# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 06:10:47 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 4-amino-1-(2-deoxy-beta-L-erythro-pentofuranosyl)pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[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
 LDC  LDC  4-amino-1-(2-deoxy-beta-L-erythro-pentofuranosyl)pyrimidin-2(1H)-one  ligand  29  16  .  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_LDC
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
 LDC  O1    O  OC    0  -0.527   2.8726   1.1970  -1.5182
 LDC  C2    C  CR6   0   0.595   2.3784   0.3024  -2.1964
 LDC  N3    N  N     0  -0.539   3.1049  -0.6993  -2.7280
 LDC  C3    C  CR6   0   0.512   2.5271  -1.6468  -3.4428
 LDC  N4    N  NH2   0  -0.812   3.2950  -2.6148  -3.9446
 LDC  C4    C  CR16  0  -0.476   1.1236  -1.6550  -3.6937
 LDC  C5    C  CR16  0   0.080   0.4058  -0.6406  -3.1638
 LDC  N2    N  NR6   0  -0.558   0.9966   0.3228  -2.4250
 LDC  C8    C  CH1   0   0.223   0.2422   1.4442  -1.8320
 LDC  C9    C  CH2   0  -0.555   0.1088   1.3312  -0.3084
 LDC  C10   C  CH1   0   0.005  -1.3453   1.7190  -0.0397
 LDC  O3    O  OH1   0  -0.663  -1.5295   3.0899   0.2177
 LDC  C11   C  CH1   0  -0.058  -2.0266   1.2517  -1.3255
 LDC  O4    O  O2    0  -0.498  -1.0552   1.4749  -2.3492
 LDC  C12   C  CH2   0  -0.175  -2.4635  -0.1993  -1.2511
 LDC  O5    O  OH1   0  -0.663  -2.9395  -0.5908  -2.5167
 LDC  HN41  H  HNH2  0   0.412   2.9039  -3.3780  -4.4676
 LDC  HN42  H  HNH2  0   0.401   4.2818  -2.6298  -3.7512
 LDC  H4    H  HCR6  0   0.283   0.6471  -2.4254  -4.2805
 LDC  H5    H  HCR6  0   0.319  -0.6613  -0.5665  -3.3133
 LDC  H8    H  HCH1  0   0.267   0.7617   2.3570  -2.1307
 LDC  H91   H  HCH2  0   0.283   0.8117   1.9725   0.2184
 LDC  H92   H  HCH2  0   0.267   0.2929   0.3058   0.0165
 LDC  H10   H  HCH1  0   0.264  -1.7404   1.1972   0.8338
 LDC  HO3   H  HOH1  0   0.450  -1.1720   3.6088  -0.5106
 LDC  H11   H  HCH1  0   0.263  -2.8939   1.8719  -1.5686
 LDC  H121  H  HCH2  0   0.231  -3.2442  -0.2720  -0.4831
 LDC  H122  H  HCH2  0   0.207  -1.6332  -0.8367  -0.9160
 LDC  HO5   H  HOH1  0   0.462  -3.1617  -1.5257  -2.4780

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
 LDC  O1   C2    double    1.226  0.020  1.226
 LDC  C2   N3    aromatic  1.347  0.020  1.347
 LDC  C2   N2    aromatic  1.401  0.020  1.401
 LDC  N3   C3    aromatic  1.320  0.020  1.320
 LDC  C3   N4    single    1.334  0.020  1.334
 LDC  C3   C4    aromatic  1.426  0.020  1.426
 LDC  N4   HN41  single    0.860  0.020  1.020
 LDC  N4   HN42  single    0.860  0.020  1.020
 LDC  C4   C5    aromatic  1.351  0.020  1.351
 LDC  C4   H4    single    0.930  0.020  1.080
 LDC  C5   N2    aromatic  1.350  0.020  1.350
 LDC  C5   H5    single    0.930  0.020  1.080
 LDC  N2   C8    single    1.476  0.020  1.476
 LDC  C8   O4    single    1.397  0.020  1.397
 LDC  C8   C9    single    1.534  0.020  1.534
 LDC  C8   H8    single    0.970  0.020  1.090
 LDC  C9   C10   single    1.529  0.020  1.529
 LDC  C9   H91   single    0.970  0.020  1.090
 LDC  C9   H92   single    0.970  0.020  1.090
 LDC  C10  C11   single    1.528  0.020  1.528
 LDC  C10  O3    single    1.407  0.020  1.407
 LDC  C10  H10   single    0.970  0.020  1.090
 LDC  O3   HO3   single    0.850  0.020  0.980
 LDC  C11  O4    single    1.429  0.020  1.429
 LDC  C11  C12   single    1.517  0.020  1.517
 LDC  C11  H11   single    0.970  0.020  1.090
 LDC  C12  O5    single    1.408  0.020  1.408
 LDC  C12  H121  single    0.970  0.020  1.090
