# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:42:17 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-(3-carboxypropanoyl)-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](NC(=O)CCC(O)=O)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
 SN0  SN0  N-(3-carboxypropanoyl)-L-norvaline  ligand  28  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SN0
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
 SN0  CA    C  CH1    0  -0.179   1.9978  -0.2529  -0.2043
 SN0  C     C  C      0   0.407   2.3897  -1.6211   0.4141
 SN0  OXT   O  OC     0  -0.620   3.4095  -2.1458  -0.0780
 SN0  O     O  O     -1  -0.598   1.6917  -2.0600   1.3432
 SN0  CB    C  CH2    0  -0.452   3.0108   0.8194   0.1955
 SN0  CG    C  CH2    0  -0.415   2.7997   2.1666  -0.4860
 SN0  CD    C  CH3    0  -0.662   3.8643   3.1836  -0.0978
 SN0  N1    N  NH1    0  -0.629   0.6694   0.1722   0.1687
 SN0  C1    C  C      0   0.565  -0.4365  -0.4535  -0.2606
 SN0  O1    O  O      0  -0.524  -0.4090  -1.3048  -1.1441
 SN0  C2    C  CH2    0  -0.574  -1.7256  -0.0344   0.4118
 SN0  C3    C  CH2    0  -0.578  -2.8877   0.0890  -0.5595
 SN0  C4    C  C      0   0.415  -4.2491   0.3829   0.0951
 SN0  OD1   O  OC    -1  -0.629  -5.1483   0.7821  -0.6740
 SN0  OD2   O  O      0  -0.610  -4.3602   0.1820   1.3207
 SN0  HA    H  HCH1   0   0.225   2.0311  -0.3584  -1.2931
 SN0  HB1   H  HCH2   0   0.232   4.0069   0.4442  -0.0489
 SN0  HB2   H  HCH2   0   0.216   2.9903   0.9510   1.2844
 SN0  HG1   H  HCH2   0   0.215   1.8120   2.5648  -0.2383
 SN0  HG2   H  HCH2   0   0.212   2.8064   2.0234  -1.5708
 SN0  HD1A  H  HCH3   0   0.216   3.8685   3.3591   0.9798
 SN0  HD2   H  HCH3   0   0.216   4.8616   2.8402  -0.3786
 SN0  HD3   H  HCH3   0   0.226   3.6951   4.1438  -0.5868
 SN0  HN1   H  HNH1   0   0.384   0.5832   0.7718   0.9738
 SN0  H21   H  HCH2   0   0.253  -1.9577  -0.7912   1.1667
 SN0  H22   H  HCH2   0   0.234  -1.5857   0.9007   0.9595
 SN0  H31   H  HCH2   0   0.222  -2.6795   0.8659  -1.3009
 SN0  H32   H  HCH2   0   0.233  -2.9836  -0.8394  -1.1317

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
 SN0  CA  C     single  1.552  0.020  1.552
 SN0  CA  CB    single  1.528  0.020  1.528
 SN0  CA  N1    single  1.444  0.020  1.444
 SN0  CA  HA    single  0.970  0.020  1.090
 SN0  C   OXT   deloc   1.248  0.020  1.248
 SN0  C   O     deloc   1.242  0.020  1.242
 SN0  CB  CG    single  1.525  0.020  1.525
 SN0  CB  HB1   single  0.970  0.020  1.090
 SN0  CB  HB2   single  0.970  0.020  1.090
 SN0  CG  CD    single  1.523  0.020  1.523
 SN0  CG  HG1   single  0.970  0.020  1.090
 SN0  CG  HG2   single  0.970  0.020  1.090
 SN0  CD  HD1A  single  0.970  0.020  1.090
 SN0  CD  HD2   single  0.970  0.020  1.090
 SN0  CD  HD3   single  0.970  0.020  1.090
 SN0  N1  C1    single  1.341  0.020  1.341
 SN0  N1  HN1   single  0.860  0.020  1.020
 SN0  C1  O1    double  1.227  0.020  1.227
 SN0  C1  C2    single  1.513  0.020  1.513
 SN0  C2  C3    single  1.520  0.020  1.520
