# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:27:51 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2R,4R)-4-amino-2-methyl-5-phenylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C[C@@H](N)Cc1ccccc1)C(O)=O
#
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
 55P  55P  '(2R,4R)-4-amino-2-methyl-5-phenylpentanoic acid'  ligand  31  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_55P
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
 55P  NBI  N  NH2    0  -0.784  -0.0923   0.8643   1.2749
 55P  CBJ  C  CH1    0  -0.091   0.0879   0.0829   0.0610
 55P  CBL  C  CH2    0  -0.395   1.5034   0.2865  -0.4753
 55P  CBT  C  CH1    0  -0.366   2.6082  -0.2268   0.4427
 55P  CBX  C  CH3    0  -0.665   2.6211  -1.7554   0.5140
 55P  CBU  C  C      0   0.420   4.0180   0.2717   0.0546
 55P  OXT  O  OC     0  -0.629   4.9396  -0.0310   0.8431
 55P  O    O  O     -1  -0.606   4.1485   0.9215  -1.0029
 55P  CBM  C  CH2    0  -0.510  -0.9448   0.3896  -1.0449
 55P  CBN  C  CR6    0   0.134  -2.3575   0.1872  -0.5810
 55P  CBO  C  CR16   0  -0.307  -2.9237  -1.0877  -0.5649
 55P  CBP  C  CR16   0  -0.240  -4.2071  -1.2943  -0.0786
 55P  CBQ  C  CR16   0  -0.274  -4.9523  -0.2249   0.4034
 55P  CBR  C  CR16   0  -0.241  -4.4029   1.0499   0.3912
 55P  CBS  C  CR16   0  -0.322  -3.1169   1.2504  -0.0956
 55P  H43  H  HNH2   0   0.331  -0.0422   1.8528   1.0514
 55P  H44  H  HCH1   0   0.220  -0.0459  -0.9690   0.3372
 55P  H45  H  HCH2   0   0.202   1.5873  -0.1948  -1.4550
 55P  H46  H  HCH2   0   0.207   1.6420   1.3572  -0.6584
 55P  H47  H  HCH1   0   0.213   2.4035   0.1447   1.4531
 55P  H48  H  HCH3   0   0.207   2.8451  -2.1915  -0.4636
 55P  H49  H  HCH3   0   0.223   3.3772  -2.1056   1.2152
 55P  H50  H  HCH3   0   0.217   1.6606  -2.1602   0.8378
 55P  H52  H  HCH2   0   0.232  -0.8045   1.4219  -1.3822
 55P  H53  H  HCH2   0   0.235  -0.7390  -0.2558  -1.9035
 55P  H54  H  HCR6   0   0.244  -2.3529  -1.9298  -0.9400
 55P  H55  H  HCR6   0   0.251  -4.6271  -2.2924  -0.0760
 55P  H56  H  HCR6   0   0.252  -5.9535  -0.3856   0.7822
 55P  H57  H  HCR6   0   0.251  -4.9753   1.8921   0.7595
 55P  H58  H  HCR6   0   0.246  -2.6989   2.2504  -0.1060
 55P  H2   H  HNH2   0   0.345  -1.0190   0.7128   1.6544

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
 55P  CBL  CBT  single    1.525  0.020  1.525
 55P  CBL  CBJ  single    1.527  0.020  1.527
 55P  CBX  CBT  single    1.530  0.020  1.530
 55P  CBM  CBJ  single    1.544  0.020  1.544
 55P  CBM  CBN  single    1.501  0.020  1.501
 55P  CBO  CBN  aromatic  1.395  0.020  1.395
 55P  CBO  CBP  aromatic  1.388  0.020  1.388
 55P  CBT  CBU  single    1.545  0.020  1.545
 55P  NBI  CBJ  single    1.455  0.020  1.455
 55P  CBN  CBS  aromatic  1.394  0.020  1.394
 55P  CBP  CBQ  aromatic  1.390  0.020  1.390
 55P  CBU  O    deloc     1.248  0.020  1.248
 55P  CBU  OXT  deloc     1.250  0.020  1.250
 55P  CBS  CBR  aromatic  1.390  0.020  1.390
 55P  CBQ  CBR  aromatic  1.388  0.020  1.388
 55P  NBI  H43  single    0.890  0.020  1.040
 55P  CBJ  H44  single    0.970  0.020  1.090
 55P  CBL  H45  single    0.970  0.020  1.090
 55P  CBL  H46  single    0.970  0.020  1.090
 55P  CBT  H47  single    0.970  0.020  1.090
 55P  CBX  H48  single    0.970  0.020  1.090
 55P  CBX  H49  single    0.970  0.020  1.090
 55P  CBX  H50  single    0.970  0.020  1.090
 55P  CBM  H52  single    0.970  0.020  1.090
 55P  CBM  H53  single    0.970  0.020  1.090
 55P  CBO  H54  single    0.930  0.020  1.080
