# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 22:17:15 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  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 PERFECT
;

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  -0.629  -1.8409   1.2058   1.5089
 3DZ  CAB  C  C      0   0.447  -1.8603   0.9546   0.2845
 3DZ  OAC  O  OC    -1  -0.625  -2.0508   1.7768  -0.6318
 3DZ  CAD  C  CH1    0  -0.318  -1.6992  -0.5272  -0.1062
 3DZ  CAE  C  CH2    0  -0.489  -2.9139  -1.3247   0.4012
 3DZ  CAF  C  CR6    0   0.162  -4.2265  -0.8526  -0.1564
 3DZ  CAK  C  CR16   0  -0.346  -4.7291  -1.3808  -1.3416
 3DZ  CAJ  C  CR16   0  -0.228  -5.9401  -0.9348  -1.8580
 3DZ  CAI  C  CR16   0  -0.310  -6.6653   0.0440  -1.1960
 3DZ  CAH  C  CR6    0   0.121  -6.1780   0.5957  -0.0121
 3DZ  CAZ  C  CH2    0  -0.351  -6.9465   1.6768   0.7038
 3DZ  NBA  N  NH2    0  -0.791  -8.3474   1.3188   0.8651
 3DZ  CAG  C  CR16   0  -0.363  -4.9666   0.1365   0.4908
 3DZ  CAL  C  CH2    0  -0.699  -0.4201  -1.1448   0.4593
 3DZ  PAM  P  P      0   1.170   1.1098  -0.4917  -0.3273
 3DZ  OAN  O  O      0  -0.833   1.1375  -0.9508  -1.7784
 3DZ  OAO  O  OP    -1  -0.801   1.2274   0.9933  -0.0354
 3DZ  CAP  C  CH1    0  -0.327   2.4534  -1.4314   0.5574
 3DZ  NAQ  N  NH2    0  -0.807   2.3183  -2.8817   0.3808
 3DZ  CAR  C  CH2    0  -0.415   3.8515  -1.0170   0.0925
 3DZ  CAS  C  CH2    0  -0.520   4.2929   0.3810   0.5299
 3DZ  CAT  C  CR6    0   0.144   5.7200   0.6544   0.1468
 3DZ  CAU  C  CR16   0  -0.312   6.7727   0.2354   0.9597
 3DZ  CAY  C  CR16   0  -0.319   6.0278   1.2979  -1.0503
 3DZ  CAX  C  CR16   0  -0.240   7.3469   1.5195  -1.4252
 3DZ  CAW  C  CR16   0  -0.277   8.3853   1.0979  -0.6050
 3DZ  CAV  C  CR16   0  -0.240   8.0931   0.4543   0.5913
 3DZ  H2   H  HCH1   0   0.197  -1.6764  -0.6093  -1.1982
 3DZ  H3   H  HCH2   0   0.225  -2.7707  -2.3784   0.1449
 3DZ  H4   H  HCH2   0   0.225  -2.9326  -1.2675   1.4924
 3DZ  H5   H  HCR6   0   0.236  -4.1722  -2.1525  -1.8614
 3DZ  H6   H  HCR6   0   0.243  -6.3217  -1.3598  -2.7783
 3DZ  H7   H  HCR6   0   0.238  -7.6161   0.3784  -1.5923
 3DZ  H8   H  HCH2   0   0.212  -6.4338   1.9093   1.6468
 3DZ  H9   H  HCH2   0   0.233  -6.9073   2.5935   0.1073
 3DZ  H10  H  HNH2   0   0.341  -8.4254   0.5559   1.5260
 3DZ  H11  H  HNH2   0   0.350  -8.8466   2.0970   1.2768
 3DZ  H13  H  HCR6   0   0.230  -4.5791   0.5616   1.4105
 3DZ  H14  H  HCH2   0   0.220  -0.3813  -0.9750   1.5390
 3DZ  H15  H  HCH2   0   0.213  -0.4554  -2.2294   0.3121
 3DZ  H17  H  HCH1   0   0.217   2.3784  -1.2229   1.6312
 3DZ  H18  H  HNH2   0   0.345   1.4887  -3.2093   0.8600
 3DZ  H19  H  HNH2   0   0.330   2.1503  -3.0672  -0.6026
