# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 05:36:42 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  22  11  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.776  -4.3165   0.9645   0.6497
 9YT  C02   C  C      0   0.513  -3.2444  -0.0452   0.3161
 9YT  O03   O  O      0  -0.515  -3.4622  -1.2500   0.3750
 9YT  N04   N  NH1    0  -0.627  -2.0616   0.4750  -0.0454
 9YT  C05   C  CH2    0  -0.246  -0.8974  -0.2959  -0.4265
 9YT  C06   C  CH2    0  -0.450   0.3720   0.2988   0.1641
 9YT  C07   C  CH1    0  -0.218   1.6335  -0.4254  -0.3086
 9YT  N08   N  NH2    0  -0.787   1.5747  -1.8240   0.0886
 9YT  C09   C  C      0   0.387   2.8832   0.3566   0.1692
 9YT  O10   O  OC    -1  -0.623   3.0565   1.4768  -0.3550
 9YT  O11   O  O      0  -0.606   3.5989  -0.1743   1.0405
 9YT  H013  H  HCH3   0   0.263  -5.1439   0.8555  -0.0520
 9YT  H011  H  HCH3   0   0.262  -4.7090   0.7636   1.6461
 9YT  H012  H  HCH3   0   0.245  -3.9724   1.9967   0.6158
 9YT  H041  H  HNH1   0   0.394  -1.9822   1.4775  -0.1019
 9YT  H051  H  HCH2   0   0.241  -1.0300  -1.3198  -0.0864
 9YT  H052  H  HCH2   0   0.222  -0.8114  -0.3299  -1.5186
 9YT  H062  H  HCH2   0   0.228   0.4486   1.3530  -0.1135
 9YT  H061  H  HCH2   0   0.219   0.3123   0.2649   1.2580
 9YT  H071  H  HCH1   0   0.213   1.6296  -0.3971  -1.4054
 9YT  H082  H  HNH2   0   0.336   2.3454  -2.3180  -0.3448
 9YT  H1    H  HNH2   0   0.324   1.7741  -1.8743   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
 9YT  O11  C09   deloc   1.246  0.020  1.246
 9YT  O10  C09   deloc   1.249  0.020  1.249
 9YT  C09  C07   single  1.550  0.020  1.550
 9YT  C06  C07   single  1.529  0.020  1.529
 9YT  C06  C05   single  1.521  0.020  1.521
 9YT  C07  N08   single  1.455  0.020  1.455
 9YT  C05  N04   single  1.447  0.020  1.447
 9YT  N04  C02   single  1.342  0.020  1.342
 9YT  C02  O03   double  1.226  0.020  1.226
 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

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  108.49  3.000
 9YT  H012  C01  H013  108.34  3.000
 9YT  H011  C01  H013  107.26  3.000
 9YT  H012  C01  C02   113.75  3.000
 9YT  H011  C01  C02   109.54  3.000
 9YT  H013  C01  C02   109.26  3.000
 9YT  N04   C02  O03   123.41  3.000
 9YT  O03   C02  C01   121.37  3.000
 9YT  N04   C02  C01   115.22  3.000
 9YT  H041  N04  C05   116.87  3.000
 9YT  H041  N04  C02   118.07  3.000
 9YT  C05   N04  C02   124.99  3.000
 9YT  H052  C05  H051  106.99  3.000
 9YT  H052  C05  C06   109.48  3.000
 9YT  H051  C05  C06   110.40  3.000
 9YT  H052  C05  N04   110.00  3.000
 9YT  H051  C05  N04   108.73  3.000
 9YT  C06   C05  N04   111.15  3.000
 9YT  H061  C06  H062  106.69  3.000
 9YT  H061  C06  C07   109.80  3.000
 9YT  H062  C06  C07   108.69  3.000
 9YT  H061  C06  C05   109.27  3.000
 9YT  H062  C06  C05   109.69  3.000
 9YT  C07   C06  C05   112.53  3.000
 9YT  H071  C07  C09   107.34  3.000
 9YT  H071  C07  N08   107.31  3.000
 9YT  C09   C07  N08   115.69  3.000
 9YT  H071  C07  C06   107.08  3.000
 9YT  N08   C07  C06   109.72  3.000
 9YT  C09   C07  C06   109.32  3.000
 9YT  H1    N08  H082  104.19  3.000
 9YT  H1    N08  C07   107.88  3.000
 9YT  H082  N08  C07   108.74  3.000
 9YT  O11   C09  O10   126.57  3.000
 9YT  O10   C09  C07   115.79  3.000
 9YT  O11   C09  C07   117.63  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  Var_01    C06   C05  N04  C02  -138.90  30.0  1
 9YT  Var_02    C07   C06  C05  N04  -175.46  30.0  1
 9YT  Var_03    H013  C01  C02  O03   -62.36  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

