# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:59:15 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (4R)-4-(2-carboxyethyl)imidazolidin-2-iminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@H]1CNC(=[NH2+])N1
#
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
 ECD  ECD  (4R)-4-(2-carboxyethyl)imidazolidin-2-iminium  ligand  22  11  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ECD
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
 ECD  O01   O  OC    -1  -0.628  -3.9855   0.8823  -0.4523
 ECD  C02   C  C      0   0.420  -3.1537   0.0310  -0.0765
 ECD  O03   O  O      0  -0.604  -3.3893  -0.9908   0.5963
 ECD  C04   C  CH2    0  -0.599  -1.6950   0.2870  -0.5037
 ECD  C06   C  CH2    0  -0.425  -0.6872  -0.7360  -0.0065
 ECD  C07   C  CR15   0  -0.088   0.7066  -0.5216  -0.5636
 ECD  C08   C  CH2    0  -0.263   1.7337  -1.5527  -0.0761
 ECD  N09   N  NR15   0  -0.639   2.9417  -0.7510   0.0458
 ECD  C10   C  CR5    0   0.843   2.6272   0.5390   0.1230
 ECD  N11   N  NC2    1  -0.823   3.4832   1.5007   0.3961
 ECD  N12   N  NR15   0  -0.642   1.3304   0.7250  -0.1100
 ECD  H04   H  HCH2   0   0.230  -1.6638   0.3336  -1.5985
 ECD  H04A  H  HCH2   0   0.225  -1.4202   1.2926  -0.1662
 ECD  H06   H  HCH2   0   0.225  -0.6368  -0.7328   1.0853
 ECD  H06A  H  HCH2   0   0.236  -1.0061  -1.7391  -0.3002
 ECD  H07   H  HCR5   0   0.271   0.6701  -0.5200  -1.6586
 ECD  H08   H  HCH2   0   0.261   1.4479  -1.9706   0.8933
 ECD  HN11  H  HNC2   0   0.435   4.4538   1.2994   0.5685
 ECD  HN1A  H  HNC2   0   0.436   3.1972   2.4653   0.4045
 ECD  H08A  H  HCH2   0   0.276   1.8678  -2.3672  -0.7834
 ECD  HN09  H  HNR5   0   0.428   3.7927  -1.1176   0.4417
 ECD  HN12  H  HNR5   0   0.424   0.9729   1.6279  -0.3800

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
 ECD  C02  O01   deloc   1.248  0.020  1.248
 ECD  C04  C02   single  1.541  0.020  1.541
 ECD  O03  C02   deloc   1.246  0.020  1.246
 ECD  C04  C06   single  1.520  0.020  1.520
 ECD  C04  H04   single  0.970  0.020  1.090
 ECD  C04  H04A  single  0.970  0.020  1.090
 ECD  C06  C07   single  1.516  0.020  1.516
 ECD  C06  H06   single  0.970  0.020  1.090
 ECD  C06  H06A  single  0.970  0.020  1.090
 ECD  C07  N12   single  1.466  0.020  1.466
 ECD  C07  C08   single  1.535  0.020  1.535
 ECD  C07  H07   single  0.970  0.020  1.090
 ECD  C08  N09   single  1.455  0.020  1.455
 ECD  C08  H08   single  0.970  0.020  1.090
 ECD  C10  N09   single  1.330  0.020  1.330
 ECD  N12  C10   single  1.331  0.020  1.331
 ECD  C10  N11   double  1.316  0.020  1.316
 ECD  N11  HN11  single  0.860  0.020  1.020
 ECD  N11  HN1A  single  0.860  0.020  1.020
 ECD  C08  H08A  single  0.970  0.020  1.090
 ECD  N09  HN09  single  0.890  0.020  1.040
 ECD  N12  HN12  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
 ECD  C04   C02  O03   117.70  3.000
 ECD  O03   C02  O01   126.58  3.000
 ECD  C04   C02  O01   115.72  3.000
 ECD  H04A  C04  H04   105.16  3.000
 ECD  H04A  C04  C06   110.53  3.000
 ECD  H04   C04  C06   109.66  3.000
 ECD  H04A  C04  C02   107.72  3.000
 ECD  H04   C04  C02   108.10  3.000
 ECD  C06   C04  C02   115.16  3.000
 ECD  H06A  C06  H06   106.53  3.000
 ECD  H06A  C06  C07   107.42  3.000
 ECD  H06   C06  C07   108.92  3.000
 ECD  H06A  C06  C04   109.66  3.000
 ECD  H06   C06  C04   110.82  3.000
 ECD  C07   C06  C04   113.22  3.000
 ECD  H07   C07  N12   108.80  3.000
 ECD  H07   C07  C08   109.92  3.000
 ECD  N12   C07  C08   100.85  3.000
 ECD  H07   C07  C06   109.68  3.000
 ECD  C08   C07  C06   113.79  3.000
 ECD  N12   C07  C06   113.43  3.000
 ECD  H08A  C08  H08   108.83  3.000
 ECD  H08A  C08  N09   111.40  3.000
 ECD  H08   C08  N09   110.69  3.000
 ECD  H08A  C08  C07   112.28  3.000
 ECD  H08   C08  C07   111.31  3.000
 ECD  N09   C08  C07   102.24  3.000
 ECD  HN09  N09  C10   122.00  3.000
 ECD  HN09  N09  C08   122.25  3.000
 ECD  C10   N09  C08   110.05  3.000
 ECD  N12   C10  N11   124.61  3.000
 ECD  N11   C10  N09   124.54  3.000
 ECD  N12   C10  N09   110.85  3.000
 ECD  HN1A  N11  HN11  117.68  3.000
 ECD  HN1A  N11  C10   121.16  3.000
 ECD  HN11  N11  C10   121.12  3.000
 ECD  HN12  N12  C10   121.18  3.000
 ECD  HN12  N12  C07   121.87  3.000
 ECD  C10   N12  C07   110.49  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
 ECD  CONST_01  N09   C10  N12  C07    0.00   0.0  0
 ECD  CONST_03  N12   C10  N09  C08    0.00   0.0  0
 ECD  CONST_04  N11   C10  N12  C07  180.00   0.0  0
 ECD  CONST_05  N11   C10  N09  C08  180.00   0.0  0
 ECD  CONST_06  HN09  N09  C08  C07  180.00   0.0  0
 ECD  CONST_08  HN11  N11  C10  N09    0.00   0.0  0
 ECD  CONST_09  HN1A  N11  C10  N09  180.00   0.0  0
 ECD  Var_01    H08   C08  N09  C10  -98.92  30.0  1
 ECD  Var_02    C07   C06  C04  C02  174.25  30.0  3
 ECD  Var_03    C06   C04  C02  O01  178.35  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
 ECD  chir_01  C07  C06  N12  C08  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
 ECD  plan-1  C07   0.020
 ECD  plan-1  C08   0.020
 ECD  plan-1  N09   0.020
 ECD  plan-1  C10   0.020
 ECD  plan-1  N11   0.020
 ECD  plan-1  N12   0.020
 ECD  plan-1  HN11  0.020
 ECD  plan-1  HN1A  0.020
 ECD  plan-1  HN09  0.020
 ECD  plan-1  HN12  0.020
 ECD  plan-2  O01   0.020
 ECD  plan-2  C02   0.020
 ECD  plan-2  O03   0.020
 ECD  plan-2  C04   0.020

