# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 05:43:36 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (2S,3S,4R,5R,6R)-5-(acetylamino)-4-amino-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](N)[C@H](O)[C@H](O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)C(O)=O
#
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
 MJZ  MJZ  '(2S,3S,4R,5R,6R)-5-(acetylamino)-4-amino-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  ligand  63  40  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MJZ
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
 MJZ  N1    N  NR6    0  -0.571   2.2915   1.1358  -0.8284
 MJZ  C2    C  CR6    0   0.740   1.9404   1.3351   0.4952
 MJZ  O2    O  O      0  -0.452   2.0027   0.4735   1.3422
 MJZ  N3    N  NR16   0  -0.740   1.5178   2.6085   0.7856
 MJZ  C4    C  CR6    0   0.585   1.4967   3.7200  -0.0427
 MJZ  O4    O  O      0  -0.467   1.1725   4.8088   0.3898
 MJZ  C5    C  CR16   0  -0.488   1.9192   3.4300  -1.3909
 MJZ  C6    C  CR16   0   0.051   2.2807   2.1814  -1.7142
 MJZ  PA    P  P      0   1.377  -0.0880  -3.0975   2.0322
 MJZ  PB    P  P      0   1.358  -2.5343  -1.5286   1.7973
 MJZ  O'P   O  O      0  -0.564  -5.0236   3.7604   0.4355
 MJZ  O'Q   O  OC    -1  -0.619  -3.1613   4.8629  -0.0932
 MJZ  C1'   C  CH1    0   0.282  -3.3328   0.1637  -0.1356
 MJZ  O1A   O  OP    -1  -0.793   0.7202  -2.6248   3.1991
 MJZ  O1B   O  OP    -1  -0.784  -3.4668  -2.4807   1.1182
 MJZ  C1C   C  CH1    0   0.244   2.7769  -0.1557  -1.2916
 MJZ  C2'   C  CH1    0  -0.100  -2.4437   0.0553  -1.3834
 MJZ  N2'   N  NH1    0  -0.649  -1.7663  -1.2177  -1.4391
 MJZ  O2A   O  O      0  -0.798  -0.9599  -4.3085   2.1394
 MJZ  O2B   O  O      0  -0.792  -2.6354  -1.2676   3.2671
 MJZ  C2C   C  CH1    0  -0.056   4.0942  -0.6175  -0.6727
 MJZ  O2C   O  OH1    0  -0.658   5.1568   0.0347  -1.3085
 MJZ  C3'   C  CH1    0  -0.136  -1.4410   1.2004  -1.4698
 MJZ  N3'   N  NH2    0  -0.813  -0.7668   1.1504  -2.7568
 MJZ  O3A   O  O2     0  -0.738  -0.9689  -1.8489   1.4268
 MJZ  O3B   O  O2     0  -0.632  -2.5981  -0.0653   1.0393
 MJZ  C3C   C  CH1    0  -0.038   4.0128  -2.1210  -0.9415
 MJZ  O3C   O  OH1    0  -0.671   4.3360  -2.4093  -2.2790
 MJZ  C4'   C  CH1    0   0.071  -2.1902   2.5175  -1.3302
 MJZ  O4'   O  OH1    0  -0.691  -1.2673   3.5712  -1.3245
 MJZ  C4C   C  CH1    0  -0.025   2.5258  -2.3918  -0.7294
 MJZ  O4C   O  O2     0  -0.485   1.8495  -1.1719  -1.0677
 MJZ  C5'   C  CH1    0  -0.155  -3.0377   2.5101  -0.0501
 MJZ  O5'   O  O2     0  -0.491  -3.9320   1.4159  -0.0578
 MJZ  C5C   C  CH2    0  -0.144   2.2079  -2.8407   0.6835
 MJZ  O5C   O  O2     0  -0.618   0.8865  -3.3309   0.7343
