# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:49:12 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (3-chloranyl-4-phenyl-phenyl)methyl-propyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[NH2+]Cc1ccc(c(Cl)c1)c2ccccc2
#
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
 JMB  JMB  (3-chloranyl-4-phenyl-phenyl)methyl-propyl-azanium  ligand  37  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JMB
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
 JMB  C    C   CH3   0  -0.666   7.3937  -0.0690  -0.9566
 JMB  N    N   NT2   1  -0.657   3.6719   0.1820  -0.1080
 JMB  C8   C   CR6   0  -0.106  -0.6463  -0.7881   0.5892
 JMB  C7   C   CR6   0   0.152  -1.3247   0.3644   0.1920
 JMB  C10  C   CR6   0   0.058  -2.7634   0.3822  -0.1499
 JMB  C15  C   CR16  0  -0.281  -3.2673  -0.3980  -1.1897
 JMB  C14  C   CR16  0  -0.243  -4.6110  -0.3341  -1.5262
 JMB  C13  C   CR16  0  -0.260  -5.4687   0.5042  -0.8244
 JMB  C12  C   CR16  0  -0.242  -4.9741   1.2841   0.2116
 JMB  C11  C   CR16  0  -0.289  -3.6276   1.2261   0.5446
 JMB  C6   C   CR16  0  -0.295  -0.5924   1.5504   0.1376
 JMB  C5   C   CR16  0  -0.257   0.7554   1.5870   0.4497
 JMB  C9   C   CR16  0  -0.220   0.7032  -0.7671   0.9036
 JMB  C4   C   CR6   0   0.057   1.4140   0.4238   0.8299
 JMB  C3   C   CH2   0  -0.382   2.8811   0.4431   1.1310
 JMB  C2   C   CH2   0  -0.283   5.1463   0.1858   0.1049
 JMB  C1   C   CH2   0  -0.464   5.8891  -0.1005  -1.1848
 JMB  H1   H   HCH3  0   0.231   7.6973  -0.8059  -0.2122
 JMB  H2   H   HCH3  0   0.246   7.9254  -0.2920  -1.8804
 JMB  H3   H   HCH3  0   0.232   7.7214   0.9118  -0.6113
 JMB  H4   H   HNT2  0   0.469   3.3895  -0.7175  -0.5016
 JMB  H5   H   HNT2  0   0.469   3.4314   0.8776  -0.8171
 JMB  H6   H   HCR6  0   0.257  -2.6046  -1.0454  -1.7494
 JMB  H7   H   HCR6  0   0.260  -4.9890  -0.9369  -2.3418
 JMB  H8   H   HCR6  0   0.260  -6.5173   0.5513  -1.0875
 JMB  H9   H   HCR6  0   0.260  -5.6349   1.9407   0.7622
 JMB  H10  H   HCR6  0   0.258  -3.2465   1.8329   1.3567
 JMB  H11  H   HCR6  0   0.271  -1.0936   2.4597  -0.1674
 JMB  H12  H   HCR6  0   0.272   1.2932   2.5256   0.3988
 JMB  H13  H   HCR6  0   0.288   1.1955  -1.6777   1.2207
 JMB  H14  H   HCH2  0   0.320   3.1607  -0.3245   1.8498
 JMB  H15  H   HCH2  0   0.320   3.2002   1.4117   1.5110
 JMB  H16  H   HCH2  0   0.292   5.4016   1.1658   0.5056
 JMB  H17  H   HCH2  0   0.292   5.3551  -0.5661   0.8644
 JMB  H18  H   HCH2  0   0.249   5.6137   0.6391  -1.9407
 JMB  H19  H   HCH2  0   0.249   5.5943  -1.0794  -1.5707
 JMB  CL   CL  CL    0  -0.115  -1.4906  -2.2912   0.7525

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
 JMB  C14  C15  aromatic  1.387  0.020  1.387
 JMB  C14  C13  aromatic  1.390  0.020  1.390
 JMB  C15  C10  aromatic  1.394  0.020  1.394
 JMB  CL   C8   single    1.732  0.020  1.732
 JMB  C13  C12  aromatic  1.388  0.020  1.388
 JMB  C10  C7   single    1.479  0.020  1.479
 JMB  C10  C11  aromatic  1.393  0.020  1.393
 JMB  C12  C11  aromatic  1.388  0.020  1.388
 JMB  C8   C7   aromatic  1.395  0.020  1.395
