# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 01:17:06 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[6-[(phenylmethyl)amino]purin-9-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23
#
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
 KYK  KYK  '[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[6-[(phenylmethyl)amino]purin-9-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  54  34  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KYK
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
 KYK  N1    N  N      0  -0.488  -12.2110  22.8161  -36.9485
 KYK  N3    N  N      0  -0.455  -14.2957  21.6665  -36.8696
 KYK  C4    C  CR56   0   0.496  -14.0728  21.5645  -35.5612
 KYK  C5    C  CR56   0   0.009  -12.9709  22.0415  -34.8580
 KYK  C6    C  CR6    0   0.424  -11.9955  22.7023  -35.6299
 KYK  C8    C  CR15   0   0.169  -14.2340  21.1083  -33.4223
 KYK  C22   C  CR16   0  -0.263  -12.5196  26.1846  -31.3304
 KYK  C24   C  CR16   0  -0.274  -11.9076  25.3653  -33.5127
 KYK  C26   C  CR16   0  -0.285  -11.1733  24.2038  -31.5513
 KYK  O1B   O  OP    -1  -0.943  -16.5197  21.9187  -29.5066
 KYK  O2B   O  OP    -1  -0.878  -14.5745  21.0608  -28.0620
 KYK  O3B   O  O      0  -0.790  -14.6692  20.4566  -30.5477
 KYK  PA    P  P      0   1.213  -17.9421  18.7336  -29.6620
 KYK  O1A   O  OP    -1  -0.790  -19.0963  19.6080  -29.2430
 KYK  O2A   O  O      0  -0.816  -18.0883  17.2314  -29.5590
 KYK  C3A   C  CH2    0  -0.965  -16.4006  19.2423  -28.8330
 KYK  C5'   C  CH2    0  -0.148  -16.7646  18.4068  -32.0230
 KYK  C4'   C  CH1    0  -0.020  -16.9670  18.7046  -33.4878
 KYK  O4'   O  O2     0  -0.481  -16.8322  20.1050  -33.7423
 KYK  C3'   C  CH1    0   0.017  -15.9248  18.0492  -34.3976
 KYK  O3'   O  OH1    0  -0.646  -16.2171  16.7393  -34.7906
 KYK  C2'   C  CH1    0  -0.103  -15.9511  18.9772  -35.6079
 KYK  O2'   O  OH1    0  -0.688  -17.0820  18.7558  -36.4080
 KYK  C1'   C  CH1    0   0.213  -16.1443  20.3337  -34.9288
 KYK  N9    N  NR5    0  -0.545  -14.8696  20.9732  -34.6292
 KYK  N7    N  N      0  -0.519  -13.1001  21.7439  -33.5242
 KYK  N6    N  NH1    0  -0.641  -10.8548  23.2238  -35.1545
 KYK  C2    C  CR16   0   0.083  -13.3139  22.3060  -37.4812
 KYK  C23   C  CR16   0  -0.235  -12.5615  26.2954  -32.7126
 KYK  C25   C  CR6    0   0.056  -11.2083  24.3095  -32.9400
 KYK  C27   C  CR16   0  -0.234  -11.8190  25.1335  -30.7507
 KYK  H8    H  HCR5   0   0.298  -14.6406  20.7523  -32.4726
 KYK  H3    H  HCH2   0   0.274  -10.5764  22.3026  -33.3076
 KYK  H1    H  HCH2   0   0.251   -9.4008  23.5132  -33.7514
 KYK  H23   H  HCR6   0   0.216  -11.9532  25.4670  -34.5899
 KYK  H25   H  HCR6   0   0.265  -10.6424  23.3778  -31.0912
 KYK  H3A2  H  HCH2   0   0.182  -16.6706  19.3002  -27.7717
