# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:57:17 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-amino-1-(3-O-phosphono-beta-L-lyxofuranosyl)pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@H]2O[C@@H](CO)[C@@H](O[P](O)(O)=O)[C@H]2O
#
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
 C6B  C6B  4-amino-1-(3-O-phosphono-beta-L-lyxofuranosyl)pyrimidin-2(1H)-one  ligand  35  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_C6B
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
 C6B  O1P   O  OH1   0  -0.769  -2.0420   2.3264  -1.0970
 C6B  P     P  P     0   1.440  -2.3380   1.5829   0.2752
 C6B  O2P   O  OH1   0  -0.727  -1.5418   2.3419   1.4286
 C6B  O3P   O  O     0  -0.704  -3.7842   1.4010   0.5042
 C6B  O3'   O  O2    0  -0.594  -1.4418   0.2485   0.2378
 C6B  C3'   C  CH1   0  -0.098  -1.4868  -0.6377  -0.8764
 C6B  C2'   C  CH1   0   0.028  -0.2540  -0.4375  -1.7534
 C6B  O2'   O  OH1   0  -0.671   0.0584   0.9183  -1.8867
 C6B  C4'   C  CH1   0   0.003  -1.2778  -2.0627  -0.4083
 C6B  C5'   C  CH2   0  -0.156  -2.0140  -2.4461   0.8530
 C6B  O5'   O  OH1   0  -0.667  -1.8576  -3.8310   1.0417
 C6B  O4'   O  O2    0  -0.495   0.1332  -2.1956  -0.2296
 C6B  C1'   C  CH1   0   0.176   0.8248  -1.2898  -1.0314
 C6B  N1    N  NR6   0  -0.541   1.7249  -0.4757  -0.2141
 C6B  C6    C  CR16  0   0.111   1.5430  -0.3023   1.1128
 C6B  C5    C  CR16  0  -0.477   2.3846   0.4617   1.8393
 C6B  C4    C  CR6   0   0.516   3.4680   1.0679   1.1369
 C6B  N4    N  NH2   0  -0.810   4.3508   1.8153   1.7979
 C6B  N3    N  N     0  -0.538   3.6336   0.9129  -0.1642
 C6B  C2    C  CR6   0   0.599   2.7747   0.1693  -0.8827
 C6B  O2    O  O     0  -0.536   2.8711   0.0283  -2.0993
 C6B  HO1P  H  HOH1  0   0.498  -1.2044   2.0340  -1.5274
 C6B  HO2P  H  HOH1  0   0.502  -2.1102   2.8653   2.0090
 C6B  H3'   H  HCH1  0   0.305  -2.4211  -0.5423  -1.4362
 C6B  H2'   H  HCH1  0   0.282  -0.4580  -0.8996  -2.7247
 C6B  HO2'  H  HOH1  0   0.484   0.6609   1.0458  -2.6286
 C6B  H4'   H  HCH1  0   0.263  -1.6050  -2.7253  -1.2208
 C6B  H5'   H  HCH2  0   0.215  -1.6300  -1.8730   1.7038
 C6B  H5'A  H  HCH2  0   0.212  -3.0677  -2.1653   0.7238
 C6B  HO5'  H  HOH1  0   0.460  -2.2534  -4.0658   1.8857
 C6B  H1'   H  HCH1  0   0.276   1.4468  -1.8244  -1.7498
 C6B  H6    H  HCR6  0   0.310   0.7133  -0.8150   1.5719
 C6B  H5    H  HCR6  0   0.285   2.2428   0.5899   2.9016
 C6B  HN4   H  HNH2  0   0.413   4.2756   1.9677   2.7879
 C6B  HN4A  H  HNH2  0   0.402   5.1219   2.2377   1.3099

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
 C6B  O1P  P     single  1.588  0.020  1.588
 C6B  P    O2P   single  1.594  0.020  1.594
 C6B  P    O3P   double  1.475  0.020  1.475
 C6B  P    O3'   single  1.608  0.020  1.608
 C6B  O3'  C3'   single  1.424  0.020  1.424
 C6B  C3'  C2'   single  1.526  0.020  1.526
 C6B  C3'  C4'   single  1.514  0.020  1.514
 C6B  C2'  O2'   single  1.398  0.020  1.398
 C6B  C2'  C1'   single  1.553  0.020  1.553
 C6B  C4'  C5'   single  1.510  0.020  1.510
 C6B  C4'  O4'   single  1.428  0.020  1.428
 C6B  C5'  O5'   single  1.407  0.020  1.407
 C6B  O4'  C1'   single  1.393  0.020  1.393
 C6B  C1'  N1    single  1.463  0.020  1.463
 C6B  N1   C6    single  1.351  0.020  1.351
 C6B  N1   C2    single  1.402  0.020  1.402
 C6B  C6   C5    double  1.349  0.020  1.349
 C6B  C5   C4    single  1.426  0.020  1.426
 C6B  C4   N4    single  1.332  0.020  1.332
 C6B  C4   N3    double  1.321  0.020  1.321
 C6B  N3   C2    single  1.344  0.020  1.344
 C6B  C2   O2    double  1.229  0.020  1.229
 C6B  O1P  HO1P  single  0.850  0.020  0.980
 C6B  O2P  HO2P  single  0.850  0.020  0.980
 C6B  C3'  H3'   single  0.970  0.020  1.090
 C6B  C2'  H2'   single  0.970  0.020  1.090
 C6B  O2'  HO2'  single  0.850  0.020  0.980
