# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:18:40 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-amino-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2CS[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
 3TC  3TC  4-amino-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]pyrimidin-2(1H)-one  ligand  26  15  .  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_3TC
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
 3TC  O1    O  OC    0  -0.513   3.5086  -2.1266  -1.1247
 3TC  C1    C  CR6   0   0.601   3.5171  -1.2906  -0.2324
 3TC  N2    N  N     0  -0.541   4.6332  -0.6364   0.1420
 3TC  C3    C  CR6   0   0.520   4.6117   0.2601   1.1086
 3TC  N3    N  NH2   0  -0.804   5.7493   0.8687   1.4314
 3TC  C5    C  CR16  0  -0.473   3.4116   0.5916   1.8142
 3TC  C7    C  CR16  0   0.105   2.2977  -0.0593   1.4368
 3TC  N1    N  NR6   0  -0.561   2.3160  -0.9800   0.4374
 3TC  C4    C  CR15  0   0.189   1.0940  -1.6597   0.0848
 3TC  C6    C  CH2   0  -0.578   0.0126  -0.7275  -0.4594
 3TC  O2    O  O     0  -0.472   0.5772  -2.2503   1.2537
 3TC  C2    C  CR15  0  -0.093  -0.7038  -2.7658   1.0348
 3TC  S1    S  S2    0  -0.026  -1.5125  -1.6671  -0.2202
 3TC  C8    C  CH2   0  -0.192  -1.4618  -2.8080   2.3457
 3TC  O3    O  OH1   0  -0.650  -1.6372  -1.5503   2.9338
 3TC  HN31  H  HNH2  0   0.416   5.7881   1.5666   2.1534
 3TC  HN32  H  HNH2  0   0.405   6.5971   0.6543   0.9340
 3TC  H5    H  HCR6  0   0.293   3.3922   1.3206   2.6095
 3TC  H7    H  HCR6  0   0.316   1.3479   0.1222   1.9197
 3TC  H4    H  HCR5  0   0.290   1.3370  -2.4163  -0.6622
 3TC  H61   H  HCH2  0   0.283  -0.0228   0.2209   0.0776
 3TC  H62   H  HCH2  0   0.296   0.1731  -0.5270  -1.5170
 3TC  H2    H  HCR5  0   0.267  -0.6579  -3.7730   0.6075
 3TC  H81   H  HCH2  0   0.230  -0.9444  -3.5098   3.0137
 3TC  H82   H  HCH2  0   0.242  -2.4506  -3.2282   2.1535
 3TC  HO3   H  HOH1  0   0.448  -0.7756  -1.2161   3.1991

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
 3TC  O1  C1    double    1.223  0.020  1.223
 3TC  C1  N2    aromatic  1.347  0.020  1.347
 3TC  C1  N1    aromatic  1.410  0.020  1.410
 3TC  N2  C3    aromatic  1.319  0.020  1.319
 3TC  C3  N3    single    1.330  0.020  1.330
 3TC  C3  C5    aromatic  1.431  0.020  1.431
 3TC  N3  HN31  single    0.860  0.020  1.020
 3TC  N3  HN32  single    0.860  0.020  1.020
 3TC  C5  C7    aromatic  1.344  0.020  1.344
 3TC  C5  H5    single    0.930  0.020  1.080
 3TC  C7  N1    aromatic  1.359  0.020  1.359
 3TC  C7  H7    single    0.930  0.020  1.080
 3TC  N1  C4    single    1.442  0.020  1.442
 3TC  C4  O2    single    1.408  0.020  1.408
 3TC  C4  C6    single    1.528  0.020  1.528
 3TC  C4  H4    single    0.970  0.020  1.090
 3TC  C6  S1    single    1.807  0.020  1.807
 3TC  C6  H61   single    0.970  0.020  1.090
 3TC  C6  H62   single    0.970  0.020  1.090
 3TC  O2  C2    single    1.398  0.020  1.398
 3TC  C2  C8    single    1.515  0.020  1.515
 3TC  C2  S1    single    1.854  0.020  1.854
 3TC  C2  H2    single    0.970  0.020  1.090
 3TC  C8  O3    single    1.399  0.020  1.399
 3TC  C8  H81   single    0.970  0.020  1.090
 3TC  C8  H82   single    0.970  0.020  1.090
