# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 15:46:16 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2R)-2-[4-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(C[C@@H](C[P](O)(=O)[C@@H](N)CCc2ccccc2)C(O)=O)cc1
#
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
 32R  32R  '(2R)-2-[4-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid'  ligand  52  27  .  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_32R
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
 32R  P11   P  P      0   1.182  -1.1826   0.3776  -0.1722
 32R  C1    C  CH2    0  -0.413  -3.9283   0.8468   0.2491
 32R  C3    C  CH1    0  -0.330  -2.5416   1.3265   0.6773
 32R  C6    C  CH2    0  -0.519  -4.3014  -0.5662   0.7027
 32R  C8    C  CR6    0   0.143  -5.7083  -0.9123   0.3044
 32R  N10   N  NH2    0  -0.806  -2.4581   2.7674   0.4107
 32R  C11   C  CH2    0  -0.709   0.3265   1.2468   0.4287
 32R  O12   O  O      0  -0.821  -1.3579   0.5998  -1.6639
 32R  C13   C  CH1    0  -0.317   1.6237   0.5340   0.0477
 32R  O13   O  OP    -1  -0.821  -1.1387  -1.0475   0.3568
 32R  C15   C  C      0   0.438   1.8866   0.6033  -1.4694
 32R  C16   C  CH2    0  -0.482   2.8019   1.1648   0.8075
 32R  C17   C  CR16   0  -0.316  -5.9723  -1.5322  -0.9158
 32R  C18   C  CR6    0   0.125   4.1137   0.4856   0.5370
 32R  C19   C  CR16   0  -0.240  -7.2745  -1.8139  -1.3082
 32R  C20   C  CR16   0  -0.277  -8.3397  -1.4789  -0.4823
 32R  C21   C  CR16   0  -0.240  -8.0911  -0.8626   0.7377
 32R  C22   C  CR16   0  -0.312  -6.7869  -0.5822   1.1234
 32R  O23   O  O      0  -0.627   2.0045   1.7483  -1.9569
 32R  O24   O  OC    -1  -0.624   1.9972  -0.4719  -2.0891
 32R  N24   N  NH2    0  -0.793   8.5023  -2.0354   0.9021
 32R  C36   C  CR16   0  -0.288   4.9913   0.9621  -0.4321
 32R  C37   C  CR16   0  -0.300   6.1953   0.3183  -0.6875
 32R  C38   C  CR6    0   0.072   6.5591  -0.8293   0.0094
 32R  C39   C  CR16   0  -0.273   5.6836  -1.3083   0.9821
 32R  C40   C  CR16   0  -0.308   4.4840  -0.6611   1.2381
 32R  H11   H  HCH2   0   0.219  -4.6636   1.5518   0.6506
 32R  H12   H  HCH2   0   0.214  -4.0075   0.9094  -0.8415
 32R  H31   H  HCH1   0   0.215  -2.4459   1.1855   1.7606
 32R  H61   H  HCH2   0   0.248  -3.6014  -1.2869   0.2812
 32R  H62   H  HCH2   0   0.225  -4.2006  -0.6310   1.7902
 32R  H101  H  HNH2   0   0.347  -1.6035   3.1391   0.8072
 32R  H102  H  HNH2   0   0.330  -2.3686   2.9012  -0.5915
 32R  H111  H  HCH2   0   0.219   0.3629   2.2711   0.0509
 32R  H112  H  HCH2   0   0.216   0.2548   1.3153   1.5212
 32R  H131  H  HCH1   0   0.199   1.5466  -0.5154   0.3478
 32R  H161  H  HCH2   0   0.223   2.8699   2.2214   0.5377
 32R  H162  H  HCH2   0   0.223   2.5887   1.1262   1.8803
 32R  H171  H  HCR6   0   0.243  -5.1468  -1.8006  -1.5660
 32R  H191  H  HCR6   0   0.250  -7.4581  -2.2993  -2.2585
 32R  H201  H  HCR6   0   0.251  -9.3552  -1.6981  -0.7862
 32R  H211  H  HCR6   0   0.250  -8.9144  -0.6021   1.3911
 32R  H221  H  HCR6   0   0.242  -6.6010  -0.1020   2.0779
 32R  H231  H  HCH2   0   0.210   8.4817  -0.8731  -0.9039
