# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:09:41 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (3S)-3-amino-1-chloro-4-phenylbutan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)C(=O)CCl
#
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
 PHM  PHM  (3S)-3-amino-1-chloro-4-phenylbutan-2-one  peptide  25  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PHM
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
 PHM  C1   C   CH2   0  -0.579   2.5623   0.9233  -0.2921
 PHM  N1   N   NH2   0  -0.765  -0.0404  -1.7215  -0.9674
 PHM  C2   C   CH1   0  -0.197   0.4113  -0.4438  -0.4782
 PHM  C3   C   CH2   0  -0.544  -0.4020  -0.0250   0.7621
 PHM  C4   C   CR6   0   0.170  -1.8621   0.1350   0.4512
 PHM  C5   C   CR16  0  -0.312  -2.7747  -0.8683   0.7623
 PHM  C6   C   CR16  0  -0.306  -2.3280   1.2914  -0.1704
 PHM  C7   C   CR16  0  -0.244  -4.1233  -0.7204   0.4654
 PHM  C8   C   CR16  0  -0.241  -3.6741   1.4424  -0.4739
 PHM  C9   C   CR16  0  -0.272  -4.5772   0.4355  -0.1560
 PHM  C10  C   C     0   0.396   1.8866  -0.4102  -0.0860
 PHM  O1   O   O     0  -0.366   2.4580  -1.3726   0.3564
 PHM  CL1  CL  CL    0  -0.133   4.2010   0.9697   0.3882
 PHM  HM2  H   HCH2  0   0.327   2.6238   1.1230  -1.3636
 PHM  HM3  H   HCH2  0   0.313   1.9747   1.7272   0.1529
 PHM  H2   H   HNH2  0   0.346   0.1501  -2.4447  -0.2839
 PHM  HA   H   HCH1  0   0.271   0.2461   0.3058  -1.2601
 PHM  HB2  H   HCH2  0   0.265  -0.2647  -0.7803   1.5409
 PHM  HB3  H   HCH2  0   0.266  -0.0076   0.9127   1.1633
 PHM  HD1  H   HCR6  0   0.244  -2.4278  -1.7726   1.2479
 PHM  HD2  H   HCR6  0   0.245  -1.6312   2.0852  -0.4159
 PHM  HE1  H   HCR6  0   0.253  -4.8201  -1.5091   0.7194
 PHM  HE2  H   HCR6  0   0.253  -4.0195   2.3491  -0.9539
 PHM  HZ   H   HCR6  0   0.254  -5.6279   0.5533  -0.3877
 PHM  H    H   HNH2  0   0.356   0.4690  -1.9777  -1.8039

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
 PHM  C1   C10  single    1.509  0.020  1.509
 PHM  C1   CL1  single    1.775  0.020  1.775
 PHM  C1   HM2  single    0.970  0.020  1.090
 PHM  C1   HM3  single    0.970  0.020  1.090
 PHM  N1   C2   single    1.441  0.020  1.441
 PHM  N1   H    single    0.890  0.020  1.040
 PHM  N1   H2   single    0.890  0.020  1.040
 PHM  C2   C3   single    1.541  0.020  1.541
 PHM  C2   C10  single    1.527  0.020  1.527
 PHM  C2   HA   single    0.970  0.020  1.090
 PHM  C3   C4   single    1.501  0.020  1.501
 PHM  C3   HB2  single    0.970  0.020  1.090
 PHM  C3   HB3  single    0.970  0.020  1.090
 PHM  C4   C5   aromatic  1.391  0.020  1.391
 PHM  C4   C6   aromatic  1.393  0.020  1.393
 PHM  C5   C7   aromatic  1.389  0.020  1.389
 PHM  C5   HD1  single    0.930  0.020  1.080
 PHM  C6   C8   aromatic  1.388  0.020  1.388
 PHM  C6   HD2  single    0.930  0.020  1.080
 PHM  C7   C9   aromatic  1.389  0.020  1.389
 PHM  C7   HE1  single    0.930  0.020  1.080
 PHM  C8   C9   aromatic  1.389  0.020  1.389
