# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 14:13:46 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: N-[3-(2,4-dichlorophenoxy)propyl]-N-methylprop-2-yn-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCCOc1ccc(Cl)cc1Cl)CC#C
#
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
 MLG  MLG  N-[3-(2,4-dichlorophenoxy)propyl]-N-methylprop-2-yn-1-amine  ligand  32  17  .  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_MLG
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
 MLG  C06   C   CR16   0  -0.395  -1.3322   0.0501  -1.8640
 MLG  C05   C   CR16   0  -0.193  -1.6940   0.1077  -3.2029
 MLG  C04   C   CR6    0  -0.073  -0.7148   0.1746  -4.1760
 MLG  CL08  CL  CL     0  -0.126  -1.1584   0.2455  -5.8490
 MLG  C03   C   CR16   0  -0.163   0.6280   0.1863  -3.8293
 MLG  C02   C   CR6    0  -0.163   0.9754   0.1281  -2.4934
 MLG  CL07  CL  CL     0  -0.099   2.6426   0.1436  -2.0470
 MLG  C01   C   CR6    0   0.474   0.0072   0.0572  -1.4848
 MLG  O09   O   O2     0  -0.456   0.4496   0.0008  -0.2251
 MLG  C11   C   CH2    0  -0.484   0.2692  -0.1163   2.1400
 MLG  C10   C   CH2    0  -0.174  -0.4963  -0.0339   0.8357
 MLG  C12   C   CH2    0  -0.268  -0.7013  -0.1519   3.3137
 MLG  N13   N   NT    -1  -0.417  -0.0382  -0.0798   4.6054
 MLG  C17   C   CH3    0  -0.540   0.7459  -1.2658   4.8902
 MLG  C14   C   CH2    0  -0.408  -1.0197   0.1644   5.6491
 MLG  C15   C   CSP    0   0.278  -0.4029   0.4869   6.9339
 MLG  C16   C   CSP1   0  -0.555   0.0890   0.7548   7.9974
 MLG  H06   H   HCR6   0   0.301  -2.1185   0.0002  -1.1244
 MLG  H05   H   HCR6   0   0.288  -2.7413   0.0998  -3.4718
 MLG  H03   H   HCR6   0   0.301   1.3971   0.2401  -4.5871
 MLG  H111  H   HCH2   0   0.245   0.8980  -1.0089   2.1236
 MLG  H112  H   HCH2   0   0.242   0.9267   0.7505   2.2411
 MLG  H101  H   HCH2   0   0.231  -1.1579  -0.9008   0.7260
 MLG  H102  H   HCH2   0   0.231  -1.1205   0.8665   0.8108
 MLG  H121  H   HCH2   0   0.201  -1.3413  -1.0480   3.2366
 MLG  H122  H   HCH2   0   0.238  -1.3693   0.7107   3.2353
 MLG  H171  H   HCH3   0   0.245   1.2274  -1.1736   5.8637
 MLG  H172  H   HCH3   0   0.199   0.1413  -2.1861   4.8993
 MLG  H173  H   HCH3   0   0.245   1.5379  -1.3893   4.1538
 MLG  H141  H   HCH2   0   0.278  -1.6451   1.0104   5.3523
 MLG  H142  H   HCH2   0   0.239  -1.7047  -0.6887   5.7910
 MLG  H16   H   H      0   0.279   0.5248   0.9902   8.9415

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
 MLG  C06  C05   aromatic  1.388  0.020  1.388
 MLG  C06  C01   aromatic  1.392  0.020  1.392
 MLG  C06  H06   single    0.929  0.020  1.085
 MLG  C05  C04   aromatic  1.382  0.020  1.382
 MLG  C05  H05   single    0.929  0.020  1.085
 MLG  C04  CL08  single    1.732  0.020  1.732
 MLG  C04  C03   aromatic  1.387  0.020  1.387
 MLG  C03  C02   aromatic  1.382  0.020  1.382
 MLG  C03  H03   single    0.929  0.020  1.085
 MLG  C02  CL07  single    1.726  0.020  1.726
 MLG  C02  C01   aromatic  1.400  0.020  1.400
 MLG  C01  O09   single    1.336  0.020  1.336
 MLG  O09  C10   single    1.422  0.020  1.422
 MLG  C11  C10   single    1.515  0.020  1.515
 MLG  C11  C12   single    1.523  0.020  1.523
 MLG  C11  H111  single    0.939  0.020  1.096
 MLG  C11  H112  single    0.939  0.020  1.096
 MLG  C10  H101  single    0.939  0.020  1.096
 MLG  C10  H102  single    0.939  0.020  1.096
 MLG  C12  N13   single    1.454  0.020  1.454
 MLG  C12  H121  single    0.939  0.020  1.096
 MLG  C12  H122  single    0.939  0.020  1.096
 MLG  N13  C17   single    1.450  0.020  1.450
 MLG  N13  C14   single    1.453  0.020  1.453
 MLG  C17  H171  single    0.939  0.020  1.096
 MLG  C17  H172  single    0.939  0.020  1.096
 MLG  C17  H173  single    0.939  0.020  1.096
 MLG  C14  C15   single    1.461  0.020  1.461
 MLG  C14  H141  single    0.939  0.020  1.096
 MLG  C14  H142  single    0.939  0.020  1.096
 MLG  C15  C16   triple    1.202  0.020  1.202
 MLG  C16  H16   single    0.913  0.020  1.066

