# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 02:39:01 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC1=NC(=O)NC(=O)C1)Cc2occc2
#
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
 P0K  P0K  6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione  ligand  30  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P0K
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
 P0K  C10  C  C     0   0.265  22.5652  -27.0596  24.9584
 P0K  C01  C  CH3   0  -0.533  22.9157  -30.4116  26.5157
 P0K  C03  C  CH2   0  -0.379  23.6763  -28.4270  27.5982
 P0K  C04  C  CR5   0   0.353  23.5244  -26.9638  27.7990
 P0K  C05  C  CR15  0  -0.353  22.7153  -26.2269  28.5961
 P0K  C06  C  CR15  0  -0.318  22.9385  -24.8601  28.2504
 P0K  C07  C  CR15  0  -0.033  23.8745  -24.8706  27.2735
 P0K  C09  C  CH2   0  -0.337  23.1694  -28.4080  25.2358
 P0K  C11  C  CH2   0  -0.677  23.2709  -26.2481  23.9248
 P0K  C12  C  C     0   0.576  22.6956  -24.8850  23.6916
 P0K  C14  C  C     0   0.605  20.9276  -25.4710  25.2899
 P0K  N02  N  NT    0  -0.400  22.8420  -28.9629  26.5255
 P0K  N13  N  NH1   0  -0.692  21.5702  -24.6113  24.4138
 P0K  N15  N  N     0  -0.417  21.4931  -26.7122  25.5498
 P0K  O08  O  O     0  -0.416  24.2454  -26.1399  27.0005
 P0K  O16  O  O     0  -0.429  19.8950  -25.1350  25.8174
 P0K  O17  O  O     0  -0.433  23.1800  -24.0805  22.9289
 P0K  H1   H  HCH3  0   0.241  22.6140  -30.7999  27.4890
 P0K  H2   H  HCH3  0   0.244  22.2305  -30.8138  25.7694
 P0K  H3   H  HCH3  0   0.203  23.9214  -30.8011  26.2985
 P0K  H4   H  HCH2  0   0.268  23.3788  -28.9198  28.5254
 P0K  H5   H  HCH2  0   0.227  24.7399  -28.6714  27.4380
 P0K  H6   H  HCR5  0   0.258  22.0245  -26.6132  29.3284
 P0K  H7   H  HCR5  0   0.263  22.4669  -23.9887  28.6747
 P0K  H8   H  HCR5  0   0.281  24.3706  -24.0897  26.7199
 P0K  H9   H  HCH2  0   0.297  22.7694  -29.0628  24.4525
 P0K  H10  H  HCH2  0   0.241  24.2539  -28.3647  25.0456
 P0K  H11  H  HCH2  0   0.342  23.2646  -26.7989  22.9772
 P0K  H12  H  HCH2  0   0.329  24.3270  -26.1474  24.1859
 P0K  H14  H  HNH1  0   0.423  21.1436  -23.7020  24.2806

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
 P0K  O17  C12  double    1.210  0.020  1.210
 P0K  C12  C11  single    1.498  0.020  1.498
 P0K  C12  N13  single    1.365  0.020  1.365
 P0K  C11  C10  single    1.492  0.020  1.492
 P0K  N13  C14  single    1.386  0.020  1.386
 P0K  C10  C09  single    1.503  0.020  1.503
 P0K  C10  N15  double    1.273  0.020  1.273
 P0K  C14  N15  single    1.388  0.020  1.388
 P0K  C14  O16  double    1.207  0.020  1.207
 P0K  C09  N02  single    1.442  0.020  1.442
 P0K  C01  N02  single    1.451  0.020  1.451
 P0K  N02  C03  single    1.461  0.020  1.461
 P0K  O08  C07  aromatic  1.350  0.020  1.350
 P0K  O08  C04  aromatic  1.355  0.020  1.355
 P0K  C07  C06  aromatic  1.353  0.020  1.353
 P0K  C04  C03  single    1.485  0.020  1.485
 P0K  C04  C05  aromatic  1.354  0.020  1.354
 P0K  C06  C05  aromatic  1.427  0.020  1.427
 P0K  C01  H1   single    0.970  0.020  1.090
 P0K  C01  H2   single    0.970  0.020  1.090
 P0K  C01  H3   single    0.970  0.020  1.090
 P0K  C03  H4   single    0.970  0.020  1.090
 P0K  C03  H5   single    0.970  0.020  1.090
 P0K  C05  H6   single    0.930  0.020  1.080
 P0K  C06  H7   single    0.930  0.020  1.080
 P0K  C07  H8   single    0.930  0.020  1.080
 P0K  C09  H9   single    0.970  0.020  1.090
 P0K  C09  H10  single    0.970  0.020  1.090
 P0K  C11  H11  single    0.970  0.020  1.090
 P0K  C11  H12  single    0.970  0.020  1.090
 P0K  N13  H14  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
 P0K  N15  C10  C11  124.89  3.000
