# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:14:47 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-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
 32Q  32Q  '(2S)-2-[4-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid'  ligand  54  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_32Q
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
 32Q  P11   P  P     0   1.249  -1.1087   0.4491  -0.2636
 32Q  C1    C  CH2   0  -0.444  -3.8851   0.9195  -0.4154
 32Q  C3    C  CH1   0  -0.336  -2.5435   1.5701  -0.0597
 32Q  C6    C  CH2   0  -0.530  -4.4004  -0.1399   0.5621
 32Q  C8    C  CR6   0   0.139  -5.7827  -0.5911   0.1804
 32Q  N10   N  NH2   0  -0.795  -2.2210   2.7312  -0.8788
 32Q  C11   C  CH2   0  -0.723   0.3665   1.3960   0.2107
 32Q  O12   O  O     0  -0.720  -1.0246  -0.1532  -1.6266
 32Q  C13   C  CH1   0  -0.353   1.6604   0.5937   0.0630
 32Q  O13   O  OH1   0  -0.751  -1.2320  -0.7381   0.8374
 32Q  C15   C  C     0   0.556   1.7446  -0.5134   1.0913
 32Q  C16   C  CH2   0  -0.496   2.8770   1.5221   0.2446
 32Q  C17   C  CR16  0  -0.311  -5.9636  -1.6697  -0.6828
 32Q  C18   C  CR6   0   0.103   4.1873   0.7977   0.1134
 32Q  C19   C  CR16  0  -0.240  -7.2355  -2.0601  -1.0810
 32Q  C20   C  CR16  0  -0.273  -8.3514  -1.3734  -0.6205
 32Q  C21   C  CR16  0  -0.240  -8.1843  -0.2969   0.2414
 32Q  C22   C  CR16  0  -0.309  -6.9102   0.0888   0.6367
 32Q  O23   O  O     0  -0.445   1.6175  -0.3324   2.2779
 32Q  O24   O  OH1   0  -0.581   2.0110  -1.6937   0.5558
 32Q  N24   N  NH2   0  -0.793   8.6994  -0.9512  -1.3929
 32Q  C36   C  CR16  0  -0.295   4.6979   0.4701  -1.1416
 32Q  C37   C  CR16  0  -0.271   5.8909  -0.2229  -1.2703
 32Q  C38   C  CR6   0   0.078   6.6125  -0.6182  -0.1448
 32Q  C39   C  CR16  0  -0.295   6.1076  -0.2847   1.1069
 32Q  C40   C  CR16  0  -0.291   4.9113   0.4100   1.2354
 32Q  H11   H  HCH2  0   0.252  -4.6192   1.7297  -0.4656
 32Q  H12   H  HCH2  0   0.238  -3.8263   0.4984  -1.4238
 32Q  H31   H  HCH1  0   0.276  -2.5601   1.8949   0.9865
 32Q  H61   H  HCH2  0   0.253  -3.7311  -1.0003   0.5828
 32Q  H62   H  HCH2  0   0.243  -4.4095   0.2783   1.5726
 32Q  H101  H  HNH2  0   0.352  -2.3725   2.5155  -1.8571
 32Q  H102  H  HNH2  0   0.365  -2.8532   3.4894  -0.6537
 32Q  H111  H  HCH2  0   0.300   0.3994   2.2622  -0.4516
 32Q  H112  H  HCH2  0   0.285   0.2551   1.7844   1.2266
 32Q  H131  H  HCH1  0   0.282   1.7028   0.1614  -0.9391
 32Q  H132  H  HOH1  0   0.484  -1.2806  -0.4476   1.7573
 32Q  H161  H  HCH2  0   0.267   2.8050   2.3081  -0.5103
 32Q  H162  H  HCH2  0   0.257   2.8116   2.0109   1.2196
 32Q  H171  H  HCR6  0   0.245  -5.0986  -2.2137  -1.0456
 32Q  H191  H  HCR6  0   0.253  -7.3542  -2.9034  -1.7494
 32Q  H201  H  HCR6  0   0.253  -9.3440  -1.6768  -0.9271
 32Q  H211  H  HCR6  0   0.253  -9.0478   0.2437   0.6079
 32Q  H221  H  HCR6  0   0.245  -6.7904   0.9273   1.3132
 32Q  H231  H  HCH2  0   0.238   7.6360  -2.4553  -0.4566
 32Q  H232  H  HCH2  0   0.213   8.4143  -1.3905   0.6909
 32Q  H3    H  HOH1  0   0.479   2.0925  -2.3642   1.2515
