# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 18:14:50 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-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: NCCN[C@H]1CC[C@@H](CC1)CC(=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
 K9B  K9B  '(4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid'  ligand  57  29  .  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_K9B
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
 K9B  C15   C  CR16   0  -0.283   4.3328  -3.1383   0.1846
 K9B  C16   C  CR16   0  -0.335   3.0948  -2.5117   0.1708
 K9B  C19   C  CH2    0  -0.556  -1.7658   2.3609   0.6308
 K9B  C20   C  CH1    0  -0.228  -2.9956   1.4849   0.8606
 K9B  C21   C  CH2    0  -0.420  -4.2757   2.3118   0.7680
 K9B  C22   C  CH2    0  -0.435  -5.5212   1.4580   0.9734
 K9B  C23   C  CH1    0  -0.054  -5.5887   0.2933  -0.0097
 K9B  B05   B  B     -1   0.453   2.7353   1.5880  -1.1238
 K9B  C02   C  C      0   0.530  -0.4718   1.6244   0.9122
 K9B  C04   C  CH1    0  -0.238   1.7086   0.9478  -0.0365
 K9B  C09   C  CR6    0   0.363   4.0688  -0.5065  -0.7665
 K9B  C10   C  CR6    0  -0.189   5.3276  -1.1437  -0.7752
 K9B  C11   C  C      0   0.359   6.5750  -0.4786  -1.3327
 K9B  C14   C  CR16   0  -0.302   5.4382  -2.4375  -0.2760
 K9B  C17   C  CR6    0  -0.006   2.9421  -1.2106  -0.2930
 K9B  C18   C  CH2    0  -0.507   1.5890  -0.5537  -0.2923
 K9B  C28   C  CH2    0  -0.441  -4.3030  -0.5352   0.0790
 K9B  C29   C  CH2    0  -0.421  -3.0574   0.3212  -0.1266
 K9B  N03   N  NH1    0  -0.643   0.4114   1.5966  -0.0900
 K9B  O01   O  O      0  -0.528  -0.2663   1.1130   2.0117
 K9B  O06   O  OB     0  -0.719   3.1275   2.9294  -0.7049
 K9B  O07   O  OB     0  -0.738   2.0852   1.5442  -2.4365
 K9B  O08   O  OC2    0  -0.528   3.9931   0.7541  -1.1594
 K9B  O12   O  OC    -1  -0.617   7.6155  -0.5976  -0.6508
 K9B  O13   O  O      0  -0.599   6.4777   0.0862  -2.4376
 K9B  H151  H  HCR6   0   0.228   4.4365  -4.1488   0.5593
 K9B  H161  H  HCR6   0   0.228   2.2192  -3.0376   0.5377
 K9B  H191  H  HCH2   0   0.232  -1.7840   2.7621  -0.3873
 K9B  H192  H  HCH2   0   0.256  -1.8027   3.2217   1.3067
 K9B  H201  H  HCH1   0   0.217  -2.9363   1.0713   1.8745
 K9B  H211  H  HCH2   0   0.228  -4.2526   3.1177   1.5073
 K9B  H212  H  HCH2   0   0.207  -4.3220   2.7972  -0.2146
 K9B  H222  H  HCH2   0   0.207  -5.5206   1.0586   1.9952
 K9B  H221  H  HCH2   0   0.227  -6.4209   2.0705   0.8765
 K9B  H1    H  HCH1   0   0.208  -5.6505   0.7111  -1.0238
 K9B  H141  H  HCR6   0   0.229   6.4142  -2.9078  -0.2558
 K9B  H182  H  HCH2   0   0.222   0.9468  -1.0388   0.4494
 K9B  H181  H  HCH2   0   0.220   1.1047  -0.7100  -1.2632
 K9B  H282  H  HCH2   0   0.204  -4.2626  -1.0137   1.0658
 K9B  H281  H  HCH2   0   0.231  -4.3160  -1.3433  -0.6568
 K9B  H291  H  HCH2   0   0.208  -3.0564   0.7227  -1.1474
 K9B  H292  H  HCH2   0   0.232  -2.1643  -0.3045  -0.0410
 K9B  H031  H  HNH1   0   0.383   0.1378   2.0069  -0.9682
 K9B  H061  H  H      0   0.436   3.7845   3.3016  -1.3002
 K9B  H071  H  H      0   0.432   2.6828   1.8364  -3.1301
 K9B  N1    N  NH1    0  -0.605  -6.8154  -0.4553   0.2144
 K9B  C2    C  CH2    0  -0.267  -7.1110  -1.4791  -0.7688
