# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:50:21 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: {[(4S)-4-amino-4-carboxybutyl]amino}{[(2R)-2-amino-2-carboxyethyl]sulfanyl}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=[NH2+])SC[C@H](N)C(O)=O)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
 CYR  CYR  {[(4S)-4-amino-4-carboxybutyl]amino}{[(2R)-2-amino-2-carboxyethyl]sulfanyl}methaniminium  L-peptide  35  18  .  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_CYR
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
 CYR  O1    O  OC    -1  -0.607  25.9695  48.5256  0.4107
 CYR  C1    C  C      0   0.400  26.2035  49.5768  1.0382
 CYR  O2    O  O      0  -0.606  25.3646  50.3351  1.5682
 CYR  C2    C  CH1    0  -0.172  27.6875  49.9681  1.2254
 CYR  N2    N  NH2    0  -0.799  27.8414  51.4088  1.0664
 CYR  C3    C  CH2    0  -0.449  28.1939  49.4674  2.5862
 CYR  C4    C  CH2    0  -0.433  28.1702  47.9552  2.7721
 CYR  C5    C  CH2    0  -0.293  28.8823  47.5697  4.0609
 CYR  N6    N  NH1    0  -0.579  28.8654  46.1383  4.3317
 CYR  C7    C  C      0   0.445  27.9369  45.4717  4.9840
 CYR  N7    N  NC2    1  -0.767  28.0451  44.2032  5.2774
 CYR  SG    S  S2     0   0.050  26.4307  46.3033  5.3682
 CYR  CB    C  CH2    0  -0.559  26.1572  46.0438  7.1671
 CYR  CA    C  CH1    0  -0.226  26.3212  44.6394  7.7360
 CYR  C     C  C      0   0.428  25.6605  44.5745  9.1471
 CYR  O     O  O      0  -0.593  25.8523  45.5675  9.8724
 CYR  N     N  NH2    0  -0.811  25.8737  43.6205  6.7966
 CYR  OXT   O  OC    -1  -0.584  25.0423  43.5325  9.4200
 CYR  HC2   H  HCH1   0   0.191  28.2775  49.4716  0.4472
 CYR  HN21  H  HNH2   0   0.327  28.7469  51.6964  1.4192
 CYR  HN22  H  HNH2   0   0.324  27.1508  51.8591  1.6556
 CYR  H31   H  HCH2   0   0.213  27.6066  49.9421  3.3802
 CYR  H32   H  HCH2   0   0.216  29.2235  49.8224  2.7157
 CYR  H41   H  HCH2   0   0.227  28.6568  47.4612  1.9264
 CYR  H42   H  HCH2   0   0.231  27.1418  47.5889  2.8007
 CYR  H51   H  HCH2   0   0.262  28.4468  48.0919  4.9128
 CYR  H52   H  HCH2   0   0.273  29.9324  47.8574  4.0120
 CYR  HN6   H  HNH1   0   0.427  29.6477  45.6036  3.9757
 CYR  HN71  H  HNC2   0   0.420  28.9053  43.6999  5.1094
 CYR  HN72  H  HNC2   0   0.466  27.2229  43.7333  5.7398
 CYR  HB3   H  HCH2   0   0.294  25.1242  46.3875  7.2588
 CYR  HB2   H  HCH2   0   0.303  26.7872  46.7469  7.7029
 CYR  HA    H  HCH1   0   0.251  27.3931  44.4732  7.8974
 CYR  H     H  HNH2   0   0.362  24.9502  43.8428  6.4407
 CYR  H2    H  HNH2   0   0.369  25.7691  42.7483  7.3026

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
 CYR  O1  C1    deloc   1.246  0.020  1.246
 CYR  C1  O2    deloc   1.249  0.020  1.249
 CYR  C1  C2    single  1.546  0.020  1.546
 CYR  C2  N2    single  1.458  0.020  1.458
 CYR  C2  C3    single  1.536  0.020  1.536
 CYR  C2  HC2   single  0.970  0.020  1.090
 CYR  N2  HN21  single  0.890  0.020  1.040
 CYR  N2  HN22  single  0.890  0.020  1.040
 CYR  C3  C4    single  1.524  0.020  1.524
 CYR  C3  H31   single  0.970  0.020  1.090
 CYR  C3  H32   single  0.970  0.020  1.090
 CYR  C4  C5    single  1.522  0.020  1.522
 CYR  C4  H41   single  0.970  0.020  1.090
 CYR  C4  H42   single  0.970  0.020  1.090
 CYR  C5  N6    single  1.457  0.020  1.457
 CYR  C5  H51   single  0.970  0.020  1.090
 CYR  C5  H52   single  0.970  0.020  1.090
 CYR  N6  C7    single  1.316  0.020  1.316
 CYR  N6  HN6   single  0.860  0.020  1.020
 CYR  C7  N7    double  1.306  0.020  1.306
 CYR  C7  SG    single  1.763  0.020  1.763
 CYR  N7  HN71  single  0.860  0.020  1.020
 CYR  N7  HN72  single  0.860  0.020  1.020
