# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 15:24:35 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC2=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C(=O)N=C2N1
#
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
 P0C  P0C  6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one  ligand  35  20  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P0C
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
 P0C  C14  C  CR56  0  -0.063  -2.4998   0.4911  -0.5781
 P0C  C16  C  CR5   0   0.364  -4.6850   0.0331  -0.4120
 P0C  C17  C  CH3   0  -0.737  -6.1640  -0.0363  -0.4882
 P0C  O01  O  OH1   0  -0.669   3.6443   2.1472  -0.6512
 P0C  C02  C  CH1   0  -0.049   3.3864   1.0318   0.1623
 P0C  C03  C  CH1   0  -0.030   3.2612  -0.2677  -0.6405
 P0C  C04  C  CH2   0  -0.152   3.6422  -1.4886   0.1714
 P0C  O05  O  OH1   0  -0.673   3.4566  -2.6346  -0.6238
 P0C  O06  O  O2    0  -0.488   1.9006  -0.3295  -1.0789
 P0C  C07  C  CH1   0   0.240   1.1527   0.6762  -0.4704
 P0C  C08  C  CH1   0  -0.023   1.9677   1.1718   0.7221
 P0C  O09  O  OH1   0  -0.658   1.5576   2.4622   1.0549
 P0C  N10  N  NR6   0  -0.562  -0.2028   0.2181  -0.1804
 P0C  C11  C  CR6   0   0.595  -0.4271  -0.8769   0.6954
 P0C  N12  N  N     0  -0.513  -1.7009  -1.2781   0.9017
 P0C  C13  C  CR56  0   0.511  -2.6574  -0.6236   0.2969
 P0C  C15  C  CR15  0  -0.472  -3.8142   0.8827  -1.0097
 P0C  N18  N  NR15  0  -0.702  -3.9781  -0.8734   0.3761
 P0C  C19  C  CR16  0   0.034  -1.2172   0.8746  -0.7938
 P0C  O20  O  O     0  -0.506   0.5262  -1.4194   1.2354
 P0C  H1   H  HCH3  0   0.258  -6.4973  -1.0157  -0.8355
 P0C  H2   H  HCH3  0   0.259  -6.6195   0.1357   0.4889
 P0C  H3   H  HCH3  0   0.261  -6.5427   0.7158  -1.1761
 P0C  H5   H  HCH1  0   0.246   4.1337   0.9374   0.9606
 P0C  H6   H  HCH1  0   0.247   3.9009  -0.2310  -1.5304
 P0C  H7   H  HCH2  0   0.195   4.6933  -1.3670   0.4671
 P0C  H8   H  HCH2  0   0.214   3.0469  -1.5287   1.0877
 P0C  H9   H  HOH1  0   0.455   3.5798  -3.4067  -0.0651
 P0C  H10  H  HCH1  0   0.244   1.0181   1.5192  -1.1592
 P0C  H11  H  HCH1  0   0.259   1.8670   0.4820   1.5638
 P0C  H12  H  HOH1  0   0.462   1.9416   2.6961   1.9052
 P0C  H14  H  HCR5  0   0.261  -4.0705   1.6924  -1.6736
 P0C  H15  H  HNR5  0   0.414  -4.3921  -1.6168   0.9169
 P0C  H16  H  HCR6  0   0.323  -0.9465   1.6927  -1.4476
 P0C  H4   H  HOH1  0   0.455   4.5128   2.0353  -1.0501

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
 P0C  O20  C11  double  1.223  0.020  1.223
 P0C  C11  N12  single  1.351  0.020  1.351
 P0C  C11  N10  single  1.420  0.020  1.420
 P0C  N12  C13  double  1.307  0.020  1.307
 P0C  O09  C08  single  1.394  0.020  1.394
 P0C  C08  C07  single  1.527  0.020  1.527
 P0C  C08  C02  single  1.532  0.020  1.532
 P0C  C13  N18  single  1.346  0.020  1.346
 P0C  C13  C14  single  1.426  0.020  1.426
 P0C  N10  C07  single  1.460  0.020  1.460
 P0C  N10  C19  single  1.355  0.020  1.355
 P0C  C07  O06  single  1.393  0.020  1.393
 P0C  N18  C16  single  1.394  0.020  1.394
 P0C  O06  C03  single  1.431  0.020  1.431
 P0C  C19  C14  double  1.356  0.020  1.356
 P0C  C14  C15  single  1.438  0.020  1.438
 P0C  C02  O01  single  1.404  0.020  1.404
 P0C  C02  C03  single  1.533  0.020  1.533
 P0C  C16  C15  double  1.356  0.020  1.356
 P0C  C16  C17  single  1.483  0.020  1.483
 P0C  C03  C04  single  1.515  0.020  1.515
 P0C  C04  O05  single  1.407  0.020  1.407
 P0C  C17  H1   single  0.970  0.020  1.090
 P0C  C17  H2   single  0.970  0.020  1.090
 P0C  C17  H3   single  0.970  0.020  1.090
 P0C  O01  H4   single  0.850  0.020  0.980
 P0C  C02  H5   single  0.970  0.020  1.090
 P0C  C03  H6   single  0.970  0.020  1.090
 P0C  C04  H7   single  0.970  0.020  1.090
 P0C  C04  H8   single  0.970  0.020  1.090
 P0C  O05  H9   single  0.850  0.020  0.980
 P0C  C07  H10  single  0.970  0.020  1.090
 P0C  C08  H11  single  0.970  0.020  1.090
