# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 14:14:08 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethyl-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C=C(C)C1=O)[C@H]2C[C@H](O)[C@@H](CO)O2
#
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
 3DT  3DT  1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,5-dimethyl-pyrimidine-2,4-dione  ligand  34  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3DT
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
 3DT  N1    N  NR6   0  -0.571  -0.5195  -0.5189  -0.1253
 3DT  C2    C  CR6   0   0.777  -1.5868  -1.2693   0.3140
 3DT  O2    O  O     0  -0.489  -1.4725  -2.4255   0.6696
 3DT  N3    N  NR6   0  -0.597  -2.8087  -0.6285   0.3140
 3DT  C4    C  CR6   0   0.587  -3.0076   0.7173   0.0177
 3DT  O4    O  O     0  -0.459  -4.1118   1.2211   0.1167
 3DT  C5    C  CR6   0  -0.178  -1.8328   1.4519  -0.4092
 3DT  C6    C  CR16  0   0.072  -0.6629   0.8003  -0.4552
 3DT  C7    C  CH3   0  -0.709  -1.9781   2.8964  -0.7577
 3DT  CN    C  CH3   0  -0.529  -3.9612  -1.4185   0.7327
 3DT  C1'   C  CH1   0   0.169   0.8134  -1.1094  -0.1540
 3DT  C2'   C  CH2   0  -0.570   1.5290  -0.9711  -1.5040
 3DT  C3'   C  CH1   0   0.021   2.6596   0.0229  -1.2341
 3DT  O3'   O  OH1   0  -0.662   3.8516  -0.2271  -1.9250
 3DT  C4'   C  CH1   0   0.012   2.8867  -0.1548   0.2644
 3DT  O4'   O  O2    0  -0.490   1.6049  -0.4393   0.7990
 3DT  C5'   C  CH2   0  -0.157   3.4624   1.0703   0.9294
 3DT  O5'   O  OH1   0  -0.669   3.7339   0.7838   2.2794
 3DT  H6    H  HCR6  0   0.305   0.2398   1.3096  -0.7632
 3DT  H7    H  HCH3  0   0.247  -2.3339   3.4778   0.0939
 3DT  H7A   H  HCH3  0   0.246  -1.0238   3.3155  -1.0728
 3DT  H7B   H  HCH3  0   0.247  -2.6925   3.0408  -1.5689
 3DT  HN    H  HCH3  0   0.257  -4.0531  -1.4300   1.8182
 3DT  HNA   H  HCH3  0   0.263  -4.8604  -0.9870   0.3090
 3DT  HNB   H  HCH3  0   0.261  -3.8588  -2.4377   0.3763
 3DT  H1'   H  HCH1  0   0.276   0.6883  -2.1558   0.1157
 3DT  H2'   H  HCH2  0   0.280   1.9598  -1.9344  -1.7818
 3DT  H2'A  H  HCH2  0   0.283   0.8592  -0.6660  -2.3081
 3DT  H3'   H  HCH1  0   0.219   2.3127   1.0484  -1.4272
 3DT  HO3'  H  HOH1  0   0.460   3.7335   0.0348  -2.8430
 3DT  H4'   H  HCH1  0   0.233   3.5624  -1.0099   0.4170
 3DT  H5'   H  HCH2  0   0.208   4.3699   1.3500   0.3789
 3DT  H5'A  H  HCH2  0   0.197   2.7506   1.9001   0.8197
 3DT  HO5'  H  HOH1  0   0.458   4.0878   1.5783   2.6890

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
 3DT  N1   C2    single  1.377  0.020  1.377
 3DT  N1   C6    single  1.367  0.020  1.367
 3DT  N1   C1'   single  1.458  0.020  1.458
 3DT  C2   O2    double  1.215  0.020  1.215
 3DT  C2   N3    single  1.380  0.020  1.380
 3DT  N3   C4    single  1.392  0.020  1.392
 3DT  N3   CN    single  1.459  0.020  1.459
 3DT  C4   O4    double  1.218  0.020  1.218
 3DT  C4   C5    single  1.450  0.020  1.450
 3DT  C5   C6    double  1.340  0.020  1.340
 3DT  C5   C7    single  1.493  0.020  1.493
 3DT  C1'  C2'   single  1.534  0.020  1.534
 3DT  C1'  O4'   single  1.408  0.020  1.408
 3DT  C2'  C3'   single  1.529  0.020  1.529
 3DT  C3'  O3'   single  1.400  0.020  1.400
 3DT  C3'  C4'   single  1.526  0.020  1.526
 3DT  C4'  O4'   single  1.418  0.020  1.418
 3DT  C4'  C5'   single  1.508  0.020  1.508
 3DT  C5'  O5'   single  1.407  0.020  1.407
 3DT  C6   H6    single  0.930  0.020  1.080
 3DT  C7   H7    single  0.970  0.020  1.090
 3DT  C7   H7A   single  0.970  0.020  1.090
 3DT  C7   H7B   single  0.970  0.020  1.090
 3DT  CN   HN    single  0.970  0.020  1.090
 3DT  CN   HNA   single  0.970  0.020  1.090
 3DT  CN   HNB   single  0.970  0.020  1.090
 3DT  C1'  H1'   single  0.970  0.020  1.090
 3DT  C2'  H2'   single  0.970  0.020  1.090
 3DT  C2'  H2'A  single  0.970  0.020  1.090
