# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:32:49 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: (2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](C[C@](C)(N)C1=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=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
 JHZ  JHZ  '(2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  60  35  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JHZ
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
 JHZ  P     P  P      0   1.380  -0.9607   2.5008  -1.6768
 JHZ  C1    C  CH1    0   0.284  -2.0181  -1.0583  -1.0204
 JHZ  O1    O  O2     0  -0.628  -1.0838  -1.3309  -2.0156
 JHZ  C2    C  CH2    0  -0.486  -1.4016  -1.3009   0.3410
 JHZ  P2    P  P      0   1.389  -0.5266  -0.1262  -2.9943
 JHZ  C3    C  CT     0  -0.048  -2.4032  -1.0762   1.4739
 JHZ  N3    N  NH2    0  -0.772  -1.8720  -1.6627   2.6891
 JHZ  C4    C  C      0   0.397  -3.7783  -1.6446   1.0983
 JHZ  O4    O  O      0  -0.396  -4.5699  -1.9794   1.9502
 JHZ  C5    C  CH1    0  -0.093  -4.1818  -1.7404  -0.3710
 JHZ  O5    O  O2     0  -0.490  -3.0817  -1.9607  -1.2247
 JHZ  C6    C  CH3    0  -0.699  -5.0299  -0.5343  -0.7842
 JHZ  C1X   C  CH1    0   0.203   2.3999   0.5072   1.7781
 JHZ  N11   N  NR6    0  -0.558   2.3945  -0.6739   0.9101
 JHZ  O1P   O  OP    -1  -0.771  -2.4196   2.3406  -1.3840
 JHZ  C2X   C  CH2    0  -0.547   3.6576   1.3750   1.7660
 JHZ  C21   C  CR6    0   0.739   2.5001  -0.5091  -0.4550
 JHZ  O21   O  O      0  -0.478   2.9260   0.5100  -0.9578
 JHZ  O2P   O  O      0  -0.800  -0.4830   3.4183  -2.7579
 JHZ  C3X   C  CH1    0   0.020   3.2418   2.7006   1.1205
 JHZ  O3X   O  OH1    0  -0.672   3.6625   3.8449   1.8257
 JHZ  N31   N  NR16   0  -0.755   2.0993  -1.5797  -1.2065
 JHZ  C3M   C  CH3    0  -0.660  -2.5969   0.4265   1.7205
 JHZ  O3P   O  OP    -1  -0.773   0.7941  -0.6395  -3.5022
 JHZ  C4X   C  CH1    0   0.012   1.7063   2.6495   1.1219
 JHZ  O4X   O  O2     0  -0.471   1.3205   1.3238   1.4412
 JHZ  C41   C  CR6    0   0.550   1.7110  -2.8187  -0.7439
 JHZ  O41   O  O      0  -0.468   1.3766  -3.6993  -1.5192
 JHZ  O4P   O  O      0  -0.781  -1.5877   0.3148  -3.9459
 JHZ  C5X   C  CH2    0  -0.167   1.1455   3.0767  -0.2205
 JHZ  O5X   O  O2     0  -0.611  -0.2551   2.8955  -0.2546
 JHZ  C51   C  CR6    0  -0.186   1.7377  -2.9691   0.6985
 JHZ  C5A   C  CH3    0  -0.709   1.3442  -4.2783   1.2985
 JHZ  C61   C  CR16   0   0.052   2.0287  -1.8846   1.4358
