# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 12:11:27 2021
#   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  62  35  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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   1.487  22.4965  12.9720  -2.1752
 JHZ  C1    C  CH1   0   0.297  19.6319  14.6723   1.3497
 JHZ  O1    O  O2    0  -0.593  19.3772  14.0979   0.0550
 JHZ  C2    C  CH2   0  -0.553  18.7369  15.8972   1.4683
 JHZ  P2    P  P     0   1.495  20.1321  12.8243  -0.5225
 JHZ  C3    C  CT    0  -0.032  19.3534  16.9698   2.3721
 JHZ  N3    N  NH2   0  -0.773  18.4511  18.1031   2.4044
 JHZ  C4    C  C     0   0.413  20.7316  17.3174   1.7979
 JHZ  O4    O  O     0  -0.382  21.2288  18.4098   1.9205
 JHZ  C5    C  CH1   0  -0.093  21.4193  16.2076   1.0162
 JHZ  O5    O  O2    0  -0.481  20.9735  14.9526   1.5087
 JHZ  C6    C  CH3   0  -0.680  22.9288  16.2423   1.1080
 JHZ  C1X   C  CH1   0   0.200  24.8116   7.6526  -3.0974
 JHZ  N11   N  NR6   0  -0.566  25.3341   7.4159  -4.4315
 JHZ  O1P   O  OH1   0  -0.714  23.9211  13.5125  -1.7294
 JHZ  C2X   C  CH2   0  -0.536  25.5969   8.6578  -2.2672
 JHZ  C21   C  CR6   0   0.735  25.6713   6.1332  -4.8071
 JHZ  O21   O  O     0  -0.480  25.6023   5.1730  -4.0680
 JHZ  O2P   O  O     0  -0.679  22.0142  13.3967  -3.4972
 JHZ  C3X   C  CH1   0  -0.013  24.5326   9.1691  -1.3132
 JHZ  O3X   O  OH1   0  -0.669  24.4143   8.2413  -0.2624
 JHZ  N31   N  NR16  0  -0.736  26.1064   6.0223  -6.1009
 JHZ  C3M   C  CH3   0  -0.654  19.5448  16.4726   3.8093
 JHZ  O3P   O  OH1   0  -0.730  20.5431  11.9060   0.7058
 JHZ  C4X   C  CH1   0  -0.020  23.2879   9.1761  -2.2150
 JHZ  O4X   O  O2    0  -0.498  23.5099   8.1870  -3.2101
 JHZ  C41   C  CR6   0   0.563  26.2231   7.0193  -7.0525
 JHZ  O41   O  O     0  -0.449  26.6218   6.7631  -8.1728
 JHZ  O4P   O  O     0  -0.677  19.4050  12.2071  -1.6407
 JHZ  C5X   C  CH2   0  -0.199  23.0509  10.5084  -2.9066
 JHZ  O5X   O  O2    0  -0.590  22.5872  11.4110  -1.8964
 JHZ  C51   C  CR6   0  -0.185  25.8340   8.3381  -6.5899
 JHZ  C5A   C  CH3   0  -0.707  25.9086   9.4865  -7.5409
 JHZ  C61   C  CR16  0   0.076  25.4125   8.4574  -5.3212
 JHZ  OPP   O  O2    0  -0.682  21.5880  13.4162  -0.9145
 JHZ  H1    H  HCH1  0   0.270  19.3879  13.9254   2.1071
 JHZ  H2    H  HCH2  0   0.273  18.5642  16.3270   0.4764
 JHZ  H2A   H  HCH2  0   0.287  17.7621  15.6037   1.8601
 JHZ  HN3   H  HNH2  0   0.352  18.8444  18.8458   2.9700
 JHZ  HN3A  H  HNH2  0   0.350  18.3334  18.4893   1.4746
 JHZ  H5    H  HCH1  0   0.276  21.1250  16.3378  -0.0370
 JHZ  H6    H  HCH3  0   0.247  23.3585  15.4458   0.5022
 JHZ  H6A   H  HCH3  0   0.246  23.3070  17.1906   0.7332
 JHZ  H6B   H  HCH3  0   0.240  23.2674  16.1196   2.1371
 JHZ  H1X   H  HCH1  0   0.277  24.7820   6.6831  -2.6013
