# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:26:04 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N~2~-({6-[difluoro(phosphono)methyl]naphthalen-2-yl}carbonyl)-L-alpha-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@H](CCC(O)=O)NC(=O)c1ccc2cc(ccc2c1)C(F)(F)[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
 TPI  TPI  N~2~-({6-[difluoro(phosphono)methyl]naphthalen-2-yl}carbonyl)-L-alpha-glutamine  ligand  43  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TPI
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
 TPI  P     P  P      0   1.103  -0.5876   0.5236  -6.1963
 TPI  O1    O  OP    -1  -0.875  -1.8823   0.7978  -5.4411
 TPI  O2    O  OP    -1  -0.873   0.4388   1.6518  -6.1691
 TPI  O3    O  O      0  -0.885  -0.7572  -0.1603  -7.5502
 TPI  C1    C  CT     0   0.454   0.2320  -0.8047  -5.1319
 TPI  F1    F  F      0  -0.380   1.4305  -1.2017  -5.6987
 TPI  F2    F  F      0  -0.372  -0.5382  -1.9496  -5.1227
 TPI  C2    C  CR16   0  -0.382  -0.3431  -0.7414  -2.6998
 TPI  C3    C  CR6    0  -0.035   0.4999  -0.3906  -3.7215
 TPI  C4    C  CR16   0  -0.277   1.6288   0.4195  -3.4448
 TPI  C5    C  CR16   0  -0.305   1.9060   0.8189  -2.1690
 TPI  C6    C  C1     0  -0.341   1.3371   0.8235   0.2362
 TPI  C7    C  C      0  -0.040   0.5215   0.4278   1.2675
 TPI  C8    C  C1     0  -0.296  -0.6330  -0.3423   0.9847
 TPI  C9    C  C1     0  -0.303  -0.9253  -0.7103  -0.2981
 TPI  C10   C  CR6    0   0.139  -0.0803  -0.3422  -1.3708
 TPI  C11   C  CR6    0   0.131   1.0656   0.4443  -1.0942
 TPI  C12   C  C      0   0.542   0.8912   0.8406   2.6527
 TPI  O4    O  O      0  -0.479   1.5900   1.8204   2.8699
 TPI  N1    N  NH1    0  -0.677   0.4268   0.0642   3.6520
 TPI  C13   C  CH1    0  -0.165   0.6759   0.3767   5.0393
 TPI  C14   C  C      0   0.508   2.1217   0.1262   5.4678
 TPI  N2    N  NH2    0  -0.794   2.7947  -0.7986   4.7753
 TPI  O5    O  O      0  -0.494   2.5852   0.7173   6.4329
 TPI  C15   C  CH2    0  -0.458  -0.2717  -0.4219   5.9386
 TPI  C16   C  CH2    0  -0.584  -1.7304  -0.0449   5.7339
 TPI  C17   C  C      0   0.418  -2.7272  -0.7485   6.6738
 TPI  O6    O  O      0  -0.605  -2.2699  -1.5349   7.5254
 TPI  O7    O  OC    -1  -0.629  -3.9291  -0.4605   6.4985
 TPI  H41   H  HCR6   0   0.253   2.2782   0.7243  -4.2527
 TPI  H51   H  HCR6   0   0.254   2.7767   1.4308  -1.9663
 TPI  H61   H  H      0   0.257   2.2154   1.4238   0.4404
 TPI  H81   H  H      0   0.252  -1.3170  -0.6258   1.7749
 TPI  H91   H  H      0   0.260  -1.8146  -1.2929  -0.5046
 TPI  HN11  H  HNH1   0   0.412  -0.0619  -0.7906   3.4378
 TPI  H131  H  HCH1   0   0.271   0.4935   1.4427   5.1985
 TPI  HN21  H  HNH2   0   0.403   3.7387  -1.0378   5.0312
 TPI  HN22  H  HNH2   0   0.405   2.3973  -1.2677   3.9802
