# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:55:41 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CNC(=O)C[C@@](O)(CC(=O)NCCNC(=O)CCC(=O)C(O)=O)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
 SE8  SE8  '5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoic acid'  ligand  52  31  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SE8
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
 SE8  C1    C  C      0   0.391    7.5687  -2.5194  -2.3385
 SE8  C2    C  CH1    0  -0.256    6.6470  -2.1348  -1.1535
 SE8  C3    C  CH2    0  -0.248    6.1593  -0.6983  -1.3509
 SE8  N4    N  NH1    0  -0.628    5.3279  -0.3088  -0.2369
 SE8  C5    C  C      0   0.547    4.4525   0.7031  -0.2672
 SE8  C6    C  CH2    0  -0.583    3.7151   0.9578   1.0287
 SE8  C7    C  CT     0   0.068    2.2180   0.6381   0.9085
 SE8  C8    C  CH2    0  -0.539    1.5867   0.7999   2.3044
 SE8  C9    C  C      0   0.514    0.0709   0.8230   2.3365
 SE8  N10   N  NH1    0  -0.622   -0.5434  -0.0962   1.5710
 SE8  C11   C  CH2    0  -0.302   -1.9672  -0.0959   1.3432
 SE8  C12   C  CH2    0  -0.295   -2.3614   0.9004   0.2500
 SE8  N13   N  NH1    0  -0.637   -3.7883   0.9419   0.0348
 SE8  C14   C  C      0   0.566   -4.4461   0.0811  -0.7604
 SE8  C15   C  CH2    0  -0.579   -5.9328   0.3408  -0.8875
 SE8  C16   C  CH2    0  -0.544   -6.7271  -0.9335  -1.1083
 SE8  C17   C  C      0   0.237   -8.1933  -0.6925  -1.3456
 SE8  C18   C  C      0   0.348   -9.0993  -1.9444  -1.5473
 SE8  O19   O  OC    -1  -0.618    7.0402  -2.4731  -3.4681
 SE8  O20   O  O      0  -0.600    8.7471  -2.8246  -2.0768
 SE8  N21   N  NH2    0  -0.794    7.2232  -2.2722   0.1748
 SE8  O22   O  O      0  -0.509    4.2478   1.3789  -1.2696
 SE8  C23   C  C      0   0.449    1.5231   1.6189  -0.0781
 SE8  O24   O  O      0  -0.592    1.0099   1.1467  -1.1020
 SE8  O25   O  OC    -1  -0.614    1.5285   2.8078   0.2953
 SE8  O26   O  OH1    0  -0.667    2.0480  -0.6820   0.4234
 SE8  O27   O  O      0  -0.510   -0.5435   1.6073   3.0500
 SE8  O28   O  O      0  -0.505   -3.8821  -0.8207  -1.3664
 SE8  O29   O  O      0  -0.399   -8.6650   0.4202  -1.3844
 SE8  O30   O  O      0  -0.578   -8.5259  -3.0415  -1.4395
 SE8  O31   O  OC    -1  -0.583  -10.2902  -1.7091  -1.7910
 SE8  H2    H  HCH1   0   0.233    5.7648  -2.7837  -1.1923
 SE8  H3    H  HCH2   0   0.220    7.0184  -0.0208  -1.4404
 SE8  H3A   H  HCH2   0   0.239    5.5943  -0.6281  -2.2782
 SE8  HN4   H  HNH1   0   0.387    5.5366  -0.7744   0.6345
 SE8  H6    H  HCH2   0   0.248    4.1481   0.3707   1.8455
 SE8  H6A   H  HCH2   0   0.266    3.8352   2.0084   1.2955
 SE8  H8    H  HCH2   0   0.263    1.9375  -0.0082   2.9577
 SE8  H8A   H  HCH2   0   0.253    1.9283   1.7302   2.7542
 SE8  HN10  H  HNH1   0   0.401    0.0357  -0.6435   0.9496
