# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:33:55 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: [4-(3-aminocarbonylphenyl)-1,2,3-triazol-1-yl]methyl-phosphonooxy-borinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc(c1)c2cn(CB(O)O[P](O)(O)=O)nn2
#
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
 PKY  PKY  '[4-(3-aminocarbonylphenyl)-1,2,3-triazol-1-yl]methyl-phosphonooxy-borinic acid'  ligand  34  22  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PKY
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
 PKY  O7   O  O     0  -0.480  23.0299   -5.7865  -32.9085
 PKY  C2   C  C     0   0.492  22.6647   -5.0160  -33.7862
 PKY  N8   N  NH2   0  -0.814  22.3979   -3.7233  -33.5526
 PKY  C12  C  CR6   0  -0.015  22.4907   -5.4857  -35.1980
 PKY  C11  C  CR16  0  -0.320  23.1693   -6.6356  -35.5845
 PKY  C13  C  CR16  0  -0.296  21.6565   -4.8427  -36.1095
 PKY  C14  C  CR16  0  -0.221  21.5207   -5.3465  -37.3948
 PKY  C15  C  CR16  0  -0.331  22.2139   -6.4816  -37.7803
 PKY  C10  C  CR6   0   0.090  23.0470   -7.1410  -36.8760
 PKY  C8   C  CR5   0   0.170  23.7752   -8.3451  -37.2668
 PKY  N7   N  N     0  -0.324  24.6893   -8.9390  -36.4677
 PKY  N6   N  N     0  -0.083  25.1620   -9.9802  -37.0571
 PKY  C9   C  CR15  0  -0.107  23.6964   -9.0871  -38.4238
 PKY  N5   N  NR5   0  -0.269  24.5727  -10.0862  -38.2347
 PKY  C1   C  CH2   0  -0.555  24.9150  -11.1603  -39.1449
 PKY  B1   B  B     0   0.596  25.7943  -10.7054  -40.3841
 PKY  O2   O  OH1   0  -0.582  26.2268   -9.4587  -40.6205
 PKY  O4   O  O2    0  -0.569  26.1069  -11.7165  -41.2642
 PKY  P1   P  P     0   1.496  26.9932  -11.7550  -42.5973
 PKY  O6   O  OH1   0  -0.739  28.3989  -11.1048  -42.2153
 PKY  O3   O  O     0  -0.692  27.0470  -13.1139  -43.1640
 PKY  O5   O  OH1   0  -0.739  26.2992  -10.6167  -43.4631
 PKY  H1   H  HNH2  0   0.406  22.5065   -3.3524  -32.6224
 PKY  H2   H  HNH2  0   0.414  22.2166   -3.0627  -34.2879
 PKY  H3   H  HCR6  0   0.261  23.8059   -7.1425  -34.8720
 PKY  H4   H  HCR6  0   0.262  21.0897   -3.9640  -35.8309
 PKY  H5   H  HCR6  0   0.269  20.8665   -4.8514  -38.0995
 PKY  H6   H  HCR6  0   0.257  22.1017   -6.8500  -38.7922
 PKY  H7   H  HCR5  0   0.317  23.0968   -9.0010  -39.3143
 PKY  H8   H  HCH2  0   0.302  23.9946  -11.6392  -39.4860
 PKY  H9   H  HCH2  0   0.304  25.4538  -11.9130  -38.5673
 PKY  H10  H  HOH1  0   0.495  25.9797   -8.7949  -39.9687
 PKY  H11  H  HOH1  0   0.500  29.0679  -11.7484  -41.9456
 PKY  H12  H  HOH1  0   0.504  26.5523  -10.6162  -44.3965

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
 PKY  O3   P1   double    1.473  0.020  1.473
 PKY  O6   P1   single    1.595  0.020  1.595
 PKY  P1   O5   single    1.590  0.020  1.590
 PKY  P1   O4   single    1.601  0.020  1.601
 PKY  O4   B1   single    1.376  0.020  1.376
 PKY  B1   O2   single    1.341  0.020  1.341