 CYR  SG  CB    single  1.838  0.020  1.838
 CYR  CB  CA    single  1.530  0.020  1.530
 CYR  CB  HB3   single  0.970  0.020  1.090
 CYR  CB  HB2   single  0.970  0.020  1.090
 CYR  CA  C     single  1.525  0.021  1.525
 CYR  CA  N     single  1.458  0.019  1.458
 CYR  CA  HA    single  0.970  0.020  0.970
 CYR  C   O     deloc   1.231  0.020  1.231
 CYR  C   OXT   deloc   1.242  0.020  1.242
 CYR  N   H     single  0.860  0.020  0.860
 CYR  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
 CYR  C2    C1  O2    116.08  3.000
 CYR  C2    C1  O1    117.04  3.000
 CYR  O2    C1  O1    126.85  3.000
 CYR  HC2   C2  C3    107.70  3.000
 CYR  HC2   C2  N2    108.28  3.000
 CYR  C3    C2  N2    112.58  3.000
 CYR  HC2   C2  C1    108.43  3.000
 CYR  C3    C2  C1    109.95  3.000
 CYR  N2    C2  C1    109.78  3.000
 CYR  HN22  N2  HN21  106.29  3.000
 CYR  HN22  N2  C2    107.69  3.000
 CYR  HN21  N2  C2    109.69  3.000
 CYR  H32   C3  H31   106.10  3.000
 CYR  H32   C3  C4    108.75  3.000
 CYR  H31   C3  C4    109.46  3.000
 CYR  H32   C3  C2    107.98  3.000
 CYR  H31   C3  C2    108.91  3.000
 CYR  C4    C3  C2    115.25  3.000
 CYR  H42   C4  H41   106.72  3.000
 CYR  H42   C4  C5    109.48  3.000
 CYR  H41   C4  C5    109.41  3.000
 CYR  H42   C4  C3    110.53  3.000
 CYR  H41   C4  C3    110.30  3.000
 CYR  C5    C4  C3    110.33  3.000
 CYR  H52   C5  H51   107.07  3.000
 CYR  H52   C5  N6    106.19  3.000
 CYR  H51   C5  N6    108.71  3.000
 CYR  H52   C5  C4    110.24  3.000
 CYR  H51   C5  C4    110.71  3.000
 CYR  N6    C5  C4    113.63  3.000
 CYR  HN6   N6  C7    116.87  3.000
 CYR  HN6   N6  C5    116.40  3.000
 CYR  C7    N6  C5    126.73  3.000
 CYR  SG    C7  N7    118.67  3.000
 CYR  SG    C7  N6    118.16  3.000
 CYR  N7    C7  N6    123.01  3.000
 CYR  HN72  N7  HN71  120.99  3.000
 CYR  HN72  N7  C7    117.83  3.000
 CYR  HN71  N7  C7    121.11  3.000
 CYR  CB    SG  C7    105.90  3.000
 CYR  HB2   CB  HB3   107.67  3.000
 CYR  HB2   CB  CA    110.49  3.000
 CYR  HB3   CB  CA    111.12  3.000
 CYR  HB2   CB  SG    107.78  3.000
 CYR  HB3   CB  SG    100.28  3.000
 CYR  CA    CB  SG    118.64  3.000
 CYR  HA    CA  N     110.00  3.000
 CYR  HA    CA  C     109.00  3.000
 CYR  N     CA  C     111.00  2.800
 CYR  HA    CA  CB    109.00  3.000
 CYR  N     CA  CB    110.50  1.700
 CYR  C     CA  CB    110.10  1.900
 CYR  OXT   C   O     128.18  3.000
 CYR  OXT   C   CA    116.40  3.000
 CYR  O     C   CA    120.80  1.700
 CYR  H2    N   H     105.65  3.000
 CYR  H2    N   CA    108.16  3.000
 CYR  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
 CYR  CONST_01  N7    C7  N6  C5  180.00   0.0  0
 CYR  CONST_02  SG    C7  N6  C5    0.00   0.0  0
 CYR  CONST_03  HN71  N7  C7  N6    0.00   0.0  0
 CYR  CONST_04  HN72  N7  C7  N6  180.00   0.0  0
 CYR  CONST_05  HN6   N6  C7  N7    0.00   0.0  0
 CYR  Var_01    C5    C4  C3  C2  171.52  30.0  3
 CYR  Var_02    N6    C5  C4  C3  178.17  30.0  3
 CYR  Var_03    C7    N6  C5  C4  -88.30  30.0  3
 CYR  Var_04    CA    CB  SG  C7  -46.92  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
 CYR  chir_01  C2  C1  N2  C3  negativ
 CYR  chir_02  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
 CYR  plan-1  C5    0.020
 CYR  plan-1  N6    0.020
 CYR  plan-1  C7    0.020
 CYR  plan-1  N7    0.020
 CYR  plan-1  SG    0.020
 CYR  plan-1  HN6   0.020
 CYR  plan-1  HN71  0.020
 CYR  plan-1  HN72  0.020
 CYR  plan-2  O1    0.020
 CYR  plan-2  C1    0.020
 CYR  plan-2  O2    0.020
 CYR  plan-2  C2    0.020
 CYR  plan-3  CA    0.020
 CYR  plan-3  C     0.020
 CYR  plan-3  O     0.020
 CYR  plan-3  OXT   0.020

