# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:58:03 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2CC[C@@H](CO)O2)C(=O)NC1=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
 38S  38S  1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  30  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_38S
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
 38S  OAC  O  O     0  -0.490   1.5016   2.5988   0.2585
 38S  CAM  C  CR6   0   0.729   1.5498   1.3881   0.1511
 38S  NAI  N  NR16  0  -0.731   2.7283   0.7168  -0.0401
 38S  CAL  C  CR6   0   0.557   2.9120  -0.6458  -0.1937
 38S  OAB  O  O     0  -0.459   4.0271  -1.1053  -0.3669
 38S  CAK  C  CR6   0  -0.182   1.6924  -1.4209  -0.1216
 38S  CAA  C  CH3   0  -0.705   1.7709  -2.9063  -0.2585
 38S  CAE  C  CR16  0   0.052   0.5332  -0.7653   0.0788
 38S  NAP  N  NR6   0  -0.563   0.4351   0.5900   0.2088
 38S  CAO  C  CR15  0   0.206  -0.8660   1.2865   0.3942
 38S  OAJ  O  O     0  -0.500  -1.8269   0.3700   0.8043
 38S  CAH  C  CH2   0  -0.504  -1.3739   1.8992  -0.9103
 38S  CAG  C  CH2   0  -0.502  -2.2557   0.7894  -1.4630
 38S  CAN  C  CR15  0   0.013  -2.8544   0.2164  -0.1900
 38S  CAF  C  CH2   0  -0.158  -3.2755  -1.2276  -0.3008
 38S  OAD  O  OH1   0  -0.669  -3.7890  -1.6584   0.9354
 38S  H1   H  HNR6  0   0.424   3.5559   1.2988  -0.0815
 38S  H2   H  HCH3  0   0.246   2.4170  -3.3437   0.5037
 38S  H3   H  HCH3  0   0.244   0.7848  -3.3573  -0.1589
 38S  H4   H  HCH3  0   0.246   2.1749  -3.1962  -1.2294
 38S  H5   H  HCR6  0   0.307  -0.3925  -1.3130   0.1657
 38S  H6   H  HCR5  0   0.274  -0.7049   2.0304   1.1747
 38S  H7   H  HCH2  0   0.262  -1.9704   2.7831  -0.6767
 38S  H8   H  HCH2  0   0.274  -0.5729   2.2056  -1.5795
 38S  H9   H  HCH2  0   0.272  -3.0184   1.1515  -2.1501
 38S  H10  H  HCH2  0   0.245  -1.6582   0.0377  -1.9878
 38S  H11  H  HCR5  0   0.241  -3.7187   0.8166   0.1207
 38S  H12  H  HCH2  0   0.217  -4.0253  -1.2861  -1.1001
 38S  H13  H  HCH2  0   0.192  -2.4224  -1.8388  -0.6285
 38S  H14  H  HOH1  0   0.459  -4.1249  -2.5523   0.8256

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
 38S  OAC  CAM  double  1.216  0.020  1.216
 38S  NAI  CAM  single  1.370  0.020  1.370
 38S  NAI  CAL  single  1.383  0.020  1.383
 38S  OAB  CAL  double  1.218  0.020  1.218
 38S  CAM  NAP  single  1.372  0.020  1.372
 38S  CAL  CAK  single  1.447  0.020  1.447
 38S  CAH  CAO  single  1.528  0.020  1.528
 38S  CAH  CAG  single  1.521  0.020  1.521
 38S  NAP  CAO  single  1.487  0.020  1.487
 38S  NAP  CAE  single  1.365  0.020  1.365
 38S  CAK  CAE  double  1.347  0.020  1.347
 38S  CAK  CAA  single  1.494  0.020  1.494
 38S  CAO  OAJ  single  1.390  0.020  1.390
 38S  CAG  CAN  single  1.519  0.020  1.519
 38S  OAJ  CAN  single  1.438  0.020  1.438
 38S  CAN  CAF  single  1.508  0.020  1.508
 38S  OAD  CAF  single  1.406  0.020  1.406
 38S  NAI  H1   single  0.860  0.020  1.020
 38S  CAA  H2   single  0.970  0.020  1.090
 38S  CAA  H3   single  0.970  0.020  1.090
 38S  CAA  H4   single  0.970  0.020  1.090
 38S  CAE  H5   single  0.930  0.020  1.080
 38S  CAO  H6   single  0.970  0.020  1.090
 38S  CAH  H7   single  0.970  0.020  1.090
 38S  CAH  H8   single  0.970  0.020  1.090