 PKY  B1   C1   single    1.586  0.020  1.586
 PKY  C1   N5   single    1.449  0.020  1.449
 PKY  C9   N5   aromatic  1.342  0.020  1.342
 PKY  C9   C8   aromatic  1.377  0.020  1.377
 PKY  N5   N6   aromatic  1.321  0.020  1.321
 PKY  C15  C14  aromatic  1.385  0.020  1.385
 PKY  C15  C10  aromatic  1.395  0.020  1.395
 PKY  C14  C13  aromatic  1.387  0.020  1.387
 PKY  C8   C10  single    1.460  0.020  1.460
 PKY  C8   N7   aromatic  1.352  0.020  1.352
 PKY  C10  C11  aromatic  1.392  0.020  1.392
 PKY  N6   N7   aromatic  1.286  0.020  1.286
 PKY  C13  C12  aromatic  1.393  0.020  1.393
 PKY  C11  C12  aromatic  1.390  0.020  1.390
 PKY  C12  C2   single    1.498  0.020  1.498
 PKY  C2   N8   single    1.341  0.020  1.341
 PKY  C2   O7   double    1.224  0.020  1.224
 PKY  N8   H1   single    0.860  0.020  1.020
 PKY  N8   H2   single    0.860  0.020  1.020
 PKY  C11  H3   single    0.930  0.020  1.080
 PKY  C13  H4   single    0.930  0.020  1.080
 PKY  C14  H5   single    0.930  0.020  1.080
 PKY  C15  H6   single    0.930  0.020  1.080
 PKY  C9   H7   single    0.930  0.020  1.080
 PKY  C1   H8   single    0.970  0.020  1.090
 PKY  C1   H9   single    0.970  0.020  1.090
 PKY  O2   H10  single    0.850  0.020  0.980
 PKY  O6   H11  single    0.850  0.020  0.980
 PKY  O5   H12  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
 PKY  C12  C2   N8   116.32  3.000
 PKY  N8   C2   O7   122.80  3.000
 PKY  C12  C2   O7   120.88  3.000
 PKY  H2   N8   H1   116.94  3.000
 PKY  H2   N8   C2   122.85  3.000
 PKY  H1   N8   C2   119.63  3.000
 PKY  C13  C12  C11  119.49  3.000
 PKY  C11  C12  C2   117.69  3.000
 PKY  C13  C12  C2   122.79  3.000
 PKY  H3   C11  C10  119.52  3.000
 PKY  H3   C11  C12  119.46  3.000
 PKY  C10  C11  C12  121.02  3.000
 PKY  H4   C13  C14  118.83  3.000
 PKY  H4   C13  C12  121.34  3.000
 PKY  C14  C13  C12  119.82  3.000
 PKY  H5   C14  C15  119.78  3.000
 PKY  H5   C14  C13  119.78  3.000
 PKY  C15  C14  C13  120.44  3.000
 PKY  H6   C15  C10  120.45  3.000
 PKY  H6   C15  C14  119.16  3.000
 PKY  C10  C15  C14  120.40  3.000
 PKY  C8   C10  C15  120.93  3.000
 PKY  C8   C10  C11  120.25  3.000
 PKY  C15  C10  C11  118.82  3.000
 PKY  C9   C8   N7   107.38  3.000
 PKY  N7   C8   C10  122.77  3.000
 PKY  C9   C8   C10  129.85  3.000
 PKY  N6   N7   C8   109.47  3.000
 PKY  N5   N6   N7   108.03  3.000
 PKY  H7   C9   N5   122.65  3.000
 PKY  H7   C9   C8   133.13  3.000
 PKY  N5   C9   C8   104.20  3.000
 PKY  C1   N5   C9   128.13  3.000
 PKY  C9   N5   N6   110.92  3.000
 PKY  C1   N5   N6   120.94  3.000
 PKY  H9   C1   H8   106.20  3.000
 PKY  H9   C1   B1   109.73  3.000
 PKY  H8   C1   B1   110.43  3.000
 PKY  H9   C1   N5   107.19  3.000
 PKY  H8   C1   N5   108.79  3.000
 PKY  B1   C1   N5   114.15  3.000
 PKY  O4   B1   O2   119.81  3.000
 PKY  O2   B1   C1   125.69  3.000
 PKY  O4   B1   C1   114.50  3.000
 PKY  H10  O2   B1   116.04  3.000