 KYK  H3A1  H  HCH2   0   0.162  -15.6875  18.4145  -28.9029
 KYK  H5'2  H  HCH2   0   0.198  -16.8651  17.3195  -31.8991
 KYK  H5'1  H  HCH2   0   0.221  -15.7512  18.6889  -31.7164
 KYK  H4'   H  HCH1   0   0.230  -17.9711  18.3824  -33.7923
 KYK  H3'   H  HCH1   0   0.238  -14.9344  18.1154  -33.9237
 KYK  HO3'  H  HOH1   0   0.439  -16.1241  16.1516  -34.0344
 KYK  H2'   H  HCH1   0   0.274  -15.0233  18.9375  -36.1912
 KYK  HO2'  H  HOH1   0   0.424  -17.1383  17.8136  -36.6024
 KYK  H1'   H  HCH1   0   0.257  -16.7018  21.0170  -35.5772
 KYK  HN61  H  HNH1   0   0.401  -10.2789  23.6987  -35.8312
 KYK  H2    H  HCR6   0   0.283  -13.4185  22.4333  -38.5537
 KYK  H22   H  HCR6   0   0.262  -13.1074  27.1082  -33.1749
 KYK  H26   H  HCR6   0   0.240  -11.7851  25.0320  -29.6734
 KYK  O5'   O  O2     0  -0.621  -17.7218  19.1057  -31.2719
 KYK  C21   C  CH2    0  -0.339  -10.4677  23.2843  -33.7690
 KYK  H21   H  HCR6   0   0.257  -13.0317  26.9078  -30.7087
 KYK  PB    P  P      0   1.115  -15.4745  20.8219  -29.2805

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
 KYK  C2   N3    aromatic  1.322  0.020  1.322
 KYK  C2   N1    aromatic  1.327  0.020  1.327
 KYK  N3   C4    aromatic  1.331  0.020  1.331
 KYK  N1   C6    aromatic  1.341  0.020  1.341
 KYK  O2'  C2'   single    1.403  0.020  1.403
 KYK  C4   C5    aromatic  1.391  0.020  1.391
 KYK  C4   N9    aromatic  1.361  0.020  1.361
 KYK  C2'  C1'   single    1.529  0.020  1.529
 KYK  C2'  C3'   single    1.525  0.020  1.525
 KYK  C6   N6    single    1.341  0.020  1.341
 KYK  C6   C5    aromatic  1.408  0.020  1.408
 KYK  C1'  N9    single    1.457  0.020  1.457
 KYK  C1'  O4'   single    1.390  0.020  1.390
 KYK  N6   C21   single    1.440  0.020  1.440
 KYK  C5   N7    aromatic  1.373  0.020  1.373
 KYK  N9   C8    aromatic  1.371  0.020  1.371
 KYK  O3'  C3'   single    1.399  0.020  1.399
 KYK  C3'  C4'   single    1.531  0.020  1.531
 KYK  O4'  C4'   single    1.430  0.020  1.430
 KYK  C4'  C5'   single    1.508  0.020  1.508
 KYK  C21  C25   single    1.512  0.020  1.512
 KYK  C8   N7    aromatic  1.304  0.020  1.304
 KYK  C26  C25   aromatic  1.393  0.020  1.393
 KYK  C26  C27   aromatic  1.387  0.020  1.387
 KYK  C25  C24   aromatic  1.390  0.020  1.390
 KYK  C27  C22   aromatic  1.390  0.020  1.390
 KYK  C24  C23   aromatic  1.390  0.020  1.390
 KYK  C22  C23   aromatic  1.387  0.020  1.387
 KYK  C5'  O5'   single    1.403  0.020  1.403
 KYK  O5'  PA    single    1.667  0.020  1.667
 KYK  O2A  PA    deloc     1.513  0.020  1.513
 KYK  PA   O1A   deloc     1.507  0.020  1.507
 KYK  PA   C3A   single    1.823  0.020  1.823
 KYK  O3B  PB    deloc     1.545  0.020  1.545
 KYK  C3A  PB    single    1.885  0.020  1.885
