FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: 196JZ

Calculation Name: 2A31-A-Xray547

Preferred Name: Trypsin

Target Type: SINGLE PROTEIN

Ligand Name: guanidine-3-propanol | borate ion

Ligand 3-letter code: PG3 | BO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A31

Chain ID: A

ChEMBL ID: CHEMBL2366

UniProt ID: P00761

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2548159.962007
FMO2-HF: Nuclear repulsion 2463376.826626
FMO2-HF: Total energy -84783.135381
FMO2-MP2: Total energy -85022.455636


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:16:ILE)


Summations of interaction energy for fragment #1(A:16:ILE)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-138.75-123.53338.377-22.008-31.58-0.231
Interaction energy analysis for fragmet #1(A:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.728 / q_NPA : 0.859
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A18GLY00.0460.0133.3883.6425.3030.063-0.672-1.052-0.001
4A19GLY0-0.042-0.0182.4033.7414.4961.034-0.746-1.0430.000
5A20TYR0-0.025-0.0153.2114.4804.0370.0280.651-0.2360.000
7A22CYS0-0.075-0.0222.743-1.1870.8700.733-1.007-1.783-0.014
117A138ILE00.0030.0152.5740.5120.9420.857-0.207-1.0800.001
118A139SER0-0.003-0.0342.521-2.584-1.3890.762-0.594-1.362-0.002
119A140GLY00.004-0.0022.8850.8191.8690.906-0.273-1.684-0.009
120A141TRP0-0.0010.0013.235-6.660-5.8400.101-0.249-0.672-0.004
121A142GLY00.0320.0102.9879.50310.1660.047-0.261-0.448-0.001
122A143ASN0-0.023-0.0302.563-18.402-16.3811.801-1.944-1.879-0.021
123A144THR00.031-0.0051.921-29.281-29.2446.665-3.661-3.040-0.045
124A145LYS10.8570.9444.21333.03633.144-0.001-0.026-0.0810.000
131A152PRO0-0.0410.0073.8234.8745.030-0.001-0.017-0.1380.000
135A156GLN0-0.051-0.0382.3341.1541.8282.358-0.952-2.080-0.004
136A158LEU00.0120.0022.264-2.077-1.4342.854-0.849-2.648-0.005
137A159LYS10.9060.9643.69524.13824.2790.0110.010-0.1610.000
168A189ASP-1-0.753-0.8684.284-32.237-32.006-0.001-0.028-0.2020.000
169A190SER0-0.0420.0032.248-16.073-12.9091.889-2.496-2.557-0.015
170A191CYS0-0.048-0.0303.2777.6037.8140.0190.342-0.571-0.001
171A192GLN00.1050.0264.813-2.273-2.145-0.001-0.004-0.1220.000
172A193GLY00.0230.0215.177-7.148-7.126-0.001-0.001-0.0190.000
173A194ASP-1-0.766-0.8681.921-132.915-133.62118.256-8.988-8.562-0.110
174A195SER00.002-0.0154.6764.0394.139-0.001-0.028-0.0710.000
187A213VAL0-0.048-0.0254.3120.8750.974-0.001-0.008-0.0890.000
6A21THR00.0500.0265.264-4.632-4.6320.0000.0000.0000.000
8A23ALA00.0560.0238.2731.1071.1070.0000.0000.0000.000
9A24ALA00.0660.03911.430-0.808-0.8080.0000.0000.0000.000
10A25ASN0-0.013-0.01312.3622.0042.0040.0000.0000.0000.000
11A26SER0-0.056-0.04110.9990.2880.2880.0000.0000.0000.000
12A27ILE0-0.025-0.0077.3770.3950.3950.0000.0000.0000.000
13A28PRO00.0470.02810.801-0.678-0.6780.0000.0000.0000.000
14A29TYR00.0260.0219.1021.1921.1920.0000.0000.0000.000
15A30GLN0-0.0080.0046.177-2.196-2.1960.0000.0000.0000.000
