# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 07:34:23 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  58  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  -0.236    4.9729  -3.0875  -0.7289
 K9B  C16   C  CR16   0  -0.297    3.6855  -2.5608  -0.8114
 K9B  C19   C  CH2    0  -0.559   -1.8223   1.8764  -0.1447
 K9B  C20   C  CH1    0  -0.256   -3.1583   1.3227   0.3351
 K9B  C21   C  CH2    0  -0.443   -4.3086   2.1970  -0.1607
 K9B  C22   C  CH2    0  -0.435   -5.6660   1.6714   0.2918
 K9B  C23   C  CH1    0  -0.057   -5.8897   0.2308  -0.1541
 K9B  B05   B  B     -1   0.463    2.9547   1.6311  -0.2221
 K9B  C02   C  C      0   0.507   -0.6148   1.1971   0.4806
 K9B  C04   C  CH1    0  -0.277    1.7511   0.5764   0.0551
 K9B  C09   C  CR6    0   0.406    4.4694  -0.3633  -0.1869
 K9B  C10   C  CR6    0  -0.197    5.7806  -0.8985  -0.1064
 K9B  C11   C  C      0   0.478    6.9152  -0.0409   0.2910
 K9B  C14   C  CR16   0  -0.263    6.0145  -2.2495  -0.3907
 K9B  C17   C  CR6    0  -0.013    3.4112  -1.2264  -0.5685
 K9B  C18   C  CH2    0  -0.526    2.0069  -0.7077  -0.7335
 K9B  C28   C  CH2    0  -0.438   -4.7410  -0.6490   0.3452
 K9B  C29   C  CH2    0  -0.383   -3.3794  -0.1242  -0.1043
 K9B  N03   N  NH1    0  -0.632    0.4537   1.1180  -0.3113
 K9B  O01   O  O      0  -0.479   -0.6414   0.7991   1.6453
 K9B  O06   O  OB     0  -0.642    2.8926   2.7374   0.7108
 K9B  O07   O  OB     0  -0.791    2.9371   1.9983  -1.6250
 K9B  O08   O  OC2    0  -0.515    4.2730   0.8990   0.0793
 K9B  O12   O  OH1    0  -0.714    8.0802  -0.4891  -0.1859
 K9B  O13   O  O      0  -0.307    6.8530   0.9549   0.9742
 K9B  H151  H  HCR6   0   0.254    5.1517  -4.1364  -0.9251
 K9B  H161  H  HCR6   0   0.251    2.8608  -3.2140  -1.0783
 K9B  H191  H  HCH2   0   0.259   -1.7692   1.8237  -1.2370
 K9B  H192  H  HCH2   0   0.282   -1.7630   2.9419   0.1084
 K9B  H201  H  HCH1   0   0.238   -3.1628   1.3519   1.4310
 K9B  H211  H  HCH2   0   0.206   -4.1708   3.2270   0.1823
 K9B  H212  H  HCH2   0   0.242   -4.2835   2.2325  -1.2568
 K9B  H222  H  HCH2   0   0.253   -5.7293   1.7208   1.3863
 K9B  H221  H  HCH2   0   0.181   -6.4684   2.3033  -0.0979
 K9B  H1    H  HCH1   0   0.241   -5.8814   0.2122  -1.2524
 K9B  H141  H  HCR6   0   0.247    7.0183  -2.6468  -0.3305
 K9B  H182  H  HCH2   0   0.236    1.2970  -1.4946  -0.4581
 K9B  H181  H  HCH2   0   0.224    1.8388  -0.5075  -1.7974
 K9B  H282  H  HCH2   0   0.218   -4.7808  -0.6789   1.4415
 K9B  H281  H  HCH2   0   0.209   -4.8742  -1.6775  -0.0002
 K9B  H291  H  HCH2   0   0.138   -3.3106  -0.1799  -1.1974
 K9B  H292  H  HCH2   0   0.206   -2.5908  -0.7670   0.2929
 K9B  H031  H  HNH1   0   0.382    0.3781   1.5093  -1.2385
 K9B  H061  H  H      0   0.414    3.6216   3.3512   0.5753
 K9B  H071  H  H      0   0.408    3.6651   2.5838  -1.8540
 K9B  H2    H  HOH1   0   0.446    8.7935   0.0826   0.1344
 K9B  N1    N  NH1    0  -0.578   -7.2139  -0.2006   0.2583
 K9B  C2    C  CH2    0  -0.255   -7.6599  -1.4625  -0.3014
 K9B  C3    C  CH2    0  -0.305   -9.1081  -1.7316   0.0767
 K9B  N2    N  NH2    0  -0.783   -9.5592  -2.9843  -0.5016
 K9B  H3    H  HNH1   0   0.325   -7.2281  -0.2673   1.2710
 K9B  H5    H  HNH2   0   0.344  -10.4705  -3.2281  -0.1412
 K9B  H4    H  HNH2   0   0.305   -9.6666  -2.8840  -1.5021
