# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:19:18 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: dicyclopentyl amidophosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[P](=O)(OC1CCCC1)OC2CCCC2
#
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
 DI9  DI9  'dicyclopentyl amidophosphate'  ligand  35  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DI9
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
 DI9  CAB   C  CH2   0  -0.468  -3.0411   0.8473  -0.6043
 DI9  CAJ   C  CH2   0  -0.449  -4.4924   0.4299  -0.9245
 DI9  CAK   C  CH2   0  -0.459  -4.7748  -0.7969  -0.0426
 DI9  CAL   C  CH2   0  -0.465  -3.4019  -1.4299   0.1476
 DI9  CAC   C  CR15  0   0.044  -2.5156  -0.2148   0.3731
 DI9  OAD   O  O2    0  -0.595  -1.1409  -0.5472   0.1496
 DI9  PAE   P  P     0   1.405   0.0046   0.1839   1.0046
 DI9  NAM   N  NH2   0  -0.959   0.0181   1.8047   0.6913
 DI9  OAA   O  O     0  -0.725  -0.0353  -0.0794   2.4633
 DI9  OAF   O  O2    0  -0.594   1.2214  -0.4467   0.1867
 DI9  CAG   C  CH1   0   0.047   2.5790  -0.2599   0.6272
 DI9  CAH   C  CH2   0  -0.475   3.4420  -1.4354   0.1321
 DI9  CAI   C  CH2   0  -0.446   4.3873  -0.8429  -0.9140
 DI9  CAO   C  CH2   0  -0.451   4.6122   0.5775  -0.4029
 DI9  CAN   C  CH2   0  -0.470   3.2090   1.0056   0.0241
 DI9  HAB1  H  HCH2  0   0.239  -2.9817   1.8489  -0.1783
 DI9  HAB2  H  HCH2  0   0.240  -2.4263   0.8479  -1.5063
 DI9  HAJ1  H  HCH2  0   0.236  -5.2058   1.2343  -0.7471
 DI9  HAJ2  H  HCH2  0   0.232  -4.5800   0.1576  -1.9773
 DI9  HAK1  H  HCH2  0   0.226  -5.1787  -0.4862   0.9246
 DI9  HAK2  H  HCH2  0   0.240  -5.4977  -1.4803  -0.4884
 DI9  HAL1  H  HCH2  0   0.230  -3.0919  -1.9416  -0.7686
 DI9  HAL2  H  HCH2  0   0.244  -3.3546  -2.1460   0.9688
 DI9  HAC   H  HCR5  0   0.235  -2.6518   0.1281   1.4051
 DI9  HAM1  H  HNH2  0   0.403  -0.0433   2.1296  -0.2625
 DI9  HAM2  H  HNH2  0   0.406  -0.4597   2.4116   1.3402
 DI9  HAG   H  HCH1  0   0.242   2.5911  -0.2198   1.7190
 DI9  HAH1  H  HCH2  0   0.240   4.0200  -1.8283   0.9706
 DI9  HAH2  H  HCH2  0   0.248   2.8313  -2.2564  -0.2448
 DI9  HAI1  H  HCH2  0   0.236   5.3071  -1.4179  -1.0250
 DI9  HAI2  H  HCH2  0   0.223   3.9015  -0.8083  -1.8931
 DI9  HAO1  H  HCH2  0   0.223   5.2872   0.5619   0.4574
 DI9  HAO2  H  HCH2  0   0.237   5.0469   1.2451  -1.1474
 DI9  HAN1  H  HCH2  0   0.235   2.6366   1.2983  -0.8599
 DI9  HAN2  H  HCH2  0   0.243   3.1969   1.8496   0.7134

