# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 08:00:55 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-carboxy-2,3-dideoxy-D-erythro-pentaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]([C@H](CC(O)=O)C(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
 N81  N81  '3-carboxy-2,3-dideoxy-D-erythro-pentaric acid'  ligand  21  13  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N81
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
 N81  O01   O  OH1   0  -0.649  -1.4149   1.1573   1.4042
 N81  C02   C  CH1   0  -0.061  -1.3711   0.7305   0.0786
 N81  C03   C  CH1   0  -0.424   0.0511   0.2974  -0.3478
 N81  C04   C  CH2   0  -0.595   0.5149  -0.9717   0.3495
 N81  C05   C  C     0   0.562   1.8823  -1.4055  -0.1066
 N81  O06   O  O     0  -0.442   2.4126  -1.0381  -1.1248
 N81  O07   O  OH1   0  -0.590   2.4245  -2.2816   0.7274
 N81  C08   C  C     0   0.583   0.9999   1.4378  -0.0401
 N81  O09   O  OH1   0  -0.591   0.7442   2.5069  -0.7785
 N81  O10   O  O     0  -0.428   1.8774   1.3893   0.7833
 N81  C11   C  C     0   0.499  -2.3640  -0.3931  -0.1713
 N81  O12   O  OH1   0  -0.579  -2.4971  -0.6570  -1.4574
 N81  O13   O  O     0  -0.425  -2.9395  -0.9730   0.7134
 N81  HO01  H  HOH1  0   0.455  -1.5531   0.4016   1.9874
 N81  H02   H  HCH1  0   0.309  -1.6705   1.5772  -0.5466
 N81  H03   H  HCH1  0   0.316   0.0469   0.1461  -1.4307
 N81  H04   H  HCH2  0   0.287   0.5093  -0.8646   1.4353
 N81  H04A  H  HCH2  0   0.311  -0.1604  -1.8034   0.1227
 N81  HO07  H  HOH1  0   0.482   3.2850  -2.5739   0.3906
 N81  HO09  H  HOH1  0   0.486   1.3441   3.2306  -0.5413
 N81  HO12  H  HOH1  0   0.493  -3.1124  -1.3941  -1.5942

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
 N81  C02  O01   single  1.393  0.020  1.393
 N81  O01  HO01  single  0.850  0.020  0.980
 N81  C11  C02   single  1.520  0.020  1.520
 N81  C03  C02   single  1.547  0.020  1.547
 N81  C02  H02   single  0.970  0.020  1.090
 N81  C08  C03   single  1.515  0.020  1.515
 N81  C03  C04   single  1.520  0.020  1.520
 N81  C03  H03   single  0.970  0.020  1.090
 N81  C05  C04   single  1.505  0.020  1.505
 N81  C04  H04   single  0.970  0.020  1.090
 N81  C04  H04A  single  0.970  0.020  1.090
 N81  O06  C05   double  1.205  0.020  1.205
 N81  C05  O07   single  1.326  0.020  1.326
 N81  O07  HO07  single  0.850  0.020  0.980
 N81  O10  C08   double  1.204  0.020  1.204
 N81  O09  C08   single  1.324  0.020  1.324
 N81  O09  HO09  single  0.850  0.020  0.980
 N81  O13  C11   double  1.204  0.020  1.204
 N81  C11  O12   single  1.320  0.020  1.320
 N81  O12  HO12  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
 N81  HO01  O01  C02  109.86  3.000
 N81  H02   C02  C11  107.41  3.000
 N81  H02   C02  C03  108.10  3.000
 N81  C11   C02  C03  110.38  3.000
 N81  H02   C02  O01  107.34  3.000
 N81  C03   C02  O01  112.15  3.000
 N81  C11   C02  O01  111.24  3.000
 N81  H03   C03  C08  107.92  3.000
 N81  H03   C03  C04  109.88  3.000
 N81  C08   C03  C04  110.13  3.000
 N81  H03   C03  C02  107.95  3.000
 N81  C04   C03  C02  112.82  3.000
 N81  C08   C03  C02  108.00  3.000
 N81  H04A  C04  H04  106.11  3.000
 N81  H04A  C04  C05  106.17  3.000
 N81  H04   C04  C05  109.54  3.000
 N81  H04A  C04  C03  110.53  3.000
 N81  H04   C04  C03  111.90  3.000
 N81  C05   C04  C03  112.25  3.000
 N81  O07   C05  O06  123.57  3.000
 N81  O07   C05  C04  111.80  3.000
 N81  O06   C05  C04  124.60  3.000
 N81  HO07  O07  C05  110.11  3.000
 N81  O10   C08  O09  123.67  3.000
 N81  O09   C08  C03  111.94  3.000
 N81  O10   C08  C03  124.39  3.000
 N81  HO09  O09  C08  110.29  3.000
 N81  O13   C11  O12  124.86  3.000
 N81  O12   C11  C02  111.96  3.000
 N81  O13   C11  C02  123.18  3.000
 N81  HO12  O12  C11  110.69  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
 N81  CONST_01  HO12  O12  C11  C02  180.00   0.0  0
 N81  CONST_02  HO09  O09  C08  C03  180.00   0.0  0
 N81  CONST_03  HO07  O07  C05  C04  180.00   0.0  0
 N81  Var_01    O06   C05  C04  C03  -18.49  30.0  2

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
 N81  chir_01  C02  O01  C11  C03  positiv
 N81  chir_02  C03  C02  C08  C04  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
 N81  plan-1  C04   0.020
 N81  plan-1  C05   0.020
 N81  plan-1  O06   0.020
 N81  plan-1  O07   0.020
 N81  plan-1  HO07  0.020
 N81  plan-2  C03   0.020
 N81  plan-2  C08   0.020
 N81  plan-2  O09   0.020
 N81  plan-2  O10   0.020
 N81  plan-2  HO09  0.020
 N81  plan-3  C02   0.020
 N81  plan-3  C11   0.020
 N81  plan-3  O12   0.020
 N81  plan-3  O13   0.020
 N81  plan-3  HO12  0.020

