# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:26:50 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-[(1R)-3-amino-1-phenyl-propoxy]-4-chloro-benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@@H](Oc1cc(Cl)ccc1C#N)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
 A54  A54  2-[(1R)-3-amino-1-phenyl-propoxy]-4-chloro-benzonitrile  ligand  35  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A54
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
 A54  C1    C   CR16  0  -0.263  -4.0308   0.1626   1.8755
 A54  C2    C   CR16  0  -0.240  -3.4130  -1.0683   2.0484
 A54  C3    C   CR16  0  -0.302  -2.3543  -1.4351   1.2282
 A54  C4    C   CR6   0   0.089  -1.9085  -0.5819   0.2251
 A54  C5    C   CR16  0  -0.291  -2.5349   0.6493   0.0519
 A54  C6    C   CR16  0  -0.239  -3.5880   1.0200   0.8761
 A54  C7    C   CH1   0  -0.062  -0.7910  -1.0214  -0.6883
 A54  C8    C   CH2   0  -0.444  -1.3168  -1.5533  -2.0125
 A54  C9    C   CH2   0  -0.281  -0.2336  -2.1429  -2.9067
 A54  N10   N   NH2   0  -0.801  -0.8268  -2.6727  -4.1263
 A54  O11   O   O2    0  -0.470   0.0754   0.0709  -1.0040
 A54  C12   C   CR6   0   0.453   0.8838   0.5849  -0.0804
 A54  C13   C   CR16  0  -0.309   1.0167   0.1146   1.2222
 A54  C14   C   CR6   0  -0.016   1.9096   0.7447   2.0749
 A54  C15   C   CR16  0  -0.240   2.6783   1.8315   1.6842
 A54  C16   C   CR16  0  -0.234   2.5412   2.2969   0.3905
 A54  C17   C   CR6   0  -0.119   1.6536   1.6857  -0.4905
 A54  C18   C   CSP   0   0.071   1.5147   2.1671  -1.8219
 A54  N19   N   NS    0  -0.251   1.4151   2.5688  -2.8976
 A54  CL2   CL  CL    0  -0.097   2.0597   0.1485   3.6876
 A54  H1    H   HCR6  0   0.259  -4.8520   0.4549   2.5171
 A54  H2    H   HCR6  0   0.259  -3.7504  -1.7416   2.8257
 A54  H6    H   HCR6  0   0.258  -4.0636   1.9822   0.7370
 A54  H3    H   HCR6  0   0.258  -1.8699  -2.3942   1.3741
 A54  H5    H   HCR6  0   0.255  -2.2022   1.3292  -0.7227
 A54  H7    H   HCH1  0   0.259  -0.2087  -1.8141  -0.2006
 A54  H81C  H   HCH2  0   0.249  -2.0551  -2.3270  -1.7901
 A54  H82C  H   HCH2  0   0.239  -1.8511  -0.7522  -2.5350
 A54  H91C  H   HCH2  0   0.205   0.5449  -1.3917  -3.0894
 A54  H92C  H   HCH2  0   0.219   0.2497  -2.9676  -2.3754
 A54  H101  H   HNH2  0   0.340  -1.1706  -1.9034  -4.6886
 A54  H102  H   HNH2  0   0.349  -0.1039  -3.1095  -4.6837
 A54  H13   H   HCR6  0   0.312   0.4410  -0.7258   1.5813
 A54  H15   H   HCR6  0   0.293   3.3660   2.3045   2.3696
 A54  H16   H   HCR6  0   0.294   3.1250   3.1436   0.0569

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
 A54  C1   C2    aromatic  1.388  0.020  1.388
 A54  C1   C6    aromatic  1.389  0.020  1.389
 A54  C2   C3    aromatic  1.389  0.020  1.389
 A54  C3   C4    aromatic  1.390  0.020  1.390
 A54  C4   C5    aromatic  1.392  0.020  1.392
 A54  C4   C7    single    1.509  0.020  1.509
 A54  C5   C6    aromatic  1.388  0.020  1.388
 A54  C7   C8    single    1.521  0.020  1.521
