# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:21:03 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@H](O)[C@H](O)[C@H](O)CO
#
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
 Y19  Y19  1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol  ligand  43  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y19
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
 Y19  O2    O  O     0  -0.465   2.2148  -4.3994  -0.2224
 Y19  C2    C  C     0   0.588   2.2355  -3.1860  -0.2451
 Y19  N3    N  NH1   0  -0.709   3.4154  -2.5489  -0.6506
 Y19  C4    C  C     0   0.596   3.6290  -1.2098  -0.6625
 Y19  O4    O  O     0  -0.421   4.6019  -0.6898  -1.1554
 Y19  N1    N  N     0  -0.536   1.1498  -2.4288   0.0582
 Y19  C6    C  C     0   0.567   1.2462  -1.1316   0.1100
 Y19  C5    C  CH1   0  -0.344   2.5718  -0.4078   0.0773
 Y19  N13   N  NH1   0  -0.654   2.4809   0.9341  -0.3962
 Y19  C14   C  C     0   0.573   3.1582   1.9559   0.2011
 Y19  C15   C  CH2   0  -0.588   3.1469   3.2442  -0.5864
 Y19  C16   C  CH3   0  -0.659   3.7860   4.4106   0.1430
 Y19  O23   O  O     0  -0.467   3.7062   1.8271   1.2786
 Y19  N7    N  NH1   0  -0.612   0.1746  -0.3825   0.2604
 Y19  C8    C  CH2   0  -0.271  -1.1717  -0.9040   0.3658
 Y19  C9    C  CH1   0  -0.038  -2.1638   0.1890  -0.0282
 Y19  O9    O  OH1   0  -0.658  -1.9020   1.3765   0.6892
 Y19  C10   C  CH1   0  -0.027  -3.6171  -0.2827   0.1727
 Y19  O10   O  OH1   0  -0.655  -3.7774  -1.6567  -0.0987
 Y19  C11   C  CH1   0  -0.015  -4.6334   0.5324  -0.6512
 Y19  O11   O  OH1   0  -0.656  -4.3627   1.9110  -0.6829
 Y19  C12   C  CH2   0  -0.158  -6.0482   0.2436  -0.1730
 Y19  O12   O  OH1   0  -0.672  -6.9618   0.8377  -1.0644
 Y19  H3    H  HNH1  0   0.420   4.1449  -3.1438  -1.0244
 Y19  H5    H  HCH1  0   0.360   2.9161  -0.3725   1.1204
 Y19  H7    H  HNH1  0   0.410   0.3025   0.6141   0.3701
 Y19  H13   H  HNH1  0   0.416   2.1740   1.0666  -1.3492
 Y19  H151  H  HCH2  0   0.275   3.6641   3.0569  -1.5326
 Y19  H152  H  HCH2  0   0.273   2.1150   3.4794  -0.8607
 Y19  H161  H  HCH3  0   0.237   3.7659   5.2975  -0.4890
 Y19  H162  H  HCH3  0   0.231   3.2564   4.6492   1.0646
 Y19  H163  H  HCH3  0   0.231   4.8259   4.2078   0.3951
 Y19  H8C1  H  HCH2  0   0.264  -1.2584  -1.7667  -0.2902
 Y19  H8C2  H  HCH2  0   0.253  -1.3611  -1.2494   1.3885
 Y19  H9    H  HCH1  0   0.253  -1.9945   0.4389  -1.0811
 Y19  HA    H  HOH1  0   0.451  -2.0375   1.2071   1.6291
 Y19  H10   H  HCH1  0   0.236  -3.8460  -0.1744   1.2418
 Y19  HB    H  HOH1  0   0.451  -3.6708  -1.8032  -1.0458
 Y19  H11   H  HCH1  0   0.229  -4.5417   0.2005  -1.6938
 Y19  HC    H  HOH1  0   0.441  -4.3060   2.2412   0.2197
 Y19  H121  H  HCH2  0   0.204  -6.1909  -0.8410  -0.1108
 Y19  H122  H  HCH2  0   0.192  -6.1624   0.6377   0.8487
 Y19  H12   H  HOH1  0   0.455  -7.8497   0.6065  -0.7785

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
 Y19  O2   C2    double  1.214  0.020  1.214
 Y19  C2   N3    single  1.401  0.020  1.401
 Y19  C2   N1    single  1.358  0.020  1.358
 Y19  N3   C4    single  1.356  0.020  1.356