 P0K  N15  C10  C09  119.84  3.000
 P0K  C11  C10  C09  115.20  3.000
 P0K  H3   C01  H2   107.99  3.000
 P0K  H3   C01  H1   107.64  3.000
 P0K  H2   C01  H1   107.81  3.000
 P0K  H3   C01  N02  113.66  3.000
 P0K  H2   C01  N02  109.95  3.000
 P0K  H1   C01  N02  109.60  3.000
 P0K  H5   C03  H4   106.63  3.000
 P0K  H5   C03  N02  111.28  3.000
 P0K  H4   C03  N02  107.61  3.000
 P0K  H5   C03  C04  109.67  3.000
 P0K  H4   C03  C04  107.59  3.000
 P0K  N02  C03  C04  113.73  3.000
 P0K  O08  C04  C05  109.52  3.000
 P0K  C05  C04  C03  132.62  3.000
 P0K  O08  C04  C03  117.71  3.000
 P0K  H6   C05  C06  127.42  3.000
 P0K  H6   C05  C04  126.00  3.000
 P0K  C06  C05  C04  106.56  3.000
 P0K  H7   C06  C07  126.38  3.000
 P0K  H7   C06  C05  127.62  3.000
 P0K  C07  C06  C05  106.00  3.000
 P0K  H8   C07  O08  116.78  3.000
 P0K  H8   C07  C06  133.12  3.000
 P0K  O08  C07  C06  110.08  3.000
 P0K  H10  C09  H9   105.02  3.000
 P0K  H10  C09  N02  113.14  3.000
 P0K  H9   C09  N02  109.05  3.000
 P0K  H10  C09  C10  109.17  3.000
 P0K  H9   C09  C10  104.91  3.000
 P0K  N02  C09  C10  114.77  3.000
 P0K  H12  C11  H11  104.98  3.000
 P0K  H12  C11  C12  108.95  3.000
 P0K  H11  C11  C12  108.69  3.000
 P0K  H12  C11  C10  109.98  3.000
 P0K  H11  C11  C10  108.84  3.000
 P0K  C12  C11  C10  114.91  3.000
 P0K  O17  C12  N13  122.03  3.000
 P0K  N13  C12  C11  114.64  3.000
 P0K  O17  C12  C11  123.33  3.000
 P0K  O16  C14  N15  121.02  3.000
 P0K  O16  C14  N13  120.02  3.000
 P0K  N15  C14  N13  118.96  3.000
 P0K  C09  N02  C03  112.71  3.000
 P0K  C03  N02  C01  110.02  3.000
 P0K  C09  N02  C01  111.52  3.000
 P0K  H14  N13  C14  116.41  3.000
 P0K  H14  N13  C12  117.23  3.000
 P0K  C14  N13  C12  126.33  3.000
 P0K  C14  N15  C10  120.01  3.000
 P0K  C07  O08  C04  107.83  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
 P0K  CONST_01  C06  C07  O08  C04     0.00   0.0  0
 P0K  CONST_02  C07  C06  C05  C04     0.00   0.0  0
 P0K  CONST_03  C07  O08  C04  C05     0.00   0.0  0
 P0K  CONST_04  O08  C07  C06  C05     0.00   0.0  0
 P0K  CONST_05  O08  C04  C05  C06     0.00   0.0  0
 P0K  CONST_06  N13  C14  N15  C10     0.00   0.0  0
 P0K  CONST_07  C14  N13  C12  C11     0.00   0.0  0
 P0K  CONST_08  N15  C14  N13  C12     0.00   0.0  0
 P0K  CONST_09  C07  O08  C04  C03   180.00   0.0  0
 P0K  CONST_10  C06  C05  C04  C03   180.00   0.0  0
 P0K  CONST_11  O16  C14  N15  C10   180.00   0.0  0
 P0K  CONST_12  O16  C14  N13  C12   180.00   0.0  0
 P0K  CONST_13  O17  C12  N13  C14   180.00   0.0  0
 P0K  CONST_14  H8   C07  O08  C04   180.00   0.0  0
 P0K  CONST_15  H7   C06  C05  C04   180.00   0.0  0
 P0K  CONST_16  H6   C05  C06  C07   180.00   0.0  0
 P0K  CONST_17  H14  N13  C12  C11   180.00   0.0  0
 P0K  Var_01    C12  C11  C10  C09  -177.72  30.0  1
 P0K  Var_02    H11  C11  C12  N13   119.19  30.0  1
 P0K  Var_03    N02  C03  C04  C05    91.54  30.0  2
 P0K  Var_04    N02  C09  C10  C11   157.38  30.0  3
 P0K  Var_05    C01  N02  C09  C10   154.31  30.0  3
 P0K  Var_06    C04  C03  N02  C01  -172.39  30.0  3
 P0K  Var_07    H1   C01  N02  C03    57.04  30.0  3

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
 P0K  plan-1  C03  0.020
 P0K  plan-1  C04  0.020
 P0K  plan-1  C05  0.020
 P0K  plan-1  C06  0.020
 P0K  plan-1  C07  0.020
 P0K  plan-1  O08  0.020
 P0K  plan-1  H6   0.020
 P0K  plan-1  H7   0.020
 P0K  plan-1  H8   0.020
 P0K  plan-2  C10  0.020
 P0K  plan-2  C11  0.020
 P0K  plan-2  C12  0.020
 P0K  plan-2  C14  0.020
 P0K  plan-2  N13  0.020
 P0K  plan-2  N15  0.020
 P0K  plan-2  O16  0.020
 P0K  plan-2  O17  0.020
 P0K  plan-2  H14  0.020

