# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 05:32:58 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2R,4R,5R,6R)-2-{[(S)-{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[C@]3(C[C@@H](O)[C@@H](O)[C@H](O3)[C@H](O)CO)C(O)=O)[C@@H](O)[C@H]2O
#
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
 CMK  CMK  '(2R,4R,5R,6R)-2-{[(S)-{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  ligand  60  36  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CMK
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
 CMK  N1C   N  NR6    0  -0.557   0.4302  -0.6648   5.4422
 CMK  C2C   C  CR6    0   0.603   0.4261   0.7073   5.7448
 CMK  N3C   N  N      0  -0.541   1.3533   1.1750   6.6037
 CMK  C4C   C  CR6    0   0.515   2.2533   0.3739   7.1395
 CMK  C5C   C  CR16   0  -0.478   2.3033  -1.0218   6.8369
 CMK  C6C   C  CR16   0   0.102   1.3709  -1.4799   5.9804
 CMK  O2C   O  OC     0  -0.509  -0.4166   1.4283   5.2293
 CMK  N4C   N  NH2    0  -0.808   3.1395   0.8954   7.9854
 CMK  C1'   C  CR15   0   0.210  -0.5202  -1.2193   4.4941
 CMK  C2'   C  CR15   0  -0.049  -2.0118  -0.9779   4.7900
 CMK  O2'   O  OH1    0  -0.677  -2.6619  -2.2234   4.7326
 CMK  C3'   C  CR15   0  -0.028  -2.4665  -0.0808   3.6250
 CMK  C4'   C  CR15   0   0.014  -1.4484  -0.4052   2.5334
 CMK  O4'   O  O      0  -0.492  -0.2473  -0.7176   3.2149
 CMK  O3'   O  OH1    0  -0.665  -3.7629  -0.3902   3.1762
 CMK  C5'   C  CH2    0  -0.151  -1.2229   0.7449   1.5856
 CMK  O5'   O  O2     0  -0.621  -0.3721   0.3316   0.5406
 CMK  PA    P  P      0   1.331  -0.1737   1.3663  -0.7333
 CMK  O1A   O  OP    -1  -0.780  -1.5161   1.7040  -1.2998
 CMK  O2A   O  O      0  -0.790   0.7778   2.4526  -0.3370
 CMK  O6    O  O2     0  -0.495  -0.2530   0.1676  -3.6536
 CMK  C2    C  CT     0   0.436   0.9521   0.3042  -2.9504
 CMK  O2    O  O2     0  -0.649   0.6158   0.2033  -1.5955
 CMK  C3    C  CH2    0  -0.517   1.8496  -0.8899  -3.2713
 CMK  C4    C  CH1    0   0.018   2.0291  -1.0367  -4.7767
 CMK  O4    O  OH1    0  -0.680   2.7353  -2.2130  -5.1198
 CMK  C5    C  CH1    0   0.037   0.6751  -1.1030  -5.4812
 CMK  C6    C  CH1    0  -0.015  -0.1327   0.1151  -5.0522
 CMK  C7    C  CH1    0  -0.016  -1.5567   0.1555  -5.6112
 CMK  C1    C  C      0   0.349   1.6533   1.6782  -3.2371
 CMK  O1X   O  OC    -1  -0.580   0.9307   2.6047  -3.6339
 CMK  O1Y   O  O      0  -0.596   2.8794   1.7089  -3.0236
 CMK  O5    O  OH1    0  -0.680  -0.0289  -2.2733  -5.1442
 CMK  C8    C  CH2    0  -0.175  -2.2457   1.4459  -5.1923
 CMK  O8    O  OH1    0  -0.676  -3.5774   1.4205  -5.6603
 CMK  O7    O  OH1    0  -0.666  -1.5544  -0.0127  -7.0111