 PHM  C8   HE2  single    0.930  0.020  1.080
 PHM  C9   HZ   single    0.930  0.020  1.080
 PHM  C10  O1   double    1.204  0.020  1.204

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
 PHM  HM3  C1   HM2  107.21  3.000
 PHM  HM3  C1   CL1  108.77  3.000
 PHM  HM2  C1   CL1  108.63  3.000
 PHM  HM3  C1   C10  110.75  3.000
 PHM  HM2  C1   C10  108.72  3.000
 PHM  CL1  C1   C10  112.59  3.000
 PHM  H2   N1   H    106.39  3.000
 PHM  H2   N1   C2   110.18  3.000
 PHM  H    N1   C2   110.32  3.000
 PHM  HA   C2   C10  108.29  3.000
 PHM  HA   C2   C3   107.99  3.000
 PHM  C10  C2   C3   107.29  3.000
 PHM  HA   C2   N1   108.49  3.000
 PHM  C10  C2   N1   114.18  3.000
 PHM  C3   C2   N1   110.42  3.000
 PHM  HB3  C3   HB2  106.60  3.000
 PHM  HB3  C3   C4   109.59  3.000
 PHM  HB2  C3   C4   110.07  3.000
 PHM  HB3  C3   C2   109.76  3.000
 PHM  HB2  C3   C2   108.61  3.000
 PHM  C4   C3   C2   112.06  3.000
 PHM  C6   C4   C5   118.62  3.000
 PHM  C6   C4   C3   120.40  3.000
 PHM  C5   C4   C3   120.98  3.000
 PHM  HD1  C5   C7   119.70  3.000
 PHM  HD1  C5   C4   119.48  3.000
 PHM  C7   C5   C4   120.82  3.000
 PHM  HD2  C6   C8   119.60  3.000
 PHM  HD2  C6   C4   119.59  3.000
 PHM  C8   C6   C4   120.81  3.000
 PHM  HE1  C7   C9   120.07  3.000
 PHM  HE1  C7   C5   119.82  3.000
 PHM  C9   C7   C5   120.11  3.000
 PHM  HE2  C8   C9   120.07  3.000
 PHM  HE2  C8   C6   119.84  3.000
 PHM  C9   C8   C6   120.09  3.000
 PHM  HZ   C9   C8   120.21  3.000
 PHM  HZ   C9   C7   120.24  3.000
 PHM  C8   C9   C7   119.55  3.000
 PHM  O1   C10  C2   122.38  3.000
 PHM  O1   C10  C1   122.97  3.000
 PHM  C2   C10  C1   114.65  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
 PHM  CONST_01  C9   C7  C5   C4    0.00   0.0  0
 PHM  CONST_02  C9   C8  C6   C4    0.00   0.0  0
 PHM  CONST_03  C8   C6  C4   C5    0.00   0.0  0
 PHM  CONST_04  C8   C9  C7   C5    0.00   0.0  0
 PHM  CONST_05  C7   C5  C4   C6    0.00   0.0  0
 PHM  CONST_06  C7   C9  C8   C6    0.00   0.0  0
 PHM  CONST_07  C7   C5  C4   C3  180.00   0.0  0
 PHM  CONST_08  C8   C6  C4   C3  180.00   0.0  0
 PHM  CONST_09  HE1  C7  C5   C4  180.00   0.0  0
 PHM  CONST_10  HE2  C8  C6   C4  180.00   0.0  0
 PHM  CONST_11  HD2  C6  C4   C5  180.00   0.0  0
 PHM  CONST_12  HZ   C9  C7   C5  180.00   0.0  0
 PHM  CONST_13  HD1  C5  C4   C6  180.00   0.0  0
 PHM  Var_01    C5   C4  C3   C2   99.91  30.0  2
 PHM  Var_02    CL1  C1  C10  C2  171.94  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
 PHM  chir_01  C2  N1  C3  C10  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
 PHM  plan-1  C3   0.020
 PHM  plan-1  C4   0.020
 PHM  plan-1  C5   0.020
 PHM  plan-1  C6   0.020
 PHM  plan-1  C7   0.020
 PHM  plan-1  C8   0.020
 PHM  plan-1  C9   0.020
 PHM  plan-1  HD1  0.020
 PHM  plan-1  HD2  0.020
 PHM  plan-1  HE1  0.020
 PHM  plan-1  HE2  0.020
 PHM  plan-1  HZ   0.020
 PHM  plan-2  C1   0.020
 PHM  plan-2  C2   0.020
 PHM  plan-2  C10  0.020
 PHM  plan-2  O1   0.020

