# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 17:25:20 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCc1ccccc1)[P@@](O)(=O)C[C@@H](Cc2ccccc2)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
 BEY  BEY  '(2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid'  ligand  49  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BEY
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
 BEY  O3    O  OH1   0  -0.769  -0.8477   1.2524   1.3752
 BEY  P     P  P     0   1.231  -0.4749   0.4561   0.0141
 BEY  O4    O  O     0  -0.719  -0.3823  -1.0326   0.1538
 BEY  C19   C  CH1   0  -0.336  -1.7733   1.1022  -1.1144
 BEY  C18   C  CH2   0  -0.425  -3.1980   0.8478  -0.6200
 BEY  C15   C  CH2   0  -0.530  -3.5715  -0.6171  -0.3846
 BEY  C16   C  CR6   0   0.141  -5.0260  -0.7428  -0.0265
 BEY  C10   C  CR16  0  -0.311  -5.9948  -0.9299  -1.0099
 BEY  C11   C  CR16  0  -0.241  -7.3418  -1.0024  -0.6790
 BEY  C12   C  CR16  0  -0.274  -7.7420  -0.8862   0.6459
 BEY  C14   C  CR16  0  -0.239  -6.7855  -0.6987   1.6356
 BEY  C13   C  CR16  0  -0.311  -5.4402  -0.6280   1.2990
 BEY  N     N  NH2   0  -0.790  -1.6109   2.5186  -1.3950
 BEY  C17   C  CH2   0  -0.751   1.1131   1.1526  -0.5674
 BEY  C8    C  CH1   0  -0.342   2.3015   0.2376  -0.2760
 BEY  C9    C  C     0   0.572   2.3186  -0.2172   1.1622
 BEY  O2    O  O     0  -0.466   1.8536   0.4238   2.0799
 BEY  O1    O  OH1   0  -0.568   2.9437  -1.3650   1.3300
 BEY  C7    C  CH2   0  -0.521   3.6148   0.9910  -0.5894
 BEY  C1    C  CR6   0   0.151   4.8502   0.1374  -0.5315
 BEY  C2    C  CR16  0  -0.308   5.1076  -0.7908  -1.5385
 BEY  C3    C  CR16  0  -0.239   6.2399  -1.5903  -1.4964
 BEY  C4    C  CR16  0  -0.272   7.1374  -1.4716  -0.4417
 BEY  C6    C  CR16  0  -0.240   6.8930  -0.5479   0.5648
 BEY  C5    C  CR16  0  -0.312   5.7564   0.2498   0.5179
 BEY  H19   H  HCH1  0   0.278  -1.6286   0.5549  -2.0522
 BEY  H18   H  HCH2  0   0.239  -3.3782   1.4218   0.2937
 BEY  H18A  H  HCH2  0   0.251  -3.8650   1.2675  -1.3780
 BEY  H15   H  HCH2  0   0.242  -3.3563  -1.1961  -1.2862
 BEY  H15A  H  HCH2  0   0.253  -2.9612  -1.0442   0.4119
 BEY  H10   H  HCR6  0   0.245  -5.6920  -1.0239  -2.0467
 BEY  H11   H  HCR6  0   0.253  -8.0795  -1.1520  -1.4571
 BEY  H12   H  HCR6  0   0.252  -8.7915  -0.9439   0.9047
 BEY  H14   H  HCR6  0   0.252  -7.0859  -0.6108   2.6721
 BEY  H13   H  HCR6  0   0.245  -4.6995  -0.4856   2.0779
 BEY  HN    H  HNH2  0   0.352  -1.6236   3.0668  -0.5439
 BEY  HNA   H  HNH2  0   0.367  -0.7371   2.7130  -1.8654
 BEY  H17   H  HCH2  0   0.296   1.0489   1.2778  -1.6515
 BEY  H17A  H  HCH2  0   0.292   1.2661   2.1497  -0.1498
 BEY  H8    H  HCH1  0   0.293   2.2447  -0.6425  -0.9196
 BEY  H7    H  HCH2  0   0.273   3.5083   1.4105  -1.5929
 BEY  H7A   H  HCH2  0   0.263   3.7061   1.8403   0.0916
