# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 20:38:25 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: (3R)-3-aminobutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)CC(N)=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
 XEJ  XEJ  '(3R)-3-aminobutanamide   '  ligand  17  7  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XEJ
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
 XEJ  C01   C  CH3   0  -0.663  -13.7252  11.9008  12.8600
 XEJ  C02   C  CH1   0  -0.074  -12.8058  11.7799  14.0666
 XEJ  N03   N  NH2   0  -0.798  -11.6160  12.5937  13.8451
 XEJ  C04   C  CH2   0  -0.557  -13.4920  12.2739  15.3422
 XEJ  C05   C  C     0   0.503  -14.6761  11.4141  15.7266
 XEJ  N06   N  NH2   0  -0.799  -15.8427  12.0635  15.8627
 XEJ  O07   O  O     0  -0.490  -14.5666  10.2080  15.9012
 XEJ  H011  H  HCH3  0   0.228  -14.6197  11.2869  12.9708
 XEJ  H013  H  HCH3  0   0.220  -14.0381  12.9363  12.7132
 XEJ  H012  H  HCH3  0   0.232  -13.2182  11.5707  11.9515
 XEJ  H021  H  HCH1  0   0.205  -12.5632  10.7174  14.2061
 XEJ  H1    H  HNH2  0   0.342  -10.9600  12.4458  14.6033
 XEJ  H031  H  HNH2  0   0.343  -11.1428  12.2704  13.0097
 XEJ  H042  H  HCH2  0   0.266  -12.7796  12.2353  16.1726
 XEJ  H041  H  HCH2  0   0.244  -13.7770  13.3211  15.2156
 XEJ  H061  H  HNH2  0   0.395  -16.6770  11.5652  16.1280
 XEJ  H062  H  HNH2  0   0.405  -15.9226  13.0540  15.7131

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
 XEJ  C02  C01   single  1.522  0.020  1.522
 XEJ  N03  C02   single  1.458  0.020  1.458
 XEJ  C04  C02   single  1.530  0.020  1.530
 XEJ  C05  C04   single  1.513  0.020  1.513
 XEJ  N06  C05   single  1.342  0.020  1.342
 XEJ  O07  C05   double  1.224  0.020  1.224
 XEJ  C01  H011  single  0.970  0.020  1.090
 XEJ  C01  H013  single  0.970  0.020  1.090
 XEJ  C01  H012  single  0.970  0.020  1.090
 XEJ  C02  H021  single  0.970  0.020  1.090
 XEJ  N03  H1    single  0.890  0.020  1.040
 XEJ  N03  H031  single  0.890  0.020  1.040
 XEJ  C04  H042  single  0.970  0.020  1.090
 XEJ  C04  H041  single  0.970  0.020  1.090
 XEJ  N06  H061  single  0.860  0.020  1.020
 XEJ  N06  H062  single  0.860  0.020  1.020

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
 XEJ  H012  C01  H013  107.94  3.000
 XEJ  H012  C01  H011  107.18  3.000
 XEJ  H013  C01  H011  108.21  3.000
 XEJ  H012  C01  C02   110.81  3.000
 XEJ  H013  C01  C02   110.81  3.000
 XEJ  H011  C01  C02   111.74  3.000
 XEJ  H021  C02  C04   107.78  3.000
 XEJ  H021  C02  N03   112.26  3.000
 XEJ  C04   C02  N03   108.19  3.000
 XEJ  H021  C02  C01   108.11  3.000
 XEJ  C04   C02  C01   111.37  3.000
 XEJ  N03   C02  C01   109.16  3.000
 XEJ  H031  N03  H1    105.55  3.000
 XEJ  H031  N03  C02   109.15  3.000
 XEJ  H1    N03  C02   109.45  3.000
 XEJ  H041  C04  H042  106.94  3.000
 XEJ  H041  C04  C05   111.71  3.000
 XEJ  H042  C04  C05   107.25  3.000
 XEJ  H041  C04  C02   109.25  3.000
 XEJ  H042  C04  C02   109.22  3.000
 XEJ  C05   C04  C02   112.29  3.000
 XEJ  O07   C05  N06   122.70  3.000
 XEJ  O07   C05  C04   121.76  3.000
 XEJ  N06   C05  C04   115.54  3.000
 XEJ  H062  N06  H061  117.45  3.000
 XEJ  H062  N06  C05   122.07  3.000
 XEJ  H061  N06  C05   120.48  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
 XEJ  CONST_01  H061  N06  C05  C04   180.00   0.0  0
 XEJ  CONST_02  H062  N06  C05  C04     0.00   0.0  0
 XEJ  Var_01    N06   C05  C04  C02  -124.00  30.0  1

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
 XEJ  chir_01  C02  C01  N03  C04  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
 XEJ  plan-1  C04   0.020
 XEJ  plan-1  C05   0.020
 XEJ  plan-1  N06   0.020
 XEJ  plan-1  O07   0.020
 XEJ  plan-1  H061  0.020
 XEJ  plan-1  H062  0.020

