# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:11:56 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: amino{[(4S)-4-amino-9-carboxy-5-oxononyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=[NH2+])C(=O)CCCCC(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
 A5R  A5R  amino{[(4S)-4-amino-9-carboxy-5-oxononyl]amino}methaniminium  peptide  41  18  .  2022-03-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A5R
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
 A5R  C     C  C     0   0.391   0.6682   1.7411  -0.2637
 A5R  N     N  NH2   0  -0.777  -1.3473   3.0831   0.3553
 A5R  O     O  O     0  -0.398   1.0201   2.5951  -1.0458
 A5R  CA    C  CH1   0  -0.200  -0.7238   1.7793   0.3706
 A5R  CB    C  CH2   0  -0.436  -1.6256   0.7555  -0.3327
 A5R  CD    C  CH2   0  -0.276  -3.8419  -0.4247  -0.3411
 A5R  NE    N  NH1   0  -0.637  -5.1182  -0.5408   0.3444
 A5R  CG    C  CH2   0  -0.465  -2.9619   0.5854   0.3745
 A5R  CZ    C  C     0   0.830  -6.0716  -1.4026   0.0188
 A5R  NH1   N  NH2   0  -0.816  -5.8734  -2.2951  -0.9409
 A5R  NH2   N  NC2   1  -0.823  -7.2275  -1.3848   0.6713
 A5R  C1    C  C     0   0.550   6.2127  -1.3712   0.2614
 A5R  O1    O  O     0  -0.446   5.8794  -2.2539   1.0125
 A5R  C2    C  CH2   0  -0.580   5.3151  -0.2785  -0.2489
 A5R  C3    C  CH2   0  -0.420   3.8668  -0.4212   0.1881
 A5R  C4    C  CH2   0  -0.415   3.0103   0.7322  -0.3192
 A5R  C5    C  CH2   0  -0.569   1.5663   0.5990   0.1366
 A5R  H1N   H  HNH2  0   0.352  -0.8102   3.7346   0.9139
 A5R  H2N   H  HNH2  0   0.341  -1.3397   3.4520  -0.5884
 A5R  HA    H  HCH1  0   0.253  -0.6114   1.4645   1.4141
 A5R  H1B   H  HCH2  0   0.239  -1.7875   1.0784  -1.3669
 A5R  H2B   H  HCH2  0   0.244  -1.1203  -0.2118  -0.3876
 A5R  H1D   H  HCH2  0   0.256  -3.3428  -1.3972  -0.3553
 A5R  H2D   H  HCH2  0   0.258  -3.9993  -0.1155  -1.3788
 A5R  HNE   H  HNH1  0   0.426  -5.3375   0.1530   1.0424
 A5R  H1G   H  HCH2  0   0.243  -2.7926   0.2531   1.4028
 A5R  H2G   H  HCH2  0   0.250  -3.4740   1.5481   0.4273
 A5R  H1H1  H  HNH2  0   0.448  -5.0198  -2.3300  -1.4712
 A5R  H2H1  H  HNH2  0   0.432  -6.5981  -2.9408  -1.2038
 A5R  H1H2  H  HNC2  0   0.433  -7.4155  -0.6982   1.3816
 A5R  H2H2  H  HNC2  0   0.429  -7.9779  -2.0059   0.4217
 A5R  O3    O  OH1   0  -0.598   7.4511  -1.2543  -0.2112
 A5R  H12   H  HCH2  0   0.277   5.7265   0.6772   0.0933
 A5R  H22   H  HCH2  0   0.275   5.3936  -0.2550  -1.3397
 A5R  H13   H  HCH2  0   0.229   3.4609  -1.3680  -0.1782
 A5R  H23   H  HCH2  0   0.229   3.8111  -0.4624   1.2789
 A5R  H14   H  HCH2  0   0.227   3.4235   1.6779   0.0430
 A5R  H24   H  HCH2  0   0.228   3.0569   0.7732  -1.4103
 A5R  H15   H  HCH2  0   0.264   1.5116   0.4900   1.2250
 A5R  H25   H  HCH2  0   0.271   1.1321  -0.3283  -0.2559
 A5R  H231  H  HOH1  0   0.478   8.0083  -1.9613   0.1463

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
 A5R  C    CA    single  1.525  0.021  1.525