16A31VAL0-0.0150.00010.0781.3761.3760.0000.0000.0000.000
17A32SER0-0.005-0.0159.677-2.022-2.0220.0000.0000.0000.000
18A33LEU0-0.033-0.01111.1852.6832.6830.0000.0000.0000.000
19A34ASN00.0470.01112.854-0.279-0.2790.0000.0000.0000.000
20A37SER0-0.021-0.02815.4130.7920.7920.0000.0000.0000.000
21A38GLY00.0050.01618.0660.5430.5430.0000.0000.0000.000
22A39SER00.0140.00714.0210.1760.1760.0000.0000.0000.000
23A40HIS00.0410.0326.9644.0374.0370.0000.0000.0000.000
24A41PHE0-0.024-0.03010.682-0.701-0.7010.0000.0000.0000.000
25A42CYS0-0.083-0.0168.944-2.380-2.3800.0000.0000.0000.000
26A43GLY00.0420.0337.1410.2550.2550.0000.0000.0000.000
27A44GLY00.0230.0058.1602.1702.1700.0000.0000.0000.000
28A45SER0-0.015-0.0089.704-1.328-1.3280.0000.0000.0000.000
29A46LEU0-0.0140.00011.7381.0581.0580.0000.0000.0000.000
30A47ILE0-0.020-0.02015.087-0.010-0.0100.0000.0000.0000.000
31A48ASN00.0150.00317.5860.8340.8340.0000.0000.0000.000
32A49SER00.0570.03320.219-0.444-0.4440.0000.0000.0000.000
33A50GLN00.0280.00722.391-0.035-0.0350.0000.0000.0000.000
34A51TRP00.0290.01520.072-0.055-0.0550.0000.0000.0000.000
35A52VAL00.0300.02113.692-0.265-0.2650.0000.0000.0000.000
36A53VAL0-0.026-0.00513.3550.7180.7180.0000.0000.0000.000
37A54SER00.015-0.00211.187-1.306-1.3060.0000.0000.0000.000
38A55ALA00.0570.03111.4141.0391.0390.0000.0000.0000.000
39A56ALA0-0.040-0.01813.1900.4250.4250.0000.0000.0000.000
40A57HIS0-0.045-0.04110.864-1.106-1.1060.0000.0000.0000.000
41A59TYR00.0130.00214.5430.4040.4040.0000.0000.0000.000
42A60LYS10.8910.95415.46419.22919.2290.0000.0000.0000.000
43A61SER00.0100.01120.139-0.021-0.0210.0000.0000.0000.000
44A62ARG10.9360.96221.98512.30212.3020.0000.0000.0000.000
45A63ILE00.0200.01316.540-0.595-0.5950.0000.0000.0000.000
46A64GLN00.0080.01918.5180.3010.3010.0000.0000.0000.000
47A65VAL00.0150.00515.179-1.303-1.3030.0000.0000.0000.000
48A66ARG10.8500.93914.23619.09819.0980.0000.0000.0000.000
49A67LEU00.0440.01013.902-1.541-1.5410.0000.0000.0000.000
50A69GLY00.0500.01915.0630.6040.6040.0000.0000.0000.000
51A70GLU-1-0.855-0.94812.120-20.469-20.4690.0000.0000.0000.000
52A71HIS0-0.086-0.0409.456-1.247-1.2470.0000.0000.0000.000
53A72ASN00.008-0.01910.572-3.974-3.9740.0000.0000.0000.000
54A73ILE00.0260.0279.3551.2181.2180.0000.0000.0000.000
55A74ASP-1-0.890-0.91512.354-23.315-23.3150.0000.0000.0000.000
56A75VAL0-0.099-0.06014.9901.4031.4030.0000.0000.0000.000
57A76LEU0-0.0230.00017.403-0.338-0.3380.0000.0000.0000.000
58A77GLU-1-0.839-0.93815.237-19.517-19.5170.0000.0000.0000.000
59A78GLY0-0.037-0.01319.6220.6480.6480.0000.0000.0000.000
60A79ASN0-0.050-0.03318.4851.0201.0200.0000.0000.0000.000
61A80GLU-1-0.789-0.86916.602-16.345-16.3450.0000.0000.0000.000
62A81GLN0-0.022-0.02018.3961.0451.0450.0000.0000.0000.000
63A82PHE0-0.009-0.00817.125-0.680-0.6800.0000.0000.0000.000
64A83ILE0-0.0060.00319.7680.7670.7670.0000.0000.0000.000
65A84ASN00.0250.01020.323-1.146-1.1460.0000.0000.0000.000
66A85ALA00.0310.02720.3810.3310.3310.0000.0000.0000.000
