# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:55:55 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-(6-chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)OCCCCC1=C(Cl)NC(=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
 JCL  JCL  '4-(6-chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl dihydrogen phosphate'  ligand  30  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JCL
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
 JCL  N3    N   NR16  0  -0.721  -4.2691  -1.5532   0.1065
 JCL  N1    N   NR16  0  -0.698  -4.4777   0.7075   0.4145
 JCL  C6    C   CR6   0   0.280  -3.2512   0.8938  -0.1520
 JCL  CL    CL  CL    0  -0.039  -2.7558   2.5298  -0.2138
 JCL  C5    C   CR6   0  -0.094  -2.4874  -0.1108  -0.6196
 JCL  C7    C   CH2   0  -0.495  -1.1295   0.0667  -1.2228
 JCL  C2    C   CR6   0   0.687  -5.0494  -0.5292   0.5686
 JCL  C4    C   CR6   0   0.581  -3.0154  -1.4596  -0.4725
 JCL  O1    O   OC    0  -0.467  -6.1406  -0.6904   1.0696
 JCL  O2    O   OC    0  -0.447  -2.4280  -2.4656  -0.8219
 JCL  C8    C   CH2   0  -0.426  -0.0115  -0.0131  -0.1825
 JCL  C9    C   CH2   0  -0.466   1.3648   0.1431  -0.8180
 JCL  C10   C   CH2   0  -0.158   2.4546   0.0583   0.2266
 JCL  O27   O   O2    0  -0.592   3.7262   0.2423  -0.4194
 JCL  P     P   P     0   1.452   5.0575  -0.1550   0.3618
 JCL  O1P   O   OH1   0  -0.732   6.0887   0.4449  -0.6960
 JCL  O2P   O   OH1   0  -0.741   5.1757  -1.7490   0.3066
 JCL  O3P   O   O     0  -0.714   5.1624   0.2971   1.7620
 JCL  H3    H   HNR6  0   0.431  -4.6518  -2.4845   0.2136
 JCL  H1    H   HNR6  0   0.442  -5.0121   1.5025   0.7371
 JCL  H7C1  H   HCH2  0   0.249  -1.0753   1.0227  -1.7466
 JCL  H7C2  H   HCH2  0   0.258  -0.9775  -0.7051  -1.9787
 JCL  H8C1  H   HCH2  0   0.236  -0.0699  -0.9713   0.3415
 JCL  H8C2  H   HCH2  0   0.231  -0.1608   0.7649   0.5717
 JCL  H9C1  H   HCH2  0   0.238   1.4244   1.1055  -1.3349
 JCL  H9C2  H   HCH2  0   0.237   1.5159  -0.6374  -1.5688
 JCL  H101  H   HCH2  0   0.231   2.4166  -0.9140   0.7270
 JCL  H102  H   HCH2  0   0.238   2.3217   0.8320   0.9860
 JCL  H1P   H   HOH1  0   0.503   7.0138   0.3841  -0.4222
 JCL  H2P   H   HOH1  0   0.495   5.1498  -2.1378  -0.5780

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
 JCL  N3   C2    aromatic  1.368  0.020  1.368
 JCL  N3   C4    aromatic  1.384  0.020  1.384
 JCL  N3   H3    single    0.860  0.020  1.020
 JCL  N1   C6    aromatic  1.364  0.020  1.364
 JCL  N1   C2    aromatic  1.371  0.020  1.371
 JCL  N1   H1    single    0.860  0.020  1.020
 JCL  C6   CL    single    1.711  0.020  1.711
 JCL  C6   C5    aromatic  1.346  0.020  1.346
 JCL  C5   C7    single    1.496  0.020  1.496
 JCL  C5   C4    aromatic  1.456  0.020  1.456
 JCL  C7   C8    single    1.529  0.020  1.529
 JCL  C7   H7C1  single    0.970  0.020  1.090
 JCL  C7   H7C2  single    0.970  0.020  1.090
 JCL  C2   O1    double    1.211  0.020  1.211
 JCL  C4   O2    double    1.216  0.020  1.216
 JCL  C8   C9    single    1.524  0.020  1.524
 JCL  C8   H8C1  single    0.970  0.020  1.090
 JCL  C8   H8C2  single    0.970  0.020  1.090
 JCL  C9   C10   single    1.512  0.020  1.512
 JCL  C9   H9C1  single    0.970  0.020  1.090
 JCL  C9   H9C2  single    0.970  0.020  1.090
 JCL  C10  O27   single    1.438  0.020  1.438
 JCL  C10  H101  single    0.970  0.020  1.090
 JCL  C10  H102  single    0.970  0.020  1.090
 JCL  O27  P     single    1.594  0.020  1.594
 JCL  P    O1P   single    1.594  0.020  1.594
 JCL  P    O2P   single    1.599  0.020  1.599