 JHZ  OPP   O  O2     0  -0.747  -0.2342   1.0305  -1.8854
 JHZ  H1    H  HCH1   0   0.221  -2.3901  -0.0310  -1.0975
 JHZ  H2    H  HCH2   0   0.236  -1.0334  -2.3314   0.3704
 JHZ  H2A   H  HCH2   0   0.266  -0.5499  -0.6354   0.4842
 JHZ  HN3   H  HNH2   0   0.343  -2.5490  -1.5789   3.4385
 JHZ  HN3A  H  HNH2   0   0.341  -1.7178  -2.6558   2.5591
 JHZ  H5    H  HCH1   0   0.274  -4.8072  -2.6332  -0.4579
 JHZ  H6    H  HCH3   0   0.244  -4.4679   0.4002  -0.7960
 JHZ  H6A   H  HCH3   0   0.252  -5.4277  -0.6967  -1.7859
 JHZ  H6B   H  HCH3   0   0.244  -5.8734  -0.4145  -0.1051
 JHZ  H1X   H  HCH1   0   0.247   2.2455   0.0959   2.7782
 JHZ  H2X   H  HCH2   0   0.263   3.9539   1.5629   2.7995
 JHZ  H2XA  H  HCH2   0   0.272   4.4977   0.8985   1.2653
 JHZ  H3X   H  HCH1   0   0.230   3.6080   2.7386   0.0904
 JHZ  HO3X  H  HOH1   0   0.454   4.6010   3.9710   1.6576
 JHZ  HN31  H  HNR6   0   0.427   1.8626  -1.3481  -2.1859
 JHZ  H3M   H  HCH3   0   0.244  -2.9305   0.9644   0.8349
 JHZ  H3MA  H  HCH3   0   0.230  -3.3199   0.6001   2.5193
 JHZ  H3MB  H  HCH3   0   0.252  -1.6380   0.8536   2.0144
 JHZ  H4X   H  HCH1   0   0.227   1.3285   3.3140   1.9102
 JHZ  H5X   H  HCH2   0   0.207   1.4005   4.1337  -0.3651
 JHZ  H5XA  H  HCH2   0   0.229   1.6454   2.5104  -1.0067
 JHZ  H5A   H  HCH3   0   0.241   0.3121  -4.5347   1.0506
 JHZ  H5AA  H  HCH3   0   0.244   1.9729  -5.0921   0.9348
 JHZ  H5AB  H  HCH3   0   0.243   1.4290  -4.2512   2.3839
 JHZ  H61   H  HCR6   0   0.306   1.9958  -1.9223   2.5168

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
 JHZ  O2P  P     deloc   1.496  0.020  1.496
 JHZ  P    O1P   deloc   1.497  0.020  1.497
 JHZ  P    O5X   single  1.636  0.020  1.636
 JHZ  P    OPP   single  1.653  0.020  1.653
 JHZ  O1   C1    single  1.392  0.020  1.392
 JHZ  O5   C1    single  1.410  0.020  1.410
 JHZ  C1   C2    single  1.514  0.020  1.514
 JHZ  C1   H1    single  0.970  0.020  1.090
 JHZ  P2   O1    single  1.649  0.020  1.649
 JHZ  C2   C3    single  1.529  0.020  1.529
 JHZ  C2   H2    single  0.970  0.020  1.090
 JHZ  C2   H2A   single  0.970  0.020  1.090
 JHZ  O4P  P2    deloc   1.492  0.020  1.492
 JHZ  OPP  P2    single  1.629  0.020  1.629
 JHZ  P2   O3P   deloc   1.505  0.020  1.505
 JHZ  C4   C3    single  1.535  0.020  1.535
 JHZ  C3   N3    single  1.450  0.020  1.450
 JHZ  C3   C3M   single  1.535  0.020  1.535
 JHZ  N3   HN3   single  0.890  0.020  1.040
 JHZ  N3   HN3A  single  0.890  0.020  1.040
 JHZ  C5   C4    single  1.527  0.020  1.527