 Y19  C4   O4    double  1.208  0.020  1.208
 Y19  C4   C5    single  1.519  0.020  1.519
 Y19  N1   C6    double  1.302  0.020  1.302
 Y19  C6   C5    single  1.511  0.020  1.511
 Y19  C6   N7    single  1.316  0.020  1.316
 Y19  C5   N13   single  1.426  0.020  1.426
 Y19  N13  C14   single  1.364  0.020  1.364
 Y19  C14  C15   single  1.510  0.020  1.510
 Y19  C14  O23   double  1.216  0.020  1.216
 Y19  C15  C16   single  1.517  0.020  1.517
 Y19  N7   C8    single  1.448  0.020  1.448
 Y19  C8   C9    single  1.528  0.020  1.528
 Y19  C9   O9    single  1.412  0.020  1.412
 Y19  C9   C10   single  1.541  0.020  1.541
 Y19  C10  O10   single  1.410  0.020  1.410
 Y19  C10  C11   single  1.541  0.020  1.541
 Y19  C11  O11   single  1.405  0.020  1.405
 Y19  C11  C12   single  1.521  0.020  1.521
 Y19  C12  O12   single  1.408  0.020  1.408
 Y19  N3   H3    single  0.860  0.020  1.020
 Y19  C5   H5    single  0.970  0.020  1.090
 Y19  N7   H7    single  0.860  0.020  1.020
 Y19  N13  H13   single  0.890  0.020  1.040
 Y19  C15  H151  single  0.970  0.020  1.090
 Y19  C15  H152  single  0.970  0.020  1.090
 Y19  C16  H161  single  0.970  0.020  1.090
 Y19  C16  H162  single  0.970  0.020  1.090
 Y19  C16  H163  single  0.970  0.020  1.090
 Y19  C8   H8C1  single  0.970  0.020  1.090
 Y19  C8   H8C2  single  0.970  0.020  1.090
 Y19  C9   H9    single  0.970  0.020  1.090
 Y19  O9   HA    single  0.850  0.020  0.980
 Y19  C10  H10   single  0.970  0.020  1.090
 Y19  O10  HB    single  0.850  0.020  0.980
 Y19  C11  H11   single  0.970  0.020  1.090
 Y19  O11  HC    single  0.850  0.020  0.980
 Y19  C12  H121  single  0.970  0.020  1.090
 Y19  C12  H122  single  0.970  0.020  1.090
 Y19  O12  H12   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
 Y19  N1    C2   N3    118.97  3.000
 Y19  N1    C2   O2    122.66  3.000
 Y19  N3    C2   O2    118.33  3.000
 Y19  H3    N3   C4    117.61  3.000
 Y19  H3    N3   C2    116.50  3.000
 Y19  C4    N3   C2    125.76  3.000
 Y19  C5    C4   O4    122.12  3.000
 Y19  C5    C4   N3    114.04  3.000
 Y19  O4    C4   N3    123.74  3.000
 Y19  C6    N1   C2    120.36  3.000
 Y19  N7    C6   C5    116.37  3.000
 Y19  N7    C6   N1    120.76  3.000
 Y19  C5    C6   N1    122.79  3.000
 Y19  H5    C5   N13   107.76  3.000
 Y19  H5    C5   C6    105.65  3.000
 Y19  N13   C5   C6    113.72  3.000
 Y19  H5    C5   C4    105.13  3.000
 Y19  N13   C5   C4    112.29  3.000
 Y19  C6    C5   C4    111.60  3.000
 Y19  H13   N13  C14   117.77  3.000
 Y19  H13   N13  C5    117.14  3.000
 Y19  C14   N13  C5    121.87  3.000
 Y19  O23   C14  C15   123.78  3.000
 Y19  O23   C14  N13   122.19  3.000
 Y19  C15   C14  N13   114.02  3.000
 Y19  H152  C15  H151  105.42  3.000
 Y19  H152  C15  C16   110.66  3.000
 Y19  H151  C15  C16   110.38  3.000
 Y19  H152  C15  C14   108.75  3.000
 Y19  H151  C15  C14   107.54  3.000
 Y19  C16   C15  C14   113.71  3.000
 Y19  H163  C16  H162  108.01  3.000
 Y19  H163  C16  H161  107.67  3.000
 Y19  H162  C16  H161  107.67  3.000
 Y19  H163  C16  C15   111.74  3.000
 Y19  H162  C16  C15   111.74  3.000
 Y19  H161  C16  C15   109.83  3.000
