# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 03:27:55 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  40  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  -3.9171  -0.1416  -0.3313
 RTY  N    N   NH2   0  -0.786  -2.3517  -1.0590   1.4411
 RTY  O    O   OH1   0  -0.654  -4.5701  -1.3561  -0.6008
 RTY  C1   C   CH2   0  -0.165   4.7247   0.2018  -0.1582
 RTY  O1   O   O     0  -0.443   8.9452  -0.1662   0.7243
 RTY  C2   C   C     0   0.554   8.5041   0.8271   0.2025
 RTY  C3   C   CH2   0  -0.588   7.0615   1.0521  -0.1546
 RTY  C4   C   CH2   0  -0.462   6.1523  -0.0959   0.2519
 RTY  C6   C   CH2   0  -0.544  -4.6976   0.7296   0.6373
 RTY  CA   C   CH1   0  -0.108  -2.4746  -0.3448   0.1862
 RTY  CB   C   CH2   0  -0.517  -1.6344  -1.0512  -0.8851
 RTY  CG   C   CR6   0   0.138  -0.1619  -0.9983  -0.5980
 RTY  CZ   C   CR6   0   0.366   2.5973  -0.8596  -0.0509
 RTY  CD1  C   CR16  0  -0.300   0.6031   0.0858  -1.0080
 RTY  CD2  C   CR16  0  -0.291   0.4874  -2.0155   0.1006
 RTY  CE1  C   CR16  0  -0.369   1.9663   0.1697  -0.7438
 RTY  CE2  C   CR16  0  -0.338   1.8429  -1.9560   0.3704
 RTY  H    H   HCH1  0   0.247  -3.8464   0.3843  -1.2884
 RTY  HN   H   HNH2  0   0.355  -2.8341  -0.5971   2.1999
 RTY  HNA  H   HNH2  0   0.339  -2.7099  -2.0031   1.3746
 RTY  HO   H   HOH1  0   0.440  -4.6538  -1.8536   0.2204
 RTY  H1   H   HCH2  0   0.222   4.3788   1.1311   0.3107
 RTY  H1A  H   HCH2  0   0.221   4.6665   0.3414  -1.2442
 RTY  O2   O   OH1   0  -0.596   9.2598   1.8685  -0.1309
 RTY  H3   H   HCH2  0   0.282   6.7361   1.9884   0.3094
 RTY  H3A  H   HCH2  0   0.284   7.0056   1.2271  -1.2340
 RTY  H4   H   HCH2  0   0.245   6.2001  -0.2469   1.3323
 RTY  H4A  H   HCH2  0   0.245   6.4816  -1.0228  -0.2222
 RTY  BR1  BR  BR    0  -0.138  -6.4946   1.1324  -0.0455
 RTY  H6   H   HCH2  0   0.281  -4.8436   0.2471   1.6048
 RTY  H6A  H   HCH2  0   0.296  -4.1996   1.6857   0.7943
 RTY  HA   H   HCH1  0   0.243  -2.0527   0.6561   0.3351
 RTY  HB   H   HCH2  0   0.243  -1.9638  -2.0903  -0.9735
 RTY  HBA  H   HCH2  0   0.246  -1.8343  -0.5828  -1.8522
 RTY  HD1  H   HCR6  0   0.246   0.1319   0.8953  -1.5543
 RTY  HD2  H   HCR6  0   0.241  -0.0749  -2.8780   0.4365
 RTY  HE1  H   HCR6  0   0.274   2.5112   1.0365  -1.0923
 RTY  HE2  H   HCR6  0   0.255   2.3286  -2.7614   0.9079
 RTY  H20  H   HOH1  0   0.480  10.1839   1.6950   0.1024
 RTY  OH   O   O2    0  -0.479   3.9138  -0.8861   0.2468

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   double    1.206  0.020  1.206
 RTY  C2   O2   single    1.329  0.020  1.329
 RTY  C3   C2   single    1.503  0.020  1.503
 RTY  C3   H3   single    0.970  0.020  1.090
 RTY  C3   H3A  single    0.970  0.020  1.090
 RTY  C4   C1   single    1.515  0.020  1.515
 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    1.416  0.020  1.416
 RTY  OH   CZ   single    1.350  0.020  1.350
 RTY  CZ   CE2  aromatic  1.396  0.020  1.396
 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  1.392  0.020  1.392