 JHZ  HO1P  H  HOH1  0   0.509  24.2304  14.2809  -2.2290
 JHZ  H2X   H  HCH2  0   0.290  26.4402   8.2002  -1.7519
 JHZ  H2XA  H  HCH2  0   0.273  25.9895   9.4747  -2.8759
 JHZ  H3X   H  HCH1  0   0.257  24.7618  10.1728  -0.9380
 JHZ  HO3X  H  HOH1  0   0.456  23.7258   8.5422   0.3393
 JHZ  HN31  H  HNR6  0   0.427  26.3611   5.0859  -6.3903
 JHZ  H3M   H  HCH3  0   0.245  19.9171  17.2809   4.4408
 JHZ  H3MA  H  HCH3  0   0.250  18.5849  16.1439   4.2096
 JHZ  H3MB  H  HCH3  0   0.245  20.2496  15.6466   3.8868
 JHZ  HO3P  H  HOH1  0   0.510  19.8724  11.2563   0.9603
 JHZ  H4X   H  HCH1  0   0.266  22.3878   8.9153  -1.6467
 JHZ  H5X   H  HCH2  0   0.240  23.9689  10.8870  -3.3681
 JHZ  H5XA  H  HCH2  0   0.274  22.2947  10.4022  -3.6863
 JHZ  H5A   H  HCH3  0   0.248  25.5805  10.4089  -7.0646
 JHZ  H5AA  H  HCH3  0   0.249  26.9269   9.6389  -7.9006
 JHZ  H5AB  H  HCH3  0   0.249  25.2787   9.3174  -8.4151
 JHZ  H61   H  HCR6  0   0.301  25.1036   9.4202  -4.9407

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     double  1.470  0.020  1.470
 JHZ  P    O1P   single  1.588  0.020  1.588
 JHZ  P    O5X   single  1.588  0.020  1.588
 JHZ  P    OPP   single  1.616  0.020  1.616
 JHZ  O1   C1    single  1.439  0.020  1.439
 JHZ  O5   C1    single  1.380  0.020  1.380
 JHZ  C1   C2    single  1.522  0.020  1.522
 JHZ  C1   H1    single  0.970  0.020  1.090
 JHZ  P2   O1    single  1.589  0.020  1.589
 JHZ  C2   C3    single  1.532  0.020  1.532
 JHZ  C2   H2    single  0.970  0.020  1.090
 JHZ  C2   H2A   single  0.970  0.020  1.090
 JHZ  O4P  P2    double  1.470  0.020  1.470
 JHZ  OPP  P2    single  1.620  0.020  1.620
 JHZ  P2   O3P   single  1.588  0.020  1.588
 JHZ  C4   C3    single  1.533  0.020  1.533
 JHZ  C3   N3    single  1.449  0.020  1.449
 JHZ  C3   C3M   single  1.533  0.020  1.533
 JHZ  N3   HN3   single  0.890  0.020  1.040
 JHZ  N3   HN3A  single  0.890  0.020  1.040
 JHZ  C5   C4    single  1.522  0.020  1.522
 JHZ  O4   C4    double  1.206  0.020  1.206
 JHZ  C6   C5    single  1.513  0.020  1.513
 JHZ  C5   O5    single  1.420  0.020  1.420
 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  1.452  0.020  1.452
 JHZ  O4X  C1X   single  1.412  0.020  1.412
 JHZ  C1X  C2X   single  1.522  0.020  1.522
 JHZ  C1X  H1X   single  0.970  0.020  1.090
 JHZ  C21  N11   single  1.378  0.020  1.378
 JHZ  C61  N11   single  1.372  0.020  1.372
 JHZ  O1P  HO1P  single  0.850  0.020  0.980
 JHZ  C2X  C3X   single  1.518  0.020  1.518
 JHZ  C2X  H2X   single  0.970  0.020  1.090
 JHZ  C2X  H2XA  single  0.970  0.020  1.090
 JHZ  N31  C21   single  1.370  0.020  1.370
 JHZ  C21  O21   double  1.214  0.020  1.214
 JHZ  C4X  C3X   single  1.537  0.020  1.537
 JHZ  C3X  O3X   single  1.407  0.020  1.407
 JHZ  C3X  H3X   single  0.970  0.020  1.090
 JHZ  O3X  HO3X  single  0.850  0.020  0.980
