# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 15:30:23 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  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_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   1.180  -1.1422   0.2464  -0.1765
 32Q  C1    C  CH2    0  -0.434  -3.8644   0.9214  -0.4500
 32Q  C3    C  CH1    0  -0.316  -2.4960   1.5194  -0.0982
 32Q  C6    C  CH2    0  -0.521  -4.4646  -0.0353   0.5842
 32Q  C8    C  CR6    0   0.143  -5.8352  -0.4877   0.1685
 32Q  N10   N  NH2    0  -0.795  -2.1332   2.6255  -0.9807
 32Q  C11   C  CH2    0  -0.688   0.3516   1.2081   0.2889
 32Q  O12   O  O      0  -0.831  -1.0208  -0.1684  -1.6351
 32Q  C13   C  CH1    0  -0.322   1.6525   0.4234   0.1146
 32Q  O13   O  OP    -1  -0.805  -1.4012  -0.8278   0.8647
 32Q  C15   C  C      0   0.438   1.7552  -0.7551   1.1009
 32Q  C16   C  CH2    0  -0.480   2.8523   1.3661   0.3008
 32Q  C17   C  CR16   0  -0.314  -5.9929  -1.5976  -0.6608
 32Q  C18   C  CR6    0   0.123   4.1803   0.6903   0.1087
 32Q  C19   C  CR16   0  -0.240  -7.2501  -1.9931  -1.0979
 32Q  C20   C  CR16   0  -0.277  -8.3787  -1.2814  -0.7109
 32Q  C21   C  CR16   0  -0.240  -8.2370  -0.1747   0.1163
 32Q  C22   C  CR16   0  -0.315  -6.9764   0.2158   0.5499
 32Q  O23   O  O      0  -0.627   1.7629  -0.4592   2.3150
 32Q  O24   O  OC    -1  -0.627   1.8549  -1.9026   0.6240
 32Q  N24   N  NH2    0  -0.791   8.8699  -0.5297  -1.3326
 32Q  C36   C  CR16   0  -0.310   4.7291   0.5409  -1.1652
 32Q  C37   C  CR16   0  -0.271   5.9480  -0.0914  -1.3559
 32Q  C38   C  CR6    0   0.080   6.6629  -0.6044  -0.2745
 32Q  C39   C  CR16   0  -0.301   6.1197  -0.4544   0.9964
 32Q  C40   C  CR16   0  -0.286   4.8971   0.1786   1.1854
 32Q  H11   H  HCH2   0   0.218  -4.5676   1.7507  -0.5927
 32Q  H12   H  HCH2   0   0.213  -3.7922   0.4151  -1.4188
 32Q  H31   H  HCH1   0   0.213  -2.5350   1.9062   0.9284
 32Q  H61   H  HCH2   0   0.252  -3.8044  -0.8916   0.7140
 32Q  H62   H  HCH2   0   0.223  -4.5157   0.4724   1.5522
 32Q  H101  H  HNH2   0   0.328  -2.0193   2.2646  -1.9210
 32Q  H102  H  HNH2   0   0.334  -2.9009   3.2861  -1.0291
 32Q  H111  H  HCH2   0   0.225   0.3734   2.1040  -0.3373
 32Q  H112  H  HCH2   0   0.215   0.2616   1.5514   1.3241
 32Q  H131  H  HCH1   0   0.196   1.6856   0.0330  -0.9075
 32Q  H161  H  HCH2   0   0.223   2.7630   2.1922  -0.4112
 32Q  H162  H  HCH2   0   0.222   2.8015   1.8030   1.3011
 32Q  H171  H  HCR6   0   0.243  -5.1181  -2.1602  -0.9679
 32Q  H191  H  HCR6   0   0.250  -7.3488  -2.8598  -1.7394
 32Q  H201  H  HCR6   0   0.250  -9.3604  -1.5883  -1.0480
 32Q  H211  H  HCR6   0   0.250  -9.1102   0.3861   0.4256
 32Q  H221  H  HCR6   0   0.242  -6.8778   1.0787   1.1988
 32Q  H231  H  HCH2   0   0.233   7.8051  -2.2657  -0.9676
