20     0.00   0.0  0
 RH5  CONST_08  C25  C23  C21  C20     0.00   0.0  0
 RH5  CONST_09  N27  C28  C20  C21     0.00   0.0  0
 RH5  CONST_10  N27  C25  C23  C21     0.00   0.0  0
 RH5  CONST_11  C23  C25  N27  C28     0.00   0.0  0
 RH5  CONST_12  C23  C21  C20  C28     0.00   0.0  0
 RH5  CONST_13  C40  C42  C44  C35     0.00   0.0  0
 RH5  CONST_14  C40  C38  C36  C35     0.00   0.0  0
 RH5  CONST_15  C42  C44  C35  C36     0.00   0.0  0
 RH5  CONST_16  C42  C40  C38  C36     0.00   0.0  0
 RH5  CONST_17  C44  C42  C40  C38     0.00   0.0  0
 RH5  CONST_18  C44  C35  C36  C38     0.00   0.0  0
 RH5  CONST_19  C30  C12  C13  C15   180.00   0.0  0
 RH5  CONST_20  C30  C12  C10  C08   180.00   0.0  0
 RH5  CONST_21  C04  C07  C08  C10   180.00   0.0  0
 RH5  CONST_22  O16  C15  C13  C12   180.00   0.0  0
 RH5  CONST_23  C04  C07  C15  C13   180.00   0.0  0
 RH5  CONST_24  N27  C28  C20  C17   180.00   0.0  0
 RH5  CONST_25  C23  C21  C20  C17   180.00   0.0  0
 RH5  CONST_26  O16  C15  C07  C08   180.00   0.0  0
 RH5  CONST_27  H2   C13  C12  C10   180.00   0.0  0
 RH5  CONST_28  H10  C08  C10  C12   180.00   0.0  0
 RH5  CONST_29  H1   C10  C12  C13   180.00   0.0  0
 RH5  CONST_30  H11  C23  C21  C20   180.00   0.0  0
 RH5  CONST_31  H6   C28  C20  C21   180.00   0.0  0
 RH5  CONST_32  H12  C25  C23  C21   180.00   0.0  0
 RH5  CONST_33  H5   C21  C20  C28   180.00   0.0  0
 RH5  CONST_34  H16  C36  C35  C32     0.00   0.0  0
 RH5  CONST_35  H19  C42  C44  C35   180.00   0.0  0
 RH5  CONST_36  H17  C38  C36  C35   180.00   0.0  0
 RH5  CONST_37  H18  C40  C38  C36   180.00   0.0  0
 RH5  CONST_38  H7   N01  C04  C07     0.00   0.0  0
 RH5  CONST_39  H8   N05  C04  C07   180.00   0.0  0
 RH5  Var_01    C44  B45  O48  C30     8.39  30.0  1
 RH5  Var_02    C44  C35  C32  C30   -34.50  30.0  1
 RH5  Var_03    O48  B45  C44  C35    14.12  30.0  1
 RH5  Var_04    N01  C04  C07  C15   -51.44  30.0  2
 RH5  Var_05    C20  C17  O16  C15  -174.55  30.0  3
 RH5  Var_06    C07  C15  O16  C17   176.30  30.0  1
 RH5  Var_07    O16  C17  C20  C21    64.41  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
 RH5  chir_01  C30  O48  C12  C32  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
 RH5  plan-1  C17  0.020
 RH5  plan-1  C20  0.020
 RH5  plan-1  C21  0.020
 RH5  plan-1  C28  0.020
 RH5  plan-1  C23  0.020
 RH5  plan-1  C25  0.020
 RH5  plan-1  N27  0.020
 RH5  plan-1  H5   0.020
 RH5  plan-1  H6   0.020
 RH5  plan-1  H11  0.020
 RH5  plan-1  H12  0.020
 RH5  plan-2  C10  0.020
 RH5  plan-2  C12  0.020
 RH5  plan-2  C13  0.020
 RH5  plan-2  C15  0.020
 RH5  plan-2  C07  0.020
 RH5  plan-2  C08  0.020
 RH5  plan-2  O16  0.020
 RH5  plan-2  C30  0.020
 RH5  plan-2  H1   0.020
 RH5  plan-2  H2   0.020
 RH5  plan-2  H10  0.020
 RH5  plan-2  C04  0.020
 RH5  plan-3  C32  0.020
 RH5  plan-3  C35  0.020
 RH5  plan-3  C36  0.020
 RH5  plan-3  C38  0.020
 RH5  plan-3  C40  0.020
 RH5  plan-3  C42  0.020
 RH5  plan-3  C44  0.020
 RH5  plan-3  B45  0.020
 RH5  plan-3  H16  0.020
 RH5  plan-3  H17  0.020
 RH5  plan-3  H18  0.020
 RH5  plan-3  H19  0.020
 RH5  plan-4  N01  0.020
 RH5  plan-4  N05  0.020
 RH5  plan-4  C07  0.020
 RH5  plan-4  H7   0.020
 RH5  plan-4  H8   0.020
 RH5  plan-4  H9   0.020
 RH5  plan-4  C04  0.020

