# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 21:26:20 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 5-[[4-(2-azanylethylamino)cyclohexyl]methyl]-3-oxidanyl-2,4-dioxa-6-aza-3$l^{4}-boratricyclo[7.4.0.0^{3,7}]trideca-1(13),5,9,11-tetraene-13-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN[C@@H]1CC[C@H](CC1)CC2=N[C@H]3Cc4cccc(C(O)=O)c4O[B]3(O)O2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 K9K  K9K  '5-[[4-(2-azanylethylamino)cyclohexyl]methyl]-3-oxidanyl-2,4-dioxa-6-aza-3$l^{4}-boratricyclo[7.4.0.0^{3,7}]trideca-1(13),5,9,11-tetraene-13-carboxylic acid'  ligand  55  28  .  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_K9K
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
 K9K  B13   B  B     0   0.561    2.3029  -1.0696   0.1087
 K9K  C05   C  CH1   0  -0.022   -5.3637  -0.2664   0.6126
 K9K  C06   C  CH2   0  -0.454   -4.7788   0.2104   1.9385
 K9K  C07   C  CH2   0  -0.421   -3.4531  -0.4676   2.2622
 K9K  C08   C  CH1   0  -0.230   -2.4316  -0.2602   1.1463
 K9K  C09   C  CH2   0  -0.533   -1.1171  -0.9567   1.4771
 K9K  C10   C  CR5   0   0.527    0.0353  -0.5596   0.6121
 K9K  C12   C  C     0  -0.231    1.1425   0.8428  -0.8624
 K9K  C17   C  CR66  0   0.414    3.9695   0.5841   0.1876
 K9K  C18   C  CR6   0  -0.171    5.3349   0.2916   0.2074
 K9K  C19   C  C     0   0.552    5.8511  -0.9056   0.9167
 K9K  C22   C  CR16  0  -0.284    6.2078   1.1575  -0.4621
 K9K  C23   C  CR16  0  -0.240    5.7295   2.2649  -1.1339
 K9K  C24   C  CR16  0  -0.317    4.3663   2.5355  -1.1407
 K9K  C25   C  CR66  0   0.042    3.4735   1.7058  -0.4823
 K9K  C26   C  C     0  -0.516    1.9954   2.0004  -0.4236
 K9K  C27   C  CH2   0  -0.422   -3.0144  -0.7489  -0.1778
 K9K  C28   C  CH2   0  -0.436   -4.3398  -0.0688  -0.5025
 K9K  N11   N  N     0  -0.369    0.0503   0.4931  -0.0875
 K9K  O14   O  OB    0  -0.597    2.8627  -1.7555  -0.9123
 K9K  O15   O  O     0  -0.480    1.0614  -1.4301   0.6495
 K9K  O16   O  O     0  -0.491    3.0563  -0.1765   0.8376
 K9K  O20   O  O     0  -0.427    5.1764  -1.7294   1.4846
 K9K  O21   O  OH1   0  -0.598    7.1769  -0.9865   0.8630
 K9K  H051  H  HCH1  0   0.179   -5.5547  -1.3521   0.7012
 K9K  H061  H  HCH2  0   0.213   -4.6334   1.2951   1.8863
 K9K  H062  H  HCH2  0   0.230   -5.4961   0.0289   2.7452
 K9K  H072  H  HCH2  0   0.231   -3.0614  -0.0796   3.2065
 K9K  H071  H  HCH2  0   0.211   -3.6158  -1.5411   2.4132
 K9K  H081  H  HCH1  0   0.222   -2.2397   0.8155   1.0620
 K9K  H092  H  HCH2  0   0.278   -0.8247  -0.7444   2.5131
 K9K  H091  H  HCH2  0   0.260   -1.2383  -2.0429   1.4228
 K9K  H221  H  HCR6  0   0.273    7.2698   0.9591  -0.4666
 K9K  H231  H  HCR6  0   0.265    6.4160   2.9223  -1.6496
 K9K  H241  H  HCR6  0   0.264    3.9920   3.4089  -1.6610
 K9K  H262  H  H     0   0.270    1.7898   2.8779  -1.0446
 K9K  H261  H  H     0   0.272    1.7246   2.2752   0.5995
 K9K  H272  H  HCH2  0   0.236   -2.3069  -0.5808  -0.9926
 K9K  H271  H  HCH2  0   0.208   -3.1657  -1.8335  -0.1178
 K9K  H281  H  HCH2  0   0.231   -4.7199  -0.4572  -1.4504
 K9K  H282  H  HCH2  0   0.208   -4.1803   1.0058  -0.6450
 K9K  H141  H  H     0   0.494    2.2521  -2.3338  -1.3814
