# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:10:09 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(cc1)C(=O)N[C@H]2Cc3cccc(C(O)=O)c3O[B-]2(O)O
#
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
 OK3  OK3  '(4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid'  ligand  44  26  .  2021-08-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OK3
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
 OK3  N01   N  NH2    0  -0.793  55.3350  10.6826  30.5524
 OK3  C02   C  CH2    0  -0.339  55.2765  11.6786  29.4974
 OK3  C03   C  CR6    0   0.088  56.1581  11.3187  28.3291
 OK3  C04   C  CR16   0  -0.296  55.7577  11.6105  27.0279
 OK3  C05   C  CR16   0  -0.261  56.5742  11.3216  25.9463
 OK3  C06   C  CR6    0  -0.044  57.8086  10.7071  26.1354
 OK3  C07   C  CR16   0  -0.281  58.2144  10.4154  27.4369
 OK3  C08   C  CR16   0  -0.274  57.4001  10.7173  28.5176
 OK3  C09   C  C      0   0.520  58.6573  10.4171  24.9357
 OK3  O10   O  O      0  -0.511  58.5321  11.0839  23.9107
 OK3  N11   N  NH1    0  -0.652  59.5179   9.4042  25.0604
 OK3  C12   C  CH1    0  -0.286  60.4587   8.9796  24.0374
 OK3  C13   C  CH2    0  -0.517  61.5283  10.0482  23.7953
 OK3  C14   C  CR6    0   0.028  62.3325  10.2777  25.0384
 OK3  C15   C  CR6    0   0.401  62.7459   9.1434  25.7771
 OK3  O16   O  OC2    0  -0.535  62.4428   7.9441  25.3508
 OK3  B17   B  B     -1   0.505  61.2146   7.6004  24.4986
 OK3  O18   O  OB     0  -0.713  61.6723   6.9192  23.3033
 OK3  O19   O  OB     0  -0.733  60.3509   6.7947  25.3574
 OK3  C20   C  CR6    0  -0.226  63.5106   9.3361  26.9507
 OK3  C21   C  CR16   0  -0.276  63.8466  10.6411  27.3443
 OK3  C22   C  CR16   0  -0.273  63.4314  11.7383  26.6269
 OK3  C23   C  CR16   0  -0.319  62.6673  11.5412  25.4750
 OK3  C24   C  C      0   0.520  63.9923   8.2543  27.8336
 OK3  O25   O  O      0  -0.468  64.6981   8.4540  28.8021
 OK3  O26   O  OH1    0  -0.584  63.5933   7.0281  27.5169
 OK3  H011  H  HNH2   0   0.354  54.8146  11.0151  31.3538
 OK3  H012  H  HNH2   0   0.344  54.8655   9.8394  30.2466
 OK3  H021  H  HCH2   0   0.217  54.2634  11.8740  29.1213
 OK3  H022  H  HCH2   0   0.243  55.6263  12.6283  29.9136
 OK3  H04   H  HCR6   0   0.250  54.7910  12.0691  26.8550
 OK3  H08   H  HCR6   0   0.251  57.7330  10.4837  29.5203
 OK3  H05   H  HCR6   0   0.252  56.2407  11.5617  24.9453
 OK3  H07   H  HCR6   0   0.247  59.1835   9.9690  27.6252
 OK3  H11   H  HNH1   0   0.395  59.4377   8.7992  25.8626
 OK3  H12   H  HCH1   0   0.204  59.9096   8.8197  23.1015
 OK3  H131  H  HCH2   0   0.238  62.1777   9.6956  22.9861
 OK3  H132  H  HCH2   0   0.237  61.1029  10.9933  23.4530
 OK3  H23   H  HCR6   0   0.242  62.3316  12.3980  24.9007
 OK3  H18   H  H      0   0.441  62.1196   6.0986  23.5276
