# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 01:09:37 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: (2E)-2-({(2S)-2-carboxy-2-[(phenoxyacetyl)amino]ethoxy}imino)pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC\C(=N/OC[C@H](NC(=O)COc1ccccc1)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
 PL7  PL7  '(2E)-2-({(2S)-2-carboxy-2-[(phenoxyacetyl)amino]ethoxy}imino)pentanedioic acid'  ligand  42  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PL7
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
 PL7  O16   O  OC    -1  -0.633   1.5057   3.5094  -5.5374
 PL7  C9    C  C      0   0.412   2.1871   3.6640  -4.5013
 PL7  O17   O  O      0  -0.609   3.4313   3.7051  -4.4373
 PL7  C10   C  CH2    0  -0.581   1.3894   3.8249  -3.1952
 PL7  C11   C  CH2    0  -0.469   2.2346   3.9236  -1.9267
 PL7  C8    C  C      0   0.017   1.3753   4.1414  -0.7197
 PL7  C12   C  C      0   0.385   1.0195   5.5702  -0.2961
 PL7  O19   O  O      0  -0.601   0.4003   5.7179   0.7707
 PL7  O18   O  OC    -1  -0.589   1.3870   6.4616  -1.0850
 PL7  N1    N  N      0  -0.107   0.8433   3.2165  -0.0244
 PL7  O13   O  O2     0  -0.401   1.1582   1.9606  -0.4656
 PL7  C5    C  CH2    0  -0.122   0.4589   0.9887   0.2839
 PL7  C3    C  CH1    0  -0.271   0.9339  -0.3742  -0.1858
 PL7  C4    C  C      0   0.440   0.6726  -0.5595  -1.7068
 PL7  O14   O  O      0  -0.593   1.6508  -0.8543  -2.4171
 PL7  N2    N  NH1    0  -0.630   2.3332  -0.5935   0.0938
 PL7  C6    C  C      0   0.511   2.8330  -0.8582   1.3013
 PL7  O15   O  O      0  -0.494   2.1696  -0.9475   2.3232
 PL7  C7    C  CH2    0  -0.301   4.3488  -1.0004   1.3105
 PL7  O34   O  O2     0  -0.465   4.7075  -1.6614   2.4943
 PL7  C35   C  C      0   0.385   6.0175  -1.8220   2.7744
 PL7  C40   C  C1     0  -0.379   7.0563  -1.4236   1.9371
 PL7  C39   C  C1     0  -0.241   8.3742  -1.6384   2.3291
 PL7  C38   C  C1     0  -0.281   8.6696  -2.2435   3.5397
 PL7  C37   C  C1     0  -0.240   7.6254  -2.6416   4.3691
 PL7  C36   C  C1     0  -0.346   6.3097  -2.4347   3.9950
 PL7  OXT   O  OC    -1  -0.604  -0.5077  -0.4094  -2.0613
 PL7  H101  H  HCH2   0   0.226   0.7652   4.7202  -3.2838
 PL7  H102  H  HCH2   0   0.228   0.6916   2.9862  -3.1102
 PL7  H111  H  HCH2   0   0.222   2.9281   4.7564  -2.0207
 PL7  H112  H  HCH2   0   0.227   2.8301   3.0166  -1.8198
 PL7  H5C1  H  HCH2   0   0.216   0.6482   1.1160   1.3541
 PL7  H5C2  H  HCH2   0   0.210  -0.6202   1.0670   0.1227
 PL7  H3    H  HCH1   0   0.260   0.3352  -1.1210   0.3466
 PL7  H2    H  HNH1   0   0.391   2.9219  -0.6328  -0.7275
 PL7  H7C1  H  HCH2   0   0.252   4.6878  -1.5467   0.4228
 PL7  H7C2  H  HCH2   0   0.263   4.7878   0.0046   1.2613
 PL7  H40   H  H      0   0.281   6.8628  -0.9516   0.9832
 PL7  H36   H  H      0   0.262   5.4982  -2.7423   4.6431
 PL7  H39   H  H      0   0.259   9.1737  -1.3247   1.6700
 PL7  H38   H  H      0   0.253   9.6970  -2.4041   3.8372
 PL7  H37   H  H      0   0.257   7.8378  -3.1171   5.3181

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
 PL7  O16  C9    deloc     1.250  0.020  1.250
 PL7  C9   O17   deloc     1.247  0.020  1.247
 PL7  C9   C10   single    1.539  0.020  1.539
 PL7  C10  C11   single    1.528  0.020  1.528
 PL7  C10  H101  single    0.970  0.020  1.090
 PL7  C10  H102  single    0.970  0.020  1.090
