# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:10:29 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2~{R})-2-[[(3~{R},4~{R},5~{S})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexyl]amino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@@H](O)[C@@H](O)C(=O)CN[C@H](CCC(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
 N72  N72  '(2~{R})-2-[[(3~{R},4~{R},5~{S})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexyl]amino]pentanedioic acid'  ligand  38  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N72
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
 N72  OAB  O  OH1    0  -0.676   6.4556   1.4849  -0.9358
 N72  CAF  C  CH2    0  -0.167   5.1029   1.7206  -0.6055
 N72  CAG  C  CH1    0  -0.006   4.4828   0.3793  -0.2499
 N72  OAC  O  OH1    0  -0.682   4.5187  -0.5144  -1.3421
 N72  CAH  C  CH1    0  -0.025   3.0225   0.5400   0.1580
 N72  OAM  O  OH1    0  -0.662   2.2345   1.0634  -0.8847
 N72  CAI  C  CH1    0  -0.077   2.4146  -0.7787   0.6839
 N72  OAD  O  OH1    0  -0.655   3.1395  -1.2940   1.7672
 N72  CAJ  C  C      0   0.353   0.9646  -0.5111   1.0872
 N72  OAE  O  O      0  -0.400   0.7332   0.0009   2.1588
 N72  CAK  C  CH2    0  -0.370  -0.1036  -0.9387   0.1287
 N72  N    N  NH1    0  -0.587  -1.4109  -0.4610   0.4825
 N72  CA   C  CH1    0  -0.191  -2.4359  -0.8583  -0.4680
 N72  C    C  C      0   0.395  -2.7476  -2.3743  -0.4716
 N72  O    O  O      0  -0.612  -2.5037  -3.0057   0.5776
 N72  CB   C  CH2    0  -0.422  -3.7265  -0.0805  -0.1925
 N72  CG   C  CH2    0  -0.567  -3.5697   1.4221  -0.3593
 N72  CD   C  C      0   0.404  -4.8124   2.2648  -0.0337
 N72  OE1  O  O      0  -0.615  -5.6798   1.7601   0.7085
 N72  OE2  O  OC    -1  -0.634  -4.8429   3.4167  -0.5187
 N72  OXT  O  OC    -1  -0.618  -3.2570  -2.8355  -1.5135
 N72  H1   H  HOH1   0   0.461   6.8120   2.2760  -1.3495
 N72  H2   H  HCH2   0   0.202   5.0057   2.3962   0.2537
 N72  H3   H  HCH2   0   0.206   4.5601   2.1723  -1.4435
 N72  H4   H  HCH1   0   0.219   5.0344  -0.0257   0.6101
 N72  H5   H  HOH1   0   0.455   5.3867  -0.4535  -1.7557
 N72  H6   H  HCH1   0   0.253   2.9810   1.2711   0.9742
 N72  H7   H  HOH1   0   0.448   2.4086   0.5440  -1.6788
 N72  H8   H  HCH1   0   0.263   2.4429  -1.5349  -0.1065
 N72  H9   H  HOH1   0   0.447   3.0101  -0.7090   2.5236
 N72  H10  H  HCH2   0   0.255   0.1741  -0.5703  -0.8642
 N72  H11  H  HCH2   0   0.236  -0.0135  -2.0381   0.0551
 N72  H12  H  HNH1   0   0.329  -1.6654  -0.8429   1.3866
 N72  H14  H  HCH1   0   0.202  -2.0830  -0.5805  -1.4692
 N72  H15  H  HCH2   0   0.210  -4.5030  -0.4491  -0.8681
 N72  H16  H  HCH2   0   0.202  -4.0737  -0.3072   0.8200
 N72  H17  H  HCH2   0   0.225  -2.7519   1.7651   0.2841
 N72  H18  H  HCH2   0   0.201  -3.2424   1.6453  -1.3802

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
 N72  OAB  CAF  single  1.412  0.020  1.412
 N72  OAC  CAG  single  1.412  0.020  1.412
 N72  CAF  CAG  single  1.520  0.020  1.520
 N72  CAG  CAH  single  1.525  0.020  1.525
 N72  OAD  CAI  single  1.402  0.020  1.402
 N72  CAH  CAI  single  1.544  0.020  1.544
 N72  CAH  OAM  single  1.408  0.020  1.408
 N72  CAI  CAJ  single  1.529  0.020  1.529
 N72  CAJ  CAK  single  1.498  0.020  1.498
 N72  CAJ  OAE  double  1.210  0.020  1.210
 N72  CAK  N    single  1.436  0.020  1.436
 N72  N    CA   single  1.453  0.020  1.453
 N72  O    C    deloc   1.249  0.020  1.249
 N72  C    CA   single  1.548  0.020  1.548
 N72  C    OXT  deloc   1.248  0.020  1.248
 N72  CA   CB   single  1.532  0.020  1.532
 N72  CB   CG   single  1.520  0.020  1.520
 N72  CG   CD   single  1.536  0.020  1.536
 N72  CD   OE1  deloc   1.248  0.020  1.248
 N72  CD   OE2  deloc   1.250  0.020  1.250
 N72  OAB  H1   single  0.850  0.020  0.980
