# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:48:31 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: (E)-N~6~-[(2E)-1-carboxy-3-(2-carboxyphenyl)prop-2-en-1-ylidene]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C(\C=C\c1ccccc1C(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
 9KP  9KP  (E)-N~6~-[(2E)-1-carboxy-3-(2-carboxyphenyl)prop-2-en-1-ylidene]-L-lysine  L-peptide  42  25  .  2019-07-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_9KP
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
 9KP  C10  C  C      0   0.128  25.1829  20.1477  64.9381
 9KP  C11  C  C      0   0.352  24.2802  19.6722  66.0805
 9KP  O13  O  O      0  -0.601  23.1717  19.2265  65.7281
 9KP  C15  C  C1     0  -0.282  23.6218  21.9693  64.3002
 9KP  C16  C  CR6    0   0.101  23.1968  23.1203  63.4962
 9KP  C17  C  CR6    0  -0.086  21.8377  23.4728  63.3866
 9KP  C18  C  CR16   0  -0.279  21.4851  24.5234  62.5394
 9KP  C19  C  CR16   0  -0.255  22.4369  25.2586  61.8520
 9KP  C20  C  CR16   0  -0.250  23.7803  24.9278  61.9785
 9KP  C22  C  C      0   0.358  20.7025  22.7787  64.1419
 9KP  N    N  NH2    0  -0.807  32.9344  17.8318  62.0725
 9KP  CA   C  CH1    0  -0.155  31.7839  18.6861  61.7851
 9KP  C    C  C      0   0.384  32.2152  20.1612  61.5953
 9KP  O    O  O      0  -0.606  33.0277  20.6269  62.4186
 9KP  CB   C  CH2    0  -0.421  30.7924  18.5645  62.9428
 9KP  CG   C  CH2    0  -0.427  29.4910  19.3343  62.7563
 9KP  CD   C  CH2    0  -0.417  28.4791  19.0349  63.8545
 9KP  CE   C  CH2    0  -0.315  27.1972  19.8417  63.7152
 9KP  NZ   N  N      0  -0.408  26.2742  19.5062  64.7815
 9KP  O12  O  OC    -1  -0.587  24.7461  19.7533  67.2289
 9KP  C14  C  C1     0  -0.320  24.7446  21.2643  64.0936
 9KP  C21  C  CR16   0  -0.319  24.1463  23.8653  62.7843
 9KP  O23  O  OC    -1  -0.585  20.8851  22.5506  65.3531
 9KP  O24  O  O      0  -0.582  19.6783  22.5414  63.4771
 9KP  H1   H  H      0   0.262  22.9475  21.6758  65.0915
 9KP  H2   H  HCR6   0   0.245  20.4390  24.7776  62.4273
 9KP  H3   H  HCR6   0   0.248  22.1337  26.0847  61.2213
 9KP  H4   H  HCR6   0   0.251  24.5382  25.4958  61.4545
 9KP  H8   H  HCH1   0   0.165  31.2581  18.3762  60.8689
 9KP  OXT  O  OC    -1  -0.615  31.6881  20.7707  60.6408
 9KP  H10  H  HCH2   0   0.205  30.5548  17.5027  63.0837
 9KP  H11  H  HCH2   0   0.203  31.2846  18.8898  63.8648
 9KP  H12  H  HCH2   0   0.211  29.6908  20.4100  62.7346
 9KP  H13  H  HCH2   0   0.204  29.0545  19.0884  61.7820
 9KP  H14  H  HCH2   0   0.208  28.2347  17.9679  63.8493
 9KP  H15  H  HCH2   0   0.207  28.9236  19.2435  64.8332
 9KP  H16  H  HCH2   0   0.211  27.4513  20.9098  63.7178
 9KP  H17  H  HCH2   0   0.216  26.7533  19.6401  62.7315
 9KP  H19  H  H      0   0.254  25.3912  21.5310  63.2647
 9KP  H20  H  HCR6   0   0.245  25.1967  23.6205  62.8811
 9KP  H    H  HNH2   0   0.329  32.6264  16.8663  62.0795
 9KP  H7   H  HNH2   0   0.332  33.6009  17.8937  61.3124

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
 9KP  C    CA   single    1.525  0.021  1.525
 9KP  C    O    deloc     1.231  0.020  1.231
 9KP  C19  C20  aromatic  1.389  0.020  1.389
 9KP  C19  C18  aromatic  1.385  0.020  1.385
 9KP  C20  C21  aromatic  1.383  0.020  1.383
