# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 01:42:12 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2Z)-4-[(3-carbamoylphenyl)amino]-4-oxobut-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc(NC(=O)\C=C/C(O)=O)c1
#
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
 0RY  0RY  '(2Z)-4-[(3-carbamoylphenyl)amino]-4-oxobut-2-enoic acid'  ligand  26  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0RY
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
 0RY  OAB  O  O      0  -0.600   4.4278  -1.5452  -0.7278
 0RY  CAM  C  C      0   0.389   4.2640  -0.9741   0.3625
 0RY  OAE  O  OC    -1  -0.600   4.3374  -1.4528   1.5058
 0RY  CAF  C  C1     0  -0.303   4.0605   0.5232   0.2918
 0RY  CAG  C  C1     0  -0.387   2.9176   1.2104   0.2259
 0RY  CAO  C  C      0   0.544   1.5935   0.5626   0.2083
 0RY  OAD  O  O      0  -0.469   1.4356  -0.6464   0.2544
 0RY  NAL  N  NH1    0  -0.767   0.5616   1.4545   0.1343
 0RY  CAP  C  CR6    0   0.401  -0.8107   1.2221   0.0803
 0RY  CAK  C  CR16   0  -0.352  -1.3993  -0.0416   0.1167
 0RY  CAI  C  CR16   0  -0.347  -1.6347   2.3491  -0.0152
 0RY  CAH  C  CR16   0  -0.229  -3.0082   2.2138  -0.0780
 0RY  CAJ  C  CR16   0  -0.310  -3.5944   0.9561  -0.0602
 0RY  CAQ  C  CR6    0  -0.018  -2.7832  -0.1696   0.0303
 0RY  CAN  C  C      0   0.487  -3.3492  -1.5567   0.0716
 0RY  OAC  O  O      0  -0.481  -2.7431  -2.4736   0.6085
 0RY  NAA  N  NH2    0  -0.811  -4.5481  -1.7184  -0.5084
 0RY  H2   H  H      0   0.272   4.9778   1.1073   0.2968
 0RY  H3   H  H      0   0.260   2.9531   2.2937   0.1817
 0RY  H4   H  HNH1   0   0.417   0.8226   2.4283   0.1006
 0RY  H5   H  HCR6   0   0.285  -0.7908  -0.9265   0.2003
 0RY  H6   H  HCR6   0   0.276  -1.1922   3.3384  -0.0390
 0RY  H7   H  HCR6   0   0.267  -3.6287   3.0977  -0.1398
 0RY  H8   H  HCR6   0   0.260  -4.6726   0.8726  -0.0927
 0RY  H9   H  HNH2   0   0.412  -4.9715  -1.0055  -1.0765
 0RY  H10  H  HNH2   0   0.405  -4.9638  -2.6349  -0.5443

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
 0RY  NAA  CAN  single    1.342  0.020  1.342
 0RY  OAC  CAN  double    1.223  0.020  1.223
 0RY  CAN  CAQ  single    1.499  0.020  1.499
 0RY  CAQ  CAK  aromatic  1.392  0.020  1.392
 0RY  CAQ  CAJ  aromatic  1.390  0.020  1.390
 0RY  OAD  CAO  double    1.220  0.020  1.220
 0RY  CAK  CAP  aromatic  1.395  0.020  1.395
 0RY  CAJ  CAH  aromatic  1.388  0.020  1.388
 0RY  CAO  NAL  single    1.366  0.020  1.366
 0RY  CAO  CAG  single    1.474  0.020  1.474
 0RY  CAP  NAL  single    1.393  0.020  1.393
 0RY  CAP  CAI  aromatic  1.399  0.020  1.399
 0RY  CAG  CAF  double    1.335  0.020  1.335
 0RY  CAH  CAI  aromatic  1.382  0.020  1.382
 0RY  CAF  CAM  single    1.513  0.020  1.513
 0RY  OAB  CAM  deloc     1.242  0.020  1.242
 0RY  CAM  OAE  deloc     1.242  0.020  1.242
 0RY  CAF  H2   single    0.930  0.020  1.080
 0RY  CAG  H3   single    0.930  0.020  1.080
 0RY  NAL  H4   single    0.860  0.020  1.020
 0RY  CAK  H5   single    0.930  0.020  1.080
 0RY  CAI  H6   single    0.930  0.020  1.080
 0RY  CAH  H7   single    0.930  0.020  1.080
 0RY  CAJ  H8   single    0.930  0.020  1.080
 0RY  NAA  H9   single    0.860  0.020  1.020
 0RY  NAA  H10  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
 0RY  CAF  CAM  OAE  115.63  3.000
 0RY  OAE  CAM  OAB  128.57  3.000
 0RY  CAF  CAM  OAB  115.59  3.000
 0RY  H2   CAF  CAG  116.47  3.000
 0RY  H2   CAF  CAM  114.71  3.000
