# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:57:09 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: N~2~-methyl-L-arginine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](CCCNC(N)=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
 MMO  MMO  'N~2~-methyl-L-arginine   '  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_MMO
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
 MMO  N     N  NH1    0  -0.600  13.1164  -11.4024  15.9485
 MMO  CA    C  CH1    0  -0.205  14.4640  -11.6627  16.4589
 MMO  C     C  C      0   0.413  14.7429  -10.6926  17.6415
 MMO  O     O  O      0  -0.604  15.4419   -9.6844  17.4094
 MMO  CB    C  CH2    0  -0.435  15.5703  -11.6514  15.4032
 MMO  CG    C  CH2    0  -0.474  15.3247  -12.6288  14.2576
 MMO  CD    C  CH2    0  -0.268  16.4698  -12.7015  13.2581
 MMO  NE    N  NH1    0  -0.630  16.5870  -11.4609  12.5150
 MMO  CZ    C  C      0   0.522  17.6747  -11.1197  11.7596
 MMO  NH2   N  NH2    0  -0.829  18.4711  -12.1756  11.3808
 MMO  NH1   N  N      0  -0.724  17.8904   -9.8812  11.4899
 MMO  CN    C  CH3    0  -0.524  12.9631  -10.1863  15.1748
 MMO  H2    H  HNH1   0   0.341  12.8147  -12.1876  15.3868
 MMO  HA    H  HCH1   0   0.203  14.4199  -12.6742  16.8790
 MMO  HCB1  H  HCH2   0   0.211  15.7080  -10.6364  15.0239
 MMO  HCB2  H  HCH2   0   0.214  16.5163  -11.9147  15.8876
 MMO  HCG1  H  HCH2   0   0.233  15.1758  -13.6336  14.6630
 MMO  HCG2  H  HCH2   0   0.223  14.4047  -12.3758  13.7214
 MMO  HCD1  H  HCH2   0   0.218  17.3984  -12.9384  13.7914
 MMO  HCD2  H  HCH2   0   0.229  16.2819  -13.5317  12.5695
 MMO  HH21  H  HNH2   0   0.387  19.1327  -11.9752  10.6483
 MMO  HH22  H  HNH2   0   0.388  18.0295  -13.0733  11.2567
 MMO  HH11  H  H      0   0.310  18.6815   -9.7833  10.8648
 MMO  HC1   H  HCH3   0   0.223  11.9312  -10.1110  14.8301
 MMO  HC2   H  HCH3   0   0.220  13.1639   -9.3123  15.7949
 MMO  HC3   H  HCH3   0   0.191  13.6093  -10.1115  14.2895
 MMO  OXT   O  OC    -1  -0.611  14.2182  -10.9953  18.7317
 MMO  HE    H  HNH1   0   0.377  16.1201  -10.6598  12.9090

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
 MMO  N    CA    single  1.458  0.019  1.458
 MMO  N    CN    single  1.449  0.020  1.449
 MMO  N    H2    single  0.890  0.020  1.040
 MMO  CA   C     single  1.525  0.021  1.525
 MMO  CA   CB    single  1.530  0.020  1.530
 MMO  CA   HA    single  0.970  0.020  0.970
 MMO  C    O     deloc   1.231  0.020  1.231
 MMO  CB   CG    single  1.526  0.020  1.526
 MMO  CB   HCB1  single  0.970  0.020  1.090
 MMO  CB   HCB2  single  0.970  0.020  1.090
 MMO  CG   CD    single  1.522  0.020  1.522
 MMO  CG   HCG1  single  0.970  0.020  1.090
 MMO  CG   HCG2  single  0.970  0.020  1.090
 MMO  CD   NE    single  1.451  0.020  1.451
 MMO  CD   HCD1  single  0.970  0.020  1.090
 MMO  CD   HCD2  single  0.970  0.020  1.090
 MMO  NE   CZ    single  1.368  0.020  1.368
 MMO  CZ   NH2   single  1.376  0.020  1.376
 MMO  CZ   NH1   double  1.286  0.020  1.286
