# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 03:27:21 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  36  20  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.200  -3.0772  -0.1929   0.4685
 EKQ  C15  C  C     0   0.534  -3.4216  -1.4831   1.2054
 EKQ  O01  O  OH1   0  -0.589   5.1490   1.7358   1.9617
 EKQ  O03  O  O     0  -0.438   3.3978   2.4769   0.7956
 EKQ  C04  C  CH2   0  -0.604   4.1902   0.2239   0.4542
 EKQ  C05  C  CH1   0  -0.171   2.9828  -0.0500  -0.4435
 EKQ  N06  N  NH1   0  -0.604   1.7862  -0.2157   0.3457
 EKQ  C07  C  CH2   0  -0.289   0.5638  -0.1897  -0.4392
 EKQ  C08  C  CH2   0  -0.284  -0.6456  -0.3050   0.4736
 EKQ  N09  N  NH1   0  -0.588  -1.8681  -0.2702  -0.3057
 EKQ  C11  C  CH2   0  -0.577  -4.2438   0.1706  -0.4529
 EKQ  C12  C  C     0   0.557  -4.0063   1.5192  -1.0831
 EKQ  O13  O  OH1   0  -0.588  -4.2999   1.5316  -2.3764
 EKQ  O14  O  O     0  -0.445  -3.6290   2.4917  -0.4799
 EKQ  O16  O  OH1   0  -0.589  -4.2607  -1.2740   2.2103
 EKQ  O17  O  O     0  -0.433  -3.0028  -2.5698   0.8970
 EKQ  C18  C  C     0   0.539   3.2793  -1.3288  -1.2131
 EKQ  O19  O  O     0  -0.428   2.9074  -2.4283  -0.8979
 EKQ  O20  O  OH1   0  -0.591   4.0417  -1.0841  -2.2720
 EKQ  H1   H  HCH1  0   0.284  -2.9631   0.6006   1.2123
 EKQ  H2   H  HOH1  0   0.484   5.1363   2.6297   2.3363
 EKQ  H3   H  HCH2  0   0.313   5.1214   0.1404  -0.1135
 EKQ  H4   H  HCH2  0   0.298   4.2441  -0.5289   1.2452
 EKQ  H5   H  HCH1  0   0.255   2.8995   0.7649  -1.1788
 EKQ  H6   H  HNH1  0   0.354   1.7380   0.5375   1.0207
 EKQ  H8   H  HCH2  0   0.205   0.4699   0.7216  -1.0478
 EKQ  H9   H  HCH2  0   0.229   0.5666  -1.0337  -1.1349
 EKQ  H10  H  HCH2  0   0.208  -0.5408  -1.2054   1.0943
 EKQ  H11  H  HCH2  0   0.227  -0.6583   0.5489   1.1585
 EKQ  H12  H  HNH1  0   0.348  -1.9073  -1.0680  -0.9300
 EKQ  H14  H  HCH2  0   0.278  -4.3762  -0.5959  -1.2180
 EKQ  H15  H  HCH2  0   0.304  -5.1804   0.2304   0.1082
 EKQ  H16  H  HOH1  0   0.480  -4.1767   2.4243  -2.7339
 EKQ  H17  H  HOH1  0   0.484  -4.4926  -2.1134   2.6365
 EKQ  H18  H  HOH1  0   0.484   4.2679  -1.9130  -2.7202
 EKQ  C02  C  C     0   0.553   4.1751   1.5984   1.0731

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  double  1.205  0.020  1.205
 EKQ  C12  C11  single  1.507  0.020  1.507
 EKQ  C12  O13  single  1.326  0.020  1.326
 EKQ  C11  C10  single  1.530  0.020  1.530
 EKQ  O17  C15  double  1.205  0.020  1.205
 EKQ  C10  C15  single  1.525  0.020  1.525
 EKQ  C10  N09  single  1.438  0.020  1.438
 EKQ  C15  O16  single  1.326  0.020  1.326
 EKQ  N09  C08  single  1.450  0.020  1.450
 EKQ  O19  C18  double  1.203  0.020  1.203
 EKQ  C08  C07  single  1.520  0.020  1.520
 EKQ  C18  O20  single  1.328  0.020  1.328
 EKQ  C18  C05  single  1.522  0.020  1.522
 EKQ  C07  N06  single  1.453  0.020  1.453
 EKQ  N06  C05  single  1.443  0.020  1.443
 EKQ  C05  C04  single  1.529  0.020  1.529
 EKQ  C04  C02  single  1.507  0.020  1.507
 EKQ  C02  O03  double  1.205  0.020  1.205
 EKQ  C02  O01  single  1.326  0.020  1.326
 EKQ  C10  H1   single  0.970  0.020  1.090
