# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Nov 21 17:35:51 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@H](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)[C@H](O)[C@H](O)[C@H]1O
#
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
 TRH  TRH  "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE"  ligand  61  35  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TRH
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
 TRH  O4P   O  OH1   0  -0.706  15.0064  63.0339  52.3616
 TRH  P2    P  P     0   1.479  15.0927  61.5584  52.9168
 TRH  O3P   O  O     0  -0.673  15.4447  60.5712  51.8886
 TRH  O1    O  O2    0  -0.602  15.9842  61.5755  54.2456
 TRH  C1    C  CH1   0   0.300  17.3381  61.1940  54.1653
 TRH  C2    C  CH1   0  -0.033  17.9676  61.3000  55.5418
 TRH  O2    O  OH1   0  -0.662  17.7917  62.6031  56.0229
 TRH  C3    C  CH1   0  -0.004  19.4416  60.9320  55.3751
 TRH  O3    O  OH1   0  -0.666  20.0577  61.0862  56.6269
 TRH  C4    C  CH1   0   0.018  20.0947  61.7935  54.2979
 TRH  O4    O  OH1   0  -0.669  21.4127  61.3210  54.1396
 TRH  C5    C  CH1   0   0.005  19.2985  61.6906  52.9906
 TRH  O5    O  O2    0  -0.497  17.9440  62.0427  53.2473
 TRH  C6    C  CH3   0  -0.690  19.8134  62.6132  51.9089
 TRH  OPP   O  O2    0  -0.691  13.6264  61.3553  53.5785
 TRH  P     P  P     0   1.514  12.9787  59.9307  54.0041
 TRH  O1P   O  OH1   0  -0.718  11.6804  60.5398  54.6805
 TRH  O2P   O  O     0  -0.667  13.8431  59.0507  54.8022
 TRH  O5'   O  O2    0  -0.582  12.5556  59.2378  52.6400
 TRH  C5'   C  CH2   0  -0.216  11.8526  59.8908  51.5784
 TRH  C4'   C  CH1   0   0.003  11.7243  58.9476  50.4048
 TRH  O4'   O  O2    0  -0.492  13.0072  58.6167  49.8928
 TRH  C3'   C  CH1   0  -0.022  11.0123  57.6184  50.7012
 TRH  O3'   O  OH1   0  -0.666  10.1967  57.3350  49.5868
 TRH  C2'   C  CH2   0  -0.534  12.1749  56.6429  50.8237
 TRH  C1'   C  CH1   0   0.208  13.1617  57.2177  49.8174
 TRH  N11   N  NR6   0  -0.572  14.5548  56.8905  50.0628
 TRH  C21   C  CR6   0   0.728  15.2968  56.2928  49.0654
 TRH  O21   O  O     0  -0.474  14.8505  55.9869  47.9793
 TRH  N31   N  NR16  0  -0.737  16.6042  56.0571  49.4035
 TRH  C41   C  CR6   0   0.555  17.2522  56.3581  50.5898
 TRH  O41   O  O     0  -0.444  18.4295  56.0898  50.7368
 TRH  C51   C  CR6   0  -0.183  16.4110  57.0002  51.5800
 TRH  C5A   C  CH3   0  -0.722  17.0007  57.3894  52.8948
 TRH  C61   C  CR16  0   0.071  15.1289  57.2377  51.2594
 TRH  H4PO  H  HOH1  0   0.507  14.8807  63.7458  53.0063
 TRH  HC1   H  HCH1  0   0.242  17.4089  60.1474  53.8341
 TRH  HC2   H  HCH1  0   0.246  17.4909  60.5547  56.1963
 TRH  HO2   H  HOH1  0   0.454  18.3355  62.7006  56.8122
 TRH  HC3   H  HCH1  0   0.217  19.4876  59.8828  55.0387
 TRH  HO3   H  HOH1  0   0.453  21.0099  60.9981  56.5080
