# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:36:04 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 2,2'-[ethane-1,2-diylbis(oxy)]diacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)COCCOCC(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
 OGG  OGG  2,2'-[ethane-1,2-diylbis(oxy)]diacetamide  ligand  24  12  .  2021-08-17  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OGG
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
 OGG  NB    N  NH2   0  -0.802   0.7989  -0.3211   4.6765
 OGG  CC    C  C     0   0.461   0.6173   0.2118   3.4595
 OGG  OL    O  O     0  -0.479   1.3199   1.0902   2.9915
 OGG  CD    C  CH2   0  -0.245  -0.5695  -0.3722   2.7109
 OGG  OE    O  O2    0  -0.477  -0.5946   0.1434   1.4176
 OGG  CF    C  CH2   0  -0.174  -1.7191  -0.2913   0.6922
 OGG  CG    C  CH2   0  -0.173  -1.7110   0.3327  -0.6786
 OGG  OH    O  O2    0  -0.477  -0.6173  -0.1559  -1.4159
 OGG  CI    C  CH2   0  -0.245  -0.5595   0.3836  -2.6979
 OGG  CJ    C  C     0   0.460   0.6129  -0.2303  -3.4458
 OGG  OM    O  O     0  -0.479   1.3323  -1.0809  -2.9526
 OGG  NK    N  NH2   0  -0.802   0.7651   0.2489  -4.6887
 OGG  HNB1  H  HNH2  0   0.405   1.5288   0.0189   5.2808
 OGG  HNB2  H  HNH2  0   0.409   0.2041  -1.0484   5.0358
 OGG  HD1   H  HCH2  0   0.240  -1.4851  -0.1212   3.2678
 OGG  HD2   H  HCH2  0   0.238  -0.4981  -1.4699   2.7155
 OGG  HF1   H  HCH2  0   0.214  -2.6505   0.0051   1.1935
 OGG  HF2   H  HCH2  0   0.212  -1.7360  -1.3871   0.6068
 OGG  HG1   H  HCH2  0   0.211  -1.6731   1.4276  -0.5920
 OGG  HG2   H  HCH2  0   0.213  -2.6610   0.0825  -1.1700
 OGG  HI1   H  HCH2  0   0.239  -0.4373   1.4769  -2.6778
 OGG  HI2   H  HCH2  0   0.239  -1.4804   0.1867  -3.2675
 OGG  HNK1  H  HNH2  0   0.405   1.5043  -0.0903  -5.2820
 OGG  HNK2  H  HNH2  0   0.409   0.1618   0.9609  -5.0641

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
 OGG  NB  CC    single  1.341  0.020  1.341
 OGG  NB  HNB1  single  0.860  0.020  1.020
 OGG  NB  HNB2  single  0.860  0.020  1.020
 OGG  CC  OL    double  1.218  0.020  1.218
 OGG  CC  CD    single  1.520  0.020  1.520
 OGG  CD  OE    single  1.392  0.020  1.392
 OGG  CD  HD1   single  0.970  0.020  1.090
 OGG  CD  HD2   single  0.970  0.020  1.090
 OGG  OE  CF    single  1.407  0.020  1.407
 OGG  CF  CG    single  1.506  0.020  1.506
 OGG  CF  HF1   single  0.970  0.020  1.090
 OGG  CF  HF2   single  0.970  0.020  1.090
 OGG  CG  OH    single  1.407  0.020  1.407
 OGG  CG  HG1   single  0.970  0.020  1.090
 OGG  CG  HG2   single  0.970  0.020  1.090
 OGG  OH  CI    single  1.392  0.020  1.392
 OGG  CI  CJ    single  1.520  0.020  1.520
 OGG  CI  HI1   single  0.970  0.020  1.090
 OGG  CI  HI2   single  0.970  0.020  1.090
 OGG  CJ  OM    double  1.218  0.020  1.218
 OGG  CJ  NK    single  1.341  0.020  1.341
 OGG  NK  HNK1  single  0.860  0.020  1.020
 OGG  NK  HNK2  single  0.860  0.020  1.020

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
 OGG  HNB2  NB  HNB1  117.29  3.000
 OGG  HNB2  NB  CC    122.10  3.000
 OGG  HNB1  NB  CC    120.59  3.000
 OGG  CD    CC  OL    122.56  3.000
 OGG  CD    CC  NB    113.58  3.000
 OGG  OL    CC  NB    123.85  3.000
 OGG  HD2   CD  HD1   106.23  3.000
 OGG  HD2   CD  OE    112.00  3.000
 OGG  HD1   CD  OE    111.75  3.000
 OGG  HD2   CD  CC    109.31  3.000
 OGG  HD1   CD  CC    108.22  3.000
 OGG  OE    CD  CC    109.22  3.000
 OGG  CF    OE  CD    112.26  3.000
 OGG  HF2   CF  HF1   106.95  3.000
 OGG  HF2   CF  CG    110.02  3.000
 OGG  HF1   CF  CG    107.94  3.000
 OGG  HF2   CF  OE    111.12  3.000
 OGG  HF1   CF  OE    111.04  3.000
 OGG  CG    CF  OE    109.69  3.000
 OGG  HG2   CG  HG1   106.98  3.000
 OGG  HG2   CG  OH    111.03  3.000
 OGG  HG1   CG  OH    111.14  3.000
 OGG  HG2   CG  CF    107.95  3.000
 OGG  HG1   CG  CF    109.95  3.000
 OGG  OH    CG  CF    109.71  3.000
 OGG  CI    OH  CG    112.35  3.000
 OGG  HI2   CI  HI1   106.27  3.000
 OGG  HI2   CI  CJ    108.57  3.000
 OGG  HI1   CI  CJ    108.94  3.000
 OGG  HI2   CI  OH    111.87  3.000
 OGG  HI1   CI  OH    111.90  3.000
 OGG  CJ    CI  OH    109.18  3.000
 OGG  NK    CJ  OM    123.90  3.000
 OGG  NK    CJ  CI    113.54  3.000
 OGG  OM    CJ  CI    122.56  3.000
 OGG  HNK2  NK  HNK1  117.32  3.000
 OGG  HNK2  NK  CJ    122.06  3.000
 OGG  HNK1  NK  CJ    120.62  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
 OGG  CONST_01  HNB1  NB  CC  OL     0.00   0.0  0
 OGG  CONST_02  HNB2  NB  CC  OL   180.00   0.0  0
 OGG  CONST_03  HNK1  NK  CJ  CI   180.00   0.0  0
 OGG  CONST_04  HNK2  NK  CJ  CI     0.00   0.0  0
 OGG  Var_01    OE    CD  CC  NB  -174.10  30.0  3
 OGG  Var_02    CG    CF  OE  CD   178.24  30.0  3
 OGG  Var_03    OH    CG  CF  OE    66.21  30.0  3
 OGG  Var_04    CJ    CI  OH  CG  -177.88  30.0  3
 OGG  Var_05    OM    CJ  CI  OH     1.56  30.0  3

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
 OGG  plan-1  NB    0.020
 OGG  plan-1  CC    0.020
 OGG  plan-1  OL    0.020
 OGG  plan-1  CD    0.020
 OGG  plan-1  HNB1  0.020
 OGG  plan-1  HNB2  0.020
 OGG  plan-2  CI    0.020
 OGG  plan-2  CJ    0.020
 OGG  plan-2  OM    0.020
 OGG  plan-2  NK    0.020
 OGG  plan-2  HNK1  0.020
 OGG  plan-2  HNK2  0.020

