# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 21:55:52 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: amino{[(4S,5S)-4-amino-6,6,6-trifluoro-5-hydroxyhexyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=[NH2+])[C@H](O)C(F)(F)F
#
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
 M9P  M9P  amino{[(4S,5S)-4-amino-6,6,6-trifluoro-5-hydroxyhexyl]amino}methaniminium  ligand  31  15  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M9P
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
 M9P  N     N  NH2   0  -0.788  -1.1186   1.5876   0.5554
 M9P  F1    F  F     0  -0.317  -3.7254   0.4740  -1.2176
 M9P  F2    F  F     0  -0.310  -3.9470   0.9569   0.8732
 M9P  F3    F  F     0  -0.308  -4.6220  -0.9392   0.1336
 M9P  CA    C  CH1   0  -0.162  -1.0817   0.2666  -0.0364
 M9P  CB    C  CH2   0  -0.414   0.2230  -0.4228   0.3707
 M9P  CD    C  CH2   0  -0.274   2.7323  -0.3762   0.2676
 M9P  NE    N  NH1   0  -0.636   3.8790   0.3455  -0.2598
 M9P  CG    C  CH2   0  -0.469   1.4461   0.2902  -0.1872
 M9P  CI    C  CH1   0  -0.168  -2.2750  -0.6589   0.3026
 M9P  CZ    C  C     0   0.827   5.1410  -0.0212  -0.0866
 M9P  NH1   N  NH2   0  -0.817   5.4316  -1.1303   0.5797
 M9P  NH2   N  NC2   1  -0.823   6.1205   0.7327  -0.5707
 M9P  OI2   O  OH1   0  -0.651  -2.2009  -1.8863  -0.3700
 M9P  HN    H  HNH2  0   0.355  -1.8340   2.1742   0.1511
 M9P  HA    H  HCH1  0   0.245  -1.0696   0.4018  -1.1249
 M9P  HNE   H  HNH1  0   0.426   3.7078   1.2230  -0.7255
 M9P  HNH1  H  HNH2  0   0.447   4.7145  -1.7408   0.9323
 M9P  HNHA  H  HNH2  0   0.434   6.3805  -1.4548   0.6568
 M9P  HNH2  H  HNC2  0   0.431   7.0842   0.4603  -0.4801
 M9P  HB    H  HCH2  0   0.228   0.2781  -0.4522   1.4650
 M9P  HBA   H  HCH2  0   0.240   0.2246  -1.4609   0.0341
 M9P  HD    H  HCH2  0   0.255   2.7560  -1.4106  -0.0855
 M9P  HDA   H  HCH2  0   0.256   2.7758  -0.3968   1.3607
 M9P  HG    H  HCH2  0   0.240   1.4046   0.2870  -1.2807
 M9P  HGA   H  HCH2  0   0.248   1.4387   1.3340   0.1323
 M9P  HOI2  H  HOH1  0   0.456  -1.9984  -1.7322  -1.3002
 M9P  HNA   H  HNH2  0   0.346  -1.2901   1.5394   1.5519
 M9P  HI    H  HCH1  0   0.272  -2.2511  -0.8853   1.3746
 M9P  HNHB  H  HNC2  0   0.432   5.9243   1.5599  -1.1078
 M9P  CF    C  CT    0   0.999  -3.6436  -0.0334   0.0237

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
 M9P  N     HN    single  0.890  0.020  1.040
 M9P  N     HNA   single  0.890  0.020  1.040
 M9P  F1    CF    single  1.344  0.020  1.344
 M9P  F2    CF    single  1.340  0.020  1.340
 M9P  CA    N     single  1.448  0.020  1.448
 M9P  CA    HA    single  0.970  0.020  1.090
 M9P  CB    CA    single  1.531  0.020  1.531
 M9P  CB    HBA   single  0.970  0.020  1.090
 M9P  CD    NE    single  1.454  0.020  1.454
 M9P  CD    CG    single  1.518  0.020  1.518
 M9P  NE    HNE   single  0.860  0.020  1.020
 M9P  CF    F3    single  1.338  0.020  1.338
 M9P  CG    CB    single  1.522  0.020  1.522
 M9P  CG    HG    single  0.970  0.020  1.090
 M9P  CI    CA    single  1.548  0.020  1.548
 M9P  CI    CF    single  1.530  0.020  1.530
 M9P  CI    HI    single  0.970  0.020  1.090
 M9P  CZ    NE    single  1.325  0.020  1.325
 M9P  CZ    NH1   single  1.326  0.020  1.326
 M9P  NH1   HNH1  single  0.860  0.020  1.020
 M9P  NH2   CZ    double  1.327  0.020  1.327
 M9P  NH2   HNHB  single  0.860  0.020  1.020
 M9P  OI2   CI    single  1.402  0.020  1.402
 M9P  HNHA  NH1   single  0.860  0.020  1.020
 M9P  HNH2  NH2   single  0.860  0.020  1.020
 M9P  HB    CB    single  0.970  0.020  1.090
 M9P  HD    CD    single  0.970  0.020  1.090
 M9P  HDA   CD    single  0.970  0.020  1.090
 M9P  HGA   CG    single  0.970  0.020  1.090
 M9P  HOI2  OI2   single  0.850  0.020  0.980