 TRH  HC4   H  HCH1  0   0.223  20.0858  62.8412  54.6280
 TRH  HO4   H  HOH1  0   0.461  21.9642  62.0302  53.7973
 TRH  HC5   H  HCH1  0   0.227  19.3431  60.6483  52.6369
 TRH  HC61  H  HCH3  0   0.249  19.2128  62.5234  51.0039
 TRH  HC62  H  HCH3  0   0.234  19.7931  63.6535  52.2375
 TRH  HC63  H  HCH3  0   0.238  20.8393  62.3580  51.6463
 TRH  H1PO  H  HOH1  0   0.509  11.1243  59.8963  55.1434
 TRH  H5'1  H  HCH2  0   0.258  10.8538  60.1853  51.9084
 TRH  H5'2  H  HCH2  0   0.265  12.3879  60.7898  51.2654
 TRH  H4'C  H  HCH1  0   0.265  11.1536  59.4948  49.6454
 TRH  H3'C  H  HCH1  0   0.253  10.4216  57.6697  51.6231
 TRH  H3'O  H  HOH1  0   0.453   9.7932  56.4709  49.7187
 TRH  H2'1  H  HCH2  0   0.266  12.5738  56.6541  51.8390
 TRH  H2'2  H  HCH2  0   0.280  11.9003  55.6144  50.5883
 TRH  H1'C  H  HCH1  0   0.269  12.9349  56.8573  48.8139
 TRH  H31N  H  HNR6  0   0.422  17.1603  55.6125  48.6830
 TRH  HCA1  H  HCH3  0   0.244  16.2521  57.8619  53.5287
 TRH  HCA2  H  HCH3  0   0.248  17.3936  56.5232  53.4284
 TRH  HCA3  H  HCH3  0   0.246  17.8260  58.0925  52.7683
 TRH  H61C  H  HCR6  0   0.315  14.4771  57.7361  51.9608

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
 TRH  O4P  P2    single  1.579  0.020  1.579
 TRH  O4P  H4PO  single  0.850  0.020  0.980
 TRH  P2   O3P   double  1.468  0.020  1.468
 TRH  P2   O1    single  1.600  0.020  1.600
 TRH  P2   OPP   single  1.621  0.020  1.621
 TRH  O1   C1    single  1.409  0.020  1.409
 TRH  C1   C2    single  1.517  0.020  1.517
 TRH  C1   O5    single  1.389  0.020  1.389
 TRH  C1   HC1   single  0.970  0.020  1.090
 TRH  C2   O2    single  1.400  0.020  1.400
 TRH  C2   C3    single  1.528  0.020  1.528
 TRH  C2   HC2   single  0.970  0.020  1.090
 TRH  O2   HO2   single  0.850  0.020  0.980
 TRH  C3   O3    single  1.404  0.020  1.404
 TRH  C3   C4    single  1.526  0.020  1.526
 TRH  C3   HC3   single  0.970  0.020  1.090
 TRH  O3   HO3   single  0.850  0.020  0.980
 TRH  C4   O4    single  1.409  0.020  1.409
 TRH  C4   C5    single  1.534  0.020  1.534
 TRH  C4   HC4   single  0.970  0.020  1.090
 TRH  O4   HO4   single  0.850  0.020  0.980
 TRH  C5   O5    single  1.423  0.020  1.423
 TRH  C5   C6    single  1.512  0.020  1.512
 TRH  C5   HC5   single  0.970  0.020  1.090
 TRH  C6   HC61  single  0.970  0.020  1.090
 TRH  C6   HC62  single  0.970  0.020  1.090
 TRH  C6   HC63  single  0.970  0.020  1.090
 TRH  OPP  P     single  1.622  0.020  1.622
 TRH  P    O1P   single  1.586  0.020  1.586
 TRH  P    O2P   double  1.469  0.020  1.469
 TRH  P    O5'   single  1.587  0.020  1.587
 TRH  O1P  H1PO  single  0.850  0.020  0.980
 TRH  O5'  C5'   single  1.431  0.020  1.431
 TRH  C5'  C4'   single  1.511  0.020  1.511
 TRH  C5'  H5'1  single  0.970  0.020  1.090