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
 DI9  CAB  CAJ   single  1.544  0.020  1.544
 DI9  CAB  CAC   single  1.536  0.020  1.536
 DI9  CAB  HAB1  single  0.970  0.020  1.090
 DI9  CAB  HAB2  single  0.970  0.020  1.090
 DI9  CAJ  CAK   single  1.537  0.020  1.537
 DI9  CAJ  HAJ1  single  0.970  0.020  1.090
 DI9  CAJ  HAJ2  single  0.970  0.020  1.090
 DI9  CAK  CAL   single  1.524  0.020  1.524
 DI9  CAK  HAK1  single  0.970  0.020  1.090
 DI9  CAK  HAK2  single  0.970  0.020  1.090
 DI9  CAL  CAC   single  1.521  0.020  1.521
 DI9  CAL  HAL1  single  0.970  0.020  1.090
 DI9  CAL  HAL2  single  0.970  0.020  1.090
 DI9  CAC  OAD   single  1.432  0.020  1.432
 DI9  CAC  HAC   single  0.970  0.020  1.090
 DI9  OAD  PAE   single  1.605  0.020  1.605
 DI9  PAE  NAM   single  1.651  0.020  1.651
 DI9  PAE  OAA   double  1.483  0.020  1.483
 DI9  PAE  OAF   single  1.596  0.020  1.596
 DI9  NAM  HAM1  single  0.890  0.020  1.040
 DI9  NAM  HAM2  single  0.890  0.020  1.040
 DI9  OAF  CAG   single  1.440  0.020  1.440
 DI9  CAG  CAH   single  1.540  0.020  1.540
 DI9  CAG  CAN   single  1.537  0.020  1.537
 DI9  CAG  HAG   single  0.970  0.020  1.090
 DI9  CAH  CAI   single  1.529  0.020  1.529
 DI9  CAH  HAH1  single  0.970  0.020  1.090
 DI9  CAH  HAH2  single  0.970  0.020  1.090
 DI9  CAI  CAO   single  1.526  0.020  1.526
 DI9  CAI  HAI1  single  0.970  0.020  1.090
 DI9  CAI  HAI2  single  0.970  0.020  1.090
 DI9  CAO  CAN   single  1.528  0.020  1.528
 DI9  CAO  HAO1  single  0.970  0.020  1.090
 DI9  CAO  HAO2  single  0.970  0.020  1.090
 DI9  CAN  HAN1  single  0.970  0.020  1.090
 DI9  CAN  HAN2  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
 DI9  HAB2  CAB  HAB1  106.96  3.000
 DI9  HAB2  CAB  CAC   109.47  3.000
 DI9  HAB1  CAB  CAC   111.59  3.000
 DI9  HAB2  CAB  CAJ   110.99  3.000
 DI9  HAB1  CAB  CAJ   112.39  3.000
 DI9  CAC   CAB  CAJ   105.47  3.000
 DI9  HAJ2  CAJ  HAJ1  106.79  3.000
 DI9  HAJ2  CAJ  CAK   109.86  3.000
 DI9  HAJ1  CAJ  CAK   112.05  3.000
 DI9  HAJ2  CAJ  CAB   110.07  3.000
 DI9  HAJ1  CAJ  CAB   112.46  3.000
 DI9  CAK   CAJ  CAB   105.64  3.000
 DI9  HAK2  CAK  HAK1  107.16  3.000
 DI9  HAK2  CAK  CAL   112.84  3.000
 DI9  HAK1  CAK  CAL   109.91  3.000
 DI9  HAK2  CAK  CAJ   112.80  3.000
 DI9  HAK1  CAK  CAJ   110.40  3.000
 DI9  CAL   CAK  CAJ   103.75  3.000
 DI9  HAL2  CAL  HAL1  108.13  3.000
 DI9  HAL2  CAL  CAC   112.81  3.000
