# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:13:20 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2R)-3-[(benzylcarbamoyl)amino]-2-hydroxypropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](CNC(=O)NCc1ccccc1)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
 J54  J54  '(2R)-3-[(benzylcarbamoyl)amino]-2-hydroxypropanoic acid'  ligand  30  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J54
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
 J54  O02   O  O      0  -0.605  -5.3421   0.2310  -1.0770
 J54  C06   C  C      0   0.394  -4.2051   0.6262  -1.4195
 J54  C05   C  CH1    0  -0.111  -3.0402  -0.2623  -0.9276
 J54  O18   O  OH1    0  -0.699  -3.5522  -1.3646  -0.2199
 J54  C04   C  CH2    0  -0.261  -2.0947   0.5544  -0.0563
 J54  N02   N  NH1    0  -0.683  -1.0291  -0.2799   0.4504
 J54  C03   C  C      0   0.730   0.1542   0.2414   0.8698
 J54  O01   O  O      0  -0.540   0.4775   1.4096   0.6856
 J54  N01   N  NH1    0  -0.680   0.9704  -0.6390   1.5154
 J54  C02   C  CH2    0  -0.336   2.3193  -0.2788   1.8600
 J54  C01   C  CR6    0   0.104   3.2711  -0.1558   0.6915
 J54  CE1   C  CR16   0  -0.297   3.1091  -0.9138  -0.4641
 J54  CD1   C  CR16   0  -0.242   4.0212  -0.8187  -1.5075
 J54  CG    C  CR16   0  -0.272   5.1121   0.0349  -1.4083
 J54  CD2   C  CR16   0  -0.243   5.2825   0.7941  -0.2577
 J54  CE2   C  CR16   0  -0.305   4.3664   0.6988   0.7811
 J54  OXT   O  OC    -1  -0.592  -3.9192   1.6321  -2.0852
 J54  H05   H  HCH1   0   0.209  -2.4760  -0.6148  -1.8033
 J54  H18   H  HOH1   0   0.430  -4.5102  -1.1771  -0.2119
 J54  H041  H  HCH2   0   0.238  -1.6673   1.3555  -0.6550
 J54  H042  H  HCH2   0   0.217  -2.6580   1.0208   0.7626
 J54  H02   H  HNH1   0   0.384  -1.3134  -1.1709   0.8279
 J54  H01   H  HNH1   0   0.394   0.7348  -1.6174   1.5181
 J54  H021  H  HCH2   0   0.251   2.3217   0.6530   2.4282
 J54  H022  H  HCH2   0   0.269   2.6889  -1.0476   2.5415
 J54  HE1   H  HCR6   0   0.243   2.2616  -1.5820  -0.5579
 J54  HE2   H  HCR6   0   0.246   4.5030   1.3019   1.6719
 J54  HD1   H  HCR6   0   0.252   3.8783  -1.4139  -2.4007
 J54  HG    H  HCR6   0   0.253   5.8207   0.1116  -2.2227
 J54  HD2   H  HCR6   0   0.253   6.1262   1.4668  -0.1710

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
 J54  O02  C06   deloc     1.252  0.020  1.252
 J54  C06  C05   single    1.545  0.020  1.545
 J54  C06  OXT   deloc     1.240  0.020  1.240
 J54  C05  O18   single    1.406  0.020  1.406
 J54  C05  C04   single    1.523  0.020  1.523
 J54  C05  H05   single    0.970  0.020  1.090
 J54  O18  H18   single    0.850  0.020  0.980
 J54  C04  N02   single    1.445  0.020  1.445
 J54  C04  H041  single    0.970  0.020  1.090
 J54  C04  H042  single    0.970  0.020  1.090
 J54  N02  C03   single    1.359  0.020  1.359
 J54  N02  H02   single    0.890  0.020  1.040
 J54  C03  O01   double    1.226  0.020  1.226
 J54  C03  N01   single    1.363  0.020  1.363
 J54  N01  C02   single    1.438  0.020  1.438
 J54  N01  H01   single    0.860  0.020  1.020
 J54  C02  C01   single    1.512  0.020  1.512
 J54  C02  H021  single    0.970  0.020  1.090
 J54  C02  H022  single    0.970  0.020  1.090
 J54  C01  CE1   aromatic  1.391  0.020  1.391
 J54  C01  CE2   aromatic  1.392  0.020  1.392
 J54  CE1  CD1   aromatic  1.389  0.020  1.389
 J54  CE1  HE1   single    0.930  0.020  1.080
 J54  CD1  CG    aromatic  1.389  0.020  1.389
 J54  CD1  HD1   single    0.930  0.020  1.080
 J54  CG   CD2   aromatic  1.389  0.020  1.389
 J54  CG   HG    single    0.930  0.020  1.080
 J54  CD2  CE2   aromatic  1.388  0.020  1.388
 J54  CD2  HD2   single    0.930  0.020  1.080
 J54  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