 32Q  H241  H  HNH2  0   0.343   9.0859  -0.0396  -1.1821
 32Q  H242  H  HNH2  0   0.353   9.4902  -1.5713  -1.5089
 32Q  H361  H  HCR6  0   0.243   4.1578   0.7667  -2.0339
 32Q  H371  H  HCR6  0   0.244   6.2748  -0.4528  -2.2558
 32Q  H391  H  HCR6  0   0.245   6.6572  -0.5641   1.9987
 32Q  H401  H  HCR6  0   0.246   4.5445   0.6607   2.2237
 32Q  C23   C  CH2   0  -0.340   7.8909  -1.4066  -0.2750

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
 32Q  P11  C3    single    1.832  0.020  1.832
 32Q  P11  C11   single    1.816  0.020  1.816
 32Q  P11  O12   double    1.492  0.020  1.492
 32Q  P11  O13   single    1.624  0.020  1.624
 32Q  C1   C3    single    1.533  0.020  1.533
 32Q  C1   C6    single    1.531  0.020  1.531
 32Q  C3   N10   single    1.457  0.020  1.457
 32Q  C6   C8    single    1.503  0.020  1.503
 32Q  C8   C17   aromatic  1.393  0.020  1.393
 32Q  C8   C22   aromatic  1.393  0.020  1.393
 32Q  C11  C13   single    1.530  0.020  1.530
 32Q  C13  C15   single    1.513  0.020  1.513
 32Q  C13  C16   single    1.541  0.020  1.541
 32Q  C15  O23   double    1.207  0.020  1.207
 32Q  C15  O24   single    1.323  0.020  1.323
 32Q  C16  C18   single    1.503  0.020  1.503
 32Q  C17  C19   aromatic  1.389  0.020  1.389
 32Q  C18  C36   aromatic  1.394  0.020  1.394
 32Q  C18  C40   aromatic  1.390  0.020  1.390
 32Q  C19  C20   aromatic  1.389  0.020  1.389
 32Q  C20  C21   aromatic  1.389  0.020  1.389
 32Q  C21  C22   aromatic  1.389  0.020  1.389
 32Q  C23  N24   single    1.453  0.020  1.453
 32Q  C23  C38   single    1.508  0.020  1.508
 32Q  C36  C37   aromatic  1.386  0.020  1.386
 32Q  C37  C38   aromatic  1.394  0.020  1.394
 32Q  C38  C39   aromatic  1.390  0.020  1.390
 32Q  C39  C40   aromatic  1.389  0.020  1.389
 32Q  C1   H11   single    0.970  0.020  1.090
 32Q  C1   H12   single    0.970  0.020  1.090
 32Q  C3   H31   single    0.970  0.020  1.090
 32Q  C6   H61   single    0.970  0.020  1.090
 32Q  C6   H62   single    0.970  0.020  1.090
 32Q  N10  H101  single    0.890  0.020  1.040
 32Q  N10  H102  single    0.890  0.020  1.040
 32Q  C11  H111  single    0.970  0.020  1.090
 32Q  C11  H112  single    0.970  0.020  1.090
 32Q  C13  H131  single    0.970  0.020  1.090
 32Q  O13  H132  single    0.850  0.020  0.980
 32Q  C16  H161  single    0.970  0.020  1.090
 32Q  C16  H162  single    0.970  0.020  1.090
 32Q  C17  H171  single    0.930  0.020  1.080
 32Q  C19  H191  single    0.930  0.020  1.080
 32Q  C20  H201  single    0.930  0.020  1.080
 32Q  C21  H211  single    0.930  0.020  1.080
 32Q  C22  H221  single    0.930  0.020  1.080
 32Q  C23  H231  single    0.970  0.020  1.090
 32Q  C23  H232  single    0.970  0.020  1.090
 32Q  O24  H3    single    0.850  0.020  0.980
 32Q  N24  H241  single    0.890  0.020  1.040
 32Q  N24  H242  single    0.890  0.020  1.040
 32Q  C36  H361  single    0.930  0.020  1.080
 32Q  C37  H371  single    0.930  0.020  1.080
 32Q  C39  H391  single    0.930  0.020  1.080
 32Q  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
 32Q  O13   P11  O12   109.18  3.000
 32Q  O13   P11  C11   105.42  3.000
