# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:56:01 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2-methyl-3-naphthalen-1-ylpropanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Cc1cccc2ccccc12)C=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
 NPD  NPD  (2S)-2-methyl-3-naphthalen-1-ylpropanal  ligand  29  15  .  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_NPD
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
 NPD  CN    C  CH3   0  -0.664   1.1289   1.2493   2.5418
 NPD  CA    C  CH1   0  -0.364  -0.0494   0.3021   2.3209
 NPD  CB    C  CH2   0  -0.556   0.3476  -0.9344   1.4860
 NPD  CG    C  CR6   0   0.128   0.7961  -0.5846   0.0947
 NPD  CD1   C  CR16  0  -0.330   2.1350  -0.5652  -0.2063
 NPD  CE1   C  CR16  0  -0.243   2.6027  -0.2115  -1.4877
 NPD  CZ1   C  CR16  0  -0.335   1.7176   0.1217  -2.4729
 NPD  CE2   C  CR66  0   0.114   0.3266   0.1074  -2.2162
 NPD  CZ2   C  CR16  0  -0.311  -0.6045   0.4382  -3.2290
 NPD  CH2   C  CR16  0  -0.261  -1.9493   0.4156  -2.9827
 NPD  CZ3   C  CR16  0  -0.251  -2.4227   0.0559  -1.7053
 NPD  CE3   C  CR16  0  -0.338  -1.5452  -0.2664  -0.7051
 NPD  CD2   C  CR66  0   0.086  -0.1455  -0.2501  -0.9234
 NPD  C     C  C1    0   0.204  -0.5352  -0.1787   3.6579
 NPD  O     O  O     0  -0.374  -1.6491  -0.0272   4.0934
 NPD  HCN1  H  HCH3  0   0.230   1.9523   0.7436   3.0498
 NPD  HCN2  H  HCH3  0   0.252   1.5058   1.6250   1.5918
 NPD  HCN3  H  HCH3  0   0.248   0.8362   2.1088   3.1455
 NPD  HA    H  HCH1  0   0.262  -0.8665   0.8381   1.8313
 NPD  HB1   H  HCH2  0   0.268   1.1586  -1.4605   1.9970
 NPD  HB2   H  HCH2  0   0.268  -0.4923  -1.6333   1.4517
 NPD  HD11  H  HCR6  0   0.252   2.8535  -0.8243   0.5624
 NPD  HE11  H  HCR6  0   0.257   3.6672  -0.2057  -1.6830
 NPD  HZ11  H  HCR6  0   0.255   2.0680   0.3993  -3.4597
 NPD  HZ21  H  HCR6  0   0.255  -0.2326   0.7115  -4.2092
 NPD  HH21  H  HCR6  0   0.258  -2.6518   0.6689  -3.7660
 NPD  HZ31  H  HCR6  0   0.259  -3.4880   0.0330  -1.5147
 NPD  HE31  H  HCR6  0   0.248  -1.9373  -0.5470   0.2631
 NPD  HC    H  H     0   0.181   0.2350  -0.7097   4.2510

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
 NPD  CN   CA    single    1.528  0.020  1.528
 NPD  CN   HCN1  single    0.970  0.020  1.090
 NPD  CN   HCN2  single    0.970  0.020  1.090
 NPD  CN   HCN3  single    0.970  0.020  1.090
 NPD  CA   CB    single    1.544  0.020  1.544
 NPD  CA   C     single    1.502  0.020  1.502
 NPD  CA   HA    single    0.970  0.020  1.090
 NPD  CB   CG    single    1.503  0.020  1.503
 NPD  CB   HB1   single    0.970  0.020  1.090