 EKQ  O01  H2   single  0.850  0.020  0.980
 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
 EKQ  O13  H16  single  0.850  0.020  0.980
 EKQ  O16  H17  single  0.850  0.020  0.980
 EKQ  O20  H18  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
 EKQ  H1   C10  C11  108.47  3.000
 EKQ  H1   C10  N09  108.51  3.000
 EKQ  C11  C10  N09  109.25  3.000
 EKQ  H1   C10  C15  107.98  3.000
 EKQ  N09  C10  C15  113.86  3.000
 EKQ  C11  C10  C15  108.64  3.000
 EKQ  O17  C15  O16  123.80  3.000
 EKQ  O16  C15  C10  112.07  3.000
 EKQ  O17  C15  C10  124.12  3.000
 EKQ  H2   O01  C02  110.19  3.000
 EKQ  H4   C04  H3   106.32  3.000
 EKQ  H4   C04  C05  109.89  3.000
 EKQ  H3   C04  C05  110.72  3.000
 EKQ  H4   C04  C02  109.35  3.000
 EKQ  H3   C04  C02  106.93  3.000
 EKQ  C05  C04  C02  113.35  3.000
 EKQ  H5   C05  C18  107.40  3.000
 EKQ  H5   C05  N06  112.81  3.000
 EKQ  C18  C05  N06  109.98  3.000
 EKQ  H5   C05  C04  108.62  3.000
 EKQ  N06  C05  C04  110.75  3.000
 EKQ  C18  C05  C04  107.07  3.000
 EKQ  H6   N06  C07  107.87  3.000
 EKQ  H6   N06  C05  108.58  3.000
 EKQ  C07  N06  C05  113.59  3.000
 EKQ  H9   C07  H8   106.72  3.000
 EKQ  H9   C07  C08  109.00  3.000
 EKQ  H8   C07  C08  109.11  3.000
 EKQ  H9   C07  N06  109.12  3.000
 EKQ  H8   C07  N06  112.68  3.000
 EKQ  C08  C07  N06  110.10  3.000
 EKQ  H11  C08  H10  106.68  3.000
 EKQ  H11  C08  N09  107.92  3.000
 EKQ  H10  C08  N09  113.80  3.000
 EKQ  H11  C08  C07  109.02  3.000
 EKQ  H10  C08  C07  109.01  3.000
 EKQ  N09  C08  C07  110.26  3.000
 EKQ  H12  N09  C08  110.16  3.000
 EKQ  H12  N09  C10  109.96  3.000
 EKQ  C08  N09  C10  114.89  3.000
 EKQ  H15  C11  H14  107.11  3.000
 EKQ  H15  C11  C12  107.49  3.000
 EKQ  H14  C11  C12  110.76  3.000
 EKQ  H15  C11  C10  110.92  3.000
 EKQ  H14  C11  C10  110.36  3.000
 EKQ  C12  C11  C10  110.13  3.000
 EKQ  O14  C12  O13  123.36  3.000
 EKQ  O13  C12  C11  112.41  3.000
 EKQ  O14  C12  C11  124.20  3.000
 EKQ  H16  O13  C12  109.88  3.000
 EKQ  H17  O16  C15  110.37  3.000
 EKQ  O20  C18  O19  123.72  3.000
 EKQ  O20  C18  C05  111.13  3.000
 EKQ  O19  C18  C05  125.13  3.000
 EKQ  H18  O20  C18  110.20  3.000
 EKQ  C04  C02  O03  125.21  3.000
 EKQ  O03  C02  O01  123.54  3.000
 EKQ  C04  C02  O01  111.24  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  CONST_01  H17  O16  C15  C10   180.00   0.0  0
 EKQ  CONST_02  H2   O01  C02  O03     0.00   0.0  0
 EKQ  CONST_03  H18  O20  C18  C05   180.00   0.0  0
 EKQ  CONST_04  H16  O13  C12  C11   180.00   0.0  0
 EKQ  Var_01    O14  C12  C11  C10   -45.76  30.0  2
 EKQ  Var_02    C07  C08  N09  C10  -172.09  30.0  3
 EKQ  Var_03    C05  C04  C02  O01   172.59  30.0  2
 EKQ  Var_04    C08  C07  N06  C05  -177.36  30.0  1
 EKQ  Var_05    N09  C08  C07  N06   179.61  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-1  H17  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-2  H16  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-3  H18  0.020
 EKQ  plan-4  O01  0.020
 EKQ  plan-4  O03  0.020
 EKQ  plan-4  C04  0.020
 EKQ  plan-4  H2   0.020
 EKQ  plan-4  C02  0.020

