# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 09:30:00 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: N-formyl-D-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H](NC=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
 C5S  C5S  'N-formyl-D-aspartic acid '  ligand  16  11  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C5S
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
 C5S  C01  C  CH2    0  -0.591  -0.9731   0.9474  -0.1993
 C5S  C02  C  CH1    0  -0.187   0.2912   0.1763   0.1602
 C5S  C03  C  C      0   0.412   1.5496   1.0713   0.0256
 C5S  O04  O  O      0  -0.599   2.3800   0.7864  -0.8536
 C5S  O05  O  OC    -1  -0.622   1.5999   2.0245   0.8302
 C5S  N06  N  NH1    0  -0.568   0.3654  -1.0181  -0.6510
 C5S  C07  C  C1     0   0.244   1.1346  -2.0627  -0.3547
 C5S  O08  O  O      0  -0.515   1.7672  -2.2134   0.6810
 C5S  C09  C  C      0   0.407  -2.2710   0.1652   0.0732
 C5S  O10  O  O      0  -0.614  -2.3529  -0.4134   1.1753
 C5S  O11  O  OC    -1  -0.620  -3.1486   0.1940  -0.8138
 C5S  H1   H  HCH2   0   0.240  -0.9860   1.8582   0.4051
 C5S  H2   H  HCH2   0   0.206  -0.9309   1.2693  -1.2451
 C5S  H3   H  HCH1   0   0.230   0.2073  -0.1319   1.2046
 C5S  H5   H  HNH1   0   0.390  -0.0254  -0.9882  -1.5794
 C5S  H7   H  H      0   0.187   1.1272  -2.8229  -1.1522

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
 C5S  C07  N06  single  1.331  0.020  1.331
 C5S  C07  O08  double  1.223  0.020  1.223
 C5S  N06  C02  single  1.446  0.020  1.446
 C5S  C02  C03  single  1.550  0.020  1.550
 C5S  C02  C01  single  1.524  0.020  1.524
 C5S  O04  C03  deloc   1.243  0.020  1.243
 C5S  C03  O05  deloc   1.248  0.020  1.248
 C5S  C01  C09  single  1.540  0.020  1.540
 C5S  C09  O10  deloc   1.247  0.020  1.247
 C5S  C09  O11  deloc   1.248  0.020  1.248
 C5S  C01  H1   single  0.970  0.020  1.090
 C5S  C01  H2   single  0.970  0.020  1.090
 C5S  C02  H3   single  0.970  0.020  1.090
 C5S  N06  H5   single  0.860  0.020  1.020
 C5S  C07  H7   single  0.930  0.020  1.080

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
 C5S  H2   C01  H1   106.47  3.000
 C5S  H2   C01  C09  110.54  3.000
 C5S  H1   C01  C09  108.39  3.000
 C5S  H2   C01  C02  110.00  3.000
 C5S  H1   C01  C02  107.51  3.000
 C5S  C09  C01  C02  113.61  3.000
 C5S  H3   C02  N06  107.90  3.000
 C5S  H3   C02  C03  107.96  3.000
 C5S  N06  C02  C03  112.74  3.000
 C5S  H3   C02  C01  107.74  3.000
 C5S  C03  C02  C01  111.16  3.000
 C5S  N06  C02  C01  109.16  3.000
 C5S  O05  C03  O04  127.17  3.000
 C5S  O05  C03  C02  114.68  3.000
 C5S  O04  C03  C02  118.14  3.000
 C5S  H5   N06  C07  116.91  3.000
 C5S  H5   N06  C02  118.20  3.000
 C5S  C07  N06  C02  123.59  3.000
 C5S  H7   C07  O08  122.10  3.000
 C5S  H7   C07  N06  112.12  3.000
 C5S  O08  C07  N06  125.76  3.000
 C5S  O11  C09  O10  126.33  3.000
 C5S  O11  C09  C01  117.08  3.000
 C5S  O10  C09  C01  116.57  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
 C5S  CONST_01  O08  C07  N06  C02    0.00   0.0  0
 C5S  CONST_02  H5   N06  C07  O08  180.00   0.0  0
 C5S  Var_01    O10  C09  C01  C02   46.14  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
 C5S  chir_01  C02  N06  C03  C01  negativ

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
 C5S  plan-1  C02  0.020
 C5S  plan-1  N06  0.020
 C5S  plan-1  C07  0.020
 C5S  plan-1  O08  0.020
 C5S  plan-1  H5   0.020
 C5S  plan-1  H7   0.020
 C5S  plan-2  C02  0.020
 C5S  plan-2  C03  0.020
 C5S  plan-2  O04  0.020
 C5S  plan-2  O05  0.020
 C5S  plan-3  C01  0.020
 C5S  plan-3  C09  0.020
 C5S  plan-3  O10  0.020
 C5S  plan-3  O11  0.020