 TRH  C5'  H5'2  single  0.970  0.020  1.090
 TRH  C4'  O4'   single  1.420  0.020  1.420
 TRH  C4'  C3'   single  1.537  0.020  1.537
 TRH  C4'  H4'C  single  0.970  0.020  1.090
 TRH  O4'  C1'   single  1.409  0.020  1.409
 TRH  C3'  O3'   single  1.410  0.020  1.410
 TRH  C3'  C2'   single  1.523  0.020  1.523
 TRH  C3'  H3'C  single  0.970  0.020  1.090
 TRH  O3'  H3'O  single  0.850  0.020  0.980
 TRH  C2'  C1'   single  1.522  0.020  1.522
 TRH  C2'  H2'1  single  0.970  0.020  1.090
 TRH  C2'  H2'2  single  0.970  0.020  1.090
 TRH  C1'  N11   single  1.452  0.020  1.452
 TRH  C1'  H1'C  single  0.970  0.020  1.090
 TRH  N11  C21   single  1.379  0.020  1.379
 TRH  N11  C61   single  1.372  0.020  1.372
 TRH  C21  O21   double  1.213  0.020  1.213
 TRH  C21  N31   single  1.371  0.020  1.371
 TRH  N31  C41   single  1.385  0.020  1.385
 TRH  N31  H31N  single  0.860  0.020  1.020
 TRH  C41  O41   double  1.216  0.020  1.216
 TRH  C41  C51   single  1.449  0.020  1.449
 TRH  C51  C5A   single  1.493  0.020  1.493
 TRH  C51  C61   double  1.343  0.020  1.343
 TRH  C5A  HCA1  single  0.970  0.020  1.090
 TRH  C5A  HCA2  single  0.970  0.020  1.090
 TRH  C5A  HCA3  single  0.970  0.020  1.090
 TRH  C61  H61C  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
 TRH  H4PO  O4P  P2    117.38  3.000
 TRH  OPP   P2   O1     99.57  3.000
 TRH  OPP   P2   O3P   114.73  3.000
 TRH  O1    P2   O3P   117.07  3.000
 TRH  OPP   P2   O4P   102.19  3.000
 TRH  O1    P2   O4P   108.21  3.000
 TRH  O3P   P2   O4P   113.28  3.000
 TRH  C1    O1   P2    119.02  3.000
 TRH  HC1   C1   O5    110.74  3.000
 TRH  HC1   C1   C2    108.24  3.000
 TRH  O5    C1   C2    112.07  3.000
 TRH  HC1   C1   O1    109.67  3.000
 TRH  O5    C1   O1    106.94  3.000
 TRH  C2    C1   O1    109.15  3.000
 TRH  HC2   C2   C3    108.64  3.000
 TRH  HC2   C2   O2    111.81  3.000
 TRH  C3    C2   O2    112.50  3.000
 TRH  HC2   C2   C1    108.21  3.000
 TRH  C3    C2   C1    106.52  3.000
 TRH  O2    C2   C1    108.94  3.000
 TRH  HO2   O2   C2    107.75  3.000
 TRH  HC3   C3   C4    107.69  3.000
 TRH  HC3   C3   O3    110.99  3.000
 TRH  C4    C3   O3    112.31  3.000
 TRH  HC3   C3   C2    107.61  3.000
 TRH  C4    C3   C2    110.72  3.000
 TRH  O3    C3   C2    107.44  3.000
 TRH  HO3   O3   C3    108.28  3.000
 TRH  HC4   C4   C5    108.41  3.000
 TRH  HC4   C4   O4    111.17  3.000
 TRH  C5    C4   O4    111.55  3.000
 TRH  HC4   C4   C3    108.83  3.000
 TRH  C5    C4   C3    109.97  3.000
 TRH  O4    C4   C3    106.87  3.000
 TRH  HO4   O4   C4    109.22  3.000
 TRH  HC5   C5   C6    109.50  3.000
 TRH  HC5   C5   O5    109.30  3.000
 TRH  C6    C5   O5    107.59  3.000
 TRH  HC5   C5   C4    108.43  3.000
 TRH  C6    C5   C4    113.08  3.000
 TRH  O5    C5   C4    108.89  3.000
 TRH  C5    O5   C1    112.53  3.000