 MJZ  C6'   C  C      0   0.427  -3.8352   3.8170   0.1114
 MJZ  C7'   C  C      0   0.517  -2.3615  -2.3403  -1.8960
 MJZ  O7'   O  O      0  -0.509  -3.4330  -2.3290  -2.4868
 MJZ  C8'   C  CH3    0  -0.793  -1.6039  -3.6120  -1.6231
 MJZ  H5    H  HCR6   0   0.288   1.9245   4.2122  -2.1331
 MJZ  H6    H  HCR6   0   0.329   2.5899   1.9331  -2.7199
 MJZ  H1'   H  HCH1   0   0.233  -4.1492  -0.5587  -0.2191
 MJZ  H1C   H  HCH1   0   0.247   2.9392  -0.0162  -2.3674
 MJZ  H2'   H  HCH1   0   0.248  -3.1016   0.1245  -2.2536
 MJZ  HN2'  H  HNH1   0   0.407  -0.9557  -1.3317  -0.8451
 MJZ  H2C   H  HCH1   0   0.264   4.1026  -0.4449   0.4068
 MJZ  HO2C  H  HOH1   0   0.469   5.9279   0.0032  -0.7341
 MJZ  H3'   H  HCH1   0   0.216  -0.7473   1.1220  -0.6167
 MJZ  HN3'  H  HNH2   0   0.357  -0.0763   1.8893  -2.8004
 MJZ  HN3A  H  HNH2   0   0.343  -0.2561   0.2794  -2.8367
 MJZ  H3C   H  HCH1   0   0.246   4.6373  -2.6961  -0.2462
 MJZ  HO3C  H  HOH1   0   0.447   5.1417  -1.9263  -2.4983
 MJZ  H4'   H  HCH1   0   0.178  -2.8801   2.5977  -2.1902
 MJZ  HO4'  H  HOH1   0   0.438  -1.7516   4.3057  -0.8812
 MJZ  H4C   H  HCH1   0   0.249   2.1914  -3.1704  -1.4234
 MJZ  H5'   H  HCH1   0   0.227  -2.3506   2.4454   0.8083
 MJZ  H5C   H  HCH2   0   0.204   2.9018  -3.6494   0.9412
 MJZ  H5CA  H  HCH2   0   0.236   2.3701  -2.0292   1.3927
 MJZ  H8'   H  HCH3   0   0.248  -0.5257  -3.4734  -1.6717
 MJZ  H8'A  H  HCH3   0   0.274  -1.8396  -3.9449  -0.6110
 MJZ  H8'B  H  HCH3   0   0.246  -1.9008  -4.3869  -2.3262
 MJZ  HN3   H  HNR6   0   0.421   1.2518   2.7568   1.7514

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
 MJZ  C1C  N1    single  1.455  0.020  1.455
 MJZ  N1   C6    single  1.370  0.020  1.370
 MJZ  N1   C2    single  1.384  0.020  1.384
 MJZ  O2   C2    double  1.210  0.020  1.210
 MJZ  C2   N3    single  1.373  0.020  1.373
 MJZ  N3   C4    single  1.386  0.020  1.386
 MJZ  C5   C4    single  1.442  0.020  1.442
 MJZ  C4   O4    double  1.216  0.020  1.216
 MJZ  C6   C5    double  1.339  0.020  1.339
 MJZ  C5   H5    single  0.930  0.020  1.080
 MJZ  C6   H6    single  0.930  0.020  1.080
 MJZ  O3A  PA    single  1.644  0.020  1.644
 MJZ  O5C  PA    single  1.640  0.020  1.640
 MJZ  O2A  PA    deloc   1.496  0.020  1.496
 MJZ  PA   O1A   deloc   1.496  0.020  1.496
 MJZ  O3B  PB    single  1.649  0.020  1.649
 MJZ  O2B  PB    deloc   1.496  0.020  1.496
 MJZ  PB   O3A   single  1.640  0.020  1.640
 MJZ  PB   O1B   deloc   1.496  0.020  1.496
 MJZ  O'P  C6'   deloc   1.233  0.020  1.233
 MJZ  C6'  O'Q   deloc   1.261  0.020  1.261
 MJZ  C2'  C1'   single  1.536  0.020  1.536
 MJZ  O5'  C1'   single  1.390  0.020  1.390
 MJZ  O3B  C1'   single  1.405  0.020  1.405
 MJZ  C1'  H1'   single  0.970  0.020  1.090