 3DT  C3'  H3'   single  0.970  0.020  1.090
 3DT  O3'  HO3'  single  0.850  0.020  0.980
 3DT  C4'  H4'   single  0.970  0.020  1.090
 3DT  C5'  H5'   single  0.970  0.020  1.090
 3DT  C5'  H5'A  single  0.970  0.020  1.090
 3DT  O5'  HO5'  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
 3DT  C1'   N1   C6   118.80  3.000
 3DT  C1'   N1   C2   119.62  3.000
 3DT  C6    N1   C2   121.44  3.000
 3DT  N3    C2   O2   121.68  3.000
 3DT  N3    C2   N1   115.69  3.000
 3DT  O2    C2   N1   122.63  3.000
 3DT  CN    N3   C4   118.15  3.000
 3DT  CN    N3   C2   116.63  3.000
 3DT  C4    N3   C2   125.13  3.000
 3DT  C5    C4   O4   123.30  3.000
 3DT  C5    C4   N3   115.89  3.000
 3DT  O4    C4   N3   120.81  3.000
 3DT  C7    C5   C6   123.19  3.000
 3DT  C7    C5   C4   118.69  3.000
 3DT  C6    C5   C4   118.11  3.000
 3DT  H6    C6   C5   120.64  3.000
 3DT  H6    C6   N1   115.83  3.000
 3DT  C5    C6   N1   123.53  3.000
 3DT  H7B   C7   H7A  107.94  3.000
 3DT  H7B   C7   H7   107.25  3.000
 3DT  H7A   C7   H7   107.86  3.000
 3DT  H7B   C7   C5   111.44  3.000
 3DT  H7A   C7   C5   110.77  3.000
 3DT  H7    C7   C5   111.42  3.000
 3DT  HNB   CN   HNA  108.91  3.000
 3DT  HNB   CN   HN   109.00  3.000
 3DT  HNA   CN   HN   108.89  3.000
 3DT  HNB   CN   N3   109.88  3.000
 3DT  HNA   CN   N3   109.13  3.000
 3DT  HN    CN   N3   110.99  3.000
 3DT  H1'   C1'  O4'  110.76  3.000
 3DT  H1'   C1'  C2'  111.01  3.000
 3DT  O4'   C1'  C2'  106.88  3.000
 3DT  H1'   C1'  N1   106.23  3.000
 3DT  O4'   C1'  N1   107.92  3.000
 3DT  C2'   C1'  N1   114.03  3.000
 3DT  H2'A  C2'  H2'  107.57  3.000
 3DT  H2'A  C2'  C3'  113.74  3.000
 3DT  H2'   C2'  C3'  109.08  3.000
 3DT  H2'A  C2'  C1'  112.81  3.000
 3DT  H2'   C2'  C1'  109.18  3.000
 3DT  C3'   C2'  C1'  104.37  3.000
 3DT  H3'   C3'  C4'  109.14  3.000
 3DT  H3'   C3'  O3'  110.39  3.000
 3DT  C4'   C3'  O3'  109.70  3.000
 3DT  H3'   C3'  C2'  109.99  3.000
 3DT  C4'   C3'  C2'  101.98  3.000
 3DT  O3'   C3'  C2'  115.23  3.000
 3DT  HO3'  O3'  C3'  108.53  3.000
 3DT  H4'   C4'  C5'  109.61  3.000
 3DT  H4'   C4'  O4'  110.30  3.000
 3DT  C5'   C4'  O4'  110.00  3.000
 3DT  H4'   C4'  C3'  108.54  3.000
 3DT  C5'   C4'  C3'  113.28  3.000
 3DT  O4'   C4'  C3'  105.02  3.000
 3DT  C4'   O4'  C1'  110.40  3.000
 3DT  H5'A  C5'  H5'  107.05  3.000
 3DT  H5'A  C5'  O5'  112.01  3.000
 3DT  H5'   C5'  O5'  111.94  3.000
 3DT  H5'A  C5'  C4'  108.79  3.000
 3DT  H5'   C5'  C4'  107.55  3.000
 3DT  O5'   C5'  C4'  109.35  3.000
 3DT  HO5'  O5'  C5'  108.15  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
 3DT  CONST_01  C4   N3  C2  N1    0.00   0.0  0
 3DT  CONST_02  C5   C4  N3  C2    0.00   0.0  0
 3DT  CONST_03  C6   N1  C2  N3    0.00   0.0  0
 3DT  CONST_04  C1'  N1  C2  N3  180.00   0.0  0
 3DT  CONST_05  CN   N3  C2  N1  180.00   0.0  0
 3DT  CONST_06  O4   C4  N3  C2  180.00   0.0  0
 3DT  CONST_07  C6   N1  C2  O2  180.00   0.0  0
 3DT  CONST_08  C1'  N1  C2  O2    0.00   0.0  0
 3DT  CONST_09  C4   N3  C2  O2  180.00   0.0  0
 3DT  CONST_10  CN   N3  C4  C5  180.00   0.0  0
 3DT  CONST_11  CN   N3  C2  O2    0.00   0.0  0
 3DT  CONST_12  CN   N3  C4  O4    0.00   0.0  0
 3DT  Var_01    HN   CN  N3  C2   83.76  30.0  3
 3DT  Var_02    H7   C7  C5  C4   60.72  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
 3DT  chir_01  C1'  N1   C2'  O4'  negativ
 3DT  chir_02  C3'  O3'  C4'  C2'  positiv
 3DT  chir_03  C4'  O4'  C3'  C5'  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
 3DT  plan-1  N1   0.020
 3DT  plan-1  C2   0.020
 3DT  plan-1  O2   0.020
 3DT  plan-1  N3   0.020
 3DT  plan-1  C4   0.020
 3DT  plan-1  O4   0.020
 3DT  plan-1  C5   0.020
 3DT  plan-1  C6   0.020
 3DT  plan-1  C7   0.020
 3DT  plan-1  CN   0.020
 3DT  plan-1  C1'  0.020
 3DT  plan-1  H6   0.020