 K9B  C3    C  CH2    0  -0.294  -8.4910  -2.0710  -0.5256
 K9B  N2    N  NH2    0  -0.803  -8.7810  -3.1072  -1.5054
 K9B  H3    H  HNH1   0   0.330  -6.7785  -0.8794   1.1360
 K9B  H5    H  HNH2   0   0.348  -9.6740  -3.5323  -1.2929
 K9B  H4    H  HNH2   0   0.339  -8.8948  -2.6810  -2.4171
 K9B  H6    H  HCH2   0   0.211  -7.0914  -1.0132  -1.7605
 K9B  H7    H  HCH2   0   0.191  -6.3809  -2.3007  -0.7990
 K9B  H8    H  HCH2   0   0.213  -8.5106  -2.5267   0.4692
 K9B  H9    H  HCH2   0   0.191  -9.2250  -1.2540  -0.5078
 K9B  H10   H  HCH1   0   0.195   2.1009   1.0882   0.9771

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
 K9B  C28  C23   single    1.532  0.020  1.532
 K9B  C28  C29   single    1.526  0.020  1.526
 K9B  C23  C22   single    1.526  0.020  1.526
 K9B  C22  C21   single    1.524  0.020  1.524
 K9B  C29  C20   single    1.527  0.020  1.527
 K9B  C20  C21   single    1.527  0.020  1.527
 K9B  C20  C19   single    1.527  0.020  1.527
 K9B  O01  C02   double    1.230  0.020  1.230
 K9B  C19  C02   single    1.515  0.020  1.515
 K9B  C02  N03   single    1.336  0.020  1.336
 K9B  N03  C04   single    1.451  0.020  1.451
 K9B  C04  C18   single    1.528  0.020  1.528
 K9B  C04  B05   single    1.627  0.020  1.627
 K9B  O06  B05   single    1.459  0.020  1.459
 K9B  C18  C17   single    1.504  0.020  1.504
 K9B  B05  O07   single    1.466  0.020  1.466
 K9B  B05  O08   single    1.510  0.020  1.510
 K9B  C17  C16   aromatic  1.390  0.020  1.390
 K9B  C17  C09   aromatic  1.410  0.020  1.410
 K9B  O08  C09   single    1.323  0.020  1.323
 K9B  C16  C15   aromatic  1.388  0.020  1.388
 K9B  C09  C10   aromatic  1.411  0.020  1.411
 K9B  C15  C14   aromatic  1.387  0.020  1.387
 K9B  C10  C14   aromatic  1.391  0.020  1.391
 K9B  C10  C11   single    1.520  0.020  1.520
 K9B  O13  C11   deloc     1.245  0.020  1.245
 K9B  C11  O12   deloc     1.250  0.020  1.250
 K9B  C15  H151  single    0.930  0.020  1.080
 K9B  C16  H161  single    0.930  0.020  1.080
 K9B  C19  H191  single    0.970  0.020  1.090
 K9B  C19  H192  single    0.970  0.020  1.090
 K9B  C20  H201  single    0.970  0.020  1.090
 K9B  C21  H211  single    0.970  0.020  1.090
 K9B  C21  H212  single    0.970  0.020  1.090
 K9B  C22  H222  single    0.970  0.020  1.090
 K9B  C22  H221  single    0.970  0.020  1.090
 K9B  C23  H1    single    0.970  0.020  1.090
 K9B  C14  H141  single    0.930  0.020  1.080
 K9B  C18  H182  single    0.970  0.020  1.090
 K9B  C18  H181  single    0.970  0.020  1.090
 K9B  C28  H282  single    0.970  0.020  1.090
 K9B  C28  H281  single    0.970  0.020  1.090
 K9B  C29  H291  single    0.970  0.020  1.090
 K9B  C29  H292  single    0.970  0.020  1.090
 K9B  N03  H031  single    0.860  0.020  1.020
 K9B  O06  H061  single    0.850  0.020  0.980
 K9B  O07  H071  single    0.850  0.020  0.980
 K9B  C23  N1    single    1.454  0.020  1.454
 K9B  N1   C2    single    1.450  0.020  1.450
 K9B  C2   C3    single    1.521  0.020  1.521
 K9B  C3   N2    single    1.455  0.020  1.455
 K9B  N1   H3    single    0.890  0.020  1.040
 K9B  N2   H5    single    0.890  0.020  1.040
 K9B  N2   H4    single    0.890  0.020  1.040
 K9B  C2   H6    single    0.970  0.020  1.090