 32Q  H232  H  HCH2   0   0.211   8.4089  -1.5404   0.5066
 32Q  H241  H  HNH2   0   0.340   9.1488   0.3139  -0.8475
 32Q  H242  H  HNH2   0   0.350   9.7210  -1.0540  -1.4907
 32Q  H361  H  HCR6   0   0.235   4.1954   0.9353  -2.0232
 32Q  H371  H  HCR6   0   0.237   6.3550  -0.1819  -2.3555
 32Q  H391  H  HCR6   0   0.239   6.6608  -0.8324   1.8569
 32Q  H401  H  HCR6   0   0.235   4.4944   0.2774   2.1858
 32Q  C23   C  CH2    0  -0.348   7.9823  -1.3034  -0.4776

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    1.860  0.020  1.860
 32Q  P11  C11   single    1.837  0.020  1.837
 32Q  P11  O12   deloc     1.521  0.020  1.521
 32Q  P11  O13   deloc     1.518  0.020  1.518
 32Q  C1   C3    single    1.534  0.020  1.534
 32Q  C1   C6    single    1.531  0.020  1.531
 32Q  C3   N10   single    1.461  0.020  1.461
 32Q  C6   C8    single    1.502  0.020  1.502
 32Q  C8   C17   aromatic  1.394  0.020  1.394
 32Q  C8   C22   aromatic  1.394  0.020  1.394
 32Q  C11  C13   single    1.529  0.020  1.529
 32Q  C13  C15   single    1.540  0.020  1.540
 32Q  C13  C16   single    1.537  0.020  1.537
 32Q  C15  O23   deloc     1.250  0.020  1.250
 32Q  C15  O24   deloc     1.247  0.020  1.247
 32Q  C16  C18   single    1.502  0.020  1.502
 32Q  C17  C19   aromatic  1.388  0.020  1.388
 32Q  C18  C36   aromatic  1.395  0.020  1.395
 32Q  C18  C40   aromatic  1.391  0.020  1.391
 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    1.455  0.020  1.455
 32Q  C23  C38   single    1.507  0.020  1.507
 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  1.390  0.020  1.390
 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  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  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   118.57  3.000
 32Q  O13   P11  C11   109.60  3.000
 32Q  O12   P11  C11   108.71  3.000
 32Q  O13   P11  C3    109.34  3.000
 32Q  O12   P11  C3    106.56  3.000
 32Q  C11   P11  C3    102.89  3.000
 32Q  H12   C1   H11   106.06  3.000
 32Q  H12   C1   C6    109.54  3.000
 32Q  H11   C1   C6    108.00  3.000
 32Q  H12   C1   C3    108.92  3.000
 32Q  H11   C1   C3    107.88  3.000
 32Q  C6    C1   C3    115.98  3.000
 32Q  H31   C3   N10   107.87  3.000
 32Q  H31   C3   C1    108.68  3.000
 32Q  N10   C3   C1    112.22  3.000
 32Q  H31   C3   P11   107.84  3.000
 32Q  N10   C3   P11   108.18  3.000
 32Q  C1    C3   P11   111.89  3.000
 32Q  H62   C6   H61   106.72  3.000
 32Q  H62   C6   C8    110.00  3.000
 32Q  H61   C6   C8    110.45  3.000
 32Q  H62   C6   C1    109.02  3.000
 32Q  H61   C6   C1    109.52  3.000
 32Q  C8    C6   C1    111.03  3.000
 32Q  C22   C8   C17   118.16  3.000
 32Q  C22   C8   C6    121.29  3.000
 32Q  C17   C8   C6    120.50  3.000
 32Q  H102  N10  H101  105.82  3.000
 32Q  H102  N10  C3    109.52  3.000
 32Q  H101  N10  C3    108.59  3.000