 JHZ  O4   C4    double  1.210  0.020  1.210
 JHZ  C6   C5    single  1.531  0.020  1.531
 JHZ  C5   O5    single  1.410  0.020  1.410
 JHZ  C5   H5    single  0.970  0.020  1.090
 JHZ  C6   H6    single  0.970  0.020  1.090
 JHZ  C6   H6A   single  0.970  0.020  1.090
 JHZ  C6   H6B   single  0.970  0.020  1.090
 JHZ  N11  C1X   single  1.466  0.020  1.466
 JHZ  O4X  C1X   single  1.395  0.020  1.395
 JHZ  C1X  C2X   single  1.528  0.020  1.528
 JHZ  C1X  H1X   single  0.970  0.020  1.090
 JHZ  C21  N11   single  1.379  0.020  1.379
 JHZ  C61  N11   single  1.370  0.020  1.370
 JHZ  C2X  C3X   single  1.532  0.020  1.532
 JHZ  C2X  H2X   single  0.970  0.020  1.090
 JHZ  C2X  H2XA  single  0.970  0.020  1.090
 JHZ  N31  C21   single  1.368  0.020  1.368
 JHZ  C21  O21   double  1.214  0.020  1.214
 JHZ  C4X  C3X   single  1.536  0.020  1.536
 JHZ  C3X  O3X   single  1.409  0.020  1.409
 JHZ  C3X  H3X   single  0.970  0.020  1.090
 JHZ  O3X  HO3X  single  0.850  0.020  0.980
 JHZ  C41  N31   single  1.378  0.020  1.378
 JHZ  N31  HN31  single  0.860  0.020  1.020
 JHZ  C3M  H3M   single  0.970  0.020  1.090
 JHZ  C3M  H3MA  single  0.970  0.020  1.090
 JHZ  C3M  H3MB  single  0.970  0.020  1.090
 JHZ  O4X  C4X   single  1.417  0.020  1.417
 JHZ  C5X  C4X   single  1.516  0.020  1.516
 JHZ  C4X  H4X   single  0.970  0.020  1.090
 JHZ  O41  C41   double  1.220  0.020  1.220
 JHZ  C41  C51   single  1.450  0.020  1.450
 JHZ  C5X  O5X   single  1.413  0.020  1.413
 JHZ  C5X  H5X   single  0.970  0.020  1.090
 JHZ  C5X  H5XA  single  0.970  0.020  1.090
 JHZ  C5A  C51   single  1.493  0.020  1.493
 JHZ  C51  C61   double  1.343  0.020  1.343
 JHZ  C5A  H5A   single  0.970  0.020  1.090
 JHZ  C5A  H5AA  single  0.970  0.020  1.090
 JHZ  C5A  H5AB  single  0.970  0.020  1.090
 JHZ  C61  H61   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
 JHZ  OPP   P    O5X    97.74  3.000
 JHZ  OPP   P    O2P   108.29  3.000
 JHZ  O5X   P    O2P   110.03  3.000
 JHZ  OPP   P    O1P   110.97  3.000
 JHZ  O5X   P    O1P   106.03  3.000
 JHZ  O2P   P    O1P   121.21  3.000
 JHZ  H1    C1   O5    109.51  3.000
 JHZ  H1    C1   C2    110.60  3.000
 JHZ  O5    C1   C2    109.57  3.000
 JHZ  H1    C1   O1    111.19  3.000
 JHZ  C2    C1   O1    109.76  3.000
 JHZ  O5    C1   O1    106.11  3.000
 JHZ  P2    O1   C1    120.53  3.000
 JHZ  H2A   C2   H2    107.96  3.000
 JHZ  H2A   C2   C3    108.95  3.000
 JHZ  H2    C2   C3    109.80  3.000
 JHZ  H2A   C2   C1    109.78  3.000
