# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 18:53:07 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 3-[(2~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-6-methyl-7~{H}-pyrrolo[2,3-d]pyrimidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC2=CN([C@H]3C[C@H](O)[C@@H](CO)O3)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
 8LK  8LK  "Pyrrolo-dC"
  ligand  34  19  .  2022-09-16  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_8LK
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
 8LK  O5'  O  OH1   0  -0.658  52.9600  -50.0079  -18.9842
 8LK  C5'  C  CH2   0  -0.176  52.3668  -49.3638  -17.8815
 8LK  C4'  C  CH1   0  -0.005  51.6361  -48.1167  -18.3301
 8LK  O4'  O  O2    0  -0.498  52.5528  -47.1376  -18.8120
 8LK  C3'  C  CH1   0  -0.013  50.6083  -48.3319  -19.4583
 8LK  O3'  O  OH1   0  -0.669  49.5011  -47.4677  -19.3294
 8LK  C2'  C  CH2   0  -0.514  51.3851  -47.9034  -20.6885
 8LK  C1'  C  CH1   0   0.202  52.2578  -46.7825  -20.1382
 8LK  N1   N  NR6   0  -0.553  53.5126  -46.5935  -20.8630
 8LK  C2   C  CR6   0   0.582  53.6986  -45.4029  -21.6101
 8LK  O2   O  O     0  -0.513  52.7954  -44.5774  -21.6587
 8LK  N3   N  N     0  -0.513  54.8788  -45.2308  -22.2458
 8LK  C4   C  CR56  0   0.508  55.7708  -46.1821  -22.1446
 8LK  C5   C  CR56  0  -0.067  55.6317  -47.4056  -21.4255
 8LK  C6   C  CR16  0   0.037  54.4498  -47.5653  -20.7784
 8LK  C14  C  CR15  0  -0.477  56.8575  -48.1380  -21.5919
 8LK  C15  C  CR5   0   0.364  57.6628  -47.3729  -22.3685
 8LK  C16  C  CH3   0  -0.735  59.0403  -47.6205  -22.8575
 8LK  N17  N  NR15  0  -0.703  56.9990  -46.1925  -22.6980
 8LK  H1   H  HOH1  0   0.463  53.4730  -50.7557  -18.6641
 8LK  H2   H  HCH2  0   0.209  51.6363  -50.0109  -17.3790
 8LK  H3   H  HCH2  0   0.219  53.1124  -49.0828  -17.1272
 8LK  H4   H  HCH1  0   0.248  51.1312  -47.7176  -17.4419
 8LK  H5   H  HCH1  0   0.244  50.2894  -49.3791  -19.5132
 8LK  H6   H  HOH1  0   0.450  49.0350  -47.6843  -18.5158
 8LK  H7   H  HCH2  0   0.271  50.7416  -47.5659  -21.5002
 8LK  H8   H  HCH2  0   0.269  51.9903  -48.7305  -21.0606
 8LK  H9   H  HCH1  0   0.266  51.7380  -45.8258  -20.1744
 8LK  H13  H  HCR5  0   0.257  57.1031  -49.1053  -21.1841
 8LK  H14  H  HCH3  0   0.260  59.3976  -48.5867  -22.5088
 8LK  H15  H  HCH3  0   0.256  59.0826  -47.6147  -23.9483
 8LK  H16  H  HCH3  0   0.257  59.7308  -46.8534  -22.5019
 8LK  H17  H  HNR5  0   0.412  57.3796  -45.4528  -23.2682
 8LK  H10  H  HCR6  0   0.324  54.2046  -48.4372  -20.1850

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
 8LK  N17  C15  single  1.394  0.020  1.394
 8LK  N17  C4   single  1.347  0.020  1.347
 8LK  C16  C15  single  1.483  0.020  1.483
 8LK  N3   C4   double  1.308  0.020  1.308
