# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:24:20 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: [2-(pentylamino)ethane-1,1-diyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCNCC([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
 0M7  0M7  '[2-(pentylamino)ethane-1,1-diyl]bis(phosphonic acid)'  ligand  35  16  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0M7
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
 0M7  O11  O  OH1   0  -0.764   1.5069  -1.3125  -1.5033
 0M7  P3   P  P     0   1.388   2.0852  -1.5527  -0.0156
 0M7  O13  O  O     0  -0.689   1.6360  -2.7958   0.6472
 0M7  O12  O  OH1   0  -0.740   3.6793  -1.5152  -0.1212
 0M7  C2   C  CH1   0  -0.874   1.5590  -0.0149   0.8031
 0M7  P1   P  P     0   1.388   1.8139   1.5292  -0.1301
 0M7  O15  O  OH1   0  -0.742   1.0417   1.4877  -1.5264
 0M7  O14  O  O     0  -0.696   1.4708   2.7583   0.6184
 0M7  O16  O  OH1   0  -0.762   3.3814   1.3407  -0.4789
 0M7  C4   C  CH2   0  -0.276   0.1380  -0.0990   1.3753
 0M7  N5   N  NH1   0  -0.592  -0.8796  -0.0671   0.3520
 0M7  C6   C  CH2   0  -0.252  -2.2193   0.0003   0.9088
 0M7  C7   C  CH2   0  -0.442  -3.2770  -0.0251  -0.1814
 0M7  C8   C  CH2   0  -0.410  -4.6911   0.0488   0.3800
 0M7  C9   C  CH2   0  -0.418  -5.7690  -0.0004  -0.6953
 0M7  C10  C  CH3   0  -0.661  -7.1770   0.0899  -0.1237
 0M7  H1   H  HOH1  0   0.508   1.6516  -2.0354  -2.1314
 0M7  H2   H  HOH1  0   0.493   4.0453  -0.6759  -0.4418
 0M7  H3   H  HCH1  0   0.360   2.2354   0.0702   1.6632
 0M7  H4   H  HOH1  0   0.493   1.0178   0.6143  -1.9481
 0M7  H5   H  HOH1  0   0.503   3.7683   2.0363  -1.0299
 0M7  H6   H  HCH2  0   0.240   0.0826  -0.9799   2.0296
 0M7  H7   H  HCH2  0   0.260  -0.0040   0.7673   2.0251
 0M7  H8   H  HNH1  0   0.343  -0.8182  -0.8962  -0.2282
 0M7  H10  H  HCH2  0   0.190  -2.4138  -0.8149   1.6242
 0M7  H11  H  HCH2  0   0.219  -2.3032   0.9311   1.4791
 0M7  H12  H  HCH2  0   0.218  -3.1062   0.8072  -0.8708
 0M7  H13  H  HCH2  0   0.214  -3.1689  -0.9425  -0.7716
 0M7  H14  H  HCH2  0   0.209  -4.8462  -0.7755   1.0851
 0M7  H15  H  HCH2  0   0.210  -4.8020   0.9692   0.9638
 0M7  H16  H  HCH2  0   0.211  -5.6099   0.8156  -1.4067
 0M7  H17  H  HCH2  0   0.211  -5.6649  -0.9264  -1.2694
 0M7  H18  H  HCH3  0   0.215  -7.3707  -0.7221   0.5801
 0M7  H19  H  HCH3  0   0.216  -7.3249   1.0294   0.4122
 0M7  H20  H  HCH3  0   0.226  -7.9327   0.0344  -0.9080

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
 0M7  C10  C9   single  1.522  0.020  1.522
 0M7  C8   C9   single  1.523  0.020  1.523
 0M7  C8   C7   single  1.523  0.020  1.523
 0M7  C7   C6   single  1.519  0.020  1.519
 0M7  C6   N5   single  1.452  0.020  1.452
 0M7  O13  P3   double  1.479  0.020  1.479
 0M7  O12  P3   single  1.598  0.020  1.598
 0M7  C4   N5   single  1.444  0.020  1.444
 0M7  C4   C2   single  1.534  0.020  1.534
 0M7  P3   C2   single  1.820  0.020  1.820
 0M7  P3   O11  single  1.614  0.020  1.614
 0M7  O14  P1   double  1.479  0.020  1.479
 0M7  C2   P1   single  1.822  0.020  1.822
 0M7  P1   O16  single  1.617  0.020  1.617
 0M7  P1   O15  single  1.596  0.020  1.596
 0M7  O11  H1   single  0.850  0.020  0.980
 0M7  O12  H2   single  0.850  0.020  0.980
 0M7  C2   H3   single  0.970  0.020  1.090
 0M7  O15  H4   single  0.850  0.020  0.980
