# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 23:18:30 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: (2R)-2-aminobutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](N)C(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
 XKV  XKV  '(2R)-2-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_XKV
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
 XKV  C01   C  CH3   0  -0.675  -46.3692  21.8502  -2.0129
 XKV  C02   C  CH2   0  -0.423  -44.9012  22.2078  -1.8281
 XKV  C03   C  CH1   0  -0.199  -44.3202  21.7945  -0.4746
 XKV  N04   N  NH2   0  -0.779  -42.9445  22.2492  -0.3766
 XKV  C05   C  C     0   0.497  -44.4498  20.2800  -0.3071
 XKV  N06   N  NH2   0  -0.798  -45.3762  19.8676   0.5695
 XKV  O07   O  O     0  -0.489  -43.7453  19.5120  -0.9486
 XKV  H012  H  HCH3  0   0.235  -46.7440  22.2473  -2.9560
 XKV  H013  H  HCH3  0   0.225  -46.5339  20.7722  -2.0282
 XKV  H011  H  HCH3  0   0.222  -46.9828  22.2675  -1.2125
 XKV  H022  H  HCH2  0   0.221  -44.3044  21.7515  -2.6237
 XKV  H021  H  HCH2  0   0.234  -44.7694  23.2876  -1.9228
 XKV  H031  H  HCH1  0   0.242  -44.8936  22.2978   0.3107
 XKV  H041  H  HNH2  0   0.348  -42.5715  22.0332   0.5402
 XKV  H042  H  HNH2  0   0.339  -42.3753  21.7328  -1.0375
 XKV  H062  H  HNH2  0   0.395  -45.5526  18.8856   0.7114
 XKV  H061  H  HNH2  0   0.405  -45.9469  20.5180   1.0816

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
 XKV  C02  C01   single  1.522  0.020  1.522
 XKV  C03  C02   single  1.530  0.020  1.530
 XKV  N04  C03   single  1.452  0.020  1.452
 XKV  C05  C03   single  1.529  0.020  1.529
 XKV  N06  C05   single  1.340  0.020  1.340
 XKV  O07  C05   double  1.224  0.020  1.224
 XKV  C01  H012  single  0.970  0.020  1.090
 XKV  C01  H013  single  0.970  0.020  1.090
 XKV  C01  H011  single  0.970  0.020  1.090
 XKV  C02  H022  single  0.970  0.020  1.090
 XKV  C02  H021  single  0.970  0.020  1.090
 XKV  C03  H031  single  0.970  0.020  1.090
 XKV  N04  H041  single  0.890  0.020  1.040
 XKV  N04  H042  single  0.890  0.020  1.040
 XKV  N06  H062  single  0.860  0.020  1.020
 XKV  N06  H061  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
 XKV  H011  C01  H013  107.66  3.000
 XKV  H011  C01  H012  107.57  3.000
 XKV  H013  C01  H012  107.23  3.000
 XKV  H011  C01  C02   111.30  3.000
 XKV  H013  C01  C02   112.31  3.000
 XKV  H012  C01  C02   110.56  3.000
 XKV  H021  C02  H022  106.47  3.000
 XKV  H021  C02  C03   107.34  3.000
 XKV  H022  C02  C03   108.88  3.000
 XKV  H021  C02  C01   109.77  3.000
 XKV  H022  C02  C01   109.86  3.000
 XKV  C03   C02  C01   114.22  3.000
 XKV  H031  C03  C05   109.41  3.000
 XKV  H031  C03  N04   107.68  3.000
 XKV  C05   C03  N04   112.52  3.000
 XKV  H031  C03  C02   108.15  3.000
 XKV  C05   C03  C02   109.41  3.000
 XKV  N04   C03  C02   109.56  3.000
 XKV  H042  N04  H041  105.94  3.000
 XKV  H042  N04  C03   109.17  3.000
 XKV  H041  N04  C03   110.06  3.000
 XKV  O07   C05  N06   123.21  3.000
 XKV  O07   C05  C03   121.02  3.000
 XKV  N06   C05  C03   115.78  3.000
 XKV  H061  N06  H062  117.34  3.000
 XKV  H061  N06  C05   121.76  3.000
 XKV  H062  N06  C05   120.85  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
 XKV  CONST_01  H062  N06  C05  C03  180.00   0.0  0
 XKV  CONST_02  H061  N06  C05  C03    0.00   0.0  0
 XKV  Var_01    H012  C01  C02  C03  175.01  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
 XKV  chir_01  C03  C02  N04  C05  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
 XKV  plan-1  C03   0.020
 XKV  plan-1  C05   0.020
 XKV  plan-1  N06   0.020
 XKV  plan-1  O07   0.020
 XKV  plan-1  H062  0.020
 XKV  plan-1  H061  0.020