 8LK  N3   C2   single  1.351  0.020  1.351
 8LK  C15  C14  double  1.355  0.020  1.355
 8LK  C4   C5   single  1.426  0.020  1.426
 8LK  O2   C2   double  1.225  0.020  1.225
 8LK  C2   N1   single  1.418  0.020  1.418
 8LK  C14  C5   single  1.438  0.020  1.438
 8LK  C5   C6   double  1.357  0.020  1.357
 8LK  N1   C6   single  1.353  0.020  1.353
 8LK  N1   C1'  single  1.461  0.020  1.461
 8LK  C2'  C1'  single  1.523  0.020  1.523
 8LK  C2'  C3'  single  1.517  0.020  1.517
 8LK  C1'  O4'  single  1.404  0.020  1.404
 8LK  C3'  O3'  single  1.410  0.020  1.410
 8LK  C3'  C4'  single  1.541  0.020  1.541
 8LK  O5'  C5'  single  1.408  0.020  1.408
 8LK  O4'  C4'  single  1.425  0.020  1.425
 8LK  C4'  C5'  single  1.513  0.020  1.513
 8LK  O5'  H1   single  0.850  0.020  0.980
 8LK  C5'  H2   single  0.970  0.020  1.090
 8LK  C5'  H3   single  0.970  0.020  1.090
 8LK  C4'  H4   single  0.970  0.020  1.090
 8LK  C3'  H5   single  0.970  0.020  1.090
 8LK  O3'  H6   single  0.850  0.020  0.980
 8LK  C2'  H7   single  0.970  0.020  1.090
 8LK  C2'  H8   single  0.970  0.020  1.090
 8LK  C1'  H9   single  0.970  0.020  1.090
 8LK  C14  H13  single  0.930  0.020  1.080
 8LK  C16  H14  single  0.970  0.020  1.090
 8LK  C16  H15  single  0.970  0.020  1.090
 8LK  C16  H16  single  0.970  0.020  1.090
 8LK  N17  H17  single  0.860  0.020  1.020
 8LK  C6   H10  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
 8LK  H1   O5'  C5'  108.65  3.000
 8LK  H3   C5'  H2   106.77  3.000
 8LK  H3   C5'  C4'  108.71  3.000
 8LK  H2   C5'  C4'  107.46  3.000
 8LK  H3   C5'  O5'  111.67  3.000
 8LK  H2   C5'  O5'  111.67  3.000
 8LK  C4'  C5'  O5'  110.38  3.000
 8LK  H4   C4'  C3'  109.67  3.000
 8LK  H4   C4'  O4'  108.67  3.000
 8LK  C3'  C4'  O4'  106.10  3.000
 8LK  H4   C4'  C5'  106.38  3.000
 8LK  O4'  C4'  C5'  110.84  3.000
 8LK  C3'  C4'  C5'  115.08  3.000
 8LK  C1'  O4'  C4'  110.97  3.000
 8LK  H5   C3'  C2'  112.23  3.000
 8LK  H5   C3'  O3'  111.20  3.000
 8LK  C2'  C3'  O3'  107.64  3.000
 8LK  H5   C3'  C4'  111.35  3.000
 8LK  O3'  C3'  C4'  111.78  3.000
 8LK  C2'  C3'  C4'  102.28  3.000
 8LK  H6   O3'  C3'  108.64  3.000
 8LK  H8   C2'  H7   107.97  3.000
 8LK  H8   C2'  C1'  111.31  3.000
 8LK  H7   C2'  C1'  112.31  3.000
 8LK  H8   C2'  C3'  110.29  3.000
 8LK  H7   C2'  C3'  112.91  3.000
 8LK  C1'  C2'  C3'  102.03  3.000
 8LK  H9   C1'  N1   106.24  3.000
 8LK  H9   C1'  C2'  111.15  3.000
 8LK  N1   C1'  C2'  114.08  3.000
 8LK  H9   C1'  O4'  110.71  3.000
 8LK  C2'  C1'  O4'  105.99  3.000
 8LK  N1   C1'  O4'  108.71  3.000
 8LK  C6   N1   C2   123.05  3.000
 8LK  C6   N1   C1'  118.09  3.000
 8LK  C2   N1   C1'  118.86  3.000
 8LK  N3   C2   O2   122.65  3.000
 8LK  O2   C2   N1   119.35  3.000
