# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 02:40:45 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: benzyl (cyanomethyl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC#N)OCc1ccccc1
#
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
 3S9  3S9  'benzyl (cyanomethyl)carbamate'  ligand  24  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3S9
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
 3S9  N14  N  NS    0  -0.265   4.7482  -0.0518  -1.9148
 3S9  C13  C  CSP   0   0.126   4.3202   0.0117  -0.8498
 3S9  C12  C  CH2   0  -0.375   3.7750   0.0872   0.5119
 3S9  N11  N  NH1   0  -0.660   2.3641   0.3333   0.5272
 3S9  C9   C  C     0   0.777   1.4998  -0.6228   0.1210
 3S9  O10  O  O     0  -0.507   1.8388  -1.7324  -0.2308
 3S9  O8   O  O2    0  -0.472   0.2443  -0.1869   0.1673
 3S9  C7   C  CH2   0  -0.243  -0.7800  -1.1079  -0.2393
 3S9  C2   C  CR16  0  -0.289  -2.5831   0.3608  -1.1811
 3S9  C3   C  CR16  0  -0.242  -3.7784   1.0555  -1.0570
 3S9  C4   C  CR16  0  -0.261  -4.4870   1.0109   0.1367
 3S9  C5   C  CR16  0  -0.242  -3.9977   0.2687   1.2040
 3S9  C6   C  CR16  0  -0.288  -2.8017  -0.4244   1.0765
 3S9  C1   C  CR6   0   0.075  -2.0856  -0.3846  -0.1161
 3S9  H1   H  HCH2  0   0.318   4.0311  -0.8370   1.0312
 3S9  H2   H  HCH2  0   0.335   4.2790   0.8984   1.0346
 3S9  H3   H  HNH1  0   0.420   2.0404   1.2693   0.7101
 3S9  H4   H  HCH2  0   0.253  -0.6047  -1.4292  -1.2678
 3S9  H5   H  HCH2  0   0.253  -0.7618  -1.9903   0.4035
 3S9  H6   H  HCR6  0   0.256  -2.0363   0.3928  -2.1162
 3S9  H7   H  HCR6  0   0.259  -4.1573   1.6304  -1.8920
 3S9  H8   H  HCR6  0   0.260  -5.4201   1.5504   0.2336
 3S9  H9   H  HCR6  0   0.259  -4.5478   0.2297   2.1353
 3S9  H10  H  HCR6  0   0.256  -2.4247  -1.0058   1.9097

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
 3S9  C4   C3   aromatic  1.389  0.020  1.389
 3S9  C4   C5   aromatic  1.389  0.020  1.389
 3S9  C3   C2   aromatic  1.388  0.020  1.388
 3S9  C5   C6   aromatic  1.388  0.020  1.388
 3S9  C12  N11  single    1.432  0.020  1.432
 3S9  C12  C13  single    1.469  0.020  1.469
 3S9  N11  C9   single    1.351  0.020  1.351
 3S9  C2   C1   aromatic  1.392  0.020  1.392
 3S9  C6   C1   aromatic  1.392  0.020  1.392
 3S9  C1   C7   single    1.498  0.020  1.498
 3S9  O8   C9   single    1.330  0.020  1.330
 3S9  O8   C7   single    1.436  0.020  1.436
 3S9  C9   O10  double    1.212  0.020  1.212
 3S9  C13  N14  triple    1.150  0.020  1.150
 3S9  C12  H1   single    0.970  0.020  1.090
 3S9  C12  H2   single    0.970  0.020  1.090
 3S9  N11  H3   single    0.860  0.020  1.020
 3S9  C7   H4   single    0.970  0.020  1.090
 3S9  C7   H5   single    0.970  0.020  1.090
 3S9  C2   H6   single    0.930  0.020  1.080
 3S9  C3   H7   single    0.930  0.020  1.080
 3S9  C4   H8   single    0.930  0.020  1.080
 3S9  C5   H9   single    0.930  0.020  1.080
