# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:01:37 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2S,4R)-2-amino-5-hydroxy-4-methyl-1-phenylpentan-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CO)C(=O)[C@@H](N)Cc1ccccc1
#
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
 39C  39C  (2S,4R)-2-amino-5-hydroxy-4-methyl-1-phenylpentan-3-one  ligand  32  15  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_39C
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
 39C  N22  N  NH2   0  -0.766   0.3459   1.9921  -0.9522
 39C  C8   C  CH1   0  -0.196  -0.2473   0.7603  -0.4947
 39C  C9   C  C     0   0.393  -1.7278   0.8495  -0.1381
 39C  O20  O  O     0  -0.394  -2.2260   1.8936   0.2186
 39C  C10  C  CH1   0  -0.408  -2.5292  -0.4255  -0.2688
 39C  C11  C  CH3   0  -0.655  -3.0764  -0.4923  -1.7009
 39C  C12  C  CH2   0  -0.119  -3.6309  -0.5007   0.7773
 39C  O13  O  OH1   0  -0.671  -4.2782  -1.7457   0.6502
 39C  C7   C  CH2   0  -0.543   0.4863   0.2410   0.7585
 39C  C6   C  CR6   0   0.165   1.9145  -0.1244   0.4752
 39C  C5   C  CR16  0  -0.312   2.2348  -1.3938  -0.0009
 39C  C4   C  CR16  0  -0.241   3.5502  -1.7387  -0.2810
 39C  C3   C  CR16  0  -0.273   4.5684  -0.8145  -0.0859
 39C  C2   C  CR16  0  -0.245   4.2605   0.4540   0.3888
 39C  C1   C  CR16  0  -0.304   2.9428   0.7949   0.6635
 39C  H28  H  HNH2  0   0.352  -0.1248   2.3107  -1.7901
 39C  H29  H  HCH1  0   0.265  -0.1367   0.0070  -1.2836
 39C  H35  H  HCH3  0   0.231  -3.8054   0.3005  -1.8761
 39C  H36  H  HCH3  0   0.242  -2.2806  -0.3892  -2.4398
 39C  H37  H  HCH3  0   0.251  -3.5642  -1.4492  -1.8774
 39C  H38  H  HCH2  0   0.207  -3.1929  -0.3809   1.7773
 39C  H39  H  HCH2  0   0.199  -4.3273   0.3329   0.6301
 39C  H40  H  HOH1  0   0.456  -5.0150  -1.7643   1.2674
 39C  H45  H  HCH2  0   0.262   0.4378   1.0120   1.5330
 39C  H46  H  HCH2  0   0.265  -0.0407  -0.6310   1.1538
 39C  H47  H  HCR6  0   0.244   1.4476  -2.1253  -0.1467
 39C  H48  H  HCR6  0   0.253   3.7817  -2.7317  -0.6449
 39C  H49  H  HCR6  0   0.253   5.5954  -1.0834  -0.2966
 39C  H50  H  HCR6  0   0.252   5.0486   1.1794   0.5467
 39C  H51  H  HCR6  0   0.242   2.7105   1.7846   1.0371
 39C  H2   H  HNH2  0   0.342   0.2115   2.7192  -0.2596
 39C  H32  H  HCH1  0   0.254  -1.8487  -1.2734  -0.1307

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
 39C  C10  C9   single    1.512  0.020  1.512
 39C  C10  C11  single    1.535  0.020  1.535
 39C  C10  C12  single    1.521  0.020  1.521
 39C  C9   O20  double    1.211  0.020  1.211
 39C  C9   C8   single    1.525  0.020  1.525
 39C  C7   C8   single    1.542  0.020  1.542
 39C  C7   C6   single    1.501  0.020  1.501
 39C  C12  O13  single    1.409  0.020  1.409
 39C  C8   N22  single    1.442  0.020  1.442
 39C  C5   C6   aromatic  1.393  0.020  1.393
 39C  C5   C4   aromatic  1.388  0.020  1.388
 39C  C6   C1   aromatic  1.392  0.020  1.392
 39C  C4   C3   aromatic  1.389  0.020  1.389
 39C  C1   C2   aromatic  1.389  0.020  1.389
 39C  C3   C2   aromatic  1.389  0.020  1.389
 39C  N22  H28  single    0.890  0.020  1.040
 39C  C8   H29  single    0.970  0.020  1.090
 39C  C7   H45  single    0.970  0.020  1.090
 39C  C7   H46  single    0.970  0.020  1.090
 39C  C1   H51  single    0.930  0.020  1.080
 39C  C2   H50  single    0.930  0.020  1.080
 39C  C3   H49  single    0.930  0.020  1.080
 39C  C4   H48  single    0.930  0.020  1.080
 39C  C5   H47  single    0.930  0.020  1.080
 39C  C10  H32  single    0.970  0.020  1.090
 39C  C11  H35  single    0.970  0.020  1.090
