# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:05:43 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-2-[3-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(C[C@H](C[P](O)(=O)[C@@H](N)CCc2ccccc2)C(O)=O)c1
#
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
 3DZ  3DZ  '(2S)-2-[3-(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_3DZ
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
 3DZ  OAA  O  O     0  -0.446  -1.8267   1.1750   1.4532
 3DZ  CAB  C  C     0   0.559  -1.8398   0.8358   0.2950
 3DZ  OAC  O  OH1   0  -0.579  -2.0479   1.6701  -0.7101
 3DZ  CAD  C  CH1   0  -0.349  -1.6753  -0.5989  -0.1583
 3DZ  CAE  C  CH2   0  -0.495  -2.9280  -1.3919   0.2660
 3DZ  CAF  C  CR6   0   0.137  -4.2080  -0.7919  -0.2446
 3DZ  CAK  C  CR16  0  -0.328  -4.5988  -0.9638  -1.5697
 3DZ  CAJ  C  CR16  0  -0.224  -5.7703  -0.3823  -2.0325
 3DZ  CAI  C  CR16  0  -0.308  -6.5636   0.3768  -1.1823
 3DZ  CAH  C  CR6   0   0.112  -6.1908   0.5623   0.1457
 3DZ  CAZ  C  CH2   0  -0.338  -7.0147   1.4081   1.0846
 3DZ  NBA  N  NH2   0  -0.793  -8.4383   1.2917   0.8227
 3DZ  CAG  C  CR16  0  -0.367  -5.0157  -0.0326   0.5966
 3DZ  CAL  C  CH2   0  -0.741  -0.4314  -1.2428   0.4578
 3DZ  PAM  P  P     0   1.228   1.1255  -0.5737  -0.2033
 3DZ  OAN  O  O     0  -0.718   1.2358  -0.6796  -1.6880
 3DZ  OAO  O  OH1   0  -0.753   1.1226   0.9927   0.2284
 3DZ  CAP  C  CH1   0  -0.334   2.4819  -1.4274   0.7020
 3DZ  NAQ  N  NH2   0  -0.794   2.3328  -2.8712   0.6002
 3DZ  CAR  C  CH2   0  -0.429   3.8657  -1.0278   0.1859
 3DZ  CAS  C  CH2   0  -0.529   4.2921   0.4106   0.4839
 3DZ  CAT  C  CR6   0   0.141   5.7352   0.6327   0.1223
 3DZ  CAU  C  CR16  0  -0.306   6.7544   0.2507   0.9933
 3DZ  CAY  C  CR16  0  -0.316   6.0859   1.1919  -1.1041
 3DZ  CAX  C  CR16  0  -0.239   7.4192   1.3669  -1.4531
 3DZ  CAW  C  CR16  0  -0.274   8.4251   0.9836  -0.5764
 3DZ  CAV  C  CR16  0  -0.240   8.0881   0.4246   0.6505
 3DZ  H1   H  HOH1  0   0.479  -2.1885   2.5682  -0.3727
 3DZ  H2   H  HCH1  0   0.283  -1.5976  -0.6305  -1.2472
 3DZ  H3   H  HCH2  0   0.269  -2.8100  -2.4113  -0.1081
 3DZ  H4   H  HCH2  0   0.257  -2.9538  -1.4564   1.3558
 3DZ  H5   H  HCR6  0   0.245  -3.9920  -1.5628  -2.2390
 3DZ  H6   H  HCR6  0   0.249  -6.0704  -0.5256  -3.0630
 3DZ  H7   H  HCR6  0   0.245  -7.4813   0.8203  -1.5458
 3DZ  H8   H  HCH2  0   0.213  -6.7283   1.1617   2.1159
 3DZ  H9   H  HCH2  0   0.240  -6.7353   2.4566   0.9420
