# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:29:24 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-{4-[(2S,3R)-2-amino-4-bromo-3-hydroxybutyl]phenoxy}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(OCCCC(O)=O)cc1)[C@@H](O)CBr
#
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
 RTY  RTY  '4-{4-[(2S,3R)-2-amino-4-bromo-3-hydroxybutyl]phenoxy}butanoic acid'  ligand  39  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RTY
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
 RTY  C    C   CH1    0   0.035  -3.9244  -0.1429  -0.3403
 RTY  N    N   NH2    0  -0.786  -2.3355  -1.0506   1.4152
 RTY  O    O   OH1    0  -0.654  -4.5867  -1.3590  -0.5777
 RTY  C1   C   CH2    0  -0.164   4.7209   0.1729  -0.2465
 RTY  O1   O   O      0  -0.607   8.9082  -0.2056   0.6176
 RTY  C2   C   C      0   0.417   8.5395   0.8967   0.1682
 RTY  C3   C   CH2    0  -0.591   7.0543   1.0614  -0.2040
 RTY  C4   C   CH2    0  -0.451   6.1518  -0.1064   0.1613
 RTY  C6   C   CH2    0  -0.544  -4.6842   0.7496   0.6254
 RTY  CA   C   CH1    0  -0.107  -2.4743  -0.3446   0.1574
 RTY  CB   C   CH2    0  -0.517  -1.6514  -1.0592  -0.9218
 RTY  CG   C   CR6    0   0.138  -0.1751  -1.0163  -0.6535
 RTY  CZ   C   CR6    0   0.366   2.5935  -0.8944  -0.1407
 RTY  CD1  C   CR16   0  -0.300   0.5906   0.0664  -1.0661
 RTY  CD2  C   CR16   0  -0.292   0.4784  -2.0405   0.0306
 RTY  CE1  C   CR16   0  -0.370   1.9574   0.1421  -0.8192
 RTY  CE2  C   CR16   0  -0.340   1.8377  -1.9896   0.2829
 RTY  H    H   HCH1   0   0.246  -3.8677   0.3654  -1.3077
 RTY  HN   H   HNH2   0   0.354  -2.8082  -0.5837   2.1770
 RTY  HNA  H   HNH2   0   0.339  -2.6947  -1.9949   1.3589
 RTY  HO   H   HOH1   0   0.440  -4.6663  -1.8381   0.2549
 RTY  H1   H   HCH2   0   0.213   4.3609   1.0919   0.2328
 RTY  H1A  H   HCH2   0   0.213   4.6605   0.3264  -1.3308
 RTY  O2   O   OC    -1  -0.631   9.2605   1.8981  -0.0241
 RTY  H3   H   HCH2   0   0.222   6.6826   1.9798   0.2638
 RTY  H3A  H   HCH2   0   0.226   6.9961   1.2502  -1.2827
 RTY  H4   H   HCH2   0   0.221   6.1946  -0.2897   1.2377
 RTY  H4A  H   HCH2   0   0.222   6.5005  -1.0177  -0.3298
 RTY  BR1  BR  BR     0  -0.138  -6.4931   1.1442  -0.0305
 RTY  H6   H   HCH2   0   0.281  -4.8128   0.2872   1.6050
 RTY  H6A  H   HCH2   0   0.296  -4.1806   1.7070   0.7533
 RTY  HA   H   HCH1   0   0.242  -2.0477   0.6560   0.2937
 RTY  HB   H   HCH2   0   0.243  -1.9893  -2.0960  -1.0042
 RTY  HBA  H   HCH2   0   0.246  -1.8599  -0.5909  -1.8871
 RTY  HD1  H   HCR6   0   0.245   0.1161   0.8825  -1.5997
 RTY  HD2  H   HCR6   0   0.240  -0.0837  -2.9023   0.3690
 RTY  HE1  H   HCR6   0   0.273   2.5023   1.0080  -1.1696
 RTY  HE2  H   HCR6   0   0.254   2.3259  -2.8011   0.8088
 RTY  OH   O   O2     0  -0.479   3.9118  -0.9279   0.1404

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
 RTY  C    O    single    1.405  0.020  1.405
