# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 17:32:59 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  30  16  .  2021-08-24  2023-02-16
;
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   0.558  -3.4648  -0.8485   0.1867
 X3J  O1'   O  OH1   0  -0.586  -4.1185  -1.9878   0.3582
 X3J  O2'   O  O     0  -0.434  -3.8484   0.2102   0.6174
 X3J  C1    C  CH2   0  -0.585  -2.2169  -1.0219  -0.6355
 X3J  C3    C  CH2   0  -0.321   4.8357  -0.9356   0.0091
 X3J  N3    N  NH2   0  -0.799   6.0911  -0.3718   0.4712
 X3J  O3    O  OH1   0  -0.653  -0.7410  -0.4972   1.2079
 X3J  CM3   C  C     0   0.568  -1.3963   1.3135  -0.1112
 X3J  O3'   O  OH1   0  -0.597  -1.7526   1.7230  -1.3208
 X3J  C4    C  CH2   0  -0.255   3.7528   0.1317   0.0435
 X3J  N4    N  NH1   0  -0.642   2.4850  -0.4286  -0.3737
 X3J  CAP   C  CT    0   0.092  -1.0424  -0.1756  -0.1206
 X3J  O4    O  O     0  -0.495   1.3760   1.5302  -0.4510
 X3J  CM4   C  CH2   0  -0.591   0.1632  -0.4429  -1.0370
 X3J  OAF   O  O     0  -0.434  -1.3630   2.0187   0.8582
 X3J  H1'   H  HOH1  0   0.483  -4.9359  -1.8315   0.8557
 X3J  H11C  H  HCH2  0   0.291  -1.9158  -2.0712  -0.6518
 X3J  H12C  H  HCH2  0   0.308  -2.4595  -0.7599  -1.6688
 X3J  H31C  H  HCH2  0   0.234   4.9664  -1.2767  -1.0206
 X3J  H32C  H  HCH2  0   0.206   4.4997  -1.8077   0.5890
 X3J  H31N  H  HNH2  0   0.344   6.0459  -0.2173   1.4707
 X3J  H32N  H  HNH2  0   0.354   6.8335  -1.0442   0.3312
 X3J  H41C  H  HCH2  0   0.233   3.6692   0.5426   1.0551
 X3J  H42C  H  HCH2  0   0.239   4.0322   0.9553  -0.6162
 X3J  H3    H  HOH1  0   0.457  -0.4792  -1.4238   1.2485
 X3J  H3'   H  HOH1  0   0.485  -1.9689   2.6670  -1.2999
 X3J  H4    H  HNH1  0   0.404   2.4137  -1.4294  -0.4618
 X3J  HM41  H  HCH2  0   0.293  -0.0619  -0.1465  -2.0637
 X3J  HM42  H  HCH2  0   0.276   0.3402  -1.5214  -1.0618
 X3J  C4'   C  C     0   0.571   1.3935   0.3135  -0.5868

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'   single  1.325  0.020  1.325
 X3J  C'   O2'   double  1.206  0.020  1.206
 X3J  C'   C1    single  1.504  0.020  1.504
 X3J  C1   CAP   single  1.537  0.020  1.537
 X3J  C3   N3    single  1.452  0.020  1.452
 X3J  C3   C4    single  1.521  0.020  1.521
 X3J  O3   CAP   single  1.400  0.020  1.400
 X3J  CM3  O3'   single  1.326  0.020  1.326
 X3J  CM3  CAP   single  1.531  0.020  1.531
 X3J  CM3  OAF   double  1.199  0.020  1.199
 X3J  C4   N4    single  1.447  0.020  1.447
 X3J  N4   C4'   single  1.337  0.020  1.337
 X3J  C4'  O4    double  1.224  0.020  1.224
 X3J  C4'  CM4   single  1.513  0.020  1.513
 X3J  CM4  CAP   single  1.538  0.020  1.538
 X3J  O1'  H1'   single  0.850  0.020  0.980
 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  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'   124.08  3.000
 X3J  C1    C'   O1'   112.39  3.000
 X3J  O2'   C'   O1'   123.50  3.000
 X3J  H1'   O1'  C'    110.11  3.000
 X3J  H12C  C1   H11C  106.11  3.000
 X3J  H12C  C1   CAP   110.75  3.000
 X3J  H11C  C1   CAP   108.88  3.000
 X3J  H12C  C1   C'    107.75  3.000
 X3J  H11C  C1   C'    110.35  3.000
 X3J  CAP   C1   C'    112.79  3.000
 X3J  H32C  C3   H31C  106.62  3.000
 X3J  H32C  C3   C4    109.09  3.000
 X3J  H31C  C3   C4    109.00  3.000
 X3J  H32C  C3   N3    113.85  3.000
 X3J  H31C  C3   N3    108.52  3.000
 X3J  C4    C3   N3    109.63  3.000
 X3J  H32N  N3   H31N  105.72  3.000
 X3J  H32N  N3   C3    109.42  3.000
 X3J  H31N  N3   C3    109.56  3.000
 X3J  H3    O3   CAP   108.63  3.000
 X3J  OAF   CM3  CAP   124.79  3.000
 X3J  OAF   CM3  O3'   124.28  3.000
 X3J  CAP   CM3  O3'   110.92  3.000
 X3J  H3'   O3'  CM3   109.96  3.000
 X3J  H42C  C4   H41C  107.13  3.000
 X3J  H42C  C4   N4    110.00  3.000
 X3J  H41C  C4   N4    110.15  3.000
 X3J  H42C  C4   C3    109.49  3.000
 X3J  H41C  C4   C3    109.79  3.000
 X3J  N4    C4   C3    110.21  3.000
 X3J  H4    N4   C4'   118.67  3.000
 X3J  H4    N4   C4    118.15  3.000
 X3J  C4'   N4   C4    123.11  3.000
 X3J  CM4   CAP  CM3   110.73  3.000
 X3J  CM4   CAP  O3    110.91  3.000
 X3J  CM3   CAP  O3    105.52  3.000
 X3J  CM4   CAP  C1    107.69  3.000
 X3J  CM3   CAP  C1    111.17  3.000
 X3J  O3    CAP  C1    110.86  3.000
 X3J  HM42  CM4  HM41  106.25  3.000
 X3J  HM42  CM4  CAP   108.18  3.000
 X3J  HM41  CM4  CAP   110.58  3.000
 X3J  HM42  CM4  C4'   111.61  3.000
 X3J  HM41  CM4  C4'   108.16  3.000
 X3J  CAP   CM4  C4'   111.92  3.000
 X3J  CM4   C4'  O4    121.21  3.000
 X3J  CM4   C4'  N4    115.71  3.000
 X3J  O4    C4'  N4    123.06  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  CONST_04  H1'   O1'  C'   O2'     0.00   0.0  0
 X3J  CONST_05  H3'   O3'  CM3  CAP   180.00   0.0  0
 X3J  Var_01    CAP   C1   C'   O1'  -140.74  30.0  3
 X3J  Var_02    C4'   N4   C4   C3   -172.04  30.0  3
 X3J  Var_03    N4    C4   C3   N3   -178.14  30.0  3
 X3J  Var_04    CAP   CM4  C4'  N4    125.01  30.0  3
 X3J  Var_05    H31N  N3   C3   C4     72.04  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-2  H1'  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
 X3J  plan-3  H3'  0.020

