# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 06:43:39 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  31  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 PERFECT
;

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  OP    -1  -0.859   0.6332  -1.7552  -1.0107
 0M7  P3   P  P      0   1.142   1.7725  -1.6469   0.0330
 0M7  O13  O  O      0  -0.897   1.5908  -2.6696   1.1759
 0M7  O12  O  OP    -1  -1.014   3.1679  -1.7270  -0.5994
 0M7  C2   C  CH1    0  -0.780   1.6041   0.0179   0.8513
 0M7  P1   P  P      0   1.135   2.1637   1.5192  -0.0997
 0M7  O15  O  OP    -1  -1.005   1.6044   1.4421  -1.5280
 0M7  O14  O  O      0  -0.806   1.6024   2.7254   0.6893
 0M7  O16  O  OP    -1  -1.013   3.7034   1.4944  -0.0562
 0M7  C4   C  CH2    0  -0.297   0.2018   0.1760   1.4360
 0M7  N5   N  NH1    0  -0.505  -0.8170   0.2776   0.4080
 0M7  C6   C  CH2    0  -0.269  -2.1467   0.0342   0.9060
 0M7  C7   C  CH2    0  -0.431  -3.1912   0.1241  -0.1975
 0M7  C8   C  CH2    0  -0.383  -4.6162  -0.0564   0.3092
 0M7  C9   C  CH2    0  -0.398  -5.6652   0.0344  -0.7921
 0M7  C10  C  CH3    0  -0.653  -7.0879  -0.1236  -0.2735
 0M7  H3   H  HCH1   0   0.198   2.2808  -0.0220   1.7175
 0M7  H6   H  HCH2   0   0.157   0.0041  -0.6806   2.1072
 0M7  H7   H  HCH2   0   0.161   0.1642   1.0745   2.0635
 0M7  H8   H  HNH1   0   0.329  -0.5650  -0.4184  -0.2967
 0M7  H10  H  HCH2   0   0.209  -2.2441  -0.9449   1.4140
 0M7  H11  H  HCH2   0   0.156  -2.3814   0.7820   1.6750
 0M7  H12  H  HCH2   0   0.225  -3.1003   1.0950  -0.6957
 0M7  H13  H  HCH2   0   0.163  -2.9776  -0.6328  -0.9611
 0M7  H14  H  HCH2   0   0.185  -4.7055  -1.0234   0.8169
 0M7  H15  H  HCH2   0   0.253  -4.8263   0.7034   1.0704
 0M7  H16  H  HCH2   0   0.158  -5.5684   0.9969  -1.3045
 0M7  H17  H  HCH2   0   0.206  -5.4643  -0.7311  -1.5479
 0M7  H18  H  HCH3   0   0.224  -7.2290  -1.0957   0.2030
 0M7  H19  H  HCH3   0   0.188  -7.3251   0.6419   0.4681
 0M7  H20  H  HCH3   0   0.222  -7.8196  -0.0406  -1.0780

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  1.524  0.020  1.524
 0M7  C8   C7   single  1.523  0.020  1.523
 0M7  C7   C6   single  1.522  0.020  1.522
 0M7  C6   N5   single  1.441  0.020  1.441
 0M7  O13  P3   deloc   1.544  0.020  1.544
 0M7  O12  P3   deloc   1.534  0.020  1.534
 0M7  C4   N5   single  1.451  0.020  1.451
 0M7  C4   C2   single  1.527  0.020  1.527
 0M7  P3   C2   single  1.863  0.020  1.863
 0M7  P3   O11  deloc   1.549  0.020  1.549
 0M7  O14  P1   deloc   1.547  0.020  1.547
 0M7  C2   P1   single  1.863  0.020  1.863
 0M7  P1   O16  deloc   1.541  0.020  1.541
 0M7  P1   O15  deloc   1.536  0.020  1.536
 0M7  C2   H3   single  0.970  0.020  1.090
 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  C2   P3   O12  108.06  3.000
 0M7  C2   P3   O13  104.84  3.000
 0M7  O12  P3   O13  112.18  3.000
 0M7  C2   P3   O11  106.98  3.000
 0M7  O12  P3   O11  112.81  3.000
 0M7  O13  P3   O11  111.46  3.000
 0M7  H3   C2   C4   105.49  3.000
 0M7  H3   C2   P1   104.26  3.000
 0M7  C4   C2   P1   112.81  3.000
 0M7  H3   C2   P3   104.95  3.000
 0M7  P1   C2   P3   117.95  3.000
 0M7  C4   C2   P3   110.10  3.000
 0M7  O16  P1   O14  111.15  3.000
 0M7  O16  P1   O15  112.91  3.000
 0M7  O14  P1   O15  112.42  3.000
 0M7  O15  P1   C2   108.96  3.000
 0M7  O16  P1   C2   105.83  3.000
 0M7  O14  P1   C2   105.01  3.000
 0M7  H7   C4   H6   106.33  3.000
 0M7  H7   C4   N5   108.90  3.000
 0M7  H6   C4   N5   111.02  3.000
 0M7  H7   C4   C2   109.59  3.000
 0M7  H6   C4   C2   108.44  3.000
 0M7  N5   C4   C2   112.38  3.000
 0M7  H8   N5   C6   110.54  3.000
 0M7  H8   N5   C4   105.53  3.000
 0M7  C6   N5   C4   113.04  3.000
 0M7  H11  C6   H10  105.19  3.000
 0M7  H11  C6   C7   108.72  3.000
 0M7  H10  C6   C7   108.94  3.000
 0M7  H11  C6   N5   108.92  3.000
 0M7  H10  C6   N5   112.90  3.000
 0M7  C7   C6   N5   111.89  3.000
 0M7  H13  C7   H12  106.21  3.000
 0M7  H13  C7   C8   109.40  3.000
 0M7  H12  C7   C8   109.52  3.000
 0M7  H13  C7   C6   109.30  3.000
 0M7  H12  C7   C6   108.98  3.000
 0M7  C8   C7   C6   113.19  3.000
 0M7  H15  C8   H14  105.93  3.000
 0M7  H15  C8   C9   109.19  3.000
 0M7  H14  C8   C9   109.35  3.000
 0M7  H15  C8   C7   109.17  3.000
 0M7  H14  C8   C7   109.57  3.000
 0M7  C9   C8   C7   113.37  3.000
 0M7  H17  C9   H16  106.00  3.000
 0M7  H17  C9   C10  109.52  3.000
 0M7  H16  C9   C10  109.47  3.000
 0M7  H17  C9   C8   109.34  3.000
 0M7  H16  C9   C8   109.26  3.000
 0M7  C10  C9   C8   113.01  3.000
 0M7  H20  C10  H19  107.57  3.000
 0M7  H20  C10  H18  107.64  3.000
 0M7  H19  C10  H18  107.44  3.000
 0M7  H20  C10  C9   111.58  3.000
 0M7  H19  C10  C9   111.20  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    55.37  30.0  3
 0M7  Var_02  N5   C4   C2  P3    -68.66  30.0  3
 0M7  Var_03  O14  P1   C2  P3    167.35  30.0  3
 0M7  Var_04  C6   N5   C4  C2    162.87  30.0  3
 0M7  Var_05  C7   C6   N5  C4   -179.03  30.0  2
 0M7  Var_06  C8   C7   C6  N5   -176.99  30.0  1
 0M7  Var_07  C9   C8   C7  C6    179.93  30.0  1
 0M7  Var_08  C10  C9   C8  C7   -179.03  30.0  3
 0M7  Var_09  H18  C10  C9  C8    -60.61  30.0  3

