# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:35:46 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{S})-2-[2-[[(2~{S})-1,4-bis(oxidanyl)-1,4-bis(oxidanylidene)butan-2-yl]amino]ethylamino]butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](NCCN[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
 EKQ  EKQ  '(2~{S})-2-[2-[[(2~{S})-1,4-bis(oxidanyl)-1,4-bis(oxidanylidene)butan-2-yl]amino]ethylamino]butanedioic acid'  ligand  32  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EKQ
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
 EKQ  C10  C  CH1    0  -0.179  -3.0582  -0.0675   0.4858
 EKQ  C15  C  C      0   0.389  -3.2675  -1.2146   1.5007
 EKQ  O01  O  OC    -1  -0.625   5.2544   1.1696   2.2427
 EKQ  O03  O  O      0  -0.608   3.4652   2.1316   1.3373
 EKQ  C04  C  CH2    0  -0.601   4.2332   0.0470   0.4269
 EKQ  C05  C  CH1    0  -0.144   3.0143   0.0007  -0.4926
 EKQ  N06  N  NH1    0  -0.610   1.8109  -0.1526   0.3041
 EKQ  C07  C  CH2    0  -0.275   0.5863  -0.1098  -0.4678
 EKQ  C08  C  CH2    0  -0.278  -0.6292  -0.0989   0.4477
 EKQ  N09  N  NH1    0  -0.588  -1.8557  -0.1768  -0.3208
 EKQ  C11  C  CH2    0  -0.565  -4.2727  -0.0111  -0.4408
 EKQ  C12  C  C      0   0.406  -4.2376   1.1839  -1.4054
 EKQ  O13  O  OC    -1  -0.626  -4.3739   0.9458  -2.6238
 EKQ  O14  O  O      0  -0.627  -4.1020   2.3136  -0.8898
 EKQ  O16  O  OC    -1  -0.624  -3.9006  -0.9358   2.5414
 EKQ  O17  O  O      0  -0.616  -2.8331  -2.3409   1.1808
 EKQ  C18  C  C      0   0.390   3.2289  -1.1513  -1.4980
 EKQ  O19  O  O      0  -0.610   2.7899  -2.2797  -1.2044
 EKQ  O20  O  OC    -1  -0.628   3.8858  -0.8602  -2.5219
 EKQ  H1   H  HCH1   0   0.193  -3.0103   0.8796   1.0326
 EKQ  H3   H  HCH2   0   0.227   5.1388   0.0780  -0.1886
 EKQ  H4   H  HCH2   0   0.216   4.2892  -0.8922   0.9881
 EKQ  H5   H  HCH1   0   0.157   2.9917   0.9382  -1.0737
 EKQ  H6   H  HNH1   0   0.328   1.8021   0.6317   0.9474
 EKQ  H8   H  HCH2   0   0.167   0.5302   0.7624  -1.1416
 EKQ  H9   H  HCH2   0   0.205   0.5412  -0.9969  -1.1055
 EKQ  H10  H  HCH2   0   0.183  -0.5226  -0.9096   1.1833
 EKQ  H11  H  HCH2   0   0.200  -0.6398   0.8374   1.0180
 EKQ  H12  H  HNH1   0   0.318  -1.8795  -1.0814  -0.7811
 EKQ  H14  H  HCH2   0   0.193  -4.3434  -0.9516  -0.9963
 EKQ  H15  H  HCH2   0   0.219  -5.1770   0.0583   0.1737
 EKQ  C02  C  C      0   0.414   4.3151   1.2200   1.4223

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
 EKQ  O14  C12  deloc   1.249  0.020  1.249
 EKQ  C12  C11  single  1.536  0.020  1.536
 EKQ  C12  O13  deloc   1.249  0.020  1.249
 EKQ  C11  C10  single  1.529  0.020  1.529
 EKQ  O17  C15  deloc   1.249  0.020  1.249
 EKQ  C10  C15  single  1.546  0.020  1.546
 EKQ  C10  N09  single  1.452  0.020  1.452
 EKQ  C15  O16  deloc   1.250  0.020  1.250
 EKQ  N09  C08  single  1.450  0.020  1.450
 EKQ  O19  C18  deloc   1.246  0.020  1.246
 EKQ  C08  C07  single  1.522  0.020  1.522
 EKQ  C18  O20  deloc   1.251  0.020  1.251
 EKQ  C18  C05  single  1.544  0.020  1.544
 EKQ  C07  N06  single  1.448  0.020  1.448
 EKQ  N06  C05  single  1.451  0.020  1.451
 EKQ  C05  C04  single  1.528  0.020  1.528
 EKQ  C04  C02  single  1.541  0.020  1.541
 EKQ  C02  O03  deloc   1.249  0.020  1.249
 EKQ  C02  O01  deloc   1.248  0.020  1.248
 EKQ  C10  H1   single  0.970  0.020  1.090
 EKQ  C04  H3   single  0.970  0.020  1.090
 EKQ  C04  H4   single  0.970  0.020  1.090
 EKQ  C05  H5   single  0.970  0.020  1.090
 EKQ  N06  H6   single  0.890  0.020  1.040
 EKQ  C07  H8   single  0.970  0.020  1.090
 EKQ  C07  H9   single  0.970  0.020  1.090
 EKQ  C08  H10  single  0.970  0.020  1.090
 EKQ  C08  H11  single  0.970  0.020  1.090
 EKQ  N09  H12  single  0.890  0.020  1.040
 EKQ  C11  H14  single  0.970  0.020  1.090
 EKQ  C11  H15  single  0.970  0.020  1.090

