# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 21:42:42 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: [2-(propylamino)ethane-1,1-diyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNCC([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
 0M9  0M9  '[2-(propylamino)ethane-1,1-diyl]bis(phosphonic acid)'  ligand  25  14  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0M9
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
 0M9  O1   O  OP    -1  -0.937   0.7379   2.6452  -1.0797
 0M9  P1   P  P      0   1.171   1.0039   1.6097   0.0354
 0M9  O3   O  OP    -1  -0.912   2.4428   1.6813   0.5626
 0M9  O2   O  O      0  -0.907  -0.0555   1.7070   1.1613
 0M9  C9   C  CH1    0  -0.774   0.7668  -0.0463  -0.7837
 0M9  P2   P  P      0   1.167   1.4085  -1.5563   0.0981
 0M9  O4   O  OP    -1  -0.939   0.7694  -2.7540  -0.6425
 0M9  O5   O  OP    -1  -0.938   2.9372  -1.5374  -0.0885
 0M9  O6   O  O      0  -0.929   0.9863  -1.4870   1.5730
 0M9  C8   C  CH2    0  -0.238  -0.6808  -0.1959  -1.2489
 0M9  N1   N  NH1    0  -0.617  -1.6154  -0.3083  -0.1419
 0M9  C7   C  CH2    0  -0.237  -2.9676   0.0140  -0.5221
 0M9  C6   C  CH2    0  -0.438  -3.9297  -0.0942   0.6523
 0M9  C5   C  CH3    0  -0.666  -5.3627   0.2505   0.2726
 0M9  H3   H  HCH1   0   0.150   1.3663   0.0041  -1.7047
 0M9  H6   H  HCH2   0   0.136  -0.9300   0.6711  -1.8877
 0M9  H7   H  HCH2   0   0.164  -0.7721  -1.0847  -1.8846
 0M9  H8   H  HNH1   0   0.343  -1.2846   0.3615   0.5572
 0M9  H10  H  HCH2   0   0.151  -3.0585   1.0249  -0.9648
 0M9  H11  H  HCH2   0   0.182  -3.2954  -0.6755  -1.3116
 0M9  H12  H  HCH2   0   0.206  -3.8857  -1.1087   1.0586
 0M9  H13  H  HCH2   0   0.207  -3.5928   0.5707   1.4548
 0M9  H14  H  HCH3   0   0.225  -6.0381   0.1537   1.1232
 0M9  H15  H  HCH3   0   0.214  -5.4412   1.2755  -0.0951
 0M9  H16  H  HCH3   0   0.214  -5.7311  -0.4086  -0.5161

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
 0M9  C6  C5   single  1.522  0.020  1.522
 0M9  C6  C7   single  1.522  0.020  1.522
 0M9  O2  P1   deloc   1.549  0.020  1.549
 0M9  C7  N1   single  1.441  0.020  1.441
 0M9  O1  P1   deloc   1.545  0.020  1.545
 0M9  N1  C8   single  1.453  0.020  1.453
 0M9  P1  C9   single  1.863  0.020  1.863
 0M9  P1  O3   deloc   1.534  0.020  1.534
 0M9  C9  C8   single  1.528  0.020  1.528
 0M9  C9  P2   single  1.863  0.020  1.863
 0M9  O6  P2   deloc   1.536  0.020  1.536
 0M9  P2  O4   deloc   1.546  0.020  1.546
 0M9  P2  O5   deloc   1.540  0.020  1.540
 0M9  C9  H3   single  0.970  0.020  1.090
 0M9  C8  H6   single  0.970  0.020  1.090
 0M9  C8  H7   single  0.970  0.020  1.090
 0M9  N1  H8   single  0.890  0.020  1.040
 0M9  C7  H10  single  0.970  0.020  1.090
 0M9  C7  H11  single  0.970  0.020  1.090
 0M9  C6  H12  single  0.970  0.020  1.090
 0M9  C6  H13  single  0.970  0.020  1.090
 0M9  C5  H14  single  0.970  0.020  1.090
 0M9  C5  H15  single  0.970  0.020  1.090
 0M9  C5  H16  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
 0M9  C9   P1  O2   106.76  3.000
 0M9  C9   P1  O3   108.18  3.000
 0M9  O2   P1  O3   112.88  3.000
 0M9  O3   P1  O1   112.23  3.000
 0M9  C9   P1  O1   104.87  3.000
 0M9  O2   P1  O1   111.39  3.000
 0M9  H3   C9  C8   105.42  3.000
 0M9  H3   C9  P2   104.22  3.000
 0M9  C8   C9  P2   113.02  3.000
 0M9  H3   C9  P1   104.96  3.000
 0M9  P2   C9  P1   117.95  3.000
 0M9  C8   C9  P1   109.97  3.000
 0M9  O6   P2  O5   112.87  3.000
 0M9  O5   P2  O4   111.20  3.000
 0M9  O6   P2  O4   112.41  3.000
 0M9  O5   P2  C9   105.94  3.000
 0M9  O4   P2  C9   105.00  3.000
 0M9  O6   P2  C9   108.86  3.000
 0M9  H7   C8  H6   106.37  3.000
 0M9  H7   C8  N1   108.99  3.000
 0M9  H6   C8  N1   110.85  3.000
 0M9  H7   C8  C9   109.56  3.000
 0M9  H6   C8  C9   108.22  3.000
 0M9  N1   C8  C9   112.64  3.000
 0M9  H8   N1  C7   109.71  3.000
 0M9  H8   N1  C8   105.19  3.000
 0M9  C7   N1  C8   112.66  3.000
 0M9  H11  C7  H10  105.15  3.000
 0M9  H11  C7  C6   108.75  3.000
 0M9  H10  C7  C6   108.75  3.000
 0M9  H11  C7  N1   109.23  3.000
 0M9  H10  C7  N1   112.75  3.000
 0M9  C6   C7  N1   111.94  3.000
 0M9  H13  C6  H12  106.18  3.000
 0M9  H13  C6  C5   109.57  3.000
 0M9  H12  C6  C5   109.92  3.000
 0M9  H13  C6  C7   109.13  3.000
 0M9  H12  C6  C7   109.09  3.000
 0M9  C5   C6  C7   112.74  3.000
 0M9  H16  C5  H15  107.41  3.000
 0M9  H16  C5  H14  107.52  3.000
 0M9  H15  C5  H14  107.55  3.000
 0M9  H16  C5  C6   111.17  3.000
 0M9  H15  C5  C6   111.36  3.000
 0M9  H14  C5  C6   111.62  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
 0M9  Var_01  C8   C9  P1  O1   -63.53  30.0  3
 0M9  Var_02  N1   C8  C9  P1   -68.64  30.0  3
 0M9  Var_03  O6   P2  C9  P1    46.16  30.0  3
 0M9  Var_04  C7   N1  C8  C9   159.76  30.0  1
 0M9  Var_05  C6   C7  N1  C8  -179.38  30.0  1
 0M9  Var_06  C5   C6  C7  N1   179.66  30.0  1
 0M9  Var_07  H14  C5  C6  C7   179.21  30.0  3

