# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:34:32 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  32  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 OK
;

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  OC    -1  -0.589  -1.8672  -3.0850   0.1702
 YRO  CAL  C  C      0   0.411  -0.9022  -2.3002   0.2362
 YRO  OAG  O  O      0  -0.538   0.2976  -2.5718   0.3470
 YRO  CAN  C  CR6    0   0.195  -1.2969  -0.8124   0.1458
 YRO  NAJ  N  NR16   0  -0.707  -2.6135  -0.6625  -0.2008
 YRO  CAO  C  CR6    0   0.654  -3.2510   0.5198  -0.3841
 YRO  OAE  O  O      0  -0.495  -4.4233   0.6198  -0.6985
 YRO  NAK  N  NR16   0  -0.714  -2.4389   1.6042  -0.1804
 YRO  CAP  C  CR6    0   0.565  -1.1057   1.5874   0.1870
 YRO  OAF  O  O      0  -0.468  -0.5143   2.6445   0.3382
 YRO  CAM  C  CR6    0  -0.146  -0.5082   0.2685   0.3639
 YRO  CAH  C  CH2    0  -0.495   0.9449   0.2446   0.7390
 YRO  CAI  C  CH2    0  -0.378   1.8450   0.3747  -0.4913
 YRO  CAQ  C  CT     0  -0.091   3.3580   0.3518  -0.2244
 YRO  CAB  C  CH3    0  -0.648   3.7585   1.4721   0.7374
 YRO  CAC  C  CH3    0  -0.633   3.7890  -0.9983   0.3495
 YRO  CAA  C  CH3    0  -0.635   4.0732   0.5683  -1.5602
 YRO  H2   H  HNR6   0   0.418  -2.8617   2.5134  -0.3164
 YRO  H4   H  HCH2   0   0.229   1.1332   1.0747   1.4228
 YRO  H5   H  HCH2   0   0.250   1.1731  -0.6746   1.2677
 YRO  H6   H  HCH2   0   0.217   1.6029  -0.4381  -1.1826
 YRO  H7   H  HCH2   0   0.213   1.6008   1.3091  -1.0069
 YRO  H8   H  HCH3   0   0.223   3.3650   1.3104   1.7427
 YRO  H9   H  HCH3   0   0.221   4.8456   1.5391   0.8227
 YRO  H10  H  HCH3   0   0.218   3.3934   2.4414   0.3900
 YRO  H11  H  HCH3   0   0.217   3.5106  -1.8156  -0.3191
 YRO  H12  H  HCH3   0   0.216   4.8725  -1.0341   0.4854
 YRO  H13  H  HCH3   0   0.221   3.3322  -1.1990   1.3196
 YRO  H14  H  HCH3   0   0.218   3.8081   1.5322  -2.0011
 YRO  H15  H  HCH3   0   0.219   5.1580   0.5488  -1.4323
 YRO  H16  H  HCH3   0   0.218   3.8109  -0.2099  -2.2812
 YRO  H17  H  HNR6   0   0.415  -3.1320  -1.5270  -0.3086

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  1.218  0.020  1.218
 YRO  CAO  NAJ  single  1.356  0.020  1.356
 YRO  CAO  NAK  single  1.370  0.020  1.370
 YRO  NAJ  CAN  single  1.370  0.020  1.370
 YRO  NAK  CAP  single  1.383  0.020  1.383
 YRO  CAL  OAG  deloc   1.235  0.020  1.235
 YRO  CAL  CAN  single  1.542  0.020  1.542
 YRO  CAL  OAD  deloc   1.246  0.020  1.246
 YRO  CAN  CAM  double  1.356  0.020  1.356
 YRO  CAP  CAM  single  1.459  0.020  1.459
 YRO  CAP  OAF  double  1.221  0.020  1.221
 YRO  CAM  CAH  single  1.501  0.020  1.501