 32Q  O12   P11  C11   113.78  3.000
 32Q  O13   P11  C3    108.20  3.000
 32Q  O12   P11  C3    113.12  3.000
 32Q  C11   P11  C3    106.74  3.000
 32Q  H12   C1   H11   106.18  3.000
 32Q  H12   C1   C6    109.89  3.000
 32Q  H11   C1   C6    108.41  3.000
 32Q  H12   C1   C3    109.27  3.000
 32Q  H11   C1   C3    106.47  3.000
 32Q  C6    C1   C3    116.11  3.000
 32Q  H31   C3   N10   107.69  3.000
 32Q  H31   C3   C1    109.52  3.000
 32Q  N10   C3   C1    113.67  3.000
 32Q  H31   C3   P11   107.43  3.000
 32Q  N10   C3   P11   104.58  3.000
 32Q  C1    C3   P11   113.57  3.000
 32Q  H62   C6   H61   106.82  3.000
 32Q  H62   C6   C8    109.98  3.000
 32Q  H61   C6   C8    109.42  3.000
 32Q  H62   C6   C1    109.15  3.000
 32Q  H61   C6   C1    110.59  3.000
 32Q  C8    C6   C1    110.80  3.000
 32Q  C22   C8   C17   118.40  3.000
 32Q  C22   C8   C6    120.96  3.000
 32Q  C17   C8   C6    120.60  3.000
 32Q  H102  N10  H101  106.30  3.000
 32Q  H102  N10  C3    109.49  3.000
 32Q  H101  N10  C3    109.88  3.000
 32Q  H112  C11  H111  106.57  3.000
 32Q  H112  C11  C13   111.24  3.000
 32Q  H111  C11  C13   109.41  3.000
 32Q  H112  C11  P11   110.19  3.000
 32Q  H111  C11  P11   106.25  3.000
 32Q  C13   C11  P11   112.85  3.000
 32Q  H131  C13  C16   108.42  3.000
 32Q  H131  C13  C15   109.38  3.000
 32Q  C16   C13  C15   108.46  3.000
 32Q  H131  C13  C11   109.21  3.000
 32Q  C16   C13  C11   109.90  3.000
 32Q  C15   C13  C11   111.42  3.000
 32Q  H132  O13  P11   115.45  3.000
 32Q  O24   C15  O23   123.56  3.000
 32Q  O24   C15  C13   112.87  3.000
 32Q  O23   C15  C13   123.54  3.000
 32Q  H162  C16  H161  106.91  3.000
 32Q  H162  C16  C18   110.23  3.000
 32Q  H161  C16  C18   110.12  3.000
 32Q  H162  C16  C13   109.11  3.000
 32Q  H161  C16  C13   107.46  3.000
 32Q  C18   C16  C13   112.81  3.000
 32Q  H171  C17  C19   119.58  3.000
 32Q  H171  C17  C8    119.48  3.000
 32Q  C19   C17  C8    120.94  3.000
 32Q  C40   C18  C36   118.05  3.000
 32Q  C40   C18  C16   121.19  3.000
 32Q  C36   C18  C16   120.74  3.000
 32Q  H191  C19  C20   120.12  3.000
 32Q  H191  C19  C17   119.77  3.000
 32Q  C20   C19  C17   120.12  3.000
 32Q  H201  C20  C21   120.22  3.000
 32Q  H201  C20  C19   120.29  3.000
 32Q  C21   C20  C19   119.49  3.000
 32Q  H211  C21  C22   119.78  3.000
 32Q  H211  C21  C20   120.07  3.000
 32Q  C22   C21  C20   120.15  3.000
 32Q  H221  C22  C21   119.60  3.000
 32Q  H221  C22  C8    119.49  3.000
 32Q  C21   C22  C8    120.91  3.000
 32Q  H3    O24  C15   110.08  3.000
 32Q  H242  N24  H241  106.11  3.000
 32Q  H242  N24  C23   109.34  3.000
 32Q  H241  N24  C23   109.54  3.000
 32Q  H361  C36  C37   119.29  3.000
 32Q  H361  C36  C18   119.61  3.000
 32Q  C37   C36  C18   121.10  3.000
 32Q  H371  C37  C38   119.42  3.000
 32Q  H371  C37  C36   119.75  3.000
 32Q  C38   C37  C36   120.83  3.000
 32Q  C39   C38  C37   118.09  3.000
 32Q  C39   C38  C23   120.74  3.000
 32Q  C37   C38  C23   121.16  3.000
 32Q  H391  C39  C40   119.30  3.000
 32Q  H391  C39  C38   119.65  3.000
 32Q  C40   C39  C38   121.05  3.000
 32Q  H401  C40  C39   119.44  3.000