 JHZ  C41  N31   single  1.383  0.020  1.383
 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  O3P  HO3P  single  0.850  0.020  0.980
 JHZ  O4X  C4X   single  1.421  0.020  1.421
 JHZ  C5X  C4X   single  1.520  0.020  1.520
 JHZ  C4X  H4X   single  0.970  0.020  1.090
 JHZ  O41  C41   double  1.216  0.020  1.216
 JHZ  C41  C51   single  1.451  0.020  1.451
 JHZ  C5X  O5X   single  1.432  0.020  1.432
 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  1.342  0.020  1.342
 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    99.52  3.000
 JHZ  OPP   P    O2P   115.96  3.000
 JHZ  O5X   P    O2P   117.42  3.000
 JHZ  OPP   P    O1P   101.06  3.000
 JHZ  O5X   P    O1P   103.54  3.000
 JHZ  O2P   P    O1P   116.65  3.000
 JHZ  H1    C1   O5    106.05  3.000
 JHZ  H1    C1   C2    111.43  3.000
 JHZ  O5    C1   C2    113.54  3.000
 JHZ  H1    C1   O1    108.16  3.000
 JHZ  C2    C1   O1    106.70  3.000
 JHZ  O5    C1   O1    110.91  3.000
 JHZ  P2    O1   C1    124.25  3.000
 JHZ  H2A   C2   H2    106.86  3.000
 JHZ  H2A   C2   C3    109.64  3.000
 JHZ  H2    C2   C3    108.85  3.000
 JHZ  H2A   C2   C1    109.70  3.000
 JHZ  H2    C2   C1    109.77  3.000
 JHZ  C3    C2   C1    111.89  3.000
 JHZ  OPP   P2   O4P   114.45  3.000
 JHZ  OPP   P2   O3P    99.55  3.000
 JHZ  O4P   P2   O3P   118.28  3.000
 JHZ  O3P   P2   O1    107.78  3.000
 JHZ  OPP   P2   O1    102.83  3.000
 JHZ  O4P   P2   O1    112.22  3.000
 JHZ  C3M   C3   C4    108.21  3.000
 JHZ  C3M   C3   N3    108.09  3.000
 JHZ  C4    C3   N3    113.01  3.000
 JHZ  C3M   C3   C2    112.10  3.000
 JHZ  N3    C3   C2    108.07  3.000
 JHZ  C4    C3   C2    107.43  3.000
 JHZ  HN3A  N3   HN3   106.14  3.000
 JHZ  HN3A  N3   C3    110.48  3.000
 JHZ  HN3   N3   C3    110.13  3.000
 JHZ  C5    C4   O4    121.76  3.000
 JHZ  O4    C4   C3    122.53  3.000
 JHZ  C5    C4   C3    115.68  3.000
 JHZ  H5    C5   C6    108.78  3.000
 JHZ  H5    C5   O5    110.63  3.000
 JHZ  C6    C5   O5    108.21  3.000
 JHZ  H5    C5   C4    106.51  3.000
 JHZ  O5    C5   C4    108.94  3.000
 JHZ  C6    C5   C4    113.77  3.000
 JHZ  C5    O5   C1    116.42  3.000
 JHZ  H6B   C6   H6A   108.38  3.000
 JHZ  H6B   C6   H6    108.67  3.000
 JHZ  H6A   C6   H6    107.98  3.000
 JHZ  H6B   C6   C5    111.39  3.000
 JHZ  H6A   C6   C5    110.25  3.000
 JHZ  H6    C6   C5    110.08  3.000
 JHZ  H1X   C1X  O4X   110.38  3.000
 JHZ  H1X   C1X  C2X   110.69  3.000
 JHZ  O4X   C1X  C2X   105.62  3.000
 JHZ  H1X   C1X  N11   106.45  3.000
 JHZ  C2X   C1X  N11   115.03  3.000
 JHZ  O4X   C1X  N11   108.67  3.000
 JHZ  C61   N11  C21   121.04  3.000
 JHZ  C61   N11  C1X   119.52  3.000
 JHZ  C21   N11  C1X   119.34  3.000
 JHZ  HO1P  O1P  P     114.36  3.000
 JHZ  H2XA  C2X  H2X   107.45  3.000
 JHZ  H2XA  C2X  C3X   110.52  3.000