 A5R  N    H1N   single  0.890  0.020  1.040
 A5R  N    H2N   single  0.890  0.020  1.040
 A5R  O    C     double  1.231  0.020  1.231
 A5R  CA   N     single  1.458  0.019  1.458
 A5R  CA   CB    single  1.521  0.033  1.521
 A5R  CA   HA    single  0.970  0.020  0.970
 A5R  CB   CG    single  1.521  0.020  1.521
 A5R  CB   H1B   single  0.970  0.020  1.090
 A5R  CB   H2B   single  0.970  0.020  1.090
 A5R  CD   NE    single  1.453  0.020  1.453
 A5R  CD   H1D   single  0.970  0.020  1.090
 A5R  CD   H2D   single  0.970  0.020  1.090
 A5R  NE   CZ    single  1.326  0.020  1.326
 A5R  NE   HNE   single  0.860  0.020  1.020
 A5R  CG   CD    single  1.519  0.020  1.519
 A5R  CG   H1G   single  0.970  0.020  1.090
 A5R  CG   H2G   single  0.970  0.020  1.090
 A5R  CZ   NH1   single  1.325  0.020  1.325
 A5R  CZ   NH2   double  1.327  0.020  1.327
 A5R  NH1  H1H1  single  0.860  0.020  1.020
 A5R  NH1  H2H1  single  0.860  0.020  1.020
 A5R  NH2  H1H2  single  0.860  0.020  1.020
 A5R  NH2  H2H2  single  0.860  0.020  1.020
 A5R  C1   O1    double  1.206  0.020  1.206
 A5R  C1   C2    single  1.503  0.020  1.503
 A5R  C1   O3    single  1.331  0.020  1.331
 A5R  C2   C3    single  1.519  0.020  1.519
 A5R  C2   H12   single  0.970  0.020  1.090
 A5R  C2   H22   single  0.970  0.020  1.090
 A5R  C3   C4    single  1.524  0.020  1.524
 A5R  C3   H13   single  0.970  0.020  1.090
 A5R  C3   H23   single  0.970  0.020  1.090
 A5R  C4   C5    single  1.520  0.020  1.520
 A5R  C4   H14   single  0.970  0.020  1.090
 A5R  C4   H24   single  0.970  0.020  1.090
 A5R  C5   C     single  1.507  0.020  1.507
 A5R  C5   H15   single  0.970  0.020  1.090
 A5R  C5   H25   single  0.970  0.020  1.090
 A5R  O3   H231  single  0.850  0.020  0.980

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
 A5R  C5    C    CA    116.80  3.000
 A5R  C5    C    O     122.22  3.000
 A5R  CA    C    O     120.80  1.700
 A5R  H2N   N    H1N   106.00  3.000
 A5R  H2N   N    CA    109.58  3.000
 A5R  H1N   N    CA    110.24  3.000
 A5R  HA    CA   CB    109.00  3.000
 A5R  HA    CA   N     110.00  3.000
 A5R  CB    CA   N     110.40  1.500
 A5R  HA    CA   C     110.00  3.000
 A5R  CB    CA   C     110.50  1.500
 A5R  N     CA   C     111.00  2.800
 A5R  H2B   CB   H1B   106.37  3.000
 A5R  H2B   CB   CG    109.30  3.000
 A5R  H1B   CB   CG    110.00  3.000
 A5R  H2B   CB   CA    109.99  3.000
 A5R  H1B   CB   CA    108.84  3.000
 A5R  CG    CB   CA    112.18  3.000
 A5R  H2D   CD   H1D   107.75  3.000
 A5R  H2D   CD   CG    110.02  3.000
 A5R  H1D   CD   CG    109.47  3.000
 A5R  CG    CD   NE    109.86  3.000
 A5R  H2D   CD   NE    110.10  3.000
 A5R  H1D   CD   NE    109.63  3.000
 A5R  HNE   NE   CZ    117.44  3.000
 A5R  HNE   NE   CD    117.56  3.000
 A5R  CZ    NE   CD    124.58  3.000
 A5R  H2G   CG   H1G   107.16  3.000
 A5R  H2G   CG   CD    109.72  3.000
 A5R  H1G   CG   CD    109.30  3.000
 A5R  H2G   CG   CB    109.63  3.000