 K9K  H5    H  HOH1  0   0.486    7.4720  -1.7825   1.3290
 K9K  C3    C  CH2   0  -0.298   -8.6788   0.7410  -0.8948
 K9K  N2    N  NH2   0  -0.802   -9.5282   0.1648  -1.9263
 K9K  H6    H  HNH2  0   0.348  -10.3788   0.7073  -2.0017
 K9K  H2    H  HNH2  0   0.339   -9.0704   0.2551  -2.8252
 K9K  H1    H  HCH2  0   0.216   -6.8744  -0.1437  -1.6290
 K9K  H3    H  HCH2  0   0.187   -7.7378  -1.1446  -0.4702
 K9K  H4    H  HCH2  0   0.214   -9.2486   0.7687   0.0390
 K9K  H8    H  HCH2  0   0.193   -8.3651   1.7740  -1.0991
 K9K  H9    H  H     0   0.266    1.0569   0.6511  -1.9290
 K9K  N1    N  NH1   0  -0.616   -6.5927   0.4652   0.3433
 K9K  C2    C  CH2   0  -0.272   -7.4342  -0.1085  -0.6896
 K9K  H7    H  HNH1  0   0.337   -7.1332   0.4994   1.2008

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
 K9K  C05  C06   single    1.526  0.020  1.526
 K9K  C05  C28   single    1.527  0.020  1.527
 K9K  C06  C07   single    1.524  0.020  1.524
 K9K  C28  C27   single    1.525  0.020  1.525
 K9K  C07  C08   single    1.527  0.020  1.527
 K9K  C27  C08   single    1.527  0.020  1.527
 K9K  C08  C09   single    1.524  0.020  1.524
 K9K  N11  C12   single    1.384  0.020  1.384
 K9K  N11  C10   double    1.264  0.020  1.264
 K9K  C09  C10   single    1.495  0.020  1.495
 K9K  C12  C26   single    1.503  0.020  1.503
 K9K  C12  B13   single    2.439  0.020  2.439
 K9K  C10  O15   single    1.346  0.020  1.346
 K9K  O14  B13   single    1.351  0.020  1.351
 K9K  C26  C25   single    1.508  0.020  1.508
 K9K  B13  O15   single    1.401  0.020  1.401
 K9K  B13  O16   single    1.377  0.020  1.377
 K9K  C25  C24   aromatic  1.385  0.020  1.385
 K9K  C25  C17   aromatic  1.397  0.020  1.397
 K9K  O16  C17   single    1.355  0.020  1.355
 K9K  C24  C23   aromatic  1.390  0.020  1.390
 K9K  C17  C18   aromatic  1.397  0.020  1.397
 K9K  C23  C22   aromatic  1.381  0.020  1.381
 K9K  C18  C22   aromatic  1.400  0.020  1.400
 K9K  C18  C19   single    1.484  0.020  1.484
 K9K  O20  C19   double    1.207  0.020  1.207
 K9K  C19  O21   single    1.329  0.020  1.329
 K9K  C05  H051  single    0.970  0.020  1.090
 K9K  C06  H061  single    0.970  0.020  1.090
 K9K  C06  H062  single    0.970  0.020  1.090
 K9K  C07  H072  single    0.970  0.020  1.090
 K9K  C07  H071  single    0.970  0.020  1.090
 K9K  C08  H081  single    0.970  0.020  1.090
 K9K  C09  H092  single    0.970  0.020  1.090
 K9K  C09  H091  single    0.970  0.020  1.090
 K9K  C22  H221  single    0.930  0.020  1.080
 K9K  C23  H231  single    0.930  0.020  1.080
 K9K  C24  H241  single    0.930  0.020  1.080
 K9K  C26  H262  single    0.970  0.020  1.090
 K9K  C26  H261  single    0.970  0.020  1.090
 K9K  C27  H272  single    0.970  0.020  1.090
 K9K  C27  H271  single    0.970  0.020  1.090
 K9K  C28  H281  single    0.970  0.020  1.090
 K9K  C28  H282  single    0.970  0.020  1.090
 K9K  O14  H141  single    0.850  0.020  0.980
 K9K  O21  H5    single    0.850  0.020  0.980
 K9K  C05  N1    single    1.455  0.020  1.455
 K9K  N1   C2    single    1.451  0.020  1.451
 K9K  C2   C3    single    1.521  0.020  1.521
 K9K  C3   N2    single    1.455  0.020  1.455
