# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 01:12:18 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (E)-N~6~-(1-carboxyethylidene)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=NCCCC[C@H](N)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
 MCL  MCL  (E)-N~6~-(1-carboxyethylidene)-L-lysine  L-peptide  29  15  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MCL
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
 MCL  N    N  NH2    0  -0.787   3.9288   1.5527   0.7079
 MCL  CA   C  CH1    0  -0.209   3.6296   0.1483   0.4683
 MCL  CB   C  CH2    0  -0.413   2.2436   0.0101  -0.1702
 MCL  CG   C  CH2    0  -0.408   1.1041   0.5198   0.7025
 MCL  CD   C  CH2    0  -0.428  -0.2512   0.4045   0.0173
 MCL  CE   C  CH2    0  -0.318  -1.4052   0.8701   0.9024
 MCL  NZ   N  N      0  -0.353  -2.6481   0.8299   0.1666
 MCL  CX1  C  C      0   0.062  -3.4580  -0.1364   0.2967
 MCL  C1   C  CH3    0  -0.741  -3.2916  -1.3251   1.2062
 MCL  CX2  C  C      0   0.370  -4.7706  -0.0689  -0.5038
 MCL  O1   O  OC    -1  -0.596  -4.8058   0.6921  -1.4839
 MCL  O2   O  O      0  -0.598  -5.6919  -0.7894  -0.0711
 MCL  C    C  C      0   0.383   4.6623  -0.6071  -0.4034
 MCL  O    O  O      0  -0.610   5.4330   0.0769  -1.1072
 MCL  OXT  O  OC    -1  -0.625   4.6165  -1.8545  -0.3530
 MCL  H    H  HNH2   0   0.333   4.7790   1.6155   1.2554
 MCL  H2   H  HNH2   0   0.321   4.1733   1.9707  -0.1832
 MCL  HA   H  HCH1   0   0.203   3.5909  -0.3516   1.4431
 MCL  HB2  H  HCH2   0   0.202   2.2393   0.5461  -1.1276
 MCL  HB3  H  HCH2   0   0.214   2.0710  -1.0429  -0.4078
 MCL  HG2  H  HCH2   0   0.202   1.0885  -0.0512   1.6376
 MCL  HG3  H  HCH2   0   0.213   1.2932   1.5597   0.9799
 MCL  HD2  H  HCH2   0   0.215  -0.2520   0.9928  -0.9055
 MCL  HD3  H  HCH2   0   0.212  -0.4311  -0.6348  -0.2780
 MCL  HE2  H  HCH2   0   0.201  -1.4107   0.2811   1.8269
 MCL  HE3  H  HCH2   0   0.223  -1.2239   1.9085   1.1961
 MCL  H11  H  HCH3   0   0.248  -3.7739  -1.1398   2.1690
 MCL  H12  H  HCH3   0   0.246  -3.7678  -2.2054   0.7816
 MCL  H13  H  HCH3   0   0.237  -2.2489  -1.5646   1.4055

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
 MCL  N    CA   single  1.458  0.019  1.458
 MCL  N    H    single  0.860  0.020  0.860
 MCL  N    H2   single  0.890  0.020  1.040
 MCL  CA   CB   single  1.530  0.020  1.530
 MCL  CA   C    single  1.525  0.021  1.525
 MCL  CA   HA   single  0.970  0.020  0.970
 MCL  CB   CG   single  1.523  0.020  1.523
 MCL  CB   HB2  single  0.970  0.020  1.090
 MCL  CB   HB3  single  0.970  0.020  1.090
 MCL  CG   CD   single  1.523  0.020  1.523
 MCL  CG   HG2  single  0.970  0.020  1.090
 MCL  CG   HG3  single  0.970  0.020  1.090
 MCL  CD   CE   single  1.527  0.020  1.527
 MCL  CD   HD2  single  0.970  0.020  1.090
 MCL  CD   HD3  single  0.970  0.020  1.090
 MCL  CE   NZ   single  1.445  0.020  1.445
 MCL  CE   HE2  single  0.970  0.020  1.090
 MCL  CE   HE3  single  0.970  0.020  1.090
 MCL  NZ   CX1  double  1.267  0.020  1.267
 MCL  CX1  C1   single  1.506  0.020  1.506
 MCL  CX1  CX2  single  1.539  0.020  1.539
 MCL  C1   H11  single  0.970  0.020  1.090
 MCL  C1   H12  single  0.970  0.020  1.090
 MCL  C1   H13  single  0.970  0.020  1.090
 MCL  CX2  O1   deloc   1.241  0.020  1.241
 MCL  CX2  O2   deloc   1.247  0.020  1.247
 MCL  C    O    deloc   1.231  0.020  1.231
 MCL  C    OXT  deloc   1.249  0.020  1.249

