# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 14:10:01 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-({[4-(aminomethyl)-5-hydroxy-6-methylpyridin-3-yl]methyl}disulfanyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CSSC[C@H](N)C(O)=O)c(CN)c1O
#
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
 PYX  PYX  3-({[4-(aminomethyl)-5-hydroxy-6-methylpyridin-3-yl]methyl}disulfanyl)-L-alanine  L-peptide  35  19  .  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_PYX
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
 PYX  N     N  NH2    0  -0.788  2.6016  33.0114  25.4060
 PYX  CA    C  CH1    0  -0.214  3.0937  33.9759  24.4437
 PYX  C     C  C      0   0.411  1.9533  34.9098  23.9414
 PYX  O     O  O      0  -0.590  0.7925  34.4694  24.0277
 PYX  OXT   O  OC    -1  -0.602  2.3200  35.9983  23.4618
 PYX  CB    C  CH2    0  -0.552  3.7408  33.3517  23.1977
 PYX  SG    S  S2     0  -0.070  5.2482  32.4367  23.6883
 PYX  SD    S  S2     0  -0.034  5.5033  31.0542  22.1998
 PYX  CE    C  CH2    0  -0.661  6.4562  31.9775  20.9344
 PYX  C1    C  CR6    0  -0.003  6.7871  31.0307  19.8227
 PYX  C2    C  CR16   0  -0.125  6.0174  31.0682  18.6655
 PYX  C6    C  CR6    0   0.101  7.8216  30.0948  19.8993
 PYX  N3    N  N      0  -0.405  6.2166  30.2800  17.6221
 PYX  C5    C  CR6    0   0.268  8.0211  29.2733  18.7902
 PYX  CM6   C  CH2    0  -0.371  8.7122  29.9385  21.1056
 PYX  C4    C  CR6    0   0.128  7.1998  29.3905  17.6624
 PYX  O5    O  OH1    0  -0.623  9.0276  28.3780  18.8554
 PYX  N6    N  NH2    0  -0.791  8.4067  28.7118  21.8334
 PYX  CM4   C  CH3    0  -0.781  7.4127  28.5162  16.4625
 PYX  H     H  HNH2   0   0.331  3.2704  32.2604  25.5283
 PYX  H2    H  HNH2   0   0.329  1.7550  32.5965  25.0369
 PYX  HA    H  HCH1   0   0.220  3.8433  34.6099  24.9308
 PYX  HB2   H  HCH2   0   0.266  3.0546  32.6454  22.7270
 PYX  HB3   H  HCH2   0   0.268  4.0154  34.1179  22.4737
 PYX  HE2   H  HCH2   0   0.301  5.8414  32.7982  20.5660
 PYX  HE3   H  HCH2   0   0.295  7.3415  32.3997  21.4073
 PYX  HC2   H  HCR6   0   0.255  5.2031  31.7814  18.5854
 PYX  HM61  H  HCH2   0   0.224  9.7580  30.0107  20.7801
 PYX  HM62  H  HCH2   0   0.245  8.5522  30.7733  21.7859
 PYX  HO5   H  HOH1   0   0.486  9.0800  27.8455  18.0537
 PYX  HN61  H  HNH2   0   0.352  8.9228  28.7191  22.7041
 PYX  HN62  H  HNH2   0   0.346  8.7550  27.9143  21.3173
 PYX  HM41  H  HCH3   0   0.257  8.4039  28.6581  16.0240
 PYX  HM42  H  HCH3   0   0.256  7.3114  27.4543  16.7024
 PYX  HM43  H  HCH3   0   0.270  6.6768  28.7523  15.6978

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
 PYX  N    CA    single    1.458  0.019  1.458
 PYX  N    H     single    0.860  0.020  0.860
 PYX  N    H2    single    0.890  0.020  1.040
 PYX  CA   C     single    1.525  0.021  1.525
 PYX  CA   CB    single    1.530  0.020  1.530
 PYX  CA   HA    single    0.970  0.020  0.970
 PYX  C    O     deloc     1.231  0.020  1.231
 PYX  C    OXT   deloc     1.245  0.020  1.245
 PYX  CB   SG    single    1.830  0.020  1.830
 PYX  CB   HB2   single    0.970  0.020  1.090
 PYX  CB   HB3   single    0.970  0.020  1.090
 PYX  SG   SD    single    2.047  0.020  2.047
 PYX  SD   CE    single    1.833  0.020  1.833
 PYX  CE   C1    single    1.497  0.020  1.497
 PYX  CE   HE2   single    0.970  0.020  1.090
 PYX  CE   HE3   single    0.970  0.020  1.090
 PYX  C1   C2    aromatic  1.390  0.020  1.390
 PYX  C1   C6    aromatic  1.397  0.020  1.397
 PYX  C2   N3    aromatic  1.323  0.020  1.323
 PYX  C2   HC2   single    0.930  0.020  1.080
 PYX  C6   C5    aromatic  1.395  0.020  1.395
 PYX  C6   CM6   single    1.508  0.020  1.508
 PYX  N3   C4    aromatic  1.326  0.020  1.326
 PYX  C5   C4    aromatic  1.400  0.020  1.400
 PYX  C5   O5    single    1.349  0.020  1.349
 PYX  CM6  N6    single    1.459  0.020  1.459
 PYX  CM6  HM61  single    0.970  0.020  1.090
 PYX  CM6  HM62  single    0.970  0.020  1.090
 PYX  C4   CM4   single    1.500  0.020  1.500
 PYX  O5   HO5   single    0.850  0.020  0.980
 PYX  N6   HN61  single    0.890  0.020  1.040