 0M7  O16  H5   single  0.850  0.020  0.980
 0M7  C4   H6   single  0.970  0.020  1.090
 0M7  C4   H7   single  0.970  0.020  1.090
 0M7  N5   H8   single  0.890  0.020  1.040
 0M7  C6   H10  single  0.970  0.020  1.090
 0M7  C6   H11  single  0.970  0.020  1.090
 0M7  C7   H12  single  0.970  0.020  1.090
 0M7  C7   H13  single  0.970  0.020  1.090
 0M7  C8   H14  single  0.970  0.020  1.090
 0M7  C8   H15  single  0.970  0.020  1.090
 0M7  C9   H16  single  0.970  0.020  1.090
 0M7  C9   H17  single  0.970  0.020  1.090
 0M7  C10  H18  single  0.970  0.020  1.090
 0M7  C10  H19  single  0.970  0.020  1.090
 0M7  C10  H20  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
 0M7  H1   O11  P3   115.66  3.000
 0M7  C2   P3   O12  107.35  3.000
 0M7  C2   P3   O13  114.89  3.000
 0M7  O12  P3   O13  110.63  3.000
 0M7  C2   P3   O11  100.68  3.000
 0M7  O12  P3   O11  107.04  3.000
 0M7  O13  P3   O11  115.43  3.000
 0M7  H2   O12  P3   114.73  3.000
 0M7  H3   C2   C4   106.42  3.000
 0M7  H3   C2   P1   104.45  3.000
 0M7  C4   C2   P1   111.53  3.000
 0M7  H3   C2   P3   103.88  3.000
 0M7  P1   C2   P3   116.44  3.000
 0M7  C4   C2   P3   112.91  3.000
 0M7  O16  P1   O14  115.52  3.000
 0M7  O16  P1   O15  106.09  3.000
 0M7  O14  P1   O15  110.61  3.000
 0M7  O15  P1   C2   111.00  3.000
 0M7  O16  P1   C2    98.47  3.000
 0M7  O14  P1   C2   114.36  3.000
 0M7  H4   O15  P1   114.55  3.000
 0M7  H5   O16  P1   115.24  3.000
 0M7  H7   C4   H6   105.97  3.000
 0M7  H7   C4   N5   108.22  3.000
 0M7  H6   C4   N5   113.85  3.000
 0M7  H7   C4   C2   107.39  3.000
 0M7  H6   C4   C2   108.22  3.000
 0M7  N5   C4   C2   112.79  3.000
 0M7  H8   N5   C6   108.26  3.000
 0M7  H8   N5   C4   110.18  3.000
 0M7  C6   N5   C4   112.30  3.000
 0M7  H11  C6   H10  106.09  3.000
 0M7  H11  C6   C7   109.55  3.000
 0M7  H10  C6   C7   109.30  3.000
 0M7  H11  C6   N5   108.06  3.000
 0M7  H10  C6   N5   112.17  3.000
 0M7  C7   C6   N5   111.49  3.000
 0M7  H13  C7   H12  106.38  3.000
 0M7  H13  C7   C8   109.31  3.000
 0M7  H12  C7   C8   109.89  3.000
 0M7  H13  C7   C6   109.37  3.000
 0M7  H12  C7   C6   109.31  3.000
 0M7  C8   C7   C6   112.40  3.000
 0M7  H15  C8   H14  105.95  3.000
 0M7  H15  C8   C9   109.37  3.000
 0M7  H14  C8   C9   109.25  3.000
 0M7  H15  C8   C7   109.34  3.000
 0M7  H14  C8   C7   109.39  3.000
 0M7  C9   C8   C7   113.28  3.000
 0M7  H17  C9   H16  106.02  3.000
 0M7  H17  C9   C10  109.58  3.000
 0M7  H16  C9   C10  109.53  3.000
 0M7  H17  C9   C8   109.29  3.000
 0M7  H16  C9   C8   109.38  3.000
 0M7  C10  C9   C8   112.80  3.000
 0M7  H20  C10  H19  107.64  3.000
 0M7  H20  C10  H18  107.62  3.000
 0M7  H19  C10  H18  107.43  3.000
 0M7  H20  C10  C9   111.59  3.000
 0M7  H19  C10  C9   111.14  3.000
 0M7  H18  C10  C9   111.22  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
 0M7  Var_01  C4   C2   P3  O11    86.70  30.0  3
 0M7  Var_02  N5   C4   C2  P3    -73.07  30.0  1
 0M7  Var_03  O14  P1   C2  P3   -175.38  30.0  3
 0M7  Var_04  C6   N5   C4  C2   -173.70  30.0  3
 0M7  Var_05  C7   C6   N5  C4   -177.64  30.0  1
 0M7  Var_06  C8   C7   C6  N5   -179.83  30.0  1
 0M7  Var_07  C9   C8   C7  C6   -178.97  30.0  1
 0M7  Var_08  C10  C9   C8  C7   -179.36  30.0  3
 0M7  Var_09  H18  C10  C9  C8    -58.76  30.0  3

