# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:00:31 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: N~5~-(N-methylcarbamimidoyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=N)NCCC[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
 NMM  NMM  N~5~-(N-methylcarbamimidoyl)-L-ornithine  L-peptide  28  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_NMM
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
 NMM  CAA   C  CH3    0  -0.497  -0.9952  -22.7960  39.5626
 NMM  NH2   N  NH1    0  -0.640   0.3769  -22.3657  39.4645
 NMM  CZ    C  C      0   0.583   0.8487  -21.3768  40.2850
 NMM  NH1   N  N      0  -0.733   0.0359  -20.7262  41.0405
 NMM  NE    N  NH1    0  -0.667   2.2051  -21.1752  40.2145
 NMM  CD    C  CH2    0  -0.281   3.0224  -21.5810  39.0837
 NMM  CG    C  CH2    0  -0.454   4.4026  -20.9429  39.1457
 NMM  CB    C  CH2    0  -0.431   4.3845  -19.4266  38.9771
 NMM  CA    C  CH1    0  -0.215   5.7703  -18.8102  38.7955
 NMM  C     C  C      0   0.389   5.6710  -17.2823  38.5252
 NMM  O     O  O      0  -0.602   6.4159  -16.5352  39.1897
 NMM  OXT   O  OC    -1  -0.613   4.8640  -16.9312  37.6390
 NMM  N     N  NH2    0  -0.789   6.6342  -19.1898  39.9055
 NMM  HAA1  H  HCH3   0   0.235  -1.1557  -23.5964  38.8437
 NMM  HAA2  H  HCH3   0   0.229  -1.6750  -21.9813  39.3171
 NMM  HAA3  H  HCH3   0   0.213  -1.2636  -23.1663  40.5563
 NMM  HH2   H  HNH1   0   0.388   1.0318  -23.0861  39.2096
 NMM  HH1   H  H      0   0.310   0.5150  -19.9703  41.5164
 NMM  HE    H  HNH1   0   0.384   2.5218  -20.3535  40.7035
 NMM  HD3   H  HCH2   0   0.219   2.5455  -21.3154  38.1328
 NMM  HD2   H  HCH2   0   0.230   3.1459  -22.6687  39.0841
 NMM  HG3   H  HCH2   0   0.229   5.0018  -21.3836  38.3440
 NMM  HG2   H  HCH2   0   0.226   4.8909  -21.2243  40.0812
 NMM  HB3   H  HCH2   0   0.207   3.9000  -18.9513  39.8397
 NMM  HB2   H  HCH2   0   0.222   3.7748  -19.1702  38.1092
 NMM  HA    H  HCH1   0   0.207   6.2011  -19.2541  37.8859
 NMM  H     H  HNH2   0   0.320   6.2008  -18.8743  40.7674
 NMM  H2    H  HNH2   0   0.330   7.4840  -18.6421  39.8432

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
 NMM  CAA  NH2   single  1.441  0.020  1.441
 NMM  CAA  HAA1  single  0.970  0.020  1.090
 NMM  CAA  HAA2  single  0.970  0.020  1.090
 NMM  CAA  HAA3  single  0.970  0.020  1.090
 NMM  NH2  CZ    single  1.369  0.020  1.369
 NMM  NH2  HH2   single  0.890  0.020  1.040
 NMM  CZ   NH1   double  1.286  0.020  1.286
 NMM  CZ   NE    single  1.373  0.020  1.373
 NMM  NH1  HH1   single  0.890  0.020  1.040
 NMM  NE   CD    single  1.453  0.020  1.453
 NMM  NE   HE    single  0.890  0.020  1.040
 NMM  CD   CG    single  1.522  0.020  1.522
 NMM  CD   HD3   single  0.970  0.020  1.090
 NMM  CD   HD2   single  0.970  0.020  1.090
 NMM  CG   CB    single  1.526  0.020  1.526
 NMM  CG   HG3   single  0.970  0.020  1.090
 NMM  CG   HG2   single  0.970  0.020  1.090
 NMM  CB   CA    single  1.530  0.020  1.530
 NMM  CB   HB3   single  0.970  0.020  1.090