 K9B  C2   H7    single    0.970  0.020  1.090
 K9B  C3   H8    single    0.970  0.020  1.090
 K9B  C3   H9    single    0.970  0.020  1.090
 K9B  C04  H10   single    0.970  0.020  1.090

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
 K9B  H151  C15  C14   120.66  3.000
 K9B  H151  C15  C16   120.69  3.000
 K9B  C14   C15  C16   118.64  3.000
 K9B  H161  C16  C17   118.54  3.000
 K9B  H161  C16  C15   119.84  3.000
 K9B  C17   C16  C15   121.61  3.000
 K9B  H192  C19  H191  106.58  3.000
 K9B  H192  C19  C02   107.23  3.000
 K9B  H191  C19  C02   111.42  3.000
 K9B  H192  C19  C20   109.32  3.000
 K9B  H191  C19  C20   109.68  3.000
 K9B  C02   C19  C20   112.39  3.000
 K9B  H201  C20  C29   108.21  3.000
 K9B  H201  C20  C21   107.80  3.000
 K9B  C29   C20  C21   109.85  3.000
 K9B  H201  C20  C19   108.17  3.000
 K9B  C21   C20  C19   110.82  3.000
 K9B  C29   C20  C19   111.86  3.000
 K9B  H212  C21  H211  106.28  3.000
 K9B  H212  C21  C22   109.52  3.000
 K9B  H211  C21  C22   109.81  3.000
 K9B  H212  C21  C20   109.23  3.000
 K9B  H211  C21  C20   109.90  3.000
 K9B  C22   C21  C20   111.94  3.000
 K9B  H221  C22  H222  106.68  3.000
 K9B  H221  C22  C23   109.53  3.000
 K9B  H222  C22  C23   108.80  3.000
 K9B  H221  C22  C21   110.30  3.000
 K9B  H222  C22  C21   109.22  3.000
 K9B  C23   C22  C21   112.15  3.000
 K9B  N1    C23  H1    106.89  3.000
 K9B  N1    C23  C28   114.86  3.000
 K9B  H1    C23  C28   107.84  3.000
 K9B  N1    C23  C22   109.33  3.000
 K9B  H1    C23  C22   107.88  3.000
 K9B  C28   C23  C22   109.78  3.000
 K9B  O08   B05  O07   109.39  3.000
 K9B  O08   B05  O06   106.90  3.000
 K9B  O07   B05  O06   113.82  3.000
 K9B  O08   B05  C04   108.92  3.000
 K9B  O07   B05  C04   107.87  3.000
 K9B  O06   B05  C04   109.85  3.000
 K9B  O01   C02  N03   123.47  3.000
 K9B  N03   C02  C19   115.80  3.000
 K9B  O01   C02  C19   120.72  3.000
 K9B  H10   C04  N03   107.26  3.000
 K9B  H10   C04  C18   107.99  3.000
 K9B  N03   C04  C18   111.30  3.000
 K9B  H10   C04  B05   109.99  3.000
 K9B  C18   C04  B05   108.92  3.000
 K9B  N03   C04  B05   111.32  3.000
 K9B  O08   C09  C17   121.99  3.000
 K9B  O08   C09  C10   118.67  3.000
 K9B  C17   C09  C10   119.29  3.000
 K9B  C14   C10  C11   118.26  3.000
 K9B  C11   C10  C09   122.47  3.000
 K9B  C14   C10  C09   119.26  3.000
 K9B  O13   C11  O12   126.35  3.000
 K9B  O12   C11  C10   116.20  3.000
 K9B  O13   C11  C10   117.39  3.000
 K9B  H141  C14  C10   118.81  3.000
 K9B  H141  C14  C15   119.48  3.000
 K9B  C10   C14  C15   121.70  3.000
 K9B  C18   C17  C09   120.05  3.000
 K9B  C09   C17  C16   119.45  3.000
 K9B  C18   C17  C16   120.50  3.000
 K9B  H181  C18  H182  106.12  3.000
 K9B  H181  C18  C17   109.55  3.000
 K9B  H182  C18  C17   109.55  3.000
 K9B  H181  C18  C04   108.84  3.000
 K9B  H182  C18  C04   111.60  3.000
 K9B  C17   C18  C04   111.03  3.000
 K9B  H281  C28  H282  106.46  3.000
 K9B  H281  C28  C29   109.51  3.000
 K9B  H282  C28  C29   109.63  3.000
 K9B  H281  C28  C23   110.54  3.000
 K9B  H282  C28  C23   108.59  3.000
 K9B  C29   C28  C23   111.95  3.000
 K9B  H292  C29  H291  106.35  3.000
 K9B  H292  C29  C28   109.57  3.000
