# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:07:25 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S},3~{R},4~{R},5~{R})-2,3,4,5,6-pentakis(oxidanyl)hexyl]amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CC[C@H](NC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)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
 GOP  GOP  '(2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S},3~{R},4~{R},5~{R})-2,3,4,5,6-pentakis(oxidanyl)hexyl]amino]pentanoic acid'  ligand  42  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GOP
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
 GOP  OAN  O  OH1    0  -0.673  -7.1742   0.7073  -0.2087
 GOP  CAM  C  CH2    0  -0.158  -5.9518   0.9371   0.4554
 GOP  CAL  C  CH1    0  -0.021  -4.8327   0.2673  -0.3268
 GOP  OAT  O  OH1    0  -0.664  -4.7691   0.7471  -1.6528
 GOP  CAK  C  CH1    0  -0.024  -3.4803   0.4304   0.3882
 GOP  OAS  O  OH1    0  -0.665  -3.5490  -0.0432   1.7155
 GOP  CAJ  C  CH1    0   0.013  -2.3260  -0.2028  -0.3943
 GOP  OAR  O  OH1    0  -0.685  -2.5415  -1.5799  -0.6049
 GOP  CAI  C  CH1    0  -0.022  -0.9668  -0.0001   0.3109
 GOP  OAQ  O  OH1    0  -0.724  -0.7847  -1.0349   1.2483
 GOP  CAH  C  CH2    0  -0.286   0.1667   0.0457  -0.7107
 GOP  N    N  NH1    0  -0.610   1.4628   0.3056  -0.1035
 GOP  CA   C  CH1    0  -0.216   2.5286  -0.6060  -0.4547
 GOP  C    C  C      0   0.445   2.3536  -2.0727   0.0146
 GOP  O    O  O      0  -0.609   1.4138  -2.3404   0.8094
 GOP  CB   C  CH2    0  -0.433   3.8634  -0.0667   0.0675
 GOP  CG   C  CH2    0  -0.565   4.2156   1.2894  -0.5269
 GOP  CD   C  C      0   0.522   5.5337   1.8364  -0.0244
 GOP  OE1  O  O      0  -0.502   6.4878   1.1154   0.2380
 GOP  NE2  N  NH2    0  -0.805   5.5864   3.1732   0.0887
 GOP  OXT  O  OC    -1  -0.586   3.1776  -2.8936  -0.4149
 GOP  H1   H  HOH1   0   0.454  -7.8819   1.0137   0.3646
 GOP  H2   H  HCH2   0   0.184  -5.7358   2.0143   0.5392
 GOP  H3   H  HCH2   0   0.207  -5.9672   0.5372   1.4738
 GOP  H4   H  HCH1   0   0.226  -5.0590  -0.8017  -0.4113
 GOP  H5   H  HOH1   0   0.442  -4.5961   1.6948  -1.6264
 GOP  H6   H  HCH1   0   0.226  -3.2670   1.5049   0.4687
 GOP  H7   H  HOH1   0   0.439  -3.6495  -1.0010   1.6911
 GOP  H8   H  HCH1   0   0.222  -2.2854   0.2895  -1.3711
 GOP  H9   H  HOH1   0   0.437  -2.0338  -2.0194   0.0951
 GOP  H10  H  HCH1   0   0.205  -0.9840   0.9723   0.8264
 GOP  H11  H  HOH1   0   0.462   0.0935  -1.4810   1.0843
 GOP  H12  H  HCH2   0   0.211   0.1718  -0.8973  -1.2723
 GOP  H13  H  HCH2   0   0.216  -0.0719   0.8293  -1.4396
 GOP  H14  H  HNH1   0   0.338   1.3886   0.3715   0.9034
 GOP  H16  H  HCH1   0   0.228   2.5950  -0.6320  -1.5495
 GOP  H17  H  HCH2   0   0.223   3.8176   0.0084   1.1598
