# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 20:49:43 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 5-(3,3-dimethylbutyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)CCC1=C(NC(=O)NC1=O)C(O)=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
 YRO  YRO  '5-(3,3-dimethylbutyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  33  17  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YRO
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
 YRO  OAD  O  OH1   0  -0.592  -1.7709  -3.0753   0.5392
 YRO  CAL  C  C     0   0.513  -0.7912  -2.2437   0.2294
 YRO  OAG  O  O     0  -0.392   0.3500  -2.5681   0.0480
 YRO  CAN  C  CR6   0   0.280  -1.2929  -0.8365   0.1164
 YRO  NAJ  N  NR16  0  -0.732  -2.6197  -0.7226  -0.2220
 YRO  CAO  C  CR6   0   0.668  -3.2630   0.4640  -0.4102
 YRO  OAE  O  O     0  -0.475  -4.4305   0.5472  -0.7295
 YRO  NAK  N  NR16  0  -0.716  -2.4625   1.5571  -0.2049
 YRO  CAP  C  CR6   0   0.586  -1.1321   1.5627   0.1578
 YRO  OAF  O  O     0  -0.439  -0.5454   2.6152   0.3154
 YRO  CAM  C  CR6   0  -0.106  -0.5109   0.2445   0.3268
 YRO  CAH  C  CH2   0  -0.518   0.9373   0.2370   0.7119
 YRO  CAI  C  CH2   0  -0.383   1.8479   0.4099  -0.5080
 YRO  CAQ  C  CT    0  -0.094   3.3566   0.3921  -0.2137
 YRO  CAB  C  CH3   0  -0.649   3.7261   1.4764   0.7999
 YRO  CAC  C  CH3   0  -0.636   3.7925  -0.9768   0.3114
 YRO  CAA  C  CH3   0  -0.635   4.0899   0.6693  -1.5282
 YRO  H1   H  HOH1  0   0.502  -1.4479  -3.9896   0.5686
 YRO  H2   H  HNR6  0   0.430  -2.9007   2.4600  -0.3404
 YRO  H4   H  HCH2  0   0.254   1.0989   1.0605   1.4090
 YRO  H5   H  HCH2  0   0.254   1.1855  -0.6770   1.2447
 YRO  H6   H  HCH2  0   0.228   1.6246  -0.3793  -1.2318
 YRO  H7   H  HCH2  0   0.225   1.6016   1.3597  -0.9920
 YRO  H8   H  HCH3  0   0.224   3.3105   1.2726   1.7886
 YRO  H9   H  HCH3  0   0.225   4.8102   1.5441   0.9139
 YRO  H10  H  HCH3  0   0.221   3.3639   2.4566   0.4810
 YRO  H11  H  HCH3  0   0.220   3.5610  -1.7646  -0.4086
 YRO  H12  H  HCH3  0   0.220   4.8697  -0.9968   0.4912
 YRO  H13  H  HCH3  0   0.221   3.3023  -1.2348   1.2511
 YRO  H14  H  HCH3  0   0.220   3.8227   1.6473  -1.9353
 YRO  H15  H  HCH3  0   0.221   5.1726   0.6540  -1.3842
 YRO  H16  H  HCH3  0   0.220   3.8467  -0.0824  -2.2830
 YRO  H17  H  HNR6  0   0.437  -3.1704  -1.5560  -0.3724

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
 YRO  OAE  CAO  double  1.213  0.020  1.213
 YRO  CAO  NAJ  single  1.363  0.020  1.363
 YRO  CAO  NAK  single  1.370  0.020  1.370
 YRO  NAJ  CAN  single  1.374  0.020  1.374
 YRO  NAK  CAP  single  1.379  0.020  1.379
 YRO  CAL  OAG  double  1.200  0.020  1.200
 YRO  CAL  CAN  single  1.498  0.020  1.498
 YRO  CAL  OAD  single  1.322  0.020  1.322
 YRO  CAN  CAM  double  1.351  0.020  1.351
 YRO  CAP  CAM  single  1.467  0.020  1.467
 YRO  CAP  OAF  double  1.215  0.020  1.215
 YRO  CAM  CAH  single  1.499  0.020  1.499
 YRO  CAH  CAI  single  1.532  0.020  1.532
 YRO  CAA  CAQ  single  1.531  0.020  1.531
 YRO  CAI  CAQ  single  1.537  0.020  1.537
 YRO  CAB  CAQ  single  1.530  0.020  1.530
 YRO  CAQ  CAC  single  1.530  0.020  1.530
 YRO  OAD  H1   single  0.850  0.020  0.980
 YRO  NAK  H2   single  0.860  0.020  1.020
 YRO  CAH  H4   single  0.970  0.020  1.090
 YRO  CAH  H5   single  0.970  0.020  1.090
 YRO  CAI  H6   single  0.970  0.020  1.090
 YRO  CAI  H7   single  0.970  0.020  1.090
 YRO  CAB  H8   single  0.970  0.020  1.090
 YRO  CAB  H9   single  0.970  0.020  1.090
 YRO  CAB  H10  single  0.970  0.020  1.090
 YRO  CAC  H11  single  0.970  0.020  1.090
 YRO  CAC  H12  single  0.970  0.020  1.090