 3DZ  H10  H  HNH2  0   0.343  -8.7605   0.3729   1.0998
 3DZ  H11  H  HNH2  0   0.353  -8.9398   1.9516   1.4028
 3DZ  H13  H  HCR6  0   0.240  -4.7245   0.0921   1.6347
 3DZ  H14  H  HCH2  0   0.290  -0.4437  -1.1474   1.5469
 3DZ  H15  H  HCH2  0   0.293  -0.4519  -2.3123   0.2371
 3DZ  H16  H  HOH1  0   0.485   1.0833   1.1597   1.1792
 3DZ  H17  H  HCH1  0   0.275   2.4064  -1.1555   1.7603
 3DZ  H18  H  HNH2  0   0.367   1.4957  -3.1991   1.0629
 3DZ  H19  H  HNH2  0   0.356   2.2823  -3.1686  -0.3668
 3DZ  H21  H  HCH2  0   0.253   4.5740  -1.7119   0.6598
 3DZ  H22  H  HCH2  0   0.241   3.9269  -1.2163  -0.8901
 3DZ  H23  H  HCH2  0   0.252   3.6734   1.1208  -0.0649
 3DZ  H24  H  HCH2  0   0.243   4.1429   0.6170   1.5476
 3DZ  H25  H  HCR6  0   0.246   6.4989  -0.1846   1.9530
 3DZ  H26  H  HCR6  0   0.245   5.3069   1.4974  -1.7936
 3DZ  H27  H  HCR6  0   0.253   7.6725   1.8070  -2.4092
 3DZ  H28  H  HCR6  0   0.253   9.4643   1.1212  -0.8459
 3DZ  H29  H  HCR6  0   0.252   8.8656   0.1269   1.3428

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
 3DZ  OAN  PAM  double    1.493  0.020  1.493
 3DZ  CAE  CAF  single    1.503  0.020  1.503
 3DZ  CAE  CAD  single    1.542  0.020  1.542
 3DZ  CAP  PAM  single    1.841  0.020  1.841
 3DZ  CAP  NAQ  single    1.455  0.020  1.455
 3DZ  CAP  CAR  single    1.530  0.020  1.530
 3DZ  CAL  PAM  single    1.819  0.020  1.819
 3DZ  CAL  CAD  single    1.530  0.020  1.530
 3DZ  PAM  OAO  single    1.625  0.020  1.625
 3DZ  CAU  CAV  aromatic  1.388  0.020  1.388
 3DZ  CAU  CAT  aromatic  1.394  0.020  1.394
 3DZ  CAV  CAW  aromatic  1.390  0.020  1.390
 3DZ  CAF  CAK  aromatic  1.392  0.020  1.392
 3DZ  CAF  CAG  aromatic  1.392  0.020  1.392
 3DZ  CAK  CAJ  aromatic  1.387  0.020  1.387
 3DZ  CAG  CAH  aromatic  1.392  0.020  1.392
 3DZ  CAJ  CAI  aromatic  1.389  0.020  1.389
 3DZ  CAH  CAI  aromatic  1.392  0.020  1.392
 3DZ  CAH  CAZ  single    1.509  0.020  1.509
 3DZ  CAD  CAB  single    1.514  0.020  1.514
 3DZ  CAZ  NBA  single    1.452  0.020  1.452
 3DZ  CAS  CAR  single    1.530  0.020  1.530
 3DZ  CAS  CAT  single    1.504  0.020  1.504
 3DZ  CAT  CAY  aromatic  1.393  0.020  1.393
 3DZ  CAW  CAX  aromatic  1.388  0.020  1.388
 3DZ  OAA  CAB  double    1.207  0.020  1.207
 3DZ  CAB  OAC  single    1.323  0.020  1.323
 3DZ  CAX  CAY  aromatic  1.389  0.020  1.389
 3DZ  OAC  H1   single    0.850  0.020  0.980