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
 MLG  H06   C06  C01   120.92  3.000
 MLG  H06   C06  C05   118.19  3.000
 MLG  C01   C06  C05   120.88  3.000
 MLG  H05   C05  C04   120.76  3.000
 MLG  H05   C05  C06   119.47  3.000
 MLG  C04   C05  C06   119.77  3.000
 MLG  C03   C04  CL08  119.28  3.000
 MLG  C03   C04  C05   120.69  3.000
 MLG  CL08  C04  C05   120.03  3.000
 MLG  H03   C03  C02   120.07  3.000
 MLG  H03   C03  C04   120.93  3.000
 MLG  C02   C03  C04   119.00  3.000
 MLG  C01   C02  CL07  118.83  3.000
 MLG  C01   C02  C03   121.66  3.000
 MLG  CL07  C02  C03   119.51  3.000
 MLG  O09   C01  C02   116.89  3.000
 MLG  O09   C01  C06   125.11  3.000
 MLG  C02   C01  C06   118.00  3.000
 MLG  C10   O09  C01   118.95  3.000
 MLG  H112  C11  H111  107.66  3.000
 MLG  H112  C11  C12   109.31  3.000
 MLG  H111  C11  C12   111.05  3.000
 MLG  H112  C11  C10   109.92  3.000
 MLG  H111  C11  C10   108.82  3.000
 MLG  C12   C11  C10   110.04  3.000
 MLG  H102  C10  H101  107.69  3.000
 MLG  H102  C10  C11   110.62  3.000
 MLG  H101  C10  C11   110.38  3.000
 MLG  H102  C10  O09   110.00  3.000
 MLG  H101  C10  O09   110.26  3.000
 MLG  C11   C10  O09   107.91  3.000
 MLG  H122  C12  H121  106.32  3.000
 MLG  H122  C12  N13   107.64  3.000
 MLG  H121  C12  N13   111.52  3.000
 MLG  H122  C12  C11   108.38  3.000
 MLG  H121  C12  C11   109.55  3.000
 MLG  N13   C12  C11   113.13  3.000
 MLG  C14   N13  C17   111.20  3.000
 MLG  C14   N13  C12   109.78  3.000
 MLG  C17   N13  C12   112.37  3.000
 MLG  H173  C17  H172  108.07  3.000
 MLG  H173  C17  H171  107.00  3.000
 MLG  H172  C17  H171  107.81  3.000
 MLG  H173  C17  N13   110.69  3.000
 MLG  H172  C17  N13   112.86  3.000
 MLG  H171  C17  N13   110.19  3.000
 MLG  H142  C14  H141  106.15  3.000
 MLG  H142  C14  C15   108.64  3.000
 MLG  H141  C14  C15   108.02  3.000
 MLG  H142  C14  N13   112.44  3.000
 MLG  H141  C14  N13   108.75  3.000
 MLG  C15   C14  N13   112.55  3.000
 MLG  C16   C15  C14   180.00  3.000
 MLG  H16   C16  C15   180.00  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
 MLG  CONST_01  C03   C04  C05  C06      0.00   0.0  0
 MLG  CONST_02  C03   C02  C01  C06      0.00   0.0  0
 MLG  CONST_03  C02   C01  C06  C05      0.00   0.0  0
 MLG  CONST_04  C02   C03  C04  C05      0.00   0.0  0
 MLG  CONST_05  C01   C06  C05  C04      0.00   0.0  0
 MLG  CONST_06  C01   C02  C03  C04      0.00   0.0  0
 MLG  CONST_07  CL08  C04  C05  C06    180.00   0.0  0
 MLG  CONST_08  CL07  C02  C01  C06    180.00   0.0  0
 MLG  CONST_09  O09   C01  C06  C05    180.00   0.0  0
 MLG  CONST_10  CL07  C02  C03  C04    180.00   0.0  0
 MLG  CONST_11  C02   C03  C04  CL08   180.00   0.0  0
 MLG  CONST_12  O09   C01  C02  C03    180.00   0.0  0
 MLG  CONST_13  H03   C03  C04  C05    180.00   0.0  0
 MLG  CONST_14  H06   C06  C05  C04    180.00   0.0  0
 MLG  CONST_15  H05   C05  C04  C03    180.00   0.0  0
 MLG  Var_01    C11   C10  O09  C01    179.17  30.0  3
 MLG  Var_02    C12   C11  C10  O09    179.83  30.0  1
 MLG  Var_03    N13   C12  C11  C10   -173.50  30.0  3
 MLG  Var_04    H141  C14  C15  C16     56.29  30.0  1

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
 MLG  chir_01  N13  C12  C17  C14  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
 MLG  plan-1  C06   0.020
 MLG  plan-1  C05   0.020
 MLG  plan-1  C04   0.020
 MLG  plan-1  CL08  0.020
 MLG  plan-1  C03   0.020
 MLG  plan-1  C02   0.020
 MLG  plan-1  CL07  0.020
 MLG  plan-1  C01   0.020
 MLG  plan-1  O09   0.020
 MLG  plan-1  H06   0.020
 MLG  plan-1  H05   0.020
 MLG  plan-1  H03   0.020

