# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:36:25 2021
#   Inital geometry file: a 60 line input string
#   Ligand name: 2-[2-(2-aminoethoxy)ethoxy]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCOCCOCC(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
 XDV  XDV  2-[2-(2-aminoethoxy)ethoxy]acetamide  ligand  25  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XDV
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
 XDV  N10   N  NH2   0  -0.802  -37.4041  -5.2324  15.2289
 XDV  C02   C  CH2   0  -0.315  -39.0399  -8.2116   9.6084
 XDV  C03   C  CH2   0  -0.151  -38.9906  -6.9533  10.4454
 XDV  C05   C  CH2   0  -0.203  -39.1934  -4.5896  10.2003
 XDV  C06   C  CH2   0  -0.194  -37.9206  -3.9320  10.7054
 XDV  C08   C  CH2   0  -0.255  -37.8670  -4.5571  12.9747
 XDV  C09   C  C     0   0.469  -37.1424  -5.4817  13.9381
 XDV  N01   N  NH2   0  -0.800  -37.8287  -8.3723   8.8186
 XDV  O04   O  O2    0  -0.493  -38.9863  -5.8347   9.5809
 XDV  O07   O  O2    0  -0.477  -37.2512  -4.6372  11.7269
 XDV  O11   O  O     0  -0.480  -36.4179  -6.3839  13.5548
 XDV  H101  H  HNH2  0   0.404  -37.0543  -5.8439  15.9483
 XDV  H102  H  HNH2  0   0.409  -38.0028  -4.4769  15.5160
 XDV  H021  H  HCH2  0   0.196  -39.9657  -8.2073   9.0147
 XDV  H022  H  HCH2  0   0.224  -39.1186  -9.0564  10.2968
 XDV  H032  H  HCH2  0   0.197  -39.8709  -6.9256  11.1026
 XDV  H031  H  HCH2  0   0.207  -38.1029  -6.9728  11.0868
 XDV  H052  H  HCH2  0   0.239  -39.6187  -3.9193   9.4475
 XDV  H051  H  HCH2  0   0.207  -39.9430  -4.6723  10.9989
 XDV  H062  H  HCH2  0   0.238  -37.2091  -3.8488   9.8809
 XDV  H061  H  HCH2  0   0.208  -38.1683  -2.9102  11.0263
 XDV  H082  H  HCH2  0   0.244  -37.8680  -3.5273  13.3598
 XDV  H081  H  HCH2  0   0.241  -38.9181  -4.8779  12.9510
 XDV  H1    H  HNH2  0   0.348  -37.8773  -9.2411   8.3025
 XDV  H2    H  HNH2  0   0.339  -37.7821  -7.6425   8.1193

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
 XDV  N01  C02   single  1.455  0.020  1.455
 XDV  C02  C03   single  1.512  0.020  1.512
 XDV  O04  C03   single  1.414  0.020  1.414
 XDV  O04  C05   single  1.406  0.020  1.406
 XDV  C05  C06   single  1.519  0.020  1.519
 XDV  C06  O07   single  1.410  0.020  1.410
 XDV  O07  C08   single  1.394  0.020  1.394
 XDV  C08  C09   single  1.519  0.020  1.519
 XDV  O11  C09   double  1.219  0.020  1.219
 XDV  C09  N10   single  1.340  0.020  1.340
 XDV  N10  H101  single  0.860  0.020  1.020
 XDV  N10  H102  single  0.860  0.020  1.020
 XDV  C02  H021  single  0.970  0.020  1.090
 XDV  C02  H022  single  0.970  0.020  1.090
 XDV  C03  H032  single  0.970  0.020  1.090
 XDV  C03  H031  single  0.970  0.020  1.090
 XDV  C05  H052  single  0.970  0.020  1.090
 XDV  C05  H051  single  0.970  0.020  1.090
 XDV  C06  H062  single  0.970  0.020  1.090
 XDV  C06  H061  single  0.970  0.020  1.090
 XDV  C08  H082  single  0.970  0.020  1.090
 XDV  C08  H081  single  0.970  0.020  1.090
 XDV  N01  H1    single  0.890  0.020  1.040
 XDV  N01  H2    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
 XDV  H102  N10  H101  117.32  3.000
 XDV  H102  N10  C09   122.06  3.000
 XDV  H101  N10  C09   120.48  3.000
 XDV  H022  C02  H021  106.41  3.000
 XDV  H022  C02  N01   108.46  3.000
 XDV  H021  C02  N01   114.09  3.000
 XDV  H022  C02  C03   107.28  3.000
 XDV  H021  C02  C03   108.84  3.000
 XDV  N01   C02  C03   111.42  3.000
 XDV  H031  C03  H032  107.43  3.000
 XDV  H031  C03  O04   111.70  3.000
 XDV  H032  C03  O04   110.37  3.000
 XDV  H031  C03  C02   109.62  3.000
 XDV  H032  C03  C02   109.02  3.000
 XDV  O04   C03  C02   108.66  3.000
 XDV  H051  C05  H052  106.33  3.000
 XDV  H051  C05  O04   110.74  3.000
 XDV  H052  C05  O04   107.26  3.000
 XDV  H051  C05  C06   111.26  3.000
 XDV  H052  C05  C06   106.82  3.000
 XDV  O04   C05  C06   113.98  3.000
 XDV  H061  C06  H062  107.23  3.000
 XDV  H061  C06  O07   111.12  3.000
 XDV  H062  C06  O07   106.01  3.000
 XDV  H061  C06  C05   108.10  3.000
 XDV  H062  C06  C05   109.13  3.000
 XDV  O07   C06  C05   114.97  3.000
 XDV  H081  C08  H082  106.26  3.000
 XDV  H081  C08  O07   112.74  3.000
 XDV  H082  C08  O07   111.58  3.000
 XDV  H081  C08  C09   106.99  3.000
 XDV  H082  C08  C09   110.39  3.000
 XDV  O07   C08  C09   108.79  3.000
 XDV  O11   C09  C08   122.31  3.000
 XDV  O11   C09  N10   123.81  3.000
 XDV  C08   C09  N10   113.85  3.000
 XDV  H2    N01  H1    105.61  3.000
 XDV  H2    N01  C02   109.50  3.000
 XDV  H1    N01  C02   109.38  3.000
 XDV  C05   O04  C03   115.52  3.000
 XDV  C08   O07  C06   114.21  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
 XDV  CONST_01  H101  N10  C09  C08  180.00   0.0  0
 XDV  CONST_02  H102  N10  C09  C08    0.00   0.0  0
 XDV  Var_01    O07   C08  C09  N10  163.18  30.0  1
 XDV  Var_02    C06   C05  O04  C03   87.67  30.0  3
 XDV  Var_03    C09   C08  O07  C06  173.54  30.0  3
 XDV  Var_04    O04   C03  C02  N01   65.63  30.0  3
 XDV  Var_05    O07   C06  C05  O04  -63.84  30.0  3
 XDV  Var_06    H1    N01  C02  C03  177.59  30.0  3
 XDV  Var_07    H062  C06  O07  C08  164.84  30.0  1

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
 XDV  plan-1  N10   0.020
 XDV  plan-1  C08   0.020
 XDV  plan-1  C09   0.020
 XDV  plan-1  O11   0.020
 XDV  plan-1  H101  0.020
 XDV  plan-1  H102  0.020

