# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:09:11 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (2~{S})-4-acetamido-2-azanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCC[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
 9YT  9YT  '(2~{S})-4-acetamido-2-azanyl-butanoic acid'  ligand  23  11  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9YT
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
 9YT  C01   C  CH3   0  -0.780  -4.3044   0.9729   0.5870
 9YT  C02   C  C     0   0.510  -3.2343  -0.0357   0.2456
 9YT  O03   O  O     0  -0.508  -3.4731  -1.2343   0.1731
 9YT  N04   N  NH1   0  -0.628  -2.0192   0.4878   0.0073
 9YT  C05   C  CH2   0  -0.240  -0.8703  -0.2756  -0.4250
 9YT  C06   C  CH2   0  -0.468   0.4030   0.2833   0.1939
 9YT  C07   C  CH1   0  -0.213   1.6516  -0.4187  -0.3516
 9YT  N08   N  NH2   0  -0.776   1.6007  -1.8328  -0.0712
 9YT  C09   C  C     0   0.524   2.8970   0.2687   0.1949
 9YT  O10   O  OH1   0  -0.593   3.0622   1.4821  -0.3189
 9YT  O11   O  O     0  -0.438   3.6457  -0.2155   1.0057
 9YT  H013  H  HCH3  0   0.260  -5.0271   0.5320   1.2704
 9YT  H011  H  HCH3  0   0.250  -3.9066   1.8833   1.0326
 9YT  H012  H  HCH3  0   0.269  -4.8368   1.2531  -0.3240
 9YT  H041  H  HNH1  0   0.397  -1.9221   1.4906   0.0304
 9YT  H051  H  HCH2  0   0.249  -1.0111  -1.3135  -0.1345
 9YT  H052  H  HCH2  0   0.231  -0.7856  -0.2557  -1.5174
 9YT  H062  H  HCH2  0   0.252   0.4673   1.3532  -0.0176
 9YT  H061  H  HCH2  0   0.246   0.3631   0.1783   1.2825
 9YT  H071  H  HCH1  0   0.273   1.6627  -0.2887  -1.4393
 9YT  H082  H  HNH2  0   0.356   2.3829  -2.3084  -0.5019
 9YT  H1    H  HNH2  0   0.345   1.6802  -1.9963   0.9251
 9YT  H2    H  HOH1  0   0.482   3.8405   1.9081   0.0709

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
 9YT  O11  C09   double  1.205  0.020  1.205
 9YT  O10  C09   single  1.328  0.020  1.328
 9YT  C09  C07   single  1.524  0.020  1.524
 9YT  C06  C07   single  1.533  0.020  1.533
 9YT  C06  C05   single  1.522  0.020  1.522
 9YT  C07  N08   single  1.443  0.020  1.443
 9YT  C05  N04   single  1.446  0.020  1.446
 9YT  N04  C02   single  1.344  0.020  1.344
 9YT  C02  O03   double  1.224  0.020  1.224
 9YT  C02  C01   single  1.510  0.020  1.510
 9YT  C01  H013  single  0.970  0.020  1.090
 9YT  C01  H011  single  0.970  0.020  1.090
 9YT  C01  H012  single  0.970  0.020  1.090
 9YT  N04  H041  single  0.860  0.020  1.020
 9YT  C05  H051  single  0.970  0.020  1.090
 9YT  C05  H052  single  0.970  0.020  1.090
 9YT  C06  H062  single  0.970  0.020  1.090
 9YT  C06  H061  single  0.970  0.020  1.090
 9YT  C07  H071  single  0.970  0.020  1.090
 9YT  N08  H082  single  0.890  0.020  1.040
 9YT  N08  H1    single  0.890  0.020  1.040
 9YT  O10  H2    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
 9YT  H012  C01  H011  107.76  3.000
 9YT  H012  C01  H013  107.71  3.000
 9YT  H011  C01  H013  108.93  3.000
 9YT  H012  C01  C02   109.18  3.000
 9YT  H011  C01  C02   113.09  3.000
 9YT  H013  C01  C02   110.00  3.000
 9YT  N04   C02  O03   123.16  3.000
 9YT  O03   C02  C01   121.95  3.000
 9YT  N04   C02  C01   114.87  3.000
 9YT  H041  N04  C05   117.11  3.000
 9YT  H041  N04  C02   118.07  3.000
 9YT  C05   N04  C02   124.45  3.000
 9YT  H052  C05  H051  107.08  3.000
 9YT  H052  C05  C06   109.52  3.000
 9YT  H051  C05  C06   110.50  3.000
 9YT  H052  C05  N04   110.48  3.000
 9YT  H051  C05  N04   108.75  3.000
 9YT  C06   C05  N04   110.45  3.000
 9YT  H061  C06  H062  106.79  3.000
 9YT  H061  C06  C07   109.87  3.000
 9YT  H062  C06  C07   109.37  3.000
 9YT  H061  C06  C05   109.80  3.000
 9YT  H062  C06  C05   109.27  3.000
 9YT  C07   C06  C05   111.63  3.000
 9YT  H071  C07  C09   107.12  3.000
 9YT  H071  C07  N08   108.04  3.000
 9YT  C09   C07  N08   113.66  3.000
 9YT  H071  C07  C06   107.90  3.000
 9YT  N08   C07  C06   110.55  3.000
 9YT  C09   C07  C06   109.36  3.000
 9YT  H1    N08  H082  106.39  3.000
 9YT  H1    N08  C07   110.28  3.000
 9YT  H082  N08  C07   110.53  3.000
 9YT  O11   C09  O10   123.38  3.000
 9YT  O10   C09  C07   112.03  3.000
 9YT  O11   C09  C07   124.59  3.000
 9YT  H2    O10  C09   110.23  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
 9YT  CONST_01  C05   N04  C02  C01   180.00   0.0  0
 9YT  CONST_02  C05   N04  C02  O03     0.00   0.0  0
 9YT  CONST_03  H041  N04  C02  C01     0.00   0.0  0
 9YT  CONST_04  H2    O10  C09  C07   180.00   0.0  0
 9YT  Var_01    C06   C05  N04  C02  -144.54  30.0  1
 9YT  Var_02    C07   C06  C05  N04  -174.46  30.0  1
 9YT  Var_03    H013  C01  C02  O03    32.80  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
 9YT  chir_01  C07  C09  C06  N08  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
 9YT  plan-1  C01   0.020
 9YT  plan-1  C02   0.020
 9YT  plan-1  O03   0.020
 9YT  plan-1  N04   0.020
 9YT  plan-1  C05   0.020
 9YT  plan-1  H041  0.020
 9YT  plan-2  C07   0.020
 9YT  plan-2  C09   0.020
 9YT  plan-2  O10   0.020
 9YT  plan-2  O11   0.020
 9YT  plan-2  H2    0.020