 JMB  C8   C9   aromatic  1.386  0.020  1.386
 JMB  C7   C6   aromatic  1.395  0.020  1.395
 JMB  C9   C4   aromatic  1.389  0.020  1.389
 JMB  C6   C5   aromatic  1.384  0.020  1.384
 JMB  C4   C5   aromatic  1.390  0.020  1.390
 JMB  C4   C3   single    1.498  0.020  1.498
 JMB  N    C3   single    1.493  0.020  1.493
 JMB  N    C2   single    1.490  0.020  1.490
 JMB  C1   C2   single    1.516  0.020  1.516
 JMB  C1   C    single    1.522  0.020  1.522
 JMB  C    H1   single    0.970  0.020  1.090
 JMB  C    H2   single    0.970  0.020  1.090
 JMB  C    H3   single    0.970  0.020  1.090
 JMB  N    H4   single    0.890  0.020  1.040
 JMB  N    H5   single    0.890  0.020  1.040
 JMB  C15  H6   single    0.930  0.020  1.080
 JMB  C14  H7   single    0.930  0.020  1.080
 JMB  C13  H8   single    0.930  0.020  1.080
 JMB  C12  H9   single    0.930  0.020  1.080
 JMB  C11  H10  single    0.930  0.020  1.080
 JMB  C6   H11  single    0.930  0.020  1.080
 JMB  C5   H12  single    0.930  0.020  1.080
 JMB  C9   H13  single    0.930  0.020  1.080
 JMB  C3   H14  single    0.970  0.020  1.090
 JMB  C3   H15  single    0.970  0.020  1.090
 JMB  C2   H16  single    0.970  0.020  1.090
 JMB  C2   H17  single    0.970  0.020  1.090
 JMB  C1   H18  single    0.970  0.020  1.090
 JMB  C1   H19  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
 JMB  H3   C    H2   107.82  3.000
 JMB  H3   C    H1   107.94  3.000
 JMB  H2   C    H1   107.74  3.000
 JMB  H3   C    C1   111.29  3.000
 JMB  H2   C    C1   110.56  3.000
 JMB  H1   C    C1   111.32  3.000
 JMB  H5   N    H4   105.48  3.000
 JMB  H5   N    C2   109.29  3.000
 JMB  H4   N    C2   109.32  3.000
 JMB  H5   N    C3   109.39  3.000
 JMB  H4   N    C3   109.11  3.000
 JMB  C2   N    C3   113.91  3.000
 JMB  C9   C8   C7   121.71  3.000
 JMB  C9   C8   CL   117.81  3.000
 JMB  C7   C8   CL   120.45  3.000
 JMB  C6   C7   C10  119.44  3.000
 JMB  C6   C7   C8   117.27  3.000
 JMB  C10  C7   C8   123.28  3.000
 JMB  C11  C10  C15  119.11  3.000
 JMB  C11  C10  C7   119.70  3.000
 JMB  C15  C10  C7   121.15  3.000
 JMB  H6   C15  C14  119.69  3.000
 JMB  H6   C15  C10  119.94  3.000
 JMB  C14  C15  C10  120.36  3.000
 JMB  H7   C14  C13  120.07  3.000
 JMB  H7   C14  C15  119.71  3.000
 JMB  C13  C14  C15  120.22  3.000
 JMB  H8   C13  C12  120.16  3.000
 JMB  H8   C13  C14  120.10  3.000
 JMB  C12  C13  C14  119.74  3.000
 JMB  H9   C12  C11  119.72  3.000
 JMB  H9   C12  C13  120.21  3.000
 JMB  C11  C12  C13  120.08  3.000
 JMB  H10  C11  C12  119.85  3.000
 JMB  H10  C11  C10  119.66  3.000
 JMB  C12  C11  C10  120.49  3.000
 JMB  H11  C6   C5   119.49  3.000
 JMB  H11  C6   C7   118.83  3.000
 JMB  C5   C6   C7   121.67  3.000
 JMB  H12  C5   C4   120.20  3.000
 JMB  H12  C5   C6   119.73  3.000
 JMB  C4   C5   C6   120.07  3.000
 JMB  H13  C9   C4   120.27  3.000
 JMB  H13  C9   C8   119.77  3.000
 JMB  C4   C9   C8   119.96  3.000
 JMB  C3   C4   C9   120.11  3.000
 JMB  C3   C4   C5   120.56  3.000
 JMB  C9   C4   C5   119.32  3.000
 JMB  H15  C3   H14  108.77  3.000
