# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 13:42:12 2022
#   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  32  22  .  2022-03-23  2022-03-23
;
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  -0.471  22.7714   -5.7910  -33.1896
 PKY  C2   C  C      0   0.488  22.5088   -5.0382  -34.1165
 PKY  N8   N  NH2    0  -0.815  22.2457   -3.7338  -33.9374
 PKY  C12  C  CR6    0  -0.014  22.4624   -5.5375  -35.5288
 PKY  C11  C  CR16   0  -0.326  23.1404   -6.7157  -35.8203
 PKY  C13  C  CR16   0  -0.300  21.7479   -4.8906  -36.5349
 PKY  C14  C  CR16   0  -0.218  21.7352   -5.4177  -37.8179
 PKY  C15  C  CR16   0  -0.336  22.4304   -6.5799  -38.1065
 PKY  C10  C  CR6    0   0.091  23.1412   -7.2477  -37.1078
 PKY  C8   C  CR5    0   0.147  23.8580   -8.4857  -37.3995
 PKY  N7   N  N      0  -0.339  24.5498   -9.1715  -36.4667
 PKY  N6   N  N      0  -0.113  25.0553  -10.2308  -37.0087
 PKY  C9   C  CR15   0  -0.093  23.9627   -9.1840  -38.5847
 PKY  N5   N  NR5    0  -0.232  24.7048  -10.2535  -38.2791
 PKY  C1   C  CH2    0  -0.567  25.1873  -11.2873  -39.1825
 PKY  B1   B  B      0   0.578  26.5507  -10.8324  -39.9869
 PKY  O2   O  OH1    0  -0.694  27.6283  -10.4681  -39.1025
 PKY  O4   O  O2     0  -0.722  26.8771  -11.9041  -41.0073
 PKY  P1   P  P      0   1.271  26.6021  -10.8125  -42.1915
 PKY  O6   O  OP    -1  -0.818  27.8480  -10.4683  -42.9636
 PKY  O3   O  O      0  -0.824  25.3581  -11.1320  -42.9784
 PKY  O5   O  OP    -1  -0.715  26.3086   -9.7442  -40.9813
 PKY  H1   H  HNH2   0   0.403  22.2884   -3.3431  -33.0101
 PKY  H2   H  HNH2   0   0.411  22.1708   -3.0840  -34.7002
 PKY  H3   H  HCR6   0   0.255  23.6805   -7.2250  -35.0338
 PKY  H4   H  HCR6   0   0.258  21.1762   -3.9938  -36.3340
 PKY  H5   H  HCR6   0   0.264  21.1737   -4.9207  -38.5977
 PKY  H6   H  HCR6   0   0.257  22.4097   -6.9703  -39.1163
 PKY  H7   H  HCR5   0   0.293  23.5748   -9.0145  -39.5743
 PKY  H8   H  HCH2   0   0.228  24.3707  -11.5125  -39.8712
 PKY  H9   H  HCH2   0   0.226  25.3434  -12.1797  -38.5723
 PKY  H10  H  HOH1   0   0.430  27.6913  -11.0817  -38.3670

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   deloc     1.506  0.020  1.506
 PKY  O6   P1   deloc     1.506  0.020  1.506
 PKY  P1   O5   deloc     1.641  0.020  1.641
 PKY  P1   O4   single    1.634  0.020  1.634
 PKY  O4   B1   single    1.515  0.020  1.515
 PKY  B1   O2   single    1.441  0.020  1.441
 PKY  B1   C1   single    1.647  0.020  1.647
 PKY  C1   N5   single    1.455  0.020  1.455
 PKY  C9   N5   aromatic  1.337  0.020  1.337
 PKY  C9   C8   aromatic  1.380  0.020  1.380
 PKY  N5   N6   aromatic  1.318  0.020  1.318
 PKY  C15  C14  aromatic  1.385  0.020  1.385
 PKY  C15  C10  aromatic  1.396  0.020  1.396
 PKY  C14  C13  aromatic  1.387  0.020  1.387
 PKY  C8   C10  single    1.460  0.020  1.460
 PKY  C8   N7   aromatic  1.349  0.020  1.349
 PKY  C10  C11  aromatic  1.393  0.020  1.393
 PKY  N6   N7   aromatic  1.293  0.020  1.293
 PKY  C13  C12  aromatic  1.393  0.020  1.393
 PKY  C11  C12  aromatic  1.390  0.020  1.390
 PKY  C12  C2   single    1.499  0.020  1.499
 PKY  C2   N8   single    1.343  0.020  1.343
 PKY  C2   O7   double    1.223  0.020  1.223
 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

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   116.31  3.000
 PKY  N8   C2   O7   122.62  3.000
 PKY  C12  C2   O7   121.06  3.000
 PKY  H2   N8   H1   116.82  3.000
 PKY  H2   N8   C2   122.79  3.000
 PKY  H1   N8   C2   119.43  3.000
 PKY  C13  C12  C11  119.48  3.000
 PKY  C11  C12  C2   117.70  3.000
 PKY  C13  C12  C2   122.80  3.000
 PKY  H3   C11  C10  119.47  3.000
 PKY  H3   C11  C12  119.35  3.000
 PKY  C10  C11  C12  121.18  3.000
 PKY  H4   C13  C14  118.80  3.000
 PKY  H4   C13  C12  121.44  3.000
 PKY  C14  C13  C12  119.74  3.000
 PKY  H5   C14  C15  119.73  3.000
 PKY  H5   C14  C13  119.79  3.000
 PKY  C15  C14  C13  120.48  3.000
 PKY  H6   C15  C10  120.29  3.000
 PKY  H6   C15  C14  119.17  3.000
 PKY  C10  C15  C14  120.54  3.000
 PKY  C8   C10  C15  120.85  3.000
 PKY  C8   C10  C11  120.58  3.000
 PKY  C15  C10  C11  118.57  3.000
 PKY  C9   C8   N7   107.33  3.000
 PKY  N7   C8   C10  123.01  3.000
 PKY  C9   C8   C10  129.65  3.000
 PKY  N6   N7   C8   109.10  3.000
 PKY  N5   N6   N7   108.31  3.000
 PKY  H7   C9   N5   122.41  3.000
 PKY  H7   C9   C8   133.07  3.000
 PKY  N5   C9   C8   104.52  3.000
 PKY  C1   N5   C9   127.62  3.000
 PKY  C9   N5   N6   110.73  3.000
 PKY  C1   N5   N6   121.50  3.000
 PKY  H9   C1   H8   106.91  3.000
 PKY  H9   C1   B1   112.34  3.000
 PKY  H8   C1   B1   111.60  3.000
 PKY  H9   C1   N5   106.32  3.000
 PKY  H8   C1   N5   106.87  3.000
 PKY  B1   C1   N5   112.42  3.000
 PKY  O4   B1   O2   115.53  3.000
 PKY  O2   B1   C1   112.90  3.000
 PKY  O4   B1   C1   108.17  3.000
 PKY  H10  O2   B1   110.96  3.000
 PKY  P1   O4   B1    88.81  3.000
 PKY  O5   P1   O3   112.07  3.000
 PKY  O5   P1   O6   112.18  3.000
 PKY  O3   P1   O6   117.64  3.000
 PKY  O5   P1   O4    86.02  3.000
 PKY  O6   P1   O4   112.65  3.000
 PKY  O3   P1   O4   112.08  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    157.24  30.0  2
 PKY  Var_02    B1   C1   N5   N6    -93.38  30.0  2
 PKY  Var_03    O4   B1   C1   N5   -173.66  30.0  3
 PKY  Var_04    O3   P1   O4   B1   -110.98  30.0  3

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