 3TC  O3  HO3   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
 3TC  N1    C1  N2    117.84  3.000
 3TC  N1    C1  O1    119.43  3.000
 3TC  N2    C1  O1    122.74  3.000
 3TC  C3    N2  C1    121.37  3.000
 3TC  C5    C3  N3    119.45  3.000
 3TC  C5    C3  N2    122.19  3.000
 3TC  N3    C3  N2    118.37  3.000
 3TC  HN32  N3  HN31  118.09  3.000
 3TC  HN32  N3  C3    120.21  3.000
 3TC  HN31  N3  C3    121.68  3.000
 3TC  H5    C5  C7    121.27  3.000
 3TC  H5    C5  C3    122.35  3.000
 3TC  C7    C5  C3    116.38  3.000
 3TC  H7    C7  N1    117.01  3.000
 3TC  H7    C7  C5    121.43  3.000
 3TC  N1    C7  C5    121.56  3.000
 3TC  C4    N1  C7    119.19  3.000
 3TC  C4    N1  C1    120.13  3.000
 3TC  C7    N1  C1    120.67  3.000
 3TC  H4    C4  O2    111.06  3.000
 3TC  H4    C4  C6    109.70  3.000
 3TC  O2    C4  C6    106.97  3.000
 3TC  H4    C4  N1    107.79  3.000
 3TC  C6    C4  N1    113.53  3.000
 3TC  O2    C4  N1    107.81  3.000
 3TC  H62   C6  H61   108.85  3.000
 3TC  H62   C6  S1    110.41  3.000
 3TC  H61   C6  S1    111.07  3.000
 3TC  H62   C6  C4    110.74  3.000
 3TC  H61   C6  C4    112.22  3.000
 3TC  S1    C6  C4    103.47  3.000
 3TC  C2    O2  C4    111.16  3.000
 3TC  H2    C2  C8    109.45  3.000
 3TC  H2    C2  S1    107.41  3.000
 3TC  C8    C2  S1    112.59  3.000
 3TC  H2    C2  O2    111.21  3.000
 3TC  S1    C2  O2    106.69  3.000
 3TC  C8    C2  O2    109.47  3.000
 3TC  C2    S1  C6     91.70  3.000
 3TC  H82   C8  H81   106.73  3.000
 3TC  H82   C8  O3    107.84  3.000
 3TC  H81   C8  O3    112.19  3.000
 3TC  H82   C8  C2    108.16  3.000
 3TC  H81   C8  C2    107.96  3.000
 3TC  O3    C8  C2    113.66  3.000
 3TC  HO3   O3  C8    108.42  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
 3TC  CONST_01  C5    C3  N2  C1     0.00   0.0  0
 3TC  CONST_02  C5    C7  N1  C1     0.00   0.0  0
 3TC  CONST_03  C7    N1  C1  N2     0.00   0.0  0
 3TC  CONST_04  C7    C5  C3  N2     0.00   0.0  0
 3TC  CONST_05  N1    C1  N2  C3     0.00   0.0  0
 3TC  CONST_06  N1    C7  C5  C3     0.00   0.0  0
 3TC  CONST_07  C4    N1  C1  N2   180.00   0.0  0
 3TC  CONST_08  C4    N1  C7  C5   180.00   0.0  0
 3TC  CONST_09  C3    N2  C1  O1   180.00   0.0  0
 3TC  CONST_10  C7    N1  C1  O1   180.00   0.0  0
 3TC  CONST_11  C4    N1  C1  O1     0.00   0.0  0
 3TC  CONST_12  N3    C3  N2  C1   180.00   0.0  0
 3TC  CONST_13  C7    C5  C3  N3   180.00   0.0  0
 3TC  CONST_14  H7    C7  N1  C1   180.00   0.0  0
 3TC  CONST_15  H5    C5  C3  N2   180.00   0.0  0
 3TC  CONST_16  HN31  N3  C3  N2   180.00   0.0  0
 3TC  CONST_17  HN32  N3  C3  N2     0.00   0.0  0
 3TC  Var_01    H61   C6  S1  C2  -101.48  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
 3TC  chir_01  C4  N1  O2  C6  negativ
 3TC  chir_02  C2  S1  O2  C8  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
 3TC  plan-1  O1    0.020
 3TC  plan-1  C1    0.020
 3TC  plan-1  N2    0.020
 3TC  plan-1  C3    0.020
 3TC  plan-1  N3    0.020
 3TC  plan-1  C5    0.020
 3TC  plan-1  C7    0.020
 3TC  plan-1  N1    0.020
 3TC  plan-1  C4    0.020
 3TC  plan-1  H5    0.020
 3TC  plan-1  H7    0.020
 3TC  plan-2  C3    0.020
 3TC  plan-2  N3    0.020
 3TC  plan-2  HN31  0.020
 3TC  plan-2  HN32  0.020