 JHZ  H2    C2   C1    108.18  3.000
 JHZ  C3    C2   C1    112.09  3.000
 JHZ  OPP   P2   O4P   110.61  3.000
 JHZ  OPP   P2   O3P   108.32  3.000
 JHZ  O4P   P2   O3P   120.64  3.000
 JHZ  O3P   P2   O1    104.34  3.000
 JHZ  OPP   P2   O1    100.10  3.000
 JHZ  O4P   P2   O1    110.74  3.000
 JHZ  C3M   C3   C4    106.79  3.000
 JHZ  C3M   C3   N3    107.91  3.000
 JHZ  C4    C3   N3    112.55  3.000
 JHZ  C3M   C3   C2    110.21  3.000
 JHZ  N3    C3   C2    108.76  3.000
 JHZ  C4    C3   C2    110.56  3.000
 JHZ  HN3A  N3   HN3   106.12  3.000
 JHZ  HN3A  N3   C3    110.15  3.000
 JHZ  HN3   N3   C3    109.97  3.000
 JHZ  C5    C4   O4    119.16  3.000
 JHZ  O4    C4   C3    121.09  3.000
 JHZ  C5    C4   C3    119.71  3.000
 JHZ  H5    C5   C6    107.75  3.000
 JHZ  H5    C5   O5    105.70  3.000
 JHZ  C6    C5   O5    113.07  3.000
 JHZ  H5    C5   C4    106.19  3.000
 JHZ  O5    C5   C4    112.73  3.000
 JHZ  C6    C5   C4    110.89  3.000
 JHZ  C5    O5   C1    113.64  3.000
 JHZ  H6B   C6   H6A   107.86  3.000
 JHZ  H6B   C6   H6    108.15  3.000
 JHZ  H6A   C6   H6    107.81  3.000
 JHZ  H6B   C6   C5    110.32  3.000
 JHZ  H6A   C6   C5    109.44  3.000
 JHZ  H6    C6   C5    113.11  3.000
 JHZ  H1X   C1X  O4X   109.40  3.000
 JHZ  H1X   C1X  C2X   109.72  3.000
 JHZ  O4X   C1X  C2X   107.61  3.000
 JHZ  H1X   C1X  N11   103.78  3.000
 JHZ  C2X   C1X  N11   117.13  3.000
 JHZ  O4X   C1X  N11   109.01  3.000
 JHZ  C61   N11  C21   120.40  3.000
 JHZ  C61   N11  C1X   119.07  3.000
 JHZ  C21   N11  C1X   119.32  3.000
 JHZ  H2XA  C2X  H2X   107.55  3.000
 JHZ  H2XA  C2X  C3X   113.24  3.000
 JHZ  H2X   C2X  C3X   108.89  3.000
 JHZ  H2XA  C2X  C1X   112.98  3.000
 JHZ  H2X   C2X  C1X   108.28  3.000
 JHZ  C3X   C2X  C1X   105.75  3.000
 JHZ  N31   C21  O21   122.17  3.000
 JHZ  O21   C21  N11   122.50  3.000
 JHZ  N31   C21  N11   115.33  3.000
 JHZ  H3X   C3X  C4X   109.67  3.000
 JHZ  H3X   C3X  O3X   110.08  3.000
 JHZ  C4X   C3X  O3X   108.97  3.000
 JHZ  H3X   C3X  C2X   109.64  3.000
 JHZ  O3X   C3X  C2X   114.26  3.000
 JHZ  C4X   C3X  C2X   104.01  3.000
 JHZ  HO3X  O3X  C3X   108.08  3.000
 JHZ  HN31  N31  C41   117.06  3.000
 JHZ  HN31  N31  C21   114.34  3.000
 JHZ  C41   N31  C21   126.98  3.000
 JHZ  H3MB  C3M  H3MA  108.85  3.000
 JHZ  H3MB  C3M  H3M   107.18  3.000
 JHZ  H3MA  C3M  H3M   108.29  3.000
 JHZ  H3MB  C3M  C3    108.41  3.000
 JHZ  H3MA  C3M  C3    110.91  3.000
 JHZ  H3M   C3M  C3    113.06  3.000
 JHZ  H4X   C4X  C5X   109.75  3.000
