# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 14:06:23 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{S},4~{S},5~{R},6~{R},7~{S},8~{R})-5-acetamido-2,4,6,7,8,9-hexakis(oxidanyl)nonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]([C@@H](O)C[C@H](O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO
#
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
 RCJ  RCJ  '(2~{S},4~{S},5~{R},6~{R},7~{S},8~{R})-5-acetamido-2,4,6,7,8,9-hexakis(oxidanyl)nonanoic acid'  ligand  42  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RCJ
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
 RCJ  O1A  O  O     0  -0.436   5.6296  -0.5857   1.1764
 RCJ  C1   C  C     0   0.506   4.9385  -0.2757   0.2401
 RCJ  O1B  O  OH1   0  -0.590   5.1704   0.7735  -0.5362
 RCJ  C2   C  CH1   0  -0.057   3.6828  -1.0236  -0.1780
 RCJ  O2   O  OH1   0  -0.651   3.6389  -2.2872   0.4158
 RCJ  C3   C  CH2   0  -0.526   2.4491  -0.1686   0.1318
 RCJ  C4   C  CH1   0   0.065   1.1493  -0.8317  -0.3104
 RCJ  O4   O  OH1   0  -0.667   1.1451  -1.1123  -1.6930
 RCJ  C5   C  CH1   0  -0.150  -0.0694   0.0110   0.1036
 RCJ  N5   N  NH1   0  -0.647  -0.0915   1.2716  -0.6041
 RCJ  C10  C  C     0   0.529   0.1909   2.4687  -0.0488
 RCJ  C11  C  CH3   0  -0.778   0.0534   3.6492  -0.9776
 RCJ  O10  O  O     0  -0.496   0.5448   2.6014   1.1129
 RCJ  C6   C  CH1   0   0.040  -1.3938  -0.7395  -0.1236
 RCJ  O6   O  OH1   0  -0.665  -1.3815  -1.9851   0.5377
 RCJ  C7   C  CH1   0  -0.024  -2.6120   0.1022   0.2827
 RCJ  O7   O  OH1   0  -0.663  -2.5307   0.5220   1.6284
 RCJ  C8   C  CH1   0  -0.023  -3.9389  -0.6273   0.0053
 RCJ  O8   O  OH1   0  -0.660  -3.9877  -1.1183  -1.3144
 RCJ  C9   C  CH2   0  -0.157  -5.1250   0.2750   0.3107
 RCJ  O9   O  OH1   0  -0.671  -6.3130  -0.4598   0.1301
 RCJ  H1   H  HOH1  0   0.485   5.9550   1.2511  -0.2271
 RCJ  H2   H  HCH1  0   0.275   3.7395  -1.1890  -1.2578
 RCJ  H3   H  HOH1  0   0.448   3.6058  -2.1816   1.3732
 RCJ  H4   H  HCH2  0   0.255   2.3998   0.0234   1.2084
 RCJ  H5   H  HCH2  0   0.253   2.5556   0.8067  -0.3513
 RCJ  H6   H  HCH1  0   0.241   1.0668  -1.7984   0.1888
 RCJ  H7   H  HOH1  0   0.443   1.3819  -0.3107  -2.1723
 RCJ  H8   H  HCH1  0   0.262   0.0258   0.2360   1.1687
 RCJ  H9   H  HNH1  0   0.397  -0.3920   1.2623  -1.5660
 RCJ  H10  H  HCH3  0   0.248  -0.3339   3.3888  -1.9608
 RCJ  H11  H  HCH3  0   0.266  -0.6090   4.3885  -0.5282
 RCJ  H12  H  HCH3  0   0.268   1.0276   4.1217  -1.1051
 RCJ  H13  H  HCH1  0   0.237  -1.4828  -0.9669  -1.1891
 RCJ  H14  H  HOH1  0   0.444  -1.1391  -1.8526   1.4607
 RCJ  H15  H  HCH1  0   0.231  -2.6043   1.0194  -0.3165
 RCJ  H16  H  HOH1  0   0.445  -2.7596  -0.2148   2.2054
 RCJ  H17  H  HCH1  0   0.230  -3.9931  -1.5107   0.6523
