# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 11:05:55 2020
#   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  43  26  .  2021-08-17  2021-08-17  
;
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   7.9372   0.9939   0.9996
 OK3  C02   C  CH2    0  -0.335   7.5026  -0.2580   0.4081
 OK3  C03   C  C      0   0.083   6.0335  -0.2516   0.0702
 OK3  C04   C  C1     0  -0.294   5.5605  -0.9853  -1.0148
 OK3  C05   C  C1     0  -0.261   4.2111  -1.0144  -1.3249
 OK3  C06   C  C      0  -0.047   3.2880  -0.3165  -0.5500
 OK3  C07   C  C1     0  -0.285   3.7605   0.4291   0.5291
 OK3  C08   C  C1     0  -0.275   5.1131   0.4618   0.8330
 OK3  C09   C  C      0   0.514   1.8429  -0.3751  -0.9452
 OK3  O10   O  O      0  -0.513   1.5293  -0.6777  -2.0950
 OK3  N11   N  NH1    0  -0.660   0.9531  -0.0800   0.0056
 OK3  C12   C  CH1    0  -0.239  -0.4848  -0.0513  -0.1892
 OK3  C13   C  CH2    0  -0.510  -1.0905  -1.4507  -0.0817
 OK3  C14   C  CR6    0  -0.006  -2.5881  -1.4002  -0.2122
 OK3  C15   C  CR6    0   0.363  -3.3022  -0.2800   0.2613
 OK3  O16   O  OC2    0  -0.527  -2.6932   0.7716   0.7830
 OK3  B17   B  B     -1   0.458  -1.1940   0.9144   0.9122
 OK3  O18   O  OB     0  -0.718  -0.8760   2.3084   0.6341
 OK3  O19   O  OB     0  -0.738  -0.7677   0.4598   2.2373
 OK3  C20   C  CR6    0  -0.185  -4.7060  -0.2496   0.1273
 OK3  C21   C  CR16   0  -0.302  -5.3544  -1.3116  -0.4942
 OK3  C22   C  CR16   0  -0.284  -4.6600  -2.4242  -0.9469
 OK3  C23   C  CR16   0  -0.335  -3.2801  -2.4505  -0.8036
 OK3  C24   C  C      0   0.358  -5.5472   0.9053   0.6441
 OK3  O25   O  O      0  -0.601  -5.3450   1.2847   1.8121
 OK3  O26   O  OC    -1  -0.617  -6.4094   1.3515  -0.1424
 OK3  H011  H  HNH2   0   0.355   8.8926   0.8993   1.3180
 OK3  H012  H  HNH2   0   0.345   7.9461   1.7190   0.2936
 OK3  H021  H  HCH2   0   0.216   8.0641  -0.5479  -0.4903
 OK3  H022  H  HCH2   0   0.245   7.6826  -1.0529   1.1386
 OK3  H04   H  H      0   0.249   6.2588  -1.5389  -1.6320
 OK3  H08   H  H      0   0.251   5.4604   1.0577   1.6666
 OK3  H05   H  H      0   0.252   3.8714  -1.5820  -2.1810
 OK3  H07   H  H      0   0.247   3.0848   1.0204   1.1350
 OK3  H11   H  HNH1   0   0.391   1.2771   0.0726   0.9471
 OK3  H12   H  HCH1   0   0.197  -0.6740   0.3239  -1.2012
 OK3  H131  H  HCH2   0   0.225  -0.6801  -2.1273  -0.8375
 OK3  H132  H  HCH2   0   0.222  -0.8169  -1.8792   0.8895
 OK3  H23   H  HCR6   0   0.228  -2.7172  -3.3024  -1.1706
 OK3  H18   H  H      0   0.437  -1.3049   2.8968   1.2621
 OK3  H19   H  H      0   0.432  -1.0870   1.0433   2.9309
 OK3  H21   H  HCR6   0   0.229  -6.4300  -1.2658  -0.6178
 OK3  H22   H  HCR6   0   0.228  -5.1805  -3.2487  -1.4174

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    1.451  0.020  1.451
 OK3  C02  C03   single    1.507  0.020  1.507
 OK3  C03  C04   aromatic  1.393  0.020  1.393
 OK3  C03  C08   aromatic  1.392  0.020  1.392
 OK3  C04  C05   aromatic  1.385  0.020  1.385
 OK3  C05  C06   aromatic  1.393  0.020  1.393
 OK3  C06  C07   aromatic  1.394  0.020  1.394
 OK3  C06  C09   single    1.499  0.020  1.499
 OK3  C07  C08   aromatic  1.387  0.020  1.387
 OK3  C09  O10   double    1.230  0.020  1.230
 OK3  C09  N11   single    1.335  0.020  1.335
 OK3  N11  C12   single    1.451  0.020  1.451
 OK3  C12  C13   single    1.529  0.020  1.529
 OK3  C12  B17   single    1.627  0.020  1.627
 OK3  C13  C14   single    1.504  0.020  1.504
 OK3  C14  C15   aromatic  1.410  0.020  1.410
 OK3  C14  C23   aromatic  1.390  0.020  1.390
 OK3  C15  O16   single    1.323  0.020  1.323
 OK3  C15  C20   aromatic  1.410  0.020  1.410
 OK3  O16  B17   single    1.511  0.020  1.511