 GOP  H18  H  HCH2   0   0.236   4.6491  -0.7854  -0.1616
 GOP  H19  H  HCH2   0   0.262   4.3008   1.1960  -1.6158
 GOP  H20  H  HCH2   0   0.251   3.4081   2.0006  -0.3488
 GOP  H21  H  HNH2   0   0.404   4.7986   3.7548  -0.1367
 GOP  H22  H  HNH2   0   0.395   6.4402   3.6331   0.3601

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
 GOP  O    C    deloc   1.260  0.020  1.260
 GOP  CB   CA   single  1.531  0.020  1.531
 GOP  CB   CG   single  1.522  0.020  1.522
 GOP  CA   C    single  1.550  0.020  1.550
 GOP  CA   N    single  1.446  0.020  1.446
 GOP  C    OXT  deloc   1.240  0.020  1.240
 GOP  NE2  CD   single  1.343  0.020  1.343
 GOP  CAH  N    single  1.455  0.020  1.455
 GOP  CAH  CAI  single  1.527  0.020  1.527
 GOP  CG   CD   single  1.513  0.020  1.513
 GOP  CD   OE1  double  1.224  0.020  1.224
 GOP  OAR  CAJ  single  1.410  0.020  1.410
 GOP  CAJ  CAI  single  1.545  0.020  1.545
 GOP  CAJ  CAK  single  1.532  0.020  1.532
 GOP  CAI  OAQ  single  1.408  0.020  1.408
 GOP  OAS  CAK  single  1.411  0.020  1.411
 GOP  CAK  CAL  single  1.538  0.020  1.538
 GOP  OAT  CAL  single  1.412  0.020  1.412
 GOP  CAL  CAM  single  1.521  0.020  1.521
 GOP  CAM  OAN  single  1.410  0.020  1.410
 GOP  OAN  H1   single  0.850  0.020  0.980
 GOP  CAM  H2   single  0.970  0.020  1.090
 GOP  CAM  H3   single  0.970  0.020  1.090
 GOP  CAL  H4   single  0.970  0.020  1.090
 GOP  OAT  H5   single  0.850  0.020  0.980
 GOP  CAK  H6   single  0.970  0.020  1.090
 GOP  OAS  H7   single  0.850  0.020  0.980
 GOP  CAJ  H8   single  0.970  0.020  1.090
 GOP  OAR  H9   single  0.850  0.020  0.980
 GOP  CAI  H10  single  0.970  0.020  1.090
 GOP  OAQ  H11  single  0.850  0.020  0.980
 GOP  CAH  H12  single  0.970  0.020  1.090
 GOP  CAH  H13  single  0.970  0.020  1.090
 GOP  N    H14  single  0.890  0.020  1.040
 GOP  CA   H16  single  0.970  0.020  1.090
 GOP  CB   H17  single  0.970  0.020  1.090
 GOP  CB   H18  single  0.970  0.020  1.090
 GOP  CG   H19  single  0.970  0.020  1.090
 GOP  CG   H20  single  0.970  0.020  1.090
 GOP  NE2  H21  single  0.860  0.020  1.020
 GOP  NE2  H22  single  0.860  0.020  1.020

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
 GOP  H1   OAN  CAM  107.79  3.000
 GOP  H3   CAM  H2   106.82  3.000
 GOP  H3   CAM  CAL  109.15  3.000
 GOP  H2   CAM  CAL  108.99  3.000
 GOP  H3   CAM  OAN  111.50  3.000
 GOP  H2   CAM  OAN  111.42  3.000
 GOP  CAL  CAM  OAN  108.90  3.000
 GOP  H4   CAL  CAK  108.71  3.000
 GOP  H4   CAL  OAT  105.57  3.000
 GOP  CAK  CAL  OAT  111.16  3.000
 GOP  H4   CAL  CAM  108.50  3.000
 GOP  OAT  CAL  CAM  111.50  3.000
 GOP  CAK  CAL  CAM  111.17  3.000
 GOP  H5   OAT  CAL  108.46  3.000
 GOP  H6   CAK  CAJ  107.19  3.000
 GOP  H6   CAK  OAS  105.60  3.000
 GOP  CAJ  CAK  OAS  112.24  3.000