 P0C  O09  H12  single  0.850  0.020  0.980
 P0C  C15  H14  single  0.930  0.020  1.080
 P0C  N18  H15  single  0.860  0.020  1.020
 P0C  C19  H16  single  0.930  0.020  1.080

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
 P0C  C19  C14  C15  137.72  3.000
 P0C  C15  C14  C13  107.22  3.000
 P0C  C19  C14  C13  115.05  3.000
 P0C  N18  C16  C15  109.34  3.000
 P0C  C15  C16  C17  130.36  3.000
 P0C  N18  C16  C17  120.30  3.000
 P0C  H3   C17  H2   108.17  3.000
 P0C  H3   C17  H1   108.25  3.000
 P0C  H2   C17  H1   107.38  3.000
 P0C  H3   C17  C16  110.34  3.000
 P0C  H2   C17  C16  111.28  3.000
 P0C  H1   C17  C16  111.29  3.000
 P0C  H4   O01  C02  108.28  3.000
 P0C  H5   C02  C08  111.88  3.000
 P0C  H5   C02  C03  111.33  3.000
 P0C  C08  C02  C03  101.15  3.000
 P0C  H5   C02  O01  111.38  3.000
 P0C  C03  C02  O01  112.64  3.000
 P0C  C08  C02  O01  108.01  3.000
 P0C  H6   C03  O06  107.91  3.000
 P0C  H6   C03  C04  108.38  3.000
 P0C  O06  C03  C04  111.62  3.000
 P0C  H6   C03  C02  110.43  3.000
 P0C  C04  C03  C02  112.46  3.000
 P0C  O06  C03  C02  105.95  3.000
 P0C  H8   C04  H7   107.42  3.000
 P0C  H8   C04  O05  111.83  3.000
 P0C  H7   C04  O05  111.62  3.000
 P0C  H8   C04  C03  109.98  3.000
 P0C  H7   C04  C03  107.20  3.000
 P0C  O05  C04  C03  108.68  3.000
 P0C  H9   O05  C04  108.00  3.000
 P0C  C07  O06  C03  110.21  3.000
 P0C  H10  C07  N10  104.60  3.000
 P0C  H10  C07  C08  107.85  3.000
 P0C  N10  C07  C08  116.24  3.000
 P0C  H10  C07  O06  110.27  3.000
 P0C  N10  C07  O06  111.02  3.000
 P0C  C08  C07  O06  106.79  3.000
 P0C  H11  C08  O09  111.92  3.000
 P0C  H11  C08  C07  110.33  3.000
 P0C  O09  C08  C07  109.26  3.000
 P0C  H11  C08  C02  108.01  3.000
 P0C  C07  C08  C02  100.32  3.000
 P0C  O09  C08  C02  116.38  3.000
 P0C  H12  O09  C08  108.58  3.000
 P0C  C19  N10  C11  122.31  3.000
 P0C  C19  N10  C07  116.94  3.000
 P0C  C11  N10  C07  120.74  3.000
 P0C  O20  C11  N12  122.40  3.000
 P0C  N12  C11  N10  118.17  3.000
 P0C  O20  C11  N10  119.43  3.000
 P0C  C13  N12  C11  118.06  3.000
 P0C  N18  C13  N12  126.69  3.000
 P0C  N18  C13  C14  106.84  3.000
 P0C  N12  C13  C14  126.47  3.000
 P0C  H14  C15  C16  126.12  3.000
 P0C  H14  C15  C14  127.36  3.000
 P0C  C16  C15  C14  106.51  3.000
 P0C  H15  N18  C13  124.83  3.000
 P0C  H15  N18  C16  125.07  3.000
 P0C  C13  N18  C16  110.09  3.000
 P0C  H16  C19  N10  116.92  3.000
 P0C  H16  C19  C14  123.14  3.000
 P0C  N10  C19  C14  119.93  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
 P0C  CONST_01  C11  N12  C13  C14    0.00   0.0  0
 P0C  CONST_02  C16  N18  C13  C14    0.00   0.0  0
 P0C  CONST_03  N12  C13  N18  C16  180.00   0.0  0
 P0C  CONST_04  N12  C11  N10  C07  180.00   0.0  0
 P0C  CONST_05  C13  N12  C11  N10    0.00   0.0  0
 P0C  CONST_06  N18  C13  N12  C11  180.00   0.0  0
 P0C  CONST_07  C19  N10  C11  N12    0.00   0.0  0
 P0C  CONST_08  O20  C11  N10  C07    0.00   0.0  0
 P0C  CONST_09  O20  C11  N12  C13  180.00   0.0  0
 P0C  CONST_10  O20  C11  N10  C19  180.00   0.0  0
 P0C  CONST_11  H15  N18  C13  C14  180.00   0.0  0
 P0C  Var_01    C13  C14  C19  N10   -0.81   0.0  0
 P0C  Var_02    H16  C19  C14  C13  178.89   0.0  0
 P0C  Var_03    H1   C17  C16  C15  122.67  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
 P0C  chir_01  C02  C08  O01  C03  positiv
 P0C  chir_02  C03  O06  C02  C04  negativ
 P0C  chir_03  C07  O06  N10  C08  negativ
 P0C  chir_04  C08  O09  C07  C02  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
 P0C  plan-1  C14  0.020
 P0C  plan-1  C16  0.020
 P0C  plan-1  C17  0.020
 P0C  plan-1  C07  0.020
 P0C  plan-1  N10  0.020
 P0C  plan-1  C11  0.020
 P0C  plan-1  N12  0.020
 P0C  plan-1  C13  0.020
 P0C  plan-1  C15  0.020
 P0C  plan-1  N18  0.020
 P0C  plan-1  C19  0.020
 P0C  plan-1  O20  0.020
 P0C  plan-1  H14  0.020
 P0C  plan-1  H15  0.020
 P0C  plan-1  H16  0.020