 PKY  P1   O4   B1   132.50  3.000
 PKY  O5   P1   O3   117.83  3.000
 PKY  O5   P1   O6   102.90  3.000
 PKY  O3   P1   O6   115.84  3.000
 PKY  O5   P1   O4   101.22  3.000
 PKY  O6   P1   O4   106.18  3.000
 PKY  O3   P1   O4   111.26  3.000
 PKY  H11  O6   P1   113.91  3.000
 PKY  H12  O5   P1   114.31  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
 PKY  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 PKY  CONST_02  C15  C10  C11  C12     0.00   0.0  0
 PKY  CONST_03  C8   C10  C11  C12   180.00   0.0  0
 PKY  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 PKY  CONST_05  C9   C8   C10  C11   180.00   0.0  0
 PKY  CONST_06  N7   C8   C10  C11     0.00   0.0  0
 PKY  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 PKY  CONST_08  C10  C15  C14  C13     0.00   0.0  0
 PKY  CONST_09  C10  C11  C12  C13     0.00   0.0  0
 PKY  CONST_10  C8   C10  C15  C14   180.00   0.0  0
 PKY  CONST_11  C9   C8   C10  C15     0.00   0.0  0
 PKY  CONST_12  N7   C8   C10  C15   180.00   0.0  0
 PKY  CONST_13  N5   C9   C8   C10   180.00   0.0  0
 PKY  CONST_14  N6   N7   C8   C10   180.00   0.0  0
 PKY  CONST_15  N6   N5   C9   C8      0.00   0.0  0
 PKY  CONST_16  N5   N6   N7   C8      0.00   0.0  0
 PKY  CONST_17  N5   C9   C8   N7      0.00   0.0  0
 PKY  CONST_18  C9   N5   N6   N7      0.00   0.0  0
 PKY  CONST_19  C9   C8   N7   N6      0.00   0.0  0
 PKY  CONST_20  C14  C13  C12  C2    180.00   0.0  0
 PKY  CONST_21  C10  C11  C12  C2    180.00   0.0  0
 PKY  CONST_22  C1   N5   C9   C8    180.00   0.0  0
 PKY  CONST_23  C1   N5   N6   N7    180.00   0.0  0
 PKY  CONST_24  H5   C14  C13  C12   180.00   0.0  0
 PKY  CONST_25  H6   C15  C10  C11   180.00   0.0  0
 PKY  CONST_26  H4   C13  C12  C11   180.00   0.0  0
 PKY  CONST_27  H3   C11  C12  C13   180.00   0.0  0
 PKY  CONST_28  H7   C9   C8   C10     0.00   0.0  0
 PKY  CONST_29  H1   N8   C2   C12   180.00   0.0  0
 PKY  CONST_30  H2   N8   C2   C12     0.00   0.0  0
 PKY  Var_01    C13  C12  C2   O7    156.33  30.0  3
 PKY  Var_02    B1   C1   N5   N6   -106.00  30.0  2
 PKY  Var_03    O4   B1   C1   N5   -179.08  30.0  1
 PKY  Var_04    O3   P1   O4   B1    178.38  30.0  2

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
 PKY  plan-1  C10  0.020
 PKY  plan-1  C8   0.020
 PKY  plan-1  N7   0.020
 PKY  plan-1  N6   0.020
 PKY  plan-1  C9   0.020
 PKY  plan-1  N5   0.020
 PKY  plan-1  C1   0.020
 PKY  plan-1  H7   0.020
 PKY  plan-2  C2   0.020
 PKY  plan-2  C12  0.020
 PKY  plan-2  C11  0.020
 PKY  plan-2  C13  0.020
 PKY  plan-2  C14  0.020
 PKY  plan-2  C15  0.020
 PKY  plan-2  C10  0.020
 PKY  plan-2  C8   0.020
 PKY  plan-2  H3   0.020
 PKY  plan-2  H4   0.020
 PKY  plan-2  H5   0.020
 PKY  plan-2  H6   0.020
 PKY  plan-3  O7   0.020
 PKY  plan-3  C2   0.020
 PKY  plan-3  N8   0.020
 PKY  plan-3  C12  0.020
 PKY  plan-3  H1   0.020
 PKY  plan-3  H2   0.020

