# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:23:59 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2-{2-[(2-aminoethyl)amino]-2-oxoethyl}-2-hydroxybutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNC(=O)C[C@](O)(CC(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
 X3J  X3J  '(2S)-2-{2-[(2-aminoethyl)amino]-2-oxoethyl}-2-hydroxybutanedioic acid'  ligand  28  16  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X3J
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
 X3J  C'    C  C      0   0.417  -3.1828  -1.1117   0.5322
 X3J  O1'   O  OC    -1  -0.783  -2.8168  -1.4896   1.6827
 X3J  O2'   O  O      0  -0.515  -4.3153  -0.6923   0.2527
 X3J  C1    C  CH2    0  -0.582  -2.1116  -1.1695  -0.5668
 X3J  C3    C  CH2    0  -0.299   4.7097  -0.7336  -0.0401
 X3J  N3    N  NH2    0  -0.844   5.9628  -0.2043   0.4775
 X3J  O3    O  OH1    0  -0.659  -0.3085  -0.9231   0.9964
 X3J  CM3   C  C      0   0.427  -1.2524   1.1320   0.0215
 X3J  O3'   O  OC    -1  -0.636  -1.8337   1.6657  -0.9474
 X3J  C4    C  CH2    0  -0.259   3.5578   0.1884   0.3434
 X3J  N4    N  NH1    0  -0.720   2.2877  -0.3285  -0.1023
 X3J  CAP   C  CT     0   0.138  -0.8620  -0.3646  -0.1684
 X3J  O4    O  O      0  -0.334   1.7407   1.3743  -1.4884
 X3J  CM4   C  CH2    0  -0.600   0.1856  -0.4492  -1.2892
 X3J  OAF   O  O      0  -0.701  -0.9574   1.6799   1.0979
 X3J  H11C  H  HCH2   0   0.244  -1.8057  -2.2134  -0.7067
 X3J  H12C  H  HCH2   0   0.258  -2.5074  -0.8151  -1.5163
 X3J  H31C  H  HCH2   0   0.276   4.7735  -0.7821  -1.1271
 X3J  H32C  H  HCH2   0   0.156   4.4803  -1.7494   0.3111
 X3J  H31N  H  HNH2   0   0.345   5.9757  -0.2895   1.4858
 X3J  H32N  H  HNH2   0   0.343   6.7293  -0.7752   0.1475
 X3J  H41C  H  HCH2   0   0.176   3.5391   0.3015   1.4332
 X3J  H42C  H  HCH2   0   0.253   3.7198   1.1790  -0.0819
 X3J  H3    H  HOH1   0   0.419  -1.0756  -1.2573   1.5084
 X3J  H4    H  HNH1   0   0.379   1.9179  -1.1369   0.3758
 X3J  HM41  H  HCH2   0   0.285  -0.2057   0.0179  -2.1797
 X3J  HM42  H  HCH2   0   0.272   0.4095  -1.4992  -1.4921
 X3J  C4'   C  C      0   0.543   1.4756   0.2929  -0.9705

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
 X3J  C'   O1'   deloc   1.265  0.020  1.265
 X3J  C'   O2'   deloc   1.240  0.020  1.240
 X3J  C'   C1    single  1.536  0.020  1.536
 X3J  C1   CAP   single  1.539  0.020  1.539
 X3J  C3   N3    single  1.455  0.020  1.455
 X3J  C3   C4    single  1.524  0.020  1.524
 X3J  O3   CAP   single  1.405  0.020  1.405
 X3J  CM3  O3'   deloc   1.250  0.020  1.250
 X3J  CM3  CAP   single  1.558  0.020  1.558
 X3J  CM3  OAF   deloc   1.243  0.020  1.243
 X3J  C4   N4    single  1.442  0.020  1.442
 X3J  N4   C4'   single  1.341  0.020  1.341
 X3J  C4'  O4    double  1.228  0.020  1.228
 X3J  C4'  CM4   single  1.522  0.020  1.522
 X3J  CM4  CAP   single  1.536  0.020  1.536
 X3J  C1   H11C  single  0.970  0.020  1.090
 X3J  C1   H12C  single  0.970  0.020  1.090
 X3J  C3   H31C  single  0.970  0.020  1.090
 X3J  C3   H32C  single  0.970  0.020  1.090