 SE8  H11   H  HCH2   0   0.250   -2.2677  -1.1021   1.0511
 SE8  H11A  H  HCH2   0   0.240   -2.4869   0.1450   2.2704
 SE8  H12   H  HCH2   0   0.252   -2.0341   1.9006   0.5326
 SE8  H12A  H  HCH2   0   0.244   -1.8508   0.6469  -0.6788
 SE8  HN13  H  HNH1   0   0.401   -4.3168   1.6406   0.5302
 SE8  H15   H  HCH2   0   0.254   -6.3004   0.8746  -0.0089
 SE8  H15A  H  HCH2   0   0.274   -6.0694   1.0214  -1.7337
 SE8  H16   H  HCH2   0   0.267   -6.3329  -1.4944  -1.9597
 SE8  H16A  H  HCH2   0   0.267   -6.6254  -1.6117  -0.2565
 SE8  HN21  H  HNH2   0   0.346    7.2989  -3.2548   0.4044
 SE8  HN2A  H  HNH2   0   0.333    8.1800  -1.9385   0.1450
 SE8  HO26  H  HOH1   0   0.442    2.5024  -1.2864   1.0214

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
 SE8  C2   C1    single  1.550  0.020  1.550
 SE8  C1   O20   deloc   1.245  0.020  1.245
 SE8  C1   O19   deloc   1.248  0.020  1.248
 SE8  C3   C2    single  1.530  0.020  1.530
 SE8  N21  C2    single  1.454  0.020  1.454
 SE8  C2   H2    single  0.970  0.020  1.090
 SE8  N4   C3    single  1.444  0.020  1.444
 SE8  C3   H3    single  0.970  0.020  1.090
 SE8  C3   H3A   single  0.970  0.020  1.090
 SE8  C5   N4    single  1.338  0.020  1.338
 SE8  N4   HN4   single  0.860  0.020  1.020
 SE8  O22  C5    double  1.226  0.020  1.226
 SE8  C6   C5    single  1.513  0.020  1.513
 SE8  C6   C7    single  1.536  0.020  1.536
 SE8  C6   H6    single  0.970  0.020  1.090
 SE8  C6   H6A   single  0.970  0.020  1.090
 SE8  C8   C7    single  1.540  0.020  1.540
 SE8  C23  C7    single  1.555  0.020  1.555
 SE8  C7   O26   single  1.417  0.020  1.417
 SE8  C8   C9    single  1.516  0.020  1.516
 SE8  C8   H8    single  0.970  0.020  1.090
 SE8  C8   H8A   single  0.970  0.020  1.090
 SE8  O27  C9    double  1.225  0.020  1.225
 SE8  C9   N10   single  1.345  0.020  1.345
 SE8  N10  C11   single  1.442  0.020  1.442
 SE8  N10  HN10  single  0.860  0.020  1.020
 SE8  C11  C12   single  1.531  0.020  1.531
 SE8  C11  H11   single  0.970  0.020  1.090
 SE8  C11  H11A  single  0.970  0.020  1.090
 SE8  C12  N13   single  1.444  0.020  1.444
 SE8  C12  H12   single  0.970  0.020  1.090
 SE8  C12  H12A  single  0.970  0.020  1.090
 SE8  N13  C14   single  1.344  0.020  1.344
 SE8  N13  HN13  single  0.860  0.020  1.020
 SE8  C14  O28   double  1.224  0.020  1.224
 SE8  C14  C15   single  1.515  0.020  1.515
 SE8  C16  C15   single  1.518  0.020  1.518
 SE8  C15  H15   single  0.970  0.020  1.090
 SE8  C15  H15A  single  0.970  0.020  1.090
 SE8  C17  C16   single  1.505  0.020  1.505
 SE8  C16  H16   single  0.970  0.020  1.090
 SE8  C16  H16A  single  0.970  0.020  1.090
 SE8  O29  C17   double  1.209  0.020  1.209
 SE8  C17  C18   single  1.558  0.020  1.558
 SE8  O30  C18   deloc   1.243  0.020  1.243
 SE8  C18  O31   deloc   1.238  0.020  1.238