 RCJ  H18  H  HOH1  0   0.445  -4.0148  -0.3696  -1.9207
 RCJ  H19  H  HCH2  0   0.204  -5.0392   0.6559   1.3339
 RCJ  H20  H  HCH2  0   0.191  -5.0857   1.1496  -0.3574
 RCJ  H21  H  HOH1  0   0.455  -7.0523   0.1232   0.3237

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
 RCJ  O6   C6   single  1.410  0.020  1.410
 RCJ  O7   C7   single  1.412  0.020  1.412
 RCJ  C7   C6   single  1.535  0.020  1.535
 RCJ  C7   C8   single  1.539  0.020  1.539
 RCJ  C6   C5   single  1.539  0.020  1.539
 RCJ  O4   C4   single  1.411  0.020  1.411
 RCJ  O9   C9   single  1.408  0.020  1.408
 RCJ  C4   C5   single  1.538  0.020  1.538
 RCJ  C4   C3   single  1.525  0.020  1.525
 RCJ  C9   C8   single  1.521  0.020  1.521
 RCJ  O2   C2   single  1.397  0.020  1.397
 RCJ  C5   N5   single  1.446  0.020  1.446
 RCJ  C8   O8   single  1.409  0.020  1.409
 RCJ  C3   C2   single  1.533  0.020  1.533
 RCJ  C2   C1   single  1.520  0.020  1.520
 RCJ  N5   C10  single  1.349  0.020  1.349
 RCJ  O1A  C1   double  1.204  0.020  1.204
 RCJ  C1   O1B  single  1.326  0.020  1.326
 RCJ  C10  O10  double  1.222  0.020  1.222
 RCJ  C10  C11  single  1.508  0.020  1.508
 RCJ  O1B  H1   single  0.850  0.020  0.980
 RCJ  C2   H2   single  0.970  0.020  1.090
 RCJ  O2   H3   single  0.850  0.020  0.980
 RCJ  C3   H4   single  0.970  0.020  1.090
 RCJ  C3   H5   single  0.970  0.020  1.090
 RCJ  C4   H6   single  0.970  0.020  1.090
 RCJ  O4   H7   single  0.850  0.020  0.980
 RCJ  C5   H8   single  0.970  0.020  1.090
 RCJ  N5   H9   single  0.860  0.020  1.020
 RCJ  C11  H10  single  0.970  0.020  1.090
 RCJ  C11  H11  single  0.970  0.020  1.090
 RCJ  C11  H12  single  0.970  0.020  1.090
 RCJ  C6   H13  single  0.970  0.020  1.090
 RCJ  O6   H14  single  0.850  0.020  0.980
 RCJ  C7   H15  single  0.970  0.020  1.090
 RCJ  O7   H16  single  0.850  0.020  0.980
 RCJ  C8   H17  single  0.970  0.020  1.090
 RCJ  O8   H18  single  0.850  0.020  0.980
 RCJ  C9   H19  single  0.970  0.020  1.090
 RCJ  C9   H20  single  0.970  0.020  1.090
 RCJ  O9   H21  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
 RCJ  C2   C1   O1B  111.89  3.000
 RCJ  O1B  C1   O1A  123.96  3.000
 RCJ  C2   C1   O1A  124.14  3.000
 RCJ  H1   O1B  C1   110.18  3.000
 RCJ  H2   C2   C3   109.00  3.000
 RCJ  H2   C2   O2   106.52  3.000
 RCJ  C3   C2   O2   113.17  3.000
 RCJ  H2   C2   C1   107.64  3.000
 RCJ  C3   C2   C1   109.56  3.000
 RCJ  O2   C2   C1   110.74  3.000
 RCJ  H3   O2   C2   108.91  3.000
 RCJ  H5   C3   H4   106.41  3.000
 RCJ  H5   C3   C4   110.05  3.000
 RCJ  H4   C3   C4   108.85  3.000
 RCJ  H5   C3   C2   109.26  3.000
 RCJ  H4   C3   C2   109.44  3.000
 RCJ  C4   C3   C2   112.64  3.000