 NPD  CB   HB2   single    0.970  0.020  1.090
 NPD  CG   CD1   aromatic  1.372  0.020  1.372
 NPD  CG   CD2   aromatic  1.427  0.020  1.427
 NPD  CD1  CE1   aromatic  1.409  0.020  1.409
 NPD  CD1  HD11  single    0.930  0.020  1.080
 NPD  CE1  CZ1   aromatic  1.366  0.020  1.366
 NPD  CE1  HE11  single    0.930  0.020  1.080
 NPD  CZ1  CE2   aromatic  1.415  0.020  1.415
 NPD  CZ1  HZ11  single    0.930  0.020  1.080
 NPD  CE2  CZ2   aromatic  1.415  0.020  1.415
 NPD  CE2  CD2   aromatic  1.422  0.020  1.422
 NPD  CZ2  CH2   aromatic  1.367  0.020  1.367
 NPD  CZ2  HZ21  single    0.930  0.020  1.080
 NPD  CH2  CZ3   aromatic  1.409  0.020  1.409
 NPD  CH2  HH21  single    0.930  0.020  1.080
 NPD  CZ3  CE3   aromatic  1.369  0.020  1.369
 NPD  CZ3  HZ31  single    0.930  0.020  1.080
 NPD  CE3  CD2   aromatic  1.417  0.020  1.417
 NPD  CE3  HE31  single    0.930  0.020  1.080
 NPD  C    O     double    1.206  0.020  1.206
 NPD  C    HC    single    0.930  0.020  1.080

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
 NPD  HCN3  CN   HCN2  107.70  3.000
 NPD  HCN3  CN   HCN1  108.06  3.000
 NPD  HCN2  CN   HCN1  107.75  3.000
 NPD  HCN3  CN   CA    111.20  3.000
 NPD  HCN2  CN   CA    110.77  3.000
 NPD  HCN1  CN   CA    111.21  3.000
 NPD  HA    CA   C     108.30  3.000
 NPD  HA    CA   CB    110.04  3.000
 NPD  C     CA   CB    107.95  3.000
 NPD  HA    CA   CN    109.72  3.000
 NPD  C     CA   CN    108.62  3.000
 NPD  CB    CA   CN    112.11  3.000
 NPD  HB2   CB   HB1   106.07  3.000
 NPD  HB2   CB   CG    110.42  3.000
 NPD  HB1   CB   CG    108.86  3.000
 NPD  HB2   CB   CA    109.36  3.000
 NPD  HB1   CB   CA    108.87  3.000
 NPD  CG    CB   CA    113.01  3.000
 NPD  CD2   CG   CD1   118.95  3.000
 NPD  CD2   CG   CB    121.21  3.000
 NPD  CD1   CG   CB    119.83  3.000
 NPD  HD11  CD1  CE1   119.01  3.000
 NPD  HD11  CD1  CG    119.20  3.000
 NPD  CE1   CD1  CG    121.79  3.000
 NPD  HE11  CE1  CZ1   120.39  3.000
 NPD  HE11  CE1  CD1   119.47  3.000
 NPD  CZ1   CE1  CD1   120.14  3.000
 NPD  HZ11  CZ1  CE2   119.07  3.000
 NPD  HZ11  CZ1  CE1   120.67  3.000
 NPD  CE2   CZ1  CE1   120.26  3.000
 NPD  CD2   CE2  CZ2   119.41  3.000
 NPD  CD2   CE2  CZ1   119.61  3.000
 NPD  CZ2   CE2  CZ1   120.98  3.000
 NPD  HZ21  CZ2  CH2   120.31  3.000
 NPD  HZ21  CZ2  CE2   118.73  3.000
 NPD  CH2   CZ2  CE2   120.96  3.000
 NPD  HH21  CH2  CZ3   119.86  3.000
 NPD  HH21  CH2  CZ2   120.28  3.000
 NPD  CZ3   CH2  CZ2   119.86  3.000
 NPD  HZ31  CZ3  CE3   119.81  3.000
 NPD  HZ31  CZ3  CH2   119.71  3.000
 NPD  CE3   CZ3  CH2   120.47  3.000