 N72  CAF  H2   single  0.970  0.020  1.090
 N72  CAF  H3   single  0.970  0.020  1.090
 N72  CAG  H4   single  0.970  0.020  1.090
 N72  OAC  H5   single  0.850  0.020  0.980
 N72  CAH  H6   single  0.970  0.020  1.090
 N72  OAM  H7   single  0.850  0.020  0.980
 N72  CAI  H8   single  0.970  0.020  1.090
 N72  OAD  H9   single  0.850  0.020  0.980
 N72  CAK  H10  single  0.970  0.020  1.090
 N72  CAK  H11  single  0.970  0.020  1.090
 N72  N    H12  single  0.890  0.020  1.040
 N72  CA   H14  single  0.970  0.020  1.090
 N72  CB   H15  single  0.970  0.020  1.090
 N72  CB   H16  single  0.970  0.020  1.090
 N72  CG   H17  single  0.970  0.020  1.090
 N72  CG   H18  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
 N72  H1   OAB  CAF  108.57  3.000
 N72  H3   CAF  H2   107.52  3.000
 N72  H3   CAF  CAG  109.91  3.000
 N72  H2   CAF  CAG  108.90  3.000
 N72  H3   CAF  OAB  111.37  3.000
 N72  H2   CAF  OAB  111.76  3.000
 N72  CAG  CAF  OAB  107.35  3.000
 N72  H4   CAG  CAH  108.07  3.000
 N72  H4   CAG  OAC  111.06  3.000
 N72  CAH  CAG  OAC  107.34  3.000
 N72  H4   CAG  CAF  107.67  3.000
 N72  CAH  CAG  CAF  111.12  3.000
 N72  OAC  CAG  CAF  111.55  3.000
 N72  H5   OAC  CAG  108.36  3.000
 N72  H6   CAH  CAI  107.52  3.000
 N72  H6   CAH  OAM  106.39  3.000
 N72  CAI  CAH  OAM  110.45  3.000
 N72  H6   CAH  CAG  107.79  3.000
 N72  OAM  CAH  CAG  112.15  3.000
 N72  CAI  CAH  CAG  112.22  3.000
 N72  H7   OAM  CAH  107.97  3.000
 N72  H8   CAI  CAJ  109.64  3.000
 N72  H8   CAI  OAD  106.90  3.000
 N72  CAJ  CAI  OAD  110.55  3.000
 N72  H8   CAI  CAH  109.51  3.000
 N72  CAJ  CAI  CAH  108.29  3.000
 N72  OAD  CAI  CAH  111.94  3.000
 N72  H9   OAD  CAI  108.27  3.000
 N72  CAK  CAJ  OAE  123.45  3.000
 N72  OAE  CAJ  CAI  119.29  3.000
 N72  CAK  CAJ  CAI  117.24  3.000
 N72  H11  CAK  H10  104.69  3.000
 N72  H11  CAK  N    114.92  3.000
 N72  H10  CAK  N    110.03  3.000
 N72  H11  CAK  CAJ  105.57  3.000
 N72  H10  CAK  CAJ  107.66  3.000
 N72  N    CAK  CAJ  113.37  3.000
 N72  H12  N    CA   107.65  3.000
 N72  H12  N    CAK  108.84  3.000
 N72  CA   N    CAK  112.95  3.000
 N72  H14  CA   CB   107.85  3.000
 N72  H14  CA   C    108.10  3.000
 N72  CB   CA   C    109.15  3.000
 N72  H14  CA   N    107.50  3.000
 N72  CB   CA   N    109.74  3.000
 N72  C    CA   N    114.29  3.000
 N72  OXT  C    O    126.47  3.000
 N72  OXT  C    CA   116.49  3.000
 N72  O    C    CA   117.00  3.000
 N72  H16  CB   H15  106.06  3.000
 N72  H16  CB   CG   109.83  3.000
 N72  H15  CB   CG   109.80  3.000
 N72  H16  CB   CA   109.18  3.000
 N72  H15  CB   CA   108.42  3.000
 N72  CG   CB   CA   113.28  3.000
 N72  H18  CG   H17  105.11  3.000
 N72  H18  CG   CD   109.12  3.000
 N72  H17  CG   CD   107.91  3.000
 N72  H18  CG   CB   109.55  3.000
 N72  H17  CG   CB   108.79  3.000
 N72  CD   CG   CB   115.81  3.000
 N72  OE2  CD   OE1  125.89  3.000
 N72  OE2  CD   CG   116.29  3.000
 N72  OE1  CD   CG   117.80  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
 N72  Var_01  N    CAK  CAJ  CAI  -170.58  30.0  3
 N72  Var_02  CA   N    CAK  CAJ   178.83  30.0  3
 N72  Var_03  CD   CG   CB   CA   -177.28  30.0  3
 N72  Var_04  OE1  CD   CG   CB     21.72  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
 N72  chir_01  CAG  OAC  CAF  CAH  negativ
 N72  chir_02  CAH  OAM  CAG  CAI  positiv
 N72  chir_03  CAI  OAD  CAH  CAJ  positiv
 N72  chir_04  CA   N    C    CB   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
 N72  plan-1  CAI  0.020
 N72  plan-1  CAJ  0.020
 N72  plan-1  OAE  0.020
 N72  plan-1  CAK  0.020
 N72  plan-2  CA   0.020
 N72  plan-2  C    0.020
 N72  plan-2  O    0.020
 N72  plan-2  OXT  0.020
 N72  plan-3  CG   0.020
 N72  plan-3  CD   0.020
 N72  plan-3  OE1  0.020
 N72  plan-3  OE2  0.020