 K9B  H6    H  HCH2   0   0.233   -7.5789  -1.3913  -1.3917
 K9B  H7    H  HCH2   0   0.099   -7.0561  -2.3306  -0.0045
 K9B  H8    H  HCH2   0   0.264   -9.1783  -1.8216   1.1651
 K9B  H9    H  HCH2   0   0.197   -9.7106  -0.8554  -0.2015
 K9B  H10   H  HCH1   0   0.228    1.6996   0.3354   1.1202

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    1.531  0.020  1.531
 K9B  C28  C29   single    1.527  0.020  1.527
 K9B  C23  C22   single    1.524  0.020  1.524
 K9B  C22  C21   single    1.524  0.020  1.524
 K9B  C29  C20   single    1.528  0.020  1.528
 K9B  C20  C21   single    1.528  0.020  1.528
 K9B  C20  C19   single    1.524  0.020  1.524
 K9B  O01  C02   double    1.231  0.020  1.231
 K9B  C19  C02   single    1.520  0.020  1.520
 K9B  C02  N03   single    1.332  0.020  1.332
 K9B  N03  C04   single    1.453  0.020  1.453
 K9B  C04  C18   single    1.528  0.020  1.528
 K9B  C04  B05   single    1.624  0.020  1.624
 K9B  O06  B05   single    1.448  0.020  1.448
 K9B  C18  C17   single    1.506  0.020  1.506
 K9B  B05  O07   single    1.450  0.020  1.450
 K9B  B05  O08   single    1.538  0.020  1.538
 K9B  C17  C16   aromatic  1.384  0.020  1.384
 K9B  C17  C09   aromatic  1.418  0.020  1.418
 K9B  O08  C09   single    1.305  0.020  1.305
 K9B  C16  C15   aromatic  1.393  0.020  1.393
 K9B  C09  C10   aromatic  1.419  0.020  1.419
 K9B  C15  C14   aromatic  1.379  0.020  1.379
 K9B  C10  C14   aromatic  1.400  0.020  1.400
 K9B  C10  C11   single    1.477  0.020  1.477
 K9B  O13  C11   double    1.209  0.020  1.209
 K9B  C11  O12   single    1.336  0.020  1.336
 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  O12  H2    single    0.850  0.020  0.980
 K9B  C23  N1    single    1.452  0.020  1.452
 K9B  N1   C2    single    1.451  0.020  1.451
 K9B  C2   C3    single    1.521  0.020  1.521
 K9B  C3   N2    single    1.452  0.020  1.452
 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   120.58  3.000
 K9B  H151  C15  C16   120.56  3.000
 K9B  C14   C15  C16   118.86  3.000
 K9B  H161  C16  C17   118.22  3.000
 K9B  H161  C16  C15   119.28  3.000
 K9B  C17   C16  C15   122.50  3.000
 K9B  H192  C19  H191  105.93  3.000
 K9B  H192  C19  C02   107.23  3.000
 K9B  H191  C19  C02   110.51  3.000
 K9B  H192  C19  C20   109.13  3.000
 K9B  H191  C19  C20   109.83  3.000
 K9B  C02   C19  C20   113.87  3.000
 K9B  H201  C20  C29   108.18  3.000
 K9B  H201  C20  C21   107.83  3.000
 K9B  C29   C20  C21   109.85  3.000
 K9B  H201  C20  C19   107.98  3.000
 K9B  C21   C20  C19   110.49  3.000
 K9B  C29   C20  C19   112.36  3.000
 K9B  H212  C21  H211  106.25  3.000
 K9B  H212  C21  C22   109.16  3.000
 K9B  H211  C21  C22   110.10  3.000
 K9B  H212  C21  C20   109.01  3.000
 K9B  H211  C21  C20   110.01  3.000
 K9B  C22   C21  C20   112.14  3.000
 K9B  H221  C22  H222  106.69  3.000
 K9B  H221  C22  C23   109.53  3.000
 K9B  H222  C22  C23   109.02  3.000
 K9B  H221  C22  C21   110.39  3.000
 K9B  H222  C22  C21   109.38  3.000
 K9B  C23   C22  C21   111.69  3.000
 K9B  N1    C23  H1    106.60  3.000
 K9B  N1    C23  C28   114.89  3.000
 K9B  H1    C23  C28   108.11  3.000
 K9B  N1    C23  C22   109.35  3.000
 K9B  H1    C23  C22   107.90  3.000
 K9B  C28   C23  C22   109.73  3.000
 K9B  O08   B05  O07   108.70  3.000
 K9B  O08   B05  O06   105.91  3.000
 K9B  O07   B05  O06   115.42  3.000