 NPD  HE31  CE3  CD2   119.94  3.000
 NPD  HE31  CE3  CZ3   118.86  3.000
 NPD  CD2   CE3  CZ3   121.20  3.000
 NPD  CE3   CD2  CE2   118.10  3.000
 NPD  CE3   CD2  CG    122.65  3.000
 NPD  CE2   CD2  CG    119.25  3.000
 NPD  HC    C    O     120.62  3.000
 NPD  HC    C    CA    113.91  3.000
 NPD  O     C    CA    125.48  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
 NPD  CONST_01  CZ1   CE1  CD1  CG     0.00   0.0  0
 NPD  CONST_02  CZ1   CE2  CD2  CG     0.00   0.0  0
 NPD  CONST_03  CZ2   CE2  CD2  CG   180.00   0.0  0
 NPD  CONST_04  CZ3   CE3  CD2  CG   180.00   0.0  0
 NPD  CONST_05  CE2   CD2  CG   CD1    0.00   0.0  0
 NPD  CONST_06  CE3   CD2  CG   CD1  180.00   0.0  0
 NPD  CONST_07  CE2   CZ1  CE1  CD1    0.00   0.0  0
 NPD  CONST_08  CD2   CG   CD1  CE1    0.00   0.0  0
 NPD  CONST_09  CZ2   CE2  CZ1  CE1  180.00   0.0  0
 NPD  CONST_10  CD2   CE2  CZ1  CE1    0.00   0.0  0
 NPD  CONST_11  CH2   CZ2  CE2  CZ1  180.00   0.0  0
 NPD  CONST_12  CE3   CD2  CE2  CZ1  180.00   0.0  0
 NPD  CONST_13  CZ3   CH2  CZ2  CE2    0.00   0.0  0
 NPD  CONST_14  CZ3   CE3  CD2  CE2    0.00   0.0  0
 NPD  CONST_15  CE3   CD2  CE2  CZ2    0.00   0.0  0
 NPD  CONST_16  CE3   CZ3  CH2  CZ2    0.00   0.0  0
 NPD  CONST_17  CD2   CE2  CZ2  CH2    0.00   0.0  0
 NPD  CONST_18  CD2   CE3  CZ3  CH2    0.00   0.0  0
 NPD  CONST_19  CE1   CD1  CG   CB   180.00   0.0  0
 NPD  CONST_20  CE2   CD2  CG   CB   180.00   0.0  0
 NPD  CONST_21  CE3   CD2  CG   CB     0.00   0.0  0
 NPD  CONST_22  HE11  CE1  CD1  CG   180.00   0.0  0
 NPD  CONST_23  HE31  CE3  CD2  CG     0.00   0.0  0
 NPD  CONST_24  HZ11  CZ1  CE1  CD1  180.00   0.0  0
 NPD  CONST_25  HD11  CD1  CE1  CZ1  180.00   0.0  0
 NPD  CONST_26  HZ21  CZ2  CE2  CZ1    0.00   0.0  0
 NPD  CONST_27  HH21  CH2  CZ2  CE2  180.00   0.0  0
 NPD  CONST_28  HZ31  CZ3  CH2  CZ2  180.00   0.0  0
 NPD  Var_01    CD1   CG   CB   CA   101.83  30.0  2

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
 NPD  chir_01  CA  CN  CB  C  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
 NPD  plan-1  CB    0.020
 NPD  plan-1  CG    0.020
 NPD  plan-1  CD1   0.020
 NPD  plan-1  CE1   0.020
 NPD  plan-1  CZ1   0.020
 NPD  plan-1  CE2   0.020
 NPD  plan-1  CZ2   0.020
 NPD  plan-1  CH2   0.020
 NPD  plan-1  CZ3   0.020
 NPD  plan-1  CE3   0.020
 NPD  plan-1  CD2   0.020
 NPD  plan-1  HD11  0.020
 NPD  plan-1  HE11  0.020
 NPD  plan-1  HZ11  0.020
 NPD  plan-1  HZ21  0.020
 NPD  plan-1  HH21  0.020
 NPD  plan-1  HZ31  0.020
 NPD  plan-1  HE31  0.020
 NPD  plan-2  CA    0.020
 NPD  plan-2  C     0.020
 NPD  plan-2  O     0.020
 NPD  plan-2  HC    0.020