 X3J  N3   H31N  single  0.890  0.020  1.040
 X3J  N3   H32N  single  0.890  0.020  1.040
 X3J  C4   H41C  single  0.970  0.020  1.090
 X3J  C4   H42C  single  0.970  0.020  1.090
 X3J  O3   H3    single  0.850  0.020  0.980
 X3J  N4   H4    single  0.860  0.020  1.020
 X3J  CM4  HM41  single  0.970  0.020  1.090
 X3J  CM4  HM42  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
 X3J  C1    C'   O2'   119.25  3.000
 X3J  C1    C'   O1'   115.96  3.000
 X3J  O2'   C'   O1'   124.78  3.000
 X3J  H12C  C1   H11C  107.46  3.000
 X3J  H12C  C1   CAP   110.55  3.000
 X3J  H11C  C1   CAP   107.72  3.000
 X3J  H12C  C1   C'    111.01  3.000
 X3J  H11C  C1   C'    108.76  3.000
 X3J  CAP   C1   C'    111.19  3.000
 X3J  H32C  C3   H31C  106.84  3.000
 X3J  H32C  C3   C4    108.72  3.000
 X3J  H31C  C3   C4    108.78  3.000
 X3J  H32C  C3   N3    113.72  3.000
 X3J  H31C  C3   N3    108.69  3.000
 X3J  C4    C3   N3    109.95  3.000
 X3J  H32N  N3   H31N  105.55  3.000
 X3J  H32N  N3   C3    109.34  3.000
 X3J  H31N  N3   C3    109.55  3.000
 X3J  H3    O3   CAP   105.07  3.000
 X3J  OAF   CM3  CAP   117.98  3.000
 X3J  OAF   CM3  O3'   126.40  3.000
 X3J  CAP   CM3  O3'   115.61  3.000
 X3J  H42C  C4   H41C  107.26  3.000
 X3J  H42C  C4   N4    109.64  3.000
 X3J  H41C  C4   N4    109.23  3.000
 X3J  H42C  C4   C3    109.82  3.000
 X3J  H41C  C4   C3    108.99  3.000
 X3J  N4    C4   C3    111.78  3.000
 X3J  H4    N4   C4'   117.11  3.000
 X3J  H4    N4   C4    117.61  3.000
 X3J  C4'   N4   C4    124.56  3.000
 X3J  CM4   CAP  CM3   108.22  3.000
 X3J  CM4   CAP  O3    108.31  3.000
 X3J  CM3   CAP  O3    112.30  3.000
 X3J  CM4   CAP  C1    109.63  3.000
 X3J  CM3   CAP  C1    109.29  3.000
 X3J  O3    CAP  C1    109.06  3.000
 X3J  HM42  CM4  HM41  109.69  3.000
 X3J  HM42  CM4  CAP   109.16  3.000
 X3J  HM41  CM4  CAP   109.32  3.000
 X3J  HM42  CM4  C4'   109.50  3.000
 X3J  HM41  CM4  C4'   105.61  3.000
 X3J  CAP   CM4  C4'   113.47  3.000
 X3J  CM4   C4'  O4    121.60  3.000
 X3J  CM4   C4'  N4    115.01  3.000
 X3J  O4    C4'  N4    123.39  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
 X3J  CONST_01  O4    C4'  N4   C4      0.00   0.0  0
 X3J  CONST_02  CM4   C4'  N4   C4    180.00   0.0  0
 X3J  CONST_03  H4    N4   C4'  O4    180.00   0.0  0
 X3J  Var_01    CAP   C1   C'   O1'   -55.70  30.0  3
 X3J  Var_02    C4'   N4   C4   C3   -118.45  30.0  3
 X3J  Var_03    N4    C4   C3   N3   -177.57  30.0  3
 X3J  Var_04    CAP   CM4  C4'  N4     75.92  30.0  3
 X3J  Var_05    H31N  N3   C3   C4     69.91  30.0  3

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
 X3J  chir_01  CAP  O3  CM3  CM4  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
 X3J  plan-1  C4   0.020
 X3J  plan-1  N4   0.020
 X3J  plan-1  O4   0.020
 X3J  plan-1  CM4  0.020
 X3J  plan-1  H4   0.020
 X3J  plan-1  C4'  0.020
 X3J  plan-2  C'   0.020
 X3J  plan-2  O1'  0.020
 X3J  plan-2  O2'  0.020
 X3J  plan-2  C1   0.020
 X3J  plan-3  CM3  0.020
 X3J  plan-3  O3'  0.020
 X3J  plan-3  CAP  0.020
 X3J  plan-3  OAF  0.020