 9KP  CA   N    single    1.458  0.019  1.458
 9KP  CA   CB   single    1.530  0.020  1.530
 9KP  C18  C17  aromatic  1.395  0.020  1.395
 9KP  C21  C16  aromatic  1.401  0.020  1.401
 9KP  CG   CB   single    1.523  0.020  1.523
 9KP  CG   CD   single    1.523  0.020  1.523
 9KP  CE   CD   single    1.521  0.020  1.521
 9KP  CE   NZ   single    1.450  0.020  1.450
 9KP  C17  C16  aromatic  1.408  0.020  1.408
 9KP  C17  C22  single    1.530  0.020  1.530
 9KP  C16  C15  single    1.467  0.020  1.467
 9KP  O24  C22  deloc     1.244  0.020  1.244
 9KP  C14  C15  double    1.342  0.020  1.342
 9KP  C14  C10  single    1.467  0.020  1.467
 9KP  C22  O23  deloc     1.246  0.020  1.246
 9KP  NZ   C10  double    1.276  0.020  1.276
 9KP  C10  C11  single    1.532  0.020  1.532
 9KP  C11  O13  deloc     1.246  0.020  1.246
 9KP  C11  O12  deloc     1.242  0.020  1.242
 9KP  C15  H1   single    0.930  0.020  1.080
 9KP  C18  H2   single    0.930  0.020  1.080
 9KP  C19  H3   single    0.930  0.020  1.080
 9KP  C20  H4   single    0.930  0.020  1.080
 9KP  N    H    single    0.860  0.020  0.860
 9KP  N    H7   single    0.890  0.020  1.040
 9KP  CA   H8   single    0.970  0.020  1.090
 9KP  C    OXT  deloc     1.249  0.020  1.249
 9KP  CB   H10  single    0.970  0.020  1.090
 9KP  CB   H11  single    0.970  0.020  1.090
 9KP  CG   H12  single    0.970  0.020  1.090
 9KP  CG   H13  single    0.970  0.020  1.090
 9KP  CD   H14  single    0.970  0.020  1.090
 9KP  CD   H15  single    0.970  0.020  1.090
 9KP  CE   H16  single    0.970  0.020  1.090
 9KP  CE   H17  single    0.970  0.020  1.090
 9KP  C14  H19  single    0.930  0.020  1.080
 9KP  C21  H20  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
 9KP  C14  C10  NZ   124.59  3.000
 9KP  NZ   C10  C11  116.08  3.000
 9KP  C14  C10  C11  119.31  3.000
 9KP  O12  C11  O13  128.23  3.000
 9KP  O12  C11  C10  116.64  3.000
 9KP  O13  C11  C10  115.12  3.000
 9KP  H1   C15  C14  119.49  3.000
 9KP  H1   C15  C16  115.71  3.000
 9KP  C14  C15  C16  124.77  3.000
 9KP  C21  C16  C17  118.77  3.000
 9KP  C17  C16  C15  121.24  3.000
 9KP  C21  C16  C15  119.96  3.000
 9KP  C22  C17  C18  117.00  3.000
 9KP  C22  C17  C16  124.34  3.000
 9KP  C18  C17  C16  118.67  3.000
 9KP  H2   C18  C19  119.21  3.000
 9KP  H2   C18  C17  118.95  3.000
 9KP  C19  C18  C17  121.83  3.000
 9KP  H3   C19  C20  120.37  3.000
 9KP  H3   C19  C18  120.11  3.000
 9KP  C20  C19  C18  119.53  3.000
 9KP  H4   C20  C21  120.00  3.000
 9KP  H4   C20  C19  120.54  3.000
 9KP  C21  C20  C19  119.47  3.000
 9KP  O24  C22  O23  127.25  3.000
 9KP  O23  C22  C17  117.01  3.000
 9KP  O24  C22  C17  115.70  3.000
 9KP  H7   N    H    105.27  3.000
 9KP  H7   N    CA   109.56  3.000
 9KP  H    N    CA   114.00  3.000
 9KP  H8   CA   CB   107.34  3.000
 9KP  H8   CA   C    107.41  3.000
 9KP  CB   CA   C    110.10  1.900
 9KP  H8   CA   N    112.03  3.000
 9KP  CB   CA   N    110.50  1.700
 9KP  C    CA   N    111.00  2.800
 9KP  OXT  C    O    126.67  3.000
 9KP  OXT  C    CA   116.16  3.000
 9KP  O    C    CA   120.80  1.700
 9KP  H11  CB   H10  106.07  3.000
 9KP  H11  CB   CG   109.70  3.000
 9KP  H10  CB   CG   108.65  3.000
 9KP  H11  CB   CA   108.82  3.000
