# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:59:42 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2S)-3-[(S)-[(1R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl]-2-benzylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCc1cccnc1)[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
 379  379  '(2S)-3-[(S)-[(1R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl]-2-benzylpropanoic acid'  ligand  48  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_379
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
 379  P11  P  P     0   1.270  -0.4150   0.5787  -0.6030
 379  C1   C  CH2   0  -0.450  -3.1855   1.0862  -0.3173
 379  C3   C  CH1   0  -0.336  -1.7932   1.6827  -0.1005
 379  C6   C  CH2   0  -0.531  -3.5470  -0.0270   0.6686
 379  C8   C  CR6   0   0.044  -4.9584  -0.4973   0.4773
 379  N10  N  NH2   0  -0.819  -1.5508   2.9373  -0.8072
 379  C11  C  CH2   0  -0.726   1.0652   1.2495   0.2071
 379  O12  O  OH1   0  -0.762  -0.2157   0.8712  -2.1857
 379  C13  C  CH1   0  -0.359   2.3230   0.4485  -0.1300
 379  O13  O  O     0  -0.705  -0.5863  -0.8897  -0.3888
 379  C15  C  C     0   0.568   2.2419  -0.9527   0.4388
 379  C16  C  CH2   0  -0.493   3.5636   1.1430   0.4655
 379  C01  C  CR16  0  -0.112  -5.2390  -1.6927  -0.1777
 379  C17  C  CR6   0   0.119   4.8371   0.3886   0.2025
 379  N18  N  N     0  -0.401  -6.4640  -2.1525  -0.4036
 379  C19  C  CR16  0  -0.076  -7.4883  -1.4238   0.0220
 379  C20  C  CR16  0  -0.318  -7.3315  -0.2157   0.6865
 379  C21  C  CR16  0  -0.191  -6.0473   0.2502   0.9154
 379  O23  O  O     0  -0.447   2.0017  -1.1869   1.5975
 379  O24  O  OH1   0  -0.583   2.5324  -1.8877  -0.4519
 379  C36  C  CR16  0  -0.305   5.4418   0.4393  -1.0521
 379  C37  C  CR16  0  -0.239   6.5961  -0.2837  -1.3149
 379  C38  C  CR16  0  -0.271   7.1660  -1.0717  -0.3220
 379  C39  C  CR16  0  -0.240   6.5737  -1.1284   0.9317
 379  C40  C  CR16  0  -0.304   5.4176  -0.4026   1.1901
 379  H1   H  HCH2  0   0.254  -3.9038   1.9050  -0.2073
 379  H2   H  HCH2  0   0.243  -3.2880   0.7256  -1.3459
 379  H12  H  HCH1  0   0.282  -1.6532   1.8636   0.9700
 379  H6   H  HCH2  0   0.266  -2.8590  -0.8644   0.5537
 379  H7   H  HCH2  0   0.248  -3.4207   0.3469   1.6888
 379  H11  H  HNH2  0   0.363  -2.1137   2.9775  -1.6483
 379  H13  H  HNH2  0   0.372  -1.8384   3.7208  -0.2367
 379  H16  H  HCH2  0   0.295   1.1931   2.2921  -0.0933
 379  H17  H  HCH2  0   0.286   0.8939   1.2497   1.2865
 379  H4   H  HOH1  0   0.478  -0.1684   1.8188  -2.3788
 379  H18  H  HCH1  0   0.279   2.4470   0.3945  -1.2142
 379  H19  H  HCH2  0   0.267   3.6225   2.1435   0.0318
 379  H20  H  HCH2  0   0.257   3.4169   1.2729   1.5400
 379  H8   H  HCR6  0   0.252  -4.4203  -2.3118  -0.5341
 379  H10  H  HCR6  0   0.261  -8.4800  -1.8183  -0.1703
 379  H14  H  HCR6  0   0.269  -8.1976   0.3417   1.0164
 379  H15  H  HCR6  0   0.265  -5.8894   1.1879   1.4358
 379  H9   H  HOH1  0   0.476   2.5134  -2.7608  -0.0311
 379  H21  H  HCR6  0   0.246   5.0050   1.0533  -1.8315
 379  H22  H  HCR6  0   0.253   7.0530  -0.2315  -2.2949
 379  H25  H  HCR6  0   0.254   8.0683  -1.6343  -0.5241
 379  H23  H  HCR6  0   0.254   7.0120  -1.7375   1.7119
 379  H24  H  HCR6  0   0.248   4.9635  -0.4513   2.1729

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
 379  P11  C3   single    1.836  0.020  1.836
 379  P11  C11  single    1.816  0.020  1.816
 379  P11  O12  single    1.622  0.020  1.622
 379  P11  O13  double    1.494  0.020  1.494
 379  C1   C3   single    1.530  0.020  1.530
 379  C1   C6   single    1.530  0.020  1.530
 379  C3   N10  single    1.460  0.020  1.460
 379  C6   C8   single    1.500  0.020  1.500