 32Q  H112  C11  H111  106.64  3.000
 32Q  H112  C11  C13   109.81  3.000
 32Q  H111  C11  C13   109.78  3.000
 32Q  H112  C11  P11   109.69  3.000
 32Q  H111  C11  P11   107.47  3.000
 32Q  C13   C11  P11   113.22  3.000
 32Q  H131  C13  C16   107.95  3.000
 32Q  H131  C13  C15   108.85  3.000
 32Q  C16   C13  C15   109.86  3.000
 32Q  H131  C13  C11   108.37  3.000
 32Q  C16   C13  C11   109.60  3.000
 32Q  C15   C13  C11   112.11  3.000
 32Q  O24   C15  O23   126.09  3.000
 32Q  O24   C15  C13   117.69  3.000
 32Q  O23   C15  C13   116.19  3.000
 32Q  H162  C16  H161  106.86  3.000
 32Q  H162  C16  C18   109.75  3.000
 32Q  H161  C16  C18   109.18  3.000
 32Q  H162  C16  C13   108.65  3.000
 32Q  H161  C16  C13   108.69  3.000
 32Q  C18   C16  C13   113.49  3.000
 32Q  H171  C17  C19   119.57  3.000
 32Q  H171  C17  C8    119.34  3.000
 32Q  C19   C17  C8    121.08  3.000
 32Q  C40   C18  C36   117.69  3.000
 32Q  C40   C18  C16   121.47  3.000
 32Q  C36   C18  C16   120.84  3.000
 32Q  H191  C19  C20   120.07  3.000
 32Q  H191  C19  C17   119.80  3.000
 32Q  C20   C19  C17   120.13  3.000
 32Q  H201  C20  C21   120.26  3.000
 32Q  H201  C20  C19   120.32  3.000
 32Q  C21   C20  C19   119.42  3.000
 32Q  H211  C21  C22   119.81  3.000
 32Q  H211  C21  C20   120.03  3.000
 32Q  C22   C21  C20   120.16  3.000
 32Q  H221  C22  C21   119.54  3.000
 32Q  H221  C22  C8    119.42  3.000
 32Q  C21   C22  C8    121.05  3.000
 32Q  H242  N24  H241  105.96  3.000
 32Q  H242  N24  C23   109.23  3.000
 32Q  H241  N24  C23   109.24  3.000
 32Q  H361  C36  C37   119.32  3.000
 32Q  H361  C36  C18   119.33  3.000
 32Q  C37   C36  C18   121.35  3.000
 32Q  H371  C37  C38   119.50  3.000
 32Q  H371  C37  C36   119.70  3.000
 32Q  C38   C37  C36   120.80  3.000
 32Q  C39   C38  C37   117.97  3.000
 32Q  C39   C38  C23   121.02  3.000
 32Q  C37   C38  C23   121.01  3.000
 32Q  H391  C39  C40   119.33  3.000
 32Q  H391  C39  C38   119.53  3.000
 32Q  C40   C39  C38   121.14  3.000
 32Q  H401  C40  C39   119.63  3.000
 32Q  H401  C40  C18   119.33  3.000
 32Q  C39   C40  C18   121.04  3.000
 32Q  H232  C23  H231  105.92  3.000
 32Q  H232  C23  C38   108.62  3.000
 32Q  H231  C23  C38   109.05  3.000
 32Q  H232  C23  N24   113.85  3.000
 32Q  H231  C23  N24   107.65  3.000
 32Q  C38   C23  N24   111.51  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  Var_01    C17   C8   C6   C1     86.99  30.0  2
 32Q  Var_02    C36   C18  C16  C13    84.64  30.0  2
 32Q  Var_03    C37   C38  C23  N24    48.58  30.0  2
 32Q  Var_04    C8    C6   C1   C3    176.55  30.0  3
 32Q  Var_05    H241  N24  C23  C38    67.88  30.0  3
 32Q  Var_06    C13   C11  P11  C3   -172.08  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

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

