# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 12:38:16 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (6-azanyl-1-oxidanyl-1-phosphono-hexyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCC(O)([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
 NRD  NRD  '(6-azanyl-1-oxidanyl-1-phosphono-hexyl)phosphonic acid'  ligand  33  16  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NRD
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
 NRD  OAK  O  OH1   0  -0.745   1.9476  -2.6562  -0.2454
 NRD  PAI  P  P     0   1.388   2.3338  -1.1559   0.1862
 NRD  OAL  O  O     0  -0.700   2.5726  -1.0834   1.6448
 NRD  OAJ  O  OH1   0  -0.735   3.5175  -0.7232  -0.7956
 NRD  CAG  C  CT    0  -0.279   0.9255  -0.0984  -0.3905
 NRD  PAM  P  P     0   1.376   1.2765   1.6285   0.1896
 NRD  OAO  O  O     0  -0.691   2.7040   2.0134   0.1722
 NRD  OAP  O  OH1   0  -0.733   0.2977   2.4734  -0.7511
 NRD  OAN  O  OH1   0  -0.739   0.7112   1.7365   1.6869
 NRD  OAH  O  OH1   0  -0.656   0.9277  -0.0546  -1.7958
 NRD  CAF  C  CH2   0  -0.535  -0.3732  -0.6750   0.1937
 NRD  CAE  C  CH2   0  -0.422  -1.6739  -0.0136  -0.2575
 NRD  CAC  C  CH2   0  -0.417  -2.8777  -0.7587   0.3068
 NRD  CAB  C  CH2   0  -0.428  -4.2062  -0.2115  -0.1957
 NRD  CAA  C  CH2   0  -0.272  -5.3993  -0.9409   0.4022
 NRD  NAD  N  NH2   0  -0.800  -6.6521  -0.4255  -0.1313
 NRD  H1   H  HOH1  0   0.493   2.0248  -2.8628  -1.1860
 NRD  H2   H  HOH1  0   0.498   4.3969  -0.9884  -0.4910
 NRD  H3   H  HOH1  0   0.500   0.4354   3.4306  -0.7004
 NRD  H4   H  HOH1  0   0.493  -0.2482   1.7203   1.7976
 NRD  H5   H  HOH1  0   0.468   0.3595  -0.7549  -2.1370
 NRD  H6   H  HCH2  0   0.271  -0.4288  -1.7287  -0.0969
 NRD  H7   H  HCH2  0   0.268  -0.3096  -0.6828   1.2839
 NRD  H8   H  HCH2  0   0.224  -1.7322   1.0333   0.0496
 NRD  H9   H  HCH2  0   0.228  -1.7332  -0.0108  -1.3492
 NRD  H10  H  HCH2  0   0.218  -2.8002  -1.8196   0.0466
 NRD  H11  H  HCH2  0   0.218  -2.8497  -0.7128   1.4006
 NRD  H12  H  HCH2  0   0.214  -4.2774   0.8559   0.0418
 NRD  H13  H  HCH2  0   0.215  -4.2498  -0.2897  -1.2863
 NRD  H14  H  HCH2  0   0.211  -5.3312  -2.0022   0.1470
 NRD  H15  H  HCH2  0   0.187  -5.3337  -0.8868   1.4989
 NRD  H16  H  HNH2  0   0.345  -7.4241  -0.9541   0.2541
 NRD  H17  H  HNH2  0   0.337  -6.7870   0.5248   0.1921

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
 NRD  NAD  CAA  single  1.456  0.020  1.456
 NRD  CAA  CAB  single  1.521  0.020  1.521
 NRD  CAB  CAC  single  1.522  0.020  1.522
 NRD  CAC  CAE  single  1.524  0.020  1.524
 NRD  CAF  CAE  single  1.527  0.020  1.527
 NRD  CAF  CAG  single  1.536  0.020  1.536
 NRD  OAO  PAM  double  1.479  0.020  1.479
 NRD  OAP  PAM  single  1.599  0.020  1.599
 NRD  PAM  CAG  single  1.855  0.020  1.855
 NRD  PAM  OAN  single  1.604  0.020  1.604
 NRD  CAG  OAH  single  1.406  0.020  1.406
 NRD  CAG  PAI  single  1.853  0.020  1.853
 NRD  OAL  PAI  double  1.480  0.020  1.480
 NRD  PAI  OAJ  single  1.598  0.020  1.598
 NRD  PAI  OAK  single  1.608  0.020  1.608
 NRD  OAK  H1   single  0.850  0.020  0.980
