# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 20 18:58:52 2020
#   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,4S,5S,6R)-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
 18T  18T  '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  D-saccharide  59  35  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_18T
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
 18T  C2   C  CH1    0  -0.069   5.3368  -0.4647  -1.3561
 18T  C3   C  CH1    0   0.015   4.9668  -1.9010  -1.7090
 18T  C5   C  CH1    0  -0.011   4.9658  -2.3699   0.7505
 18T  C6   C  CH3    0  -0.690   5.5509  -3.1820   1.8875
 18T  O1   O  O2     0  -0.609   3.4534  -0.0597   0.0137
 18T  O2   O  OH1    0  -0.672   4.7955   0.3767  -2.3457
 18T  C41  C  C      0   0.488  -5.9943  -2.7966   0.6520
 18T  C51  C  C      0  -0.144  -5.6993  -2.9076  -0.7618
 18T  C5A  C  CH3    0  -0.782  -5.9409  -4.2095  -1.4526
 18T  C61  C  C1     0   0.004  -5.2146  -1.8221  -1.3891
 18T  N31  N  NH1    0  -0.680  -5.7313  -1.5511   1.1922
 18T  C21  C  C      0   0.682  -5.2388  -0.4394   0.5582
 18T  O21  O  O      0  -0.319  -5.0543   0.6053   1.1461
 18T  N11  N  NT     0  -0.521  -4.9924  -0.6122  -0.7840
 18T  C1,  C  CH1    0   0.206  -4.4271   0.4843  -1.5683
 18T  O4,  O  O2     0  -0.385  -3.1425   0.7719  -1.0967
 18T  C2,  C  CH2    0  -0.542  -5.2242   1.7920  -1.5701
 18T  C3,  C  CH1    0  -0.010  -4.3298   2.7998  -0.8477
 18T  O3,  O  OH1    0  -0.662  -4.3010   4.0811  -1.4262
 18T  C4,  C  CH1    0  -0.031  -2.9420   2.1693  -0.9745
 18T  C5,  C  CH2    0  -0.144  -2.0583   2.4588   0.2135
 18T  O5,  O  O2     0  -0.633  -0.7862   1.8822   0.0069
 18T  P    P  P      0   1.352   0.4562   2.4363   0.9349
 18T  O1P  O  OP    -1  -0.888   0.8629   3.7953   0.4565
 18T  O2P  O  O      0  -0.872   0.1560   2.2032   2.3815
 18T  OPP  O  O2     0  -0.697   1.5318   1.3358   0.3719
 18T  P2   P  P      0   1.383   2.5917   0.4974   1.3139
 18T  O3P  O  OP    -1  -0.829   1.9004  -0.6630   1.9489
 18T  O4P  O  O      0  -0.793   3.4355   1.4430   2.1069
 18T  C1   C  CH1    0   0.253   4.8445  -0.0989   0.0448
 18T  O3   O  OH1    0  -0.628   5.5459  -2.2849  -2.9332
 18T  C4   C  CH1    0   0.014   5.4767  -2.8303  -0.6204
 18T  O4   O  OH1    0  -0.696   5.0378  -4.1357  -0.9130
 18T  O5   O  O2     0  -0.509   5.3318  -1.0144   0.9801
 18T  H1   H  HCH1   0   0.242   6.4339  -0.3952  -1.3386
 18T  H2   H  HCH1   0   0.231   3.8698  -1.9856  -1.7556
 18T  H3   H  HCH1   0   0.271   3.8734  -2.4723   0.7717
 18T  H4   H  HCH3   0   0.243   6.6411  -3.1231   1.9010
 18T  H5   H  HCH3   0   0.236   5.1754  -2.8273   2.8474
 18T  H6   H  HCH3   0   0.196   5.2677  -4.2306   1.8014
 18T  H7   H  HOH1   0   0.454   5.2844   1.2048  -2.3503
 18T  H8   H  HCH3   0   0.200  -6.9900  -4.5020  -1.3921
 18T  H9   H  HCH3   0   0.266  -5.6721  -4.1451  -2.5055
 18T  H10  H  HCH3   0   0.265  -5.3552  -5.0134  -1.0050
 18T  H11  H  H      0   0.287  -4.9741  -1.8544  -2.4438