 3DZ  CAD  H2   single    0.970  0.020  1.090
 3DZ  CAE  H3   single    0.970  0.020  1.090
 3DZ  CAE  H4   single    0.970  0.020  1.090
 3DZ  CAK  H5   single    0.930  0.020  1.080
 3DZ  CAJ  H6   single    0.930  0.020  1.080
 3DZ  CAI  H7   single    0.930  0.020  1.080
 3DZ  CAZ  H8   single    0.970  0.020  1.090
 3DZ  CAZ  H9   single    0.970  0.020  1.090
 3DZ  NBA  H10  single    0.890  0.020  1.040
 3DZ  NBA  H11  single    0.890  0.020  1.040
 3DZ  CAG  H13  single    0.930  0.020  1.080
 3DZ  CAL  H14  single    0.970  0.020  1.090
 3DZ  CAL  H15  single    0.970  0.020  1.090
 3DZ  OAO  H16  single    0.850  0.020  0.980
 3DZ  CAP  H17  single    0.970  0.020  1.090
 3DZ  NAQ  H18  single    0.890  0.020  1.040
 3DZ  NAQ  H19  single    0.890  0.020  1.040
 3DZ  CAR  H21  single    0.970  0.020  1.090
 3DZ  CAR  H22  single    0.970  0.020  1.090
 3DZ  CAS  H23  single    0.970  0.020  1.090
 3DZ  CAS  H24  single    0.970  0.020  1.090
 3DZ  CAU  H25  single    0.930  0.020  1.080
 3DZ  CAY  H26  single    0.930  0.020  1.080
 3DZ  CAX  H27  single    0.930  0.020  1.080
 3DZ  CAW  H28  single    0.930  0.020  1.080
 3DZ  CAV  H29  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
 3DZ  CAD  CAB  OAC  112.79  3.000
 3DZ  OAC  CAB  OAA  123.62  3.000
 3DZ  CAD  CAB  OAA  123.54  3.000
 3DZ  H1   OAC  CAB  110.04  3.000
 3DZ  H2   CAD  CAL  109.35  3.000
 3DZ  H2   CAD  CAE  108.49  3.000
 3DZ  CAL  CAD  CAE  109.46  3.000
 3DZ  H2   CAD  CAB  109.50  3.000
 3DZ  CAL  CAD  CAB  111.51  3.000
 3DZ  CAE  CAD  CAB  108.47  3.000
 3DZ  H4   CAE  H3   106.81  3.000
 3DZ  H4   CAE  CAF  110.03  3.000
 3DZ  H3   CAE  CAF  110.38  3.000
 3DZ  H4   CAE  CAD  108.91  3.000
 3DZ  H3   CAE  CAD  107.33  3.000
 3DZ  CAF  CAE  CAD  113.14  3.000
 3DZ  CAG  CAF  CAK  118.67  3.000
 3DZ  CAG  CAF  CAE  120.45  3.000
 3DZ  CAK  CAF  CAE  120.87  3.000
 3DZ  H5   CAK  CAJ  119.88  3.000
 3DZ  H5   CAK  CAF  119.92  3.000
 3DZ  CAJ  CAK  CAF  120.19  3.000
 3DZ  H6   CAJ  CAI  119.78  3.000
 3DZ  H6   CAJ  CAK  119.74  3.000
 3DZ  CAI  CAJ  CAK  120.48  3.000
 3DZ  H7   CAI  CAH  119.54  3.000
 3DZ  H7   CAI  CAJ  120.18  3.000
 3DZ  CAH  CAI  CAJ  120.27  3.000
 3DZ  CAG  CAH  CAZ  119.94  3.000
 3DZ  CAZ  CAH  CAI  121.49  3.000
 3DZ  CAG  CAH  CAI  118.57  3.000
 3DZ  H9   CAZ  H8   105.71  3.000
 3DZ  H9   CAZ  NBA  107.67  3.000
 3DZ  H8   CAZ  NBA  114.02  3.000
 3DZ  H9   CAZ  CAH  108.46  3.000