 K9K  N1   H7    single    0.890  0.020  1.040
 K9K  N2   H6    single    0.890  0.020  1.040
 K9K  N2   H2    single    0.890  0.020  1.040
 K9K  C2   H1    single    0.970  0.020  1.090
 K9K  C2   H3    single    0.970  0.020  1.090
 K9K  C3   H4    single    0.970  0.020  1.090
 K9K  C3   H8    single    0.970  0.020  1.090
 K9K  C12  H9    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
 K9K  O16   B13  O15   116.57  3.000
 K9K  O16   B13  O14   120.16  3.000
 K9K  O15   B13  O14   121.87  3.000
 K9K  O16   B13  C12    87.85  3.000
 K9K  O15   B13  C12    86.21  3.000
 K9K  O14   B13  C12   107.11  3.000
 K9K  N1    C05  H051  111.25  3.000
 K9K  N1    C05  C28   111.47  3.000
 K9K  H051  C05  C28   107.54  3.000
 K9K  N1    C05  C06   109.12  3.000
 K9K  H051  C05  C06   107.66  3.000
 K9K  C28   C05  C06   109.71  3.000
 K9K  H062  C06  H061  106.63  3.000
 K9K  H062  C06  C07   109.86  3.000
 K9K  H061  C06  C07   109.58  3.000
 K9K  H062  C06  C05   109.72  3.000
 K9K  H061  C06  C05   108.60  3.000
 K9K  C07   C06  C05   112.28  3.000
 K9K  H071  C07  H072  106.37  3.000
 K9K  H071  C07  C08   109.45  3.000
 K9K  H072  C07  C08   110.07  3.000
 K9K  H071  C07  C06   109.63  3.000
 K9K  H072  C07  C06   109.71  3.000
 K9K  C08   C07  C06   111.49  3.000
 K9K  H081  C08  C27   108.31  3.000
 K9K  H081  C08  C09   108.32  3.000
 K9K  C27   C08  C09   111.78  3.000
 K9K  H081  C08  C07   107.86  3.000
 K9K  C09   C08  C07   110.87  3.000
 K9K  C27   C08  C07   109.57  3.000
 K9K  H091  C09  H092  105.57  3.000
 K9K  H091  C09  C10   108.68  3.000
 K9K  H092  C09  C10   106.83  3.000
 K9K  H091  C09  C08   110.33  3.000
 K9K  H092  C09  C08   110.27  3.000
 K9K  C10   C09  C08   114.71  3.000
 K9K  O15   C10  N11   123.01  3.000
 K9K  O15   C10  C09   113.57  3.000
 K9K  N11   C10  C09   123.42  3.000
 K9K  H9    C12  N11   116.27  3.000
 K9K  H9    C12  C26   117.83  3.000
 K9K  N11   C12  C26   118.61  3.000
 K9K  H9    C12  B13   106.85  3.000
 K9K  C26   C12  B13   102.57  3.000
 K9K  N11   C12  B13    87.38  3.000
 K9K  O16   C17  C25   116.19  3.000
 K9K  O16   C17  C18   122.32  3.000
 K9K  C25   C17  C18   121.46  3.000
 K9K  C22   C18  C19   120.70  3.000
 K9K  C19   C18  C17   121.05  3.000
 K9K  C22   C18  C17   118.25  3.000
 K9K  O21   C19  O20   122.35  3.000
 K9K  O21   C19  C18   112.12  3.000
 K9K  O20   C19  C18   125.53  3.000
 K9K  H221  C22  C23   119.07  3.000
 K9K  H221  C22  C18   120.09  3.000
 K9K  C23   C22  C18   120.84  3.000
 K9K  H231  C23  C24   120.13  3.000
 K9K  H231  C23  C22   119.98  3.000
 K9K  C24   C23  C22   119.89  3.000
 K9K  H241  C24  C25   119.24  3.000
 K9K  H241  C24  C23   119.89  3.000
 K9K  C25   C24  C23   120.87  3.000
 K9K  C26   C25  C24   122.21  3.000
 K9K  C24   C25  C17   118.68  3.000
 K9K  C26   C25  C17   119.08  3.000
 K9K  H261  C26  H262  106.44  3.000
 K9K  H261  C26  C25   109.16  3.000
 K9K  H262  C26  C25   108.58  3.000
 K9K  H261  C26  C12   109.04  3.000
 K9K  H262  C26  C12   110.19  3.000
 K9K  C25   C26  C12   113.21  3.000
 K9K  H271  C27  H272  106.40  3.000
 K9K  H271  C27  C28   109.44  3.000
 K9K  H272  C27  C28   109.61  3.000