 JHZ  H2X   C2X  C3X   112.77  3.000
 JHZ  H2XA  C2X  C1X   112.06  3.000
 JHZ  H2X   C2X  C1X   112.34  3.000
 JHZ  C3X   C2X  C1X   101.74  3.000
 JHZ  N31   C21  O21   121.96  3.000
 JHZ  O21   C21  N11   123.80  3.000
 JHZ  N31   C21  N11   114.24  3.000
 JHZ  H3X   C3X  C4X   111.47  3.000
 JHZ  H3X   C3X  O3X   111.46  3.000
 JHZ  C4X   C3X  O3X   111.91  3.000
 JHZ  H3X   C3X  C2X   112.15  3.000
 JHZ  O3X   C3X  C2X   107.84  3.000
 JHZ  C4X   C3X  C2X   101.57  3.000
 JHZ  HO3X  O3X  C3X   108.72  3.000
 JHZ  HN31  N31  C41   116.66  3.000
 JHZ  HN31  N31  C21   115.13  3.000
 JHZ  C41   N31  C21   128.20  3.000
 JHZ  H3MB  C3M  H3MA  108.36  3.000
 JHZ  H3MB  C3M  H3M   107.46  3.000
 JHZ  H3MA  C3M  H3M   108.13  3.000
 JHZ  H3MB  C3M  C3    113.18  3.000
 JHZ  H3MA  C3M  C3    109.39  3.000
 JHZ  H3M   C3M  C3    110.18  3.000
 JHZ  HO3P  O3P  P2    114.35  3.000
 JHZ  H4X   C4X  C5X   108.46  3.000
 JHZ  H4X   C4X  O4X   109.02  3.000
 JHZ  C5X   C4X  O4X   108.42  3.000
 JHZ  H4X   C4X  C3X   111.08  3.000
 JHZ  C5X   C4X  C3X   113.41  3.000
 JHZ  O4X   C4X  C3X   106.33  3.000
 JHZ  C4X   O4X  C1X   110.60  3.000
 JHZ  C51   C41  O41   124.96  3.000
 JHZ  C51   C41  N31   114.41  3.000
 JHZ  O41   C41  N31   120.63  3.000
 JHZ  H5XA  C5X  H5X   108.27  3.000
 JHZ  H5XA  C5X  O5X   109.94  3.000
 JHZ  H5X   C5X  O5X   110.54  3.000
 JHZ  H5XA  C5X  C4X   110.35  3.000
 JHZ  H5X   C5X  C4X   111.36  3.000
 JHZ  O5X   C5X  C4X   106.38  3.000
 JHZ  C5X   O5X  P     120.94  3.000
 JHZ  C61   C51  C5A   123.33  3.000
 JHZ  C61   C51  C41   117.80  3.000
 JHZ  C5A   C51  C41   118.87  3.000
 JHZ  H5AB  C5A  H5AA  107.25  3.000
 JHZ  H5AB  C5A  H5A   107.93  3.000
 JHZ  H5AA  C5A  H5A   107.90  3.000
 JHZ  H5AB  C5A  C51   111.25  3.000
 JHZ  H5AA  C5A  C51   111.36  3.000
 JHZ  H5A   C5A  C51   110.98  3.000
 JHZ  H61   C61  C51   120.13  3.000
 JHZ  H61   C61  N11   115.58  3.000
 JHZ  C51   C61  N11   124.30  3.000
 JHZ  P2    OPP  P     126.41  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_01  N31   C21  N11  C1X   180.00   0.0  0
 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_05  O21   C21  N11  C1X     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  CONST_09  HN31  N31  C21  N11   180.00   0.0  0
 JHZ  Var_01    H5A   C5A  C51  C41   179.51  30.0  3
 JHZ  Var_02    C4X   C5X  O5X  P     168.17  30.0  2
 JHZ  Var_03    O4P   P2   O1   C1    161.78  30.0  1
 JHZ  Var_04    O1    P2   OPP  P    -144.52  30.0  3
 JHZ  Var_05    O2P   P    OPP  P2     71.35  30.0  1
 JHZ  Var_06    OPP   P    O5X  C5X   165.97  30.0  2

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
 JHZ  chir_09  P    O1P  O5X  OPP  both
 JHZ  chir_10  P2   O4P  OPP  O3P  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
 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