 3DZ  H21  H  HCH2   0   0.220   4.5597  -1.7501   0.4922
 3DZ  H22  H  HCH2   0   0.214   3.9143  -1.0975  -0.9986
 3DZ  H23  H  HCH2   0   0.251   3.6343   1.1286   0.0905
 3DZ  H24  H  HCH2   0   0.224   4.1824   0.4637   1.6155
 3DZ  H25  H  HCR6   0   0.242   6.5522  -0.2675   1.8949
 3DZ  H26  H  HCR6   0   0.243   5.2232   1.6358  -1.6940
 3DZ  H27  H  HCR6   0   0.250   7.5644   2.0247  -2.3579
 3DZ  H28  H  HCR6   0   0.251   9.4137   1.2704  -0.8950
 3DZ  H29  H  HCR6   0   0.250   8.8953   0.1268   1.2410

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  deloc     1.522  0.020  1.522
 3DZ  CAE  CAF  single    1.502  0.020  1.502
 3DZ  CAE  CAD  single    1.539  0.020  1.539
 3DZ  CAP  PAM  single    1.863  0.020  1.863
 3DZ  CAP  NAQ  single    1.467  0.020  1.467
 3DZ  CAP  CAR  single    1.530  0.020  1.530
 3DZ  CAL  PAM  single    1.840  0.020  1.840
 3DZ  CAL  CAD  single    1.529  0.020  1.529
 3DZ  PAM  OAO  deloc     1.518  0.020  1.518
 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  1.395  0.020  1.395
 3DZ  CAK  CAJ  aromatic  1.390  0.020  1.390
 3DZ  CAG  CAH  aromatic  1.390  0.020  1.390
 3DZ  CAJ  CAI  aromatic  1.386  0.020  1.386
 3DZ  CAH  CAI  aromatic  1.394  0.020  1.394
 3DZ  CAH  CAZ  single    1.507  0.020  1.507
 3DZ  CAD  CAB  single    1.541  0.020  1.541
 3DZ  CAZ  NBA  single    1.455  0.020  1.455
 3DZ  CAS  CAR  single    1.530  0.020  1.530
 3DZ  CAS  CAT  single    1.503  0.020  1.503
 3DZ  CAT  CAY  aromatic  1.394  0.020  1.394
 3DZ  CAW  CAX  aromatic  1.389  0.020  1.389
 3DZ  OAA  CAB  deloc     1.250  0.020  1.250
 3DZ  CAB  OAC  deloc     1.246  0.020  1.246
 3DZ  CAX  CAY  aromatic  1.389  0.020  1.389
 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  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  117.66  3.000
 3DZ  OAC  CAB  OAA  126.17  3.000
 3DZ  CAD  CAB  OAA  116.10  3.000
 3DZ  H2   CAD  CAL  108.73  3.000
 3DZ  H2   CAD  CAE  107.83  3.000
 3DZ  CAL  CAD  CAE  109.21  3.000
 3DZ  H2   CAD  CAB  109.09  3.000
 3DZ  CAL  CAD  CAB  112.47  3.000
 3DZ  CAE  CAD  CAB  109.40  3.000
 3DZ  H4   CAE  H3   106.65  3.000
 3DZ  H4   CAE  CAF  109.83  3.000
 3DZ  H3   CAE  CAF  109.28  3.000
 3DZ  H4   CAE  CAD  108.39  3.000
 3DZ  H3   CAE  CAD  108.58  3.000
 3DZ  CAF  CAE  CAD  113.85  3.000
 3DZ  CAG  CAF  CAK  118.21  3.000
 3DZ  CAG  CAF  CAE  120.95  3.000
 3DZ  CAK  CAF  CAE  120.83  3.000
 3DZ  H5   CAK  CAJ  119.85  3.000
 3DZ  H5   CAK  CAF  119.53  3.000
 3DZ  CAJ  CAK  CAF  120.62  3.000
 3DZ  H6   CAJ  CAI  119.89  3.000
 3DZ  H6   CAJ  CAK  119.79  3.000
 3DZ  CAI  CAJ  CAK  120.32  3.000
 3DZ  H7   CAI  CAH  119.70  3.000
 3DZ  H7   CAI  CAJ  120.16  3.000
 3DZ  CAH  CAI  CAJ  120.14  3.000
 3DZ  CAG  CAH  CAZ  120.64  3.000