 KYK  PB   O1B   deloc     1.532  0.020  1.532
 KYK  PB   O2B   deloc     1.534  0.020  1.534
 KYK  C8   H8    single    0.930  0.020  1.080
 KYK  C21  H3    single    0.970  0.020  1.090
 KYK  C21  H1    single    0.970  0.020  1.090
 KYK  C22  H21   single    0.930  0.020  1.080
 KYK  C24  H23   single    0.930  0.020  1.080
 KYK  C26  H25   single    0.930  0.020  1.080
 KYK  C3A  H3A2  single    0.970  0.020  1.090
 KYK  C3A  H3A1  single    0.970  0.020  1.090
 KYK  C5'  H5'2  single    0.970  0.020  1.090
 KYK  C5'  H5'1  single    0.970  0.020  1.090
 KYK  C4'  H4'   single    0.970  0.020  1.090
 KYK  C3'  H3'   single    0.970  0.020  1.090
 KYK  O3'  HO3'  single    0.850  0.020  0.980
 KYK  C2'  H2'   single    0.970  0.020  1.090
 KYK  O2'  HO2'  single    0.850  0.020  0.980
 KYK  C1'  H1'   single    0.970  0.020  1.090
 KYK  N6   HN61  single    0.860  0.020  1.020
 KYK  C2   H2    single    0.930  0.020  1.080
 KYK  C23  H22   single    0.930  0.020  1.080
 KYK  C27  H26   single    0.930  0.020  1.080

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
 KYK  C2    N1   C6    119.72  3.000
 KYK  C2    N3   C4    111.56  3.000
 KYK  N9    C4   C5    105.45  3.000
 KYK  N9    C4   N3    127.46  3.000
 KYK  C5    C4   N3    127.09  3.000
 KYK  N7    C5   C6    134.38  3.000
 KYK  N7    C5   C4    110.01  3.000
 KYK  C6    C5   C4    115.61  3.000
 KYK  N6    C6   C5    125.24  3.000
 KYK  C5    C6   N1    117.87  3.000
 KYK  N6    C6   N1    116.88  3.000
 KYK  H8    C8   N7    123.39  3.000
 KYK  H8    C8   N9    124.10  3.000
 KYK  N7    C8   N9    112.49  3.000
 KYK  H21   C22  C27   120.28  3.000
 KYK  H21   C22  C23   120.30  3.000
 KYK  C27   C22  C23   119.42  3.000
 KYK  H23   C24  C25   120.16  3.000
 KYK  H23   C24  C23   119.33  3.000
 KYK  C25   C24  C23   120.51  3.000
 KYK  H25   C26  C27   119.59  3.000
 KYK  H25   C26  C25   119.55  3.000
 KYK  C27   C26  C25   120.86  3.000
 KYK  O5'   PA   C3A   105.38  3.000
 KYK  C3A   PA   O2A   109.14  3.000
 KYK  O5'   PA   O2A   107.47  3.000
 KYK  C3A   PA   O1A   111.05  3.000
 KYK  O2A   PA   O1A   118.89  3.000
 KYK  O5'   PA   O1A   103.89  3.000
 KYK  H3A1  C3A  H3A2  105.19  3.000
 KYK  H3A1  C3A  PA    108.10  3.000
 KYK  H3A2  C3A  PA    104.28  3.000
 KYK  H3A1  C3A  PB    107.37  3.000
 KYK  H3A2  C3A  PB    107.85  3.000
 KYK  PA    C3A  PB    122.78  3.000
 KYK  H5'1  C5'  H5'2  107.92  3.000
 KYK  H5'1  C5'  C4'   110.18  3.000
 KYK  H5'2  C5'  C4'   107.01  3.000
 KYK  H5'1  C5'  O5'   110.67  3.000
 KYK  H5'2  C5'  O5'   111.72  3.000
 KYK  C4'   C5'  O5'   109.27  3.000
 KYK  H4'   C4'  C3'   109.41  3.000
 KYK  H4'   C4'  O4'   108.93  3.000
 KYK  C3'   C4'  O4'   104.44  3.000
 KYK  H4'   C4'  C5'   109.52  3.000
 KYK  O4'   C4'  C5'   110.70  3.000