 K9K  H271  C27  C08   108.77  3.000
 K9K  H272  C27  C08   110.52  3.000
 K9K  C28   C27  C08   111.94  3.000
 K9K  H282  C28  H281  106.64  3.000
 K9K  H282  C28  C27   109.79  3.000
 K9K  H281  C28  C27   109.19  3.000
 K9K  H282  C28  C05   108.64  3.000
 K9K  H281  C28  C05   110.75  3.000
 K9K  C27   C28  C05   111.70  3.000
 K9K  C12   N11  C10   121.98  3.000
 K9K  H141  O14  B13   114.21  3.000
 K9K  C10   O15  B13   119.88  3.000
 K9K  C17   O16  B13   118.62  3.000
 K9K  H5    O21  C19   109.54  3.000
 K9K  H8    C3   H4    106.47  3.000
 K9K  H8    C3   N2    114.03  3.000
 K9K  H4    C3   N2    108.12  3.000
 K9K  H8    C3   C2    108.46  3.000
 K9K  H4    C3   C2    108.97  3.000
 K9K  N2    C3   C2    110.62  3.000
 K9K  H2    N2   H6    105.43  3.000
 K9K  H2    N2   C3    109.27  3.000
 K9K  H6    N2   C3    109.34  3.000
 K9K  H7    N1   C2    107.83  3.000
 K9K  H7    N1   C05   108.09  3.000
 K9K  C2    N1   C05   115.02  3.000
 K9K  H3    C2   H1    106.36  3.000
 K9K  H3    C2   C3    109.07  3.000
 K9K  H1    C2   C3    108.71  3.000
 K9K  H3    C2   N1    112.95  3.000
 K9K  H1    C2   N1    109.10  3.000
 K9K  C3    C2   N1    110.49  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
 K9K  CONST_01  C23   C24  C25  C17     0.00   0.0  0
 K9K  CONST_02  C23   C22  C18  C17     0.00   0.0  0
 K9K  CONST_03  C24   C25  C17  C18     0.00   0.0  0
 K9K  CONST_04  C24   C23  C22  C18     0.00   0.0  0
 K9K  CONST_05  C25   C24  C23  C22     0.00   0.0  0
 K9K  CONST_06  C25   C17  C18  C22     0.00   0.0  0
 K9K  CONST_07  C25   C17  C18  C19   180.00   0.0  0
 K9K  CONST_08  O16   C17  C18  C19     0.00   0.0  0
 K9K  CONST_09  C23   C22  C18  C19   180.00   0.0  0
 K9K  CONST_10  H241  C24  C25  C17   180.00   0.0  0
 K9K  CONST_11  H221  C22  C18  C17   180.00   0.0  0
 K9K  CONST_12  H231  C23  C22  C18   180.00   0.0  0
 K9K  CONST_13  H5    O21  C19  C18   180.00   0.0  0
 K9K  Var_01    N11   C10  O15  B13    12.48  30.0  1
 K9K  Var_02    C25   C17  O16  B13    79.85  30.0  1
 K9K  Var_03    C08   C07  C06  C05    56.51  30.0  1
 K9K  Var_04    C08   C27  C28  C05   -56.62  30.0  1
 K9K  Var_05    O15   C10  N11  C12    -0.89  30.0  1
 K9K  Var_06    C24   C25  C26  C12   127.93  30.0  1
 K9K  Var_07    O20   C19  C18  C17     2.33  30.0  2
 K9K  Var_08    C3    C2   N1   C05  -179.49  30.0  3
 K9K  Var_09    N2    C3   C2   N1   -179.74  30.0  3
 K9K  Var_10    H6    N2   C3   C2    176.07  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
 K9K  chir_01  B13  C12  O15  O16  positiv
 K9K  chir_02  C05  C06  C28  N1   positiv
 K9K  chir_03  C08  C07  C27  C09  positiv
 K9K  chir_04  C12  N11  C26  B13  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
 K9K  plan-1  C18   0.020
 K9K  plan-1  C19   0.020
 K9K  plan-1  O20   0.020
 K9K  plan-1  O21   0.020
 K9K  plan-1  H5    0.020
 K9K  plan-2  C17   0.020
 K9K  plan-2  C18   0.020
 K9K  plan-2  C19   0.020
 K9K  plan-2  C22   0.020
 K9K  plan-2  C23   0.020
 K9K  plan-2  C24   0.020
 K9K  plan-2  C25   0.020
 K9K  plan-2  C26   0.020
 K9K  plan-2  O16   0.020
 K9K  plan-2  H221  0.020
 K9K  plan-2  H231  0.020
 K9K  plan-2  H241  0.020