 MJZ  C2C  C1C   single  1.527  0.020  1.527
 MJZ  O4C  C1C   single  1.394  0.020  1.394
 MJZ  C1C  H1C   single  0.970  0.020  1.090
 MJZ  C3'  C2'   single  1.524  0.020  1.524
 MJZ  C2'  N2'   single  1.443  0.020  1.443
 MJZ  C2'  H2'   single  0.970  0.020  1.090
 MJZ  N2'  C7'   single  1.350  0.020  1.350
 MJZ  N2'  HN2'  single  0.890  0.020  1.040
 MJZ  C3C  C2C   single  1.529  0.020  1.529
 MJZ  O2C  C2C   single  1.400  0.020  1.400
 MJZ  C2C  H2C   single  0.970  0.020  1.090
 MJZ  O2C  HO2C  single  0.850  0.020  0.980
 MJZ  N3'  C3'   single  1.454  0.020  1.454
 MJZ  C4'  C3'   single  1.522  0.020  1.522
 MJZ  C3'  H3'   single  0.970  0.020  1.090
 MJZ  N3'  HN3'  single  0.890  0.020  1.040
 MJZ  N3'  HN3A  single  0.890  0.020  1.040
 MJZ  O3C  C3C   single  1.406  0.020  1.406
 MJZ  C3C  C4C   single  1.526  0.020  1.526
 MJZ  C3C  H3C   single  0.970  0.020  1.090
 MJZ  O3C  HO3C  single  0.850  0.020  0.980
 MJZ  O4'  C4'   single  1.401  0.020  1.401
 MJZ  C4'  C5'   single  1.535  0.020  1.535
 MJZ  C4'  H4'   single  0.970  0.020  1.090
 MJZ  O4'  HO4'  single  0.850  0.020  0.980
 MJZ  C5C  C4C   single  1.516  0.020  1.516
 MJZ  C4C  O4C   single  1.435  0.020  1.435
 MJZ  C4C  H4C   single  0.970  0.020  1.090
 MJZ  C6'  C5'   single  1.540  0.020  1.540
 MJZ  C5'  O5'   single  1.413  0.020  1.413
 MJZ  C5'  H5'   single  0.970  0.020  1.090
 MJZ  C5C  O5C   single  1.410  0.020  1.410
 MJZ  C5C  H5C   single  0.970  0.020  1.090
 MJZ  C5C  H5CA  single  0.970  0.020  1.090
 MJZ  O7'  C7'   double  1.224  0.020  1.224
 MJZ  C7'  C8'   single  1.505  0.020  1.505
 MJZ  C8'  H8'   single  0.970  0.020  1.090
 MJZ  C8'  H8'A  single  0.970  0.020  1.090
 MJZ  C8'  H8'B  single  0.970  0.020  1.090
 MJZ  N3   HN3   single  0.860  0.020  1.020

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
 MJZ  C1C   N1   C6    118.29  3.000
 MJZ  C6    N1   C2    120.42  3.000
 MJZ  C1C   N1   C2    121.12  3.000
 MJZ  N3    C2   O2    121.89  3.000
 MJZ  N3    C2   N1    114.46  3.000
 MJZ  O2    C2   N1    123.65  3.000
 MJZ  HN3   N3   C4    116.64  3.000
 MJZ  HN3   N3   C2    114.74  3.000
 MJZ  C4    N3   C2    128.46  3.000
 MJZ  C5    C4   O4    126.22  3.000
 MJZ  O4    C4   N3    120.63  3.000
 MJZ  C5    C4   N3    113.13  3.000
 MJZ  H5    C5   C6    120.58  3.000
 MJZ  H5    C5   C4    119.93  3.000
 MJZ  C6    C5   C4    119.48  3.000
 MJZ  H6    C6   C5    121.05  3.000
 MJZ  H6    C6   N1    115.08  3.000
 MJZ  C5    C6   N1    123.87  3.000
 MJZ  O5C   PA   O3A    97.76  3.000
 MJZ  O5C   PA   O2A   106.73  3.000
 MJZ  O3A   PA   O2A   109.20  3.000
 MJZ  O2A   PA   O1A   120.98  3.000
 MJZ  O5C   PA   O1A   109.95  3.000