 32R  H232  H  HCH2   0   0.234   7.6355  -2.4025  -0.9391
 32R  H241  H  HNH2   0   0.351   9.3253  -2.5639   0.6428
 32R  H242  H  HNH2   0   0.341   8.8358  -1.2516   1.4494
 32R  H361  H  HCR6   0   0.234   4.7291   1.8513  -0.9925
 32R  H371  H  HCR6   0   0.238   6.8649   0.7226  -1.4389
 32R  H391  H  HCR6   0   0.238   5.9511  -2.1914   1.5488
 32R  H401  H  HCR6   0   0.234   3.8230  -1.0535   2.0034
 32R  C23   C  CH2    0  -0.340   7.8518  -1.5406  -0.3002

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
 32R  P11  C3    single    1.863  0.020  1.863
 32R  P11  C11   single    1.842  0.020  1.842
 32R  P11  O12   deloc     1.518  0.020  1.518
 32R  P11  O13   deloc     1.521  0.020  1.521
 32R  C1   C3    single    1.528  0.020  1.528
 32R  C1   C6    single    1.530  0.020  1.530
 32R  C3   N10   single    1.468  0.020  1.468
 32R  C6   C8    single    1.503  0.020  1.503
 32R  C8   C17   aromatic  1.394  0.020  1.394
 32R  C8   C22   aromatic  1.394  0.020  1.394
 32R  C11  C13   single    1.528  0.020  1.528
 32R  C13  C15   single    1.541  0.020  1.541
 32R  C13  C16   single    1.537  0.020  1.537
 32R  C15  O23   deloc     1.250  0.020  1.250
 32R  C15  O24   deloc     1.246  0.020  1.246
 32R  C16  C18   single    1.502  0.020  1.502
 32R  C17  C19   aromatic  1.389  0.020  1.389
 32R  C18  C36   aromatic  1.392  0.020  1.392
 32R  C18  C40   aromatic  1.394  0.020  1.394
 32R  C19  C20   aromatic  1.389  0.020  1.389
 32R  C20  C21   aromatic  1.389  0.020  1.389
 32R  C21  C22   aromatic  1.389  0.020  1.389
 32R  C23  N24   single    1.454  0.020  1.454
 32R  C23  C38   single    1.508  0.020  1.508
 32R  C36  C37   aromatic  1.389  0.020  1.389
 32R  C37  C38   aromatic  1.391  0.020  1.391
 32R  C38  C39   aromatic  1.394  0.020  1.394
 32R  C39  C40   aromatic  1.387  0.020  1.387
 32R  C1   H11   single    0.970  0.020  1.090
 32R  C1   H12   single    0.970  0.020  1.090
 32R  C3   H31   single    0.970  0.020  1.090
 32R  C6   H61   single    0.970  0.020  1.090
 32R  C6   H62   single    0.970  0.020  1.090
 32R  N10  H101  single    0.890  0.020  1.040
 32R  N10  H102  single    0.890  0.020  1.040
 32R  C11  H111  single    0.970  0.020  1.090
 32R  C11  H112  single    0.970  0.020  1.090
 32R  C13  H131  single    0.970  0.020  1.090
 32R  C16  H161  single    0.970  0.020  1.090
 32R  C16  H162  single    0.970  0.020  1.090
 32R  C17  H171  single    0.930  0.020  1.080
 32R  C19  H191  single    0.930  0.020  1.080
 32R  C20  H201  single    0.930  0.020  1.080
 32R  C21  H211  single    0.930  0.020  1.080
 32R  C22  H221  single    0.930  0.020  1.080
 32R  C23  H231  single    0.970  0.020  1.090
 32R  C23  H232  single    0.970  0.020  1.090
 32R  N24  H241  single    0.890  0.020  1.040
 32R  N24  H242  single    0.890  0.020  1.040
 32R  C36  H361  single    0.930  0.020  1.080
 32R  C37  H371  single    0.930  0.020  1.080
 32R  C39  H391  single    0.930  0.020  1.080
 32R  C40  H401  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