 TPI  H151  H  HCH2   0   0.232  -0.1193  -1.4915   5.7662
 TPI  H152  H  HCH2   0   0.248   0.0111  -0.2332   6.9745
 TPI  H161  H  HCH2   0   0.231  -1.8460   1.0374   5.8623
 TPI  H162  H  HCH2   0   0.225  -2.0434  -0.2432   4.7035
 TPI  H21   H  HCR6   0   0.249  -1.2202  -1.3464  -2.8887

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
 TPI  P    O1    deloc     1.524  0.020  1.524
 TPI  P    O2    deloc     1.525  0.020  1.525
 TPI  P    O3    deloc     1.526  0.020  1.526
 TPI  P    C1    single    1.889  0.020  1.889
 TPI  C1   F1    single    1.384  0.020  1.384
 TPI  C1   F2    single    1.380  0.020  1.380
 TPI  C1   C3    single    1.494  0.020  1.494
 TPI  C2   C3    aromatic  1.370  0.020  1.370
 TPI  C2   C10   aromatic  1.412  0.020  1.412
 TPI  C2   H21   single    0.930  0.020  1.080
 TPI  C3   C4    aromatic  1.417  0.020  1.417
 TPI  C4   C5    aromatic  1.365  0.020  1.365
 TPI  C4   H41   single    0.930  0.020  1.080
 TPI  C5   C11   aromatic  1.415  0.020  1.415
 TPI  C5   H51   single    0.930  0.020  1.080
 TPI  C6   C7    aromatic  1.373  0.020  1.373
 TPI  C6   C11   aromatic  1.410  0.020  1.410
 TPI  C6   H61   single    0.930  0.020  1.080
 TPI  C7   C8    aromatic  1.416  0.020  1.416
 TPI  C7   C12   single    1.492  0.020  1.492
 TPI  C8   C9    aromatic  1.366  0.020  1.366
 TPI  C8   H81   single    0.930  0.020  1.080
 TPI  C9   C10   aromatic  1.414  0.020  1.414
 TPI  C9   H91   single    0.930  0.020  1.080
 TPI  C10  C11   aromatic  1.417  0.020  1.417
 TPI  C12  O4    double    1.223  0.020  1.223
 TPI  C12  N1    single    1.348  0.020  1.348
 TPI  N1   C13   single    1.444  0.020  1.444
 TPI  N1   HN11  single    0.860  0.020  1.020
 TPI  C13  C14   single    1.529  0.020  1.529
 TPI  C13  C15   single    1.531  0.020  1.531
 TPI  C13  H131  single    0.970  0.020  1.090
 TPI  C14  N2    single    1.337  0.020  1.337
 TPI  C14  O5    double    1.223  0.020  1.223
 TPI  N2   HN21  single    0.860  0.020  1.020
 TPI  N2   HN22  single    0.860  0.020  1.020
 TPI  C15  C16   single    1.521  0.020  1.521
 TPI  C15  H151  single    0.970  0.020  1.090
 TPI  C15  H152  single    0.970  0.020  1.090
 TPI  C16  C17   single    1.540  0.020  1.540
 TPI  C16  H161  single    0.970  0.020  1.090
 TPI  C16  H162  single    0.970  0.020  1.090
 TPI  C17  O6    deloc     1.246  0.020  1.246
 TPI  C17  O7    deloc     1.248  0.020  1.248

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
 TPI  C1    P    O3    103.47  3.000
 TPI  C1    P    O2    102.60  3.000
 TPI  O3    P    O2    114.96  3.000
 TPI  C1    P    O1    102.47  3.000
 TPI  O3    P    O1    115.20  3.000
 TPI  O2    P    O1    115.46  3.000
 TPI  C3    C1   F2    108.89  3.000
 TPI  C3    C1   F1    108.11  3.000
 TPI  F2    C1   F1    104.37  3.000