 OK3  H19   H  H      0   0.438  60.8652   6.3677  26.0471
 OK3  H21   H  HCR6   0   0.250  64.4365  10.7805  28.2400
 OK3  H22   H  HCR6   0   0.243  63.6895  12.7374  26.9513
 OK3  H26   H  HOH1   0   0.472  63.9528   6.4150  28.1749

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
 OK3  N01  C02   single    1.452  0.020  1.452
 OK3  C02  C03   single    1.507  0.020  1.507
 OK3  C03  C04   aromatic  1.392  0.020  1.392
 OK3  C03  C08   aromatic  1.393  0.020  1.393
 OK3  C04  C05   aromatic  1.386  0.020  1.386
 OK3  C05  C06   aromatic  1.392  0.020  1.392
 OK3  C06  C07   aromatic  1.394  0.020  1.394
 OK3  C06  C09   single    1.498  0.020  1.498
 OK3  C07  C08   aromatic  1.386  0.020  1.386
 OK3  C09  O10   double    1.229  0.020  1.229
 OK3  C09  N11   single    1.335  0.020  1.335
 OK3  N11  C12   single    1.453  0.020  1.453
 OK3  C12  C13   single    1.531  0.020  1.531
 OK3  C12  B17   single    1.639  0.020  1.639
 OK3  C13  C14   single    1.498  0.020  1.498
 OK3  C14  C15   aromatic  1.415  0.020  1.415
 OK3  C14  C23   aromatic  1.378  0.020  1.378
 OK3  C15  O16   single    1.308  0.020  1.308
 OK3  C15  C20   aromatic  1.414  0.020  1.414
 OK3  O16  B17   single    1.534  0.020  1.534
 OK3  B17  O18   single    1.450  0.020  1.450
 OK3  B17  O19   single    1.460  0.020  1.460
 OK3  C20  C21   aromatic  1.404  0.020  1.404
 OK3  C20  C24   single    1.477  0.020  1.477
 OK3  C21  C22   aromatic  1.375  0.020  1.375
 OK3  C22  C23   aromatic  1.396  0.020  1.396
 OK3  C24  O25   double    1.215  0.020  1.215
 OK3  C24  O26   single    1.328  0.020  1.328
 OK3  N01  H011  single    0.890  0.020  1.040
 OK3  N01  H012  single    0.890  0.020  1.040
 OK3  C02  H021  single    0.970  0.020  1.090
 OK3  C02  H022  single    0.970  0.020  1.090
 OK3  C04  H04   single    0.930  0.020  1.080
 OK3  C08  H08   single    0.930  0.020  1.080
 OK3  C05  H05   single    0.930  0.020  1.080
 OK3  C07  H07   single    0.930  0.020  1.080
 OK3  N11  H11   single    0.860  0.020  1.020
 OK3  C12  H12   single    0.970  0.020  1.090
 OK3  C13  H131  single    0.970  0.020  1.090
 OK3  C13  H132  single    0.970  0.020  1.090
 OK3  C23  H23   single    0.930  0.020  1.080
 OK3  O18  H18   single    0.850  0.020  0.980
 OK3  O19  H19   single    0.850  0.020  0.980
 OK3  C21  H21   single    0.930  0.020  1.080
 OK3  C22  H22   single    0.930  0.020  1.080
 OK3  O26  H26   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
 OK3  H012  N01  H011  105.93  3.000
 OK3  H012  N01  C02   109.46  3.000
 OK3  H011  N01  C02   109.23  3.000
 OK3  H022  C02  H021  105.71  3.000
 OK3  H022  C02  C03   108.37  3.000
 OK3  H021  C02  C03   108.46  3.000
 OK3  H022  C02  N01   107.82  3.000
 OK3  H021  C02  N01   114.08  3.000
