# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:53:12 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 1-[(4S)-4-amino-5-oxohexyl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@@H](N)CCCNC(N)=N
#
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
 ARM  ARM  1-[(4S)-4-amino-5-oxohexyl]guanidine  L-peptide  28  12  .  2019-03-22  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ARM
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
 ARM  N     N  NH2   0  -0.807  36.1972  12.7490  144.7332
 ARM  CA    C  CH1   0  -0.181  35.0192  12.2794  145.4376
 ARM  CB    C  CH2   0  -0.434  33.9285  11.8507  144.4458
 ARM  CG    C  CH2   0  -0.467  33.3559  13.0083  143.6362
 ARM  CD    C  CH2   0  -0.224  32.1992  12.5496  142.7605
 ARM  NE    N  NH1   0  -0.649  31.6694  13.6581  142.0009
 ARM  CZ    C  C     0   0.556  30.5007  13.5335  141.2983
 ARM  NH1   N  N     0  -0.720  29.7578  12.4982  141.4505
 ARM  NH2   N  NH2   0  -0.839  30.1863  14.6348  140.5298
 ARM  C     C  C     0   0.390  35.3466  11.0664  146.2963
 ARM  O     O  O     0  -0.398  34.7228  10.8537  147.3124
 ARM  CM    C  CH3   0  -0.766  36.4260  10.1402  145.8131
 ARM  H     H  HNH2  0   0.353  36.8596  13.1429  145.3898
 ARM  H2    H  HNH2  0   0.359  35.9493  13.5083  144.1124
 ARM  HA    H  HCH1  0   0.233  34.5776  13.0308  146.1092
 ARM  HB2   H  HCH2  0   0.233  34.3335  11.0883  143.7733
 ARM  HB3   H  HCH2  0   0.238  33.1151  11.3825  145.0066
 ARM  HG2   H  HCH2  0   0.231  33.0071  13.7944  144.3121
 ARM  HG3   H  HCH2  0   0.226  34.1285  13.4544  143.0018
 ARM  HD2   H  HCH2  0   0.209  32.5298  11.7290  142.1104
 ARM  HD3   H  HCH2  0   0.228  31.4039  12.1450  143.3881
 ARM  HE    H  HNH1  0   0.377  32.3640  14.2758  141.6104
 ARM  HH1   H  H     0   0.313  28.8996  12.5953  140.9204
 ARM  HH21  H  HNH2  0   0.384  29.5327  14.4638  139.7830
 ARM  HH22  H  HNH2  0   0.380  30.9417  15.2370  140.2418
 ARM  HM1   H  HCH3  0   0.252  36.3977   9.1991  146.3583
 ARM  HM2   H  HCH3  0   0.257  36.3377   9.9517  144.7434
 ARM  HM3   H  HCH3  0   0.265  37.4044  10.6009  145.9638

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
 ARM  N    CA    single  1.458  0.019  1.458
 ARM  N    H     single  0.860  0.020  0.860
 ARM  N    H2    single  0.890  0.020  1.040
 ARM  CA   CB    single  1.530  0.020  1.530
 ARM  CA   C     single  1.525  0.021  1.525
 ARM  CA   HA    single  0.970  0.020  0.970
 ARM  CB   CG    single  1.524  0.020  1.524
 ARM  CB   HB2   single  0.970  0.020  1.090
 ARM  CB   HB3   single  0.970  0.020  1.090
 ARM  CG   CD    single  1.522  0.020  1.522
 ARM  CG   HG2   single  0.970  0.020  1.090
 ARM  CG   HG3   single  0.970  0.020  1.090
 ARM  CD   NE    single  1.444  0.020  1.444
 ARM  CD   HD2   single  0.970  0.020  1.090
 ARM  CD   HD3   single  0.970  0.020  1.090
 ARM  NE   CZ    single  1.369  0.020  1.369
 ARM  NE   HE    single  0.890  0.020  1.040
 ARM  CZ   NH1   double  1.283  0.020  1.283