 A54  C7   O11   single    1.430  0.020  1.430
 A54  C8   C9    single    1.523  0.020  1.523
 A54  C9   N10   single    1.456  0.020  1.456
 A54  O11  C12   single    1.331  0.020  1.331
 A54  C12  C13   aromatic  1.391  0.020  1.391
 A54  C12  C17   aromatic  1.404  0.020  1.404
 A54  C13  C14   aromatic  1.386  0.020  1.386
 A54  C14  C15   aromatic  1.387  0.020  1.387
 A54  C14  CL2   single    1.726  0.020  1.726
 A54  C15  C16   aromatic  1.382  0.020  1.382
 A54  C16  C17   aromatic  1.392  0.020  1.392
 A54  C17  C18   single    1.423  0.020  1.423
 A54  C18  N19   triple    1.153  0.020  1.153
 A54  C1   H1    single    0.930  0.020  1.080
 A54  C2   H2    single    0.930  0.020  1.080
 A54  C6   H6    single    0.930  0.020  1.080
 A54  C3   H3    single    0.930  0.020  1.080
 A54  C5   H5    single    0.930  0.020  1.080
 A54  C7   H7    single    0.970  0.020  1.090
 A54  C8   H81C  single    0.970  0.020  1.090
 A54  C8   H82C  single    0.970  0.020  1.090
 A54  C9   H91C  single    0.970  0.020  1.090
 A54  C9   H92C  single    0.970  0.020  1.090
 A54  N10  H101  single    0.890  0.020  1.040
 A54  N10  H102  single    0.890  0.020  1.040
 A54  C13  H13   single    0.930  0.020  1.080
 A54  C15  H15   single    0.930  0.020  1.080
 A54  C16  H16   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
 A54  H1    C1   C6    120.11  3.000
 A54  H1    C1   C2    120.22  3.000
 A54  C6    C1   C2    119.67  3.000
 A54  H2    C2   C3    119.84  3.000
 A54  H2    C2   C1    120.16  3.000
 A54  C3    C2   C1    120.00  3.000
 A54  H3    C3   C4    119.78  3.000
 A54  H3    C3   C2    119.66  3.000
 A54  C4    C3   C2    120.56  3.000
 A54  C7    C4   C5    121.04  3.000
 A54  C7    C4   C3    119.70  3.000
 A54  C5    C4   C3    119.23  3.000
 A54  H5    C5   C6    119.35  3.000
 A54  H5    C5   C4    120.40  3.000
 A54  C6    C5   C4    120.25  3.000
 A54  H6    C6   C5    119.65  3.000
 A54  H6    C6   C1    120.07  3.000
 A54  C5    C6   C1    120.29  3.000
 A54  H7    C7   O11   109.17  3.000
 A54  H7    C7   C8    108.52  3.000
 A54  O11   C7   C8    106.53  3.000
 A54  H7    C7   C4    109.53  3.000
 A54  O11   C7   C4    111.10  3.000
 A54  C8    C7   C4    111.90  3.000
 A54  H82C  C8   H81C  106.58  3.000
 A54  H82C  C8   C9    110.48  3.000
 A54  H81C  C8   C9    109.03  3.000
 A54  H82C  C8   C7    109.16  3.000
 A54  H81C  C8   C7    107.70  3.000
 A54  C9    C8   C7    113.62  3.000
 A54  H92C  C9   H91C  106.48  3.000
 A54  H92C  C9   N10   108.22  3.000
 A54  H91C  C9   N10   113.50  3.000
 A54  H92C  C9   C8    108.72  3.000
 A54  H91C  C9   C8    109.71  3.000
 A54  N10   C9   C8    110.05  3.000
 A54  H102  N10  H101  105.33  3.000
 A54  H102  N10  C9    109.11  3.000
 A54  H101  N10  C9    109.08  3.000
 A54  C12   O11  C7    120.67  3.000
 A54  C17   C12  C13   119.08  3.000
 A54  C17   C12  O11   115.66  3.000
 A54  C13   C12  O11   125.26  3.000
 A54  H13   C13  C14   119.50  3.000
 A54  H13   C13  C12   121.56  3.000
