# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:51:04 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: {(1R)-1-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]ethyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)[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
 IN5  IN5  '{(1R)-1-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]ethyl}phosphonic acid'  ligand  40  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IN5
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
 IN5  C1    C  CR16  0  -0.132  -1.4221  -0.1369   2.6404
 IN5  C2    C  CR6   0   0.123   0.3811  -0.0481   4.0554
 IN5  C3    C  CR6   0   0.265   1.2110   0.3721   3.0067
 IN5  O4    O  O     0  -0.701  -2.8337  -0.6474  -2.3722
 IN5  O5    O  OH1   0  -0.730  -4.7312  -0.8676  -0.5667
 IN5  C9    C  CH1   0  -0.355   3.0670  -0.0206  -1.1126
 IN5  C10   C  CH3   0  -0.676   4.0982  -1.1414  -1.2057
 IN5  N1    N  N     0  -0.407  -0.9038  -0.2912   3.8526
 IN5  C4    C  CR6   0   0.057   0.6804   0.5463   1.7323
 IN5  C5    C  CR6   0  -0.066  -0.6764   0.2733   1.5451
 IN5  O1    O  OH1   0  -0.616   2.5209   0.6216   3.1859
 IN5  C6    C  CH3   0  -0.784   0.9266  -0.2324   5.4401
 IN5  O2    O  O2    0  -0.592  -2.5933  -0.1280   0.1785
 IN5  N2    N  NH1   0  -0.594   2.2143  -0.2263   0.0415
 IN5  P1    P  P     0   1.463  -3.4678  -0.1006  -1.1602
 IN5  O3    O  OH1   0  -0.743  -3.8830   1.4221  -1.4062
 IN5  P2    P  P     0   1.358   2.0872   0.1640  -2.6496
 IN5  O6    O  O     0  -0.701   1.0033   1.1768  -2.6220
 IN5  O7    O  OH1   0  -0.747   3.2340   0.3913  -3.7547
 IN5  O8    O  OH1   0  -0.752   1.4391  -1.2851  -2.9393
 IN5  H1    H  HCR6  0   0.258  -2.4781  -0.3546   2.5473
 IN5  HO5   H  HOH1  0   0.505  -5.3788  -1.1297  -1.2351
 IN5  H71   H  HCH2  0   0.261  -1.3646   1.5258  -0.0465
 IN5  H72   H  HCH2  0   0.253  -0.6773   0.0003  -0.5903
 IN5  H81   H  HCH2  0   0.258   2.3371   1.6403   0.9347
 IN5  H82   H  HCH2  0   0.242   0.9753   1.5160  -0.1496
 IN5  H9    H  HCH1  0   0.282   3.5969   0.9273  -0.9758
 IN5  H101  H  HCH3  0   0.231   3.6244  -2.1214  -1.2820
 IN5  H102  H  HCH3  0   0.245   4.7663  -1.0197  -2.0566
 IN5  H103  H  HCH3  0   0.256   4.7008  -1.1401  -0.2987
 IN5  HO1   H  HOH1  0   0.486   2.7620   0.5790   4.1179
 IN5  H61   H  HCH3  0   0.257   1.2913   0.7062   5.8657
 IN5  H62   H  HCH3  0   0.271   0.1444  -0.6063   6.0965
 IN5  H63   H  HCH3  0   0.257   1.7532  -0.9466   5.4665
 IN5  HN2   H  HNH1  0   0.355   1.5532  -0.9784  -0.1126
 IN5  HO3   H  HOH1  0   0.497  -4.3450   1.8560  -0.6760
 IN5  HO7   H  HOH1  0   0.494   2.9038   0.6488  -4.6270
 IN5  HO8   H  HOH1  0   0.488   2.0685  -2.0021  -3.0910
 IN5  C7    C  CH2   0  -0.214  -1.2959   0.4580   0.1862
 IN5  C8    C  CH2   0  -0.352   1.5619   0.9560   0.5851

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