 OK3  B17  O18   single    1.457  0.020  1.457
 OK3  B17  O19   single    1.464  0.020  1.464
 OK3  C20  C21   aromatic  1.391  0.020  1.391
 OK3  C20  C24   single    1.519  0.020  1.519
 OK3  C21  C22   aromatic  1.387  0.020  1.387
 OK3  C22  C23   aromatic  1.388  0.020  1.388
 OK3  C24  O25   deloc     1.245  0.020  1.245
 OK3  C24  O26   deloc     1.249  0.020  1.249
 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

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  106.15  3.000
 OK3  H012  N01  C02   109.66  3.000
 OK3  H011  N01  C02   109.30  3.000
 OK3  H022  C02  H021  105.67  3.000
 OK3  H022  C02  C03   108.23  3.000
 OK3  H021  C02  C03   108.41  3.000
 OK3  H022  C02  N01   107.78  3.000
 OK3  H021  C02  N01   114.08  3.000
 OK3  C03   C02  N01   112.31  3.000
 OK3  C08   C03  C04   118.19  3.000
 OK3  C08   C03  C02   121.58  3.000
 OK3  C04   C03  C02   120.23  3.000
 OK3  H04   C04  C05   119.31  3.000
 OK3  H04   C04  C03   119.60  3.000
 OK3  C05   C04  C03   121.09  3.000
 OK3  H05   C05  C06   119.67  3.000
 OK3  H05   C05  C04   119.61  3.000
 OK3  C06   C05  C04   120.71  3.000
 OK3  C09   C06  C07   123.47  3.000
 OK3  C09   C06  C05   118.20  3.000
 OK3  C07   C06  C05   118.30  3.000
 OK3  H07   C07  C08   118.22  3.000
 OK3  H07   C07  C06   120.90  3.000
 OK3  C08   C07  C06   120.85  3.000
 OK3  H08   C08  C07   119.67  3.000
 OK3  H08   C08  C03   119.48  3.000
 OK3  C07   C08  C03   120.85  3.000
 OK3  N11   C09  O10   123.39  3.000
 OK3  N11   C09  C06   116.48  3.000
 OK3  O10   C09  C06   120.12  3.000
 OK3  H11   N11  C12   116.18  3.000
 OK3  H11   N11  C09   118.99  3.000
 OK3  C12   N11  C09   124.68  3.000
 OK3  H12   C12  B17   110.28  3.000
 OK3  H12   C12  C13   108.06  3.000
 OK3  B17   C12  C13   108.84  3.000
 OK3  H12   C12  N11   107.57  3.000
 OK3  B17   C12  N11   110.65  3.000
 OK3  C13   C12  N11   111.41  3.000
 OK3  H132  C13  H131  106.06  3.000
 OK3  H132  C13  C14   109.79  3.000
 OK3  H131  C13  C14   109.53  3.000
 OK3  H132  C13  C12   108.74  3.000
 OK3  H131  C13  C12   111.64  3.000
 OK3  C14   C13  C12   110.96  3.000
 OK3  C23   C14  C15   119.40  3.000
 OK3  C23   C14  C13   120.49  3.000
 OK3  C15   C14  C13   120.11  3.000
 OK3  C20   C15  O16   118.59  3.000
 OK3  C20   C15  C14   119.29  3.000
 OK3  O16   C15  C14   122.06  3.000
 OK3  B17   O16  C15   124.44  3.000
 OK3  O19   B17  O18   113.97  3.000
 OK3  O19   B17  O16   109.68  3.000
 OK3  O18   B17  O16   106.89  3.000
 OK3  O19   B17  C12   107.54  3.000
 OK3  O18   B17  C12   110.09  3.000
 OK3  O16   B17  C12   108.56  3.000
 OK3  H18   O18  B17   111.32  3.000
 OK3  H19   O19  B17   111.58  3.000
 OK3  C24   C20  C21   118.31  3.000
 OK3  C24   C20  C15   122.35  3.000
 OK3  C21   C20  C15   119.34  3.000
 OK3  H21   C21  C22   119.56  3.000
 OK3  H21   C21  C20   118.78  3.000
 OK3  C22   C21  C20   121.65  3.000
 OK3  H22   C22  C23   120.57  3.000
 OK3  H22   C22  C21   120.79  3.000
 OK3  C23   C22  C21   118.63  3.000
 OK3  H23   C23  C22   119.73  3.000
 OK3  H23   C23  C14   118.61  3.000
 OK3  C22   C23  C14   121.66  3.000
 OK3  O26   C24  O25   126.45  3.000
 OK3  O26   C24  C20   116.06  3.000
 OK3  O25   C24  C20   117.45  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  Var_01    C15   C14  C13  C12   -32.37  30.0  1
 OK3  Var_02    C20   C15  O16  B17  -176.21  30.0  1
 OK3  Var_03    O18   B17  O16  C15   142.00  30.0  1
 OK3  Var_04    C04   C03  C02  N01   148.65  30.0  2
 OK3  Var_05    O10   C09  C06  C05   -20.97  30.0  2
 OK3  Var_06    O25   C24  C20  C15   -49.09  30.0  2
 OK3  Var_07    H011  N01  C02  C03   172.66  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