 A5R  H1G   CG   CB    109.58  3.000
 A5R  CD    CG   CB    111.36  3.000
 A5R  NH2   CZ   NH1   119.68  3.000
 A5R  NH2   CZ   NE    119.79  3.000
 A5R  NH1   CZ   NE    120.53  3.000
 A5R  H2H1  NH1  H1H1  116.85  3.000
 A5R  H2H1  NH1  CZ    120.92  3.000
 A5R  H1H1  NH1  CZ    122.15  3.000
 A5R  H2H2  NH2  H1H2  117.22  3.000
 A5R  H2H2  NH2  CZ    121.30  3.000
 A5R  H1H2  NH2  CZ    121.27  3.000
 A5R  O3    C1   C2    111.80  3.000
 A5R  O3    C1   O1    122.87  3.000
 A5R  C2    C1   O1    125.34  3.000
 A5R  H22   C2   H12   105.42  3.000
 A5R  H22   C2   C3    110.92  3.000
 A5R  H12   C2   C3    110.49  3.000
 A5R  H22   C2   C1    108.14  3.000
 A5R  H12   C2   C1    107.69  3.000
 A5R  C3    C2   C1    113.78  3.000
 A5R  H23   C3   H13   106.43  3.000
 A5R  H23   C3   C4    109.40  3.000
 A5R  H13   C3   C4    109.59  3.000
 A5R  H23   C3   C2    109.82  3.000
 A5R  H13   C3   C2    109.81  3.000
 A5R  C4    C3   C2    111.66  3.000
 A5R  H24   C4   H14   106.38  3.000
 A5R  H24   C4   C5    110.07  3.000
 A5R  H14   C4   C5    109.60  3.000
 A5R  H24   C4   C3    109.68  3.000
 A5R  H14   C4   C3    109.39  3.000
 A5R  C5    C4   C3    111.58  3.000
 A5R  H25   C5   H15   104.58  3.000
 A5R  H25   C5   C4    110.06  3.000
 A5R  H15   C5   C4    110.74  3.000
 A5R  H25   C5   C     108.05  3.000
 A5R  H15   C5   C     108.03  3.000
 A5R  C4    C5   C     114.84  3.000
 A5R  H231  O3   C1    109.89  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
 A5R  CONST_01  NH1   CZ   NE  CD      0.00   0.0  0
 A5R  CONST_02  NH2   CZ   NE  CD    180.00   0.0  0
 A5R  CONST_03  H1H1  NH1  CZ  NE      0.00   0.0  0
 A5R  CONST_04  H2H1  NH1  CZ  NE    180.00   0.0  0
 A5R  CONST_05  H1H2  NH2  CZ  NE      0.00   0.0  0
 A5R  CONST_06  H2H2  NH2  CZ  NE    180.00   0.0  0
 A5R  CONST_07  HNE   NE   CZ  NH1   180.00   0.0  0
 A5R  CONST_08  H231  O3   C1  O1      0.00   0.0  0
 A5R  Var_01    C3    C4   C5  C     176.91  30.0  1
 A5R  Var_02    C4    C5   C   O      10.17  30.0  1
 A5R  Var_03    CD    CG   CB  CA    179.66  30.0  3
 A5R  Var_04    NE    CD   CG  CB   -178.81  30.0  3
 A5R  Var_05    CZ    NE   CD  CG   -175.42  30.0  3
 A5R  Var_06    C4    C3   C2  C1    178.25  30.0  3
 A5R  Var_07    C3    C2   C1  O1     -4.22  30.0  3
 A5R  Var_08    C5    C4   C3  C2   -179.13  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
 A5R  chir_01  CA  C  N  CB  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
 A5R  plan-1  C     0.020
 A5R  plan-1  O     0.020
 A5R  plan-1  CA    0.020
 A5R  plan-1  C5    0.020
 A5R  plan-2  CD    0.020
 A5R  plan-2  NE    0.020
 A5R  plan-2  CZ    0.020
 A5R  plan-2  NH1   0.020
 A5R  plan-2  NH2   0.020
 A5R  plan-2  HNE   0.020
 A5R  plan-2  H1H1  0.020
 A5R  plan-2  H2H1  0.020
 A5R  plan-2  H1H2  0.020
 A5R  plan-2  H2H2  0.020
 A5R  plan-3  C1    0.020
 A5R  plan-3  O1    0.020
 A5R  plan-3  C2    0.020
 A5R  plan-3  O3    0.020
 A5R  plan-3  H231  0.020

