# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:05:51 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-(3-hydroxy-5-methylisoxazol-4-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(O)c1C[C@H](N)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
 AMQ  AMQ  3-(3-hydroxy-5-methylisoxazol-4-yl)-L-alanine  ligand  23  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AMQ
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
 AMQ  N     N  NH2   0  -0.786  -1.1034   1.4004  -1.1232
 AMQ  CA    C  CH1   0  -0.195   0.0139   0.5333  -1.3999
 AMQ  C     C  C     0   0.543  -0.0198   0.1176  -2.8575
 AMQ  OT1   O  O     0  -0.432  -0.9797   0.2175  -3.5770
 AMQ  OT2   O  OH1   0  -0.594   1.1375  -0.4047  -3.2444
 AMQ  CB    C  CH2   0  -0.574   0.1127  -0.7383  -0.5189
 AMQ  CG    C  CR5   0  -0.224   0.1321  -0.4075   0.9332
 AMQ  CD1   C  CR5   0   0.422  -0.9661  -0.3010   1.8336
 AMQ  CD2   C  CR5   0   0.426   1.1881  -0.0878   1.7237
 AMQ  CE2   C  CH3   0  -0.748   2.6402   0.0093   1.4574
 AMQ  OE1   O  OH1   0  -0.599  -2.2584  -0.5021   1.5935
 AMQ  NE1   N  N     0  -0.212  -0.5981   0.0418   3.0321
 AMQ  OE2   O  O     0  -0.349   0.7633   0.1802   2.9600
 AMQ  H     H  HNH2  0   0.345  -1.9824   0.9007  -1.1663
 AMQ  HN2   H  HNH2  0   0.364  -1.0208   1.7932  -0.1953
 AMQ  HA    H  HCH1  0   0.285   0.9301   1.1117  -1.2440
 AMQ  HXT   H  HOH1  0   0.484   1.0783  -0.7063  -4.1635
 AMQ  HB1   H  HCH2  0   0.279   1.0083  -1.3048  -0.7782
 AMQ  HB2   H  HCH2  0   0.268  -0.7294  -1.4019  -0.7434
 AMQ  HE21  H  HCH3  0   0.274   2.9926   1.0361   1.5644
 AMQ  HE22  H  HCH3  0   0.274   3.2099  -0.6128   2.1482
 AMQ  HE23  H  HCH3  0   0.262   2.8620  -0.3186   0.4445
 AMQ  HE1   H  HOH1  0   0.487  -2.3902  -0.8729   0.7139

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
 AMQ  N    CA    single    1.441  0.020  1.441
 AMQ  N    H     single    0.860  0.020  1.020
 AMQ  N    HN2   single    0.890  0.020  1.040
 AMQ  CA   C     single    1.516  0.020  1.516
 AMQ  CA   CB    single    1.550  0.020  1.550
 AMQ  CA   HA    single    0.970  0.020  1.090
 AMQ  C    OT1   double    1.204  0.020  1.204
 AMQ  C    OT2   single    1.327  0.020  1.327
 AMQ  OT2  HXT   single    0.850  0.020  0.980
 AMQ  CB   CG    single    1.489  0.020  1.489
 AMQ  CB   HB1   single    0.970  0.020  1.090
 AMQ  CB   HB2   single    0.970  0.020  1.090
 AMQ  CG   CD1   aromatic  1.424  0.020  1.424
 AMQ  CG   CD2   aromatic  1.357  0.020  1.357
 AMQ  CD1  OE1   single    1.330  0.020  1.330
 AMQ  CD1  NE1   aromatic  1.300  0.020  1.300
 AMQ  CD2  CE2   single    1.479  0.020  1.479
 AMQ  CD2  OE2   aromatic  1.334  0.020  1.334
 AMQ  CE2  HE21  single    0.970  0.020  1.090
 AMQ  CE2  HE22  single    0.970  0.020  1.090