 32R  O13   P11  O12   118.84  3.000
 32R  O13   P11  C11   107.76  3.000
 32R  O12   P11  C11   110.24  3.000
 32R  O13   P11  C3    109.87  3.000
 32R  O12   P11  C3    106.82  3.000
 32R  C11   P11  C3    102.04  3.000
 32R  H12   C1   H11   106.25  3.000
 32R  H12   C1   C6    109.29  3.000
 32R  H11   C1   C6    108.79  3.000
 32R  H12   C1   C3    109.06  3.000
 32R  H11   C1   C3    107.72  3.000
 32R  C6    C1   C3    115.34  3.000
 32R  H31   C3   N10   107.49  3.000
 32R  H31   C3   C1    108.40  3.000
 32R  N10   C3   C1    107.99  3.000
 32R  H31   C3   P11   108.75  3.000
 32R  N10   C3   P11   112.07  3.000
 32R  C1    C3   P11   111.98  3.000
 32R  H62   C6   H61   106.63  3.000
 32R  H62   C6   C8    109.64  3.000
 32R  H61   C6   C8    110.28  3.000
 32R  H62   C6   C1    109.08  3.000
 32R  H61   C6   C1    109.85  3.000
 32R  C8    C6   C1    111.25  3.000
 32R  C22   C8   C17   118.24  3.000
 32R  C22   C8   C6    120.94  3.000
 32R  C17   C8   C6    120.79  3.000
 32R  H102  N10  H101  105.29  3.000
 32R  H102  N10  C3    108.29  3.000
 32R  H101  N10  C3    109.71  3.000
 32R  H112  C11  H111  106.73  3.000
 32R  H112  C11  C13   109.44  3.000
 32R  H111  C11  C13   108.84  3.000
 32R  H112  C11  P11   107.51  3.000
 32R  H111  C11  P11   110.91  3.000
 32R  C13   C11  P11   113.20  3.000
 32R  H131  C13  C16   108.18  3.000
 32R  H131  C13  C15   108.97  3.000
 32R  C16   C13  C15   109.71  3.000
 32R  H131  C13  C11   108.61  3.000
 32R  C16   C13  C11   109.63  3.000
 32R  C15   C13  C11   111.66  3.000
 32R  O24   C15  O23   126.02  3.000
 32R  O24   C15  C13   117.77  3.000
 32R  O23   C15  C13   116.18  3.000
 32R  H162  C16  H161  106.75  3.000
 32R  H162  C16  C18   109.32  3.000
 32R  H161  C16  C18   109.78  3.000
 32R  H162  C16  C13   108.71  3.000
 32R  H161  C16  C13   108.81  3.000
 32R  C18   C16  C13   113.26  3.000
 32R  H171  C17  C19   119.60  3.000
 32R  H171  C17  C8    119.39  3.000
 32R  C19   C17  C8    121.01  3.000
 32R  C40   C18  C36   117.67  3.000
 32R  C40   C18  C16   120.89  3.000
 32R  C36   C18  C16   121.43  3.000
 32R  H191  C19  C20   119.99  3.000
 32R  H191  C19  C17   119.87  3.000
 32R  C20   C19  C17   120.14  3.000
 32R  H201  C20  C21   120.28  3.000
 32R  H201  C20  C19   120.25  3.000
 32R  C21   C20  C19   119.47  3.000
 32R  H211  C21  C22   119.86  3.000
 32R  H211  C21  C20   120.04  3.000
 32R  C22   C21  C20   120.10  3.000
 32R  H221  C22  C21   119.66  3.000
 32R  H221  C22  C8    119.29  3.000
 32R  C21   C22  C8    121.04  3.000
 32R  H242  N24  H241  105.96  3.000
 32R  H242  N24  C23   109.33  3.000
 32R  H241  N24  C23   109.25  3.000
 32R  H361  C36  C37   119.68  3.000
 32R  H361  C36  C18   119.25  3.000
 32R  C37   C36  C18   121.06  3.000
 32R  H371  C37  C38   119.55  3.000
 32R  H371  C37  C36   119.32  3.000
 32R  C38   C37  C36   121.13  3.000
 32R  C39   C38  C37   117.97  3.000
 32R  C39   C38  C23   121.32  3.000
 32R  C37   C38  C23   120.71  3.000
 32R  H391  C39  C40   119.84  3.000
 32R  H391  C39  C38   119.37  3.000
