# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 17:48:11 2021
#   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  57  34  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.479  -12.0713  22.6153  -36.7207
 KYK  N3    N  N     0  -0.458  -14.1594  21.4737  -36.8373
 KYK  C4    C  CR56  0   0.485  -14.0886  21.4245  -35.5094
 KYK  C5    C  CR56  0  -0.010  -13.0730  21.9290  -34.7038
 KYK  C6    C  CR6   0   0.479  -12.0075  22.5582  -35.3820
 KYK  C8    C  CR15  0   0.086  -14.5159  21.0983  -33.3899
 KYK  C21   C  CH2   0  -0.377  -10.6581  23.2145  -33.3924
 KYK  C22   C  CR16  0  -0.270  -11.7503  26.9874  -31.6236
 KYK  C24   C  CR16  0  -0.291  -12.2740  25.1384  -33.0756
 KYK  C26   C  CR16  0  -0.313  -10.1726  25.1967  -31.9264
 KYK  PB    P  P     0   1.389  -16.2813  20.4441  -29.0296
 KYK  O1B   O  OH1   0  -0.732  -17.5900  21.3367  -28.8413
 KYK  O2B   O  OH1   0  -0.739  -15.4738  20.7279  -27.6699
 KYK  O3B   O  O     0  -0.686  -15.4865  20.6573  -30.2629
 KYK  PA    P  P     0   1.385  -18.1861  18.1867  -29.9976
 KYK  O1A   O  OH1   0  -0.725  -19.4646  19.0546  -29.6057
 KYK  O2A   O  O     0  -0.698  -18.3434  16.7137  -29.9890
 KYK  C3A   C  CH2   0  -1.049  -16.9431  18.7760  -28.8263
 KYK  C5'   C  CH2   0  -0.171  -16.7820  18.2234  -32.2379
 KYK  C4'   C  CH1   0   0.007  -17.0505  18.5583  -33.6830
 KYK  O4'   O  O2    0  -0.493  -17.0011  19.9657  -33.9024
 KYK  C3'   C  CH1   0  -0.045  -16.0008  17.9672  -34.6215
 KYK  O3'   O  OH1   0  -0.655  -16.3505  16.6588  -34.9720
 KYK  C2'   C  CH1   0  -0.045  -16.0417  18.9572  -35.7899
 KYK  O2'   O  OH1   0  -0.664  -17.1667  18.7353  -36.5949
 KYK  C1'   C  CH1   0   0.177  -16.2648  20.2718  -35.0471
 KYK  N9    N  NR5   0  -0.544  -14.9985  20.8824  -34.6511
 KYK  N7    N  N     0  -0.458  -13.3691  21.7131  -33.3812
 KYK  N6    N  NH1   0  -0.629  -10.9290  23.1024  -34.8057
 KYK  C2    C  CR16  0   0.039  -13.1096  22.0874  -37.3558
 KYK  C23   C  CR16  0  -0.241  -12.6245  26.3490  -32.4951
 KYK  C25   C  CR6   0   0.119  -11.0431  24.5485  -32.7967
 KYK  C27   C  CR16  0  -0.241  -10.5225  26.4067  -31.3397
 KYK  H8    H  HCR5  0   0.315  -15.0548  20.8035  -32.5025
 KYK  H3    H  HCH2  0   0.281  -11.1798  22.4154  -32.8682
 KYK  H1    H  HCH2  0   0.276   -9.5911  23.0444  -33.2425
 KYK  H21   H  HCR6  0   0.255  -12.0238  27.9328  -31.1733
 KYK  H23   H  HCR6  0   0.249  -12.9708  24.6571  -33.7507
 KYK  H25   H  HCR6  0   0.252   -9.2078  24.7544  -31.7054
 KYK  H4    H  HOH1  0   0.499  -17.4596  22.2800  -29.0139
 KYK  H5    H  HOH1  0   0.497  -14.5257  20.5530  -27.7368
 KYK  H6    H  HOH1  0   0.501  -20.2911  18.7379  -29.9969
 KYK  H3A2  H  HCH2  0   0.340  -17.3481  18.6542  -27.8185
 KYK  H3A1  H  HCH2  0   0.338  -16.0918  18.0926  -28.8955
 KYK  H5'2  H  HCH2  0   0.253  -16.7756  17.1343  -32.1401
 KYK  H5'1  H  HCH2  0   0.240  -15.8072  18.6010  -31.9192
 KYK  H4'   H  HCH1  0   0.256  -18.0444  18.1859  -33.9596
 KYK  H3'   H  HCH1  0   0.252  -15.0093  18.0059  -34.1508
 KYK  HO3'  H  HOH1  0   0.470  -15.5678  16.2049  -35.3006
 KYK  H2'   H  HCH1  0   0.266  -15.1155  18.9619  -36.3754
 KYK  HO2'  H  HOH1  0   0.453  -17.2789  17.7811  -36.6878
 KYK  H1'   H  HCH1  0   0.288  -16.8048  20.9972  -35.6614