 55P  CBP  H55  single    0.930  0.020  1.080
 55P  CBQ  H56  single    0.930  0.020  1.080
 55P  CBR  H57  single    0.930  0.020  1.080
 55P  CBS  H58  single    0.930  0.020  1.080
 55P  NBI  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
 55P  H2   NBI  H43  105.87  3.000
 55P  H2   NBI  CBJ  110.23  3.000
 55P  H43  NBI  CBJ  109.47  3.000
 55P  H44  CBJ  CBM  106.83  3.000
 55P  H44  CBJ  CBL  109.25  3.000
 55P  CBM  CBJ  CBL  109.99  3.000
 55P  H44  CBJ  NBI  106.87  3.000
 55P  CBM  CBJ  NBI  114.08  3.000
 55P  CBL  CBJ  NBI  109.65  3.000
 55P  H46  CBL  H45  105.70  3.000
 55P  H46  CBL  CBT  109.76  3.000
 55P  H45  CBL  CBT  109.58  3.000
 55P  H46  CBL  CBJ  107.84  3.000
 55P  H45  CBL  CBJ  109.06  3.000
 55P  CBT  CBL  CBJ  114.52  3.000
 55P  H47  CBT  CBU  107.02  3.000
 55P  H47  CBT  CBX  107.29  3.000
 55P  CBU  CBT  CBX  109.04  3.000
 55P  H47  CBT  CBL  107.79  3.000
 55P  CBU  CBT  CBL  113.65  3.000
 55P  CBX  CBT  CBL  111.73  3.000
 55P  H50  CBX  H49  107.50  3.000
 55P  H50  CBX  H48  107.31  3.000
 55P  H49  CBX  H48  107.77  3.000
 55P  H50  CBX  CBT  112.14  3.000
 55P  H49  CBX  CBT  110.92  3.000
 55P  H48  CBX  CBT  111.00  3.000
 55P  O    CBU  OXT  125.69  3.000
 55P  OXT  CBU  CBT  115.86  3.000
 55P  O    CBU  CBT  118.45  3.000
 55P  H53  CBM  H52  106.88  3.000
 55P  H53  CBM  CBN  109.89  3.000
 55P  H52  CBM  CBN  110.06  3.000
 55P  H53  CBM  CBJ  108.62  3.000
 55P  H52  CBM  CBJ  108.80  3.000
 55P  CBN  CBM  CBJ  112.43  3.000
 55P  CBS  CBN  CBO  118.16  3.000
 55P  CBS  CBN  CBM  121.17  3.000
 55P  CBO  CBN  CBM  120.59  3.000
 55P  H54  CBO  CBP  119.50  3.000
 55P  H54  CBO  CBN  119.48  3.000
 55P  CBP  CBO  CBN  121.03  3.000
 55P  H55  CBP  CBQ  120.04  3.000
 55P  H55  CBP  CBO  119.78  3.000
 55P  CBQ  CBP  CBO  120.18  3.000
 55P  H56  CBQ  CBR  120.37  3.000
 55P  H56  CBQ  CBP  120.20  3.000
 55P  CBR  CBQ  CBP  119.43  3.000
 55P  H57  CBR  CBS  119.75  3.000
 55P  H57  CBR  CBQ  120.13  3.000
 55P  CBS  CBR  CBQ  120.12  3.000
 55P  H58  CBS  CBR  119.56  3.000
 55P  H58  CBS  CBN  119.36  3.000
 55P  CBR  CBS  CBN  121.08  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
 55P  CONST_01  CBQ  CBP  CBO  CBN    0.00   0.0  0
 55P  CONST_02  CBQ  CBR  CBS  CBN    0.00   0.0  0
 55P  CONST_03  CBR  CBS  CBN  CBO    0.00   0.0  0
 55P  CONST_04  CBR  CBQ  CBP  CBO    0.00   0.0  0
 55P  CONST_05  CBS  CBN  CBO  CBP    0.00   0.0  0
 55P  CONST_06  CBS  CBR  CBQ  CBP    0.00   0.0  0
 55P  CONST_07  CBP  CBO  CBN  CBM  180.00   0.0  0
 55P  CONST_08  CBR  CBS  CBN  CBM  180.00   0.0  0
 55P  CONST_09  H55  CBP  CBO  CBN  180.00   0.0  0
 55P  CONST_10  H57  CBR  CBS  CBN  180.00   0.0  0
 55P  CONST_11  H58  CBS  CBN  CBO  180.00   0.0  0
 55P  CONST_12  H56  CBQ  CBP  CBO  180.00   0.0  0
 55P  CONST_13  H54  CBO  CBP  CBQ  180.00   0.0  0
 55P  Var_01    CBO  CBN  CBM  CBJ  -81.87  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
 55P  chir_01  CBJ  CBL  CBM  NBI  positiv
 55P  chir_02  CBT  CBU  CBX  CBL  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
 55P  plan-1  CBM  0.020
 55P  plan-1  CBN  0.020
 55P  plan-1  CBO  0.020
 55P  plan-1  CBP  0.020
 55P  plan-1  CBQ  0.020
 55P  plan-1  CBR  0.020
 55P  plan-1  CBS  0.020
 55P  plan-1  H54  0.020
 55P  plan-1  H55  0.020
 55P  plan-1  H56  0.020
 55P  plan-1  H57  0.020
 55P  plan-1  H58  0.020
 55P  plan-2  CBT  0.020
 55P  plan-2  CBU  0.020
 55P  plan-2  OXT  0.020
 55P  plan-2  O    0.020