 A54  C14   C13  C12   118.93  3.000
 A54  CL2   C14  C15   119.05  3.000
 A54  CL2   C14  C13   118.28  3.000
 A54  C15   C14  C13   122.67  3.000
 A54  H15   C15  C16   120.66  3.000
 A54  H15   C15  C14   121.14  3.000
 A54  C16   C15  C14   118.20  3.000
 A54  H16   C16  C17   119.53  3.000
 A54  H16   C16  C15   119.93  3.000
 A54  C17   C16  C15   120.53  3.000
 A54  C18   C17  C16   120.40  3.000
 A54  C18   C17  C12   119.02  3.000
 A54  C16   C17  C12   120.58  3.000
 A54  N19   C18  C17   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
 A54  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 A54  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 A54  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 A54  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 A54  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 A54  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 A54  CONST_07  C15   C14  C13  C12    0.00   0.0  0
 A54  CONST_08  C15   C16  C17  C12    0.00   0.0  0
 A54  CONST_09  C16   C17  C12  C13    0.00   0.0  0
 A54  CONST_10  C16   C15  C14  C13    0.00   0.0  0
 A54  CONST_11  C17   C12  C13  C14    0.00   0.0  0
 A54  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 A54  CONST_13  C7    C4   C3   C2   180.00   0.0  0
 A54  CONST_14  C7    C4   C5   C6   180.00   0.0  0
 A54  CONST_15  C14   C13  C12  O11  180.00   0.0  0
 A54  CONST_16  C16   C17  C12  O11  180.00   0.0  0
 A54  CONST_17  CL2   C14  C13  C12  180.00   0.0  0
 A54  CONST_18  C18   C17  C12  C13  180.00   0.0  0
 A54  CONST_19  C18   C17  C16  C15  180.00   0.0  0
 A54  CONST_20  CL2   C14  C15  C16  180.00   0.0  0
 A54  CONST_21  H3    C3   C2   C1   180.00   0.0  0
 A54  CONST_22  H5    C5   C6   C1   180.00   0.0  0
 A54  CONST_23  H6    C6   C1   C2   180.00   0.0  0
 A54  CONST_24  H1    C1   C2   C3   180.00   0.0  0
 A54  CONST_25  H2    C2   C3   C4   180.00   0.0  0
 A54  CONST_26  H16   C16  C17  C12  180.00   0.0  0
 A54  CONST_27  H15   C15  C14  C13  180.00   0.0  0
 A54  CONST_28  H13   C13  C14  C15  180.00   0.0  0
 A54  Var_01    C13   C12  O11  C7     2.53  30.0  2
 A54  Var_02    N10   C9   C8   C7   177.84  30.0  3
 A54  Var_03    H101  N10  C9   C8    68.77  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
 A54  chir_01  C7  C4  C8  O11  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
 A54  plan-1  C1   0.020
 A54  plan-1  C2   0.020
 A54  plan-1  C3   0.020
 A54  plan-1  C4   0.020
 A54  plan-1  C5   0.020
 A54  plan-1  C6   0.020
 A54  plan-1  C7   0.020
 A54  plan-1  H1   0.020
 A54  plan-1  H2   0.020
 A54  plan-1  H6   0.020
 A54  plan-1  H3   0.020
 A54  plan-1  H5   0.020
 A54  plan-2  O11  0.020
 A54  plan-2  C12  0.020
 A54  plan-2  C13  0.020
 A54  plan-2  C14  0.020
 A54  plan-2  C15  0.020
 A54  plan-2  C16  0.020
 A54  plan-2  C17  0.020
 A54  plan-2  C18  0.020
 A54  plan-2  N19  0.020
 A54  plan-2  CL2  0.020
 A54  plan-2  H13  0.020
 A54  plan-2  H15  0.020
 A54  plan-2  H16  0.020

