# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 12:41:19 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-(2-deoxy-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2C[C@@H](O)[C@H](CO)O2)C(=O)NC1=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
 LLT  LLT  1-(2-deoxy-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  31  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LLT
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
 LLT  O4    O  O     0  -0.451  -4.4015   0.9328  -0.3363
 LLT  C4    C  CR6   0   0.561  -3.2577   0.5175  -0.3347
 LLT  C5    C  CR6   0  -0.184  -2.1939   1.0132   0.5181
 LLT  C7    C  CH3   0  -0.706  -2.4885   2.1216   1.4735
 LLT  C6    C  CR16  0   0.077  -0.9815   0.4491   0.3975
 LLT  N3    N  NR16  0  -0.735  -2.8773  -0.5026  -1.1872
 LLT  C2    C  CR6   0   0.733  -1.6417  -1.0801  -1.3198
 LLT  O2    O  O     0  -0.482  -1.4308  -1.9669  -2.1217
 LLT  N1    N  NR6   0  -0.561  -0.6859  -0.5725  -0.4681
 LLT  C1'   C  CH1   0   0.175   0.6829  -1.0614  -0.5487
 LLT  O4'   O  O2    0  -0.490   1.4911  -0.0090  -1.0233
 LLT  C4'   C  CH1   0   0.011   2.7070   0.0403  -0.2959
 LLT  C5'   C  CH2   0  -0.157   3.2623   1.4423  -0.3130
 LLT  O5'   O  OH1   0  -0.670   3.6385   1.7769  -1.6266
 LLT  C3'   C  CH1   0   0.024   2.3447  -0.4546   1.1011
 LLT  O3'   O  OH1   0  -0.662   3.4905  -0.9393   1.7435
 LLT  C2'   C  CH2   0  -0.573   1.2784  -1.5063   0.7935
 LLT  H7    H  HCH3  0   0.248  -3.2610   1.8369   2.1891
 LLT  H7A   H  HCH3  0   0.247  -1.5972   2.3959   2.0353
 LLT  H7B   H  HCH3  0   0.248  -2.8434   3.0113   0.9520
 LLT  H6    H  HCR6  0   0.306  -0.1598   0.7906   1.0117
 LLT  HN3   H  HNR6  0   0.426  -3.5914  -0.8682  -1.8049
 LLT  H1'   H  HCH1  0   0.275   0.6698  -1.8866  -1.2583
 LLT  H4'   H  HCH1  0   0.232   3.4422  -0.6522  -0.7333
 LLT  H5'   H  HCH2  0   0.197   2.5047   2.1308   0.0865
 LLT  H5'A  H  HCH2  0   0.210   4.1155   1.4676   0.3763
 LLT  HO5'  H  HOH1  0   0.458   4.0527   2.6442  -1.6081
 LLT  H3'   H  HCH1  0   0.219   1.9036   0.3739   1.6739
 LLT  HO3'  H  HOH1  0   0.460   3.2742  -1.1135   2.6643
 LLT  H2'   H  HCH2  0   0.283   0.5279  -1.6162   1.5763
 LLT  H2'A  H  HCH2  0   0.280   1.7640  -2.4754   0.6651

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
 LLT  O4   C4    double  1.217  0.020  1.217
 LLT  N3   C4    single  1.383  0.020  1.383
 LLT  C4   C5    single  1.451  0.020  1.451
 LLT  C5   C7    single  1.493  0.020  1.493
 LLT  C5   C6    double  1.343  0.020  1.343
 LLT  C7   H7    single  0.970  0.020  1.090
 LLT  C7   H7A   single  0.970  0.020  1.090
 LLT  C7   H7B   single  0.970  0.020  1.090
 LLT  N1   C6    single  1.371  0.020  1.371
 LLT  C6   H6    single  0.930  0.020  1.080
 LLT  N3   C2    single  1.370  0.020  1.370
 LLT  N3   HN3   single  0.860  0.020  1.020
 LLT  O2   C2    double  1.214  0.020  1.214
 LLT  C2   N1    single  1.377  0.020  1.377
 LLT  N1   C1'   single  1.456  0.020  1.456
 LLT  O4'  C1'   single  1.409  0.020  1.409
 LLT  C1'  C2'   single  1.534  0.020  1.534
 LLT  C1'  H1'   single  0.970  0.020  1.090
 LLT  O4'  C4'   single  1.418  0.020  1.418
 LLT  C4'  C5'   single  1.508  0.020  1.508
 LLT  C4'  C3'   single  1.526  0.020  1.526
 LLT  C4'  H4'   single  0.970  0.020  1.090
 LLT  O5'  C5'   single  1.407  0.020  1.407
 LLT  C5'  H5'   single  0.970  0.020  1.090
 LLT  C5'  H5'A  single  0.970  0.020  1.090
 LLT  O5'  HO5'  single  0.850  0.020  0.980