 TRH  HC63  C6   HC62  108.28  3.000
 TRH  HC63  C6   HC61  107.43  3.000
 TRH  HC62  C6   HC61  108.57  3.000
 TRH  HC63  C6   C5    110.50  3.000
 TRH  HC62  C6   C5    111.09  3.000
 TRH  HC61  C6   C5    110.86  3.000
 TRH  P     OPP  P2    125.33  3.000
 TRH  O5'   P    O2P   111.23  3.000
 TRH  O5'   P    O1P   108.42  3.000
 TRH  O2P   P    O1P   118.69  3.000
 TRH  O5'   P    OPP   105.33  3.000
 TRH  O2P   P    OPP   115.70  3.000
 TRH  O1P   P    OPP    95.83  3.000
 TRH  H1PO  O1P  P     114.76  3.000
 TRH  C5'   O5'  P     124.70  3.000
 TRH  H5'2  C5'  H5'1  108.23  3.000
 TRH  H5'2  C5'  C4'   109.45  3.000
 TRH  H5'1  C5'  C4'   108.98  3.000
 TRH  H5'2  C5'  O5'   110.34  3.000
 TRH  H5'1  C5'  O5'   110.37  3.000
 TRH  C4'   C5'  O5'   109.46  3.000
 TRH  H4'C  C4'  C3'   108.92  3.000
 TRH  H4'C  C4'  O4'   109.68  3.000
 TRH  C3'   C4'  O4'   106.65  3.000
 TRH  H4'C  C4'  C5'   105.70  3.000
 TRH  C3'   C4'  C5'   115.44  3.000
 TRH  O4'   C4'  C5'   110.40  3.000
 TRH  C1'   O4'  C4'   110.46  3.000
 TRH  H3'C  C3'  C2'   111.95  3.000
 TRH  H3'C  C3'  O3'   111.25  3.000
 TRH  C2'   C3'  O3'   112.12  3.000
 TRH  H3'C  C3'  C4'   111.80  3.000
 TRH  C2'   C3'  C4'   102.47  3.000
 TRH  O3'   C3'  C4'   106.83  3.000
 TRH  H3'O  O3'  C3'   108.34  3.000
 TRH  H2'2  C2'  H2'1  107.62  3.000
 TRH  H2'2  C2'  C1'   112.14  3.000
 TRH  H2'1  C2'  C1'   111.99  3.000
 TRH  H2'2  C2'  C3'   113.24  3.000
 TRH  H2'1  C2'  C3'   110.34  3.000
 TRH  C1'   C2'  C3'   101.53  3.000
 TRH  H1'C  C1'  N11   106.30  3.000
 TRH  H1'C  C1'  C2'   110.42  3.000
 TRH  N11   C1'  C2'   115.16  3.000
 TRH  H1'C  C1'  O4'   110.77  3.000
 TRH  N11   C1'  O4'   108.65  3.000
 TRH  C2'   C1'  O4'   105.57  3.000
 TRH  C61   N11  C21   121.02  3.000
 TRH  C61   N11  C1'   119.46  3.000
 TRH  C21   N11  C1'   119.45  3.000
 TRH  N31   C21  O21   121.88  3.000
 TRH  N31   C21  N11   114.16  3.000
 TRH  O21   C21  N11   123.96  3.000
 TRH  H31N  N31  C41   116.60  3.000
 TRH  H31N  N31  C21   115.07  3.000
 TRH  C41   N31  C21   128.33  3.000
 TRH  C51   C41  O41   125.23  3.000
 TRH  C51   C41  N31   114.20  3.000
 TRH  O41   C41  N31   120.56  3.000
 TRH  C61   C51  C5A   122.78  3.000
 TRH  C61   C51  C41   118.00  3.000
 TRH  C5A   C51  C41   119.21  3.000
 TRH  HCA3  C5A  HCA2  107.21  3.000
 TRH  HCA3  C5A  HCA1  107.92  3.000
 TRH  HCA2  C5A  HCA1  107.91  3.000
 TRH  HCA3  C5A  C51   111.39  3.000
 TRH  HCA2  C5A  C51   111.48  3.000
 TRH  HCA1  C5A  C51   110.76  3.000
 TRH  H61C  C61  C51   120.21  3.000
 TRH  H61C  C61  N11   115.53  3.000
 TRH  C51   C61  N11   124.26  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
 TRH  CONST_01  N31   C21  N11  C1'   180.00   0.0  0
 TRH  CONST_02  C41   N31  C21  N11     0.00   0.0  0