 BEY  H2    H  HCR6  0   0.248   4.4153  -0.8853  -2.3676
 BEY  H3    H  HCR6  0   0.253   6.4257  -2.3032  -2.2896
 BEY  H4    H  HCR6  0   0.254   8.0235  -2.0924  -0.4083
 BEY  H6    H  HCR6  0   0.254   7.5894  -0.4449   1.3871
 BEY  H5    H  HCR6  0   0.247   5.5766   0.9723   1.3056
 BEY  H23   H  HOH1  0   0.484  -0.1111   1.2442   2.0053
 BEY  H24   H  HOH1  0   0.483   2.9822  -1.5925   2.2718

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
 BEY  O3   P     single    1.620  0.020  1.620
 BEY  P    O4    double    1.498  0.020  1.498
 BEY  P    C19   single    1.838  0.020  1.838
 BEY  P    C17   single    1.829  0.020  1.829
 BEY  C19  C18   single    1.529  0.020  1.529
 BEY  C19  N     single    1.453  0.020  1.453
 BEY  C19  H19   single    0.970  0.020  1.090
 BEY  C18  C15   single    1.530  0.020  1.530
 BEY  C18  H18   single    0.970  0.020  1.090
 BEY  C18  H18A  single    0.970  0.020  1.090
 BEY  C15  C16   single    1.503  0.020  1.503
 BEY  C15  H15   single    0.970  0.020  1.090
 BEY  C15  H15A  single    0.970  0.020  1.090
 BEY  C16  C10   aromatic  1.393  0.020  1.393
 BEY  C16  C13   aromatic  1.393  0.020  1.393
 BEY  C10  C11   aromatic  1.389  0.020  1.389
 BEY  C10  H10   single    0.930  0.020  1.080
 BEY  C11  C12   aromatic  1.389  0.020  1.389
 BEY  C11  H11   single    0.930  0.020  1.080
 BEY  C12  C14   aromatic  1.389  0.020  1.389
 BEY  C12  H12   single    0.930  0.020  1.080
 BEY  C14  C13   aromatic  1.389  0.020  1.389
 BEY  C14  H14   single    0.930  0.020  1.080
 BEY  C13  H13   single    0.930  0.020  1.080
 BEY  N    HN    single    0.890  0.020  1.040
 BEY  N    HNA   single    0.890  0.020  1.040
 BEY  C17  C8    single    1.528  0.020  1.528
 BEY  C17  H17   single    0.970  0.020  1.090
 BEY  C17  H17A  single    0.970  0.020  1.090
 BEY  C8   C9    single    1.509  0.020  1.509
 BEY  C8   C7    single    1.546  0.020  1.546
 BEY  C8   H8    single    0.970  0.020  1.090
 BEY  C9   O2    double    1.212  0.020  1.212
 BEY  C9   O1    single    1.318  0.020  1.318
 BEY  C7   C1    single    1.503  0.020  1.503
 BEY  C7   H7    single    0.970  0.020  1.090
 BEY  C7   H7A   single    0.970  0.020  1.090
 BEY  C1   C2    aromatic  1.393  0.020  1.393
 BEY  C1   C5    aromatic  1.391  0.020  1.391
 BEY  C2   C3    aromatic  1.387  0.020  1.387
 BEY  C2   H2    single    0.930  0.020  1.080
 BEY  C3   C4    aromatic  1.390  0.020  1.390
 BEY  C3   H3    single    0.930  0.020  1.080
 BEY  C4   C6    aromatic  1.388  0.020  1.388
 BEY  C4   H4    single    0.930  0.020  1.080
 BEY  C6   C5    aromatic  1.389  0.020  1.389
 BEY  C6   H6    single    0.930  0.020  1.080
 BEY  C5   H5    single    0.930  0.020  1.080
 BEY  O3   H23   single    0.850  0.020  0.980
 BEY  O1   H24   single    0.850  0.020  0.980

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