 18T  H12  H  HNH1   0   0.418  -5.9214  -1.4335   2.1801
 18T  H13  H  HCH1   0   0.249  -4.3738   0.0860  -2.5843
 18T  H14  H  HCH2   0   0.281  -5.3593   2.1138  -2.6041
 18T  H15  H  HCH2   0   0.273  -6.2138   1.6890  -1.1279
 18T  H16  H  HCH1   0   0.262  -4.6135   2.8615   0.2066
 18T  H17  H  HOH1   0   0.403  -5.0753   4.5645  -1.1247
 18T  H18  H  HCH1   0   0.265  -2.4667   2.5560  -1.8879
 18T  H19  H  HCH2   0   0.151  -1.9984   3.5484   0.3256
 18T  H20  H  HCH2   0   0.251  -2.5268   2.0586   1.1192
 18T  H23  H  HCH1   0   0.310   5.2584   0.8696   0.3470
 18T  H24  H  HOH1   0   0.452   5.2770  -1.6413  -3.5974
 18T  H25  H  HCH1   0   0.238   6.5769  -2.7762  -0.6120
 18T  H26  H  HOH1   0   0.453   5.6100  -4.7603  -0.4589
 18T  O41  O  O      0  -0.478  -6.4348  -3.6936   1.3480

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
 18T  O3,  C3,  single  1.406  0.020  1.406
 18T  O21  C21  double  1.213  0.020  1.213
 18T  C2,  C1,  single  1.531  0.020  1.531
 18T  C2,  C3,  single  1.529  0.020  1.529
 18T  C1,  O4,  single  1.398  0.020  1.398
 18T  C1,  N11  single  1.462  0.020  1.462
 18T  C3,  C4,  single  1.530  0.020  1.530
 18T  C21  N11  single  1.376  0.020  1.376
 18T  C21  N31  single  1.371  0.020  1.371
 18T  O4,  C4,  single  1.417  0.020  1.417
 18T  C4,  C5,  single  1.509  0.020  1.509
 18T  N11  C61  single  1.371  0.020  1.371
 18T  N31  C41  single  1.383  0.020  1.383
 18T  C61  C51  double  1.344  0.020  1.344
 18T  C5,  O5,  single  1.412  0.020  1.412
 18T  C41  C51  single  1.448  0.020  1.448
 18T  C41  O41  double  1.218  0.020  1.218
 18T  O5,  P    single  1.647  0.020  1.647
 18T  C51  C5A  single  1.493  0.020  1.493
 18T  O2P  P    deloc   1.496  0.020  1.496
 18T  O1P  P    deloc   1.497  0.020  1.497
 18T  P    OPP  single  1.639  0.020  1.639
 18T  OPP  P2   single  1.647  0.020  1.647
 18T  O4P  P2   deloc   1.495  0.020  1.495
 18T  P2   O3P  deloc   1.493  0.020  1.493
 18T  P2   O1   single  1.656  0.020  1.656
 18T  O2   C2   single  1.407  0.020  1.407
 18T  C1   O1   single  1.392  0.020  1.392
 18T  C1   C2   single  1.529  0.020  1.529
 18T  C1   O5   single  1.397  0.020  1.397
 18T  C2   C3   single  1.525  0.020  1.525
 18T  O5   C5   single  1.423  0.020  1.423
 18T  C3   O3   single  1.408  0.020  1.408
 18T  C3   C4   single  1.519  0.020  1.519
 18T  C5   C4   single  1.534  0.020  1.534
 18T  C5   C6   single  1.515  0.020  1.515
 18T  C4   O4   single  1.408  0.020  1.408
 18T  C2   H1   single  0.970  0.020  1.090
 18T  C3   H2   single  0.970  0.020  1.090
 18T  C5   H3   single  0.970  0.020  1.090
 18T  C6   H4   single  0.970  0.020  1.090
 18T  C6   H5   single  0.970  0.020  1.090
 18T  C6   H6   single  0.970  0.020  1.090
 18T  O2   H7   single  0.850  0.020  0.980
 18T  C5A  H8   single  0.970  0.020  1.090
 18T  C5A  H9   single  0.970  0.020  1.090
 18T  C5A  H10  single  0.970  0.020  1.090
 18T  C61  H11  single  0.930  0.020  1.080