 JCL  P    O3P   double    1.475  0.020  1.475
 JCL  O1P  H1P   single    0.850  0.020  0.980
 JCL  O2P  H2P   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
 JCL  H3    N3   C4    116.67  3.000
 JCL  H3    N3   C2    115.92  3.000
 JCL  C4    N3   C2    127.41  3.000
 JCL  H1    N1   C2    116.94  3.000
 JCL  H1    N1   C6    120.04  3.000
 JCL  C2    N1   C6    123.01  3.000
 JCL  C5    C6   CL    122.48  3.000
 JCL  C5    C6   N1    123.56  3.000
 JCL  CL    C6   N1    113.96  3.000
 JCL  C4    C5   C7    118.66  3.000
 JCL  C4    C5   C6    116.78  3.000
 JCL  C7    C5   C6    124.51  3.000
 JCL  H7C2  C7   H7C1  106.27  3.000
 JCL  H7C2  C7   C8    109.43  3.000
 JCL  H7C1  C7   C8    109.62  3.000
 JCL  H7C2  C7   C5    108.77  3.000
 JCL  H7C1  C7   C5    110.02  3.000
 JCL  C8    C7   C5    112.52  3.000
 JCL  O1    C2   N1    122.82  3.000
 JCL  O1    C2   N3    123.64  3.000
 JCL  N1    C2   N3    113.54  3.000
 JCL  O2    C4   C5    124.21  3.000
 JCL  O2    C4   N3    120.11  3.000
 JCL  C5    C4   N3    115.68  3.000
 JCL  H8C2  C8   H8C1  106.59  3.000
 JCL  H8C2  C8   C9    109.75  3.000
 JCL  H8C1  C8   C9    109.74  3.000
 JCL  H8C2  C8   C7    109.40  3.000
 JCL  H8C1  C8   C7    109.43  3.000
 JCL  C9    C8   C7    111.79  3.000
 JCL  H9C2  C9   H9C1  107.22  3.000
 JCL  H9C2  C9   C10   109.55  3.000
 JCL  H9C1  C9   C10   109.66  3.000
 JCL  H9C2  C9   C8    109.75  3.000
 JCL  H9C1  C9   C8    109.66  3.000
 JCL  C10   C9   C8    110.92  3.000
 JCL  H102  C10  H101  107.90  3.000
 JCL  H102  C10  O27   109.23  3.000
 JCL  H101  C10  O27   110.48  3.000
 JCL  H102  C10  C9    110.67  3.000
 JCL  H101  C10  C9    109.92  3.000
 JCL  O27   C10  C9    108.65  3.000
 JCL  P     O27  C10   119.11  3.000
 JCL  O3P   P    O2P   109.45  3.000
 JCL  O3P   P    O1P   117.93  3.000
 JCL  O2P   P    O1P   107.72  3.000
 JCL  O3P   P    O27   116.63  3.000
 JCL  O2P   P    O27   107.05  3.000
 JCL  O1P   P    O27    96.97  3.000
 JCL  H1P   O1P  P     114.04  3.000
 JCL  H2P   O2P  P     115.49  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
 JCL  CONST_01  C6   N1   C2   N3      0.00   0.0  0
 JCL  CONST_02  C6   C5   C4   N3      0.00   0.0  0
 JCL  CONST_03  C4   C5   C6   N1      0.00   0.0  0
 JCL  CONST_04  C4   N3   C2   N1      0.00   0.0  0
 JCL  CONST_05  C2   N1   C6   C5      0.00   0.0  0
 JCL  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 JCL  CONST_07  C7   C5   C4   N3    180.00   0.0  0
 JCL  CONST_08  C7   C5   C6   N1    180.00   0.0  0
 JCL  CONST_09  O1   C2   N1   C6    180.00   0.0  0
 JCL  CONST_10  O2   C4   C5   C6    180.00   0.0  0
 JCL  CONST_11  C2   N1   C6   CL    180.00   0.0  0
 JCL  CONST_12  C4   C5   C6   CL    180.00   0.0  0
 JCL  CONST_13  O2   C4   N3   C2    180.00   0.0  0
 JCL  CONST_14  O1   C2   N3   C4    180.00   0.0  0
 JCL  CONST_15  H1   N1   C2   N3    180.00   0.0  0
 JCL  CONST_16  H3   N3   C2   N1    180.00   0.0  0
 JCL  Var_01    C8   C7   C5   C6     90.03  30.0  2
 JCL  Var_02    C9   C8   C7   C5    178.91  30.0  3
 JCL  Var_03    C10  C9   C8   C7   -179.88  30.0  3
 JCL  Var_04    O27  C10  C9   C8   -178.68  30.0  3
 JCL  Var_05    O1P  P    O27  C10  -172.12  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
 JCL  plan-1  N3  0.020
 JCL  plan-1  N1  0.020
 JCL  plan-1  C6  0.020
 JCL  plan-1  CL  0.020
 JCL  plan-1  C5  0.020
 JCL  plan-1  C7  0.020
 JCL  plan-1  C2  0.020
 JCL  plan-1  C4  0.020
 JCL  plan-1  O1  0.020
 JCL  plan-1  O2  0.020
 JCL  plan-1  H3  0.020
 JCL  plan-1  H1  0.020