 OK3  C03   C02  N01   112.08  3.000
 OK3  C08   C03  C04   118.25  3.000
 OK3  C08   C03  C02   121.32  3.000
 OK3  C04   C03  C02   120.41  3.000
 OK3  H04   C04  C05   119.29  3.000
 OK3  H04   C04  C03   119.62  3.000
 OK3  C05   C04  C03   121.09  3.000
 OK3  H05   C05  C06   119.81  3.000
 OK3  H05   C05  C04   119.62  3.000
 OK3  C06   C05  C04   120.57  3.000
 OK3  C09   C06  C07   122.84  3.000
 OK3  C09   C06  C05   118.63  3.000
 OK3  C07   C06  C05   118.52  3.000
 OK3  H07   C07  C08   118.66  3.000
 OK3  H07   C07  C06   120.58  3.000
 OK3  C08   C07  C06   120.74  3.000
 OK3  H08   C08  C07   119.64  3.000
 OK3  H08   C08  C03   119.54  3.000
 OK3  C07   C08  C03   120.82  3.000
 OK3  N11   C09  O10   123.72  3.000
 OK3  N11   C09  C06   115.94  3.000
 OK3  O10   C09  C06   120.34  3.000
 OK3  H11   N11  C12   115.87  3.000
 OK3  H11   N11  C09   118.58  3.000
 OK3  C12   N11  C09   124.98  3.000
 OK3  H12   C12  B17   110.38  3.000
 OK3  H12   C12  C13   108.45  3.000
 OK3  B17   C12  C13   108.03  3.000
 OK3  H12   C12  N11   108.62  3.000
 OK3  B17   C12  N11   110.27  3.000
 OK3  C13   C12  N11   111.08  3.000
 OK3  H132  C13  H131  106.14  3.000
 OK3  H132  C13  C14   109.67  3.000
 OK3  H131  C13  C14   110.11  3.000
 OK3  H132  C13  C12   112.44  3.000
 OK3  H131  C13  C12   107.83  3.000
 OK3  C14   C13  C12   110.53  3.000
 OK3  C23   C14  C15   119.90  3.000
 OK3  C23   C14  C13   122.26  3.000
 OK3  C15   C14  C13   117.84  3.000
 OK3  C20   C15  O16   121.38  3.000
 OK3  C20   C15  C14   118.81  3.000
 OK3  O16   C15  C14   119.80  3.000
 OK3  B17   O16  C15   124.88  3.000
 OK3  O19   B17  O18   114.35  3.000
 OK3  O19   B17  O16   105.69  3.000
 OK3  O18   B17  O16   108.09  3.000
 OK3  O19   B17  C12   110.91  3.000
 OK3  O18   B17  C12   108.00  3.000
 OK3  O16   B17  C12   109.70  3.000
 OK3  H18   O18  B17   110.83  3.000
 OK3  H19   O19  B17   110.54  3.000
 OK3  C24   C20  C21   115.79  3.000
 OK3  C24   C20  C15   124.94  3.000
 OK3  C21   C20  C15   119.27  3.000
 OK3  H21   C21  C22   119.60  3.000
 OK3  H21   C21  C20   118.85  3.000
 OK3  C22   C21  C20   121.55  3.000
 OK3  H22   C22  C23   120.56  3.000
 OK3  H22   C22  C21   120.56  3.000
 OK3  C23   C22  C21   118.88  3.000
 OK3  H23   C23  C22   119.65  3.000
 OK3  H23   C23  C14   118.77  3.000
 OK3  C22   C23  C14   121.59  3.000
 OK3  O26   C24  O25   121.10  3.000
 OK3  O26   C24  C20   115.83  3.000
 OK3  O25   C24  C20   123.07  3.000
 OK3  H26   O26  C24   108.11  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
 OK3  CONST_01  C06   C05  C04  C03    0.00   0.0  0
 OK3  CONST_02  C06   C07  C08  C03    0.00   0.0  0
 OK3  CONST_03  C07   C08  C03  C04    0.00   0.0  0
 OK3  CONST_04  C07   C06  C05  C04    0.00   0.0  0