 379  C8   C01  aromatic  1.392  0.020  1.392
 379  C8   C21  aromatic  1.392  0.020  1.392
 379  C11  C13  single    1.529  0.020  1.529
 379  C13  C15  single    1.514  0.020  1.514
 379  C13  C16  single    1.541  0.020  1.541
 379  C15  O23  double    1.206  0.020  1.206
 379  C15  O24  single    1.324  0.020  1.324
 379  C16  C17  single    1.503  0.020  1.503
 379  C01  N18  aromatic  1.328  0.020  1.328
 379  C17  C36  aromatic  1.394  0.020  1.394
 379  C17  C40  aromatic  1.392  0.020  1.392
 379  N18  C19  aromatic  1.327  0.020  1.327
 379  C19  C20  aromatic  1.388  0.020  1.388
 379  C20  C21  aromatic  1.385  0.020  1.385
 379  C36  C37  aromatic  1.387  0.020  1.387
 379  C37  C38  aromatic  1.390  0.020  1.390
 379  C38  C39  aromatic  1.388  0.020  1.388
 379  C39  C40  aromatic  1.389  0.020  1.389
 379  C1   H1   single    0.970  0.020  1.090
 379  C1   H2   single    0.970  0.020  1.090
 379  C3   H12  single    0.970  0.020  1.090
 379  C6   H6   single    0.970  0.020  1.090
 379  C6   H7   single    0.970  0.020  1.090
 379  N10  H11  single    0.890  0.020  1.040
 379  N10  H13  single    0.890  0.020  1.040
 379  C11  H16  single    0.970  0.020  1.090
 379  C11  H17  single    0.970  0.020  1.090
 379  O12  H4   single    0.850  0.020  0.980
 379  C13  H18  single    0.970  0.020  1.090
 379  C16  H19  single    0.970  0.020  1.090
 379  C16  H20  single    0.970  0.020  1.090
 379  C01  H8   single    0.930  0.020  1.080
 379  C19  H10  single    0.930  0.020  1.080
 379  C20  H14  single    0.930  0.020  1.080
 379  C21  H15  single    0.930  0.020  1.080
 379  O24  H9   single    0.850  0.020  0.980
 379  C36  H21  single    0.930  0.020  1.080
 379  C37  H22  single    0.930  0.020  1.080
 379  C38  H25  single    0.930  0.020  1.080
 379  C39  H23  single    0.930  0.020  1.080
 379  C40  H24  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
 379  O13  P11  O12  109.35  3.000
 379  O13  P11  C11  113.12  3.000
 379  O12  P11  C11  105.58  3.000
 379  O13  P11  C3   117.76  3.000
 379  O12  P11  C3   104.53  3.000
 379  C11  P11  C3   105.53  3.000
 379  H2   C1   H1   106.22  3.000
 379  H2   C1   C6   110.09  3.000
 379  H1   C1   C6   108.93  3.000
 379  H2   C1   C3   110.28  3.000
 379  H1   C1   C3   106.93  3.000
 379  C6   C1   C3   114.03  3.000
 379  H12  C3   N10  108.06  3.000
 379  H12  C3   C1   108.62  3.000
 379  N10  C3   C1   114.67  3.000
 379  H12  C3   P11  105.72  3.000
 379  N10  C3   P11  105.04  3.000
 379  C1   C3   P11  114.20  3.000
 379  H7   C6   H6   106.74  3.000
 379  H7   C6   C8   109.56  3.000
 379  H6   C6   C8   109.85  3.000
 379  H7   C6   C1   108.96  3.000
 379  H6   C6   C1   110.00  3.000
 379  C8   C6   C1   111.60  3.000
 379  C21  C8   C01  116.87  3.000
 379  C21  C8   C6   121.85  3.000
 379  C01  C8   C6   121.27  3.000
 379  H13  N10  H11  106.25  3.000
 379  H13  N10  C3   110.21  3.000
 379  H11  N10  C3   110.11  3.000
 379  H17  C11  H16  106.84  3.000
 379  H17  C11  C13  110.29  3.000
 379  H16  C11  C13  110.06  3.000
 379  H17  C11  P11  108.23  3.000
 379  H16  C11  P11  108.98  3.000
 379  C13  C11  P11  112.25  3.000
 379  H4   O12  P11  112.15  3.000
 379  H18  C13  C16  108.32  3.000
 379  H18  C13  C15  109.45  3.000
 379  C16  C13  C15  108.35  3.000
 379  H18  C13  C11  109.76  3.000
 379  C16  C13  C11  109.93  3.000
 379  C15  C13  C11  110.97  3.000
 379  O24  C15  O23  123.57  3.000
 379  O24  C15  C13  112.90  3.000
 379  O23  C15  C13  123.44  3.000
 379  H20  C16  H19  106.80  3.000
 379  H20  C16  C17  110.21  3.000
 379  H19  C16  C17  110.16  3.000
 379  H20  C16  C13  109.00  3.000
 379  H19  C16  C13  107.62  3.000
