# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:44:15 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-({2-[(3-carboxypropanoyl)amino]ethyl}amino)-5-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC(=O)NCCNC(=O)CCC(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
 XLX  XLX  '5-({2-[(3-carboxypropanoyl)amino]ethyl}amino)-5-oxopentanoic acid'  ligand  35  19  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XLX
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
 XLX  O13  O  O      0  -0.507   2.0088  -0.5788   1.2392
 XLX  C12  C  C      0   0.551   2.2194   0.1291   0.2622
 XLX  C11  C  CH2    0  -0.563   3.5167   0.8845   0.0858
 XLX  N8   N  NH1    0  -0.632   1.3227   0.2741  -0.7295
 XLX  C7   C  CH2    0  -0.329   0.0251  -0.3535  -0.7254
 XLX  C6   C  CH2    0  -0.249  -1.0033   0.4572   0.0559
 XLX  N1   N  NH1    0  -0.641  -2.2984  -0.1786  -0.0332
 XLX  C2   C  C      0   0.545  -3.3432   0.1804   0.7313
 XLX  O15  O  O      0  -0.514  -3.2486   1.0368   1.6036
 XLX  C3   C  CH2    0  -0.556  -4.6469  -0.5267   0.4439
 XLX  H1   H  HCH2   0   0.240   3.5224   1.4404  -0.8554
 XLX  H2   H  HCH2   0   0.255   3.5768   1.6281   0.8866
 XLX  H4   H  HNH1   0   0.403   1.5394   0.8960  -1.4905
 XLX  H5   H  HCH2   0   0.260  -0.2946  -0.4612  -1.7633
 XLX  H6   H  HCH2   0   0.253   0.1065  -1.3568  -0.3054
 XLX  H7   H  HCH2   0   0.242  -0.6986   0.5254   1.1010
 XLX  H8   H  HCH2   0   0.234  -1.0421   1.4772  -0.3394
 XLX  H9   H  HNH1   0   0.399  -2.4557  -0.8323  -0.7831
 XLX  H10  H  HCH2   0   0.236  -4.5136  -1.3145  -0.3007
 XLX  H11  H  HCH2   0   0.252  -4.9759  -1.0148   1.3629
 XLX  C1   C  CH2    0  -0.576  -5.7192   0.4546  -0.0181
 XLX  C4   C  C      0   0.414  -7.1153  -0.1695  -0.1983
 XLX  O2   O  O      0  -0.610  -7.3680  -1.2045   0.4503
 XLX  O1   O  OC    -1  -0.623  -7.8950   0.4371  -0.9599
 XLX  C9   C  CH2    0  -0.408   4.7325  -0.0393   0.1553
 XLX  C10  C  CH2    0  -0.584   6.0354   0.7311   0.0280
 XLX  C13  C  C      0   0.412   7.3188  -0.1194   0.0759
 XLX  O4   O  OC    -1  -0.632   8.3905   0.5057  -0.0678
 XLX  O3   O  O      0  -0.608   7.1970  -1.3472   0.2529
 XLX  H3   H  HCH2   0   0.237  -5.8076   1.2620   0.7169
 XLX  H12  H  HCH2   0   0.222  -5.4132   0.9342  -0.9516
 XLX  H14  H  HCH2   0   0.218   4.7155  -0.5896   1.0974
 XLX  H15  H  HCH2   0   0.217   4.6631  -0.7865  -0.6394
 XLX  H16  H  HCH2   0   0.219   6.0396   1.3056  -0.9057
 XLX  H17  H  HCH2   0   0.222   6.0957   1.4844   0.8228

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
 XLX  O13  C12  double  1.225  0.020  1.225
 XLX  C12  C11  single  1.512  0.020  1.512
 XLX  C11  H1   single  0.970  0.020  1.090
 XLX  C11  H2   single  0.970  0.020  1.090
 XLX  C11  C9   single  1.529  0.020  1.529
 XLX  N8   C7   single  1.441  0.020  1.441
 XLX  N8   C12  single  1.345  0.020  1.345
 XLX  N8   H4   single  0.860  0.020  1.020
 XLX  C7   C6   single  1.525  0.020  1.525
 XLX  C7   H5   single  0.970  0.020  1.090
 XLX  C7   H6   single  0.970  0.020  1.090
 XLX  C6   H7   single  0.970  0.020  1.090
 XLX  C6   H8   single  0.970  0.020  1.090
 XLX  N1   C2   single  1.343  0.020  1.343
 XLX  N1   C6   single  1.445  0.020  1.445
 XLX  N1   H9   single  0.860  0.020  1.020
 XLX  C2   C3   single  1.511  0.020  1.511
 XLX  O15  C2   double  1.226  0.020  1.226
 XLX  C3   H10  single  0.970  0.020  1.090
 XLX  C3   H11  single  0.970  0.020  1.090
 XLX  C3   C1   single  1.525  0.020  1.525
 XLX  C1   C4   single  1.540  0.020  1.540
 XLX  C1   H3   single  0.970  0.020  1.090
 XLX  C1   H12  single  0.970  0.020  1.090
 XLX  C4   O2   deloc   1.247  0.020  1.247
 XLX  C4   O1   deloc   1.247  0.020  1.247
 XLX  C9   C10  single  1.519  0.020  1.519
 XLX  C9   H14  single  0.970  0.020  1.090
 XLX  C9   H15  single  0.970  0.020  1.090
