# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 04:44:10 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (4aS,7aR)-octahydro-1H-cyclopenta[b]pyridine-6,6-diylbis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C1(C[C@@H]2CCCN[C@@H]2C1)[P](O)(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
 RSX  RSX  '(4aS,7aR)-octahydro-1H-cyclopenta[b]pyridine-6,6-diylbis(phosphonic acid)'  ligand  34  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RSX
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
 RSX  O1   O  O     0  -0.697   2.8362   0.5108   1.1605
 RSX  P1   P  P     0   1.392   2.0196   0.8290  -0.0316
 RSX  O3   O  OH1   0  -0.739   1.6025   2.3685  -0.2097
 RSX  O2   O  OH1   0  -0.747   2.8143   0.4392  -1.3752
 RSX  C3   C  CT    0  -0.627   0.3917  -0.0012  -0.1031
 RSX  P2   P  P     0   1.396   0.6887  -1.7575   0.3387
 RSX  O5   O  OH1   0  -0.743   2.0386  -2.2239  -0.4025
 RSX  O4   O  O     0  -0.702   0.8135  -2.0145   1.7914
 RSX  O6   O  OH1   0  -0.727  -0.5053  -2.5217  -0.4043
 RSX  C4   C  CH2   0  -0.461  -0.3098   0.2415  -1.4766
 RSX  C5   C  CH1   0  -0.077  -1.7073   0.7579  -1.1410
 RSX  C2   C  CH2   0  -0.442  -0.5628   0.6337   0.9563
 RSX  C1   C  CH1   0  -0.231  -1.4907   1.5432   0.1531
 RSX  C9   C  CH2   0  -0.434  -2.7921   1.9219   0.8550
 RSX  C8   C  CH2   0  -0.433  -3.7716   0.7569   0.9375
 RSX  C7   C  CH2   0  -0.292  -3.9163   0.1010  -0.4268
 RSX  N1   N  NH1   0  -0.576  -2.6137  -0.3407  -0.8853
 RSX  HO3  H  HOH1  0   0.498   2.3055   2.9939   0.0168
 RSX  HO2  H  HOH1  0   0.494   2.4986   0.8438  -2.1932
 RSX  HO5  H  HOH1  0   0.486   2.0365  -2.1769  -1.3672
 RSX  HO6  H  HOH1  0   0.494  -0.5795  -3.4533  -0.1536
 RSX  H4   H  HCH2  0   0.254   0.2025   1.0134  -2.0539
 RSX  H4A  H  HCH2  0   0.269  -0.3330  -0.6416  -2.1150
 RSX  H5   H  HCH1  0   0.218  -2.0703   1.4217  -1.9432
 RSX  H2   H  HCH2  0   0.263  -1.1429  -0.1419   1.4558
 RSX  H2A  H  HCH2  0   0.261  -0.0269   1.1659   1.7434
 RSX  H1   H  HCH1  0   0.248  -0.9548   2.4615  -0.0984
 RSX  H9   H  HCH2  0   0.232  -2.5802   2.3251   1.8489
 RSX  H9A  H  HCH2  0   0.223  -3.2595   2.7346   0.2899
 RSX  H8   H  HCH2  0   0.216  -3.4265   0.0097   1.6573
 RSX  H8A  H  HCH2  0   0.228  -4.7436   1.1089   1.2900
 RSX  H7   H  HCH2  0   0.231  -4.5769  -0.7659  -0.3644
 RSX  H7A  H  HCH2  0   0.179  -4.3949   0.8153  -1.1195
 RSX  HN1  H  HNH1  0   0.346  -2.7025  -0.9132  -1.7139

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
 RSX  O1  P1   double  1.480  0.020  1.480
 RSX  C3  P1   single  1.829  0.020  1.829
 RSX  P1  O2   single  1.609  0.020  1.609
 RSX  P1  O3   single  1.605  0.020  1.605
 RSX  O3  HO3  single  0.850  0.020  0.980
 RSX  O2  HO2  single  0.850  0.020  0.980
 RSX  P2  C3   single  1.835  0.020  1.835
 RSX  C4  C3   single  1.561  0.020  1.561
 RSX  C3  C2   single  1.561  0.020  1.561
 RSX  O4  P2   double  1.480  0.020  1.480
 RSX  O6  P2   single  1.601  0.020  1.601
 RSX  P2  O5   single  1.609  0.020  1.609
 RSX  O5  HO5  single  0.850  0.020  0.980
 RSX  O6  HO6  single  0.850  0.020  0.980
 RSX  C4  C5   single  1.527  0.020  1.527
 RSX  C4  H4   single  0.970  0.020  1.090
 RSX  C4  H4A  single  0.970  0.020  1.090
 RSX  N1  C5   single  1.447  0.020  1.447
 RSX  C5  C1   single  1.529  0.020  1.529
 RSX  C5  H5   single  0.970  0.020  1.090
