# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:21:49 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 4-[(2~{R})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)CC[C@H](Cc1ccc(cc1)C(O)=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
 5PU  5PU  '4-[(2~{R})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid'  ligand  33  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5PU
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
 5PU  CAG  C  CR16   0  -0.298  -1.9490   1.4618   0.6720
 5PU  CAI  C  CR16   0  -0.276  -3.1422   0.7784   0.8464
 5PU  CAS  C  CR6    0  -0.117  -3.6029  -0.1202  -0.1146
 5PU  CAO  C  C      0   0.391  -4.9171  -0.8634   0.0737
 5PU  OAE  O  O      0  -0.597  -5.5451  -0.6331   1.1260
 5PU  OAA  O  OC    -1  -0.597  -5.2581  -1.6403  -0.8399
 5PU  CAJ  C  CR16   0  -0.276  -2.8268  -0.3116  -1.2537
 5PU  CAH  C  CR16   0  -0.305  -1.6313   0.3731  -1.4280
 5PU  CAR  C  CR6    0   0.131  -1.1709   1.2727  -0.4701
 5PU  CAM  C  CH2    0  -0.511   0.1283   2.0084  -0.6407
 5PU  CAT  C  CH1    0  -0.327   1.2509   1.4805   0.2701
 5PU  CAP  C  C      0   0.402   2.4602   2.4324   0.1738
 5PU  OAF  O  OC    -1  -0.613   2.7145   3.1414   1.1685
 5PU  OAB  O  O      0  -0.615   3.0782   2.4320  -0.9113
 5PU  CAL  C  CH2    0  -0.404   1.6243   0.0482  -0.0957
 5PU  CAK  C  CH2    0  -0.587   2.7108  -0.5224   0.8118
 5PU  CAQ  C  C      0   0.528   2.9528  -1.9920   0.5610
 5PU  OAC  O  O      0  -0.483   2.0588  -2.8196   0.5130
 5PU  NAN  N  NH1    0  -0.377   4.2511  -2.2999   0.3722
 5PU  OAD  O  OH1    0  -0.547   4.6450  -3.6041   0.3295
 5PU  H1   H  HCR6   0   0.236  -1.6168   2.1584   1.4345
 5PU  H2   H  HCR6   0   0.237  -3.7302   0.9461   1.7396
 5PU  H4   H  HCR6   0   0.237  -3.1635  -1.0026  -2.0157
 5PU  H5   H  HCR6   0   0.237  -1.0468   0.2090  -2.3266
 5PU  H6   H  HCH2   0   0.233   0.4547   1.9503  -1.6821
 5PU  H7   H  HCH2   0   0.241  -0.0325   3.0683  -0.4196
 5PU  H8   H  HCH1   0   0.204   0.8809   1.4895   1.3017
 5PU  H10  H  HCH2   0   0.231   0.7399  -0.5894  -0.0369
 5PU  H11  H  HCH2   0   0.218   1.9636   0.0194  -1.1349
 5PU  H12  H  HCH2   0   0.251   3.6348   0.0498   0.7012
 5PU  H13  H  HCH2   0   0.263   2.4068  -0.4215   1.8589
 5PU  H14  H  HNH1   0   0.414   4.9927  -1.6438   0.5684
 5PU  H15  H  HOH1   0   0.477   4.7127  -3.8332  -0.6060

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
 5PU  OAE  CAO  deloc     1.247  0.020  1.247
 5PU  CAO  OAA  deloc     1.247  0.020  1.247
 5PU  CAO  CAS  single    1.521  0.020  1.521
 5PU  CAI  CAS  aromatic  1.394  0.020  1.394