 379  C17  C16  C13  112.84  3.000
 379  H8   C01  N18  116.23  3.000
 379  H8   C01  C8   119.47  3.000
 379  N18  C01  C8   124.30  3.000
 379  C40  C17  C36  118.58  3.000
 379  C40  C17  C16  120.95  3.000
 379  C36  C17  C16  120.45  3.000
 379  C19  N18  C01  117.86  3.000
 379  H10  C19  C20  120.33  3.000
 379  H10  C19  N18  116.69  3.000
 379  C20  C19  N18  122.98  3.000
 379  H14  C20  C21  121.24  3.000
 379  H14  C20  C19  120.28  3.000
 379  C21  C20  C19  118.48  3.000
 379  H15  C21  C20  120.36  3.000
 379  H15  C21  C8   120.12  3.000
 379  C20  C21  C8   119.52  3.000
 379  H9   O24  C15  109.87  3.000
 379  H21  C36  C37  119.62  3.000
 379  H21  C36  C17  119.53  3.000
 379  C37  C36  C17  120.84  3.000
 379  H22  C37  C38  120.07  3.000
 379  H22  C37  C36  119.84  3.000
 379  C38  C37  C36  120.09  3.000
 379  H25  C38  C39  120.22  3.000
 379  H25  C38  C37  120.21  3.000
 379  C39  C38  C37  119.58  3.000
 379  H23  C39  C40  119.79  3.000
 379  H23  C39  C38  120.09  3.000
 379  C40  C39  C38  120.12  3.000
 379  H24  C40  C39  119.60  3.000
 379  H24  C40  C17  119.61  3.000
 379  C39  C40  C17  120.79  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
 379  CONST_01  C19  N18  C01  C8      0.00   0.0  0
 379  CONST_02  C19  C20  C21  C8      0.00   0.0  0
 379  CONST_03  C20  C21  C8   C01     0.00   0.0  0
 379  CONST_04  C20  C19  N18  C01     0.00   0.0  0
 379  CONST_05  C38  C37  C36  C17     0.00   0.0  0
 379  CONST_06  C38  C39  C40  C17     0.00   0.0  0
 379  CONST_07  C21  C8   C01  N18     0.00   0.0  0
 379  CONST_08  C21  C20  C19  N18     0.00   0.0  0
 379  CONST_09  C39  C40  C17  C36     0.00   0.0  0
 379  CONST_10  C39  C38  C37  C36     0.00   0.0  0
 379  CONST_11  C40  C17  C36  C37     0.00   0.0  0
 379  CONST_12  C40  C39  C38  C37     0.00   0.0  0
 379  CONST_13  N18  C01  C8   C6    180.00   0.0  0
 379  CONST_14  C20  C21  C8   C6    180.00   0.0  0
 379  CONST_15  C37  C36  C17  C16   180.00   0.0  0
 379  CONST_16  C39  C40  C17  C16   180.00   0.0  0
 379  CONST_17  H14  C20  C21  C8    180.00   0.0  0
 379  CONST_18  H15  C21  C8   C01   180.00   0.0  0
 379  CONST_19  H10  C19  N18  C01   180.00   0.0  0
 379  CONST_20  H22  C37  C36  C17   180.00   0.0  0
 379  CONST_21  H23  C39  C40  C17   180.00   0.0  0
 379  CONST_22  H8   C01  N18  C19   180.00   0.0  0
 379  CONST_23  H24  C40  C17  C36   180.00   0.0  0
 379  CONST_24  H25  C38  C37  C36   180.00   0.0  0
 379  CONST_25  H21  C36  C37  C38   180.00   0.0  0
 379  CONST_26  H9   O24  C15  C13   180.00   0.0  0
 379  Var_01    C01  C8   C6   C1    102.96  30.0  2
 379  Var_02    C36  C17  C16  C13    76.99  30.0  2
 379  Var_03    C8   C6   C1   C3    175.52  30.0  3
 379  Var_04    C13  C11  P11  C3   -179.07  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
 379  chir_02  C3   P11  C1   N10  positiv
 379  chir_03  C13  C16  C15  C11  negativ
 379  chir_04  P11  C11  O12  O13  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
 379  plan-1  C6   0.020
 379  plan-1  C8   0.020
 379  plan-1  C01  0.020
 379  plan-1  N18  0.020
 379  plan-1  C19  0.020
 379  plan-1  C20  0.020
 379  plan-1  C21  0.020
 379  plan-1  H8   0.020
 379  plan-1  H10  0.020
 379  plan-1  H14  0.020
 379  plan-1  H15  0.020
 379  plan-2  C16  0.020
 379  plan-2  C17  0.020
 379  plan-2  C36  0.020
 379  plan-2  C37  0.020
 379  plan-2  C38  0.020
 379  plan-2  C39  0.020
 379  plan-2  C40  0.020
 379  plan-2  H21  0.020
 379  plan-2  H22  0.020
 379  plan-2  H25  0.020
 379  plan-2  H23  0.020
 379  plan-2  H24  0.020
 379  plan-3  C13  0.020
 379  plan-3  C15  0.020
 379  plan-3  O23  0.020
 379  plan-3  O24  0.020
 379  plan-3  H9   0.020