 18T  N31  H12  single  0.860  0.020  1.020
 18T  C1,  H13  single  0.970  0.020  1.090
 18T  C2,  H14  single  0.970  0.020  1.090
 18T  C2,  H15  single  0.970  0.020  1.090
 18T  C3,  H16  single  0.970  0.020  1.090
 18T  O3,  H17  single  0.850  0.020  0.980
 18T  C4,  H18  single  0.970  0.020  1.090
 18T  C5,  H19  single  0.970  0.020  1.090
 18T  C5,  H20  single  0.970  0.020  1.090
 18T  C1   H23  single  0.970  0.020  1.090
 18T  O3   H24  single  0.850  0.020  0.980
 18T  C4   H25  single  0.970  0.020  1.090
 18T  O4   H26  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
 18T  H1   C2   C1   106.95  3.000
 18T  H1   C2   O2   110.93  3.000
 18T  C1   C2   O2   112.17  3.000
 18T  H1   C2   C3   107.78  3.000
 18T  C1   C2   C3   111.06  3.000
 18T  O2   C2   C3   107.89  3.000
 18T  H2   C3   C4   108.52  3.000
 18T  H2   C3   O3   110.61  3.000
 18T  C4   C3   O3   108.55  3.000
 18T  H2   C3   C2   108.90  3.000
 18T  C4   C3   C2   109.20  3.000
 18T  O3   C3   C2   111.01  3.000
 18T  H3   C5   O5   109.99  3.000
 18T  H3   C5   C4   108.72  3.000
 18T  O5   C5   C4   110.16  3.000
 18T  H3   C5   C6   108.66  3.000
 18T  C4   C5   C6   112.41  3.000
 18T  O5   C5   C6   106.87  3.000
 18T  H6   C6   H5   107.05  3.000
 18T  H6   C6   H4   108.21  3.000
 18T  H5   C6   H4   108.39  3.000
 18T  H6   C6   C5   110.87  3.000
 18T  H5   C6   C5   110.70  3.000
 18T  H4   C6   C5   111.47  3.000
 18T  C1   O1   P2   120.78  3.000
 18T  H7   O2   C2   108.83  3.000
 18T  N31  C41  C51  114.30  3.000
 18T  C51  C41  O41  125.11  3.000
 18T  N31  C41  O41  120.59  3.000
 18T  C61  C51  C5A  123.12  3.000
 18T  C5A  C51  C41  119.03  3.000
 18T  C61  C51  C41  117.85  3.000
 18T  H10  C5A  H9   107.93  3.000
 18T  H10  C5A  H8   107.22  3.000
 18T  H9   C5A  H8   107.88  3.000
 18T  H10  C5A  C51  111.46  3.000
 18T  H9   C5A  C51  110.85  3.000
 18T  H8   C5A  C51  111.33  3.000
 18T  H11  C61  N11  114.87  3.000
 18T  H11  C61  C51  120.72  3.000
 18T  N11  C61  C51  124.41  3.000
 18T  H12  N31  C21  115.10  3.000
 18T  H12  N31  C41  116.74  3.000
 18T  C21  N31  C41  128.16  3.000
 18T  N11  C21  O21  123.64  3.000
 18T  N11  C21  N31  114.43  3.000
 18T  O21  C21  N31  121.92  3.000
 18T  C1,  N11  C21  119.90  3.000
 18T  C21  N11  C61  120.83  3.000
 18T  C1,  N11  C61  119.20  3.000
 18T  H13  C1,  C2,  109.61  3.000
 18T  H13  C1,  O4,  110.11  3.000
 18T  C2,  C1,  O4,  107.63  3.000
 18T  H13  C1,  N11  104.14  3.000
 18T  O4,  C1,  N11  109.18  3.000
 18T  C2,  C1,  N11  116.09  3.000
 18T  C4,  O4,  C1,  111.22  3.000
 18T  H15  C2,  H14  107.47  3.000
 18T  H15  C2,  C3,  113.71  3.000
 18T  H14  C2,  C3,  109.01  3.000
 18T  H15  C2,  C1,  113.07  3.000
 18T  H14  C2,  C1,  108.50  3.000
 18T  C3,  C2,  C1,  104.94  3.000
 18T  H16  C3,  C4,  109.79  3.000
 18T  H16  C3,  O3,  110.52  3.000
 18T  C4,  C3,  O3,  108.84  3.000
 18T  H16  C3,  C2,  109.93  3.000
 18T  C4,  C3,  C2,  102.70  3.000