 RTY  C    H    single    0.970  0.020  1.090
 RTY  N    CA   single    1.449  0.020  1.449
 RTY  N    HN   single    0.890  0.020  1.040
 RTY  N    HNA  single    0.890  0.020  1.040
 RTY  O    HO   single    0.850  0.020  0.980
 RTY  C1   H1   single    0.970  0.020  1.090
 RTY  C1   H1A  single    0.970  0.020  1.090
 RTY  C2   O1   deloc     1.246  0.020  1.246
 RTY  C2   O2   deloc     1.249  0.020  1.249
 RTY  C3   C2   single    1.540  0.020  1.540
 RTY  C3   H3   single    0.970  0.020  1.090
 RTY  C3   H3A  single    0.970  0.020  1.090
 RTY  C4   C1   single    1.514  0.020  1.514
 RTY  C4   C3   single    1.520  0.020  1.520
 RTY  C4   H4   single    0.970  0.020  1.090
 RTY  C4   H4A  single    0.970  0.020  1.090
 RTY  C6   C    single    1.519  0.020  1.519
 RTY  C6   BR1  single    1.964  0.020  1.964
 RTY  C6   H6   single    0.970  0.020  1.090
 RTY  C6   H6A  single    0.970  0.020  1.090
 RTY  CA   C    single    1.546  0.020  1.546
 RTY  CA   CB   single    1.534  0.020  1.534
 RTY  CA   HA   single    0.970  0.020  1.090
 RTY  CB   HB   single    0.970  0.020  1.090
 RTY  CB   HBA  single    0.970  0.020  1.090
 RTY  CG   CB   single    1.501  0.020  1.501
 RTY  CG   CD2  aromatic  1.394  0.020  1.394
 RTY  OH   C1   single    1.420  0.020  1.420
 RTY  OH   CZ   single    1.348  0.020  1.348
 RTY  CZ   CE2  aromatic  1.397  0.020  1.397
 RTY  CD1  CG   aromatic  1.389  0.020  1.389
 RTY  CD1  HD1  single    0.930  0.020  1.080
 RTY  CD2  HD2  single    0.930  0.020  1.080
 RTY  CE1  CZ   aromatic  1.393  0.020  1.393
 RTY  CE1  CD1  aromatic  1.391  0.020  1.391
 RTY  CE1  HE1  single    0.930  0.020  1.080
 RTY  CE2  CD2  aromatic  1.383  0.020  1.383
 RTY  CE2  HE2  single    0.930  0.020  1.080

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
 RTY  H    C    CA   107.25  3.000
 RTY  CA   C    C6   109.95  3.000
 RTY  H    C    C6   108.37  3.000
 RTY  CA   C    O    112.55  3.000
 RTY  C6   C    O    112.35  3.000
 RTY  H    C    O    106.09  3.000
 RTY  HNA  N    HN   107.87  3.000
 RTY  HNA  N    CA   111.87  3.000
 RTY  HN   N    CA   112.60  3.000
 RTY  HO   O    C    108.86  3.000
 RTY  H1A  C1   H1   107.25  3.000
 RTY  H1A  C1   OH   110.27  3.000
 RTY  H1   C1   OH   110.08  3.000
 RTY  OH   C1   C4   108.80  3.000
 RTY  H1A  C1   C4   110.13  3.000
 RTY  H1   C1   C4   110.31  3.000
 RTY  O2   C2   C3   115.71  3.000
 RTY  C3   C2   O1   117.85  3.000
 RTY  O2   C2   O1   126.44  3.000
 RTY  H3A  C3   H3   104.94  3.000
 RTY  H3A  C3   C4   109.70  3.000
 RTY  H3   C3   C4   109.86  3.000
 RTY  C4   C3   C2   115.61  3.000
 RTY  H3A  C3   C2   107.90  3.000
 RTY  H3   C3   C2   108.28  3.000
 RTY  H4A  C4   H4   106.88  3.000
 RTY  H4A  C4   C3   110.08  3.000
 RTY  H4   C4   C3   110.02  3.000
 RTY  H4A  C4   C1   109.54  3.000
 RTY  H4   C4   C1   109.47  3.000
 RTY  C3   C4   C1   110.77  3.000
 RTY  H6A  C6   H6   108.76  3.000
 RTY  H6A  C6   BR1  106.76  3.000