 0RY  CAG  CAF  CAM  128.82  3.000
 0RY  H3   CAG  CAO  117.89  3.000
 0RY  H3   CAG  CAF  119.21  3.000
 0RY  CAO  CAG  CAF  122.91  3.000
 0RY  NAL  CAO  OAD  123.45  3.000
 0RY  NAL  CAO  CAG  113.10  3.000
 0RY  OAD  CAO  CAG  123.45  3.000
 0RY  H4   NAL  CAP  114.50  3.000
 0RY  H4   NAL  CAO  115.90  3.000
 0RY  CAP  NAL  CAO  129.60  3.000
 0RY  CAI  CAP  CAK  118.89  3.000
 0RY  CAI  CAP  NAL  116.64  3.000
 0RY  CAK  CAP  NAL  124.47  3.000
 0RY  H5   CAK  CAQ  119.39  3.000
 0RY  H5   CAK  CAP  120.54  3.000
 0RY  CAQ  CAK  CAP  120.07  3.000
 0RY  H6   CAI  CAH  119.61  3.000
 0RY  H6   CAI  CAP  119.75  3.000
 0RY  CAH  CAI  CAP  120.64  3.000
 0RY  H7   CAH  CAJ  119.94  3.000
 0RY  H7   CAH  CAI  119.53  3.000
 0RY  CAJ  CAH  CAI  120.54  3.000
 0RY  H8   CAJ  CAQ  121.39  3.000
 0RY  H8   CAJ  CAH  119.37  3.000
 0RY  CAQ  CAJ  CAH  119.22  3.000
 0RY  CAN  CAQ  CAJ  122.05  3.000
 0RY  CAJ  CAQ  CAK  120.63  3.000
 0RY  CAN  CAQ  CAK  117.30  3.000
 0RY  NAA  CAN  OAC  122.83  3.000
 0RY  OAC  CAN  CAQ  121.25  3.000
 0RY  NAA  CAN  CAQ  115.92  3.000
 0RY  H10  NAA  H9   116.84  3.000
 0RY  H10  NAA  CAN  119.60  3.000
 0RY  H9   NAA  CAN  122.37  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
 0RY  CONST_01  CAJ  CAQ  CAK  CAP     0.00   0.0  0
 0RY  CONST_02  CAJ  CAH  CAI  CAP     0.00   0.0  0
 0RY  CONST_03  CAH  CAJ  CAQ  CAK     0.00   0.0  0
 0RY  CONST_04  CAH  CAI  CAP  CAK     0.00   0.0  0
 0RY  CONST_05  CAQ  CAK  CAP  CAI     0.00   0.0  0
 0RY  CONST_06  CAQ  CAJ  CAH  CAI     0.00   0.0  0
 0RY  CONST_07  CAQ  CAK  CAP  NAL   180.00   0.0  0
 0RY  CONST_08  CAH  CAI  CAP  NAL   180.00   0.0  0
 0RY  CONST_09  CAN  CAQ  CAK  CAP   180.00   0.0  0
 0RY  CONST_10  CAN  CAQ  CAJ  CAH   180.00   0.0  0
 0RY  CONST_11  H7   CAH  CAI  CAP   180.00   0.0  0
 0RY  CONST_12  H8   CAJ  CAQ  CAK   180.00   0.0  0
 0RY  CONST_13  H6   CAI  CAP  CAK   180.00   0.0  0
 0RY  CONST_14  H5   CAK  CAP  CAI   180.00   0.0  0
 0RY  CONST_15  CAK  CAP  NAL  CAO     0.00   0.0  0
 0RY  CONST_16  CAI  CAP  NAL  CAO   180.00   0.0  0
 0RY  CONST_17  H4   NAL  CAP  CAK   180.00   0.0  0
 0RY  CONST_18  CAP  NAL  CAO  CAG   180.00   0.0  0
 0RY  CONST_19  CAP  NAL  CAO  OAD     0.00   0.0  0
 0RY  CONST_20  H9   NAA  CAN  CAQ     0.00   0.0  0
 0RY  CONST_21  H10  NAA  CAN  CAQ   180.00   0.0  0
 0RY  Var_01    NAA  CAN  CAQ  CAK  -155.20  30.0  2
 0RY  Var_02    CAO  CAG  CAF  CAM    -0.15   0.0  2
 0RY  Var_03    CAG  CAF  CAM  OAB    92.90  30.0  2
 0RY  Var_04    OAD  CAO  CAG  CAF     0.12  30.0  2

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
 0RY  plan-1  NAL  0.020
 0RY  plan-1  CAP  0.020
 0RY  plan-1  CAK  0.020
 0RY  plan-1  CAI  0.020
 0RY  plan-1  CAH  0.020
 0RY  plan-1  CAJ  0.020
 0RY  plan-1  CAQ  0.020
 0RY  plan-1  CAN  0.020
 0RY  plan-1  H5   0.020
 0RY  plan-1  H6   0.020
 0RY  plan-1  H7   0.020
 0RY  plan-1  H8   0.020
 0RY  plan-2  CAM  0.020
 0RY  plan-2  CAF  0.020
 0RY  plan-2  CAG  0.020
 0RY  plan-2  CAO  0.020
 0RY  plan-2  H2   0.020
 0RY  plan-2  H3   0.020
 0RY  plan-3  CAG  0.020
 0RY  plan-3  CAO  0.020
 0RY  plan-3  OAD  0.020
 0RY  plan-3  NAL  0.020
 0RY  plan-3  CAP  0.020
 0RY  plan-3  H4   0.020
 0RY  plan-4  CAQ  0.020
 0RY  plan-4  CAN  0.020
 0RY  plan-4  OAC  0.020
 0RY  plan-4  NAA  0.020
 0RY  plan-4  H9   0.020
 0RY  plan-4  H10  0.020
 0RY  plan-5  OAB  0.020
 0RY  plan-5  CAM  0.020
 0RY  plan-5  OAE  0.020
 0RY  plan-5  CAF  0.020