 SE8  N21  HN21  single  0.890  0.020  1.040
 SE8  N21  HN2A  single  0.890  0.020  1.040
 SE8  O24  C23   deloc   1.239  0.020  1.239
 SE8  C23  O25   deloc   1.246  0.020  1.246
 SE8  O26  HO26  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
 SE8  O20   C1   O19   126.88  3.000
 SE8  O19   C1   C2    115.54  3.000
 SE8  O20   C1   C2    117.58  3.000
 SE8  H2    C2   N21   107.18  3.000
 SE8  H2    C2   C3    107.14  3.000
 SE8  N21   C2   C3    109.44  3.000
 SE8  H2    C2   C1    107.75  3.000
 SE8  N21   C2   C1    116.06  3.000
 SE8  C3    C2   C1    108.90  3.000
 SE8  H3A   C3   H3    107.28  3.000
 SE8  H3A   C3   N4    109.95  3.000
 SE8  H3    C3   N4    110.31  3.000
 SE8  H3A   C3   C2    109.64  3.000
 SE8  H3    C3   C2    109.91  3.000
 SE8  N4    C3   C2    109.72  3.000
 SE8  HN4   N4   C5    120.22  3.000
 SE8  HN4   N4   C3    114.99  3.000
 SE8  C5    N4   C3    124.28  3.000
 SE8  O22   C5   C6    121.75  3.000
 SE8  C6    C5   N4    115.26  3.000
 SE8  O22   C5   N4    122.99  3.000
 SE8  H6A   C6   H6    106.88  3.000
 SE8  H6A   C6   C7    109.09  3.000
 SE8  H6    C6   C7    109.40  3.000
 SE8  H6A   C6   C5    108.55  3.000
 SE8  H6    C6   C5    110.85  3.000
 SE8  C7    C6   C5    111.91  3.000
 SE8  O26   C7   C23   108.47  3.000
 SE8  O26   C7   C8    111.04  3.000
 SE8  C23   C7   C8    108.99  3.000
 SE8  O26   C7   C6    109.74  3.000
 SE8  C23   C7   C6    110.73  3.000
 SE8  C8    C7   C6    107.86  3.000
 SE8  H8A   C8   H8    106.45  3.000
 SE8  H8A   C8   C9    106.97  3.000
 SE8  H8    C8   C9    108.56  3.000
 SE8  H8A   C8   C7    109.61  3.000
 SE8  H8    C8   C7    109.34  3.000
 SE8  C9    C8   C7    115.50  3.000
 SE8  O27   C9   N10   122.68  3.000
 SE8  N10   C9   C8    115.73  3.000
 SE8  O27   C9   C8    121.56  3.000
 SE8  HN10  N10  C11   117.96  3.000
 SE8  HN10  N10  C9    117.29  3.000
 SE8  C11   N10  C9    122.74  3.000
 SE8  H11A  C11  H11   107.49  3.000
 SE8  H11A  C11  C12   109.93  3.000
 SE8  H11   C11  C12   109.78  3.000
 SE8  H11A  C11  N10   109.66  3.000
 SE8  H11   C11  N10   108.33  3.000
 SE8  C12   C11  N10   111.55  3.000
 SE8  H12A  C12  H12   107.08  3.000
 SE8  H12A  C12  N13   110.04  3.000
 SE8  H12   C12  N13   108.01  3.000
 SE8  H12A  C12  C11   109.67  3.000
 SE8  H12   C12  C11   109.57  3.000
 SE8  N13   C12  C11   112.32  3.000
 SE8  HN13  N13  C14   118.62  3.000
 SE8  HN13  N13  C12   117.75  3.000
 SE8  C14   N13  C12   123.61  3.000
 SE8  O28   C14  C15   122.48  3.000
 SE8  C15   C14  N13   114.85  3.000
 SE8  O28   C14  N13   122.63  3.000
 SE8  H15A  C15  H15   106.03  3.000
 SE8  H15A  C15  C16   110.14  3.000
 SE8  H15   C15  C16   110.57  3.000
 SE8  H15A  C15  C14   107.10  3.000
 SE8  H15   C15  C14   110.29  3.000
 SE8  C16   C15  C14   112.45  3.000