 IN5  C1   N1    aromatic  1.327  0.020  1.327
 IN5  C1   C5    aromatic  1.387  0.020  1.387
 IN5  C1   H1    single    0.930  0.020  1.080
 IN5  C2   C3    aromatic  1.402  0.020  1.402
 IN5  C2   N1    aromatic  1.323  0.020  1.323
 IN5  C2   C6    single    1.500  0.020  1.500
 IN5  C3   C4    aromatic  1.391  0.020  1.391
 IN5  C3   O1    single    1.345  0.020  1.345
 IN5  O4   P1    double    1.473  0.020  1.473
 IN5  O5   P1    single    1.593  0.020  1.593
 IN5  O5   HO5   single    0.850  0.020  0.980
 IN5  C7   C5    single    1.505  0.020  1.505
 IN5  C7   O2    single    1.424  0.020  1.424
 IN5  C7   H71   single    0.970  0.020  1.090
 IN5  C7   H72   single    0.970  0.020  1.090
 IN5  C8   C4    single    1.504  0.020  1.504
 IN5  C8   N2    single    1.456  0.020  1.456
 IN5  C8   H81   single    0.970  0.020  1.090
 IN5  C8   H82   single    0.970  0.020  1.090
 IN5  C9   C10   single    1.526  0.020  1.526
 IN5  C9   N2    single    1.450  0.020  1.450
 IN5  C9   P2    single    1.832  0.020  1.832
 IN5  C9   H9    single    0.970  0.020  1.090
 IN5  C10  H101  single    0.970  0.020  1.090
 IN5  C10  H102  single    0.970  0.020  1.090
 IN5  C10  H103  single    0.970  0.020  1.090
 IN5  C4   C5    aromatic  1.397  0.020  1.397
 IN5  O1   HO1   single    0.850  0.020  0.980
 IN5  C6   H61   single    0.970  0.020  1.090
 IN5  C6   H62   single    0.970  0.020  1.090
 IN5  C6   H63   single    0.970  0.020  1.090
 IN5  O2   P1    single    1.599  0.020  1.599
 IN5  N2   HN2   single    0.890  0.020  1.040
 IN5  P1   O3    single    1.597  0.020  1.597
 IN5  O3   HO3   single    0.850  0.020  0.980
 IN5  P2   O6    double    1.484  0.020  1.484
 IN5  P2   O7    single    1.609  0.020  1.609
 IN5  P2   O8    single    1.614  0.020  1.614
 IN5  O7   HO7   single    0.850  0.020  0.980
 IN5  O8   HO8   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
 IN5  H1    C1   C5    121.07  3.000
 IN5  H1    C1   N1    115.87  3.000
 IN5  C5    C1   N1    123.06  3.000
 IN5  C6    C2   N1    118.17  3.000
 IN5  C6    C2   C3    120.81  3.000
 IN5  N1    C2   C3    121.01  3.000
 IN5  O1    C3   C4    118.04  3.000
 IN5  O1    C3   C2    122.16  3.000
 IN5  C4    C3   C2    119.80  3.000
 IN5  HO5   O5   P1    113.84  3.000
 IN5  H9    C9   P2    106.05  3.000
 IN5  H9    C9   N2    107.94  3.000
 IN5  P2    C9   N2    111.57  3.000
 IN5  H9    C9   C10   108.46  3.000
 IN5  P2    C9   C10   112.60  3.000
 IN5  N2    C9   C10   109.99  3.000
 IN5  H103  C10  H102  108.14  3.000
 IN5  H103  C10  H101  107.43  3.000
 IN5  H102  C10  H101  108.19  3.000
 IN5  H103  C10  C9    108.81  3.000
 IN5  H102  C10  C9    112.35  3.000
 IN5  H101  C10  C9    111.75  3.000
 IN5  C2    N1   C1    119.86  3.000
 IN5  C5    C4   C8    121.37  3.000
 IN5  C5    C4   C3    117.96  3.000
 IN5  C8    C4   C3    120.62  3.000
 IN5  C4    C5   C7    119.81  3.000