 YRO  CAH  CAI  single  1.530  0.020  1.530
 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  1.529  0.020  1.529
 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  CAN  CAL  OAG  117.78  3.000
 YRO  CAN  CAL  OAD  113.99  3.000
 YRO  OAG  CAL  OAD  128.22  3.000
 YRO  CAM  CAN  NAJ  120.84  3.000
 YRO  CAM  CAN  CAL  127.66  3.000
 YRO  NAJ  CAN  CAL  111.50  3.000
 YRO  H17  NAJ  CAO  119.26  3.000
 YRO  H17  NAJ  CAN  115.16  3.000
 YRO  CAO  NAJ  CAN  125.57  3.000
 YRO  NAK  CAO  OAE  122.96  3.000
 YRO  NAK  CAO  NAJ  113.05  3.000
 YRO  OAE  CAO  NAJ  124.00  3.000
 YRO  H2   NAK  CAP  116.70  3.000
 YRO  H2   NAK  CAO  116.33  3.000
 YRO  CAP  NAK  CAO  126.96  3.000
 YRO  CAM  CAP  OAF  124.71  3.000
 YRO  OAF  CAP  NAK  119.31  3.000
 YRO  CAM  CAP  NAK  115.98  3.000
 YRO  CAH  CAM  CAP  116.18  3.000
 YRO  CAH  CAM  CAN  126.21  3.000
 YRO  CAP  CAM  CAN  117.59  3.000
 YRO  H5   CAH  H4   107.62  3.000
 YRO  H5   CAH  CAI  109.89  3.000
 YRO  H4   CAH  CAI  109.73  3.000
 YRO  H5   CAH  CAM  109.82  3.000
 YRO  H4   CAH  CAM  108.15  3.000
 YRO  CAI  CAH  CAM  111.54  3.000
 YRO  H7   CAI  H6   106.68  3.000
 YRO  H7   CAI  CAQ  108.31  3.000
 YRO  H6   CAI  CAQ  108.45  3.000
 YRO  H7   CAI  CAH  108.67  3.000
 YRO  H6   CAI  CAH  108.35  3.000
 YRO  CAQ  CAI  CAH  116.00  3.000
 YRO  CAA  CAQ  CAC  108.71  3.000
 YRO  CAC  CAQ  CAB  109.69  3.000
 YRO  CAA  CAQ  CAB  108.83  3.000
 YRO  CAC  CAQ  CAI  110.85  3.000
 YRO  CAB  CAQ  CAI  110.86  3.000
 YRO  CAA  CAQ  CAI  107.84  3.000
 YRO  H10  CAB  H9   107.64  3.000
 YRO  H10  CAB  H8   107.69  3.000
 YRO  H9   CAB  H8   107.21  3.000
 YRO  H10  CAB  CAQ  111.24  3.000
 YRO  H9   CAB  CAQ  110.76  3.000
 YRO  H8   CAB  CAQ  112.09  3.000
 YRO  H13  CAC  H12  107.38  3.000
 YRO  H13  CAC  H11  107.46  3.000
 YRO  H12  CAC  H11  107.73  3.000
 YRO  H13  CAC  CAQ  112.22  3.000
 YRO  H12  CAC  CAQ  110.80  3.000
 YRO  H11  CAC  CAQ  111.05  3.000
 YRO  H16  CAA  H15  107.63  3.000
 YRO  H16  CAA  H14  107.69  3.000
 YRO  H15  CAA  H14  107.69  3.000
 YRO  H16  CAA  CAQ  111.28  3.000
 YRO  H15  CAA  CAQ  111.05  3.000
 YRO  H14  CAA  CAQ  111.32  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  Var_01    NAJ  CAN  CAL  OAD    -9.60  30.0  2
 YRO  Var_02    CAI  CAH  CAM  CAN    94.87  30.0  3
 YRO  Var_03    CAQ  CAI  CAH  CAM  -179.57  30.0  3
 YRO  Var_04    CAA  CAQ  CAI  CAH  -177.02  30.0  3
 YRO  Var_05    H14  CAA  CAQ  CAI    60.73  30.0  3
 YRO  Var_06    H8   CAB  CAQ  CAI    67.84  30.0  3
 YRO  Var_07    H11  CAC  CAQ  CAI    57.07  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

