# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 18:58:46 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{R})-4-azanyl-2-[[(1~{S})-1-oxidanylethyl]amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)N[C@H](CCN)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
 P4B  P4B  '(2~{R})-4-azanyl-2-[[(1~{S})-1-oxidanylethyl]amino]butanoic acid'  ligand  24  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P4B
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
 P4B  C10   C  CH3    0  -0.665   3.5575  24.8803  -11.4909
 P4B  C02   C  CH2    0  -0.262   1.9562  22.1065   -9.3672
 P4B  C03   C  CH2    0  -0.411   0.6508  22.3656  -10.1015
 P4B  C04   C  CH1    0  -0.257   0.7213  23.5849  -11.0183
 P4B  C05   C  C      0   0.460  -0.6735  24.0200  -11.5566
 P4B  C09   C  CH1    0   0.163   2.4982  24.4974  -12.5153
 P4B  N01   N  NH2    0  -0.799   1.8423  20.9400   -8.5019
 P4B  N08   N  NH1    0  -0.618   1.7110  23.3728  -12.0667
 P4B  O21   O  OH1    0  -0.730   1.7474  25.6455  -12.8457
 P4B  H102  H  HCH3   0   0.211   4.2432  24.0500  -11.3237
 P4B  H101  H  HCH3   0   0.220   4.1403  25.7325  -11.8440
 P4B  H103  H  HCH3   0   0.215   3.1152  25.1560  -10.5310
 P4B  H021  H  HCH2   0   0.207   2.7463  21.9181  -10.0965
 P4B  H022  H  HCH2   0   0.176   2.2431  23.0224   -8.8271
 P4B  H032  H  HCH2   0   0.210  -0.1451  22.5142   -9.3690
 P4B  H031  H  HCH2   0   0.201   0.3807  21.4758  -10.6798
 P4B  H041  H  HCH1   0   0.235   1.0684  24.4243  -10.3993
 P4B  H1    H  HCH1   0   0.175   3.0268  24.1304  -13.4085
 P4B  H2    H  HNH2   0   0.340   2.7306  20.7621   -8.0504
 P4B  H012  H  HNH2   0   0.333   1.1904  21.1404   -7.7535
 P4B  H3    H  HNH1   0   0.339   1.2857  22.9091  -12.8581
 P4B  H211  H  HOH1   0   0.440   0.7980  25.3511  -12.8710
 P4B  O06   O  OC    -1  -0.569  -1.6808  23.7069  -10.9080
 P4B  O07   O  O      0  -0.613  -0.6732  24.6982  -12.6205

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
 P4B  O21  C09   single  1.411  0.020  1.411
 P4B  C09  N08   single  1.444  0.020  1.444
 P4B  C09  C10   single  1.523  0.020  1.523
 P4B  O07  C05   deloc   1.262  0.020  1.262
 P4B  N08  C04   single  1.457  0.020  1.457
 P4B  C05  O06   deloc   1.238  0.020  1.238
 P4B  C05  C04   single  1.557  0.020  1.557
 P4B  C04  C03   single  1.527  0.020  1.527
 P4B  C03  C02   single  1.520  0.020  1.520
 P4B  C02  N01   single  1.457  0.020  1.457
 P4B  C10  H102  single  0.970  0.020  1.090
 P4B  C10  H101  single  0.970  0.020  1.090
 P4B  C10  H103  single  0.970  0.020  1.090
 P4B  C02  H021  single  0.970  0.020  1.090
 P4B  C02  H022  single  0.970  0.020  1.090
 P4B  C03  H032  single  0.970  0.020  1.090
 P4B  C03  H031  single  0.970  0.020  1.090
 P4B  C04  H041  single  0.970  0.020  1.090
 P4B  C09  H1    single  0.970  0.020  1.090
 P4B  N01  H2    single  0.890  0.020  1.040
 P4B  N01  H012  single  0.890  0.020  1.040
 P4B  N08  H3    single  0.890  0.020  1.040
 P4B  O21  H211  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
 P4B  H103  C10  H101  107.67  3.000
 P4B  H103  C10  H102  108.20  3.000
 P4B  H101  C10  H102  107.98  3.000
 P4B  H103  C10  C09   111.90  3.000
 P4B  H101  C10  C09   110.50  3.000
 P4B  H102  C10  C09   110.45  3.000
 P4B  H022  C02  H021  106.42  3.000
 P4B  H022  C02  N01   113.26  3.000
 P4B  H021  C02  N01   108.37  3.000
 P4B  H022  C02  C03   108.60  3.000
 P4B  H021  C02  C03   109.16  3.000
 P4B  N01   C02  C03   110.87  3.000
 P4B  H031  C03  H032  106.56  3.000
 P4B  H031  C03  C04   110.07  3.000
 P4B  H032  C03  C04   109.13  3.000
 P4B  H031  C03  C02   109.18  3.000
 P4B  H032  C03  C02   108.98  3.000
 P4B  C04   C03  C02   112.73  3.000
 P4B  H041  C04  N08   107.57  3.000
 P4B  H041  C04  C05   105.31  3.000
 P4B  N08   C04  C05   113.60  3.000
 P4B  H041  C04  C03   106.63  3.000
 P4B  C05   C04  C03   112.91  3.000
 P4B  N08   C04  C03   110.31  3.000
 P4B  O07   C05  O06   125.30  3.000
 P4B  O06   C05  C04   118.49  3.000
 P4B  O07   C05  C04   116.20  3.000
 P4B  H1    C09  O21   109.68  3.000
 P4B  H1    C09  N08   104.72  3.000
 P4B  O21   C09  N08   114.60  3.000
 P4B  H1    C09  C10   107.20  3.000
 P4B  N08   C09  C10   111.47  3.000
 P4B  O21   C09  C10   108.85  3.000
 P4B  H012  N01  H2    105.67  3.000
 P4B  H012  N01  C02   109.32  3.000
 P4B  H2    N01  C02   109.70  3.000
 P4B  H3    N08  C09   110.08  3.000
 P4B  H3    N08  C04   110.13  3.000
 P4B  C09   N08  C04   118.70  3.000
 P4B  H211  O21  C09   105.85  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
 P4B  Var_01  N01  C02  C03  C04  179.77  30.0  3
 P4B  Var_02  H2   N01  C02  C03  177.77  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
 P4B  chir_01  C04  N08  C05  C03  negativ
 P4B  chir_02  C09  O21  N08  C10  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
 P4B  plan-1  C04  0.020
 P4B  plan-1  C05  0.020
 P4B  plan-1  O06  0.020
 P4B  plan-1  O07  0.020