 RCJ  H6   C4   C5   107.60  3.000
 RCJ  H6   C4   O4   105.78  3.000
 RCJ  C5   C4   O4   111.73  3.000
 RCJ  H6   C4   C3   108.49  3.000
 RCJ  C5   C4   C3   111.04  3.000
 RCJ  O4   C4   C3   111.92  3.000
 RCJ  H7   O4   C4   108.74  3.000
 RCJ  H8   C5   C6   108.62  3.000
 RCJ  H8   C5   N5   107.40  3.000
 RCJ  C6   C5   N5   109.86  3.000
 RCJ  H8   C5   C4   107.82  3.000
 RCJ  N5   C5   C4   110.98  3.000
 RCJ  C6   C5   C4   112.01  3.000
 RCJ  H9   N5   C10  117.60  3.000
 RCJ  H9   N5   C5   117.63  3.000
 RCJ  C10  N5   C5   124.67  3.000
 RCJ  O10  C10  C11  121.80  3.000
 RCJ  C11  C10  N5   114.95  3.000
 RCJ  O10  C10  N5   123.25  3.000
 RCJ  H12  C11  H11  107.30  3.000
 RCJ  H12  C11  H10  108.42  3.000
 RCJ  H11  C11  H10  108.58  3.000
 RCJ  H12  C11  C10  109.26  3.000
 RCJ  H11  C11  C10  109.42  3.000
 RCJ  H10  C11  C10  113.67  3.000
 RCJ  H13  C6   C7   107.90  3.000
 RCJ  H13  C6   O6   105.90  3.000
 RCJ  C7   C6   O6   111.53  3.000
 RCJ  H13  C6   C5   108.39  3.000
 RCJ  C7   C6   C5   112.11  3.000
 RCJ  O6   C6   C5   110.73  3.000
 RCJ  H14  O6   C6   109.26  3.000
 RCJ  H15  C7   C8   107.71  3.000
 RCJ  H15  C7   O7   105.78  3.000
 RCJ  C8   C7   O7   111.24  3.000
 RCJ  H15  C7   C6   107.97  3.000
 RCJ  C8   C7   C6   112.11  3.000
 RCJ  O7   C7   C6   111.68  3.000
 RCJ  H16  O7   C7   109.25  3.000
 RCJ  H17  C8   C9   108.72  3.000
 RCJ  H17  C8   O8   105.68  3.000
 RCJ  C9   C8   O8   111.57  3.000
 RCJ  H17  C8   C7   108.55  3.000
 RCJ  O8   C8   C7   111.33  3.000
 RCJ  C9   C8   C7   110.78  3.000
 RCJ  H18  O8   C8   108.63  3.000
 RCJ  H20  C9   H19  106.72  3.000
 RCJ  H20  C9   O9   111.51  3.000
 RCJ  H19  C9   O9   111.55  3.000
 RCJ  H20  C9   C8   108.75  3.000
 RCJ  H19  C9   C8   109.43  3.000
 RCJ  O9   C9   C8   108.81  3.000
 RCJ  H21  O9   C9   107.85  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
 RCJ  CONST_01  O10  C10  N5   C5     0.00   0.0  0
 RCJ  CONST_02  C11  C10  N5   C5   180.00   0.0  0
 RCJ  CONST_03  H9   N5   C10  C11    0.00   0.0  0
 RCJ  CONST_04  H1   O1B  C1   O1A    0.00   0.0  0
 RCJ  Var_01    H10  C11  C10  N5     4.56  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
 RCJ  chir_01  C2  O2  C3  C1  negativ
 RCJ  chir_02  C4  O4  C5  C3  positiv
 RCJ  chir_03  C5  N5  C6  C4  negativ
 RCJ  chir_04  C6  O6  C5  C7  positiv
 RCJ  chir_05  C7  O7  C6  C8  negativ
 RCJ  chir_06  C8  O8  C7  C9  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
 RCJ  plan-1  C5   0.020
 RCJ  plan-1  N5   0.020
 RCJ  plan-1  C10  0.020
 RCJ  plan-1  C11  0.020
 RCJ  plan-1  O10  0.020
 RCJ  plan-1  H9   0.020
 RCJ  plan-2  O1A  0.020
 RCJ  plan-2  C1   0.020
 RCJ  plan-2  O1B  0.020
 RCJ  plan-2  C2   0.020
 RCJ  plan-2  H1   0.020

