# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:40:18 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(5S)-5-amino-5-carboxypentyl]-N,N-dimethylmethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(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
 M3L  M3L  N-[(5S)-5-amino-5-carboxypentyl]-N,N-dimethylmethanaminium  L-peptide  33  13  .  2012-08-28  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_M3L
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
 M3L  N     N  NH2    0  -0.818  -2.9065  12.5554  13.2371
 M3L  CA    C  CH1    0  -0.223  -3.0001  11.5211  14.2583
 M3L  CB    C  CH2    0  -0.389  -3.9389  11.9564  15.3798
 M3L  CG    C  CH2    0  -0.420  -3.5027  13.2453  16.0648
 M3L  CD    C  CH2    0  -0.470  -4.3857  13.5821  17.2644
 M3L  CE    C  CH2    0  -0.300  -3.9386  14.8974  17.8720
 M3L  NZ    N  NT     1  -0.383  -4.6642  15.3309  19.1222
 M3L  C     C  C      0   0.414  -3.4340  10.1675  13.6339
 M3L  O     O  O      0  -0.604  -3.8374   9.2950  14.4269
 M3L  OXT   O  OC    -1  -0.601  -3.3069  10.0486  12.3983
 M3L  CM1   C  CH3    0  -0.548  -4.4569  14.3528  20.2257
 M3L  CM2   C  CH3    0  -0.544  -4.1045  16.6478  19.5403
 M3L  CM3   C  CH3    0  -0.549  -6.1215  15.4915  18.8636
 M3L  H     H  HNH2   0   0.333  -2.6248  12.1095  12.3737
 M3L  H2    H  HNH2   0   0.330  -2.1862  13.2239  13.4747
 M3L  HA    H  HCH1   0   0.192  -2.0180  11.3211  14.7245
 M3L  HB2   H  HCH2   0   0.200  -4.9491  12.0881  14.9760
 M3L  HB3   H  HCH2   0   0.207  -3.9991  11.1586  16.1226
 M3L  HG2   H  HCH2   0   0.217  -2.4635  13.1500  16.3986
 M3L  HG3   H  HCH2   0   0.222  -3.5267  14.0738  15.3513
 M3L  HD2   H  HCH2   0   0.248  -5.4261  13.6388  16.9365
 M3L  HD3   H  HCH2   0   0.249  -4.3171  12.7680  17.9889
 M3L  HE2   H  HCH2   0   0.294  -2.8819  14.8529  18.1406
 M3L  HE3   H  HCH2   0   0.296  -4.0695  15.7079  17.1537
 M3L  HM11  H  HCH3   0   0.296  -4.9119  14.7457  21.1313
 M3L  HM12  H  HCH3   0   0.294  -4.9221  13.4057  19.9719
 M3L  HM13  H  HCH3   0   0.293  -3.3895  14.2138  20.3795
 M3L  HM21  H  HCH3   0   0.293  -4.6153  16.9798  20.4402
 M3L  HM22  H  HCH3   0   0.294  -3.0417  16.5357  19.7389
 M3L  HM23  H  HCH3   0   0.294  -4.2585  17.3689  18.7415
 M3L  HM31  H  HCH3   0   0.296  -6.5934  15.8933  19.7568
 M3L  HM32  H  HCH3   0   0.293  -6.2600  16.1798  18.0336
 M3L  HM33  H  HCH3   0   0.295  -6.5633  14.5285  18.6264

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
 M3L  N    CA    single  1.458  0.019  1.458
 M3L  N    H     single  0.860  0.020  0.860
 M3L  N    H2    single  0.890  0.020  1.040
 M3L  CA   CB    single  1.530  0.020  1.530
 M3L  CA   C     single  1.525  0.021  1.525
 M3L  CA   HA    single  0.970  0.020  0.970
 M3L  CB   CG    single  1.523  0.020  1.523
 M3L  CB   HB2   single  0.970  0.020  1.090
 M3L  CB   HB3   single  0.970  0.020  1.090
 M3L  CG   CD    single  1.527  0.020  1.527
 M3L  CG   HG2   single  0.970  0.020  1.090
 M3L  CG   HG3   single  0.970  0.020  1.090
 M3L  CD   CE    single  1.516  0.020  1.516
 M3L  CD   HD2   single  0.970  0.020  1.090
 M3L  CD   HD3   single  0.970  0.020  1.090
 M3L  CE   NZ    single  1.509  0.020  1.509
 M3L  CE   HE2   single  0.970  0.020  1.090
 M3L  CE   HE3   single  0.970  0.020  1.090
 M3L  NZ   CM1   single  1.489  0.020  1.489
 M3L  NZ   CM2   single  1.491  0.020  1.491