 Y19  H7    N7   C8    117.71  3.000
 Y19  H7    N7   C6    118.07  3.000
 Y19  C8    N7   C6    124.10  3.000
 Y19  H8C2  C8   H8C1  107.41  3.000
 Y19  H8C2  C8   C9    110.73  3.000
 Y19  H8C1  C8   C9    111.12  3.000
 Y19  H8C2  C8   N7    110.01  3.000
 Y19  H8C1  C8   N7    108.42  3.000
 Y19  C9    C8   N7    109.12  3.000
 Y19  H9    C9   C10   109.93  3.000
 Y19  H9    C9   O9    105.53  3.000
 Y19  C10   C9   O9    111.48  3.000
 Y19  H9    C9   C8    108.11  3.000
 Y19  C10   C9   C8    111.09  3.000
 Y19  O9    C9   C8    110.50  3.000
 Y19  HA    O9   C9    108.74  3.000
 Y19  H10   C10  C11   109.30  3.000
 Y19  H10   C10  O10   105.05  3.000
 Y19  C11   C10  O10   109.73  3.000
 Y19  H10   C10  C9    107.05  3.000
 Y19  C11   C10  C9    112.97  3.000
 Y19  O10   C10  C9    112.36  3.000
 Y19  HB    O10  C10   108.94  3.000
 Y19  H11   C11  C12   108.59  3.000
 Y19  H11   C11  O11   105.01  3.000
 Y19  C12   C11  O11   111.87  3.000
 Y19  H11   C11  C10   107.02  3.000
 Y19  C12   C11  C10   110.17  3.000
 Y19  O11   C11  C10   113.82  3.000
 Y19  HC    O11  C11   109.06  3.000
 Y19  H122  C12  H121  106.75  3.000
 Y19  H122  C12  O12   111.66  3.000
 Y19  H121  C12  O12   111.66  3.000
 Y19  H122  C12  C11   108.68  3.000
 Y19  H121  C12  C11   109.08  3.000
 Y19  O12   C12  C11   108.93  3.000
 Y19  H12   O12  C12   108.04  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
 Y19  CONST_01  C5    C6   N1   C2      0.00   0.0  0
 Y19  CONST_02  C6    N1   C2   N3      0.00   0.0  0
 Y19  CONST_03  N1    C2   N3   C4      0.00   0.0  0
 Y19  CONST_04  C4    N3   C2   O2    180.00   0.0  0
 Y19  CONST_05  C6    N1   C2   O2    180.00   0.0  0
 Y19  CONST_06  N7    C6   N1   C2    180.00   0.0  0
 Y19  CONST_07  H3    N3   C2   N1    180.00   0.0  0
 Y19  CONST_08  C8    N7   C6   N1      0.00   0.0  0
 Y19  CONST_09  C8    N7   C6   C5    180.00   0.0  0
 Y19  CONST_10  H7    N7   C6   N1    180.00   0.0  0
 Y19  CONST_11  C15   C14  N13  C5    180.00   0.0  0
 Y19  CONST_12  O23   C14  N13  C5      0.00   0.0  0
 Y19  CONST_13  H13   N13  C14  C15     0.00   0.0  0
 Y19  Var_01    O4    C4   N3   C2   -171.52  30.0  1
 Y19  Var_02    C9    C8   N7   C6   -157.50  30.0  3
 Y19  Var_03    C16   C15  C14  N13   174.44  30.0  3
 Y19  Var_04    H161  C16  C15  C14   178.61  30.0  3

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
 Y19  chir_01  C5   C4   C6   N13  positiv
 Y19  chir_02  C9   O9   C8   C10  negativ
 Y19  chir_03  C10  O10  C11  C9   positiv
 Y19  chir_04  C11  O11  C10  C12  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
 Y19  plan-1  C5   0.020
 Y19  plan-1  N13  0.020
 Y19  plan-1  C14  0.020
 Y19  plan-1  C15  0.020
 Y19  plan-1  O23  0.020
 Y19  plan-1  H13  0.020
 Y19  plan-2  N3   0.020
 Y19  plan-2  C4   0.020
 Y19  plan-2  O4   0.020
 Y19  plan-2  C5   0.020
 Y19  plan-3  O2   0.020
 Y19  plan-3  C2   0.020
 Y19  plan-3  N3   0.020
 Y19  plan-3  C4   0.020
 Y19  plan-3  N1   0.020
 Y19  plan-3  C6   0.020
 Y19  plan-3  C5   0.020
 Y19  plan-3  N7   0.020
 Y19  plan-3  C8   0.020
 Y19  plan-3  H3   0.020
 Y19  plan-3  H7   0.020