 3DZ  H8   CAZ  CAH  108.43  3.000
 3DZ  NBA  CAZ  CAH  112.22  3.000
 3DZ  H11  NBA  H10  106.10  3.000
 3DZ  H11  NBA  CAZ  109.29  3.000
 3DZ  H10  NBA  CAZ  109.60  3.000
 3DZ  H13  CAG  CAH  119.15  3.000
 3DZ  H13  CAG  CAF  119.02  3.000
 3DZ  CAH  CAG  CAF  121.83  3.000
 3DZ  H15  CAL  H14  106.65  3.000
 3DZ  H15  CAL  PAM  107.62  3.000
 3DZ  H14  CAL  PAM  109.85  3.000
 3DZ  H15  CAL  CAD  108.39  3.000
 3DZ  H14  CAL  CAD  110.80  3.000
 3DZ  PAM  CAL  CAD  113.25  3.000
 3DZ  CAP  PAM  OAO  108.53  3.000
 3DZ  OAO  PAM  OAN  109.44  3.000
 3DZ  CAP  PAM  OAN  113.70  3.000
 3DZ  OAO  PAM  CAL  104.86  3.000
 3DZ  CAP  PAM  CAL  106.34  3.000
 3DZ  OAN  PAM  CAL  113.49  3.000
 3DZ  H16  OAO  PAM  115.35  3.000
 3DZ  H17  CAP  CAR  108.87  3.000
 3DZ  H17  CAP  NAQ  107.87  3.000
 3DZ  CAR  CAP  NAQ  109.17  3.000
 3DZ  H17  CAP  PAM  108.02  3.000
 3DZ  CAR  CAP  PAM  112.30  3.000
 3DZ  NAQ  CAP  PAM  110.50  3.000
 3DZ  H19  NAQ  H18  107.48  3.000
 3DZ  H19  NAQ  CAP  111.30  3.000
 3DZ  H18  NAQ  CAP  112.00  3.000
 3DZ  H22  CAR  H21  106.40  3.000
 3DZ  H22  CAR  CAS  109.76  3.000
 3DZ  H21  CAR  CAS  108.87  3.000
 3DZ  H22  CAR  CAP  109.71  3.000
 3DZ  H21  CAR  CAP  106.05  3.000
 3DZ  CAS  CAR  CAP  115.60  3.000
 3DZ  H24  CAS  H23  106.81  3.000
 3DZ  H24  CAS  CAT  109.69  3.000
 3DZ  H23  CAS  CAT  109.10  3.000
 3DZ  H24  CAS  CAR  109.20  3.000
 3DZ  H23  CAS  CAR  110.87  3.000
 3DZ  CAT  CAS  CAR  111.07  3.000
 3DZ  CAY  CAT  CAU  118.44  3.000
 3DZ  CAY  CAT  CAS  120.83  3.000
 3DZ  CAU  CAT  CAS  120.71  3.000
 3DZ  H25  CAU  CAV  119.69  3.000
 3DZ  H25  CAU  CAT  119.39  3.000
 3DZ  CAV  CAU  CAT  120.92  3.000
 3DZ  H26  CAY  CAX  119.62  3.000
 3DZ  H26  CAY  CAT  119.49  3.000
 3DZ  CAX  CAY  CAT  120.89  3.000
 3DZ  H27  CAX  CAW  120.03  3.000
 3DZ  H27  CAX  CAY  119.85  3.000
 3DZ  CAW  CAX  CAY  120.13  3.000
 3DZ  H28  CAW  CAV  120.25  3.000
 3DZ  H28  CAW  CAX  120.22  3.000
 3DZ  CAV  CAW  CAX  119.53  3.000
 3DZ  H29  CAV  CAW  120.06  3.000
 3DZ  H29  CAV  CAU  119.84  3.000
 3DZ  CAW  CAV  CAU  120.10  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
 3DZ  CONST_01  CAI  CAJ  CAK  CAF    0.00   0.0  0
 3DZ  CONST_02  CAI  CAH  CAG  CAF    0.00   0.0  0
 3DZ  CONST_03  CAH  CAG  CAF  CAK    0.00   0.0  0
 3DZ  CONST_04  CAH  CAI  CAJ  CAK    0.00   0.0  0
 3DZ  CONST_05  CAG  CAF  CAK  CAJ    0.00   0.0  0