 KYK  HN61  H  HNH1  0   0.395  -10.2986  23.5760  -35.4350
 KYK  H2    H  HCR6  0   0.252  -13.0900  22.1736  -38.4371
 KYK  H22   H  HCR6  0   0.255  -13.5847  26.7943  -32.7226
 KYK  H26   H  HCR6  0   0.255   -9.8319  26.8973  -30.6660
 KYK  O5'   O  O2    0  -0.591  -17.8050  18.8055  -31.4309

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    1.401  0.020  1.401
 KYK  C4   C5    aromatic  1.391  0.020  1.391
 KYK  C4   N9    aromatic  1.363  0.020  1.363
 KYK  C2'  C1'   single    1.526  0.020  1.526
 KYK  C2'  C3'   single    1.532  0.020  1.532
 KYK  C6   N6    single    1.338  0.020  1.338
 KYK  C6   C5    aromatic  1.411  0.020  1.411
 KYK  C1'  N9    single    1.461  0.020  1.461
 KYK  C1'  O4'   single    1.395  0.020  1.395
 KYK  N6   C21   single    1.443  0.020  1.443
 KYK  C5   N7    aromatic  1.372  0.020  1.372
 KYK  N9   C8    aromatic  1.368  0.020  1.368
 KYK  O3'  C3'   single    1.399  0.020  1.399
 KYK  C3'  C4'   single    1.527  0.020  1.527
 KYK  O4'  C4'   single    1.425  0.020  1.425
 KYK  C4'  C5'   single    1.508  0.020  1.508
 KYK  C21  C25   single    1.511  0.020  1.511
 KYK  C8   N7    aromatic  1.301  0.020  1.301
 KYK  C26  C25   aromatic  1.391  0.020  1.391
 KYK  C26  C27   aromatic  1.390  0.020  1.390
 KYK  C25  C24   aromatic  1.393  0.020  1.393
 KYK  C27  C22   aromatic  1.388  0.020  1.388
 KYK  C24  C23   aromatic  1.388  0.020  1.388
 KYK  C22  C23   aromatic  1.390  0.020  1.390
 KYK  C5'  O5'   single    1.427  0.020  1.427
 KYK  O5'  PA    single    1.607  0.020  1.607
 KYK  O2A  PA    double    1.481  0.020  1.481
 KYK  PA   O1A   single    1.594  0.020  1.594
 KYK  PA   C3A   single    1.807  0.020  1.807
 KYK  O3B  PB    double    1.483  0.020  1.483
 KYK  C3A  PB    single    1.806  0.020  1.806
 KYK  PB   O1B   single    1.595  0.020  1.595
 KYK  PB   O2B   single    1.607  0.020  1.607
 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  O1B  H4    single    0.850  0.020  0.980
 KYK  O2B  H5    single    0.850  0.020  0.980
 KYK  O1A  H6    single    0.850  0.020  0.980
 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    119.87  3.000
 KYK  C2    N3   C4    111.49  3.000
 KYK  N9    C4   C5    105.48  3.000
 KYK  N9    C4   N3    127.41  3.000
 KYK  C5    C4   N3    127.11  3.000
 KYK  N7    C5   C6    134.13  3.000
 KYK  N7    C5   C4    110.09  3.000
 KYK  C6    C5   C4    115.77  3.000
 KYK  N6    C6   C5    125.64  3.000
 KYK  C5    C6   N1    117.56  3.000
 KYK  N6    C6   N1    116.79  3.000
 KYK  H8    C8   N7    124.30  3.000
 KYK  H8    C8   N9    122.62  3.000
 KYK  N7    C8   N9    113.06  3.000
 KYK  H1    C21  H3    106.75  3.000
 KYK  H1    C21  C25   109.44  3.000
 KYK  H3    C21  C25   109.64  3.000
 KYK  H1    C21  N6    107.82  3.000
 KYK  H3    C21  N6    108.93  3.000
 KYK  C25   C21  N6    114.00  3.000
 KYK  H21   C22  C27   120.27  3.000
 KYK  H21   C22  C23   120.21  3.000
 KYK  C27   C22  C23   119.52  3.000
 KYK  H23   C24  C25   120.33  3.000
 KYK  H23   C24  C23   119.09  3.000
 KYK  C25   C24  C23   120.59  3.000
 KYK  H25   C26  C27   119.56  3.000
 KYK  H25   C26  C25   119.62  3.000
 KYK  C27   C26  C25   120.82  3.000
 KYK  C3A   PB   O3B   115.02  3.000
 KYK  C3A   PB   O2B   104.60  3.000
 KYK  O3B   PB   O2B   114.15  3.000