 CMK  H5C   H  HCR6   0   0.289   3.0437  -1.6803   7.2646
 CMK  H6C   H  HCR6   0   0.319   1.3321  -2.5199   5.6874
 CMK  H4C1  H  HNH2   0   0.403   3.1047   1.8738   8.2155
 CMK  H4C2  H  HNH2   0   0.415   3.8380   0.3282   8.4323
 CMK  H1'   H  HCR5   0   0.251  -0.3524  -2.3008   4.5237
 CMK  H2'   H  HCR5   0   0.245  -2.1692  -0.5044   5.7647
 CMK  HA    H  HOH1   0   0.446  -3.5112  -2.0739   4.2949
 CMK  H3'   H  HCR5   0   0.257  -2.3877   0.9667   3.9179
 CMK  H4'   H  HCR5   0   0.229  -1.8028  -1.2796   1.9677
 CMK  HB    H  HOH1   0   0.469  -4.3913   0.1858   3.6219
 CMK  H5'1  H  HCH2   0   0.213  -2.1997   1.0616   1.2022
 CMK  H5'2  H  HCH2   0   0.208  -0.7963   1.5880   2.1436
 CMK  H3C1  H  HCH2   0   0.242   2.8199  -0.7682  -2.7872
 CMK  H3C2  H  HCH2   0   0.228   1.3850  -1.7971  -2.8745
 CMK  H4    H  HCH1   0   0.206   2.5575  -0.1517  -5.1597
 CMK  HC    H  HOH1   0   0.453   3.5023  -2.2897  -4.5439
 CMK  H5    H  HCH1   0   0.213   0.8448  -1.0406  -6.5658
 CMK  H6    H  HCH1   0   0.212   0.3991   1.0003  -5.4326
 CMK  H7    H  HCH1   0   0.228  -2.1208  -0.6920  -5.2096
 CMK  HD    H  HOH1   0   0.445   0.5800  -3.0145  -5.2319
 CMK  H8C1  H  HCH2   0   0.232  -2.1948   1.5455  -4.1040
 CMK  H8C2  H  HCH2   0   0.179  -1.6865   2.2967  -5.6127
 CMK  H8    H  HOH1   0   0.452  -4.0378   2.1711  -5.2760
 CMK  HE    H  HOH1   0   0.442  -1.1297   0.7542  -7.4113

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
 CMK  N1C  C2C   aromatic  1.405  0.020  1.405
 CMK  N1C  C6C   aromatic  1.356  0.020  1.356
 CMK  N1C  C1'   single    1.452  0.020  1.452
 CMK  C2C  N3C   aromatic  1.348  0.020  1.348
 CMK  C2C  O2C   double    1.223  0.020  1.223
 CMK  N3C  C4C   aromatic  1.319  0.020  1.319
 CMK  C4C  C5C   aromatic  1.429  0.020  1.429
 CMK  C4C  N4C   single    1.331  0.020  1.331
 CMK  C5C  C6C   aromatic  1.346  0.020  1.346
 CMK  C5C  H5C   single    0.930  0.020  1.080
 CMK  C6C  H6C   single    0.930  0.020  1.080
 CMK  N4C  H4C1  single    0.860  0.020  1.020
 CMK  N4C  H4C2  single    0.860  0.020  1.020
 CMK  C1'  C2'   single    1.540  0.020  1.540
 CMK  C1'  O4'   single    1.401  0.020  1.401
 CMK  C1'  H1'   single    0.970  0.020  1.090
 CMK  C2'  O2'   single    1.406  0.020  1.406
 CMK  C2'  C3'   single    1.539  0.020  1.539
 CMK  C2'  H2'   single    0.970  0.020  1.090
 CMK  O2'  HA    single    0.850  0.020  0.980
 CMK  C3'  C4'   single    1.527  0.020  1.527
 CMK  C3'  O3'   single    1.406  0.020  1.406
 CMK  C3'  H3'   single    0.970  0.020  1.090
 CMK  C4'  O4'   single    1.416  0.020  1.416
