# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:43:13 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@H](O[C@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=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
 3KA  3KA  1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)pyrimidine-2,4(1H,3H)-dione  ligand  33  20  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3KA
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
 3KA  O4   O  O     0  -0.452  -3.8466  -3.3033  -0.2420
 3KA  C4   C  CR6   0   0.547  -3.2163  -2.2760  -0.0743
 3KA  N3   N  NR16  0  -0.689  -3.8462  -1.0442  -0.1783
 3KA  C2   C  CR6   0   0.687  -3.3019   0.1965   0.0018
 3KA  O2   O  O     0  -0.349  -3.9639   1.2125  -0.0657
 3KA  C5   C  CR16  0  -0.479  -1.8091  -2.1721   0.2144
 3KA  C6   C  CR16  0   0.083  -1.2589  -0.9617   0.4163
 3KA  N1   N  NR6   0  -0.609  -1.9606   0.2011   0.3263
 3KA  C1'  C  CH1   0   0.198  -1.3248   1.5145   0.5790
 3KA  O4'  O  O2    0  -0.521  -0.0627   1.2890   1.1424
 3KA  C2'  C  CH2   0  -0.529  -1.0923   2.3260  -0.6962
 3KA  C3'  C  CH1   0   0.032   0.2683   2.9592  -0.4384
 3KA  O3'  O  OH1   0  -0.670   0.1651   4.0817   0.3996
 3KA  C4'  C  CH1   0  -0.007   0.9751   1.8778   0.3658
 3KA  C5'  C  CH2   0  -0.175   1.6601   0.8513  -0.5175
 3KA  O5'  O  O2    0  -0.631   2.1310  -0.1830   0.3475
 3KA  P    P  P     0   1.435   3.0309  -1.3637  -0.2525
 3KA  OP1  O  O     0  -0.655   2.6081  -1.8891  -1.5625
 3KA  OP2  O  OH1   0  -0.740   4.5313  -0.8298  -0.3702
 3KA  O1   O  OH1   0  -0.694   2.9467  -2.3409   1.0009
 3KA  H1   H  HNR6  0   0.449  -4.8452  -1.0539  -0.3451
 3KA  H2   H  HCR6  0   0.296  -1.2167  -3.0677   0.3097
 3KA  H3   H  HCR6  0   0.291  -0.2191  -0.8620   0.6851
 3KA  H4   H  HCH1  0   0.249  -1.9527   2.0399   1.3003
 3KA  H5   H  HCH2  0   0.299  -1.0500   1.6755  -1.5697
 3KA  H6   H  HCH2  0   0.237  -1.8780   3.0595  -0.8718
 3KA  H7   H  HCH1  0   0.222   0.7951   3.1873  -1.3717
 3KA  H8   H  HOH1  0   0.459  -0.4023   4.7247  -0.0290
 3KA  H9   H  HCH1  0   0.246   1.7127   2.3011   1.0546
 3KA  H10  H  HCH2  0   0.273   0.9918   0.4530  -1.2866
 3KA  H11  H  HCH2  0   0.197   2.4980   1.3337  -1.0254
 3KA  H12  H  HOH1  0   0.508   4.9509  -0.5702   0.4555
 3KA  H13  H  HOH1  0   0.490   3.4649  -3.1628   0.8828

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
 3KA  C2'  C3'  single  1.523  0.020  1.523
 3KA  C2'  C1'  single  1.529  0.020  1.529
 3KA  O4   C4   double  1.217  0.020  1.217
 3KA  C5   C4   single  1.440  0.020  1.440
 3KA  C5   C6   double  1.345  0.020  1.345
 3KA  C4   N3   single  1.387  0.020  1.387
 3KA  C6   N1   single  1.361  0.020  1.361
 3KA  C3'  O3'  single  1.405  0.020  1.405
 3KA  C3'  C4'  single  1.522  0.020  1.522
 3KA  N3   C2   single  1.367  0.020  1.367
 3KA  N1   C2   single  1.380  0.020  1.380
 3KA  N1   C1'  single  1.481  0.020  1.481
 3KA  C2   O2   double  1.214  0.020  1.214
 3KA  C1'  O4'  single  1.400  0.020  1.400
 3KA  C5'  C4'  single  1.518  0.020  1.518
 3KA  C5'  O5'  single  1.428  0.020  1.428
 3KA  OP1  P    double  1.473  0.020  1.473
 3KA  C4'  O4'  single  1.424  0.020  1.424
 3KA  O5'  P    single  1.601  0.020  1.601
 3KA  P    OP2  single  1.597  0.020  1.597
 3KA  P    O1   single  1.592  0.020  1.592
 3KA  N3   H1   single  0.860  0.020  1.020
 3KA  C5   H2   single  0.930  0.020  1.080
 3KA  C6   H3   single  0.930  0.020  1.080
 3KA  C1'  H4   single  0.970  0.020  1.090
 3KA  C2'  H5   single  0.970  0.020  1.090
 3KA  C2'  H6   single  0.970  0.020  1.090