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
 M9P  HNA   N    HN    107.57  3.000
 M9P  HNA   N    CA    111.30  3.000
 M9P  HN    N    CA    112.61  3.000
 M9P  HA    CA   CI    107.43  3.000
 M9P  CI    CA   CB    109.25  3.000
 M9P  HA    CA   CB    108.06  3.000
 M9P  CI    CA   N     115.87  3.000
 M9P  CB    CA   N     108.90  3.000
 M9P  HA    CA   N     107.06  3.000
 M9P  HBA   CB   HB    106.40  3.000
 M9P  HB    CB   CG    109.77  3.000
 M9P  HBA   CB   CG    109.36  3.000
 M9P  HB    CB   CA    108.69  3.000
 M9P  CG    CB   CA    112.12  3.000
 M9P  HBA   CB   CA    110.34  3.000
 M9P  HDA   CD   HD    107.70  3.000
 M9P  HDA   CD   CG    109.95  3.000
 M9P  HD    CD   CG    109.68  3.000
 M9P  HDA   CD   NE    109.90  3.000
 M9P  HD    CD   NE    109.60  3.000
 M9P  CG    CD   NE    109.97  3.000
 M9P  HNE   NE   CZ    117.57  3.000
 M9P  CZ    NE   CD    124.48  3.000
 M9P  HNE   NE   CD    117.76  3.000
 M9P  HGA   CG   HG    107.17  3.000
 M9P  HGA   CG   CD    109.74  3.000
 M9P  HG    CG   CD    109.28  3.000
 M9P  HGA   CG   CB    109.59  3.000
 M9P  HG    CG   CB    109.54  3.000
 M9P  CD    CG   CB    111.43  3.000
 M9P  HI    CI   OI2   106.70  3.000
 M9P  OI2   CI   CF    108.53  3.000
 M9P  HI    CI   CF    106.39  3.000
 M9P  OI2   CI   CA    112.19  3.000
 M9P  HI    CI   CA    108.72  3.000
 M9P  CF    CI   CA    113.90  3.000
 M9P  NH2   CZ   NH1   119.77  3.000
 M9P  NH2   CZ   NE    119.85  3.000
 M9P  NH1   CZ   NE    120.38  3.000
 M9P  HNHA  NH1  HNH1  116.75  3.000
 M9P  HNHA  NH1  CZ    121.00  3.000
 M9P  HNH1  NH1  CZ    121.84  3.000
 M9P  HNHB  NH2  HNH2  117.25  3.000
 M9P  HNH2  NH2  CZ    121.37  3.000
 M9P  HNHB  NH2  CZ    121.20  3.000
 M9P  HOI2  OI2  CI    109.52  3.000
 M9P  CI    CF   F3    111.24  3.000
 M9P  CI    CF   F2    112.90  3.000
 M9P  F3    CF   F2    106.43  3.000
 M9P  CI    CF   F1    112.16  3.000
 M9P  F3    CF   F1    106.68  3.000
 M9P  F2    CF   F1    107.03  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
 M9P  CONST_01  NH1   CZ   NE  CD      0.00   0.0  0
 M9P  CONST_02  NH2   CZ   NE  CD    180.00   0.0  0
 M9P  CONST_03  HNH1  NH1  CZ  NE      0.00   0.0  0
 M9P  CONST_04  HNHA  NH1  CZ  NE    180.00   0.0  0
 M9P  CONST_05  HNHB  NH2  CZ  NE      0.00   0.0  0
 M9P  CONST_06  HNH2  NH2  CZ  NE    180.00   0.0  0
 M9P  CONST_07  HNE   NE   CZ  NH1   180.00   0.0  0
 M9P  Var_01    CD    CG   CB  CA    177.92  30.0  1
 M9P  Var_02    NE    CD   CG  CB   -178.82  30.0  1
 M9P  Var_03    CZ    NE   CD  CG   -177.03  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
 M9P  chir_01  CA  N    CB  CI  negativ
 M9P  chir_02  CI  OI2  CA  CF  negativ

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
 M9P  plan-1  CD    0.020
 M9P  plan-1  NE    0.020
 M9P  plan-1  CZ    0.020
 M9P  plan-1  NH1   0.020
 M9P  plan-1  NH2   0.020
 M9P  plan-1  HNE   0.020
 M9P  plan-1  HNH1  0.020
 M9P  plan-1  HNHA  0.020
 M9P  plan-1  HNH2  0.020
 M9P  plan-1  HNHB  0.020