 NRD  OAJ  H2   single  0.850  0.020  0.980
 NRD  OAP  H3   single  0.850  0.020  0.980
 NRD  OAN  H4   single  0.850  0.020  0.980
 NRD  OAH  H5   single  0.850  0.020  0.980
 NRD  CAF  H6   single  0.970  0.020  1.090
 NRD  CAF  H7   single  0.970  0.020  1.090
 NRD  CAE  H8   single  0.970  0.020  1.090
 NRD  CAE  H9   single  0.970  0.020  1.090
 NRD  CAC  H10  single  0.970  0.020  1.090
 NRD  CAC  H11  single  0.970  0.020  1.090
 NRD  CAB  H12  single  0.970  0.020  1.090
 NRD  CAB  H13  single  0.970  0.020  1.090
 NRD  CAA  H14  single  0.970  0.020  1.090
 NRD  CAA  H15  single  0.970  0.020  1.090
 NRD  NAD  H16  single  0.890  0.020  1.040
 NRD  NAD  H17  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
 NRD  H1   OAK  PAI  116.21  3.000
 NRD  CAG  PAI  OAJ  102.55  3.000
 NRD  OAJ  PAI  OAL  118.22  3.000
 NRD  CAG  PAI  OAL  113.66  3.000
 NRD  OAJ  PAI  OAK  105.41  3.000
 NRD  OAL  PAI  OAK  110.42  3.000
 NRD  CAG  PAI  OAK  105.45  3.000
 NRD  H2   OAJ  PAI  113.93  3.000
 NRD  CAF  CAG  OAH  113.15  3.000
 NRD  OAH  CAG  PAM  106.45  3.000
 NRD  CAF  CAG  PAM  112.98  3.000
 NRD  OAH  CAG  PAI  109.12  3.000
 NRD  PAM  CAG  PAI  106.86  3.000
 NRD  CAF  CAG  PAI  108.05  3.000
 NRD  OAN  PAM  OAP  107.32  3.000
 NRD  OAN  PAM  OAO  109.50  3.000
 NRD  OAP  PAM  OAO  116.52  3.000
 NRD  OAN  PAM  CAG  106.73  3.000
 NRD  OAP  PAM  CAG  101.07  3.000
 NRD  OAO  PAM  CAG  114.92  3.000
 NRD  H3   OAP  PAM  113.86  3.000
 NRD  H4   OAN  PAM  117.13  3.000
 NRD  H5   OAH  CAG  109.28  3.000
 NRD  H7   CAF  H6   105.14  3.000
 NRD  H7   CAF  CAE  110.34  3.000
 NRD  H6   CAF  CAE  107.17  3.000
 NRD  H7   CAF  CAG  109.45  3.000
 NRD  H6   CAF  CAG  107.66  3.000
 NRD  CAE  CAF  CAG  116.42  3.000
 NRD  H9   CAE  H8   105.98  3.000
 NRD  H9   CAE  CAC  109.16  3.000
 NRD  H8   CAE  CAC  108.80  3.000
 NRD  H9   CAE  CAF  110.02  3.000
 NRD  H8   CAE  CAF  112.17  3.000
 NRD  CAC  CAE  CAF  110.58  3.000
 NRD  H11  CAC  H10  106.02  3.000
 NRD  H11  CAC  CAB  109.69  3.000
 NRD  H10  CAC  CAB  109.36  3.000
 NRD  H11  CAC  CAE  109.22  3.000
 NRD  H10  CAC  CAE  109.26  3.000
 NRD  CAB  CAC  CAE  113.04  3.000
 NRD  H13  CAB  H12  106.44  3.000
 NRD  H13  CAB  CAA  109.05  3.000
 NRD  H12  CAB  CAA  109.33  3.000
 NRD  H13  CAB  CAC  109.76  3.000
 NRD  H12  CAB  CAC  109.59  3.000
 NRD  CAA  CAB  CAC  112.49  3.000
 NRD  H15  CAA  H14  106.06  3.000
 NRD  H15  CAA  NAD  113.53  3.000
 NRD  H14  CAA  NAD  108.15  3.000
 NRD  H15  CAA  CAB  108.76  3.000
 NRD  H14  CAA  CAB  108.95  3.000
 NRD  NAD  CAA  CAB  111.18  3.000
 NRD  H17  NAD  H16  105.48  3.000
 NRD  H17  NAD  CAA  109.25  3.000
 NRD  H16  NAD  CAA  109.39  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
 NRD  Var_01  CAF  CAG  PAI  OAK    54.38  30.0  3
 NRD  Var_02  CAE  CAF  CAG  PAI  -175.08  30.0  1
 NRD  Var_03  OAO  PAM  CAG  PAI    35.83  30.0  3
 NRD  Var_04  CAC  CAE  CAF  CAG   175.28  30.0  3
 NRD  Var_05  CAB  CAC  CAE  CAF  -175.54  30.0  1
 NRD  Var_06  CAA  CAB  CAC  CAE  -178.55  30.0  1
 NRD  Var_07  NAD  CAA  CAB  CAC  -178.08  30.0  1
 NRD  Var_08  H16  NAD  CAA  CAB   177.65  30.0  3

