# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 01:45:09 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-amino-1-[(2S,4S)-2-(hydroxymethyl)-1,3-dioxolan-4-yl]pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2CO[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
 LTT  LTT  4-amino-1-[(2S,4S)-2-(hydroxymethyl)-1,3-dioxolan-4-yl]pyrimidin-2(1H)-one  ligand  26  15  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LTT
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
 LTT  O1    O  OC    0  -0.526   2.4642   0.6329  -2.0107
 LTT  C1    C  CR6   0   0.597   1.7473   1.6242  -1.9122
 LTT  N2    N  N     0  -0.537   1.2741   2.3017  -2.9723
 LTT  C3    C  CR6   0   0.516   0.5119   3.3674  -2.8039
 LTT  N3    N  NH2   0  -0.809   0.0663   3.9996  -3.8886
 LTT  C5    C  CR16  0  -0.471   0.1614   3.8518  -1.5083
 LTT  C7    C  CR16  0   0.087   0.6432   3.1641  -0.4509
 LTT  N1    N  NR6   0  -0.558   1.4076   2.0640  -0.6273
 LTT  C4    C  CR15  0   0.167   2.0027   1.3134   0.4910
 LTT  O3    O  O     0  -0.492   1.6573   1.8825   1.7113
 LTT  C2    C  CR15  0   0.232   0.7863   1.0042   2.3995
 LTT  C8    C  CH2   0  -0.196  -0.6798   1.3435   2.1783
 LTT  O4    O  OH1   0  -0.664  -0.8783   2.6665   2.6121
 LTT  O2    O  O     0  -0.489   1.0982  -0.2694   1.9345
 LTT  C6    C  CH2   0  -0.226   1.4790  -0.1346   0.5778
 LTT  HN31  H  HNH2  0   0.414  -0.5140   4.8167  -3.8207
 LTT  HN32  H  HNH2  0   0.402   0.3060   3.6637  -4.8056
 LTT  H5    H  HCR6  0   0.286  -0.4552   4.7265  -1.3677
 LTT  H7    H  HCR6  0   0.317   0.4286   3.4618   0.5644
 LTT  H4    H  HCR5  0   0.283   3.0867   1.3548   0.3726
 LTT  H2    H  HCR5  0   0.257   1.0263   1.0674   3.4649
 LTT  H81   H  HCH2  0   0.232  -1.2758   0.6268   2.7568
 LTT  H82   H  HCH2  0   0.209  -0.9569   1.2093   1.1230
 LTT  HO4   H  HOH1  0   0.465  -1.8056   2.8882   2.4886
 LTT  H61   H  HCH2  0   0.241   0.6349  -0.2972  -0.0991
 LTT  H62   H  HCH2  0   0.265   2.2515  -0.8678   0.3577

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
 LTT  O1  C1    double    1.227  0.020  1.227
 LTT  C1  N2    aromatic  1.344  0.020  1.344
 LTT  C1  N1    aromatic  1.400  0.020  1.400
 LTT  N2  C3    aromatic  1.321  0.020  1.321
 LTT  C3  N3    single    1.332  0.020  1.332
 LTT  C3  C5    aromatic  1.427  0.020  1.427
 LTT  N3  HN31  single    0.860  0.020  1.020
 LTT  N3  HN32  single    0.860  0.020  1.020
 LTT  C5  C7    aromatic  1.350  0.020  1.350
 LTT  C5  H5    single    0.930  0.020  1.080
 LTT  C7  N1    aromatic  1.351  0.020  1.351
 LTT  C7  H7    single    0.930  0.020  1.080
 LTT  N1  C4    single    1.473  0.020  1.473
 LTT  C4  O3    single    1.390  0.020  1.390
 LTT  C4  C6    single    1.542  0.020  1.542
 LTT  C4  H4    single    0.970  0.020  1.090
 LTT  O3  C2    single    1.415  0.020  1.415
 LTT  C2  C8    single    1.521  0.020  1.521
 LTT  C2  O2    single    1.391  0.020  1.391
 LTT  C2  H2    single    0.970  0.020  1.090
 LTT  C8  O4    single    1.406  0.020  1.406
 LTT  C8  H81   single    0.970  0.020  1.090
 LTT  C8  H82   single    0.970  0.020  1.090
 LTT  O4  HO4   single    0.850  0.020  0.980
 LTT  O2  C6    single    1.416  0.020  1.416
 LTT  C6  H61   single    0.970  0.020  1.090