 DI9  HAL1  CAL  CAC   109.43  3.000
 DI9  HAL2  CAL  CAK   113.94  3.000
 DI9  HAL1  CAL  CAK   110.18  3.000
 DI9  CAC   CAL  CAK   102.22  3.000
 DI9  HAC   CAC  OAD   109.81  3.000
 DI9  HAC   CAC  CAL   108.49  3.000
 DI9  OAD   CAC  CAL   110.54  3.000
 DI9  HAC   CAC  CAB   109.89  3.000
 DI9  OAD   CAC  CAB   112.94  3.000
 DI9  CAL   CAC  CAB   105.00  3.000
 DI9  PAE   OAD  CAC   119.74  3.000
 DI9  OAF   PAE  OAA   117.03  3.000
 DI9  OAF   PAE  NAM   106.52  3.000
 DI9  OAA   PAE  NAM   111.18  3.000
 DI9  OAF   PAE  OAD    95.22  3.000
 DI9  OAA   PAE  OAD   115.07  3.000
 DI9  NAM   PAE  OAD   110.60  3.000
 DI9  HAM2  NAM  HAM1  112.66  3.000
 DI9  HAM2  NAM  PAE   117.69  3.000
 DI9  HAM1  NAM  PAE   119.66  3.000
 DI9  CAG   OAF  PAE   120.73  3.000
 DI9  HAG   CAG  CAN   110.93  3.000
 DI9  HAG   CAG  CAH   110.07  3.000
 DI9  CAN   CAG  CAH   105.82  3.000
 DI9  HAG   CAG  OAF   108.72  3.000
 DI9  CAN   CAG  OAF   111.92  3.000
 DI9  CAH   CAG  OAF   109.33  3.000
 DI9  HAH2  CAH  HAH1  106.92  3.000
 DI9  HAH2  CAH  CAI   113.67  3.000
 DI9  HAH1  CAH  CAI   109.73  3.000
 DI9  HAH2  CAH  CAG   111.84  3.000
 DI9  HAH1  CAH  CAG   108.94  3.000
 DI9  CAI   CAH  CAG   105.70  3.000
 DI9  HAI2  CAI  HAI1  107.48  3.000
 DI9  HAI2  CAI  CAO   109.62  3.000
 DI9  HAI1  CAI  CAO   113.61  3.000
 DI9  HAI2  CAI  CAH   110.50  3.000
 DI9  HAI1  CAI  CAH   112.75  3.000
 DI9  CAO   CAI  CAH   102.86  3.000
 DI9  HAO2  CAO  HAO1  107.45  3.000
 DI9  HAO2  CAO  CAN   112.67  3.000
 DI9  HAO1  CAO  CAN   110.54  3.000
 DI9  HAO2  CAO  CAI   113.57  3.000
 DI9  HAO1  CAO  CAI   109.95  3.000
 DI9  CAN   CAO  CAI   102.65  3.000
 DI9  HAN2  CAN  HAN1  107.36  3.000
 DI9  HAN2  CAN  CAO   113.83  3.000
 DI9  HAN1  CAN  CAO   109.27  3.000
 DI9  HAN2  CAN  CAG   112.64  3.000
 DI9  HAN1  CAN  CAG   108.85  3.000
 DI9  CAO   CAN  CAG   104.80  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
 DI9  Var_01  CAL   CAK  CAJ  CAB  -28.16  30.0  1
 DI9  Var_02  CAC   CAL  CAK  CAJ   41.59  30.0  1
 DI9  Var_03  CAC   CAB  CAJ  CAK    3.91  30.0  1
 DI9  Var_04  CAO   CAI  CAH  CAG   32.03  30.0  1
 DI9  Var_05  CAI   CAO  CAN  CAG   37.22  30.0  1
 DI9  Var_06  CAN   CAO  CAI  CAH  -42.71  30.0  1
 DI9  Var_07  NAM   PAE  OAD  CAC  -63.31  30.0  3
 DI9  Var_08  HAM1  NAM  PAE  OAD  -45.11  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
 DI9  chir_01  CAC  CAB  CAL  OAD  negativ
 DI9  chir_02  CAG  OAF  CAH  CAN  negativ