 SE8  H16A  C16  H16   104.77  3.000
 SE8  H16A  C16  C17   108.23  3.000
 SE8  H16   C16  C17   108.10  3.000
 SE8  H16A  C16  C15   111.02  3.000
 SE8  H16   C16  C15   110.81  3.000
 SE8  C17   C16  C15   113.48  3.000
 SE8  O29   C17  C18   120.55  3.000
 SE8  C18   C17  C16   117.27  3.000
 SE8  O29   C17  C16   122.18  3.000
 SE8  O31   C18  O30   128.96  3.000
 SE8  O31   C18  C17   115.59  3.000
 SE8  O30   C18  C17   115.45  3.000
 SE8  HN2A  N21  HN21  104.82  3.000
 SE8  HN2A  N21  C2    108.42  3.000
 SE8  HN21  N21  C2    109.18  3.000
 SE8  O25   C23  O24   127.81  3.000
 SE8  O25   C23  C7    114.19  3.000
 SE8  O24   C23  C7    117.97  3.000
 SE8  HO26  O26  C7    108.37  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
 SE8  CONST_01  O22   C5   N4   C3      0.00   0.0  0
 SE8  CONST_02  C6    C5   N4   C3    180.00   0.0  0
 SE8  CONST_03  C11   N10  C9   C8    180.00   0.0  0
 SE8  CONST_04  O27   C9   N10  C11     0.00   0.0  0
 SE8  CONST_05  O28   C14  N13  C12     0.00   0.0  0
 SE8  CONST_06  C15   C14  N13  C12   180.00   0.0  0
 SE8  CONST_07  HN4   N4   C5   C6      0.00   0.0  0
 SE8  CONST_08  HN10  N10  C9   C8      0.00   0.0  0
 SE8  CONST_09  HN13  N13  C14  C15     0.00   0.0  0
 SE8  Var_01    C5    N4   C3   C2   -160.10  30.0  2
 SE8  Var_02    C7    C6   C5   N4   -112.62  30.0  2
 SE8  Var_03    O27   C9   C8   C7   -138.39  30.0  3
 SE8  Var_04    C12   C11  N10  C9     81.22  30.0  3
 SE8  Var_05    N13   C12  C11  N10  -178.35  30.0  3
 SE8  Var_06    C14   N13  C12  C11   -84.15  30.0  3
 SE8  Var_07    C16   C15  C14  N13  -149.10  30.0  3
 SE8  Var_08    C17   C16  C15  C14  -175.47  30.0  2
 SE8  Var_09    O29   C17  C16  C15     1.67  30.0  2
 SE8  Var_10    O30   C18  C17  C16     2.74  30.0  2

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
 SE8  chir_01  C2  C1  C3  N21  positiv
 SE8  chir_02  C7  C6  C8  C23  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
 SE8  plan-1  C3    0.020
 SE8  plan-1  N4    0.020
 SE8  plan-1  C5    0.020
 SE8  plan-1  C6    0.020
 SE8  plan-1  O22   0.020
 SE8  plan-1  HN4   0.020
 SE8  plan-2  C7    0.020
 SE8  plan-2  C23   0.020
 SE8  plan-2  O24   0.020
 SE8  plan-2  O25   0.020
 SE8  plan-3  C8    0.020
 SE8  plan-3  C9    0.020
 SE8  plan-3  N10   0.020
 SE8  plan-3  C11   0.020
 SE8  plan-3  O27   0.020
 SE8  plan-3  HN10  0.020
 SE8  plan-4  C12   0.020
 SE8  plan-4  N13   0.020
 SE8  plan-4  C14   0.020
 SE8  plan-4  C15   0.020
 SE8  plan-4  O28   0.020
 SE8  plan-4  HN13  0.020
 SE8  plan-5  C16   0.020
 SE8  plan-5  C17   0.020
 SE8  plan-5  C18   0.020
 SE8  plan-5  O29   0.020
 SE8  plan-6  C1    0.020
 SE8  plan-6  C2    0.020
 SE8  plan-6  O19   0.020
 SE8  plan-6  O20   0.020
 SE8  plan-7  C17   0.020
 SE8  plan-7  C18   0.020
 SE8  plan-7  O30   0.020
 SE8  plan-7  O31   0.020