 3DZ  CAZ  CAH  CAI  120.60  3.000
 3DZ  CAG  CAH  CAI  118.77  3.000
 3DZ  H9   CAZ  H8   105.90  3.000
 3DZ  H9   CAZ  NBA  107.52  3.000
 3DZ  H8   CAZ  NBA  113.98  3.000
 3DZ  H9   CAZ  CAH  108.89  3.000
 3DZ  H8   CAZ  CAH  108.76  3.000
 3DZ  NBA  CAZ  CAH  111.54  3.000
 3DZ  H11  NBA  H10  106.02  3.000
 3DZ  H11  NBA  CAZ  109.32  3.000
 3DZ  H10  NBA  CAZ  109.39  3.000
 3DZ  H13  CAG  CAH  119.25  3.000
 3DZ  H13  CAG  CAF  118.80  3.000
 3DZ  CAH  CAG  CAF  121.94  3.000
 3DZ  H15  CAL  H14  106.71  3.000
 3DZ  H15  CAL  PAM  108.71  3.000
 3DZ  H14  CAL  PAM  109.72  3.000
 3DZ  H15  CAL  CAD  108.87  3.000
 3DZ  H14  CAL  CAD  109.40  3.000
 3DZ  PAM  CAL  CAD  113.21  3.000
 3DZ  CAP  PAM  OAO  110.26  3.000
 3DZ  OAO  PAM  OAN  118.49  3.000
 3DZ  CAP  PAM  OAN  106.70  3.000
 3DZ  OAO  PAM  CAL  109.23  3.000
 3DZ  CAP  PAM  CAL  102.57  3.000
 3DZ  OAN  PAM  CAL  108.40  3.000
 3DZ  H17  CAP  CAR  107.97  3.000
 3DZ  H17  CAP  NAQ  107.43  3.000
 3DZ  CAR  CAP  NAQ  108.38  3.000
 3DZ  H17  CAP  PAM  108.64  3.000
 3DZ  CAR  CAP  PAM  112.21  3.000
 3DZ  NAQ  CAP  PAM  112.02  3.000
 3DZ  H19  NAQ  H18  105.30  3.000
 3DZ  H19  NAQ  CAP  108.22  3.000
 3DZ  H18  NAQ  CAP  109.77  3.000
 3DZ  H22  CAR  H21  106.10  3.000
 3DZ  H22  CAR  CAS  109.59  3.000
 3DZ  H21  CAR  CAS  108.71  3.000
 3DZ  H22  CAR  CAP  109.57  3.000
 3DZ  H21  CAR  CAP  107.38  3.000
 3DZ  CAS  CAR  CAP  115.10  3.000
 3DZ  H24  CAS  H23  106.70  3.000
 3DZ  H24  CAS  CAT  109.57  3.000
 3DZ  H23  CAS  CAT  110.28  3.000
 3DZ  H24  CAS  CAR  108.88  3.000
 3DZ  H23  CAS  CAR  109.72  3.000
 3DZ  CAT  CAS  CAR  111.55  3.000
 3DZ  CAY  CAT  CAU  118.22  3.000
 3DZ  CAY  CAT  CAS  120.84  3.000
 3DZ  CAU  CAT  CAS  120.91  3.000
 3DZ  H25  CAU  CAV  119.69  3.000
 3DZ  H25  CAU  CAT  119.25  3.000
 3DZ  CAV  CAU  CAT  121.07  3.000
 3DZ  H26  CAY  CAX  119.65  3.000
 3DZ  H26  CAY  CAT  119.34  3.000
 3DZ  CAX  CAY  CAT  121.01  3.000
 3DZ  H27  CAX  CAW  120.01  3.000
 3DZ  H27  CAX  CAY  119.84  3.000
 3DZ  CAW  CAX  CAY  120.15  3.000
 3DZ  H28  CAW  CAV  120.28  3.000
 3DZ  H28  CAW  CAX  120.26  3.000
 3DZ  CAV  CAW  CAX  119.47  3.000
 3DZ  H29  CAV  CAW  120.05  3.000
 3DZ  H29  CAV  CAU  119.85  3.000
 3DZ  CAW  CAV  CAU  120.09  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  Var_01    CAK  CAF  CAE  CAD   89.54  30.0  2
 3DZ  Var_02    NBA  CAZ  CAH  CAI   48.88  30.0  2
 3DZ  Var_03    CAU  CAT  CAS  CAR  -84.34  30.0  2
 3DZ  Var_04    CAT  CAS  CAR  CAP  174.49  30.0  1
 3DZ  Var_05    H10  NBA  CAZ  CAH   69.09  30.0  3
 3DZ  Var_06    OAN  PAM  CAL  CAD  -67.06  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

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

