# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:15:24 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (2R)-2-amino-3-[(3-aminopropyl)sulfanyl]propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCSC[C@H](N)CO
#
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
 BPE  BPE  (2R)-2-amino-3-[(3-aminopropyl)sulfanyl]propan-1-ol  L-peptide  26  10  .  2019-03-22  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BPE
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
 BPE  N     N  NH2   0  -0.787  3.4587  49.0896  14.7561
 BPE  CA    C  CH1   0  -0.111  3.5379  48.5699  16.1112
 BPE  CB    C  CH2   0  -0.542  3.9997  47.1157  16.1126
 BPE  SG    S  S2    0  -0.038  5.5886  46.8154  15.2811
 BPE  C05   C  CH2   0  -0.549  5.4045  45.0293  14.9885
 BPE  C     C  CH2   0  -0.148  4.3787  49.4777  16.9930
 BPE  O     O  OH1   0  -0.657  5.6950  49.5685  16.5059
 BPE  C08   C  CH2   0  -0.440  6.6237  44.4626  14.2772
 BPE  C09   C  CH2   0  -0.267  6.8355  45.0209  12.8765
 BPE  N10   N  NH2   0  -0.797  7.9529  44.3518  12.2277
 BPE  HN1   H  HNH2  0   0.344  2.9886  49.9868  14.7694
 BPE  HN2   H  HNH2  0   0.343  2.8754  48.4809  14.1952
 BPE  HA    H  HCH1  0   0.222  2.5541  48.5391  16.6086
 BPE  HB1   H  HCH2  0   0.260  4.0473  46.7552  17.1424
 BPE  HB2   H  HCH2  0   0.264  3.2462  46.5134  15.5974
 BPE  H051  H  HCH2  0   0.261  5.2631  44.5235  15.9455
 BPE  H052  H  HCH2  0   0.248  4.5048  44.8569  14.3915
 BPE  H1    H  HCH2  0   0.198  3.8961  50.4652  17.0303
 BPE  H2    H  HCH2  0   0.197  4.3475  49.0752  18.0142
 BPE  HO    H  HOH1  0   0.452  6.2136  50.0727  17.1389
 BPE  H081  H  HCH2  0   0.227  7.5220  44.6275  14.8782
 BPE  H082  H  HCH2  0   0.235  6.4916  43.3776  14.2111
 BPE  H091  H  HCH2  0   0.189  5.8897  44.9447  12.3191
 BPE  H092  H  HCH2  0   0.216  7.0678  46.0867  12.9357
 BPE  H101  H  HNH2  0   0.344  8.1215  44.7730  11.3232
 BPE  H102  H  HNH2  0   0.336  7.7025  43.3891  12.0371

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
 BPE  N    CA    single  1.458  0.019  1.458
 BPE  N    HN1   single  0.890  0.020  1.040
 BPE  N    HN2   single  0.890  0.020  1.040
 BPE  CA   CB    single  1.530  0.020  1.530
 BPE  CA   C     single  1.525  0.021  1.525
 BPE  CA   HA    single  0.970  0.020  0.970
 BPE  CB   SG    single  1.818  0.020  1.818
 BPE  CB   HB1   single  0.970  0.020  1.090
 BPE  CB   HB2   single  0.970  0.020  1.090
 BPE  SG   C05   single  1.819  0.020  1.819
 BPE  C05  C08   single  1.521  0.020  1.521
 BPE  C05  H051  single  0.970  0.020  1.090
 BPE  C05  H052  single  0.970  0.020  1.090
 BPE  C    O     single  1.231  0.020  1.231
 BPE  C    H1    single  0.970  0.020  1.090
 BPE  C    H2    single  0.970  0.020  1.090
 BPE  O    HO    single  0.850  0.020  0.980
 BPE  C08  C09   single  1.523  0.020  1.523
 BPE  C08  H081  single  0.970  0.020  1.090
 BPE  C08  H082  single  0.970  0.020  1.090
 BPE  C09  N10   single  1.455  0.020  1.455
 BPE  C09  H091  single  0.970  0.020  1.090
 BPE  C09  H092  single  0.970  0.020  1.090
 BPE  N10  H101  single  0.890  0.020  1.040
 BPE  N10  H102  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
 BPE  HN2   N    HN1   105.81  3.000
 BPE  HN2   N    CA    109.44  3.000
 BPE  HN1   N    CA    109.26  3.000
 BPE  HA    CA   C     109.00  3.000
 BPE  HA    CA   CB    109.00  3.000
 BPE  C     CA   CB    110.10  1.900
 BPE  HA    CA   N     110.00  3.000
 BPE  C     CA   N     111.00  2.800
 BPE  CB    CA   N     110.50  1.700
 BPE  HB2   CB   HB1   107.01  3.000
 BPE  HB2   CB   SG    107.20  3.000
 BPE  HB1   CB   SG    109.80  3.000
 BPE  HB2   CB   CA    108.41  3.000
 BPE  HB1   CB   CA    109.18  3.000
 BPE  SG    CB   CA    114.93  3.000
 BPE  C05   SG   CB     98.46  3.000
 BPE  H052  C05  H051  107.40  3.000
 BPE  H052  C05  C08   110.21  3.000
 BPE  H051  C05  C08   109.94  3.000
 BPE  H052  C05  SG    109.02  3.000
 BPE  H051  C05  SG    109.09  3.000
 BPE  C08   C05  SG    111.09  3.000
 BPE  H2    C    H1    106.57  3.000
 BPE  H2    C    O     111.86  3.000
 BPE  H1    C    O     111.37  3.000
 BPE  H2    C    CA    107.76  3.000
 BPE  H1    C    CA    108.26  3.000
 BPE  O     C    CA    120.80  1.700
 BPE  HO    O    C     108.10  3.000
 BPE  H082  C08  H081  106.36  3.000
 BPE  H082  C08  C09   108.94  3.000
 BPE  H081  C08  C09   109.64  3.000
 BPE  H082  C08  C05   107.50  3.000
 BPE  H081  C08  C05   110.20  3.000
 BPE  C09   C08  C05   113.90  3.000
 BPE  H092  C09  H091  106.13  3.000
 BPE  H092  C09  N10   108.03  3.000
 BPE  H091  C09  N10   113.72  3.000
 BPE  H092  C09  C08   109.72  3.000
 BPE  H091  C09  C08   108.72  3.000
 BPE  N10   C09  C08   110.39  3.000
 BPE  H102  N10  H101  105.58  3.000
 BPE  H102  N10  C09   109.34  3.000
 BPE  H101  N10  C09   109.58  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
 BPE  Var_01  C08   C05  SG   CB    179.95  30.0  3
 BPE  Var_02  C09   C08  C05  SG    -64.15  30.0  3
 BPE  Var_03  N10   C09  C08  C05  -175.42  30.0  3
 BPE  Var_04  HB1   CB   SG   C05    76.47  30.0  1
 BPE  Var_05  H101  N10  C09  C08  -176.30  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
 BPE  chir_01  CA  N  CB  C  negativ