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
 EKQ  H1   C10  C11  107.80  3.000
 EKQ  H1   C10  N09  107.84  3.000
 EKQ  C11  C10  N09  108.90  3.000
 EKQ  H1   C10  C15  108.67  3.000
 EKQ  N09  C10  C15  114.90  3.000
 EKQ  C11  C10  C15  108.53  3.000
 EKQ  O17  C15  O16  126.22  3.000
 EKQ  O16  C15  C10  116.73  3.000
 EKQ  O17  C15  C10  117.00  3.000
 EKQ  H4   C04  H3   105.65  3.000
 EKQ  H4   C04  C05  108.85  3.000
 EKQ  H3   C04  C05  108.80  3.000
 EKQ  H4   C04  C02  108.61  3.000
 EKQ  H3   C04  C02  107.31  3.000
 EKQ  C05  C04  C02  117.03  3.000
 EKQ  H5   C05  C18  107.09  3.000
 EKQ  H5   C05  N06  111.21  3.000
 EKQ  C18  C05  N06  113.20  3.000
 EKQ  H5   C05  C04  107.92  3.000
 EKQ  N06  C05  C04  109.54  3.000
 EKQ  C18  C05  C04  107.68  3.000
 EKQ  H6   N06  C07  107.93  3.000
 EKQ  H6   N06  C05  105.88  3.000
 EKQ  C07  N06  C05  113.92  3.000
 EKQ  H9   C07  H8   106.44  3.000
 EKQ  H9   C07  C08  108.88  3.000
 EKQ  H8   C07  C08  108.73  3.000
 EKQ  H9   C07  N06  108.77  3.000
 EKQ  H8   C07  N06  113.06  3.000
 EKQ  C08  C07  N06  110.79  3.000
 EKQ  H11  C08  H10  106.41  3.000
 EKQ  H11  C08  N09  108.27  3.000
 EKQ  H10  C08  N09  113.39  3.000
 EKQ  H11  C08  C07  109.07  3.000
 EKQ  H10  C08  C07  108.64  3.000
 EKQ  N09  C08  C07  110.89  3.000
 EKQ  H12  N09  C08  107.94  3.000
 EKQ  H12  N09  C10  107.43  3.000
 EKQ  C08  N09  C10  113.71  3.000
 EKQ  H15  C11  H14  106.60  3.000
 EKQ  H15  C11  C12  108.77  3.000
 EKQ  H14  C11  C12  110.56  3.000
 EKQ  H15  C11  C10  108.55  3.000
 EKQ  H14  C11  C10  109.10  3.000
 EKQ  C12  C11  C10  113.03  3.000
 EKQ  O14  C12  O13  125.94  3.000
 EKQ  O13  C12  C11  117.50  3.000
 EKQ  O14  C12  C11  116.54  3.000
 EKQ  O20  C18  O19  126.07  3.000
 EKQ  O20  C18  C05  115.62  3.000
 EKQ  O19  C18  C05  118.25  3.000
 EKQ  C04  C02  O03  118.39  3.000
 EKQ  O03  C02  O01  125.89  3.000
 EKQ  C04  C02  O01  115.72  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
 EKQ  Var_01  O14  C12  C11  C10   -54.52  30.0  2
 EKQ  Var_02  C07  C08  N09  C10  -175.53  30.0  3
 EKQ  Var_03  C05  C04  C02  O01   173.73  30.0  2
 EKQ  Var_04  C08  C07  N06  C05  -172.81  30.0  1
 EKQ  Var_05  N09  C08  C07  N06  -174.89  30.0  1

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
 EKQ  chir_01  C10  C11  C15  N09  negativ
 EKQ  chir_02  C05  N06  C18  C04  positiv

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
 EKQ  plan-1  C10  0.020
 EKQ  plan-1  C15  0.020
 EKQ  plan-1  O16  0.020
 EKQ  plan-1  O17  0.020
 EKQ  plan-2  C11  0.020
 EKQ  plan-2  C12  0.020
 EKQ  plan-2  O13  0.020
 EKQ  plan-2  O14  0.020
 EKQ  plan-3  C05  0.020
 EKQ  plan-3  C18  0.020
 EKQ  plan-3  O19  0.020
 EKQ  plan-3  O20  0.020
 EKQ  plan-4  O01  0.020
 EKQ  plan-4  O03  0.020
 EKQ  plan-4  C04  0.020
 EKQ  plan-4  C02  0.020