 3KA  C3'  H7   single  0.970  0.020  1.090
 3KA  O3'  H8   single  0.850  0.020  0.980
 3KA  C4'  H9   single  0.970  0.020  1.090
 3KA  C5'  H10  single  0.970  0.020  1.090
 3KA  C5'  H11  single  0.970  0.020  1.090
 3KA  OP2  H12  single  0.850  0.020  0.980
 3KA  O1   H13  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
 3KA  C5   C4   N3   113.24  3.000
 3KA  N3   C4   O4   120.26  3.000
 3KA  C5   C4   O4   126.49  3.000
 3KA  H1   N3   C2   115.03  3.000
 3KA  H1   N3   C4   116.85  3.000
 3KA  C2   N3   C4   127.97  3.000
 3KA  N1   C2   O2   122.69  3.000
 3KA  O2   C2   N3   122.34  3.000
 3KA  N1   C2   N3   114.90  3.000
 3KA  H2   C5   C6   120.64  3.000
 3KA  H2   C5   C4   119.65  3.000
 3KA  C6   C5   C4   119.65  3.000
 3KA  H3   C6   N1   115.75  3.000
 3KA  H3   C6   C5   121.00  3.000
 3KA  N1   C6   C5   123.24  3.000
 3KA  C1'  N1   C6   121.68  3.000
 3KA  C1'  N1   C2   117.41  3.000
 3KA  C6   N1   C2   120.92  3.000
 3KA  H4   C1'  C2'  112.53  3.000
 3KA  H4   C1'  O4'  109.28  3.000
 3KA  C2'  C1'  O4'  106.49  3.000
 3KA  H4   C1'  N1   107.03  3.000
 3KA  O4'  C1'  N1   108.22  3.000
 3KA  C2'  C1'  N1   113.18  3.000
 3KA  C4'  O4'  C1'  111.77  3.000
 3KA  H6   C2'  H5   107.50  3.000
 3KA  H6   C2'  C3'  113.07  3.000
 3KA  H5   C2'  C3'  110.44  3.000
 3KA  H6   C2'  C1'  112.47  3.000
 3KA  H5   C2'  C1'  110.95  3.000
 3KA  C3'  C2'  C1'  102.44  3.000
 3KA  H7   C3'  C4'  112.01  3.000
 3KA  H7   C3'  O3'  112.16  3.000
 3KA  C4'  C3'  O3'  106.67  3.000
 3KA  H7   C3'  C2'  111.83  3.000
 3KA  C4'  C3'  C2'  102.06  3.000
 3KA  O3'  C3'  C2'  111.57  3.000
 3KA  H8   O3'  C3'  108.23  3.000
 3KA  H9   C4'  C5'  108.89  3.000
 3KA  H9   C4'  C3'  111.77  3.000
 3KA  C5'  C4'  C3'  112.50  3.000
 3KA  H9   C4'  O4'  107.94  3.000
 3KA  C5'  C4'  O4'  111.52  3.000
 3KA  C3'  C4'  O4'  104.10  3.000
 3KA  H11  C5'  H10  107.61  3.000
 3KA  H11  C5'  O5'  110.40  3.000
 3KA  H10  C5'  O5'  111.31  3.000
 3KA  H11  C5'  C4'  108.56  3.000
 3KA  H10  C5'  C4'  112.31  3.000
 3KA  O5'  C5'  C4'  106.63  3.000
 3KA  P    O5'  C5'  119.50  3.000
 3KA  O1   P    OP2  108.25  3.000
 3KA  O1   P    OP1  117.78  3.000
 3KA  OP2  P    OP1  108.86  3.000
 3KA  O1   P    O5'   97.35  3.000
 3KA  OP2  P    O5'  108.01  3.000
 3KA  OP1  P    O5'  115.77  3.000
 3KA  H12  OP2  P    115.90  3.000
 3KA  H13  O1   P    113.11  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
 3KA  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 3KA  CONST_02  C6   N1   C2   N3     0.00   0.0  0
 3KA  CONST_03  C1'  N1   C2   N3   180.00   0.0  0
 3KA  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 3KA  CONST_05  C2   N3   C4   O4   180.00   0.0  0
 3KA  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 3KA  CONST_07  C6   N1   C2   O2   180.00   0.0  0
 3KA  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 3KA  CONST_09  H1   N3   C4   C5   180.00   0.0  0
 3KA  Var_01    OP1  P    O5'  C5'  -41.29  30.0  3
 3KA  Var_02    H10  C5'  O5'  P     63.04  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
 3KA  chir_01  C1'  C2'  N1   O4'  negativ
 3KA  chir_02  C3'  O3'  C2'  C4'  positiv
 3KA  chir_03  C4'  O4'  C3'  C5'  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
 3KA  plan-1  O4   0.020
 3KA  plan-1  C4   0.020
 3KA  plan-1  N3   0.020
 3KA  plan-1  C2   0.020
 3KA  plan-1  O2   0.020
 3KA  plan-1  C5   0.020
 3KA  plan-1  C6   0.020
 3KA  plan-1  N1   0.020
 3KA  plan-1  C1'  0.020
 3KA  plan-1  H1   0.020
 3KA  plan-1  H2   0.020
 3KA  plan-1  H3   0.020

