# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:08:06 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N~5~-(N,N'-dimethylcarbamimidoyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(NCCC[C@H](N)C(O)=O)=NC
#
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
 2MR  2MR  N~5~-(N,N'-dimethylcarbamimidoyl)-L-ornithine  L-peptide  31  14  .  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_2MR
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
 2MR  N     N  NH2    0  -0.817  31.0626  13.5424  12.1391
 2MR  CA    C  CH1    0  -0.219  32.0502  13.0178  11.2050
 2MR  CB    C  CH2    0  -0.396  32.7921  14.1568  10.5105
 2MR  CG    C  CH2    0  -0.437  31.8882  15.0787   9.7033
 2MR  CD    C  CH2    0  -0.286  32.6842  16.1726   9.0077
 2MR  NE    N  NH1    0  -0.652  31.8447  17.0460   8.2018
 2MR  CZ    C  C      0   0.564  32.0191  18.4027   8.1127
 2MR  NH1   N  N      0  -0.480  31.9065  19.1091   7.0495
 2MR  CQ1   C  CH3    0  -0.575  31.7731  18.4338   5.7825
 2MR  NH2   N  NH1    0  -0.633  32.3316  19.0403   9.3023
 2MR  CQ2   C  CH3    0  -0.530  31.5197  18.7976  10.4840
 2MR  C     C  C      0   0.413  33.0325  12.0501  11.9202
 2MR  O     O  O      0  -0.605  34.0663  11.7489  11.2927
 2MR  OXT   O  OC    -1  -0.601  32.6938  11.6246  13.0434
 2MR  H     H  HNH2   0   0.333  30.8852  12.8270  12.8323
 2MR  H2    H  HNH2   0   0.329  30.1879  13.7169  11.6632
 2MR  HA    H  HCH1   0   0.190  31.5754  12.4129  10.4110
 2MR  HB2   H  HCH2   0   0.197  33.3256  14.7460  11.2654
 2MR  HB3   H  HCH2   0   0.206  33.5505  13.7311   9.8509
 2MR  HG2   H  HCH2   0   0.211  31.3424  14.4938   8.9540
 2MR  HG3   H  HCH2   0   0.217  31.1356  15.5405  10.3485
 2MR  HD2   H  HCH2   0   0.242  33.2182  16.7728   9.7436
 2MR  HD3   H  HCH2   0   0.233  33.4536  15.7153   8.3751
 2MR  HE    H  HNH1   0   0.389  31.5312  16.6129   7.3475
 2MR  HQ11  H  HCH3   0   0.228  31.9444  19.1448   4.9734
 2MR  HQ12  H  HCH3   0   0.204  32.4829  17.6091   5.6347
 2MR  HQ13  H  HCH3   0   0.211  30.7701  18.0190   5.6209
 2MR  HH2   H  HNH1   0   0.366  32.4573  20.0260   9.1263
 2MR  HQ21  H  HCH3   0   0.244  31.8245  19.5021  11.2549
 2MR  HQ22  H  HCH3   0   0.218  30.4472  18.9298  10.3094
 2MR  HQ23  H  HCH3   0   0.237  31.6742  17.7979  10.8852

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
 2MR  N    CA    single  1.458  0.019  1.458
 2MR  N    H     single  0.860  0.020  0.860
 2MR  N    H2    single  0.890  0.020  1.040
 2MR  CA   CB    single  1.530  0.020  1.530
 2MR  CA   C     single  1.525  0.021  1.525
 2MR  CA   HA    single  0.970  0.020  0.970
 2MR  CB   CG    single  1.523  0.020  1.523
 2MR  CB   HB2   single  0.970  0.020  1.090
 2MR  CB   HB3   single  0.970  0.020  1.090
 2MR  CG   CD    single  1.521  0.020  1.521
 2MR  CG   HG2   single  0.970  0.020  1.090
 2MR  CG   HG3   single  0.970  0.020  1.090
 2MR  CD   NE    single  1.455  0.020  1.455
 2MR  CD   HD2   single  0.970  0.020  1.090
 2MR  CD   HD3   single  0.970  0.020  1.090
 2MR  NE   CZ    single  1.371  0.020  1.371
 2MR  NE   HE    single  0.890  0.020  1.040
 2MR  CZ   NH1   double  1.281  0.020  1.281
 2MR  CZ   NH2   single  1.385  0.020  1.385
 2MR  NH1  CQ1   single  1.442  0.020  1.442
 2MR  CQ1  HQ11  single  0.970  0.020  1.090