 LDC  C12  H122  single    0.970  0.020  1.090
 LDC  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
 LDC  N2    C2   N3    118.59  3.000
 LDC  N2    C2   O1    118.50  3.000
 LDC  N3    C2   O1    122.92  3.000
 LDC  C3    N3   C2    120.76  3.000
 LDC  C4    C3   N4    119.77  3.000
 LDC  C4    C3   N3    122.02  3.000
 LDC  N4    C3   N3    118.21  3.000
 LDC  HN42  N4   HN41  118.09  3.000
 LDC  HN42  N4   C3    120.23  3.000
 LDC  HN41  N4   C3    121.54  3.000
 LDC  H4    C4   C5    120.97  3.000
 LDC  H4    C4   C3    122.30  3.000
 LDC  C5    C4   C3    116.73  3.000
 LDC  H5    C5   N2    117.34  3.000
 LDC  H5    C5   C4    121.47  3.000
 LDC  N2    C5   C4    121.19  3.000
 LDC  C8    N2   C5    122.57  3.000
 LDC  C8    N2   C2    116.72  3.000
 LDC  C5    N2   C2    120.71  3.000
 LDC  H8    C8   O4    108.79  3.000
 LDC  H8    C8   C9    112.01  3.000
 LDC  O4    C8   C9    106.77  3.000
 LDC  H8    C8   N2    106.39  3.000
 LDC  C9    C8   N2    112.81  3.000
 LDC  O4    C8   N2    110.04  3.000
 LDC  H92   C9   H91   107.51  3.000
 LDC  H92   C9   C10   110.27  3.000
 LDC  H91   C9   C10   112.33  3.000
 LDC  H92   C9   C8    110.51  3.000
 LDC  H91   C9   C8    112.43  3.000
 LDC  C10   C9   C8    103.81  3.000
 LDC  H10   C10  C11   111.45  3.000
 LDC  H10   C10  O3    105.78  3.000
 LDC  C11   C10  O3    113.17  3.000
 LDC  H10   C10  C9    111.33  3.000
 LDC  O3    C10  C9    113.82  3.000
 LDC  C11   C10  C9    101.45  3.000
 LDC  HO3   O3   C10   109.76  3.000
 LDC  H11   C11  C12   108.96  3.000
 LDC  H11   C11  O4    106.94  3.000
 LDC  C12   C11  O4    112.35  3.000
 LDC  H11   C11  C10   111.55  3.000
 LDC  C12   C11  C10   112.31  3.000
 LDC  O4    C11  C10   104.59  3.000
 LDC  C11   O4   C8    111.27  3.000
 LDC  H122  C12  H121  106.60  3.000
 LDC  H122  C12  O5    111.61  3.000
 LDC  H121  C12  O5    111.73  3.000
 LDC  H122  C12  C11   110.61  3.000
 LDC  H121  C12  C11   107.60  3.000
 LDC  O5    C12  C11   108.62  3.000
 LDC  HO5   O5   C12   108.20  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
 LDC  CONST_01  C4    C3  N3  C2    0.00  0.0  0
 LDC  CONST_02  C4    C5  N2  C2    0.00  0.0  0
 LDC  CONST_03  C5    N2  C2  N3    0.00  0.0  0
 LDC  CONST_04  C5    C4  C3  N3    0.00  0.0  0
 LDC  CONST_05  N2    C2  N3  C3    0.00  0.0  0
 LDC  CONST_06  N2    C5  C4  C3    0.00  0.0  0
 LDC  CONST_07  C8    N2  C2  N3  180.00  0.0  0
 LDC  CONST_08  C8    N2  C5  C4  180.00  0.0  0
 LDC  CONST_09  C3    N3  C2  O1  180.00  0.0  0
 LDC  CONST_10  C5    N2  C2  O1  180.00  0.0  0
 LDC  CONST_11  C8    N2  C2  O1    0.00  0.0  0
 LDC  CONST_12  N4    C3  N3  C2  180.00  0.0  0
 LDC  CONST_13  C5    C4  C3  N4  180.00  0.0  0
 LDC  CONST_14  H5    C5  N2  C2  180.00  0.0  0
 LDC  CONST_15  H4    C4  C3  N3  180.00  0.0  0
 LDC  CONST_16  HN41  N4  C3  N3  180.00  0.0  0
 LDC  CONST_17  HN42  N4  C3  N3    0.00  0.0  0

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
 LDC  chir_01  C8   N2  O4   C9   negativ
 LDC  chir_02  C10  O3  C11  C9   negativ
 LDC  chir_03  C11  O4  C10  C12  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
 LDC  plan-1  O1    0.020
 LDC  plan-1  C2    0.020
 LDC  plan-1  N3    0.020
 LDC  plan-1  C3    0.020
 LDC  plan-1  N4    0.020
 LDC  plan-1  C4    0.020
 LDC  plan-1  C5    0.020
 LDC  plan-1  N2    0.020
 LDC  plan-1  C8    0.020
 LDC  plan-1  H4    0.020
 LDC  plan-1  H5    0.020
 LDC  plan-2  C3    0.020
 LDC  plan-2  N4    0.020
 LDC  plan-2  HN41  0.020
 LDC  plan-2  HN42  0.020

