# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 20:19:29 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: N~6~,N~6~-dimethyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCC[C@H](N)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
 MLY  MLY  N~6~,N~6~-dimethyl-L-lysine  L-peptide  29  12  .  2009-04-28  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_MLY
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
 MLY  N     N  NH2    0  -0.816  30.2920  32.1769  86.9627
 MLY  CA    C  CH1    0  -0.224  30.1517  31.8119  85.5590
 MLY  CB    C  CH2    0  -0.401  28.9565  32.5417  84.9459
 MLY  CG    C  CH2    0  -0.428  27.6299  32.2819  85.6557
 MLY  CD    C  CH2    0  -0.449  27.2008  30.8180  85.6388
 MLY  CE    C  CH2    0  -0.244  25.8067  30.6288  86.2188
 MLY  NZ    N  NT     0  -0.404  25.4133  29.2389  86.3725
 MLY  CH1   C  CH3    0  -0.515  24.1835  29.1337  87.1267
 MLY  CH2   C  CH3    0  -0.523  25.2860  28.5544  85.1038
 MLY  C     C  C      0   0.414  31.4581  32.0864  84.7712
 MLY  O     O  O      0  -0.602  32.4922  32.3014  85.4358
 MLY  OXT   O  OC    -1  -0.608  31.3745  32.0276  83.5283
 MLY  H     H  HNH2   0   0.331  31.2478  31.9964  87.2401
 MLY  H2    H  HNH2   0   0.330  29.7023  31.5874  87.5356
 MLY  HA    H  HCH1   0   0.196  29.9771  30.7285  85.4377
 MLY  HB2   H  HCH2   0   0.202  29.1584  33.6181  84.9596
 MLY  HB3   H  HCH2   0   0.201  28.8615  32.2538  83.8970
 MLY  HG2   H  HCH2   0   0.207  27.6835  32.6383  86.6891
 MLY  HG3   H  HCH2   0   0.215  26.8529  32.8845  85.1735
 MLY  HD2   H  HCH2   0   0.215  27.2439  30.4537  84.6083
 MLY  HD3   H  HCH2   0   0.217  27.9035  30.2077  86.2143
 MLY  HE2   H  HCH2   0   0.218  25.7836  31.0903  87.2111
 MLY  HE3   H  HCH2   0   0.177  25.0775  31.1874  85.6031
 MLY  HH11  H  HCH3   0   0.228  23.9292  28.0846  87.2863
 MLY  HH12  H  HCH3   0   0.228  24.3000  29.6004  88.1063
 MLY  HH13  H  HCH3   0   0.186  23.3246  29.6118  86.6286
 MLY  HH21  H  HCH3   0   0.230  24.9889  27.5180  85.2711
 MLY  HH22  H  HCH3   0   0.185  24.5352  29.0135  84.4396
 MLY  HH23  H  HCH3   0   0.235  26.2350  28.5357  84.5690

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
 MLY  N    CA    single  1.458  0.019  1.458
 MLY  N    H     single  0.860  0.020  0.860
 MLY  N    H2    single  0.890  0.020  1.040
 MLY  CA   CB    single  1.530  0.020  1.530
 MLY  CA   C     single  1.525  0.021  1.525
 MLY  CA   HA    single  0.970  0.020  0.970
 MLY  CB   CG    single  1.527  0.020  1.527
 MLY  CB   HB2   single  0.970  0.020  1.090
 MLY  CB   HB3   single  0.970  0.020  1.090
 MLY  CG   CD    single  1.526  0.020  1.526
 MLY  CG   HG2   single  0.970  0.020  1.090
 MLY  CG   HG3   single  0.970  0.020  1.090
 MLY  CD   CE    single  1.522  0.020  1.522
 MLY  CD   HD2   single  0.970  0.020  1.090
 MLY  CD   HD3   single  0.970  0.020  1.090
 MLY  CE   NZ    single  1.453  0.020  1.453
 MLY  CE   HE2   single  0.970  0.020  1.090