 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
 RTY  O2   H20  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
 RTY  H    C    CA   107.20  3.000
 RTY  CA   C    C6   109.97  3.000
 RTY  H    C    C6   108.38  3.000
 RTY  CA   C    O    112.60  3.000
 RTY  C6   C    O    112.29  3.000
 RTY  H    C    O    106.12  3.000
 RTY  HNA  N    HN   107.86  3.000
 RTY  HNA  N    CA   111.89  3.000
 RTY  HN   N    CA   112.61  3.000
 RTY  HO   O    C    108.85  3.000
 RTY  H1A  C1   H1   107.38  3.000
 RTY  H1A  C1   OH   110.53  3.000
 RTY  H1   C1   OH   110.37  3.000
 RTY  OH   C1   C4   108.14  3.000
 RTY  H1A  C1   C4   110.07  3.000
 RTY  H1   C1   C4   110.36  3.000
 RTY  O2   C2   C3   111.64  3.000
 RTY  C3   C2   O1   125.26  3.000
 RTY  O2   C2   O1   123.10  3.000
 RTY  H3A  C3   H3   105.43  3.000
 RTY  H3A  C3   C4   110.73  3.000
 RTY  H3   C3   C4   110.79  3.000
 RTY  C4   C3   C2   113.43  3.000
 RTY  H3A  C3   C2   107.89  3.000
 RTY  H3   C3   C2   108.22  3.000
 RTY  H4A  C4   H4   107.40  3.000
 RTY  H4A  C4   C3   110.16  3.000
 RTY  H4   C4   C3   110.05  3.000
 RTY  H4A  C4   C1   109.48  3.000
 RTY  H4   C4   C1   109.65  3.000
 RTY  C3   C4   C1   110.06  3.000
 RTY  H6A  C6   H6   108.76  3.000
 RTY  H6A  C6   BR1  106.76  3.000
 RTY  H6   C6   BR1  106.06  3.000
 RTY  H6A  C6   C    111.12  3.000
 RTY  H6   C6   C    112.37  3.000
 RTY  BR1  C6   C    111.48  3.000
 RTY  HA   CA   CB   107.73  3.000
 RTY  HA   CA   N    107.44  3.000
 RTY  CB   CA   N    109.36  3.000
 RTY  HA   CA   C    106.53  3.000
 RTY  CB   CA   C    109.75  3.000
 RTY  N    CA   C    115.71  3.000
 RTY  HBA  CB   HB   106.29  3.000
 RTY  HBA  CB   CG   109.49  3.000
 RTY  HB   CB   CG   110.14  3.000
 RTY  CG   CB   CA   112.80  3.000
 RTY  HBA  CB   CA   108.69  3.000
 RTY  HB   CB   CA   109.21  3.000
 RTY  CD2  CG   CD1  117.44  3.000
 RTY  CD1  CG   CB   120.76  3.000
 RTY  CD2  CG   CB   121.79  3.000
 RTY  CE2  CZ   CE1  119.08  3.000
 RTY  CE1  CZ   OH   124.49  3.000
 RTY  CE2  CZ   OH   116.43  3.000
 RTY  HD1  CD1  CE1  118.46  3.000
 RTY  CE1  CD1  CG   122.06  3.000
 RTY  HD1  CD1  CG   119.48  3.000
 RTY  HD2  CD2  CE2  118.85  3.000
 RTY  CE2  CD2  CG   121.51  3.000
 RTY  HD2  CD2  CG   119.65  3.000
 RTY  HE1  CE1  CD1  118.74  3.000
 RTY  HE1  CE1  CZ   121.65  3.000
 RTY  CD1  CE1  CZ   119.61  3.000
 RTY  HE2  CE2  CD2  120.27  3.000
 RTY  HE2  CE2  CZ   119.44  3.000
 RTY  CD2  CE2  CZ   120.29  3.000
 RTY  H20  O2   C2   109.98  3.000
 RTY  CZ   OH   C1   118.71  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  CONST_15  H20  O2   C2   O1      0.00   0.0  0
 RTY  Var_01    CE2  CZ   OH   C1    179.98  30.0  2
 RTY  Var_02    CD2  CG   CB   CA     92.70  30.0  2
 RTY  Var_03    H1   C1   OH   CZ     61.12  30.0  3
 RTY  Var_04    C2   C3   C4   C1   -179.29  30.0  3
 RTY  Var_05    C4   C3   C2   O1      2.07  30.0  2
 RTY  Var_06    OH   C1   C4   C3   -179.61  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
 RTY  plan-2  H20  0.020