 LLT  C2'  C3'   single  1.529  0.020  1.529
 LLT  O3'  C3'   single  1.400  0.020  1.400
 LLT  C3'  H3'   single  0.970  0.020  1.090
 LLT  O3'  HO3'  single  0.850  0.020  0.980
 LLT  C2'  H2'   single  0.970  0.020  1.090
 LLT  C2'  H2'A  single  0.970  0.020  1.090

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
 LLT  N3    C4   C5   114.38  3.000
 LLT  C5    C4   O4   124.99  3.000
 LLT  N3    C4   O4   120.63  3.000
 LLT  C6    C5   C7   123.21  3.000
 LLT  C6    C5   C4   117.76  3.000
 LLT  C7    C5   C4   119.03  3.000
 LLT  H7B   C7   H7A  107.92  3.000
 LLT  H7B   C7   H7   107.22  3.000
 LLT  H7A   C7   H7   107.88  3.000
 LLT  H7B   C7   C5   111.34  3.000
 LLT  H7A   C7   C5   110.84  3.000
 LLT  H7    C7   C5   111.46  3.000
 LLT  H6    C6   N1   115.46  3.000
 LLT  H6    C6   C5   120.17  3.000
 LLT  N1    C6   C5   124.36  3.000
 LLT  HN3   N3   C2   115.13  3.000
 LLT  HN3   N3   C4   116.65  3.000
 LLT  C2    N3   C4   128.21  3.000
 LLT  N1    C2   O2   123.86  3.000
 LLT  N1    C2   N3   114.24  3.000
 LLT  O2    C2   N3   121.89  3.000
 LLT  C1'   N1   C2   119.64  3.000
 LLT  C1'   N1   C6   119.20  3.000
 LLT  C2    N1   C6   121.02  3.000
 LLT  H1'   C1'  C2'  110.80  3.000
 LLT  H1'   C1'  O4'  110.70  3.000
 LLT  C2'   C1'  O4'  106.77  3.000
 LLT  H1'   C1'  N1   106.22  3.000
 LLT  C2'   C1'  N1   114.45  3.000
 LLT  O4'   C1'  N1   107.89  3.000
 LLT  C4'   O4'  C1'  110.18  3.000
 LLT  H4'   C4'  C3'  108.57  3.000
 LLT  H4'   C4'  C5'  109.54  3.000
 LLT  C3'   C4'  C5'  113.54  3.000
 LLT  H4'   C4'  O4'  110.31  3.000
 LLT  C3'   C4'  O4'  104.77  3.000
 LLT  C5'   C4'  O4'  110.02  3.000
 LLT  H5'A  C5'  H5'  107.05  3.000
 LLT  H5'A  C5'  O5'  111.91  3.000
 LLT  H5'   C5'  O5'  112.02  3.000
 LLT  H5'A  C5'  C4'  107.50  3.000
 LLT  H5'   C5'  C4'  108.94  3.000
 LLT  O5'   C5'  C4'  109.28  3.000
 LLT  HO5'  O5'  C5'  108.17  3.000
 LLT  H3'   C3'  C2'  110.08  3.000
 LLT  H3'   C3'  O3'  110.49  3.000
 LLT  C2'   C3'  O3'  115.15  3.000
 LLT  H3'   C3'  C4'  109.14  3.000
 LLT  O3'   C3'  C4'  109.76  3.000
 LLT  C2'   C3'  C4'  101.80  3.000
 LLT  HO3'  O3'  C3'  108.54  3.000
 LLT  H2'A  C2'  H2'  107.54  3.000
 LLT  H2'A  C2'  C3'  108.91  3.000
 LLT  H2'   C2'  C3'  113.89  3.000
 LLT  H2'A  C2'  C1'  109.10  3.000
 LLT  H2'   C2'  C1'  112.97  3.000
 LLT  C3'   C2'  C1'  104.31  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
 LLT  CONST_01  N1   C2  N3  C4    0.00   0.0  0
 LLT  CONST_02  C2   N3  C4  C5    0.00   0.0  0
 LLT  CONST_03  N3   C2  N1  C6    0.00   0.0  0
 LLT  CONST_04  C1'  N1  C2  N3  180.00   0.0  0
 LLT  CONST_05  C2   N3  C4  O4  180.00   0.0  0
 LLT  CONST_06  O2   C2  N3  C4  180.00   0.0  0
 LLT  CONST_07  O2   C2  N1  C6  180.00   0.0  0
 LLT  CONST_08  C1'  N1  C2  O2    0.00   0.0  0
 LLT  CONST_09  HN3  N3  C4  C5  180.00   0.0  0
 LLT  Var_01    H7   C7  C5  C4   60.53  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
 LLT  chir_01  C1'  N1   O4'  C2'  negativ
 LLT  chir_02  C4'  O4'  C3'  C5'  positiv
 LLT  chir_03  C3'  O3'  C4'  C2'  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
 LLT  plan-1  O4   0.020
 LLT  plan-1  C4   0.020
 LLT  plan-1  C5   0.020
 LLT  plan-1  C7   0.020
 LLT  plan-1  C6   0.020
 LLT  plan-1  N3   0.020
 LLT  plan-1  C2   0.020
 LLT  plan-1  O2   0.020
 LLT  plan-1  N1   0.020
 LLT  plan-1  C1'  0.020
 LLT  plan-1  H6   0.020
 LLT  plan-1  HN3  0.020