 YRO  CAC  H13  single  0.970  0.020  1.090
 YRO  CAA  H14  single  0.970  0.020  1.090
 YRO  CAA  H15  single  0.970  0.020  1.090
 YRO  CAA  H16  single  0.970  0.020  1.090
 YRO  NAJ  H17  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
 YRO  H1   OAD  CAL  110.68  3.000
 YRO  CAN  CAL  OAG  124.12  3.000
 YRO  CAN  CAL  OAD  111.12  3.000
 YRO  OAG  CAL  OAD  124.75  3.000
 YRO  CAM  CAN  NAJ  122.08  3.000
 YRO  CAM  CAN  CAL  123.10  3.000
 YRO  NAJ  CAN  CAL  114.82  3.000
 YRO  H17  NAJ  CAO  116.13  3.000
 YRO  H17  NAJ  CAN  119.65  3.000
 YRO  CAO  NAJ  CAN  124.20  3.000
 YRO  NAK  CAO  OAE  123.15  3.000
 YRO  NAK  CAO  NAJ  113.46  3.000
 YRO  OAE  CAO  NAJ  123.39  3.000
 YRO  H2   NAK  CAP  116.68  3.000
 YRO  H2   NAK  CAO  116.01  3.000
 YRO  CAP  NAK  CAO  127.32  3.000
 YRO  CAM  CAP  OAF  123.98  3.000
 YRO  OAF  CAP  NAK  120.23  3.000
 YRO  CAM  CAP  NAK  115.79  3.000
 YRO  CAH  CAM  CAP  116.32  3.000
 YRO  CAH  CAM  CAN  126.55  3.000
 YRO  CAP  CAM  CAN  117.13  3.000
 YRO  H5   CAH  H4   106.73  3.000
 YRO  H5   CAH  CAI  110.46  3.000
 YRO  H4   CAH  CAI  109.60  3.000
 YRO  H5   CAH  CAM  110.54  3.000
 YRO  H4   CAH  CAM  107.67  3.000
 YRO  CAI  CAH  CAM  111.67  3.000
 YRO  H7   CAI  H6   106.72  3.000
 YRO  H7   CAI  CAQ  108.41  3.000
 YRO  H6   CAI  CAQ  108.59  3.000
 YRO  H7   CAI  CAH  108.44  3.000
 YRO  H6   CAI  CAH  108.91  3.000
 YRO  CAQ  CAI  CAH  115.44  3.000
 YRO  CAA  CAQ  CAC  108.68  3.000
 YRO  CAC  CAQ  CAB  109.76  3.000
 YRO  CAA  CAQ  CAB  108.96  3.000
 YRO  CAC  CAQ  CAI  110.85  3.000
 YRO  CAB  CAQ  CAI  110.84  3.000
 YRO  CAA  CAQ  CAI  107.68  3.000
 YRO  H10  CAB  H9   107.69  3.000
 YRO  H10  CAB  H8   107.79  3.000
 YRO  H9   CAB  H8   107.15  3.000
 YRO  H10  CAB  CAQ  111.26  3.000
 YRO  H9   CAB  CAQ  110.67  3.000
 YRO  H8   CAB  CAQ  112.08  3.000
 YRO  H13  CAC  H12  107.28  3.000
 YRO  H13  CAC  H11  107.58  3.000
 YRO  H12  CAC  H11  107.72  3.000
 YRO  H13  CAC  CAQ  112.29  3.000
 YRO  H12  CAC  CAQ  110.74  3.000
 YRO  H11  CAC  CAQ  111.03  3.000
 YRO  H16  CAA  H15  107.59  3.000
 YRO  H16  CAA  H14  107.70  3.000
 YRO  H15  CAA  H14  107.70  3.000
 YRO  H16  CAA  CAQ  111.22  3.000
 YRO  H15  CAA  CAQ  111.05  3.000
 YRO  H14  CAA  CAQ  111.40  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
 YRO  CONST_01  NAK  CAO  NAJ  CAN     0.00   0.0  0
 YRO  CONST_02  CAP  NAK  CAO  NAJ     0.00   0.0  0
 YRO  CONST_03  CAM  CAP  NAK  CAO     0.00   0.0  0
 YRO  CONST_04  OAE  CAO  NAJ  CAN   180.00   0.0  0
 YRO  CONST_05  OAF  CAP  NAK  CAO   180.00   0.0  0
 YRO  CONST_06  CAP  NAK  CAO  OAE   180.00   0.0  0
 YRO  CONST_07  H2   NAK  CAO  NAJ   180.00   0.0  0
 YRO  CONST_08  H17  NAJ  CAO  NAK   180.00   0.0  0
 YRO  CONST_09  H1   OAD  CAL  CAN   180.00   0.0  0
 YRO  Var_01    NAJ  CAN  CAL  OAD   -26.59  30.0  2
 YRO  Var_02    CAI  CAH  CAM  CAN    96.96  30.0  3
 YRO  Var_03    CAQ  CAI  CAH  CAM  -179.06  30.0  3
 YRO  Var_04    CAA  CAQ  CAI  CAH  -176.33  30.0  3
 YRO  Var_05    H14  CAA  CAQ  CAI    60.81  30.0  3
 YRO  Var_06    H8   CAB  CAQ  CAI    67.48  30.0  3
 YRO  Var_07    H11  CAC  CAQ  CAI    58.66  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
 YRO  plan-1  CAL  0.020
 YRO  plan-1  CAN  0.020
 YRO  plan-1  NAJ  0.020
 YRO  plan-1  CAO  0.020
 YRO  plan-1  OAE  0.020
 YRO  plan-1  NAK  0.020
 YRO  plan-1  CAP  0.020
 YRO  plan-1  OAF  0.020
 YRO  plan-1  CAM  0.020
 YRO  plan-1  CAH  0.020
 YRO  plan-1  H2   0.020
 YRO  plan-1  H17  0.020
 YRO  plan-2  OAD  0.020
 YRO  plan-2  CAL  0.020
 YRO  plan-2  OAG  0.020
 YRO  plan-2  CAN  0.020
 YRO  plan-2  H1   0.020