 39C  C11  H36  single    0.970  0.020  1.090
 39C  C11  H37  single    0.970  0.020  1.090
 39C  C12  H38  single    0.970  0.020  1.090
 39C  C12  H39  single    0.970  0.020  1.090
 39C  O13  H40  single    0.850  0.020  0.980
 39C  N22  H2   single    0.890  0.020  1.040

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
 39C  H2   N22  H28  106.16  3.000
 39C  H2   N22  C8   109.98  3.000
 39C  H28  N22  C8   109.90  3.000
 39C  H29  C8   C7   107.78  3.000
 39C  H29  C8   C9   107.83  3.000
 39C  C7   C8   C9   106.94  3.000
 39C  H29  C8   N22  108.49  3.000
 39C  C7   C8   N22  110.48  3.000
 39C  C9   C8   N22  115.06  3.000
 39C  C10  C9   O20  122.33  3.000
 39C  O20  C9   C8   121.24  3.000
 39C  C10  C9   C8   116.43  3.000
 39C  H32  C10  C12  108.96  3.000
 39C  H32  C10  C11  107.78  3.000
 39C  C12  C10  C11  112.42  3.000
 39C  H32  C10  C9   108.21  3.000
 39C  C12  C10  C9   111.48  3.000
 39C  C11  C10  C9   107.84  3.000
 39C  H37  C11  H36  107.47  3.000
 39C  H37  C11  H35  108.26  3.000
 39C  H36  C11  H35  108.07  3.000
 39C  H37  C11  C10  110.45  3.000
 39C  H36  C11  C10  111.58  3.000
 39C  H35  C11  C10  110.89  3.000
 39C  H39  C12  H38  107.02  3.000
 39C  H39  C12  O13  111.59  3.000
 39C  H38  C12  O13  111.21  3.000
 39C  H39  C12  C10  109.28  3.000
 39C  H38  C12  C10  109.38  3.000
 39C  O13  C12  C10  108.32  3.000
 39C  H40  O13  C12  108.13  3.000
 39C  H46  C7   H45  106.55  3.000
 39C  H46  C7   C6   109.44  3.000
 39C  H45  C7   C6   110.32  3.000
 39C  H46  C7   C8   109.47  3.000
 39C  H45  C7   C8   108.48  3.000
 39C  C6   C7   C8   112.41  3.000
 39C  C1   C6   C5   118.56  3.000
 39C  C1   C6   C7   121.10  3.000
 39C  C5   C6   C7   120.33  3.000
 39C  H47  C5   C4   119.54  3.000
 39C  H47  C5   C6   119.58  3.000
 39C  C4   C5   C6   120.87  3.000
 39C  H48  C4   C3   120.05  3.000
 39C  H48  C4   C5   119.88  3.000
 39C  C3   C4   C5   120.06  3.000
 39C  H49  C3   C2   120.25  3.000
 39C  H49  C3   C4   120.19  3.000
 39C  C2   C3   C4   119.55  3.000
 39C  H50  C2   C1   119.83  3.000
 39C  H50  C2   C3   120.03  3.000
 39C  C1   C2   C3   120.15  3.000
 39C  H51  C1   C2   119.75  3.000
 39C  H51  C1   C6   119.45  3.000
 39C  C2   C1   C6   120.80  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
 39C  CONST_01  C3   C4  C5  C6    0.00   0.0  0
 39C  CONST_02  C3   C2  C1  C6    0.00   0.0  0
 39C  CONST_03  C2   C1  C6  C5    0.00   0.0  0
 39C  CONST_04  C2   C3  C4  C5    0.00   0.0  0
 39C  CONST_05  C1   C6  C5  C4    0.00   0.0  0
 39C  CONST_06  C1   C2  C3  C4    0.00   0.0  0
 39C  CONST_07  C4   C5  C6  C7  180.00   0.0  0
 39C  CONST_08  C2   C1  C6  C7  180.00   0.0  0
 39C  CONST_09  H48  C4  C5  C6  180.00   0.0  0
 39C  CONST_10  H50  C2  C1  C6  180.00   0.0  0
 39C  CONST_11  H51  C1  C6  C5  180.00   0.0  0
 39C  CONST_12  H49  C3  C4  C5  180.00   0.0  0
 39C  CONST_13  H47  C5  C4  C3  180.00   0.0  0
 39C  Var_01    C5   C6  C7  C8  -86.11  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
 39C  chir_01  C8   C9   C7   N22  positiv
 39C  chir_02  C10  C12  C11  C9   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
 39C  plan-1  C7   0.020
 39C  plan-1  C6   0.020
 39C  plan-1  C5   0.020
 39C  plan-1  C4   0.020
 39C  plan-1  C3   0.020
 39C  plan-1  C2   0.020
 39C  plan-1  C1   0.020
 39C  plan-1  H47  0.020
 39C  plan-1  H48  0.020
 39C  plan-1  H49  0.020
 39C  plan-1  H50  0.020
 39C  plan-1  H51  0.020
 39C  plan-2  C8   0.020
 39C  plan-2  C9   0.020
 39C  plan-2  O20  0.020
 39C  plan-2  C10  0.020