 18T  O3,  C3,  C2,  114.72  3.000
 18T  H17  O3,  C3,  108.23  3.000
 18T  H18  C4,  C5,  109.47  3.000
 18T  H18  C4,  C3,  108.42  3.000
 18T  C5,  C4,  C3,  112.77  3.000
 18T  H18  C4,  O4,  109.65  3.000
 18T  C5,  C4,  O4,  109.88  3.000
 18T  C3,  C4,  O4,  106.57  3.000
 18T  H20  C5,  H19  107.56  3.000
 18T  H20  C5,  O5,  110.92  3.000
 18T  H19  C5,  O5,  111.80  3.000
 18T  H20  C5,  C4,  109.29  3.000
 18T  H19  C5,  C4,  107.64  3.000
 18T  O5,  C5,  C4,  109.52  3.000
 18T  P    O5,  C5,  117.38  3.000
 18T  OPP  P    O2P  111.06  3.000
 18T  OPP  P    O1P  108.76  3.000
 18T  O2P  P    O1P  120.34  3.000
 18T  OPP  P    O5,   94.33  3.000
 18T  O1P  P    O5,  109.29  3.000
 18T  O2P  P    O5,  109.95  3.000
 18T  P2   OPP  P    124.58  3.000
 18T  O4P  P2   O3P  121.84  3.000
 18T  O3P  P2   OPP  109.93  3.000
 18T  O4P  P2   OPP  110.15  3.000
 18T  O3P  P2   O1   108.27  3.000
 18T  O4P  P2   O1   109.60  3.000
 18T  OPP  P2   O1    93.27  3.000
 18T  H23  C1   O5   105.25  3.000
 18T  H23  C1   O1   111.02  3.000
 18T  O5   C1   O1   112.46  3.000
 18T  H23  C1   C2   110.03  3.000
 18T  O5   C1   C2   110.14  3.000
 18T  O1   C1   C2   107.94  3.000
 18T  H24  O3   C3   107.61  3.000
 18T  H25  C4   O4   111.01  3.000
 18T  H25  C4   C5   108.13  3.000
 18T  O4   C4   C5   111.12  3.000
 18T  H25  C4   C3   108.09  3.000
 18T  O4   C4   C3   108.28  3.000
 18T  C5   C4   C3   110.18  3.000
 18T  H26  O4   C4   108.59  3.000
 18T  C1   O5   C5   115.26  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
 18T  CONST_01  N11  C21  N31  C41    0.00   0.0  0
 18T  CONST_02  C21  N31  C41  C51    0.00   0.0  0
 18T  CONST_03  N31  C21  N11  C61    0.00   0.0  0
 18T  CONST_04  C1,  N11  C21  N31  180.00   0.0  0
 18T  CONST_05  C21  N31  C41  O41  180.00   0.0  0
 18T  CONST_06  O21  C21  N31  C41  180.00   0.0  0
 18T  CONST_07  O21  C21  N11  C61  180.00   0.0  0
 18T  CONST_08  C1,  N11  C21  O21    0.00   0.0  0
 18T  CONST_09  H12  N31  C41  C51  180.00   0.0  0
 18T  Var_01    H8   C5A  C51  C41   60.10  30.0  3
 18T  Var_02    O2P  P    O5,  C5,   60.14  30.0  3
 18T  Var_03    O4P  P2   OPP  P    -56.00  30.0  3
 18T  Var_04    H19  C5,  O5,  P     42.91  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
 18T  chir_01  C2   O2   C1   C3   negativ
 18T  chir_02  C3   O3   C2   C4   positiv
 18T  chir_03  C5   O5   C4   C6   negativ
 18T  chir_04  C1,  C2,  O4,  N11  negativ
 18T  chir_05  C3,  O3,  C4,  C2,  positiv
 18T  chir_06  C4,  O4,  C3,  C5,  negativ
 18T  chir_09  C1   O1   C2   O5   positiv
 18T  chir_10  C4   O4   C5   C3   positiv

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
 18T  plan-1  C41  0.020
 18T  plan-1  C51  0.020
 18T  plan-1  C5A  0.020
 18T  plan-1  C61  0.020
 18T  plan-1  N31  0.020
 18T  plan-1  C21  0.020
 18T  plan-1  O21  0.020
 18T  plan-1  N11  0.020
 18T  plan-1  C1,  0.020
 18T  plan-1  H11  0.020
 18T  plan-1  H12  0.020
 18T  plan-1  O41  0.020