 KYK  C3'   C4'  C5'   113.66  3.000
 KYK  C1'   O4'  C4'   111.07  3.000
 KYK  H3'   C3'  C2'   108.71  3.000
 KYK  H3'   C3'  O3'   111.44  3.000
 KYK  C2'   C3'  O3'   110.07  3.000
 KYK  H3'   C3'  C4'   109.34  3.000
 KYK  O3'   C3'  C4'   115.19  3.000
 KYK  C2'   C3'  C4'   101.50  3.000
 KYK  HO3'  O3'  C3'   109.33  3.000
 KYK  H2'   C2'  C1'   112.04  3.000
 KYK  H2'   C2'  O2'   111.90  3.000
 KYK  C1'   C2'  O2'   106.94  3.000
 KYK  H2'   C2'  C3'   112.67  3.000
 KYK  C1'   C2'  C3'   100.92  3.000
 KYK  O2'   C2'  C3'   111.74  3.000
 KYK  HO2'  O2'  C2'   108.45  3.000
 KYK  H1'   C1'  N9    107.06  3.000
 KYK  H1'   C1'  C2'   110.80  3.000
 KYK  N9    C1'  C2'   111.72  3.000
 KYK  H1'   C1'  O4'   110.86  3.000
 KYK  N9    C1'  O4'   109.24  3.000
 KYK  C2'   C1'  O4'   107.19  3.000
 KYK  C1'   N9   C8    129.04  3.000
 KYK  C8    N9   C4    106.78  3.000
 KYK  C1'   N9   C4    124.19  3.000
 KYK  C8    N7   C5    105.28  3.000
 KYK  HN61  N6   C21   118.22  3.000
 KYK  HN61  N6   C6    115.55  3.000
 KYK  C21   N6   C6    125.88  3.000
 KYK  H2    C2   N3    116.27  3.000
 KYK  H2    C2   N1    115.58  3.000
 KYK  N3    C2   N1    128.15  3.000
 KYK  H22   C23  C24   119.58  3.000
 KYK  H22   C23  C22   120.04  3.000
 KYK  C24   C23  C22   120.38  3.000
 KYK  C26   C25  C24   118.76  3.000
 KYK  C24   C25  C21   122.38  3.000
 KYK  C26   C25  C21   118.86  3.000
 KYK  H26   C27  C26   119.81  3.000
 KYK  H26   C27  C22   120.12  3.000
 KYK  C26   C27  C22   120.07  3.000
 KYK  C5'   O5'  PA    119.73  3.000
 KYK  H1    C21  H3    106.23  3.000
 KYK  H1    C21  C25   109.13  3.000
 KYK  H3    C21  C25   109.25  3.000
 KYK  H1    C21  N6    106.69  3.000
 KYK  H3    C21  N6    110.04  3.000
 KYK  C25   C21  N6    115.11  3.000
 KYK  C3A   PB   O3B   104.63  3.000
 KYK  C3A   PB   O2B   103.31  3.000
 KYK  O3B   PB   O2B   112.49  3.000
 KYK  O2B   PB   O1B   113.96  3.000
 KYK  C3A   PB   O1B   107.45  3.000
 KYK  O3B   PB   O1B   113.82  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
 KYK  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 KYK  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 KYK  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 KYK  CONST_04  C6    N1   C2   N3     0.00   0.0  0
 KYK  CONST_05  C6    C5   C4   N3     0.00   0.0  0
 KYK  CONST_06  N7    C5   C4   N3   180.00   0.0  0
 KYK  CONST_07  C8    N9   C4   N3   180.00   0.0  0
 KYK  CONST_08  C8    N7   C5   C4     0.00   0.0  0
 KYK  CONST_09  N7    C8   N9   C4     0.00   0.0  0
 KYK  CONST_10  C2    N3   C4   C5     0.00   0.0  0
 KYK  CONST_11  C8    N9   C4   C5     0.00   0.0  0
 KYK  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 KYK  CONST_13  N9    C8   N7   C5     0.00   0.0  0