 38S  CAG  H9   single  0.970  0.020  1.090
 38S  CAG  H10  single  0.970  0.020  1.090
 38S  CAN  H11  single  0.970  0.020  1.090
 38S  CAF  H12  single  0.970  0.020  1.090
 38S  CAF  H13  single  0.970  0.020  1.090
 38S  OAD  H14  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
 38S  NAP  CAM  NAI  114.82  3.000
 38S  NAP  CAM  OAC  122.89  3.000
 38S  NAI  CAM  OAC  122.29  3.000
 38S  H1   NAI  CAL  116.94  3.000
 38S  H1   NAI  CAM  115.29  3.000
 38S  CAL  NAI  CAM  127.77  3.000
 38S  CAK  CAL  OAB  125.21  3.000
 38S  CAK  CAL  NAI  114.22  3.000
 38S  OAB  CAL  NAI  120.57  3.000
 38S  CAE  CAK  CAA  122.89  3.000
 38S  CAA  CAK  CAL  118.94  3.000
 38S  CAE  CAK  CAL  118.17  3.000
 38S  H4   CAA  H3   107.86  3.000
 38S  H4   CAA  H2   107.21  3.000
 38S  H3   CAA  H2   107.84  3.000
 38S  H4   CAA  CAK  111.43  3.000
 38S  H3   CAA  CAK  110.85  3.000
 38S  H2   CAA  CAK  111.46  3.000
 38S  H5   CAE  NAP  115.76  3.000
 38S  H5   CAE  CAK  120.22  3.000
 38S  NAP  CAE  CAK  124.01  3.000
 38S  CAO  NAP  CAE  122.66  3.000
 38S  CAE  NAP  CAM  121.00  3.000
 38S  CAO  NAP  CAM  116.33  3.000
 38S  H6   CAO  CAH  112.75  3.000
 38S  H6   CAO  OAJ  109.93  3.000
 38S  CAH  CAO  OAJ  106.65  3.000
 38S  H6   CAO  NAP  106.23  3.000
 38S  OAJ  CAO  NAP  109.44  3.000
 38S  CAH  CAO  NAP  111.85  3.000
 38S  CAN  OAJ  CAO  111.12  3.000
 38S  H8   CAH  H7   107.81  3.000
 38S  H8   CAH  CAG  114.13  3.000
 38S  H7   CAH  CAG  110.59  3.000
 38S  H8   CAH  CAO  113.16  3.000
 38S  H7   CAH  CAO  108.88  3.000
 38S  CAG  CAH  CAO  102.14  3.000
 38S  H10  CAG  H9   107.97  3.000
 38S  H10  CAG  CAN  110.98  3.000
 38S  H9   CAG  CAN  112.23  3.000
 38S  H10  CAG  CAH  111.03  3.000
 38S  H9   CAG  CAH  113.13  3.000
 38S  CAN  CAG  CAH  101.48  3.000
 38S  H11  CAN  CAF  108.94  3.000
 38S  H11  CAN  CAG  109.97  3.000
 38S  CAF  CAN  CAG  114.18  3.000
 38S  H11  CAN  OAJ  107.98  3.000
 38S  CAF  CAN  OAJ  110.64  3.000
 38S  CAG  CAN  OAJ  104.93  3.000
 38S  H13  CAF  H12  106.47  3.000
 38S  H13  CAF  OAD  112.04  3.000
 38S  H12  CAF  OAD  111.99  3.000
 38S  H13  CAF  CAN  109.72  3.000
 38S  H12  CAF  CAN  107.17  3.000
 38S  OAD  CAF  CAN  109.31  3.000
 38S  H14  OAD  CAF  108.19  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
 38S  CONST_01  CAO  NAP  CAM  NAI  180.00   0.0  0
 38S  CONST_02  CAE  NAP  CAM  NAI    0.00   0.0  0
 38S  CONST_03  NAP  CAM  NAI  CAL    0.00   0.0  0
 38S  CONST_04  CAL  NAI  CAM  OAC  180.00   0.0  0
 38S  CONST_05  CAO  NAP  CAM  OAC    0.00   0.0  0
 38S  CONST_06  CAE  NAP  CAM  OAC  180.00   0.0  0
 38S  CONST_07  H1   NAI  CAM  NAP  180.00   0.0  0
 38S  Var_01    CAN  CAG  CAH  CAO   35.74  30.0  1
 38S  Var_02    H2   CAA  CAK  CAL   58.41  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
 38S  chir_01  CAO  CAH  NAP  OAJ  positiv
 38S  chir_02  CAN  OAJ  CAF  CAG  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
 38S  plan-1  OAC  0.020
 38S  plan-1  CAM  0.020
 38S  plan-1  NAI  0.020
 38S  plan-1  CAL  0.020
 38S  plan-1  OAB  0.020
 38S  plan-1  CAK  0.020
 38S  plan-1  CAA  0.020
 38S  plan-1  CAE  0.020
 38S  plan-1  NAP  0.020
 38S  plan-1  CAO  0.020
 38S  plan-1  H1   0.020
 38S  plan-1  H5   0.020