 KYK  O2B   PB   O1B   102.33  3.000
 KYK  C3A   PB   O1B   101.71  3.000
 KYK  O3B   PB   O1B   117.22  3.000
 KYK  H4    O1B  PB    114.45  3.000
 KYK  H5    O2B  PB    113.74  3.000
 KYK  O5'   PA   C3A   106.82  3.000
 KYK  C3A   PA   O2A   113.17  3.000
 KYK  O5'   PA   O2A   114.41  3.000
 KYK  C3A   PA   O1A   102.40  3.000
 KYK  O2A   PA   O1A   117.05  3.000
 KYK  O5'   PA   O1A   101.53  3.000
 KYK  H6    O1A  PA    114.04  3.000
 KYK  H3A1  C3A  H3A2  106.08  3.000
 KYK  H3A1  C3A  PA    106.90  3.000
 KYK  H3A2  C3A  PA    107.84  3.000
 KYK  H3A1  C3A  PB    106.55  3.000
 KYK  H3A2  C3A  PB    110.03  3.000
 KYK  PA    C3A  PB    118.71  3.000
 KYK  H5'1  C5'  H5'2  108.23  3.000
 KYK  H5'1  C5'  C4'   111.21  3.000
 KYK  H5'2  C5'  C4'   107.93  3.000
 KYK  H5'1  C5'  O5'   109.49  3.000
 KYK  H5'2  C5'  O5'   111.09  3.000
 KYK  C4'   C5'  O5'   108.89  3.000
 KYK  H4'   C4'  C3'   109.67  3.000
 KYK  H4'   C4'  O4'   109.14  3.000
 KYK  C3'   C4'  O4'   105.29  3.000
 KYK  H4'   C4'  C5'   109.13  3.000
 KYK  O4'   C4'  C5'   111.14  3.000
 KYK  C3'   C4'  C5'   112.38  3.000
 KYK  C1'   O4'  C4'   111.18  3.000
 KYK  H3'   C3'  C2'   109.16  3.000
 KYK  H3'   C3'  O3'   111.48  3.000
 KYK  C2'   C3'  O3'   113.99  3.000
 KYK  H3'   C3'  C4'   110.09  3.000
 KYK  O3'   C3'  C4'   110.13  3.000
 KYK  C2'   C3'  C4'   101.55  3.000
 KYK  HO3'  O3'  C3'   108.85  3.000
 KYK  H2'   C2'  C1'   112.32  3.000
 KYK  H2'   C2'  O2'   111.86  3.000
 KYK  C1'   C2'  O2'   107.38  3.000
 KYK  H2'   C2'  C3'   112.81  3.000
 KYK  C1'   C2'  C3'   100.92  3.000
 KYK  O2'   C2'  C3'   110.94  3.000
 KYK  HO2'  O2'  C2'   107.77  3.000
 KYK  H1'   C1'  N9    107.65  3.000
 KYK  H1'   C1'  C2'   111.73  3.000
 KYK  N9    C1'  C2'   111.42  3.000
 KYK  H1'   C1'  O4'   110.24  3.000
 KYK  N9    C1'  O4'   109.08  3.000
 KYK  C2'   C1'  O4'   106.70  3.000
 KYK  C1'   N9   C8    128.46  3.000
 KYK  C8    N9   C4    106.40  3.000
 KYK  C1'   N9   C4    125.05  3.000
 KYK  C8    N7   C5    104.96  3.000
 KYK  HN61  N6   C21   117.20  3.000
 KYK  HN61  N6   C6    115.20  3.000
 KYK  C21   N6   C6    127.19  3.000
 KYK  H2    C2   N3    116.24  3.000
 KYK  H2    C2   N1    115.55  3.000
 KYK  N3    C2   N1    128.20  3.000
 KYK  H22   C23  C24   119.66  3.000
 KYK  H22   C23  C22   120.05  3.000
 KYK  C24   C23  C22   120.28  3.000
 KYK  C26   C25  C24   118.74  3.000
 KYK  C24   C25  C21   121.34  3.000
 KYK  C26   C25  C21   119.91  3.000
 KYK  H26   C27  C26   119.79  3.000
 KYK  H26   C27  C22   120.15  3.000
 KYK  C26   C27  C22   120.06  3.000
 KYK  C5'   O5'  PA    121.15  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   -96.12  30.0  3
 KYK  Var_02    N6    C21  C25  C24   46.15  30.0  2
 KYK  Var_03    C4'   C5'  O5'  PA   154.49  30.0  2
 KYK  Var_04    O5'   PA   C3A  PB    35.67  30.0  1
 KYK  Var_05    PA    C3A  PB   O1B   62.02  30.0  1

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
 KYK  chir_06  PA   O2A  O1A  C3A  both

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  C21   0.020
 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  H21   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-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  C21   0.020
 KYK  plan-3  N6    0.020
 KYK  plan-3  HN61  0.020