 MMO  NH2  HH21  single  0.890  0.020  1.040
 MMO  NH2  HH22  single  0.890  0.020  1.040
 MMO  NH1  HH11  single  0.890  0.020  1.040
 MMO  CN   HC1   single  0.970  0.020  1.090
 MMO  CN   HC2   single  0.970  0.020  1.090
 MMO  CN   HC3   single  0.970  0.020  1.090
 MMO  C    OXT   deloc   1.247  0.020  1.247
 MMO  NE   HE    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
 MMO  H2    N    CN    108.86  3.000
 MMO  H2    N    CA    109.27  3.000
 MMO  CN    N    CA    115.63  3.000
 MMO  HA    CA   CB    109.00  3.000
 MMO  HA    CA   C     109.00  3.000
 MMO  CB    CA   C     110.10  1.900
 MMO  HA    CA   N     110.00  3.000
 MMO  CB    CA   N     110.50  1.700
 MMO  C     CA   N     111.00  2.800
 MMO  OXT   C    O     126.44  3.000
 MMO  OXT   C    CA    115.98  3.000
 MMO  O     C    CA    120.80  1.700
 MMO  HCB2  CB   HCB1  105.55  3.000
 MMO  HCB2  CB   CG    108.49  3.000
 MMO  HCB1  CB   CG    110.79  3.000
 MMO  HCB2  CB   CA    108.53  3.000
 MMO  HCB1  CB   CA    109.74  3.000
 MMO  CG    CB   CA    113.40  3.000
 MMO  HCG2  CG   HCG1  106.23  3.000
 MMO  HCG2  CG   CD    108.77  3.000
 MMO  HCG1  CG   CD    107.58  3.000
 MMO  HCG2  CG   CB    110.80  3.000
 MMO  HCG1  CG   CB    109.40  3.000
 MMO  CD    CG   CB    113.74  3.000
 MMO  HCD2  CD   HCD1  106.70  3.000
 MMO  HCD2  CD   NE    109.88  3.000
 MMO  HCD1  CD   NE    111.43  3.000
 MMO  HCD2  CD   CG    108.67  3.000
 MMO  HCD1  CD   CG    109.15  3.000
 MMO  NE    CD   CG    110.88  3.000
 MMO  HE    NE   CZ    112.72  3.000
 MMO  HE    NE   CD    116.24  3.000
 MMO  CZ    NE   CD    124.09  3.000
 MMO  NH1   CZ   NH2   125.77  3.000
 MMO  NH1   CZ   NE    119.32  3.000
 MMO  NH2   CZ   NE    114.90  3.000
 MMO  HH22  NH2  HH21  112.05  3.000
 MMO  HH22  NH2  CZ    117.63  3.000
 MMO  HH21  NH2  CZ    115.33  3.000
 MMO  HH11  NH1  CZ    110.70  3.000
 MMO  HC3   CN   HC2   107.18  3.000
 MMO  HC3   CN   HC1   107.29  3.000
 MMO  HC2   CN   HC1   107.37  3.000
 MMO  HC3   CN   N     115.16  3.000
 MMO  HC2   CN   N     110.45  3.000
 MMO  HC1   CN   N     109.07  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
 MMO  CONST_03  HH21  NH2  CZ  NE    180.00   0.0  0
 MMO  CONST_05  HH11  NH1  CZ  NE    180.00   0.0  0
 MMO  CONST_06  HE    NE   CZ  NH2   180.00   0.0  0
 MMO  Var_01    CD    CG   CB  CA   -175.59  30.0  3
 MMO  Var_02    NE    CD   CG  CB    -68.05  30.0  3
 MMO  Var_03    CZ    NE   CD  CG    165.67  30.0  3
 MMO  Var_04    HC1   CN   N   CA    178.67  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
 MMO  chir_01  CA  N  C  CB  positiv

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
 MMO  plan-1  CD    0.020
 MMO  plan-1  NE    0.020
 MMO  plan-1  CZ    0.020
 MMO  plan-1  NH2   0.020
 MMO  plan-1  NH1   0.020
 MMO  plan-1  HH21  0.020
 MMO  plan-1  HH22  0.020
 MMO  plan-1  HH11  0.020
 MMO  plan-1  HE    0.020
 MMO  plan-2  CA    0.020
 MMO  plan-2  C     0.020
 MMO  plan-2  O     0.020
 MMO  plan-2  OXT   0.020