 TPI  C3    C1   P     114.50  3.000
 TPI  F2    C1   P     110.18  3.000
 TPI  F1    C1   P     110.28  3.000
 TPI  H21   C2   C10   118.23  3.000
 TPI  H21   C2   C3    120.78  3.000
 TPI  C10   C2   C3    120.98  3.000
 TPI  C4    C3   C2    119.40  3.000
 TPI  C4    C3   C1    119.06  3.000
 TPI  C2    C3   C1    121.50  3.000
 TPI  H41   C4   C5    119.62  3.000
 TPI  H41   C4   C3    119.61  3.000
 TPI  C5    C4   C3    120.77  3.000
 TPI  H51   C5   C11   119.00  3.000
 TPI  H51   C5   C4    120.21  3.000
 TPI  C11   C5   C4    120.79  3.000
 TPI  H61   C6   C11   118.89  3.000
 TPI  H61   C6   C7    119.98  3.000
 TPI  C11   C6   C7    121.12  3.000
 TPI  C12   C7   C8    122.54  3.000
 TPI  C12   C7   C6    118.06  3.000
 TPI  C8    C7   C6    119.40  3.000
 TPI  H81   C8   C9    118.66  3.000
 TPI  H81   C8   C7    120.76  3.000
 TPI  C9    C8   C7    120.55  3.000
 TPI  H91   C9   C10   119.08  3.000
 TPI  H91   C9   C8    119.97  3.000
 TPI  C10   C9   C8    120.95  3.000
 TPI  C11   C10  C9    118.65  3.000
 TPI  C11   C10  C2    119.41  3.000
 TPI  C9    C10  C2    121.94  3.000
 TPI  C10   C11  C6    119.29  3.000
 TPI  C10   C11  C5    118.62  3.000
 TPI  C6    C11  C5    122.09  3.000
 TPI  N1    C12  O4    121.78  3.000
 TPI  N1    C12  C7    116.33  3.000
 TPI  O4    C12  C7    121.88  3.000
 TPI  HN11  N1   C13   118.14  3.000
 TPI  HN11  N1   C12   119.87  3.000
 TPI  C13   N1   C12   121.89  3.000
 TPI  H131  C13  C15   108.66  3.000
 TPI  H131  C13  C14   106.07  3.000
 TPI  C15   C13  C14   109.59  3.000
 TPI  H131  C13  N1    108.80  3.000
 TPI  C15   C13  N1    110.16  3.000
 TPI  C14   C13  N1    113.39  3.000
 TPI  O5    C14  N2    123.52  3.000
 TPI  O5    C14  C13   120.03  3.000
 TPI  N2    C14  C13   116.38  3.000
 TPI  HN22  N2   HN21  117.44  3.000
 TPI  HN22  N2   C14   122.24  3.000
 TPI  HN21  N2   C14   120.31  3.000
 TPI  H152  C15  H151  106.42  3.000
 TPI  H152  C15  C16   109.50  3.000
 TPI  H151  C15  C16   110.78  3.000
 TPI  H152  C15  C13   107.90  3.000
 TPI  H151  C15  C13   109.34  3.000
 TPI  C16   C15  C13   112.66  3.000
 TPI  H162  C16  H161  105.01  3.000
 TPI  H162  C16  C17   107.85  3.000
 TPI  H161  C16  C17   108.14  3.000
 TPI  H162  C16  C15   110.86  3.000
 TPI  H161  C16  C15   109.29  3.000
 TPI  C17   C16  C15   115.18  3.000
 TPI  O7    C17  O6    126.51  3.000
 TPI  O7    C17  C16   115.60  3.000
 TPI  O6    C17  C16   117.89  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
 TPI  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 TPI  CONST_02  C8    C9   C10  C2    180.00   0.0  0
 TPI  CONST_03  C5    C11  C10  C2      0.00   0.0  0
 TPI  CONST_04  C6    C11  C10  C2    180.00   0.0  0
 TPI  CONST_05  C9    C10  C2   C3    180.00   0.0  0