 32Q  H401  C40  C18   119.68  3.000
 32Q  C39   C40  C18   120.88  3.000
 32Q  H232  C23  H231  105.72  3.000
 32Q  H232  C23  C38   108.68  3.000
 32Q  H231  C23  C38   108.54  3.000
 32Q  H232  C23  N24   114.00  3.000
 32Q  H231  C23  N24   107.60  3.000
 32Q  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
 32Q  CONST_01  C20   C19  C17  C8      0.00   0.0  0
 32Q  CONST_02  C20   C21  C22  C8      0.00   0.0  0
 32Q  CONST_03  C21   C22  C8   C17     0.00   0.0  0
 32Q  CONST_04  C21   C20  C19  C17     0.00   0.0  0
 32Q  CONST_05  C38   C37  C36  C18     0.00   0.0  0
 32Q  CONST_06  C38   C39  C40  C18     0.00   0.0  0
 32Q  CONST_07  C22   C8   C17  C19     0.00   0.0  0
 32Q  CONST_08  C22   C21  C20  C19     0.00   0.0  0
 32Q  CONST_09  C39   C40  C18  C36     0.00   0.0  0
 32Q  CONST_10  C39   C38  C37  C36     0.00   0.0  0
 32Q  CONST_11  C40   C18  C36  C37     0.00   0.0  0
 32Q  CONST_12  C40   C39  C38  C37     0.00   0.0  0
 32Q  CONST_13  C19   C17  C8   C6    180.00   0.0  0
 32Q  CONST_14  C21   C22  C8   C6    180.00   0.0  0
 32Q  CONST_15  C37   C36  C18  C16   180.00   0.0  0
 32Q  CONST_16  C39   C40  C18  C16   180.00   0.0  0
 32Q  CONST_17  C36   C37  C38  C23   180.00   0.0  0
 32Q  CONST_18  C40   C39  C38  C23   180.00   0.0  0
 32Q  CONST_19  H191  C19  C17  C8    180.00   0.0  0
 32Q  CONST_20  H211  C21  C22  C8    180.00   0.0  0
 32Q  CONST_21  H221  C22  C8   C17   180.00   0.0  0
 32Q  CONST_22  H201  C20  C19  C17   180.00   0.0  0
 32Q  CONST_23  H371  C37  C36  C18   180.00   0.0  0
 32Q  CONST_24  H391  C39  C40  C18   180.00   0.0  0
 32Q  CONST_25  H171  C17  C19  C20   180.00   0.0  0
 32Q  CONST_26  H401  C40  C18  C36   180.00   0.0  0
 32Q  CONST_27  H361  C36  C37  C38   180.00   0.0  0
 32Q  CONST_28  H3    O24  C15  C13   180.00   0.0  0
 32Q  Var_01    C17   C8   C6   C1     90.22  30.0  2
 32Q  Var_02    C36   C18  C16  C13    78.59  30.0  2
 32Q  Var_03    C37   C38  C23  N24    39.10  30.0  2
 32Q  Var_04    C8    C6   C1   C3    173.97  30.0  3
 32Q  Var_05    H241  N24  C23  C38    70.59  30.0  3
 32Q  Var_06    C13   C11  P11  C3   -178.78  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
 32Q  chir_02  C3   P11  C1   N10  positiv
 32Q  chir_03  C13  C16  C15  C11  negativ
 32Q  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
 32Q  plan-1  C6    0.020
 32Q  plan-1  C8    0.020
 32Q  plan-1  C17   0.020
 32Q  plan-1  C19   0.020
 32Q  plan-1  C20   0.020
 32Q  plan-1  C21   0.020
 32Q  plan-1  C22   0.020
 32Q  plan-1  H171  0.020
 32Q  plan-1  H191  0.020
 32Q  plan-1  H201  0.020
 32Q  plan-1  H211  0.020
 32Q  plan-1  H221  0.020
 32Q  plan-2  C16   0.020
 32Q  plan-2  C18   0.020
 32Q  plan-2  C36   0.020
 32Q  plan-2  C37   0.020
 32Q  plan-2  C38   0.020
 32Q  plan-2  C39   0.020
 32Q  plan-2  C40   0.020
 32Q  plan-2  H361  0.020
 32Q  plan-2  H371  0.020
 32Q  plan-2  H391  0.020
 32Q  plan-2  H401  0.020
 32Q  plan-2  C23   0.020
 32Q  plan-3  C13   0.020
 32Q  plan-3  C15   0.020
 32Q  plan-3  O23   0.020
 32Q  plan-3  O24   0.020
 32Q  plan-3  H3    0.020