 MLY  CE   HE3   single  0.970  0.020  1.090
 MLY  NZ   CH1   single  1.446  0.020  1.446
 MLY  NZ   CH2   single  1.447  0.020  1.447
 MLY  CH1  HH11  single  0.970  0.020  1.090
 MLY  CH1  HH12  single  0.970  0.020  1.090
 MLY  CH1  HH13  single  0.970  0.020  1.090
 MLY  CH2  HH21  single  0.970  0.020  1.090
 MLY  CH2  HH22  single  0.970  0.020  1.090
 MLY  CH2  HH23  single  0.970  0.020  1.090
 MLY  C    O     deloc   1.231  0.020  1.231
 MLY  C    OXT   deloc   1.247  0.020  1.247

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
 MLY  H2    N    H     106.95  3.000
 MLY  H2    N    CA    110.08  3.000
 MLY  H     N    CA    114.00  3.000
 MLY  HA    CA   C     109.00  3.000
 MLY  HA    CA   CB    109.00  3.000
 MLY  C     CA   CB    110.10  1.900
 MLY  HA    CA   N     110.00  3.000
 MLY  C     CA   N     111.00  2.800
 MLY  CB    CA   N     110.50  1.700
 MLY  HB3   CB   HB2   106.69  3.000
 MLY  HB3   CB   CG    109.03  3.000
 MLY  HB2   CB   CG    108.76  3.000
 MLY  HB3   CB   CA    109.12  3.000
 MLY  HB2   CB   CA    108.67  3.000
 MLY  CG    CB   CA    114.31  3.000
 MLY  HG3   CG   HG2   105.74  3.000
 MLY  HG3   CG   CD    108.88  3.000
 MLY  HG2   CG   CD    109.67  3.000
 MLY  HG3   CG   CB    108.55  3.000
 MLY  HG2   CG   CB    109.93  3.000
 MLY  CD    CG   CB    113.74  3.000
 MLY  HD3   CD   HD2   106.52  3.000
 MLY  HD3   CD   CE    108.58  3.000
 MLY  HD2   CD   CE    110.71  3.000
 MLY  HD3   CD   CG    110.41  3.000
 MLY  HD2   CD   CG    108.59  3.000
 MLY  CE    CD   CG    111.88  3.000
 MLY  HE3   CE   HE2   106.14  3.000
 MLY  HE3   CE   NZ    111.33  3.000
 MLY  HE2   CE   NZ    107.57  3.000
 MLY  HE3   CE   CD    109.21  3.000
 MLY  HE2   CE   CD    108.20  3.000
 MLY  NZ    CE   CD    114.04  3.000
 MLY  CH2   NZ   CH1   110.36  3.000
 MLY  CH2   NZ   CE    112.56  3.000
 MLY  CH1   NZ   CE    110.79  3.000
 MLY  HH13  CH1  HH12  107.66  3.000
 MLY  HH13  CH1  HH11  107.55  3.000
 MLY  HH12  CH1  HH11  107.74  3.000
 MLY  HH13  CH1  NZ    113.29  3.000
 MLY  HH12  CH1  NZ    110.25  3.000
 MLY  HH11  CH1  NZ    110.14  3.000
 MLY  HH23  CH2  HH22  107.74  3.000
 MLY  HH23  CH2  HH21  107.22  3.000
 MLY  HH22  CH2  HH21  107.61  3.000
 MLY  HH23  CH2  NZ    111.21  3.000
 MLY  HH22  CH2  NZ    113.02  3.000
 MLY  HH21  CH2  NZ    109.80  3.000
 MLY  OXT   C    O     126.47  3.000
 MLY  OXT   C    CA    116.21  3.000
 MLY  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
 MLY  Var_01  CD    CG   CB  CA   -61.39  30.0  3
 MLY  Var_02  CE    CD   CG  CB  -173.69  30.0  3
 MLY  Var_03  NZ    CE   CD  CG  -173.08  30.0  3
 MLY  Var_04  CH1   NZ   CE  CD   170.49  30.0  3
 MLY  Var_05  HH11  CH1  NZ  CE  -176.68  30.0  3
 MLY  Var_06  HH21  CH2  NZ  CE  -179.94  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
 MLY  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
 MLY  plan-1  CA   0.020
 MLY  plan-1  C    0.020
 MLY  plan-1  O    0.020
 MLY  plan-1  OXT  0.020