 C6B  C4'  H4'   single  0.970  0.020  1.090
 C6B  C5'  H5'   single  0.970  0.020  1.090
 C6B  C5'  H5'A  single  0.970  0.020  1.090
 C6B  O5'  HO5'  single  0.850  0.020  0.980
 C6B  C1'  H1'   single  0.970  0.020  1.090
 C6B  C6   H6    single  0.930  0.020  1.080
 C6B  C5   H5    single  0.930  0.020  1.080
 C6B  N4   HN4   single  0.860  0.020  1.020
 C6B  N4   HN4A  single  0.860  0.020  1.020

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
 C6B  HO1P  O1P  P    113.36  3.000
 C6B  O3'   P    O3P  116.59  3.000
 C6B  O3'   P    O2P   97.68  3.000
 C6B  O3P   P    O2P  115.85  3.000
 C6B  O3'   P    O1P  105.34  3.000
 C6B  O3P   P    O1P  111.99  3.000
 C6B  O2P   P    O1P  108.01  3.000
 C6B  HO2P  O2P  P    113.50  3.000
 C6B  C3'   O3'  P    121.13  3.000
 C6B  H3'   C3'  C4'  110.99  3.000
 C6B  H3'   C3'  C2'  112.62  3.000
 C6B  C4'   C3'  C2'  100.93  3.000
 C6B  H3'   C3'  O3'  111.92  3.000
 C6B  C4'   C3'  O3'  109.84  3.000
 C6B  C2'   C3'  O3'  110.02  3.000
 C6B  H2'   C2'  C1'  108.08  3.000
 C6B  H2'   C2'  O2'  111.50  3.000
 C6B  C1'   C2'  O2'  114.93  3.000
 C6B  H2'   C2'  C3'  107.70  3.000
 C6B  C1'   C2'  C3'  102.83  3.000
 C6B  O2'   C2'  C3'  111.26  3.000
 C6B  HO2'  O2'  C2'  109.96  3.000
 C6B  H4'   C4'  O4'  109.31  3.000
 C6B  H4'   C4'  C5'  108.63  3.000
 C6B  O4'   C4'  C5'  110.70  3.000
 C6B  H4'   C4'  C3'  107.33  3.000
 C6B  O4'   C4'  C3'  105.22  3.000
 C6B  C5'   C4'  C3'  115.45  3.000
 C6B  H5'A  C5'  H5'  107.10  3.000
 C6B  H5'A  C5'  O5'  111.98  3.000
 C6B  H5'   C5'  O5'  111.84  3.000
 C6B  H5'A  C5'  C4'  107.74  3.000
 C6B  H5'   C5'  C4'  110.19  3.000
 C6B  O5'   C5'  C4'  107.93  3.000
 C6B  HO5'  O5'  C5'  108.21  3.000
 C6B  C1'   O4'  C4'  110.96  3.000
 C6B  H1'   C1'  N1   106.85  3.000
 C6B  H1'   C1'  O4'  110.09  3.000
 C6B  N1    C1'  O4'  110.22  3.000
 C6B  H1'   C1'  C2'  111.05  3.000
 C6B  N1    C1'  C2'  112.44  3.000
 C6B  O4'   C1'  C2'  106.23  3.000
 C6B  C2    N1   C6   120.69  3.000
 C6B  C2    N1   C1'  116.76  3.000
 C6B  C6    N1   C1'  122.51  3.000
 C6B  H6    C6   C5   121.35  3.000
 C6B  H6    C6   N1   117.45  3.000
 C6B  C5    C6   N1   121.19  3.000
 C6B  H5    C5   C4   122.28  3.000
 C6B  H5    C5   C6   121.02  3.000
 C6B  C4    C5   C6   116.70  3.000
 C6B  N3    C4   N4   118.14  3.000
 C6B  N3    C4   C5   122.04  3.000
 C6B  N4    C4   C5   119.83  3.000
 C6B  HN4A  N4   HN4  118.16  3.000
 C6B  HN4A  N4   C4   120.20  3.000
 C6B  HN4   N4   C4   121.64  3.000
 C6B  C2    N3   C4   120.76  3.000
 C6B  O2    C2   N3   122.87  3.000
 C6B  O2    C2   N1   118.57  3.000
 C6B  N3    C2   N1   118.56  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
 C6B  CONST_01  N3    C2  N1  C1'  180.00  0.0  0
 C6B  CONST_02  C4    N3  C2  N1     0.00  0.0  0
 C6B  CONST_03  N3    C2  N1  C6     0.00  0.0  0
 C6B  CONST_04  C2    N3  C4  C5     0.00  0.0  0
 C6B  CONST_05  O2    C2  N1  C1'    0.00  0.0  0
 C6B  CONST_06  O2    C2  N1  C6   180.00  0.0  0
 C6B  CONST_07  O2    C2  N3  C4   180.00  0.0  0
 C6B  CONST_08  C2    N3  C4  N4   180.00  0.0  0
 C6B  CONST_09  HN4   N4  C4  C5     0.00  0.0  0
 C6B  CONST_10  HN4A  N4  C4  C5   180.00  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
 C6B  chir_01  C3'  O3'  C2'  C4'  negativ
 C6B  chir_02  C2'  O2'  C1'  C3'  negativ
 C6B  chir_03  C4'  O4'  C3'  C5'  positiv
 C6B  chir_04  C1'  O4'  N1   C2'  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
 C6B  plan-1  C1'   0.020
 C6B  plan-1  N1    0.020
 C6B  plan-1  C6    0.020
 C6B  plan-1  C5    0.020
 C6B  plan-1  C4    0.020
 C6B  plan-1  N4    0.020
 C6B  plan-1  N3    0.020
 C6B  plan-1  C2    0.020
 C6B  plan-1  O2    0.020
 C6B  plan-1  H6    0.020
 C6B  plan-1  H5    0.020
 C6B  plan-1  HN4   0.020
 C6B  plan-1  HN4A  0.020