 NMM  CB   HB2   single  0.970  0.020  1.090
 NMM  CA   C     single  1.525  0.021  1.525
 NMM  CA   N     single  1.458  0.019  1.458
 NMM  CA   HA    single  0.970  0.020  0.970
 NMM  C    O     deloc   1.231  0.020  1.231
 NMM  C    OXT   deloc   1.249  0.020  1.249
 NMM  N    H     single  0.860  0.020  0.860
 NMM  N    H2    single  0.890  0.020  1.040

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
 NMM  HAA3  CAA  HAA2  107.74  3.000
 NMM  HAA3  CAA  HAA1  108.37  3.000
 NMM  HAA2  CAA  HAA1  108.02  3.000
 NMM  HAA3  CAA  NH2   113.36  3.000
 NMM  HAA2  CAA  NH2   110.82  3.000
 NMM  HAA1  CAA  NH2   108.37  3.000
 NMM  HH2   NH2  CZ    116.40  3.000
 NMM  HH2   NH2  CAA   115.03  3.000
 NMM  CZ    NH2  CAA   120.20  3.000
 NMM  NE    CZ   NH1   125.45  3.000
 NMM  NE    CZ   NH2   114.57  3.000
 NMM  NH1   CZ   NH2   119.98  3.000
 NMM  HH1   NH1  CZ    110.75  3.000
 NMM  HE    NE   CD    115.39  3.000
 NMM  HE    NE   CZ    113.92  3.000
 NMM  CD    NE   CZ    123.68  3.000
 NMM  HD2   CD   HD3   106.86  3.000
 NMM  HD2   CD   CG    108.32  3.000
 NMM  HD3   CD   CG    109.16  3.000
 NMM  HD2   CD   NE    109.92  3.000
 NMM  HD3   CD   NE    111.27  3.000
 NMM  CG    CD   NE    111.18  3.000
 NMM  HG2   CG   HG3   106.21  3.000
 NMM  HG2   CG   CB    110.86  3.000
 NMM  HG3   CG   CB    109.03  3.000
 NMM  HG2   CG   CD    109.41  3.000
 NMM  HG3   CG   CD    107.34  3.000
 NMM  CB    CG   CD    113.67  3.000
 NMM  HB2   CB   HB3   106.06  3.000
 NMM  HB2   CB   CA    108.51  3.000
 NMM  HB3   CB   CA    108.62  3.000
 NMM  HB2   CB   CG    109.15  3.000
 NMM  HB3   CB   CG    110.41  3.000
 NMM  CA    CB   CG    113.79  3.000
 NMM  HA    CA   N     110.00  3.000
 NMM  HA    CA   C     109.00  3.000
 NMM  N     CA   C     111.00  2.800
 NMM  HA    CA   CB    109.00  3.000
 NMM  N     CA   CB    110.50  1.700
 NMM  C     CA   CB    110.10  1.900
 NMM  OXT   C    O     126.57  3.000
 NMM  OXT   C    CA    116.16  3.000
 NMM  O     C    CA    120.80  1.700
 NMM  H2    N    H     104.03  3.000
 NMM  H2    N    CA    108.05  3.000
 NMM  H     N    CA    114.00  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
 NMM  CONST_01  NH1   CZ   NH2  CAA     0.00   0.0  0
 NMM  CONST_02  NE    CZ   NH2  CAA   180.00   0.0  0
 NMM  CONST_05  HH1   NH1  CZ   NH2   180.00   0.0  0
 NMM  CONST_06  HE    NE   CZ   NH2   180.00   0.0  0
 NMM  Var_01    CG    CD   NE   CZ    166.66  30.0  3
 NMM  Var_02    CB    CG   CD   NE    -66.30  30.0  3
 NMM  Var_03    CA    CB   CG   CD   -169.95  30.0  3
 NMM  Var_04    HAA1  CAA  NH2  CZ   -178.82  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
 NMM  chir_01  CA  CB  C  N  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
 NMM  plan-1  CAA  0.020
 NMM  plan-1  NH2  0.020
 NMM  plan-1  CZ   0.020
 NMM  plan-1  NH1  0.020
 NMM  plan-1  NE   0.020
 NMM  plan-1  CD   0.020
 NMM  plan-1  HH2  0.020
 NMM  plan-1  HH1  0.020
 NMM  plan-1  HE   0.020
 NMM  plan-2  CA   0.020
 NMM  plan-2  C    0.020
 NMM  plan-2  O    0.020
 NMM  plan-2  OXT  0.020