 PL7  C11  C8    single    1.498  0.020  1.498
 PL7  C11  H111  single    0.970  0.020  1.090
 PL7  C11  H112  single    0.970  0.020  1.090
 PL7  C8   C12   single    1.532  0.020  1.532
 PL7  C8   N1    double    1.274  0.020  1.274
 PL7  C12  O19   deloc     1.242  0.020  1.242
 PL7  C12  O18   deloc     1.246  0.020  1.246
 PL7  N1   O13   single    1.368  0.020  1.368
 PL7  O13  C5    single    1.413  0.020  1.413
 PL7  C5   C3    single    1.518  0.020  1.518
 PL7  C5   H5C1  single    0.970  0.020  1.090
 PL7  C5   H5C2  single    0.970  0.020  1.090
 PL7  C3   C4    single    1.554  0.020  1.554
 PL7  C3   N2    single    1.444  0.020  1.444
 PL7  C3   H3    single    0.970  0.020  1.090
 PL7  C4   O14   deloc     1.244  0.020  1.244
 PL7  C4   OXT   deloc     1.241  0.020  1.241
 PL7  N2   C6    single    1.333  0.020  1.333
 PL7  N2   H2    single    0.860  0.020  1.020
 PL7  C6   O15   double    1.222  0.020  1.222
 PL7  C6   C7    single    1.522  0.020  1.522
 PL7  C7   O34   single    1.403  0.020  1.403
 PL7  C7   H7C1  single    0.970  0.020  1.090
 PL7  C7   H7C2  single    0.970  0.020  1.090
 PL7  O34  C35   single    1.349  0.020  1.349
 PL7  C35  C40   aromatic  1.392  0.020  1.392
 PL7  C35  C36   aromatic  1.397  0.020  1.397
 PL7  C40  C39   aromatic  1.392  0.020  1.392
 PL7  C40  H40   single    0.930  0.020  1.080
 PL7  C39  C38   aromatic  1.385  0.020  1.385
 PL7  C39  H39   single    0.930  0.020  1.080
 PL7  C38  C37   aromatic  1.392  0.020  1.392
 PL7  C38  H38   single    0.930  0.020  1.080
 PL7  C37  C36   aromatic  1.383  0.020  1.383
 PL7  C37  H37   single    0.930  0.020  1.080
 PL7  C36  H36   single    0.930  0.020  1.080

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
 PL7  C10   C9   O17   118.05  3.000
 PL7  C10   C9   O16   115.72  3.000
 PL7  O17   C9   O16   126.22  3.000
 PL7  H102  C10  H101  105.64  3.000
 PL7  H102  C10  C11   109.75  3.000
 PL7  H101  C10  C11   109.26  3.000
 PL7  H102  C10  C9    108.43  3.000
 PL7  H101  C10  C9    108.19  3.000
 PL7  C11   C10  C9    115.13  3.000
 PL7  H112  C11  H111  107.29  3.000
 PL7  H112  C11  C8    110.82  3.000
 PL7  H111  C11  C8    108.91  3.000
 PL7  H112  C11  C10   109.26  3.000
 PL7  H111  C11  C10   109.29  3.000
 PL7  C8    C11  C10   111.17  3.000
 PL7  N1    C8   C12   115.43  3.000
 PL7  N1    C8   C11   125.04  3.000
 PL7  C12   C8   C11   119.45  3.000
 PL7  O18   C12  O19   127.28  3.000
 PL7  O18   C12  C8    115.07  3.000
 PL7  O19   C12  C8    117.65  3.000
 PL7  O13   N1   C8    113.24  3.000
 PL7  C5    O13  N1    110.28  3.000
 PL7  H5C2  C5   H5C1  107.84  3.000
 PL7  H5C2  C5   C3    109.11  3.000
 PL7  H5C1  C5   C3    110.67  3.000
 PL7  H5C2  C5   O13   111.16  3.000
 PL7  H5C1  C5   O13   110.69  3.000
 PL7  C3    C5   O13   107.38  3.000
 PL7  H3    C3   N2    109.39  3.000
 PL7  H3    C3   C4    107.61  3.000
 PL7  N2    C3   C4    109.53  3.000
 PL7  H3    C3   C5    106.90  3.000
 PL7  N2    C3   C5    112.32  3.000
 PL7  C4    C3   C5    110.94  3.000
 PL7  OXT   C4   O14   127.81  3.000
 PL7  OXT   C4   C3    115.14  3.000
 PL7  O14   C4   C3    117.04  3.000
 PL7  H2    N2   C6    120.63  3.000
 PL7  H2    N2   C3    114.38  3.000
 PL7  C6    N2   C3    124.67  3.000
 PL7  C7    C6   O15   121.93  3.000
 PL7  C7    C6   N2    113.40  3.000