 OK3  CONST_05  C08   C03  C04  C05    0.00   0.0  0
 OK3  CONST_06  C08   C07  C06  C05    0.00   0.0  0
 OK3  CONST_07  C21   C20  C15  C14    0.00   0.0  0
 OK3  CONST_08  C21   C22  C23  C14    0.00   0.0  0
 OK3  CONST_09  C22   C23  C14  C15    0.00   0.0  0
 OK3  CONST_10  C22   C21  C20  C15    0.00   0.0  0
 OK3  CONST_11  C23   C14  C15  C20    0.00   0.0  0
 OK3  CONST_12  C23   C22  C21  C20    0.00   0.0  0
 OK3  CONST_13  C05   C04  C03  C02  180.00   0.0  0
 OK3  CONST_14  C07   C08  C03  C02  180.00   0.0  0
 OK3  CONST_15  C09   C06  C05  C04  180.00   0.0  0
 OK3  CONST_16  C09   C06  C07  C08  180.00   0.0  0
 OK3  CONST_17  C24   C20  C15  C14  180.00   0.0  0
 OK3  CONST_18  C24   C20  C15  O16    0.00   0.0  0
 OK3  CONST_19  C24   C20  C21  C22  180.00   0.0  0
 OK3  CONST_20  H05   C05  C04  C03  180.00   0.0  0
 OK3  CONST_21  H07   C07  C08  C03  180.00   0.0  0
 OK3  CONST_22  H08   C08  C03  C04  180.00   0.0  0
 OK3  CONST_23  H04   C04  C05  C06  180.00   0.0  0
 OK3  CONST_24  H23   C23  C14  C13    0.00   0.0  0
 OK3  CONST_25  H22   C22  C23  C14  180.00   0.0  0
 OK3  CONST_26  H21   C21  C20  C15  180.00   0.0  0
 OK3  CONST_27  C12   N11  C09  C06  180.00   0.0  0
 OK3  CONST_28  C12   N11  C09  O10    0.00   0.0  0
 OK3  CONST_29  H11   N11  C09  C06    0.00   0.0  0
 OK3  CONST_30  H26   O26  C24  C20  180.00   0.0  0
 OK3  Var_01    C15   C14  C13  C12   43.41  30.0  1
 OK3  Var_02    C20   C15  O16  B17  153.53  30.0  1
 OK3  Var_03    O18   B17  O16  C15  125.11  30.0  1
 OK3  Var_04    C04   C03  C02  N01  143.70  30.0  2
 OK3  Var_05    O10   C09  C06  C05   25.24  30.0  2
 OK3  Var_06    O25   C24  C20  C15  176.60  30.0  2
 OK3  Var_07    H011  N01  C02  C03  173.61  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
 OK3  chir_01  C12  N11  C13  B17  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
 OK3  plan-1  C02  0.020
 OK3  plan-1  C03  0.020
 OK3  plan-1  C04  0.020
 OK3  plan-1  C05  0.020
 OK3  plan-1  C06  0.020
 OK3  plan-1  C07  0.020
 OK3  plan-1  C08  0.020
 OK3  plan-1  C09  0.020
 OK3  plan-1  H04  0.020
 OK3  plan-1  H08  0.020
 OK3  plan-1  H05  0.020
 OK3  plan-1  H07  0.020
 OK3  plan-2  C13  0.020
 OK3  plan-2  C14  0.020
 OK3  plan-2  C15  0.020
 OK3  plan-2  O16  0.020
 OK3  plan-2  C20  0.020
 OK3  plan-2  C21  0.020
 OK3  plan-2  C22  0.020
 OK3  plan-2  C23  0.020
 OK3  plan-2  C24  0.020
 OK3  plan-2  H23  0.020
 OK3  plan-2  H21  0.020
 OK3  plan-2  H22  0.020
 OK3  plan-3  C06  0.020
 OK3  plan-3  C09  0.020
 OK3  plan-3  O10  0.020
 OK3  plan-3  N11  0.020
 OK3  plan-3  C12  0.020
 OK3  plan-3  H11  0.020
 OK3  plan-4  C20  0.020
 OK3  plan-4  C24  0.020
 OK3  plan-4  O25  0.020
 OK3  plan-4  O26  0.020
 OK3  plan-4  H26  0.020