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
 MCL  H2   N    H    104.29  3.000
 MCL  H2   N    CA   107.61  3.000
 MCL  H    N    CA   114.00  3.000
 MCL  HA   CA   C    109.00  3.000
 MCL  HA   CA   CB   109.00  3.000
 MCL  C    CA   CB   110.10  1.900
 MCL  HA   CA   N    110.00  3.000
 MCL  C    CA   N    111.00  2.800
 MCL  CB   CA   N    110.50  1.700
 MCL  HB3  CB   HB2  106.28  3.000
 MCL  HB3  CB   CG   109.19  3.000
 MCL  HB2  CB   CG   109.48  3.000
 MCL  HB3  CB   CA   108.68  3.000
 MCL  HB2  CB   CA   108.85  3.000
 MCL  CG   CB   CA   114.07  3.000
 MCL  HG3  CG   HG2  106.36  3.000
 MCL  HG3  CG   CD   109.89  3.000
 MCL  HG2  CG   CD   109.38  3.000
 MCL  HG3  CG   CB   109.54  3.000
 MCL  HG2  CG   CB   108.98  3.000
 MCL  CD   CG   CB   112.50  3.000
 MCL  HD3  CD   HD2  106.41  3.000
 MCL  HD3  CD   CE   108.75  3.000
 MCL  HD2  CD   CE   108.93  3.000
 MCL  HD3  CD   CG   109.83  3.000
 MCL  HD2  CD   CG   109.83  3.000
 MCL  CE   CD   CG   112.87  3.000
 MCL  HE3  CE   HE2  106.53  3.000
 MCL  HE3  CE   NZ   107.79  3.000
 MCL  HE2  CE   NZ   114.22  3.000
 MCL  HE3  CE   CD   108.64  3.000
 MCL  HE2  CE   CD   109.20  3.000
 MCL  NZ   CE   CD   110.27  3.000
 MCL  CX1  NZ   CE   121.23  3.000
 MCL  CX2  CX1  C1   116.29  3.000
 MCL  CX2  CX1  NZ   117.27  3.000
 MCL  C1   CX1  NZ   126.39  3.000
 MCL  H13  C1   H12  108.25  3.000
 MCL  H13  C1   H11  107.39  3.000
 MCL  H12  C1   H11  106.75  3.000
 MCL  H13  C1   CX1  112.96  3.000
 MCL  H12  C1   CX1  110.79  3.000
 MCL  H11  C1   CX1  110.46  3.000
 MCL  O2   CX2  O1   127.39  3.000
 MCL  O2   CX2  CX1  115.11  3.000
 MCL  O1   CX2  CX1  117.50  3.000
 MCL  OXT  C    O    126.35  3.000
 MCL  OXT  C    CA   116.10  3.000
 MCL  O    C    CA   120.80  1.700

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
 MCL  Var_01  C1   CX1  NZ   CE    1.30   0.0  2
 MCL  Var_02  CD   CG   CB   CA  178.26  30.0  3
 MCL  Var_03  CE   CD   CG   CB  178.09  30.0  3
 MCL  Var_04  NZ   CE   CD   CG  175.81  30.0  3
 MCL  Var_05  O1   CX2  CX1  NZ   19.80  30.0  2
 MCL  Var_06  H11  C1   CX1  NZ   92.72  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
 MCL  chir_01  CA  N  CB  C  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
 MCL  plan-1  CX1  0.020
 MCL  plan-1  CX2  0.020
 MCL  plan-1  O1   0.020
 MCL  plan-1  O2   0.020
 MCL  plan-2  CA   0.020
 MCL  plan-2  C    0.020
 MCL  plan-2  O    0.020
 MCL  plan-2  OXT  0.020
 MCL  plan-3  CE   0.020
 MCL  plan-3  NZ   0.020
 MCL  plan-3  CX1  0.020
 MCL  plan-3  C1   0.020
 MCL  plan-3  CX2  0.020