 TPI  CONST_06  C11   C10  C2   C3      0.00   0.0  0
 TPI  CONST_07  C11   C5   C4   C3      0.00   0.0  0
 TPI  CONST_08  C10   C2   C3   C4      0.00   0.0  0
 TPI  CONST_09  C6    C11  C5   C4    180.00   0.0  0
 TPI  CONST_10  C10   C11  C5   C4      0.00   0.0  0
 TPI  CONST_11  C7    C6   C11  C5    180.00   0.0  0
 TPI  CONST_12  C9    C10  C11  C5    180.00   0.0  0
 TPI  CONST_13  C9    C8   C7   C6      0.00   0.0  0
 TPI  CONST_14  C9    C10  C11  C6      0.00   0.0  0
 TPI  CONST_15  C10   C11  C6   C7      0.00   0.0  0
 TPI  CONST_16  C10   C9   C8   C7      0.00   0.0  0
 TPI  CONST_17  C11   C6   C7   C8      0.00   0.0  0
 TPI  CONST_18  C11   C10  C9   C8      0.00   0.0  0
 TPI  CONST_19  C10   C2   C3   C1    180.00   0.0  0
 TPI  CONST_20  C5    C4   C3   C1    180.00   0.0  0
 TPI  CONST_21  C12   C7   C8   C9    180.00   0.0  0
 TPI  CONST_22  C12   C7   C6   C11   180.00   0.0  0
 TPI  CONST_23  H41   C4   C3   C2    180.00   0.0  0
 TPI  CONST_24  H91   C9   C10  C2      0.00   0.0  0
 TPI  CONST_25  H51   C5   C4   C3    180.00   0.0  0
 TPI  CONST_26  H21   C2   C3   C4    180.00   0.0  0
 TPI  CONST_27  H61   C6   C11  C5      0.00   0.0  0
 TPI  CONST_28  H81   C8   C7   C6    180.00   0.0  0
 TPI  CONST_29  C13   N1   C12  C7    180.00   0.0  0
 TPI  CONST_30  HN11  N1   C12  C7      0.00   0.0  0
 TPI  CONST_31  C13   N1   C12  O4      0.00   0.0  0
 TPI  CONST_32  HN21  N2   C14  C13   180.00   0.0  0
 TPI  CONST_33  HN22  N2   C14  C13     0.00   0.0  0
 TPI  Var_01    C2    C3   C1   P      98.64  30.0  2
 TPI  Var_02    O4    C12  C7   C6     23.84  30.0  2
 TPI  Var_03    C3    C1   P    O1    -59.21  30.0  3
 TPI  Var_04    C17   C16  C15  C13  -176.24  30.0  3
 TPI  Var_05    O6    C17  C16  C15     1.27  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
 TPI  chir_01  C13  N1  C14  C15  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 TPI  plan-1  C1    0.020
 TPI  plan-1  C2    0.020
 TPI  plan-1  C3    0.020
 TPI  plan-1  C4    0.020
 TPI  plan-1  C5    0.020
 TPI  plan-1  C6    0.020
 TPI  plan-1  C7    0.020
 TPI  plan-1  C8    0.020
 TPI  plan-1  C9    0.020
 TPI  plan-1  C10   0.020
 TPI  plan-1  C11   0.020
 TPI  plan-1  C12   0.020
 TPI  plan-1  H41   0.020
 TPI  plan-1  H51   0.020
 TPI  plan-1  H61   0.020
 TPI  plan-1  H81   0.020
 TPI  plan-1  H91   0.020
 TPI  plan-1  H21   0.020
 TPI  plan-2  C7    0.020
 TPI  plan-2  C12   0.020
 TPI  plan-2  O4    0.020
 TPI  plan-2  N1    0.020
 TPI  plan-2  C13   0.020
 TPI  plan-2  HN11  0.020
 TPI  plan-3  C13   0.020
 TPI  plan-3  C14   0.020
 TPI  plan-3  N2    0.020
 TPI  plan-3  O5    0.020
 TPI  plan-3  HN21  0.020
 TPI  plan-3  HN22  0.020
 TPI  plan-4  C16   0.020
 TPI  plan-4  C17   0.020
 TPI  plan-4  O6    0.020
 TPI  plan-4  O7    0.020