 2MR  CQ1  HQ12  single  0.970  0.020  1.090
 2MR  CQ1  HQ13  single  0.970  0.020  1.090
 2MR  NH2  CQ2   single  1.454  0.020  1.454
 2MR  NH2  HH2   single  0.890  0.020  1.040
 2MR  CQ2  HQ21  single  0.970  0.020  1.090
 2MR  CQ2  HQ22  single  0.970  0.020  1.090
 2MR  CQ2  HQ23  single  0.970  0.020  1.090
 2MR  C    O     deloc   1.231  0.020  1.231
 2MR  C    OXT   deloc   1.248  0.020  1.248

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
 2MR  H2    N    H     107.03  3.000
 2MR  H2    N    CA    110.29  3.000
 2MR  H     N    CA    114.00  3.000
 2MR  HA    CA   C     109.00  3.000
 2MR  HA    CA   CB    109.00  3.000
 2MR  C     CA   CB    110.10  1.900
 2MR  HA    CA   N     110.00  3.000
 2MR  C     CA   N     111.00  2.800
 2MR  CB    CA   N     110.50  1.700
 2MR  HB3   CB   HB2   106.71  3.000
 2MR  HB3   CB   CG    109.16  3.000
 2MR  HB2   CB   CG    109.18  3.000
 2MR  HB3   CB   CA    108.76  3.000
 2MR  HB2   CB   CA    108.92  3.000
 2MR  CG    CB   CA    113.86  3.000
 2MR  HG3   CG   HG2   106.62  3.000
 2MR  HG3   CG   CD    109.04  3.000
 2MR  HG2   CG   CD    109.37  3.000
 2MR  HG3   CG   CB    110.58  3.000
 2MR  HG2   CG   CB    109.56  3.000
 2MR  CD    CG   CB    111.54  3.000
 2MR  HD3   CD   HD2   106.00  3.000
 2MR  HD3   CD   NE    109.62  3.000
 2MR  HD2   CD   NE    109.04  3.000
 2MR  HD3   CD   CG    109.35  3.000
 2MR  HD2   CD   CG    110.11  3.000
 2MR  NE    CD   CG    112.52  3.000
 2MR  HE    NE   CZ    114.19  3.000
 2MR  HE    NE   CD    113.02  3.000
 2MR  CZ    NE   CD    123.83  3.000
 2MR  NH2   CZ   NH1   118.59  3.000
 2MR  NH2   CZ   NE    115.36  3.000
 2MR  NH1   CZ   NE    126.04  3.000
 2MR  CQ1   NH1  CZ    118.62  3.000
 2MR  HQ13  CQ1  HQ12  106.69  3.000
 2MR  HQ13  CQ1  HQ11  106.31  3.000
 2MR  HQ12  CQ1  HQ11  106.76  3.000
 2MR  HQ13  CQ1  NH1   113.01  3.000
 2MR  HQ12  CQ1  NH1   114.22  3.000
 2MR  HQ11  CQ1  NH1   109.39  3.000
 2MR  HH2   NH2  CQ2   111.97  3.000
 2MR  HH2   NH2  CZ    109.14  3.000
 2MR  CQ2   NH2  CZ    119.67  3.000
 2MR  HQ23  CQ2  HQ22  107.99  3.000
 2MR  HQ23  CQ2  HQ21  107.09  3.000
 2MR  HQ22  CQ2  HQ21  108.01  3.000
 2MR  HQ23  CQ2  NH2   111.95  3.000
 2MR  HQ22  CQ2  NH2   113.41  3.000
 2MR  HQ21  CQ2  NH2   108.14  3.000
 2MR  OXT   C    O     126.58  3.000
 2MR  OXT   C    CA    117.07  3.000
 2MR  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
 2MR  CONST_03  CQ1   NH1  CZ   NE      0.00   0.0  0
 2MR  CONST_06  NH2   CZ   NH1  CQ1   180.00   0.0  0
 2MR  CONST_07  HH2   NH2  CZ   NE    180.00   0.0  0
 2MR  CONST_08  HE    NE   CZ   NH1     0.00   0.0  0
 2MR  Var_01    CD    CG   CB   CA   -178.62  30.0  3
 2MR  Var_02    NE    CD   CG   CB    178.52  30.0  3
 2MR  Var_03    CZ    NE   CD   CG    140.81  30.0  3
 2MR  Var_04    HQ11  CQ1  NH1  CZ   -165.62  30.0  3
 2MR  Var_05    HQ21  CQ2  NH2  CZ   -171.02  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
 2MR  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
 2MR  plan-1  CD   0.020
 2MR  plan-1  NE   0.020
 2MR  plan-1  CZ   0.020
 2MR  plan-1  NH1  0.020
 2MR  plan-1  CQ1  0.020
 2MR  plan-1  NH2  0.020
 2MR  plan-1  CQ2  0.020
 2MR  plan-1  HE   0.020
 2MR  plan-1  HH2  0.020
 2MR  plan-2  CA   0.020
 2MR  plan-2  C    0.020
 2MR  plan-2  O    0.020
 2MR  plan-2  OXT  0.020