 SN0  C2  H21   single  0.970  0.020  1.090
 SN0  C2  H22   single  0.970  0.020  1.090
 SN0  C3  C4    single  1.539  0.020  1.539
 SN0  C3  H31   single  0.970  0.020  1.090
 SN0  C3  H32   single  0.970  0.020  1.090
 SN0  C4  OD1   deloc   1.249  0.020  1.249
 SN0  C4  OD2   deloc   1.247  0.020  1.247

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
 SN0  HA    CA  N1    108.27  3.000
 SN0  HA    CA  CB    107.92  3.000
 SN0  N1    CA  CB    109.61  3.000
 SN0  HA    CA  C     107.68  3.000
 SN0  N1    CA  C     112.90  3.000
 SN0  CB    CA  C     110.30  3.000
 SN0  O     C   OXT   127.27  3.000
 SN0  O     C   CA    117.88  3.000
 SN0  OXT   C   CA    114.83  3.000
 SN0  HB2   CB  HB1   106.29  3.000
 SN0  HB2   CB  CG    109.58  3.000
 SN0  HB1   CB  CG    109.26  3.000
 SN0  HB2   CB  CA    109.36  3.000
 SN0  HB1   CB  CA    107.76  3.000
 SN0  CG    CB  CA    114.29  3.000
 SN0  HG2   CG  HG1   106.13  3.000
 SN0  HG2   CG  CD    109.63  3.000
 SN0  HG1   CG  CD    109.30  3.000
 SN0  HG2   CG  CB    109.07  3.000
 SN0  HG1   CG  CB    110.22  3.000
 SN0  CD    CG  CB    112.30  3.000
 SN0  HD3   CD  HD2   107.66  3.000
 SN0  HD3   CD  HD1A  107.55  3.000
 SN0  HD2   CD  HD1A  107.52  3.000
 SN0  HD3   CD  CG    111.42  3.000
 SN0  HD2   CD  CG    111.29  3.000
 SN0  HD1A  CD  CG    111.21  3.000
 SN0  HN1   N1  C1    117.57  3.000
 SN0  HN1   N1  CA    117.41  3.000
 SN0  C1    N1  CA    122.59  3.000
 SN0  C2    C1  O1    122.08  3.000
 SN0  C2    C1  N1    115.53  3.000
 SN0  O1    C1  N1    122.38  3.000
 SN0  H22   C2  H21   105.87  3.000
 SN0  H22   C2  C3    110.41  3.000
 SN0  H21   C2  C3    109.58  3.000
 SN0  H22   C2  C1    110.53  3.000
 SN0  H21   C2  C1    107.20  3.000
 SN0  C3    C2  C1    112.95  3.000
 SN0  H32   C3  H31   105.35  3.000
 SN0  H32   C3  C4    107.86  3.000
 SN0  H31   C3  C4    108.73  3.000
 SN0  H32   C3  C2    109.40  3.000
 SN0  H31   C3  C2    110.21  3.000
 SN0  C4    C3  C2    114.84  3.000
 SN0  OD2   C4  OD1   126.35  3.000
 SN0  OD2   C4  C3    117.78  3.000
 SN0  OD1   C4  C3    115.85  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
 SN0  CONST_01  O1    C1  N1  CA     0.00   0.0  0
 SN0  CONST_02  C2    C1  N1  CA   180.00   0.0  0
 SN0  CONST_03  HN1   N1  C1  O1   180.00   0.0  0
 SN0  Var_01    CD    CG  CB  CA  -177.75  30.0  3
 SN0  Var_02    C3    C2  C1  N1   139.22  30.0  3
 SN0  Var_03    C4    C3  C2  C1   174.48  30.0  3
 SN0  Var_04    OD1   C4  C3  C2   164.54  30.0  3
 SN0  Var_05    HD1A  CD  CG  CB   -59.57  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
 SN0  chir_01  CA  C  CB  N1  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
 SN0  plan-1  CA   0.020
 SN0  plan-1  N1   0.020
 SN0  plan-1  C1   0.020
 SN0  plan-1  O1   0.020
 SN0  plan-1  C2   0.020
 SN0  plan-1  HN1  0.020
 SN0  plan-2  CA   0.020
 SN0  plan-2  C    0.020
 SN0  plan-2  OXT  0.020
 SN0  plan-2  O    0.020
 SN0  plan-3  C3   0.020
 SN0  plan-3  C4   0.020
 SN0  plan-3  OD1  0.020
 SN0  plan-3  OD2  0.020

