# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:11:33 2021
#   Inital geometry file: a 56 line input string
#   Ligand name: 1-[(2~{R},3~{S})-2-azanyl-3-oxidanyl-butyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](N)CNC(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
 G2B  G2B  1-[(2~{R},3~{S})-2-azanyl-3-oxidanyl-butyl]urea  ligand  23  10  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G2B
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
 G2B  N1   N  NH2   0  -0.807   -7.8745  53.0414  13.6042
 G2B  C2   C  CH2   0  -0.292   -9.7984  54.4537  14.3492
 G2B  N2   N  NH1   0  -0.654   -8.9236  55.5144  14.7889
 G2B  CA   C  CH1   0  -0.118   -9.1827  53.5784  13.2498
 G2B  C    C  C     0   0.659   -8.7831  56.6751  14.1048
 G2B  O    O  O     0  -0.545   -9.4237  56.9269  13.0882
 G2B  CB   C  CH1   0   0.052  -10.0959  52.4196  12.8320
 G2B  CG   C  CH3   0  -0.697  -11.4907  52.8603  12.4286
 G2B  OG1  O  OH1   0  -0.679  -10.2255  51.4594  13.8666
 G2B  H1   H  HNH2  0   0.351   -7.1834  53.7796  13.5906
 G2B  H2   H  HNH2  0   0.338   -7.8836  52.6984  14.5585
 G2B  H4   H  HCH2  0   0.241  -10.7432  54.8842  14.0159
 G2B  H5   H  HCH2  0   0.241  -10.0233  53.8370  15.2219
 G2B  H6   H  HNH1  0   0.392   -8.3628  55.3556  15.6082
 G2B  H7   H  HCH1  0   0.230   -9.0458  54.2005  12.3600
 G2B  H9   H  HCH1  0   0.207   -9.6181  51.9581  11.9565
 G2B  H10  H  HCH3  0   0.240  -12.0455  52.0310  11.9886
 G2B  H11  H  HCH3  0   0.229  -12.0667  53.2316  13.2773
 G2B  H12  H  HCH3  0   0.230  -11.4374  53.6562  11.6853
 G2B  H13  H  HOH1  0   0.446   -9.3724  51.0264  13.9724
 G2B  N3   N  NH2   0  -0.844   -7.9153  57.5720  14.6613
 G2B  H3   H  HNH2  0   0.391   -7.6120  58.3241  14.0657
 G2B  H8   H  HNH2  0   0.390   -7.2167  57.2508  15.3115

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
 G2B  CG   CB   single  1.517  0.020  1.517
 G2B  CA   CB   single  1.533  0.020  1.533
 G2B  CA   N1   single  1.458  0.020  1.458
 G2B  CA   C2   single  1.534  0.020  1.534
 G2B  CB   OG1  single  1.417  0.020  1.417
 G2B  C2   N2   single  1.444  0.020  1.444
 G2B  O    C    double  1.228  0.020  1.228
 G2B  N2   C    single  1.355  0.020  1.355
 G2B  N1   H1   single  0.890  0.020  1.040
 G2B  N1   H2   single  0.890  0.020  1.040
 G2B  C2   H4   single  0.970  0.020  1.090
 G2B  C2   H5   single  0.970  0.020  1.090
 G2B  N2   H6   single  0.860  0.020  1.020
 G2B  CA   H7   single  0.970  0.020  1.090
 G2B  CB   H9   single  0.970  0.020  1.090
 G2B  CG   H10  single  0.970  0.020  1.090
 G2B  CG   H11  single  0.970  0.020  1.090
 G2B  CG   H12  single  0.970  0.020  1.090
 G2B  OG1  H13  single  0.850  0.020  0.980
 G2B  C    N3   single  1.366  0.020  1.366
 G2B  N3   H3   single  0.890  0.020  1.040
 G2B  N3   H8   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
 G2B  H2   N1   H1   105.41  3.000
 G2B  H2   N1   CA   110.20  3.000
 G2B  H1   N1   CA   109.95  3.000
 G2B  H5   C2   H4   106.78  3.000
 G2B  H5   C2   CA   109.46  3.000
 G2B  H4   C2   CA   110.73  3.000
 G2B  H5   C2   N2   107.23  3.000
 G2B  H4   C2   N2   109.15  3.000
 G2B  CA   C2   N2   113.22  3.000
 G2B  H6   N2   C    119.28  3.000
 G2B  H6   N2   C2   118.05  3.000
 G2B  C    N2   C2   122.59  3.000
 G2B  H7   CA   CB   106.42  3.000
 G2B  H7   CA   C2   107.97  3.000
 G2B  CB   CA   C2   112.79  3.000
 G2B  H7   CA   N1   107.15  3.000
 G2B  C2   CA   N1   113.33  3.000
 G2B  CB   CA   N1   108.80  3.000
 G2B  N3   C    O    122.28  3.000
 G2B  N3   C    N2   115.00  3.000
 G2B  O    C    N2   122.67  3.000
 G2B  H9   CB   OG1  109.68  3.000
 G2B  H9   CB   CG   108.04  3.000
 G2B  OG1  CB   CG   107.86  3.000
 G2B  H9   CB   CA   105.99  3.000
 G2B  OG1  CB   CA   111.56  3.000
 G2B  CG   CB   CA   113.60  3.000
 G2B  H12  CG   H11  107.92  3.000
 G2B  H12  CG   H10  107.76  3.000
 G2B  H11  CG   H10  107.70  3.000
 G2B  H12  CG   CB   110.39  3.000
 G2B  H11  CG   CB   112.17  3.000
 G2B  H10  CG   CB   110.74  3.000
 G2B  H13  OG1  CB   107.70  3.000
 G2B  H8   N3   H3   114.30  3.000
 G2B  H8   N3   C    119.62  3.000
 G2B  H3   N3   C    116.16  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
 G2B  CONST_01  O   C   N2  C2    0.00   0.0  0
 G2B  CONST_02  N3  C   N2  C2  180.00   0.0  0
 G2B  CONST_03  H6  N2  C   O   180.00   0.0  0
 G2B  Var_01    C   N2  C2  CA   80.55  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
 G2B  chir_01  CA  CB   N1  C2  positiv
 G2B  chir_02  CB  OG1  CA  CG  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
 G2B  plan-1  C2  0.020
 G2B  plan-1  N2  0.020
 G2B  plan-1  C   0.020
 G2B  plan-1  O   0.020
 G2B  plan-1  H6  0.020
 G2B  plan-1  N3  0.020
 G2B  plan-1  H3  0.020
 G2B  plan-1  H8  0.020