 5PU  CAI  CAG  aromatic  1.386  0.020  1.386
 5PU  CAS  CAJ  aromatic  1.392  0.020  1.392
 5PU  CAG  CAR  aromatic  1.395  0.020  1.395
 5PU  CAJ  CAH  aromatic  1.389  0.020  1.389
 5PU  OAC  CAQ  double    1.219  0.020  1.219
 5PU  CAR  CAH  aromatic  1.392  0.020  1.392
 5PU  CAR  CAM  single    1.503  0.020  1.503
 5PU  CAK  CAQ  single    1.510  0.020  1.510
 5PU  CAK  CAL  single    1.526  0.020  1.526
 5PU  CAQ  NAN  single    1.348  0.020  1.348
 5PU  CAL  CAT  single    1.525  0.020  1.525
 5PU  CAT  CAM  single    1.539  0.020  1.539
 5PU  CAT  CAP  single    1.542  0.020  1.542
 5PU  NAN  OAD  single    1.363  0.020  1.363
 5PU  OAB  CAP  deloc     1.249  0.020  1.249
 5PU  CAP  OAF  deloc     1.248  0.020  1.248
 5PU  CAG  H1   single    0.930  0.020  1.080
 5PU  CAI  H2   single    0.930  0.020  1.080
 5PU  CAJ  H4   single    0.930  0.020  1.080
 5PU  CAH  H5   single    0.930  0.020  1.080
 5PU  CAM  H6   single    0.970  0.020  1.090
 5PU  CAM  H7   single    0.970  0.020  1.090
 5PU  CAT  H8   single    0.970  0.020  1.090
 5PU  CAL  H10  single    0.970  0.020  1.090
 5PU  CAL  H11  single    0.970  0.020  1.090
 5PU  CAK  H12  single    0.970  0.020  1.090
 5PU  CAK  H13  single    0.970  0.020  1.090
 5PU  NAN  H14  single    0.890  0.020  1.040
 5PU  OAD  H15  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
 5PU  H1   CAG  CAR  119.46  3.000
 5PU  H1   CAG  CAI  119.46  3.000
 5PU  CAR  CAG  CAI  121.09  3.000
 5PU  H2   CAI  CAS  119.30  3.000
 5PU  H2   CAI  CAG  119.67  3.000
 5PU  CAS  CAI  CAG  121.04  3.000
 5PU  CAJ  CAS  CAO  121.06  3.000
 5PU  CAJ  CAS  CAI  117.95  3.000
 5PU  CAO  CAS  CAI  120.99  3.000
 5PU  OAA  CAO  OAE  126.56  3.000
 5PU  OAA  CAO  CAS  116.74  3.000
 5PU  OAE  CAO  CAS  116.70  3.000
 5PU  H4   CAJ  CAH  119.62  3.000
 5PU  H4   CAJ  CAS  119.38  3.000
 5PU  CAH  CAJ  CAS  121.00  3.000
 5PU  H5   CAH  CAR  119.31  3.000
 5PU  H5   CAH  CAJ  119.57  3.000
 5PU  CAR  CAH  CAJ  121.12  3.000
 5PU  CAM  CAR  CAH  121.61  3.000
 5PU  CAM  CAR  CAG  120.58  3.000
 5PU  CAH  CAR  CAG  117.81  3.000
 5PU  H7   CAM  H6   106.73  3.000
 5PU  H7   CAM  CAT  108.64  3.000
 5PU  H6   CAM  CAT  109.14  3.000
 5PU  H7   CAM  CAR  108.92  3.000
 5PU  H6   CAM  CAR  109.90  3.000
 5PU  CAT  CAM  CAR  113.30  3.000
 5PU  H8   CAT  CAL  108.43  3.000
 5PU  H8   CAT  CAP  108.57  3.000
 5PU  CAL  CAT  CAP  111.89  3.000
 5PU  H8   CAT  CAM  107.94  3.000
 5PU  CAP  CAT  CAM  108.86  3.000
 5PU  CAL  CAT  CAM  111.03  3.000
 5PU  OAB  CAP  OAF  126.30  3.000
 5PU  OAF  CAP  CAT  117.44  3.000
 5PU  OAB  CAP  CAT  116.24  3.000