 RSX  C1  C2   single  1.528  0.020  1.528
 RSX  C2  H2   single  0.970  0.020  1.090
 RSX  C2  H2A  single  0.970  0.020  1.090
 RSX  C1  C9   single  1.526  0.020  1.526
 RSX  C1  H1   single  0.970  0.020  1.090
 RSX  C8  C9   single  1.524  0.020  1.524
 RSX  C9  H9   single  0.970  0.020  1.090
 RSX  C9  H9A  single  0.970  0.020  1.090
 RSX  C7  C8   single  1.521  0.020  1.521
 RSX  C8  H8   single  0.970  0.020  1.090
 RSX  C8  H8A  single  0.970  0.020  1.090
 RSX  N1  C7   single  1.450  0.020  1.450
 RSX  C7  H7   single  0.970  0.020  1.090
 RSX  C7  H7A  single  0.970  0.020  1.090
 RSX  N1  HN1  single  0.890  0.020  1.040

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
 RSX  C3   P1  O2  107.28  3.000
 RSX  O2   P1  O3  105.55  3.000
 RSX  C3   P1  O3  101.52  3.000
 RSX  O3   P1  O1  116.05  3.000
 RSX  O2   P1  O1  110.37  3.000
 RSX  C3   P1  O1  115.16  3.000
 RSX  HO3  O3  P1  113.90  3.000
 RSX  HO2  O2  P1  116.38  3.000
 RSX  C2   C3  C4  105.02  3.000
 RSX  C2   C3  P2  108.95  3.000
 RSX  C4   C3  P2  115.67  3.000
 RSX  C2   C3  P1  109.46  3.000
 RSX  C4   C3  P1  111.34  3.000
 RSX  P2   C3  P1  106.32  3.000
 RSX  O6   P2  O4  115.82  3.000
 RSX  O6   P2  O5  105.88  3.000
 RSX  O4   P2  O5  109.33  3.000
 RSX  O5   P2  C3  107.59  3.000
 RSX  O6   P2  C3  102.97  3.000
 RSX  O4   P2  C3  114.58  3.000
 RSX  HO5  O5  P2  116.37  3.000
 RSX  HO6  O6  P2  113.37  3.000
 RSX  H4A  C4  H4  105.85  3.000
 RSX  H4A  C4  C5  112.53  3.000
 RSX  H4   C4  C5  107.85  3.000
 RSX  H4A  C4  C3  113.52  3.000
 RSX  H4   C4  C3  111.36  3.000
 RSX  C5   C4  C3  105.69  3.000
 RSX  H5   C5  N1  112.30  3.000
 RSX  H5   C5  C1  110.68  3.000
 RSX  N1   C5  C1  109.22  3.000
 RSX  H5   C5  C4  110.18  3.000
 RSX  C1   C5  C4  103.29  3.000
 RSX  N1   C5  C4  110.81  3.000
 RSX  H2A  C2  H2  106.14  3.000
 RSX  H2A  C2  C1  112.78  3.000
 RSX  H2   C2  C1  109.96  3.000
 RSX  H2A  C2  C3  112.82  3.000
 RSX  H2   C2  C3  110.32  3.000
 RSX  C1   C2  C3  104.88  3.000
 RSX  H1   C1  C9  108.39  3.000
 RSX  H1   C1  C2  108.88  3.000
 RSX  C9   C1  C2  115.08  3.000
 RSX  H1   C1  C5  107.84  3.000
 RSX  C9   C1  C5  113.31  3.000
 RSX  C2   C1  C5  103.02  3.000
 RSX  H9A  C9  H9  106.15  3.000
 RSX  H9A  C9  C8  108.72  3.000
 RSX  H9   C9  C8  110.93  3.000
 RSX  H9A  C9  C1  108.12  3.000
 RSX  H9   C9  C1  110.14  3.000
 RSX  C8   C9  C1  112.53  3.000
 RSX  H8A  C8  H8  106.77  3.000
 RSX  H8A  C8  C7  110.12  3.000
 RSX  H8   C8  C7  109.02  3.000
 RSX  H8A  C8  C9  110.06  3.000
 RSX  H8   C8  C9  110.80  3.000
 RSX  C7   C8  C9  110.01  3.000
 RSX  H7A  C7  H7  106.70  3.000
 RSX  H7A  C7  N1  112.84  3.000
 RSX  H7   C7  N1  108.65  3.000
 RSX  H7A  C7  C8  108.97  3.000
 RSX  H7   C7  C8  110.41  3.000
 RSX  N1   C7  C8  109.25  3.000
 RSX  HN1  N1  C7  110.66  3.000
 RSX  HN1  N1  C5  109.88  3.000
 RSX  C7   N1  C5  112.79  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
 RSX  Var_01  C1  C2  C3  C4   -16.60  30.0  1
 RSX  Var_02  C2  C3  C4  C5    -9.79  30.0  1
 RSX  Var_03  C8  C7  N1  C5   -65.84  30.0  1
 RSX  Var_04  C7  C8  C9  C1   -48.98  30.0  1
 RSX  Var_05  N1  C7  C8  C9    57.67  30.0  1
 RSX  Var_06  C4  C3  P1  O1  -172.33  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
 RSX  chir_01  C5  C4  N1  C1  negativ
 RSX  chir_02  C1  C9  C2  C5  negativ