 RTY  H6   C6   BR1  106.05  3.000
 RTY  H6A  C6   C    111.10  3.000
 RTY  H6   C6   C    112.39  3.000
 RTY  BR1  C6   C    111.50  3.000
 RTY  HA   CA   CB   107.69  3.000
 RTY  HA   CA   N    107.43  3.000
 RTY  CB   CA   N    109.41  3.000
 RTY  HA   CA   C    106.61  3.000
 RTY  CB   CA   C    109.73  3.000
 RTY  N    CA   C    115.64  3.000
 RTY  HBA  CB   HB   106.30  3.000
 RTY  HBA  CB   CG   109.46  3.000
 RTY  HB   CB   CG   110.15  3.000
 RTY  CG   CB   CA   112.87  3.000
 RTY  HBA  CB   CA   108.63  3.000
 RTY  HB   CB   CA   109.21  3.000
 RTY  CD2  CG   CD1  117.39  3.000
 RTY  CD1  CG   CB   120.76  3.000
 RTY  CD2  CG   CB   121.85  3.000
 RTY  CE2  CZ   CE1  118.96  3.000
 RTY  CE1  CZ   OH   124.52  3.000
 RTY  CE2  CZ   OH   116.52  3.000
 RTY  HD1  CD1  CE1  118.45  3.000
 RTY  CE1  CD1  CG   122.10  3.000
 RTY  HD1  CD1  CG   119.45  3.000
 RTY  HD2  CD2  CE2  118.83  3.000
 RTY  CE2  CD2  CG   121.53  3.000
 RTY  HD2  CD2  CG   119.64  3.000
 RTY  HE1  CE1  CD1  118.76  3.000
 RTY  HE1  CE1  CZ   121.58  3.000
 RTY  CD1  CE1  CZ   119.66  3.000
 RTY  HE2  CE2  CD2  120.25  3.000
 RTY  HE2  CE2  CZ   119.39  3.000
 RTY  CD2  CE2  CZ   120.36  3.000
 RTY  CZ   OH   C1   118.75  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
 RTY  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 RTY  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 RTY  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 RTY  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 RTY  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 RTY  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 RTY  CONST_07  CE2  CD2  CG   CB    180.00   0.0  0
 RTY  CONST_08  CE1  CD1  CG   CB    180.00   0.0  0
 RTY  CONST_09  CD2  CE2  CZ   OH    180.00   0.0  0
 RTY  CONST_10  CD1  CE1  CZ   OH    180.00   0.0  0
 RTY  CONST_11  HE2  CE2  CD2  CG    180.00   0.0  0
 RTY  CONST_12  HE1  CE1  CD1  CG    180.00   0.0  0
 RTY  CONST_13  HD2  CD2  CE2  CZ    180.00   0.0  0
 RTY  CONST_14  HD1  CD1  CE1  CZ    180.00   0.0  0
 RTY  Var_01    CE2  CZ   OH   C1   -178.83  30.0  2
 RTY  Var_02    CD2  CG   CB   CA     93.19  30.0  2
 RTY  Var_03    H1   C1   OH   CZ     59.67  30.0  3
 RTY  Var_04    C2   C3   C4   C1    179.74  30.0  3
 RTY  Var_05    C4   C3   C2   O1      6.42  30.0  3
 RTY  Var_06    OH   C1   C4   C3   -178.69  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
 RTY  chir_01  C   O  C6  CA  negativ
 RTY  chir_02  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
 RTY  plan-1  CB   0.020
 RTY  plan-1  CG   0.020
 RTY  plan-1  CZ   0.020
 RTY  plan-1  CD1  0.020
 RTY  plan-1  CD2  0.020
 RTY  plan-1  CE1  0.020
 RTY  plan-1  CE2  0.020
 RTY  plan-1  OH   0.020
 RTY  plan-1  HD1  0.020
 RTY  plan-1  HD2  0.020
 RTY  plan-1  HE1  0.020
 RTY  plan-1  HE2  0.020
 RTY  plan-2  O1   0.020
 RTY  plan-2  C2   0.020
 RTY  plan-2  C3   0.020
 RTY  plan-2  O2   0.020