 BEY  H23   O3   P    111.54  3.000
 BEY  C17   P    C19  106.52  3.000
 BEY  C17   P    O4   110.76  3.000
 BEY  C19   P    O4   116.77  3.000
 BEY  C17   P    O3   106.24  3.000
 BEY  C19   P    O3   100.40  3.000
 BEY  O4    P    O3   115.11  3.000
 BEY  H19   C19  N    107.88  3.000
 BEY  H19   C19  C18  108.46  3.000
 BEY  N     C19  C18  109.19  3.000
 BEY  H19   C19  P    104.88  3.000
 BEY  N     C19  P    112.48  3.000
 BEY  C18   C19  P    113.65  3.000
 BEY  H18A  C18  H18  106.09  3.000
 BEY  H18A  C18  C15  108.98  3.000
 BEY  H18   C18  C15  109.49  3.000
 BEY  H18A  C18  C19  106.28  3.000
 BEY  H18   C18  C19  109.64  3.000
 BEY  C15   C18  C19  115.87  3.000
 BEY  H15A  C15  H15  106.55  3.000
 BEY  H15A  C15  C16  109.56  3.000
 BEY  H15   C15  C16  110.05  3.000
 BEY  H15A  C15  C18  110.53  3.000
 BEY  H15   C15  C18  109.41  3.000
 BEY  C16   C15  C18  110.66  3.000
 BEY  C13   C16  C10  118.42  3.000
 BEY  C13   C16  C15  120.49  3.000
 BEY  C10   C16  C15  121.06  3.000
 BEY  H10   C10  C11  119.61  3.000
 BEY  H10   C10  C16  119.51  3.000
 BEY  C11   C10  C16  120.88  3.000
 BEY  H11   C11  C12  120.05  3.000
 BEY  H11   C11  C10  119.79  3.000
 BEY  C12   C11  C10  120.16  3.000
 BEY  H12   C12  C14  120.30  3.000
 BEY  H12   C12  C11  120.19  3.000
 BEY  C14   C12  C11  119.50  3.000
 BEY  H14   C14  C13  119.78  3.000
 BEY  H14   C14  C12  120.13  3.000
 BEY  C13   C14  C12  120.09  3.000
 BEY  H13   C13  C14  119.63  3.000
 BEY  H13   C13  C16  119.41  3.000
 BEY  C14   C13  C16  120.95  3.000
 BEY  HNA   N    HN   107.32  3.000
 BEY  HNA   N    C19  111.95  3.000
 BEY  HN    N    C19  111.35  3.000
 BEY  H17A  C17  H17  106.43  3.000
 BEY  H17A  C17  C8   111.41  3.000
 BEY  H17   C17  C8   107.66  3.000
 BEY  H17A  C17  P    110.35  3.000
 BEY  H17   C17  P    107.93  3.000
 BEY  C8    C17  P    112.75  3.000
 BEY  H8    C8   C7   108.51  3.000
 BEY  H8    C8   C9   108.64  3.000
 BEY  C7    C8   C9   109.30  3.000
 BEY  H8    C8   C17  109.26  3.000
 BEY  C7    C8   C17  109.28  3.000
 BEY  C9    C8   C17  111.79  3.000
 BEY  O1    C9   O2   123.11  3.000
 BEY  O1    C9   C8   112.92  3.000
 BEY  O2    C9   C8   123.92  3.000
 BEY  H24   O1   C9   110.30  3.000
 BEY  H7A   C7   H7   106.39  3.000
 BEY  H7A   C7   C1   110.42  3.000
 BEY  H7    C7   C1   109.48  3.000
 BEY  H7A   C7   C8   108.88  3.000
 BEY  H7    C7   C8   106.88  3.000
 BEY  C1    C7   C8   114.44  3.000
 BEY  C5    C1   C2   118.59  3.000
 BEY  C5    C1   C7   121.25  3.000
 BEY  C2    C1   C7   120.16  3.000
 BEY  H2    C2   C3   119.62  3.000
 BEY  H2    C2   C1   119.52  3.000
 BEY  C3    C2   C1   120.86  3.000
 BEY  H3    C3   C4   120.09  3.000
 BEY  H3    C3   C2   119.84  3.000
 BEY  C4    C3   C2   120.07  3.000
 BEY  H4    C4   C6   120.23  3.000
 BEY  H4    C4   C3   120.20  3.000
 BEY  C6    C4   C3   119.56  3.000