 PYX  N6   HN62  single    0.890  0.020  1.040
 PYX  CM4  HM41  single    0.970  0.020  1.090
 PYX  CM4  HM42  single    0.970  0.020  1.090
 PYX  CM4  HM43  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
 PYX  H2    N    H     106.99  3.000
 PYX  H2    N    CA    108.34  3.000
 PYX  H     N    CA    114.00  3.000
 PYX  HA    CA   CB    109.00  3.000
 PYX  HA    CA   C     109.00  3.000
 PYX  CB    CA   C     110.10  1.900
 PYX  HA    CA   N     110.00  3.000
 PYX  CB    CA   N     110.50  1.700
 PYX  C     CA   N     111.00  2.800
 PYX  OXT   C    O     127.66  3.000
 PYX  OXT   C    CA    115.65  3.000
 PYX  O     C    CA    120.80  1.700
 PYX  HB3   CB   HB2   109.09  3.000
 PYX  HB3   CB   SG    108.79  3.000
 PYX  HB2   CB   SG    108.05  3.000
 PYX  HB3   CB   CA    111.06  3.000
 PYX  HB2   CB   CA    110.35  3.000
 PYX  SG    CB   CA    109.43  3.000
 PYX  SD    SG   CB    104.20  3.000
 PYX  CE    SD   SG    103.09  3.000
 PYX  HE3   CE   HE2   108.27  3.000
 PYX  HE3   CE   C1    112.82  3.000
 PYX  HE2   CE   C1    110.48  3.000
 PYX  HE3   CE   SD    108.55  3.000
 PYX  HE2   CE   SD    108.63  3.000
 PYX  C1    CE   SD    108.00  3.000
 PYX  C6    C1   C2    118.27  3.000
 PYX  C6    C1   CE    123.13  3.000
 PYX  C2    C1   CE    118.60  3.000
 PYX  HC2   C2   N3    116.50  3.000
 PYX  HC2   C2   C1    119.64  3.000
 PYX  N3    C2   C1    123.86  3.000
 PYX  CM6   C6   C5    119.39  3.000
 PYX  CM6   C6   C1    123.42  3.000
 PYX  C5    C6   C1    117.19  3.000
 PYX  C4    N3   C2    119.16  3.000
 PYX  O5    C5   C4    122.16  3.000
 PYX  O5    C5   C6    117.35  3.000
 PYX  C4    C5   C6    120.49  3.000
 PYX  HM62  CM6  HM61  105.96  3.000
 PYX  HM62  CM6  N6    107.59  3.000
 PYX  HM61  CM6  N6    113.75  3.000
 PYX  HM62  CM6  C6    109.49  3.000
 PYX  HM61  CM6  C6    108.59  3.000
 PYX  N6    CM6  C6    111.26  3.000
 PYX  CM4   C4   C5    120.82  3.000
 PYX  CM4   C4   N3    118.15  3.000
 PYX  C5    C4   N3    121.03  3.000
 PYX  HO5   O5   C5    111.54  3.000
 PYX  HN62  N6   HN61  105.60  3.000
 PYX  HN62  N6   CM6   109.65  3.000
 PYX  HN61  N6   CM6   108.44  3.000
 PYX  HM43  CM4  HM42  107.61  3.000
 PYX  HM43  CM4  HM41  107.66  3.000
 PYX  HM42  CM4  HM41  107.34  3.000
 PYX  HM43  CM4  C4    109.88  3.000
 PYX  HM42  CM4  C4    112.18  3.000
 PYX  HM41  CM4  C4    111.96  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
 PYX  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 PYX  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 PYX  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 PYX  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 PYX  CONST_05  N3    C2   C1   C6      0.00   0.0  0
 PYX  CONST_06  N3    C4   C5   C6      0.00   0.0  0
 PYX  CONST_07  N3    C2   C1   CE    180.00   0.0  0
 PYX  CONST_08  C5    C6   C1   CE    180.00   0.0  0
 PYX  CONST_09  O5    C5   C6   C1    180.00   0.0  0
 PYX  CONST_10  CM6   C6   C1   C2    180.00   0.0  0
 PYX  CONST_11  CM4   C4   N3   C2    180.00   0.0  0
 PYX  CONST_12  CM4   C4   C5   C6    180.00   0.0  0
 PYX  CONST_13  O5    C5   C4   N3    180.00   0.0  0
 PYX  CONST_14  C4    C5   C6   CM6   180.00   0.0  0
 PYX  CONST_15  HC2   C2   C1   C6    180.00   0.0  0
 PYX  Var_01    C2    C1   CE   SD    100.52  30.0  2
 PYX  Var_02    N6    CM6  C6   C1    107.65  30.0  2
 PYX  Var_03    HM41  CM4  C4   N3    119.00  30.0  2
 PYX  Var_04    C1    CE   SD   SG    176.21  30.0  3
 PYX  Var_05    HN61  N6   CM6  C6   -171.37  30.0  3
 PYX  Var_06    HB2   CB   SG   SD     35.74  30.0  2

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
 PYX  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
 PYX  plan-1  CE   0.020
 PYX  plan-1  C1   0.020
 PYX  plan-1  C2   0.020
 PYX  plan-1  C6   0.020
 PYX  plan-1  N3   0.020
 PYX  plan-1  C5   0.020
 PYX  plan-1  CM6  0.020
 PYX  plan-1  C4   0.020
 PYX  plan-1  O5   0.020
 PYX  plan-1  CM4  0.020
 PYX  plan-1  HC2  0.020
 PYX  plan-2  CA   0.020
 PYX  plan-2  C    0.020
 PYX  plan-2  O    0.020
 PYX  plan-2  OXT  0.020