 CMK  C4'  C5'   single    1.507  0.020  1.507
 CMK  C4'  H4'   single    0.970  0.020  1.090
 CMK  O3'  HB    single    0.850  0.020  0.980
 CMK  C5'  O5'   single    1.409  0.020  1.409
 CMK  C5'  H5'1  single    0.970  0.020  1.090
 CMK  C5'  H5'2  single    0.970  0.020  1.090
 CMK  O5'  PA    single    1.653  0.020  1.653
 CMK  PA   O1A   deloc     1.496  0.020  1.496
 CMK  PA   O2A   deloc     1.497  0.020  1.497
 CMK  PA   O2    single    1.649  0.020  1.649
 CMK  O6   C2    single    1.402  0.020  1.402
 CMK  O6   C6    single    1.405  0.020  1.405
 CMK  C2   O2    single    1.400  0.020  1.400
 CMK  C2   C3    single    1.528  0.020  1.528
 CMK  C2   C1    single    1.569  0.020  1.569
 CMK  C3   C4    single    1.523  0.020  1.523
 CMK  C3   H3C1  single    0.970  0.020  1.090
 CMK  C3   H3C2  single    0.970  0.020  1.090
 CMK  C4   O4    single    1.414  0.020  1.414
 CMK  C4   C5    single    1.528  0.020  1.528
 CMK  C4   H4    single    0.970  0.020  1.090
 CMK  O4   HC    single    0.850  0.020  0.980
 CMK  C5   C6    single    1.523  0.020  1.523
 CMK  C5   O5    single    1.407  0.020  1.407
 CMK  C5   H5    single    0.970  0.020  1.090
 CMK  C6   C7    single    1.530  0.020  1.530
 CMK  C6   H6    single    0.970  0.020  1.090
 CMK  C7   C8    single    1.522  0.020  1.522
 CMK  C7   O7    single    1.410  0.020  1.410
 CMK  C7   H7    single    0.970  0.020  1.090
 CMK  C1   O1X   deloc     1.240  0.020  1.240
 CMK  C1   O1Y   deloc     1.245  0.020  1.245
 CMK  O5   HD    single    0.850  0.020  0.980
 CMK  C8   O8    single    1.412  0.020  1.412
 CMK  C8   H8C1  single    0.970  0.020  1.090
 CMK  C8   H8C2  single    0.970  0.020  1.090
 CMK  O8   H8    single    0.850  0.020  0.980
 CMK  O7   HE    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
 CMK  C1'   N1C  C6C   118.91  3.000
 CMK  C1'   N1C  C2C   120.76  3.000
 CMK  C6C   N1C  C2C   120.23  3.000
 CMK  O2C   C2C  N3C   122.56  3.000
 CMK  O2C   C2C  N1C   119.14  3.000
 CMK  N3C   C2C  N1C   118.30  3.000
 CMK  C4C   N3C  C2C   121.18  3.000
 CMK  N4C   C4C  C5C   119.59  3.000
 CMK  N4C   C4C  N3C   118.32  3.000
 CMK  C5C   C4C  N3C   122.09  3.000
 CMK  H5C   C5C  C6C   121.30  3.000
 CMK  H5C   C5C  C4C   122.41  3.000
 CMK  C6C   C5C  C4C   116.28  3.000
 CMK  H6C   C6C  C5C   121.64  3.000
 CMK  H6C   C6C  N1C   116.46  3.000
 CMK  C5C   C6C  N1C   121.89  3.000
 CMK  H4C2  N4C  H4C1  118.13  3.000
 CMK  H4C2  N4C  C4C   121.62  3.000
 CMK  H4C1  N4C  C4C   120.22  3.000
 CMK  H1'   C1'  O4'   110.40  3.000
 CMK  H1'   C1'  C2'   107.35  3.000
 CMK  O4'   C1'  C2'   107.94  3.000
 CMK  H1'   C1'  N1C   105.02  3.000