 IN5  C4    C5   C1    118.31  3.000
 IN5  C7    C5   C1    121.87  3.000
 IN5  HO1   O1   C3    111.36  3.000
 IN5  H63   C6   H62   107.75  3.000
 IN5  H63   C6   H61   107.42  3.000
 IN5  H62   C6   H61   107.47  3.000
 IN5  H63   C6   C2    112.20  3.000
 IN5  H62   C6   C2    109.76  3.000
 IN5  H61   C6   C2    112.04  3.000
 IN5  P1    O2   C7    119.72  3.000
 IN5  HN2   N2   C9    111.60  3.000
 IN5  HN2   N2   C8    111.55  3.000
 IN5  C9    N2   C8    116.47  3.000
 IN5  O3    P1   O2    106.70  3.000
 IN5  O3    P1   O5    108.08  3.000
 IN5  O2    P1   O5     96.52  3.000
 IN5  O3    P1   O4    109.82  3.000
 IN5  O2    P1   O4    116.55  3.000
 IN5  O5    P1   O4    117.98  3.000
 IN5  HO3   O3   P1    115.83  3.000
 IN5  O8    P2   O7    106.85  3.000
 IN5  O8    P2   O6    108.84  3.000
 IN5  O7    P2   O6    115.92  3.000
 IN5  O8    P2   C9    105.96  3.000
 IN5  O7    P2   C9    102.08  3.000
 IN5  O6    P2   C9    116.35  3.000
 IN5  HO7   O7   P2    114.43  3.000
 IN5  HO8   O8   P2    115.66  3.000
 IN5  H72   C7   H71   107.02  3.000
 IN5  H72   C7   O2    109.85  3.000
 IN5  H71   C7   O2    110.07  3.000
 IN5  H72   C7   C5    110.92  3.000
 IN5  H71   C7   C5    109.72  3.000
 IN5  O2    C7   C5    109.24  3.000
 IN5  H82   C8   H81   105.95  3.000
 IN5  H82   C8   N2    113.90  3.000
 IN5  H81   C8   N2    108.09  3.000
 IN5  H82   C8   C4    109.72  3.000
 IN5  H81   C8   C4    110.05  3.000
 IN5  N2    C8   C4    109.05  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
 IN5  CONST_01  C3   C2  N1  C1    0.00   0.0  0
 IN5  CONST_02  C3   C4  C5  C1    0.00   0.0  0
 IN5  CONST_03  C5   C4  C3  C2    0.00   0.0  0
 IN5  CONST_04  C5   C1  N1  C2    0.00   0.0  0
 IN5  CONST_05  C4   C5  C1  N1    0.00   0.0  0
 IN5  CONST_06  C4   C3  C2  N1    0.00   0.0  0
 IN5  CONST_07  C6   C2  N1  C1  180.00   0.0  0
 IN5  CONST_08  C8   C4  C5  C1  180.00   0.0  0
 IN5  CONST_09  C8   C4  C3  C2  180.00   0.0  0
 IN5  CONST_10  C7   C5  C4  C3  180.00   0.0  0
 IN5  CONST_11  N1   C1  C5  C7  180.00   0.0  0
 IN5  CONST_12  O1   C3  C2  N1  180.00   0.0  0
 IN5  CONST_13  C6   C2  C3  C4  180.00   0.0  0
 IN5  CONST_14  O1   C3  C4  C5  180.00   0.0  0
 IN5  CONST_15  H1   C1  N1  C2  180.00   0.0  0
 IN5  Var_01    O2   C7  C5  C1  -12.95  30.0  1
 IN5  Var_02    N2   C8  C4  C3   83.17  30.0  2
 IN5  Var_03    H61  C6  C2  C3   63.45  30.0  2
 IN5  Var_04    C4   C8  N2  C9  177.67  30.0  1
 IN5  Var_05    O3   P1  O2  C7  -69.07  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
 IN5  chir_01  C9  C10  N2  P2  positiv

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
 IN5  plan-1  C1  0.020
 IN5  plan-1  C2  0.020
 IN5  plan-1  C3  0.020
 IN5  plan-1  N1  0.020
 IN5  plan-1  C4  0.020
 IN5  plan-1  C5  0.020
 IN5  plan-1  O1  0.020
 IN5  plan-1  C6  0.020
 IN5  plan-1  H1  0.020
 IN5  plan-1  C7  0.020
 IN5  plan-1  C8  0.020