 3DZ  CONST_06  CAG  CAH  CAI  CAJ    0.00   0.0  0
 3DZ  CONST_07  CAW  CAV  CAU  CAT    0.00   0.0  0
 3DZ  CONST_08  CAW  CAX  CAY  CAT    0.00   0.0  0
 3DZ  CONST_09  CAX  CAW  CAV  CAU    0.00   0.0  0
 3DZ  CONST_10  CAX  CAY  CAT  CAU    0.00   0.0  0
 3DZ  CONST_11  CAV  CAU  CAT  CAY    0.00   0.0  0
 3DZ  CONST_12  CAV  CAW  CAX  CAY    0.00   0.0  0
 3DZ  CONST_13  CAJ  CAK  CAF  CAE  180.00   0.0  0
 3DZ  CONST_14  CAH  CAG  CAF  CAE  180.00   0.0  0
 3DZ  CONST_15  CAZ  CAH  CAG  CAF  180.00   0.0  0
 3DZ  CONST_16  CAZ  CAH  CAI  CAJ  180.00   0.0  0
 3DZ  CONST_17  CAV  CAU  CAT  CAS  180.00   0.0  0
 3DZ  CONST_18  CAX  CAY  CAT  CAS  180.00   0.0  0
 3DZ  CONST_19  H6   CAJ  CAK  CAF  180.00   0.0  0
 3DZ  CONST_20  H13  CAG  CAF  CAK  180.00   0.0  0
 3DZ  CONST_21  H7   CAI  CAJ  CAK  180.00   0.0  0
 3DZ  CONST_22  H5   CAK  CAJ  CAI  180.00   0.0  0
 3DZ  CONST_23  H29  CAV  CAU  CAT  180.00   0.0  0
 3DZ  CONST_24  H27  CAX  CAY  CAT  180.00   0.0  0
 3DZ  CONST_25  H28  CAW  CAV  CAU  180.00   0.0  0
 3DZ  CONST_26  H26  CAY  CAT  CAU  180.00   0.0  0
 3DZ  CONST_27  H25  CAU  CAT  CAY  180.00   0.0  0
 3DZ  CONST_28  H1   OAC  CAB  OAA    0.00   0.0  0
 3DZ  Var_01    CAK  CAF  CAE  CAD   77.42  30.0  2
 3DZ  Var_02    NBA  CAZ  CAH  CAI   35.47  30.0  2
 3DZ  Var_03    CAU  CAT  CAS  CAR  -81.71  30.0  2
 3DZ  Var_04    CAT  CAS  CAR  CAP  171.37  30.0  2
 3DZ  Var_05    H10  NBA  CAZ  CAH   70.47  30.0  3
 3DZ  Var_06    OAN  PAM  CAL  CAD  -56.27  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
 3DZ  chir_01  CAD  CAE  CAL  CAB  positiv
 3DZ  chir_03  CAP  PAM  NAQ  CAR  negativ
 3DZ  chir_04  PAM  CAP  CAL  OAO  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
 3DZ  plan-1  CAE  0.020
 3DZ  plan-1  CAF  0.020
 3DZ  plan-1  CAK  0.020
 3DZ  plan-1  CAJ  0.020
 3DZ  plan-1  CAI  0.020
 3DZ  plan-1  CAH  0.020
 3DZ  plan-1  CAZ  0.020
 3DZ  plan-1  CAG  0.020
 3DZ  plan-1  H5   0.020
 3DZ  plan-1  H6   0.020
 3DZ  plan-1  H7   0.020
 3DZ  plan-1  H13  0.020
 3DZ  plan-2  CAS  0.020
 3DZ  plan-2  CAT  0.020
 3DZ  plan-2  CAU  0.020
 3DZ  plan-2  CAY  0.020
 3DZ  plan-2  CAX  0.020
 3DZ  plan-2  CAW  0.020
 3DZ  plan-2  CAV  0.020
 3DZ  plan-2  H25  0.020
 3DZ  plan-2  H26  0.020
 3DZ  plan-2  H27  0.020
 3DZ  plan-2  H28  0.020
 3DZ  plan-2  H29  0.020
 3DZ  plan-3  OAA  0.020
 3DZ  plan-3  CAB  0.020
 3DZ  plan-3  OAC  0.020
 3DZ  plan-3  CAD  0.020
 3DZ  plan-3  H1   0.020