 ARM  CZ   NH2   single  1.379  0.020  1.379
 ARM  NH1  HH1   single  0.890  0.020  1.040
 ARM  NH2  HH21  single  0.890  0.020  1.040
 ARM  NH2  HH22  single  0.890  0.020  1.040
 ARM  C    O     double  1.231  0.020  1.231
 ARM  C    CM    single  1.502  0.020  1.502
 ARM  CM   HM1   single  0.970  0.020  1.090
 ARM  CM   HM2   single  0.970  0.020  1.090
 ARM  CM   HM3   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
 ARM  H2    N    H     105.44  3.000
 ARM  H2    N    CA    110.00  3.000
 ARM  H     N    CA    114.00  3.000
 ARM  HA    CA   C     109.00  3.000
 ARM  HA    CA   CB    109.00  3.000
 ARM  C     CA   CB    110.10  1.900
 ARM  HA    CA   N     110.00  3.000
 ARM  C     CA   N     111.00  2.800
 ARM  CB    CA   N     110.50  1.700
 ARM  HB3   CB   HB2   106.99  3.000
 ARM  HB3   CB   CG    108.55  3.000
 ARM  HB2   CB   CG    109.98  3.000
 ARM  HB3   CB   CA    108.47  3.000
 ARM  HB2   CB   CA    109.19  3.000
 ARM  CG    CB   CA    113.45  3.000
 ARM  HG3   CG   HG2   106.88  3.000
 ARM  HG3   CG   CD    109.01  3.000
 ARM  HG2   CG   CD    109.26  3.000
 ARM  HG3   CG   CB    110.62  3.000
 ARM  HG2   CG   CB    109.72  3.000
 ARM  CD    CG   CB    111.24  3.000
 ARM  HD3   CD   HD2   106.44  3.000
 ARM  HD3   CD   NE    108.65  3.000
 ARM  HD2   CD   NE    111.88  3.000
 ARM  HD3   CD   CG    109.57  3.000
 ARM  HD2   CD   CG    109.71  3.000
 ARM  NE    CD   CG    110.50  3.000
 ARM  HE    NE   CZ    116.43  3.000
 ARM  HE    NE   CD    114.91  3.000
 ARM  CZ    NE   CD    120.87  3.000
 ARM  NH2   CZ   NH1   125.33  3.000
 ARM  NH2   CZ   NE    114.07  3.000
 ARM  NH1   CZ   NE    120.44  3.000
 ARM  HH1   NH1  CZ    110.55  3.000
 ARM  HH22  NH2  HH21  112.08  3.000
 ARM  HH22  NH2  CZ    117.73  3.000
 ARM  HH21  NH2  CZ    115.19  3.000
 ARM  CM    C    O     122.12  3.000
 ARM  CM    C    CA    117.68  3.000
 ARM  O     C    CA    120.80  1.700
 ARM  HM3   CM   HM2   106.33  3.000
 ARM  HM3   CM   HM1   108.61  3.000
 ARM  HM2   CM   HM1   109.89  3.000
 ARM  HM3   CM   C     109.83  3.000
 ARM  HM2   CM   C     111.36  3.000
 ARM  HM1   CM   C     110.69  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
 ARM  CONST_01  NH1  CZ   NE  CD     0.00   0.0  0
 ARM  CONST_02  NH2  CZ   NE  CD   180.00   0.0  0
 ARM  CONST_03  HH1  NH1  CZ  NE   180.00   0.0  0
 ARM  Var_01    CD   CG   CB  CA  -175.02  30.0  3
 ARM  Var_02    NE   CD   CG  CB  -179.98  30.0  3
 ARM  Var_03    CZ   NE   CD  CG  -170.04  30.0  3
 ARM  Var_04    HM1  CM   C   CA  -165.62  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
 ARM  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
 ARM  plan-1  CA    0.020
 ARM  plan-1  C     0.020
 ARM  plan-1  O     0.020
 ARM  plan-1  CM    0.020
 ARM  plan-2  CD    0.020
 ARM  plan-2  NE    0.020
 ARM  plan-2  CZ    0.020
 ARM  plan-2  NH1   0.020
 ARM  plan-2  NH2   0.020
 ARM  plan-2  HE    0.020
 ARM  plan-2  HH1   0.020
 ARM  plan-2  HH21  0.020
 ARM  plan-2  HH22  0.020