 MJZ  O3A   PA   O1A   109.68  3.000
 MJZ  O3B   PB   O3A    96.11  3.000
 MJZ  O3A   PB   O2B   108.69  3.000
 MJZ  O3B   PB   O2B   107.11  3.000
 MJZ  O3A   PB   O1B   111.60  3.000
 MJZ  O2B   PB   O1B   120.99  3.000
 MJZ  O3B   PB   O1B   109.39  3.000
 MJZ  H1'   C1'  O5'   106.12  3.000
 MJZ  H1'   C1'  O3B   110.29  3.000
 MJZ  O5'   C1'  O3B   108.99  3.000
 MJZ  H1'   C1'  C2'   108.88  3.000
 MJZ  O3B   C1'  C2'   111.42  3.000
 MJZ  O5'   C1'  C2'   111.01  3.000
 MJZ  H1C   C1C  O4C   110.41  3.000
 MJZ  H1C   C1C  C2C   107.96  3.000
 MJZ  O4C   C1C  C2C   106.76  3.000
 MJZ  H1C   C1C  N1    104.40  3.000
 MJZ  O4C   C1C  N1    111.96  3.000
 MJZ  C2C   C1C  N1    115.29  3.000
 MJZ  H2'   C2'  C3'   107.65  3.000
 MJZ  H2'   C2'  N2'   107.91  3.000
 MJZ  C3'   C2'  N2'   110.59  3.000
 MJZ  H2'   C2'  C1'   107.09  3.000
 MJZ  N2'   C2'  C1'   111.43  3.000
 MJZ  C3'   C2'  C1'   111.95  3.000
 MJZ  HN2'  N2'  C7'   117.27  3.000
 MJZ  HN2'  N2'  C2'   116.93  3.000
 MJZ  C7'   N2'  C2'   122.66  3.000
 MJZ  H2C   C2C  C3C   109.22  3.000
 MJZ  H2C   C2C  O2C   111.66  3.000
 MJZ  C3C   C2C  O2C   114.75  3.000
 MJZ  H2C   C2C  C1C   111.04  3.000
 MJZ  O2C   C2C  C1C   109.26  3.000
 MJZ  C3C   C2C  C1C   100.38  3.000
 MJZ  HO2C  O2C  C2C   108.79  3.000
 MJZ  H3'   C3'  C4'   107.48  3.000
 MJZ  H3'   C3'  N3'   113.00  3.000
 MJZ  C4'   C3'  N3'   109.83  3.000
 MJZ  H3'   C3'  C2'   108.46  3.000
 MJZ  C4'   C3'  C2'   108.73  3.000
 MJZ  N3'   C3'  C2'   109.24  3.000
 MJZ  HN3A  N3'  HN3'  106.29  3.000
 MJZ  HN3A  N3'  C3'   109.47  3.000
 MJZ  HN3'  N3'  C3'   109.23  3.000
 MJZ  PB    O3A  PA    125.21  3.000
 MJZ  C1'   O3B  PB    123.33  3.000
 MJZ  H3C   C3C  C4C   111.93  3.000
 MJZ  H3C   C3C  O3C   111.37  3.000
 MJZ  C4C   C3C  O3C   108.65  3.000
 MJZ  H3C   C3C  C2C   111.93  3.000
 MJZ  C4C   C3C  C2C   101.65  3.000
 MJZ  O3C   C3C  C2C   110.89  3.000
 MJZ  HO3C  O3C  C3C   107.79  3.000
 MJZ  H4'   C4'  C5'   107.73  3.000
 MJZ  H4'   C4'  O4'   111.09  3.000
 MJZ  C5'   C4'  O4'   111.34  3.000
 MJZ  H4'   C4'  C3'   107.38  3.000
 MJZ  C5'   C4'  C3'   110.13  3.000
 MJZ  O4'   C4'  C3'   109.10  3.000
 MJZ  HO4'  O4'  C4'   103.82  3.000
 MJZ  H4C   C4C  C5C   108.42  3.000
 MJZ  H4C   C4C  O4C   108.12  3.000
 MJZ  C5C   C4C  O4C   111.87  3.000
 MJZ  H4C   C4C  C3C   109.61  3.000
 MJZ  O4C   C4C  C3C   106.00  3.000
 MJZ  C5C   C4C  C3C   112.73  3.000
 MJZ  C4C   O4C  C1C   110.12  3.000
 MJZ  H5'   C5'  C6'   106.93  3.000
 MJZ  H5'   C5'  O5'   110.70  3.000
 MJZ  C6'   C5'  O5'   109.27  3.000
 MJZ  H5'   C5'  C4'   107.81  3.000
 MJZ  O5'   C5'  C4'   110.40  3.000
 MJZ  C6'   C5'  C4'   111.68  3.000
 MJZ  C5'   O5'  C1'   115.14  3.000