 M3L  NZ   CM3   single  1.489  0.020  1.489
 M3L  C    O     deloc   1.231  0.020  1.231
 M3L  C    OXT   deloc   1.248  0.020  1.248
 M3L  CM1  HM11  single  0.970  0.020  1.090
 M3L  CM1  HM12  single  0.970  0.020  1.090
 M3L  CM1  HM13  single  0.970  0.020  1.090
 M3L  CM2  HM21  single  0.970  0.020  1.090
 M3L  CM2  HM22  single  0.970  0.020  1.090
 M3L  CM2  HM23  single  0.970  0.020  1.090
 M3L  CM3  HM31  single  0.970  0.020  1.090
 M3L  CM3  HM32  single  0.970  0.020  1.090
 M3L  CM3  HM33  single  0.970  0.020  1.090

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
 M3L  H2    N    H     107.07  3.000
 M3L  H2    N    CA    110.52  3.000
 M3L  H     N    CA    114.00  3.000
 M3L  HA    CA   C     109.00  3.000
 M3L  HA    CA   CB    109.00  3.000
 M3L  C     CA   CB    110.10  1.900
 M3L  HA    CA   N     110.00  3.000
 M3L  C     CA   N     111.00  2.800
 M3L  CB    CA   N     110.50  1.700
 M3L  HB3   CB   HB2   106.72  3.000
 M3L  HB3   CB   CG    109.15  3.000
 M3L  HB2   CB   CG    109.15  3.000
 M3L  HB3   CB   CA    109.00  3.000
 M3L  HB2   CB   CA    109.31  3.000
 M3L  CG    CB   CA    113.30  3.000
 M3L  HG3   CG   HG2   106.59  3.000
 M3L  HG3   CG   CD    109.44  3.000
 M3L  HG2   CG   CD    109.16  3.000
 M3L  HG3   CG   CB    109.95  3.000
 M3L  HG2   CG   CB    109.57  3.000
 M3L  CD    CG   CB    111.98  3.000
 M3L  HD3   CD   HD2   107.32  3.000
 M3L  HD3   CD   CE    111.24  3.000
 M3L  HD2   CD   CE    110.86  3.000
 M3L  HD3   CD   CG    108.69  3.000
 M3L  HD2   CD   CG    109.05  3.000
 M3L  CE    CD   CG    109.61  3.000
 M3L  HE3   CE   HE2   107.97  3.000
 M3L  HE3   CE   NZ    105.92  3.000
 M3L  HE2   CE   NZ    105.87  3.000
 M3L  HE3   CE   CD    110.20  3.000
 M3L  HE2   CE   CD    110.42  3.000
 M3L  NZ    CE   CD    116.06  3.000
 M3L  CM3   NZ   CM2   108.72  3.000
 M3L  CM3   NZ   CM1   109.63  3.000
 M3L  CM2   NZ   CM1   108.67  3.000
 M3L  CM3   NZ   CE    110.96  3.000
 M3L  CM2   NZ   CE    107.79  3.000
 M3L  CM1   NZ   CE    110.99  3.000
 M3L  OXT   C    O     126.61  3.000
 M3L  OXT   C    CA    116.93  3.000
 M3L  O     C    CA    120.80  1.700
 M3L  HM13  CM1  HM12  110.02  3.000
 M3L  HM13  CM1  HM11  109.84  3.000
 M3L  HM12  CM1  HM11  109.32  3.000
 M3L  HM13  CM1  NZ    108.99  3.000
 M3L  HM12  CM1  NZ    109.89  3.000
 M3L  HM11  CM1  NZ    108.76  3.000
 M3L  HM23  CM2  HM22  109.95  3.000
 M3L  HM23  CM2  HM21  109.83  3.000
 M3L  HM22  CM2  HM21  109.87  3.000
 M3L  HM23  CM2  NZ    109.06  3.000
 M3L  HM22  CM2  NZ    109.10  3.000
 M3L  HM21  CM2  NZ    109.00  3.000
 M3L  HM33  CM3  HM32  110.05  3.000
 M3L  HM33  CM3  HM31  109.31  3.000
 M3L  HM32  CM3  HM31  109.75  3.000
 M3L  HM33  CM3  NZ    109.92  3.000
 M3L  HM32  CM3  NZ    109.00  3.000
 M3L  HM31  CM3  NZ    108.79  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
 M3L  Var_01  CD    CG   CB  CA  -174.59  30.0  3
 M3L  Var_02  CE    CD   CG  CB  -177.86  30.0  3
 M3L  Var_03  NZ    CE   CD  CG  -176.53  30.0  3
 M3L  Var_04  CM1   NZ   CE  CD    62.36  30.0  3
 M3L  Var_05  HM11  CM1  NZ  CE   174.59  30.0  3
 M3L  Var_06  HM21  CM2  NZ  CE   179.91  30.0  3
 M3L  Var_07  HM31  CM3  NZ  CE  -174.70  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
 M3L  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
 M3L  plan-1  CA   0.020
 M3L  plan-1  C    0.020
 M3L  plan-1  O    0.020
 M3L  plan-1  OXT  0.020