 JMB  H15  C3   C4   111.65  3.000
 JMB  H14  C3   C4   112.05  3.000
 JMB  H15  C3   N    106.87  3.000
 JMB  H14  C3   N    106.78  3.000
 JMB  C4   C3   N    110.47  3.000
 JMB  H17  C2   H16  108.65  3.000
 JMB  H17  C2   C1   111.66  3.000
 JMB  H16  C2   C1   111.60  3.000
 JMB  H17  C2   N    106.72  3.000
 JMB  H16  C2   N    106.67  3.000
 JMB  C1   C2   N    111.29  3.000
 JMB  H19  C1   H18  107.09  3.000
 JMB  H19  C1   C2   109.73  3.000
 JMB  H18  C1   C2   109.71  3.000
 JMB  H19  C1   C    109.76  3.000
 JMB  H18  C1   C    109.80  3.000
 JMB  C2   C1   C    110.67  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
 JMB  CONST_03  C5   C6   C7   C8     0.00   0.0  0
 JMB  CONST_04  C5   C4   C9   C8     0.00   0.0  0
 JMB  CONST_05  C14  C15  C10  C7   180.00   0.0  0
 JMB  CONST_06  C12  C11  C10  C7   180.00   0.0  0
 JMB  CONST_07  C4   C9   C8   C7     0.00   0.0  0
 JMB  CONST_08  C4   C5   C6   C7     0.00   0.0  0
 JMB  CONST_09  C13  C14  C15  C10    0.00   0.0  0
 JMB  CONST_10  C9   C8   C7   C10  180.00   0.0  0
 JMB  CONST_11  C5   C6   C7   C10  180.00   0.0  0
 JMB  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 JMB  CONST_13  C12  C13  C14  C15    0.00   0.0  0
 JMB  CONST_15  C12  C11  C10  C15    0.00   0.0  0
 JMB  CONST_16  C11  C10  C15  C14    0.00   0.0  0
 JMB  CONST_17  C11  C12  C13  C14    0.00   0.0  0
 JMB  CONST_19  C9   C8   C7   C6     0.00   0.0  0
 JMB  CONST_20  C9   C4   C5   C6     0.00   0.0  0
 JMB  CONST_21  C10  C7   C8   CL     0.00   0.0  0
 JMB  CONST_22  C6   C7   C8   CL   180.00   0.0  0
 JMB  CONST_23  C4   C9   C8   CL   180.00   0.0  0
 JMB  CONST_24  C3   C4   C9   C8   180.00   0.0  0
 JMB  CONST_25  C3   C4   C5   C6   180.00   0.0  0
 JMB  CONST_26  H11  C6   C7   C8   180.00   0.0  0
 JMB  CONST_27  H6   C15  C10  C7     0.00   0.0  0
 JMB  CONST_28  H10  C11  C10  C7     0.00   0.0  0
 JMB  CONST_29  H13  C9   C8   C7   180.00   0.0  0
 JMB  CONST_30  H12  C5   C6   C7   180.00   0.0  0
 JMB  CONST_31  H7   C14  C15  C10  180.00   0.0  0
 JMB  CONST_32  H9   C12  C11  C10  180.00   0.0  0
 JMB  CONST_33  H8   C13  C14  C15  180.00   0.0  0
 JMB  Var_01    C9   C4   C3   N     89.27  30.0  2
 JMB  Var_02    C2   N    C3   C4   179.92  30.0  1
 JMB  Var_03    N    C2   C1   C    179.01  30.0  3
 JMB  Var_04    C1   C2   N    C3   179.34  30.0  3
 JMB  Var_05    H1   C    C1   C2    59.29  30.0  3

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
 JMB  plan-1  C8   0.020
 JMB  plan-1  C7   0.020
 JMB  plan-1  C10  0.020
 JMB  plan-1  C6   0.020
 JMB  plan-1  C5   0.020
 JMB  plan-1  C9   0.020
 JMB  plan-1  C4   0.020
 JMB  plan-1  C3   0.020
 JMB  plan-1  H11  0.020
 JMB  plan-1  H12  0.020
 JMB  plan-1  H13  0.020
 JMB  plan-1  CL   0.020
 JMB  plan-2  C7   0.020
 JMB  plan-2  C10  0.020
 JMB  plan-2  C15  0.020
 JMB  plan-2  C14  0.020
 JMB  plan-2  C13  0.020
 JMB  plan-2  C12  0.020
 JMB  plan-2  C11  0.020
 JMB  plan-2  H6   0.020
 JMB  plan-2  H7   0.020
 JMB  plan-2  H8   0.020
 JMB  plan-2  H9   0.020
 JMB  plan-2  H10  0.020