 PL7  O15   C6   N2    124.65  3.000
 PL7  H7C2  C7   H7C1  107.23  3.000
 PL7  H7C2  C7   O34   111.54  3.000
 PL7  H7C1  C7   O34   111.69  3.000
 PL7  H7C2  C7   C6    108.20  3.000
 PL7  H7C1  C7   C6    110.46  3.000
 PL7  O34   C7   C6    107.68  3.000
 PL7  C35   O34  C7    118.66  3.000
 PL7  C36   C35  C40   119.67  3.000
 PL7  C36   C35  O34   115.90  3.000
 PL7  C40   C35  O34   124.44  3.000
 PL7  H40   C40  C39   119.02  3.000
 PL7  H40   C40  C35   121.44  3.000
 PL7  C39   C40  C35   119.53  3.000
 PL7  H39   C39  C38   120.08  3.000
 PL7  H39   C39  C40   118.89  3.000
 PL7  C38   C39  C40   121.03  3.000
 PL7  H38   C38  C37   120.42  3.000
 PL7  H38   C38  C39   120.51  3.000
 PL7  C37   C38  C39   119.07  3.000
 PL7  H37   C37  C36   119.30  3.000
 PL7  H37   C37  C38   120.06  3.000
 PL7  C36   C37  C38   120.64  3.000
 PL7  H36   C36  C37   120.55  3.000
 PL7  H36   C36  C35   119.39  3.000
 PL7  C37   C36  C35   120.06  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
 PL7  CONST_01  C38   C39  C40  C35     0.00   0.0  0
 PL7  CONST_02  C38   C37  C36  C35     0.00   0.0  0
 PL7  CONST_03  C37   C36  C35  C40     0.00   0.0  0
 PL7  CONST_04  C37   C38  C39  C40     0.00   0.0  0
 PL7  CONST_05  C36   C35  C40  C39     0.00   0.0  0
 PL7  CONST_06  C36   C37  C38  C39     0.00   0.0  0
 PL7  CONST_07  C39   C40  C35  O34   180.00   0.0  0
 PL7  CONST_08  C37   C36  C35  O34   180.00   0.0  0
 PL7  CONST_09  H39   C39  C40  C35   180.00   0.0  0
 PL7  CONST_10  H37   C37  C36  C35   180.00   0.0  0
 PL7  CONST_11  H36   C36  C35  C40   180.00   0.0  0
 PL7  CONST_12  H38   C38  C39  C40   180.00   0.0  0
 PL7  CONST_13  H40   C40  C39  C38   180.00   0.0  0
 PL7  CONST_14  O15   C6   N2   C3      0.00   0.0  0
 PL7  CONST_15  C7    C6   N2   C3    180.00   0.0  0
 PL7  CONST_16  H2    N2   C6   O15   180.00   0.0  0
 PL7  Var_01    C40   C35  O34  C7     -2.83  30.0  2
 PL7  Var_02    H7C1  C7   O34  C35    63.11  30.0  2
 PL7  Var_03    C11   C10  C9   O16   176.27  30.0  3
 PL7  Var_04    C8    C11  C10  C9    177.36  30.0  3
 PL7  Var_05    C12   C8   C11  C10   -88.85  30.0  3
 PL7  Var_06    O19   C12  C8   C11  -174.10  30.0  2
 PL7  Var_07    C3    C5   O13  N1   -175.78  30.0  3
 PL7  Var_08    O34   C7   C6   N2   -162.34  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
 PL7  chir_01  C3  C5  C4  N2  negativ

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
 PL7  plan-1  O34  0.020
 PL7  plan-1  C35  0.020
 PL7  plan-1  C40  0.020
 PL7  plan-1  C39  0.020
 PL7  plan-1  C38  0.020
 PL7  plan-1  C37  0.020
 PL7  plan-1  C36  0.020
 PL7  plan-1  H40  0.020
 PL7  plan-1  H36  0.020
 PL7  plan-1  H39  0.020
 PL7  plan-1  H38  0.020
 PL7  plan-1  H37  0.020
 PL7  plan-2  C3   0.020
 PL7  plan-2  N2   0.020
 PL7  plan-2  C6   0.020
 PL7  plan-2  O15  0.020
 PL7  plan-2  C7   0.020
 PL7  plan-2  H2   0.020
 PL7  plan-3  O16  0.020
 PL7  plan-3  C9   0.020
 PL7  plan-3  O17  0.020
 PL7  plan-3  C10  0.020
 PL7  plan-4  C8   0.020
 PL7  plan-4  C12  0.020
 PL7  plan-4  O19  0.020
 PL7  plan-4  O18  0.020
 PL7  plan-5  C3   0.020
 PL7  plan-5  C4   0.020
 PL7  plan-5  O14  0.020
 PL7  plan-5  OXT  0.020
 PL7  plan-6  C11  0.020
 PL7  plan-6  C8   0.020
 PL7  plan-6  C12  0.020
 PL7  plan-6  N1   0.020
 PL7  plan-6  O13  0.020