 3S9  C6   H10  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
 3S9  C12  C13  N14  180.00  3.000
 3S9  H2   C12  H1   107.10  3.000
 3S9  H2   C12  N11  108.84  3.000
 3S9  H1   C12  N11  111.83  3.000
 3S9  H2   C12  C13  108.15  3.000
 3S9  H1   C12  C13  108.10  3.000
 3S9  N11  C12  C13  112.60  3.000
 3S9  H3   N11  C9   120.44  3.000
 3S9  H3   N11  C12  118.57  3.000
 3S9  C9   N11  C12  120.35  3.000
 3S9  O8   C9   O10  125.04  3.000
 3S9  O10  C9   N11  123.77  3.000
 3S9  O8   C9   N11  111.19  3.000
 3S9  C7   O8   C9   116.95  3.000
 3S9  H5   C7   H4   108.30  3.000
 3S9  H5   C7   C1   110.88  3.000
 3S9  H4   C7   C1   111.07  3.000
 3S9  H5   C7   O8   109.86  3.000
 3S9  H4   C7   O8   109.94  3.000
 3S9  C1   C7   O8   106.78  3.000
 3S9  H6   C2   C1   119.71  3.000
 3S9  H6   C2   C3   119.79  3.000
 3S9  C1   C2   C3   120.49  3.000
 3S9  H7   C3   C4   120.11  3.000
 3S9  H7   C3   C2   119.89  3.000
 3S9  C4   C3   C2   120.01  3.000
 3S9  H8   C4   C5   120.08  3.000
 3S9  H8   C4   C3   120.06  3.000
 3S9  C5   C4   C3   119.86  3.000
 3S9  H9   C5   C6   119.93  3.000
 3S9  H9   C5   C4   120.09  3.000
 3S9  C6   C5   C4   119.97  3.000
 3S9  H10  C6   C1   119.68  3.000
 3S9  H10  C6   C5   119.80  3.000
 3S9  C1   C6   C5   120.52  3.000
 3S9  C6   C1   C2   119.15  3.000
 3S9  C6   C1   C7   120.35  3.000
 3S9  C2   C1   C7   120.49  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
 3S9  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 3S9  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 3S9  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 3S9  CONST_04  C6   C1   C2   C3      0.00   0.0  0
 3S9  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 3S9  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 3S9  CONST_07  C3   C2   C1   C7    180.00   0.0  0
 3S9  CONST_08  C5   C6   C1   C7    180.00   0.0  0
 3S9  CONST_09  H8   C4   C3   C2    180.00   0.0  0
 3S9  CONST_10  H10  C6   C1   C2    180.00   0.0  0
 3S9  CONST_11  H9   C5   C4   C3    180.00   0.0  0
 3S9  CONST_12  H6   C2   C3   C4    180.00   0.0  0
 3S9  CONST_13  H7   C3   C4   C5    180.00   0.0  0
 3S9  Var_01    C2   C1   C7   O8     88.72  30.0  1
 3S9  Var_02    C1   C7   O8   C9   -179.28  30.0  3
 3S9  Var_03    N11  C12  C13  N14  -118.23  30.0  1
 3S9  Var_04    C9   N11  C12  C13    70.05  30.0  3
 3S9  Var_05    O8   C9   N11  C12  -177.90  30.0  2

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
 3S9  plan-1  C7   0.020
 3S9  plan-1  C2   0.020
 3S9  plan-1  C3   0.020
 3S9  plan-1  C4   0.020
 3S9  plan-1  C5   0.020
 3S9  plan-1  C6   0.020
 3S9  plan-1  C1   0.020
 3S9  plan-1  H6   0.020
 3S9  plan-1  H7   0.020
 3S9  plan-1  H8   0.020
 3S9  plan-1  H9   0.020
 3S9  plan-1  H10  0.020
 3S9  plan-2  N11  0.020
 3S9  plan-2  C9   0.020
 3S9  plan-2  O10  0.020
 3S9  plan-2  O8   0.020