 CMK  O4'   C1'  N1C   109.38  3.000
 CMK  C2'   C1'  N1C   116.65  3.000
 CMK  H2'   C2'  C3'   112.29  3.000
 CMK  H2'   C2'  O2'   110.67  3.000
 CMK  C3'   C2'  O2'   110.41  3.000
 CMK  H2'   C2'  C1'   112.22  3.000
 CMK  C3'   C2'  C1'   103.42  3.000
 CMK  O2'   C2'  C1'   107.53  3.000
 CMK  HA    O2'  C2'   106.71  3.000
 CMK  H3'   C3'  O3'   111.33  3.000
 CMK  H3'   C3'  C4'   110.36  3.000
 CMK  O3'   C3'  C4'   109.85  3.000
 CMK  H3'   C3'  C2'   109.58  3.000
 CMK  O3'   C3'  C2'   112.68  3.000
 CMK  C4'   C3'  C2'   102.72  3.000
 CMK  H4'   C4'  C5'   109.35  3.000
 CMK  H4'   C4'  O4'   110.21  3.000
 CMK  C5'   C4'  O4'   110.12  3.000
 CMK  H4'   C4'  C3'   108.76  3.000
 CMK  C5'   C4'  C3'   112.77  3.000
 CMK  O4'   C4'  C3'   105.57  3.000
 CMK  C4'   O4'  C1'   110.68  3.000
 CMK  HB    O3'  C3'   108.82  3.000
 CMK  H5'2  C5'  H5'1  107.59  3.000
 CMK  H5'2  C5'  O5'   111.57  3.000
 CMK  H5'1  C5'  O5'   111.31  3.000
 CMK  H5'2  C5'  C4'   108.94  3.000
 CMK  H5'1  C5'  C4'   107.88  3.000
 CMK  O5'   C5'  C4'   109.44  3.000
 CMK  PA    O5'  C5'   117.40  3.000
 CMK  O2    PA   O2A   110.23  3.000
 CMK  O2    PA   O1A   113.01  3.000
 CMK  O2A   PA   O1A   120.45  3.000
 CMK  O2    PA   O5'    91.08  3.000
 CMK  O2A   PA   O5'   109.05  3.000
 CMK  O1A   PA   O5'   108.99  3.000
 CMK  C6    O6   C2    115.43  3.000
 CMK  C1    C2   C3    112.55  3.000
 CMK  C1    C2   O2    110.32  3.000
 CMK  C3    C2   O2    106.74  3.000
 CMK  C1    C2   O6    112.20  3.000
 CMK  C3    C2   O6    108.87  3.000
 CMK  O2    C2   O6    105.79  3.000
 CMK  C2    O2   PA    124.77  3.000
 CMK  H3C2  C3   H3C1  108.02  3.000
 CMK  H3C2  C3   C4    109.19  3.000
 CMK  H3C1  C3   C4    110.15  3.000
 CMK  H3C2  C3   C2    108.81  3.000
 CMK  H3C1  C3   C2    110.00  3.000
 CMK  C4    C3   C2    110.62  3.000
 CMK  H4    C4   C5    107.47  3.000
 CMK  H4    C4   O4    110.18  3.000
 CMK  C5    C4   O4    107.14  3.000
 CMK  H4    C4   C3    108.86  3.000
 CMK  C5    C4   C3    110.83  3.000
 CMK  O4    C4   C3    112.26  3.000
 CMK  HC    O4   C4    108.62  3.000
 CMK  H5    C5   O5    111.15  3.000
 CMK  H5    C5   C6    108.32  3.000
 CMK  O5    C5   C6    109.41  3.000
 CMK  H5    C5   C4    108.40  3.000
 CMK  O5    C5   C4    111.66  3.000
 CMK  C6    C5   C4    107.78  3.000
 CMK  H6    C6   C7    107.58  3.000
 CMK  H6    C6   C5    106.84  3.000
 CMK  C7    C6   C5    114.31  3.000
 CMK  H6    C6   O6    110.82  3.000
 CMK  C7    C6   O6    106.44  3.000
 CMK  C5    C6   O6    110.84  3.000
 CMK  H7    C7   O7    105.83  3.000
 CMK  H7    C7   C8    108.80  3.000