 5PU  H11  CAL  H10  106.68  3.000
 5PU  H11  CAL  CAK  109.53  3.000
 5PU  H10  CAL  CAK  109.05  3.000
 5PU  H11  CAL  CAT  109.19  3.000
 5PU  H10  CAL  CAT  109.71  3.000
 5PU  CAK  CAL  CAT  112.51  3.000
 5PU  H13  CAK  H12  106.46  3.000
 5PU  H13  CAK  CAQ  107.03  3.000
 5PU  H12  CAK  CAQ  110.93  3.000
 5PU  H13  CAK  CAL  109.67  3.000
 5PU  H12  CAK  CAL  110.25  3.000
 5PU  CAQ  CAK  CAL  112.28  3.000
 5PU  NAN  CAQ  OAC  123.08  3.000
 5PU  NAN  CAQ  CAK  113.58  3.000
 5PU  OAC  CAQ  CAK  123.34  3.000
 5PU  H14  NAN  OAD  114.57  3.000
 5PU  H14  NAN  CAQ  122.14  3.000
 5PU  OAD  NAN  CAQ  120.10  3.000
 5PU  H15  OAD  NAN  106.12  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
 5PU  CONST_01  CAJ  CAS  CAI  CAG    0.00   0.0  0
 5PU  CONST_02  CAJ  CAH  CAR  CAG    0.00   0.0  0
 5PU  CONST_03  CAH  CAJ  CAS  CAI    0.00   0.0  0
 5PU  CONST_04  CAH  CAR  CAG  CAI    0.00   0.0  0
 5PU  CONST_05  CAR  CAG  CAI  CAS    0.00   0.0  0
 5PU  CONST_06  CAR  CAH  CAJ  CAS    0.00   0.0  0
 5PU  CONST_07  CAO  CAS  CAI  CAG  180.00   0.0  0
 5PU  CONST_08  CAM  CAR  CAG  CAI  180.00   0.0  0
 5PU  CONST_09  CAH  CAJ  CAS  CAO  180.00   0.0  0
 5PU  CONST_10  CAM  CAR  CAH  CAJ  180.00   0.0  0
 5PU  CONST_11  H5   CAH  CAR  CAG  180.00   0.0  0
 5PU  CONST_12  H4   CAJ  CAS  CAI  180.00   0.0  0
 5PU  CONST_13  H1   CAG  CAI  CAS  180.00   0.0  0
 5PU  CONST_14  H2   CAI  CAS  CAJ  180.00   0.0  0
 5PU  CONST_15  OAD  NAN  CAQ  CAK  180.00   0.0  0
 5PU  CONST_16  OAD  NAN  CAQ  OAC    0.00   0.0  0
 5PU  CONST_17  H14  NAN  CAQ  CAK    0.00   0.0  0
 5PU  Var_01    CAT  CAM  CAR  CAG   72.90  30.0  2
 5PU  Var_02    OAE  CAO  CAS  CAI   -0.48  30.0  3
 5PU  Var_03    CAQ  CAK  CAL  CAT  172.73  30.0  1
 5PU  Var_04    OAC  CAQ  CAK  CAL  -49.71  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5PU  chir_01  CAT  CAL  CAM  CAP  positiv

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
 5PU  plan-1  CAG  0.020
 5PU  plan-1  CAI  0.020
 5PU  plan-1  CAS  0.020
 5PU  plan-1  CAO  0.020
 5PU  plan-1  CAJ  0.020
 5PU  plan-1  CAH  0.020
 5PU  plan-1  CAR  0.020
 5PU  plan-1  CAM  0.020
 5PU  plan-1  H1   0.020
 5PU  plan-1  H2   0.020
 5PU  plan-1  H4   0.020
 5PU  plan-1  H5   0.020
 5PU  plan-2  CAK  0.020
 5PU  plan-2  CAQ  0.020
 5PU  plan-2  OAC  0.020
 5PU  plan-2  NAN  0.020
 5PU  plan-2  OAD  0.020
 5PU  plan-2  H14  0.020
 5PU  plan-3  CAS  0.020
 5PU  plan-3  CAO  0.020
 5PU  plan-3  OAE  0.020
 5PU  plan-3  OAA  0.020
 5PU  plan-4  CAT  0.020
 5PU  plan-4  CAP  0.020
 5PU  plan-4  OAF  0.020
 5PU  plan-4  OAB  0.020