 32R  C40   C39  C38   120.78  3.000
 32R  H401  C40  C39   119.24  3.000
 32R  H401  C40  C18   119.38  3.000
 32R  C39   C40  C18   121.38  3.000
 32R  H232  C23  H231  105.73  3.000
 32R  H232  C23  C38   108.78  3.000
 32R  H231  C23  C38   108.53  3.000
 32R  H232  C23  N24   107.65  3.000
 32R  H231  C23  N24   113.88  3.000
 32R  C38   C23  N24   111.99  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
 32R  CONST_01  C20   C19  C17  C8     0.00   0.0  0
 32R  CONST_02  C20   C21  C22  C8     0.00   0.0  0
 32R  CONST_03  C21   C22  C8   C17    0.00   0.0  0
 32R  CONST_04  C21   C20  C19  C17    0.00   0.0  0
 32R  CONST_05  C38   C37  C36  C18    0.00   0.0  0
 32R  CONST_06  C38   C39  C40  C18    0.00   0.0  0
 32R  CONST_07  C22   C8   C17  C19    0.00   0.0  0
 32R  CONST_08  C22   C21  C20  C19    0.00   0.0  0
 32R  CONST_09  C39   C40  C18  C36    0.00   0.0  0
 32R  CONST_10  C39   C38  C37  C36    0.00   0.0  0
 32R  CONST_11  C40   C18  C36  C37    0.00   0.0  0
 32R  CONST_12  C40   C39  C38  C37    0.00   0.0  0
 32R  CONST_13  C19   C17  C8   C6   180.00   0.0  0
 32R  CONST_14  C21   C22  C8   C6   180.00   0.0  0
 32R  CONST_15  C37   C36  C18  C16  180.00   0.0  0
 32R  CONST_16  C39   C40  C18  C16  180.00   0.0  0
 32R  CONST_17  C36   C37  C38  C23  180.00   0.0  0
 32R  CONST_18  C40   C39  C38  C23  180.00   0.0  0
 32R  CONST_19  H191  C19  C17  C8   180.00   0.0  0
 32R  CONST_20  H211  C21  C22  C8   180.00   0.0  0
 32R  CONST_21  H221  C22  C8   C17  180.00   0.0  0
 32R  CONST_22  H201  C20  C19  C17  180.00   0.0  0
 32R  CONST_23  H371  C37  C36  C18  180.00   0.0  0
 32R  CONST_24  H391  C39  C40  C18  180.00   0.0  0
 32R  CONST_25  H171  C17  C19  C20  180.00   0.0  0
 32R  CONST_26  H401  C40  C18  C36  180.00   0.0  0
 32R  CONST_27  H361  C36  C37  C38  180.00   0.0  0
 32R  Var_01    C17   C8   C6   C1    90.85  30.0  2
 32R  Var_02    C36   C18  C16  C13   95.40  30.0  2
 32R  Var_03    C37   C38  C23  N24  141.16  30.0  2
 32R  Var_04    C8    C6   C1   C3   176.61  30.0  3
 32R  Var_05    H241  N24  C23  C38  175.75  30.0  3
 32R  Var_06    C13   C11  P11  C3   171.23  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
 32R  chir_02  C3   P11  C1   N10  positiv
 32R  chir_03  C13  C16  C15  C11  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
 32R  plan-1  C6    0.020
 32R  plan-1  C8    0.020
 32R  plan-1  C17   0.020
 32R  plan-1  C19   0.020
 32R  plan-1  C20   0.020
 32R  plan-1  C21   0.020
 32R  plan-1  C22   0.020
 32R  plan-1  H171  0.020
 32R  plan-1  H191  0.020
 32R  plan-1  H201  0.020
 32R  plan-1  H211  0.020
 32R  plan-1  H221  0.020
 32R  plan-2  C16   0.020
 32R  plan-2  C18   0.020
 32R  plan-2  C36   0.020
 32R  plan-2  C37   0.020
 32R  plan-2  C38   0.020
 32R  plan-2  C39   0.020
 32R  plan-2  C40   0.020
 32R  plan-2  H361  0.020
 32R  plan-2  H371  0.020
 32R  plan-2  H391  0.020
 32R  plan-2  H401  0.020
 32R  plan-2  C23   0.020
 32R  plan-3  C13   0.020
 32R  plan-3  C15   0.020
 32R  plan-3  O23   0.020
 32R  plan-3  O24   0.020