 KYK  CONST_14  N9    C4   C5   C6   180.00   0.0  0
 KYK  CONST_15  C8    N7   C5   C6   180.00   0.0  0
 KYK  CONST_16  C25   C26  C27  C22    0.00   0.0  0
 KYK  CONST_17  C25   C24  C23  C22    0.00   0.0  0
 KYK  CONST_18  C27   C26  C25  C24    0.00   0.0  0
 KYK  CONST_19  C27   C22  C23  C24    0.00   0.0  0
 KYK  CONST_20  C23   C24  C25  C26    0.00   0.0  0
 KYK  CONST_21  C23   C22  C27  C26    0.00   0.0  0
 KYK  CONST_22  C2    N3   C4   N9   180.00   0.0  0
 KYK  CONST_23  N7    C5   C4   N9     0.00   0.0  0
 KYK  CONST_24  C1'   N9   C4   N3     0.00   0.0  0
 KYK  CONST_25  C1'   N9   C4   C5   180.00   0.0  0
 KYK  CONST_26  N7    C8   N9   C1'  180.00   0.0  0
 KYK  CONST_27  N6    C6   C5   C4   180.00   0.0  0
 KYK  CONST_28  C27   C26  C25  C21  180.00   0.0  0
 KYK  CONST_29  C23   C24  C25  C21  180.00   0.0  0
 KYK  CONST_30  N6    C6   C5   N7     0.00   0.0  0
 KYK  CONST_31  C2    N1   C6   N6   180.00   0.0  0
 KYK  CONST_32  H2    C2   N3   C4   180.00   0.0  0
 KYK  CONST_33  H8    C8   N9   C4   180.00   0.0  0
 KYK  CONST_34  H25   C26  C27  C22  180.00   0.0  0
 KYK  CONST_35  H23   C24  C23  C22  180.00   0.0  0
 KYK  CONST_36  H21   C22  C23  C24  180.00   0.0  0
 KYK  CONST_37  H26   C27  C22  C23  180.00   0.0  0
 KYK  CONST_38  H22   C23  C24  C25  180.00   0.0  0
 KYK  CONST_39  C21   N6   C6   N1   180.00   0.0  0
 KYK  CONST_40  C21   N6   C6   C5     0.00   0.0  0
 KYK  CONST_41  HN61  N6   C6   N1     0.00   0.0  0
 KYK  Var_01    C25   C21  N6   C6   -73.59  30.0  3
 KYK  Var_02    N6    C21  C25  C24  -18.05  30.0  3
 KYK  Var_03    C4'   C5'  O5'  PA   167.58  30.0  2
 KYK  Var_04    O5'   PA   C3A  PB    39.57  30.0  1
 KYK  Var_05    PA    C3A  PB   O1B   40.86  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
 KYK  chir_02  C4'  C3'  O4'  C5'  positiv
 KYK  chir_03  C3'  O3'  C2'  C4'  negativ
 KYK  chir_04  C2'  O2'  C1'  C3'  negativ
 KYK  chir_05  C1'  O4'  N9   C2'  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
 KYK  plan-1  C22   0.020
 KYK  plan-1  C24   0.020
 KYK  plan-1  C26   0.020
 KYK  plan-1  C23   0.020
 KYK  plan-1  C25   0.020
 KYK  plan-1  C27   0.020
 KYK  plan-1  H23   0.020
 KYK  plan-1  H25   0.020
 KYK  plan-1  H22   0.020
 KYK  plan-1  H26   0.020
 KYK  plan-1  C21   0.020
 KYK  plan-1  H21   0.020
 KYK  plan-2  N1    0.020
 KYK  plan-2  N3    0.020
 KYK  plan-2  C4    0.020
 KYK  plan-2  C5    0.020
 KYK  plan-2  C6    0.020
 KYK  plan-2  C8    0.020
 KYK  plan-2  C1'   0.020
 KYK  plan-2  N9    0.020
 KYK  plan-2  N7    0.020
 KYK  plan-2  N6    0.020
 KYK  plan-2  C2    0.020
 KYK  plan-2  H8    0.020
 KYK  plan-2  H2    0.020
 KYK  plan-3  C6    0.020
 KYK  plan-3  N6    0.020
 KYK  plan-3  HN61  0.020
 KYK  plan-3  C21   0.020