 TRH  CONST_03  C51   C41  N31  C21     0.00   0.0  0
 TRH  CONST_04  C61   N11  C21  N31     0.00   0.0  0
 TRH  CONST_05  O21   C21  N11  C1'     0.00   0.0  0
 TRH  CONST_06  O41   C41  N31  C21   180.00   0.0  0
 TRH  CONST_07  C61   N11  C21  O21   180.00   0.0  0
 TRH  CONST_08  C41   N31  C21  O21   180.00   0.0  0
 TRH  CONST_09  H31N  N31  C21  N11   180.00   0.0  0
 TRH  CONST_10  H31N  N31  C41  C51   180.00   0.0  0
 TRH  CONST_11  H31N  N31  C21  O21     0.00   0.0  0
 TRH  CONST_12  H31N  N31  C41  O41     0.00   0.0  0
 TRH  Var_01    C5A   C51  C61  N11  -179.82  30.0  1
 TRH  Var_02    C5A   C51  C41  N31  -179.24  30.0  1
 TRH  Var_03    H61C  C61  N11  C1'     0.72  30.0  1
 TRH  Var_04    H61C  C61  N11  C21   177.60  30.0  1
 TRH  Var_05    H61C  C61  C51  C41  -178.49  30.0  1
 TRH  Var_06    C5A   C51  C41  O41     0.52  30.0  1
 TRH  Var_07    HCA1  C5A  C51  C41   179.78  30.0  3
 TRH  Var_08    HCA2  C5A  C51  C41   -60.05  30.0  3
 TRH  Var_09    HCA3  C5A  C51  C41    59.66  30.0  3
 TRH  Var_10    H61C  C61  C51  C5A     0.46  30.0  1
 TRH  Var_11    HCA1  C5A  C51  C61     0.84  30.0  3
 TRH  Var_12    HCA2  C5A  C51  C61   121.01  30.0  3
 TRH  Var_13    HCA3  C5A  C51  C61  -119.28  30.0  3
 TRH  Var_14    C1    O1   P2   O4P   -99.28  30.0  3
 TRH  Var_15    C1    O1   P2   O3P    30.16  30.0  3
 TRH  Var_16    OPP   P2   O1   C1    154.41  30.0  2
 TRH  Var_17    C4'   C5'  O5'  P     175.55  30.0  3
 TRH  Var_18    P     OPP  P2   O4P   164.72  30.0  3
 TRH  Var_19    O1P   P    OPP  P2    174.38  30.0  3
 TRH  Var_20    O2P   P    OPP  P2     48.60  30.0  3
 TRH  Var_21    O5'   P    OPP  P2    -74.68  30.0  3
 TRH  Var_22    P     OPP  P2   O3P    41.72  30.0  3
 TRH  Var_23    P     OPP  P2   O1    -84.14  30.0  3
 TRH  Var_24    C5'   O5'  P    OPP   -46.09  30.0  3
 TRH  Var_25    C5'   O5'  P    O1P    55.58  30.0  3
 TRH  Var_26    C5'   O5'  P    O2P  -172.18  30.0  3
 TRH  Var_27    H5'1  C5'  O5'  P     -64.51  30.0  3
 TRH  Var_28    H5'2  C5'  O5'  P      55.05  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
 TRH  chir_02  C1   O1   C2   O5   positiv
 TRH  chir_03  C2   O2   C1   C3   negativ
 TRH  chir_04  C3   O3   C2   C4   negativ
 TRH  chir_05  C4   O4   C5   C3   negativ
 TRH  chir_06  C5   O5   C4   C6   positiv
 TRH  chir_08  C4'  C5'  O4'  C3'  negativ
 TRH  chir_09  C3'  O3'  C4'  C2'  positiv
 TRH  chir_10  C1'  O4'  N11  C2'  negativ
 TRH  chir_11  P2   O3P  O1   OPP  both
 TRH  chir_12  P    O1P  O2P  O5'  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
 TRH  plan-1  C1'   0.020
 TRH  plan-1  N11   0.020
 TRH  plan-1  C21   0.020
 TRH  plan-1  O21   0.020
 TRH  plan-1  N31   0.020
 TRH  plan-1  C41   0.020
 TRH  plan-1  O41   0.020
 TRH  plan-1  C51   0.020
 TRH  plan-1  C61   0.020
 TRH  plan-1  H31N  0.020