 9KP  H10  CB   CA   108.34  3.000
 9KP  CG   CB   CA   114.90  3.000
 9KP  H13  CG   H12  106.01  3.000
 9KP  H13  CG   CD   109.41  3.000
 9KP  H12  CG   CD   109.20  3.000
 9KP  H13  CG   CB   109.62  3.000
 9KP  H12  CG   CB   110.07  3.000
 9KP  CD   CG   CB   112.33  3.000
 9KP  H15  CD   H14  106.30  3.000
 9KP  H15  CD   CE   108.84  3.000
 9KP  H14  CD   CE   109.18  3.000
 9KP  H15  CD   CG   109.71  3.000
 9KP  H14  CD   CG   109.66  3.000
 9KP  CE   CD   CG   112.93  3.000
 9KP  H17  CE   H16  105.93  3.000
 9KP  H17  CE   NZ   111.05  3.000
 9KP  H16  CE   NZ   111.76  3.000
 9KP  H17  CE   CD   108.99  3.000
 9KP  H16  CE   CD   108.71  3.000
 9KP  NZ   CE   CD   110.27  3.000
 9KP  CE   NZ   C10  121.24  3.000
 9KP  H19  C14  C15  119.16  3.000
 9KP  H19  C14  C10  116.69  3.000
 9KP  C15  C14  C10  124.14  3.000
 9KP  H20  C21  C20  118.85  3.000
 9KP  H20  C21  C16  119.45  3.000
 9KP  C20  C21  C16  121.69  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
 9KP  CONST_01  C19  C20  C21  C16     0.00   0.0  0
 9KP  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 9KP  CONST_03  C20  C19  C18  C17     0.00   0.0  0
 9KP  CONST_04  C20  C21  C16  C17     0.00   0.0  0
 9KP  CONST_05  C21  C20  C19  C18     0.00   0.0  0
 9KP  CONST_06  C21  C16  C17  C18     0.00   0.0  0
 9KP  CONST_07  C20  C21  C16  C15   180.00   0.0  0
 9KP  CONST_08  C18  C17  C16  C15   180.00   0.0  0
 9KP  CONST_09  C22  C17  C18  C19   180.00   0.0  0
 9KP  CONST_10  C21  C16  C17  C22   180.00   0.0  0
 9KP  CONST_11  H4   C20  C21  C16   180.00   0.0  0
 9KP  CONST_12  H2   C18  C17  C16   180.00   0.0  0
 9KP  CONST_13  H3   C19  C18  C17   180.00   0.0  0
 9KP  CONST_14  H20  C21  C16  C17   180.00   0.0  0
 9KP  Var_01    O24  C22  C17  C16  -136.96  30.0  2
 9KP  Var_02    C14  C15  C16  C17   154.01  30.0  2
 9KP  Var_03    C16  C15  C14  C10   177.52   0.0  2
 9KP  Var_04    C14  C10  NZ   CE     -0.18   0.0  2
 9KP  Var_05    CD   CE   NZ   C10   173.50  30.0  2
 9KP  Var_06    C15  C14  C10  C11     4.23  30.0  1
 9KP  Var_07    CD   CG   CB   CA    172.79  30.0  2
 9KP  Var_08    CE   CD   CG   CB    177.51  30.0  3
 9KP  Var_09    NZ   CE   CD   CG    179.62  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
 9KP  chir_01  CA  C  N  CB  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
 9KP  plan-1  C15  0.020
 9KP  plan-1  C16  0.020
 9KP  plan-1  C17  0.020
 9KP  plan-1  C18  0.020
 9KP  plan-1  C19  0.020
 9KP  plan-1  C20  0.020
 9KP  plan-1  C22  0.020
 9KP  plan-1  C21  0.020
 9KP  plan-1  H2   0.020
 9KP  plan-1  H3   0.020
 9KP  plan-1  H4   0.020
 9KP  plan-1  H20  0.020
 9KP  plan-2  C10  0.020
 9KP  plan-2  C11  0.020
 9KP  plan-2  O13  0.020
 9KP  plan-2  O12  0.020
 9KP  plan-3  C17  0.020
 9KP  plan-3  C22  0.020
 9KP  plan-3  O23  0.020
 9KP  plan-3  O24  0.020
 9KP  plan-4  CA   0.020
 9KP  plan-4  C    0.020
 9KP  plan-4  O    0.020
 9KP  plan-4  OXT  0.020
 9KP  plan-5  C10  0.020
 9KP  plan-5  C15  0.020
 9KP  plan-5  C16  0.020
 9KP  plan-5  C14  0.020
 9KP  plan-5  H1   0.020
 9KP  plan-5  H19  0.020
 9KP  plan-6  C10  0.020
 9KP  plan-6  C11  0.020
 9KP  plan-6  CE   0.020
 9KP  plan-6  NZ   0.020
 9KP  plan-6  C14  0.020