 AMQ  CE2  HE23  single    0.970  0.020  1.090
 AMQ  OE1  HE1   single    0.850  0.020  0.980
 AMQ  NE1  OE2   aromatic  1.370  0.020  1.370

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
 AMQ  HN2   N    H     107.57  3.000
 AMQ  HN2   N    CA    110.29  3.000
 AMQ  H     N    CA    111.60  3.000
 AMQ  HA    CA   CB    107.41  3.000
 AMQ  HA    CA   C     107.48  3.000
 AMQ  CB    CA   C     108.84  3.000
 AMQ  HA    CA   N     107.67  3.000
 AMQ  CB    CA   N     115.71  3.000
 AMQ  C     CA   N     109.41  3.000
 AMQ  OT2   C    OT1   123.62  3.000
 AMQ  OT2   C    CA    111.64  3.000
 AMQ  OT1   C    CA    124.72  3.000
 AMQ  HXT   OT2  C     110.22  3.000
 AMQ  HB2   CB   HB1   105.53  3.000
 AMQ  HB2   CB   CG    110.15  3.000
 AMQ  HB1   CB   CG    109.65  3.000
 AMQ  HB2   CB   CA    109.36  3.000
 AMQ  HB1   CB   CA    110.07  3.000
 AMQ  CG    CB   CA    111.88  3.000
 AMQ  CD2   CG   CD1   102.37  3.000
 AMQ  CD2   CG   CB    129.07  3.000
 AMQ  CD1   CG   CB    128.53  3.000
 AMQ  NE1   CD1  OE1   118.79  3.000
 AMQ  NE1   CD1  CG    112.60  3.000
 AMQ  OE1   CD1  CG    128.61  3.000
 AMQ  OE2   CD2  CE2   117.78  3.000
 AMQ  OE2   CD2  CG    109.83  3.000
 AMQ  CE2   CD2  CG    132.39  3.000
 AMQ  HE23  CE2  HE22  108.14  3.000
 AMQ  HE23  CE2  HE21  108.02  3.000
 AMQ  HE22  CE2  HE21  107.83  3.000
 AMQ  HE23  CE2  CD2   110.37  3.000
 AMQ  HE22  CE2  CD2   111.18  3.000
 AMQ  HE21  CE2  CD2   111.17  3.000
 AMQ  HE1   OE1  CD1   110.85  3.000
 AMQ  OE2   NE1  CD1   105.03  3.000
 AMQ  NE1   OE2  CD2   110.17  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
 AMQ  CONST_01  OE2   NE1  CD1  CG     0.00   0.0  0
 AMQ  CONST_02  NE1   OE2  CD2  CG     0.00   0.0  0
 AMQ  CONST_03  OE2   CD2  CG   CD1    0.00   0.0  0
 AMQ  CONST_04  CD2   OE2  NE1  CD1    0.00   0.0  0
 AMQ  CONST_05  NE1   CD1  CG   CD2    0.00   0.0  0
 AMQ  CONST_06  NE1   CD1  CG   CB   180.00   0.0  0
 AMQ  CONST_07  OE2   CD2  CG   CB   180.00   0.0  0
 AMQ  CONST_08  CE2   CD2  CG   CD1  180.00   0.0  0
 AMQ  CONST_09  OE1   CD1  CG   CD2  180.00   0.0  0
 AMQ  CONST_10  NE1   OE2  CD2  CE2  180.00   0.0  0
 AMQ  CONST_11  OE2   NE1  CD1  OE1  180.00   0.0  0
 AMQ  CONST_12  HXT   OT2  C    CA   180.00   0.0  0
 AMQ  Var_01    CD1   CG   CB   CA    91.32  30.0  2
 AMQ  Var_02    HE21  CE2  CD2  CG   114.59  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
 AMQ  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
 AMQ  plan-1  CB   0.020
 AMQ  plan-1  CG   0.020
 AMQ  plan-1  CD1  0.020
 AMQ  plan-1  CD2  0.020
 AMQ  plan-1  CE2  0.020
 AMQ  plan-1  OE1  0.020
 AMQ  plan-1  NE1  0.020
 AMQ  plan-1  OE2  0.020
 AMQ  plan-2  CA   0.020
 AMQ  plan-2  C    0.020
 AMQ  plan-2  OT1  0.020
 AMQ  plan-2  OT2  0.020
 AMQ  plan-2  HXT  0.020