 LTT  C6  H62   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
 LTT  N1    C1  N2    118.69  3.000
 LTT  N1    C1  O1    117.98  3.000
 LTT  N2    C1  O1    123.33  3.000
 LTT  C3    N2  C1    120.61  3.000
 LTT  C5    C3  N3    119.74  3.000
 LTT  C5    C3  N2    122.10  3.000
 LTT  N3    C3  N2    118.16  3.000
 LTT  HN32  N3  HN31  118.10  3.000
 LTT  HN32  N3  C3    120.29  3.000
 LTT  HN31  N3  C3    121.62  3.000
 LTT  H5    C5  C7    120.97  3.000
 LTT  H5    C5  C3    122.25  3.000
 LTT  C7    C5  C3    116.78  3.000
 LTT  H7    C7  N1    117.37  3.000
 LTT  H7    C7  C5    121.68  3.000
 LTT  N1    C7  C5    120.95  3.000
 LTT  C4    N1  C7    123.00  3.000
 LTT  C4    N1  C1    116.03  3.000
 LTT  C7    N1  C1    120.86  3.000
 LTT  H4    C4  C6    112.27  3.000
 LTT  H4    C4  O3    109.06  3.000
 LTT  C6    C4  O3    104.51  3.000
 LTT  H4    C4  N1    107.44  3.000
 LTT  C6    C4  N1    112.59  3.000
 LTT  O3    C4  N1    110.95  3.000
 LTT  C2    O3  C4    109.01  3.000
 LTT  H2    C2  O2    109.22  3.000
 LTT  H2    C2  C8    109.89  3.000
 LTT  O2    C2  C8    111.82  3.000
 LTT  H2    C2  O3    107.62  3.000
 LTT  O2    C2  O3    105.52  3.000
 LTT  C8    C2  O3    112.58  3.000
 LTT  H82   C8  H81   106.83  3.000
 LTT  H82   C8  O4    112.05  3.000
 LTT  H81   C8  O4    112.04  3.000
 LTT  H82   C8  C2    110.81  3.000
 LTT  H81   C8  C2    107.53  3.000
 LTT  O4    C8  C2    107.52  3.000
 LTT  HO4   O4  C8    108.27  3.000
 LTT  C6    O2  C2    107.07  3.000
 LTT  H62   C6  H61   108.82  3.000
 LTT  H62   C6  O2    108.71  3.000
 LTT  H61   C6  O2    111.79  3.000
 LTT  H62   C6  C4    112.36  3.000
 LTT  H61   C6  C4    111.51  3.000
 LTT  O2    C6  C4    103.57  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
 LTT  CONST_01  C5    C3  N2  C1    0.00   0.0  0
 LTT  CONST_02  C5    C7  N1  C1    0.00   0.0  0
 LTT  CONST_03  C7    N1  C1  N2    0.00   0.0  0
 LTT  CONST_04  C7    C5  C3  N2    0.00   0.0  0
 LTT  CONST_05  N1    C1  N2  C3    0.00   0.0  0
 LTT  CONST_06  N1    C7  C5  C3    0.00   0.0  0
 LTT  CONST_07  C4    N1  C1  N2  180.00   0.0  0
 LTT  CONST_08  C4    N1  C7  C5  180.00   0.0  0
 LTT  CONST_09  C3    N2  C1  O1  180.00   0.0  0
 LTT  CONST_10  C7    N1  C1  O1  180.00   0.0  0
 LTT  CONST_11  C4    N1  C1  O1    0.00   0.0  0
 LTT  CONST_12  N3    C3  N2  C1  180.00   0.0  0
 LTT  CONST_13  C7    C5  C3  N3  180.00   0.0  0
 LTT  CONST_14  H7    C7  N1  C1  180.00   0.0  0
 LTT  CONST_15  H5    C5  C3  N2  180.00   0.0  0
 LTT  CONST_16  HN31  N3  C3  N2  180.00   0.0  0
 LTT  CONST_17  HN32  N3  C3  N2    0.00   0.0  0
 LTT  Var_01    H61   C6  O2  C2  -93.94  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
 LTT  chir_01  C4  N1  O3  C6  negativ
 LTT  chir_02  C2  O3  O2  C8  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
 LTT  plan-1  O1    0.020
 LTT  plan-1  C1    0.020
 LTT  plan-1  N2    0.020
 LTT  plan-1  C3    0.020
 LTT  plan-1  N3    0.020
 LTT  plan-1  C5    0.020
 LTT  plan-1  C7    0.020
 LTT  plan-1  N1    0.020
 LTT  plan-1  C4    0.020
 LTT  plan-1  H5    0.020
 LTT  plan-1  H7    0.020
 LTT  plan-2  C3    0.020
 LTT  plan-2  N3    0.020
 LTT  plan-2  HN31  0.020
 LTT  plan-2  HN32  0.020