 CMK  O7    C7   C8    112.04  3.000
 CMK  H7    C7   C6    108.98  3.000
 CMK  O7    C7   C6    110.98  3.000
 CMK  C8    C7   C6    110.07  3.000
 CMK  O1Y   C1   O1X   127.62  3.000
 CMK  O1Y   C1   C2    115.49  3.000
 CMK  O1X   C1   C2    116.88  3.000
 CMK  HD    O5   C5    107.58  3.000
 CMK  H8C2  C8   H8C1  106.60  3.000
 CMK  H8C2  C8   O8    111.49  3.000
 CMK  H8C1  C8   O8    112.04  3.000
 CMK  H8C2  C8   C7    108.67  3.000
 CMK  H8C1  C8   C7    109.27  3.000
 CMK  O8    C8   C7    108.70  3.000
 CMK  H8    O8   C8    107.78  3.000
 CMK  HE    O7   C7    108.55  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
 CMK  CONST_01  C4C   N3C  C2C  N1C    0.00   0.0  0
 CMK  CONST_02  C4C   C5C  C6C  N1C    0.00   0.0  0
 CMK  CONST_03  C5C   C6C  N1C  C2C    0.00   0.0  0
 CMK  CONST_04  C5C   C4C  N3C  C2C    0.00   0.0  0
 CMK  CONST_05  C6C   N1C  C2C  N3C    0.00   0.0  0
 CMK  CONST_06  C6C   C5C  C4C  N3C    0.00   0.0  0
 CMK  CONST_07  C1'   N1C  C2C  N3C  180.00   0.0  0
 CMK  CONST_08  C1'   N1C  C6C  C5C  180.00   0.0  0
 CMK  CONST_09  N4C   C4C  N3C  C2C  180.00   0.0  0
 CMK  CONST_10  O2C   C2C  N3C  C4C  180.00   0.0  0
 CMK  CONST_11  O2C   C2C  N1C  C6C  180.00   0.0  0
 CMK  CONST_12  N4C   C4C  C5C  C6C  180.00   0.0  0
 CMK  CONST_13  C1'   N1C  C2C  O2C    0.00   0.0  0
 CMK  CONST_14  H5C   C5C  C6C  N1C  180.00   0.0  0
 CMK  CONST_15  H6C   C6C  N1C  C2C  180.00   0.0  0
 CMK  CONST_16  H4C1  N4C  C4C  N3C    0.00   0.0  0
 CMK  CONST_17  H4C2  N4C  C4C  N3C  180.00   0.0  0
 CMK  Var_01    O1A   PA   O5'  C5'  -55.38  30.0  3
 CMK  Var_02    H5'1  C5'  O5'  PA    51.88  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
 CMK  chir_01  C1'  N1C  C2'  O4'  negativ
 CMK  chir_02  C2'  O2'  C3'  C1'  positiv
 CMK  chir_03  C3'  O3'  C2'  C4'  negativ
 CMK  chir_04  C4'  O4'  C3'  C5'  negativ
 CMK  chir_06  C2   O6   C3   C1   negativ
 CMK  chir_07  C4   O4   C3   C5   positiv
 CMK  chir_08  C5   O5   C4   C6   positiv
 CMK  chir_09  C6   O6   C7   C5   positiv
 CMK  chir_10  C7   O7   C6   C8   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
 CMK  plan-1  N1C   0.020
 CMK  plan-1  C2C   0.020
 CMK  plan-1  N3C   0.020
 CMK  plan-1  C4C   0.020
 CMK  plan-1  C5C   0.020
 CMK  plan-1  C6C   0.020
 CMK  plan-1  O2C   0.020
 CMK  plan-1  N4C   0.020
 CMK  plan-1  C1'   0.020
 CMK  plan-1  H5C   0.020
 CMK  plan-1  H6C   0.020
 CMK  plan-2  C4C   0.020
 CMK  plan-2  N4C   0.020
 CMK  plan-2  H4C1  0.020
 CMK  plan-2  H4C2  0.020
 CMK  plan-3  C2    0.020
 CMK  plan-3  C1    0.020
 CMK  plan-3  O1X   0.020
 CMK  plan-3  O1Y   0.020