 XLX  C10  C13  single  1.540  0.020  1.540
 XLX  C10  H16  single  0.970  0.020  1.090
 XLX  C10  H17  single  0.970  0.020  1.090
 XLX  C13  O4   deloc   1.249  0.020  1.249
 XLX  C13  O3   deloc   1.246  0.020  1.246

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
 XLX  N8   C12  C11  115.62  3.000
 XLX  N8   C12  O13  122.41  3.000
 XLX  C11  C12  O13  121.97  3.000
 XLX  C9   C11  H2   109.49  3.000
 XLX  C9   C11  H1   110.02  3.000
 XLX  H2   C11  H1   106.51  3.000
 XLX  C9   C11  C12  112.04  3.000
 XLX  H2   C11  C12  107.54  3.000
 XLX  H1   C11  C12  111.04  3.000
 XLX  H4   N8   C7   117.71  3.000
 XLX  H4   N8   C12  118.73  3.000
 XLX  C7   N8   C12  123.45  3.000
 XLX  H6   C7   H5   107.30  3.000
 XLX  H6   C7   C6   110.01  3.000
 XLX  H5   C7   C6   110.01  3.000
 XLX  H6   C7   N8   109.54  3.000
 XLX  H5   C7   N8   107.69  3.000
 XLX  C6   C7   N8   112.15  3.000
 XLX  H8   C6   H7   107.32  3.000
 XLX  H8   C6   N1   110.85  3.000
 XLX  H7   C6   N1   109.68  3.000
 XLX  N1   C6   C7   109.80  3.000
 XLX  H8   C6   C7   109.53  3.000
 XLX  H7   C6   C7   109.62  3.000
 XLX  H9   N1   C2   118.40  3.000
 XLX  H9   N1   C6   118.12  3.000
 XLX  C2   N1   C6   122.97  3.000
 XLX  C3   C2   O15  121.93  3.000
 XLX  O15  C2   N1   122.11  3.000
 XLX  C3   C2   N1   115.96  3.000
 XLX  C1   C3   H11  109.32  3.000
 XLX  C1   C3   H10  110.08  3.000
 XLX  H11  C3   H10  106.76  3.000
 XLX  C1   C3   C2   111.30  3.000
 XLX  H11  C3   C2   108.02  3.000
 XLX  H10  C3   C2   111.22  3.000
 XLX  H12  C1   H3   105.80  3.000
 XLX  H12  C1   C4   109.37  3.000
 XLX  H3   C1   C4   107.70  3.000
 XLX  H12  C1   C3   110.13  3.000
 XLX  H3   C1   C3   109.13  3.000
 XLX  C4   C1   C3   114.34  3.000
 XLX  O1   C4   O2   126.46  3.000
 XLX  O1   C4   C1   116.17  3.000
 XLX  O2   C4   C1   117.34  3.000
 XLX  H15  C9   H14  106.38  3.000
 XLX  H15  C9   C10  109.89  3.000
 XLX  H14  C9   C10  109.97  3.000
 XLX  H15  C9   C11  109.24  3.000
 XLX  H14  C9   C11  109.37  3.000
 XLX  C10  C9   C11  111.84  3.000
 XLX  H17  C10  H16  104.90  3.000
 XLX  H17  C10  C13  108.12  3.000
 XLX  H16  C10  C13  108.22  3.000
 XLX  H17  C10  C9   109.56  3.000
 XLX  H16  C10  C9   109.90  3.000
 XLX  C13  C10  C9   115.60  3.000
 XLX  O3   C13  O4   126.38  3.000
 XLX  O3   C13  C10  117.83  3.000
 XLX  O4   C13  C10  115.79  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
 XLX  CONST_01  C7   N8   C12  O13     0.00   0.0  0
 XLX  CONST_02  C7   N8   C12  C11   180.00   0.0  0
 XLX  CONST_03  C3   C2   N1   C6    180.00   0.0  0
 XLX  CONST_04  O15  C2   N1   C6      0.00   0.0  0
 XLX  CONST_05  H4   N8   C12  O13   180.00   0.0  0
 XLX  CONST_06  H9   N1   C2   O15   180.00   0.0  0
 XLX  Var_01    C9   C11  C12  O13    55.31  30.0  3
 XLX  Var_02    C10  C9   C11  C12  -177.93  30.0  3
 XLX  Var_03    C6   C7   N8   C12    84.16  30.0  3
 XLX  Var_04    C13  C10  C9   C11  -179.54  30.0  3
 XLX  Var_05    N1   C6   C7   N8    176.92  30.0  3
 XLX  Var_06    C2   N1   C6   C7    168.57  30.0  1
 XLX  Var_07    C1   C3   C2   N1   -117.54  30.0  3
 XLX  Var_08    C4   C1   C3   C2   -174.30  30.0  3
 XLX  Var_09    O2   C4   C1   C3     24.22  30.0  3
 XLX  Var_10    O4   C13  C10  C9    177.98  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
 XLX  plan-1  O13  0.020
 XLX  plan-1  C12  0.020
 XLX  plan-1  C11  0.020
 XLX  plan-1  N8   0.020
 XLX  plan-1  C7   0.020
 XLX  plan-1  H4   0.020
 XLX  plan-2  C6   0.020
 XLX  plan-2  N1   0.020
 XLX  plan-2  C2   0.020
 XLX  plan-2  O15  0.020
 XLX  plan-2  C3   0.020
 XLX  plan-2  H9   0.020
 XLX  plan-3  C1   0.020
 XLX  plan-3  C4   0.020
 XLX  plan-3  O2   0.020
 XLX  plan-3  O1   0.020
 XLX  plan-4  C10  0.020
 XLX  plan-4  C13  0.020
 XLX  plan-4  O4   0.020
 XLX  plan-4  O3   0.020