 K9B  H291  C29  C28   109.37  3.000
 K9B  H292  C29  C20   110.62  3.000
 K9B  H291  C29  C20   108.82  3.000
 K9B  C28   C29  C20   111.94  3.000
 K9B  H031  N03  C04   117.19  3.000
 K9B  H031  N03  C02   117.78  3.000
 K9B  C04   N03  C02   124.92  3.000
 K9B  H061  O06  B05   111.21  3.000
 K9B  H071  O07  B05   111.20  3.000
 K9B  C09   O08  B05   124.56  3.000
 K9B  H3    N1   C2    109.15  3.000
 K9B  H3    N1   C23   108.92  3.000
 K9B  C2    N1   C23   115.53  3.000
 K9B  H7    C2   H6    106.32  3.000
 K9B  H7    C2   C3    108.43  3.000
 K9B  H6    C2   C3    109.04  3.000
 K9B  H7    C2   N1    114.26  3.000
 K9B  H6    C2   N1    108.04  3.000
 K9B  C3    C2   N1    110.57  3.000
 K9B  H9    C3   H8    106.44  3.000
 K9B  H9    C3   N2    114.04  3.000
 K9B  H8    C3   N2    108.18  3.000
 K9B  H9    C3   C2    108.62  3.000
 K9B  H8    C3   C2    108.88  3.000
 K9B  N2    C3   C2    110.50  3.000
 K9B  H4    N2   H5    105.46  3.000
 K9B  H4    N2   C3    109.20  3.000
 K9B  H5    N2   C3    109.49  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
 K9B  CONST_01  C09   C17  C16  C15     0.00   0.0  0
 K9B  CONST_02  C09   C10  C14  C15     0.00   0.0  0
 K9B  CONST_03  C10   C09  C17  C16     0.00   0.0  0
 K9B  CONST_04  C10   C14  C15  C16     0.00   0.0  0
 K9B  CONST_05  C17   C16  C15  C14     0.00   0.0  0
 K9B  CONST_06  C17   C09  C10  C14     0.00   0.0  0
 K9B  CONST_07  C11   C10  C14  C15   180.00   0.0  0
 K9B  CONST_08  C17   C09  C10  C11   180.00   0.0  0
 K9B  CONST_09  O08   C09  C10  C11     0.00   0.0  0
 K9B  CONST_10  H141  C14  C15  C16   180.00   0.0  0
 K9B  CONST_11  H161  C16  C17  C09   180.00   0.0  0
 K9B  CONST_12  H151  C15  C14  C10   180.00   0.0  0
 K9B  CONST_13  C04   N03  C02  C19   180.00   0.0  0
 K9B  CONST_14  O01   C02  N03  C04     0.00   0.0  0
 K9B  CONST_15  H031  N03  C02  C19     0.00   0.0  0
 K9B  Var_01    C04   C18  C17  C16   146.87  30.0  1
 K9B  Var_02    C23   C28  C29  C20    56.07  30.0  1
 K9B  Var_03    C23   C22  C21  C20   -56.19  30.0  1
 K9B  Var_04    C17   C09  O08  B05     1.42  30.0  1
 K9B  Var_05    O06   B05  O08  C09   140.82  30.0  1
 K9B  Var_06    O13   C11  C10  C09   -46.43  30.0  2
 K9B  Var_07    O01   C02  C19  C20   -57.00  30.0  3
 K9B  Var_08    C3    C2   N1   C23  -173.05  30.0  3
 K9B  Var_09    N2    C3   C2   N1   -179.46  30.0  3
 K9B  Var_10    H5    N2   C3   C2    176.26  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
 K9B  chir_01  C20  C29  C21  C19  positiv
 K9B  chir_02  C23  N1   C28  C22  positiv
 K9B  chir_03  C04  N03  C18  B05  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
 K9B  plan-1  C19   0.020
 K9B  plan-1  C02   0.020
 K9B  plan-1  C04   0.020
 K9B  plan-1  N03   0.020
 K9B  plan-1  O01   0.020
 K9B  plan-1  H031  0.020
 K9B  plan-2  C15   0.020
 K9B  plan-2  C16   0.020
 K9B  plan-2  C09   0.020
 K9B  plan-2  C10   0.020
 K9B  plan-2  C11   0.020
 K9B  plan-2  C14   0.020
 K9B  plan-2  C17   0.020
 K9B  plan-2  C18   0.020
 K9B  plan-2  O08   0.020
 K9B  plan-2  H151  0.020
 K9B  plan-2  H161  0.020
 K9B  plan-2  H141  0.020
 K9B  plan-3  C10   0.020
 K9B  plan-3  C11   0.020
 K9B  plan-3  O12   0.020
 K9B  plan-3  O13   0.020