 K9B  O08   B05  C04   107.02  3.000
 K9B  O07   B05  C04   108.70  3.000
 K9B  O06   B05  C04   110.74  3.000
 K9B  O01   C02  N03   124.08  3.000
 K9B  N03   C02  C19   114.78  3.000
 K9B  O01   C02  C19   121.10  3.000
 K9B  H10   C04  N03   106.61  3.000
 K9B  H10   C04  C18   108.99  3.000
 K9B  N03   C04  C18   109.42  3.000
 K9B  H10   C04  B05   110.14  3.000
 K9B  C18   C04  B05   109.47  3.000
 K9B  N03   C04  B05   112.12  3.000
 K9B  O08   C09  C17   122.10  3.000
 K9B  O08   C09  C10   119.51  3.000
 K9B  C17   C09  C10   118.39  3.000
 K9B  C14   C10  C11   119.12  3.000
 K9B  C11   C10  C09   120.42  3.000
 K9B  C14   C10  C09   120.46  3.000
 K9B  O13   C11  O12   121.52  3.000
 K9B  O12   C11  C10   112.27  3.000
 K9B  O13   C11  C10   126.21  3.000
 K9B  H141  C14  C10   119.89  3.000
 K9B  H141  C14  C15   119.44  3.000
 K9B  C10   C14  C15   120.66  3.000
 K9B  C18   C17  C09   121.04  3.000
 K9B  C09   C17  C16   119.09  3.000
 K9B  C18   C17  C16   119.85  3.000
 K9B  H181  C18  H182  106.02  3.000
 K9B  H181  C18  C17   108.21  3.000
 K9B  H182  C18  C17   109.23  3.000
 K9B  H181  C18  C04   108.78  3.000
 K9B  H182  C18  C04   111.43  3.000
 K9B  C17   C18  C04   112.89  3.000
 K9B  H281  C28  H282  106.60  3.000
 K9B  H281  C28  C29   109.82  3.000
 K9B  H282  C28  C29   109.62  3.000
 K9B  H281  C28  C23   110.26  3.000
 K9B  H282  C28  C23   108.32  3.000
 K9B  C29   C28  C23   112.06  3.000
 K9B  H292  C29  H291  106.70  3.000
 K9B  H292  C29  C28   109.55  3.000
 K9B  H291  C29  C28   109.39  3.000
 K9B  H292  C29  C20   110.37  3.000
 K9B  H291  C29  C20   109.00  3.000
 K9B  C28   C29  C20   111.70  3.000
 K9B  H031  N03  C04   116.30  3.000
 K9B  H031  N03  C02   117.58  3.000
 K9B  C04   N03  C02   126.04  3.000
 K9B  H061  O06  B05   111.34  3.000
 K9B  H071  O07  B05   112.04  3.000
 K9B  C09   O08  B05   123.34  3.000
 K9B  H2    O12  C11   109.03  3.000
 K9B  H3    N1   C2    108.87  3.000
 K9B  H3    N1   C23   108.40  3.000
 K9B  C2    N1   C23   115.41  3.000
 K9B  H7    C2   H6    106.24  3.000
 K9B  H7    C2   C3    108.45  3.000
 K9B  H6    C2   C3    109.23  3.000
 K9B  H7    C2   N1    114.47  3.000
 K9B  H6    C2   N1    107.74  3.000
 K9B  C3    C2   N1    110.54  3.000
 K9B  H9    C3   H8    106.39  3.000
 K9B  H9    C3   N2    114.63  3.000
 K9B  H8    C3   N2    107.78  3.000
 K9B  H9    C3   C2    108.54  3.000
 K9B  H8    C3   C2    108.84  3.000
 K9B  N2    C3   C2    110.46  3.000
 K9B  H4    N2   H5    106.33  3.000
 K9B  H4    N2   C3    109.98  3.000
 K9B  H5    N2   C3    110.28  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  H2    O12  C11  C10   180.00   0.0  0
 K9B  CONST_16  H031  N03  C02  C19     0.00   0.0  0
 K9B  Var_01    C04   C18  C17  C16   157.89  30.0  1
 K9B  Var_02    C23   C28  C29  C20    56.06  30.0  1
 K9B  Var_03    C23   C22  C21  C20   -56.52  30.0  1
 K9B  Var_04    C17   C09  O08  B05   -10.96  30.0  1
 K9B  Var_05    O06   B05  O08  C09   154.63  30.0  1
 K9B  Var_06    O13   C11  C10  C09    26.01  30.0  2
 K9B  Var_07    O01   C02  C19  C20   -34.76  30.0  3
 K9B  Var_08    C3    C2   N1   C23  -173.74  30.0  3
 K9B  Var_09    N2    C3   C2   N1    179.10  30.0  3
 K9B  Var_10    H5    N2   C3   C2    171.71  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
 K9B  plan-3  H2    0.020