 GOP  H6   CAK  CAL  107.97  3.000
 GOP  OAS  CAK  CAL  111.03  3.000
 GOP  CAJ  CAK  CAL  112.41  3.000
 GOP  H7   OAS  CAK  108.36  3.000
 GOP  H8   CAJ  CAI  108.40  3.000
 GOP  H8   CAJ  OAR  108.16  3.000
 GOP  CAI  CAJ  OAR  109.33  3.000
 GOP  H8   CAJ  CAK  107.33  3.000
 GOP  CAI  CAJ  CAK  112.06  3.000
 GOP  OAR  CAJ  CAK  111.41  3.000
 GOP  H9   OAR  CAJ  104.76  3.000
 GOP  H10  CAI  CAH  107.37  3.000
 GOP  H10  CAI  OAQ  109.85  3.000
 GOP  CAH  CAI  OAQ  111.80  3.000
 GOP  H10  CAI  CAJ  108.42  3.000
 GOP  OAQ  CAI  CAJ  108.74  3.000
 GOP  CAH  CAI  CAJ  110.59  3.000
 GOP  H11  OAQ  CAI  109.44  3.000
 GOP  H13  CAH  H12  105.96  3.000
 GOP  H13  CAH  N    110.10  3.000
 GOP  H12  CAH  N    111.28  3.000
 GOP  H13  CAH  CAI  107.74  3.000
 GOP  H12  CAH  CAI  108.67  3.000
 GOP  N    CAH  CAI  112.80  3.000
 GOP  H14  N    CA   109.69  3.000
 GOP  H14  N    CAH  111.20  3.000
 GOP  CA   N    CAH  116.28  3.000
 GOP  H16  CA   CB   107.21  3.000
 GOP  H16  CA   C    106.65  3.000
 GOP  CB   CA   C    109.18  3.000
 GOP  H16  CA   N    107.57  3.000
 GOP  C    CA   N    116.09  3.000
 GOP  CB   CA   N    109.74  3.000
 GOP  OXT  C    O    125.01  3.000
 GOP  OXT  C    CA   116.52  3.000
 GOP  O    C    CA   118.46  3.000
 GOP  H18  CB   H17  106.56  3.000
 GOP  H18  CB   CG   109.81  3.000
 GOP  H17  CB   CG   109.75  3.000
 GOP  H18  CB   CA   108.94  3.000
 GOP  H17  CB   CA   109.12  3.000
 GOP  CG   CB   CA   112.48  3.000
 GOP  H20  CG   H19  105.98  3.000
 GOP  H20  CG   CD   110.79  3.000
 GOP  H19  CG   CD   107.04  3.000
 GOP  H20  CG   CB   110.24  3.000
 GOP  H19  CG   CB   109.27  3.000
 GOP  CD   CG   CB   113.21  3.000
 GOP  NE2  CD   OE1  122.53  3.000
 GOP  OE1  CD   CG   122.49  3.000
 GOP  NE2  CD   CG   114.97  3.000
 GOP  H22  NE2  H21  117.44  3.000
 GOP  H22  NE2  CD   120.71  3.000
 GOP  H21  NE2  CD   121.78  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
 GOP  CONST_01  H21  NE2  CD   CG      0.00   0.0  0
 GOP  CONST_02  H22  NE2  CD   CG    180.00   0.0  0
 GOP  Var_01    CA   N    CAH  CAI   128.94  30.0  3
 GOP  Var_02    CD   CG   CB   CA   -179.86  30.0  3
 GOP  Var_03    NE2  CD   CG   CB   -146.78  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
 GOP  chir_01  CAL  CAK  OAT  CAM  positiv
 GOP  chir_02  CAK  OAS  CAL  CAJ  positiv
 GOP  chir_03  CAJ  OAR  CAK  CAI  negativ
 GOP  chir_04  CAI  OAQ  CAJ  CAH  positiv
 GOP  chir_05  CA   N    CB   C    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
 GOP  plan-1  CG   0.020
 GOP  plan-1  CD   0.020
 GOP  plan-1  OE1  0.020
 GOP  plan-1  NE2  0.020
 GOP  plan-1  H21  0.020
 GOP  plan-1  H22  0.020
 GOP  plan-2  CA   0.020
 GOP  plan-2  C    0.020
 GOP  plan-2  O    0.020
 GOP  plan-2  OXT  0.020