 J54  OXT   C06  C05   117.62  3.000
 J54  OXT   C06  O02   127.79  3.000
 J54  C05   C06  O02   114.59  3.000
 J54  H05   C05  C04   108.00  3.000
 J54  H05   C05  O18   109.65  3.000
 J54  C04   C05  O18   111.00  3.000
 J54  H05   C05  C06   108.52  3.000
 J54  C04   C05  C06   109.98  3.000
 J54  O18   C05  C06   109.65  3.000
 J54  H18   O18  C05   102.18  3.000
 J54  H042  C04  H041  107.41  3.000
 J54  H042  C04  N02   111.23  3.000
 J54  H041  C04  N02   109.18  3.000
 J54  H042  C04  C05   109.63  3.000
 J54  H041  C04  C05   108.90  3.000
 J54  N02   C04  C05   110.41  3.000
 J54  H02   N02  C03   117.95  3.000
 J54  H02   N02  C04   115.68  3.000
 J54  C03   N02  C04   121.92  3.000
 J54  N01   C03  O01   121.91  3.000
 J54  N01   C03  N02   114.81  3.000
 J54  O01   C03  N02   123.27  3.000
 J54  H01   N01  C02   117.55  3.000
 J54  H01   N01  C03   119.27  3.000
 J54  C02   N01  C03   120.89  3.000
 J54  H022  C02  H021  105.99  3.000
 J54  H022  C02  C01   109.06  3.000
 J54  H021  C02  C01   109.36  3.000
 J54  H022  C02  N01   106.90  3.000
 J54  H021  C02  N01   109.92  3.000
 J54  C01   C02  N01   115.19  3.000
 J54  CE2   C01  CE1   118.65  3.000
 J54  CE2   C01  C02   119.69  3.000
 J54  CE1   C01  C02   121.61  3.000
 J54  HE1   CE1  CD1   119.39  3.000
 J54  HE1   CE1  C01   119.94  3.000
 J54  CD1   CE1  C01   120.67  3.000
 J54  HD1   CD1  CG    120.03  3.000
 J54  HD1   CD1  CE1   119.69  3.000
 J54  CG    CD1  CE1   120.28  3.000
 J54  HG    CG   CD2   120.28  3.000
 J54  HG    CG   CD1   120.27  3.000
 J54  CD2   CG   CD1   119.44  3.000
 J54  HD2   CD2  CE2   119.80  3.000
 J54  HD2   CD2  CG    120.11  3.000
 J54  CE2   CD2  CG    120.09  3.000
 J54  HE2   CE2  CD2   119.56  3.000
 J54  HE2   CE2  C01   119.57  3.000
 J54  CD2   CE2  C01   120.87  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
 J54  CONST_01  CG   CD1  CE1  C01    0.00   0.0  0
 J54  CONST_02  CG   CD2  CE2  C01    0.00   0.0  0
 J54  CONST_03  CD2  CE2  C01  CE1    0.00   0.0  0
 J54  CONST_04  CD2  CG   CD1  CE1    0.00   0.0  0
 J54  CONST_05  CE2  C01  CE1  CD1    0.00   0.0  0
 J54  CONST_06  CE2  CD2  CG   CD1    0.00   0.0  0
 J54  CONST_07  CD1  CE1  C01  C02  180.00   0.0  0
 J54  CONST_08  CD2  CE2  C01  C02  180.00   0.0  0
 J54  CONST_09  HD1  CD1  CE1  C01  180.00   0.0  0
 J54  CONST_10  HD2  CD2  CE2  C01  180.00   0.0  0
 J54  CONST_11  HE2  CE2  C01  CE1  180.00   0.0  0
 J54  CONST_12  HG   CG   CD1  CE1  180.00   0.0  0
 J54  CONST_13  HE1  CE1  CD1  CG   180.00   0.0  0
 J54  CONST_14  O01  C03  N02  C04    0.00   0.0  0
 J54  CONST_15  C02  N01  C03  O01    0.00   0.0  0
 J54  CONST_16  N01  C03  N02  C04  180.00   0.0  0
 J54  CONST_17  C02  N01  C03  N02  180.00   0.0  0
 J54  CONST_18  H02  N02  C03  O01  180.00   0.0  0
 J54  CONST_19  H01  N01  C03  O01  180.00   0.0  0
 J54  Var_01    CE1  C01  C02  N01  -29.94  30.0  2
 J54  Var_02    C01  C02  N01  C03  -70.43  30.0  3
 J54  Var_03    C03  N02  C04  C05  158.08  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
 J54  chir_01  C05  C06  O18  C04  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
 J54  plan-1  C02  0.020
 J54  plan-1  C01  0.020
 J54  plan-1  CE1  0.020
 J54  plan-1  CD1  0.020
 J54  plan-1  CG   0.020
 J54  plan-1  CD2  0.020
 J54  plan-1  CE2  0.020
 J54  plan-1  HE1  0.020
 J54  plan-1  HE2  0.020
 J54  plan-1  HD1  0.020
 J54  plan-1  HG   0.020
 J54  plan-1  HD2  0.020
 J54  plan-2  C04  0.020
 J54  plan-2  N02  0.020
 J54  plan-2  C03  0.020
 J54  plan-2  O01  0.020
 J54  plan-2  N01  0.020
 J54  plan-2  C02  0.020
 J54  plan-2  H02  0.020
 J54  plan-2  H01  0.020
 J54  plan-3  O02  0.020
 J54  plan-3  C06  0.020
 J54  plan-3  C05  0.020
 J54  plan-3  OXT  0.020