 8LK  N3   C2   N1   117.99  3.000
 8LK  C4   N3   C2   117.81  3.000
 8LK  N17  C4   C5   106.83  3.000
 8LK  C5   C4   N3   126.62  3.000
 8LK  N17  C4   N3   126.55  3.000
 8LK  C14  C5   C6   137.55  3.000
 8LK  C6   C5   C4   115.25  3.000
 8LK  C14  C5   C4   107.19  3.000
 8LK  H10  C6   C5   123.60  3.000
 8LK  H10  C6   N1   117.13  3.000
 8LK  C5   C6   N1   119.28  3.000
 8LK  H13  C14  C15  126.00  3.000
 8LK  H13  C14  C5   127.42  3.000
 8LK  C15  C14  C5   106.58  3.000
 8LK  N17  C15  C16  120.39  3.000
 8LK  C16  C15  C14  130.30  3.000
 8LK  N17  C15  C14  109.30  3.000
 8LK  H16  C16  H15  107.30  3.000
 8LK  H16  C16  H14  108.18  3.000
 8LK  H15  C16  H14  108.20  3.000
 8LK  H16  C16  C15  111.27  3.000
 8LK  H15  C16  C15  111.39  3.000
 8LK  H14  C16  C15  110.36  3.000
 8LK  H17  N17  C15  125.11  3.000
 8LK  H17  N17  C4   124.80  3.000
 8LK  C15  N17  C4   110.09  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
 8LK  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 8LK  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 8LK  CONST_03  N17  C4   N3   C2    180.00   0.0  0
 8LK  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 8LK  CONST_05  C15  N17  C4   N3    180.00   0.0  0
 8LK  CONST_06  C6   N1   C2   N3      0.00   0.0  0
 8LK  CONST_07  C15  N17  C4   C5      0.00   0.0  0
 8LK  CONST_08  O2   C2   N1   C1'     0.00   0.0  0
 8LK  CONST_09  C4   N3   C2   O2    180.00   0.0  0
 8LK  CONST_10  C6   N1   C2   O2    180.00   0.0  0
 8LK  CONST_11  H17  N17  C4   N3      0.00   0.0  0
 8LK  CONST_12  H17  N17  C4   C5    180.00   0.0  0
 8LK  Var_01    C4   C5   C6   N1      0.45   0.0  0
 8LK  Var_02    C14  C5   C6   N1    179.23   0.0  0
 8LK  Var_03    H10  C6   C5   C4   -179.40   0.0  0
 8LK  Var_04    H10  C6   C5   C14    -0.62   0.0  0
 8LK  Var_05    H14  C16  C15  C14     0.50  30.0  3
 8LK  Var_06    H15  C16  C15  C14   120.71  30.0  3
 8LK  Var_07    H16  C16  C15  C14  -119.61  30.0  3
 8LK  Var_08    H14  C16  C15  N17  -179.78  30.0  3
 8LK  Var_09    H15  C16  C15  N17   -59.57  30.0  3
 8LK  Var_10    H16  C16  C15  N17    60.11  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
 8LK  chir_01  C4'  C3'  O4'  C5'  positiv
 8LK  chir_02  C3'  O3'  C2'  C4'  negativ
 8LK  chir_03  C1'  O4'  N1   C2'  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
 8LK  plan-1  C1'  0.020
 8LK  plan-1  N1   0.020
 8LK  plan-1  C2   0.020
 8LK  plan-1  O2   0.020
 8LK  plan-1  N3   0.020
 8LK  plan-1  C4   0.020
 8LK  plan-1  C5   0.020
 8LK  plan-1  C6   0.020
 8LK  plan-1  C14  0.020
 8LK  plan-1  C15  0.020
 8LK  plan-1  C16  0.020
 8LK  plan-1  N17  0.020
 8LK  plan-1  H13  0.020
 8LK  plan-1  H17  0.020
 8LK  plan-1  H10  0.020