 MJZ  H5CA  C5C  H5C   107.58  3.000
 MJZ  H5CA  C5C  O5C   112.01  3.000
 MJZ  H5C   C5C  O5C   109.16  3.000
 MJZ  H5CA  C5C  C4C   110.78  3.000
 MJZ  H5C   C5C  C4C   107.74  3.000
 MJZ  O5C   C5C  C4C   109.45  3.000
 MJZ  C5C   O5C  PA    122.40  3.000
 MJZ  C5'   C6'  O'Q   114.22  3.000
 MJZ  C5'   C6'  O'P   119.20  3.000
 MJZ  O'Q   C6'  O'P   126.56  3.000
 MJZ  C8'   C7'  O7'   122.42  3.000
 MJZ  C8'   C7'  N2'   114.79  3.000
 MJZ  O7'   C7'  N2'   122.80  3.000
 MJZ  H8'B  C8'  H8'A  108.86  3.000
 MJZ  H8'B  C8'  H8'   109.41  3.000
 MJZ  H8'A  C8'  H8'   107.12  3.000
 MJZ  H8'B  C8'  C7'   110.32  3.000
 MJZ  H8'A  C8'  C7'   108.49  3.000
 MJZ  H8'   C8'  C7'   112.52  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
 MJZ  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 MJZ  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 MJZ  CONST_03  C1C   N1   C2   N3    180.00   0.0  0
 MJZ  CONST_04  C6    N1   C2   N3      0.00   0.0  0
 MJZ  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 MJZ  CONST_06  C1C   N1   C2   O2      0.00   0.0  0
 MJZ  CONST_07  C6    N1   C2   O2    180.00   0.0  0
 MJZ  CONST_08  C4    N3   C2   O2    180.00   0.0  0
 MJZ  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 MJZ  CONST_10  O7'   C7'  N2'  C2'     0.00   0.0  0
 MJZ  CONST_11  C8'   C7'  N2'  C2'   180.00   0.0  0
 MJZ  CONST_12  HN2'  N2'  C7'  O7'   180.00   0.0  0
 MJZ  Var_01    C4C   C5C  O5C  PA   -143.70  30.0  2
 MJZ  Var_02    O2B   PB   O3B  C1'  -138.31  30.0  3
 MJZ  Var_03    O3B   PB   O3A  PA    171.16  30.0  2
 MJZ  Var_04    O5C   PA   O3A  PB    149.28  30.0  3
 MJZ  Var_05    H8'   C8'  C7'  N2'   -34.87  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
 MJZ  chir_03  C1'  C2'  O5'  O3B  positiv
 MJZ  chir_04  C1C  N1   C2C  O4C  negativ
 MJZ  chir_05  C2'  N2'  C3'  C1'  positiv
 MJZ  chir_06  C2C  C1C  C3C  O2C  negativ
 MJZ  chir_07  C3'  N3'  C4'  C2'  negativ
 MJZ  chir_08  C3C  O3C  C4C  C2C  positiv
 MJZ  chir_09  C4'  C3'  O4'  C5'  positiv
 MJZ  chir_10  C4C  C3C  C5C  O4C  negativ
 MJZ  chir_11  C5'  O5'  C4'  C6'  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
 MJZ  plan-1  N1    0.020
 MJZ  plan-1  C2    0.020
 MJZ  plan-1  O2    0.020
 MJZ  plan-1  N3    0.020
 MJZ  plan-1  C4    0.020
 MJZ  plan-1  O4    0.020
 MJZ  plan-1  C5    0.020
 MJZ  plan-1  C6    0.020
 MJZ  plan-1  C1C   0.020
 MJZ  plan-1  H5    0.020
 MJZ  plan-1  H6    0.020
 MJZ  plan-1  HN3   0.020
 MJZ  plan-2  C2'   0.020
 MJZ  plan-2  N2'   0.020
 MJZ  plan-2  C7'   0.020
 MJZ  plan-2  O7'   0.020
 MJZ  plan-2  C8'   0.020
 MJZ  plan-2  HN2'  0.020
 MJZ  plan-3  O'P   0.020
 MJZ  plan-3  O'Q   0.020
 MJZ  plan-3  C5'   0.020
 MJZ  plan-3  C6'   0.020