 JHZ  H4X   C4X  O4X   108.10  3.000
 JHZ  C5X   C4X  O4X   111.24  3.000
 JHZ  H4X   C4X  C3X   108.93  3.000
 JHZ  C5X   C4X  C3X   111.06  3.000
 JHZ  O4X   C4X  C3X   107.66  3.000
 JHZ  C4X   O4X  C1X   113.04  3.000
 JHZ  C51   C41  O41   124.20  3.000
 JHZ  C51   C41  N31   114.95  3.000
 JHZ  O41   C41  N31   120.84  3.000
 JHZ  H5XA  C5X  H5X   107.40  3.000
 JHZ  H5XA  C5X  O5X   111.75  3.000
 JHZ  H5X   C5X  O5X   110.54  3.000
 JHZ  H5XA  C5X  C4X   108.82  3.000
 JHZ  H5X   C5X  C4X   107.59  3.000
 JHZ  O5X   C5X  C4X   110.60  3.000
 JHZ  C5X   O5X  P     118.66  3.000
 JHZ  C61   C51  C5A   122.99  3.000
 JHZ  C61   C51  C41   117.78  3.000
 JHZ  C5A   C51  C41   119.06  3.000
 JHZ  H5AB  C5A  H5AA  107.82  3.000
 JHZ  H5AB  C5A  H5A   107.80  3.000
 JHZ  H5AA  C5A  H5A   107.10  3.000
 JHZ  H5AB  C5A  C51   110.98  3.000
 JHZ  H5AA  C5A  C51   111.61  3.000
 JHZ  H5A   C5A  C51   111.33  3.000
 JHZ  H61   C61  C51   120.90  3.000
 JHZ  H61   C61  N11   114.99  3.000
 JHZ  C51   C61  N11   124.11  3.000
 JHZ  P2    OPP  P     129.69  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
 JHZ  CONST_02  C41  N31  C21  N11     0.00   0.0  0
 JHZ  CONST_03  C51  C41  N31  C21     0.00   0.0  0
 JHZ  CONST_04  C61  N11  C21  N31     0.00   0.0  0
 JHZ  CONST_06  O41  C41  N31  C21   180.00   0.0  0
 JHZ  CONST_07  C61  N11  C21  O21   180.00   0.0  0
 JHZ  CONST_08  C41  N31  C21  O21   180.00   0.0  0
 JHZ  Var_01    H5A  C5A  C51  C41   -60.94  30.0  3
 JHZ  Var_02    C4X  C5X  O5X  P    -147.46  30.0  1
 JHZ  Var_03    O4P  P2   O1   C1    -71.23  30.0  1
 JHZ  Var_04    O1   P2   OPP  P    -114.51  30.0  3
 JHZ  Var_05    O2P  P    OPP  P2    -74.15  30.0  1
 JHZ  Var_06    OPP  P    O5X  C5X    63.85  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
 JHZ  chir_02  C1   O1   O5   C2   negativ
 JHZ  chir_04  C3   C2   C4   C3M  positiv
 JHZ  chir_05  C5   O5   C6   C4   positiv
 JHZ  chir_06  C1X  N11  O4X  C2X  positiv
 JHZ  chir_07  C3X  O3X  C4X  C2X  positiv
 JHZ  chir_08  C4X  O4X  C3X  C5X  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
 JHZ  plan-1  C3    0.020
 JHZ  plan-1  C4    0.020
 JHZ  plan-1  O4    0.020
 JHZ  plan-1  C5    0.020
 JHZ  plan-2  C1X   0.020
 JHZ  plan-2  N11   0.020
 JHZ  plan-2  C21   0.020
 JHZ  plan-2  O21   0.020
 JHZ  plan-2  N31   0.020
 JHZ  plan-2  C41   0.020
 JHZ  plan-2  O41   0.020
 JHZ  plan-2  C51   0.020
 JHZ  plan-2  C5A   0.020
 JHZ  plan-2  C61   0.020
 JHZ  plan-2  HN31  0.020
 JHZ  plan-2  H61   0.020