 BEY  H6    C6   C5   119.82  3.000
 BEY  H6    C6   C4   120.06  3.000
 BEY  C5    C6   C4   120.12  3.000
 BEY  H5    C5   C6   119.60  3.000
 BEY  H5    C5   C1   119.61  3.000
 BEY  C6    C5   C1   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
 BEY  CONST_01  C12  C11  C10  C16     0.00   0.0  0
 BEY  CONST_02  C12  C14  C13  C16     0.00   0.0  0
 BEY  CONST_03  C14  C13  C16  C10     0.00   0.0  0
 BEY  CONST_04  C14  C12  C11  C10     0.00   0.0  0
 BEY  CONST_05  C13  C16  C10  C11     0.00   0.0  0
 BEY  CONST_06  C13  C14  C12  C11     0.00   0.0  0
 BEY  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 BEY  CONST_08  C4   C6   C5   C1      0.00   0.0  0
 BEY  CONST_09  C6   C5   C1   C2      0.00   0.0  0
 BEY  CONST_10  C6   C4   C3   C2      0.00   0.0  0
 BEY  CONST_11  C5   C1   C2   C3      0.00   0.0  0
 BEY  CONST_12  C5   C6   C4   C3      0.00   0.0  0
 BEY  CONST_13  C11  C10  C16  C15   180.00   0.0  0
 BEY  CONST_14  C14  C13  C16  C15   180.00   0.0  0
 BEY  CONST_15  C3   C2   C1   C7    180.00   0.0  0
 BEY  CONST_16  C6   C5   C1   C7    180.00   0.0  0
 BEY  CONST_17  H11  C11  C10  C16   180.00   0.0  0
 BEY  CONST_18  H14  C14  C13  C16   180.00   0.0  0
 BEY  CONST_19  H13  C13  C16  C10   180.00   0.0  0
 BEY  CONST_20  H12  C12  C11  C10   180.00   0.0  0
 BEY  CONST_21  H10  C10  C11  C12   180.00   0.0  0
 BEY  CONST_22  H3   C3   C2   C1    180.00   0.0  0
 BEY  CONST_23  H6   C6   C5   C1    180.00   0.0  0
 BEY  CONST_24  H5   C5   C1   C2    180.00   0.0  0
 BEY  CONST_25  H4   C4   C3   C2    180.00   0.0  0
 BEY  CONST_26  H2   C2   C3   C4    180.00   0.0  0
 BEY  CONST_27  H24  O1   C9   C8    180.00   0.0  0
 BEY  Var_01    C10  C16  C15  C18    90.55  30.0  2
 BEY  Var_02    C2   C1   C7   C8     73.08  30.0  2
 BEY  Var_03    C16  C15  C18  C19  -174.74  30.0  3
 BEY  Var_04    C8   C17  P    O3    103.38  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
 BEY  chir_02  C19  P   C18  N    negativ
 BEY  chir_03  C8   C7  C9   C17  negativ
 BEY  chir_04  P    O4  C19  C17  both

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
 BEY  plan-1  C15  0.020
 BEY  plan-1  C16  0.020
 BEY  plan-1  C10  0.020
 BEY  plan-1  C11  0.020
 BEY  plan-1  C12  0.020
 BEY  plan-1  C14  0.020
 BEY  plan-1  C13  0.020
 BEY  plan-1  H10  0.020
 BEY  plan-1  H11  0.020
 BEY  plan-1  H12  0.020
 BEY  plan-1  H14  0.020
 BEY  plan-1  H13  0.020
 BEY  plan-2  C7   0.020
 BEY  plan-2  C1   0.020
 BEY  plan-2  C2   0.020
 BEY  plan-2  C3   0.020
 BEY  plan-2  C4   0.020
 BEY  plan-2  C6   0.020
 BEY  plan-2  C5   0.020
 BEY  plan-2  H2   0.020
 BEY  plan-2  H3   0.020
 BEY  plan-2  H4   0.020
 BEY  plan-2  H6   0.020
 BEY  plan-2  H5   0.020
 BEY  plan-3  C8   0.020
 BEY  plan-3  C9   0.020
 BEY  plan-3  O2   0.020
 BEY  plan-3  O1   0.020
 BEY  plan-3  H24  0.020