67A86ALA0-0.031-0.01522.1890.4190.4190.0000.0000.0000.000
68A87LYS10.7760.86723.81610.88810.8880.0000.0000.0000.000
69A88ILE00.0080.00619.418-0.526-0.5260.0000.0000.0000.000
70A89ILE0-0.0050.00321.0630.4170.4170.0000.0000.0000.000
71A90THR00.0510.02519.181-0.566-0.5660.0000.0000.0000.000
72A91HIS00.0180.01320.1730.6640.6640.0000.0000.0000.000
73A92PRO0-0.031-0.01422.047-0.090-0.0900.0000.0000.0000.000
74A93ASN00.0060.00024.5260.4200.4200.0000.0000.0000.000
75A94PHE0-0.014-0.00117.838-0.287-0.2870.0000.0000.0000.000
76A95ASN00.0170.01321.5910.1460.1460.0000.0000.0000.000
77A96GLY00.014-0.00120.068-0.567-0.5670.0000.0000.0000.000
78A97ASN0-0.077-0.02420.461-0.504-0.5040.0000.0000.0000.000
79A98THR00.047-0.00220.518-0.489-0.4890.0000.0000.0000.000
80A99LEU00.0190.01915.182-0.493-0.4930.0000.0000.0000.000
81A100ASP-1-0.797-0.87017.519-13.801-13.8010.0000.0000.0000.000
82A101ASN0-0.014-0.00319.3800.2670.2670.0000.0000.0000.000
83A102ASP-1-0.690-0.79213.880-20.265-20.2650.0000.0000.0000.000
84A103ILE0-0.063-0.01414.672-1.167-1.1670.0000.0000.0000.000
85A104MET0-0.007-0.00615.3251.2781.2780.0000.0000.0000.000
86A105LEU0-0.019-0.00316.298-0.746-0.7460.0000.0000.0000.000
87A106ILE00.007-0.00315.8140.3700.3700.0000.0000.0000.000
88A107LYS10.8620.93819.38810.65310.6530.0000.0000.0000.000
89A108LEU0-0.012-0.01818.560-0.116-0.1160.0000.0000.0000.000
90A109SER0-0.036-0.04522.5160.5750.5750.0000.0000.0000.000
91A110SER00.0210.01124.7920.5360.5360.0000.0000.0000.000
92A111PRO0-0.038-0.03224.112-0.497-0.4970.0000.0000.0000.000
93A112ALA00.0330.02420.2220.0310.0310.0000.0000.0000.000
94A113THR0-0.034-0.01722.1490.5300.5300.0000.0000.0000.000
95A114LEU0-0.009-0.00920.305-0.420-0.4200.0000.0000.0000.000
96A115ASN00.0120.00020.5980.1620.1620.0000.0000.0000.000
97A116SER0-0.002-0.01020.010-0.483-0.4830.0000.0000.0000.000
98A117ARG10.9120.96316.52513.90113.9010.0000.0000.0000.000
99A118VAL0-0.0150.00415.971-1.023-1.0230.0000.0000.0000.000
100A119ALA00.0150.00616.5451.0441.0440.0000.0000.0000.000
101A120THR0-0.0120.00516.210-0.626-0.6260.0000.0000.0000.000
102A121VAL0-0.009-0.00312.7930.1910.1910.0000.0000.0000.000
103A122SER0-0.041-0.01315.8710.8100.8100.0000.0000.0000.000
104A123LEU00.0570.02616.491-0.856-0.8560.0000.0000.0000.000
105A124PRO0-0.065-0.03716.7760.4720.4720.0000.0000.0000.000
106A125ARG10.9520.97019.26913.23113.2310.0000.0000.0000.000
107A127SER00.0170.01421.5680.5800.5800.0000.0000.0000.000
108A128CYS0-0.071-0.02416.4600.0940.0940.0000.0000.0000.000
109A129ALA00.0160.01416.1740.4290.4290.0000.0000.0000.000
110A130ALA00.0270.02618.2590.1440.1440.0000.0000.0000.000
111A132ALA00.0390.02117.590-0.773-0.7730.0000.0000.0000.000
112A133GLY0-0.006-0.00416.9320.6290.6290.0000.0000.0000.000
113A134THR0-0.088-0.05615.1950.2660.2660.0000.0000.0000.000
114A135GLU-1-0.874-0.94712.064-20.683-20.6830.0000.0000.0000.000
115A136CYS0-0.037-0.0109.2810.3980.3980.0000.0000.0000.000
116A137LEU0-0.052-0.0336.089-0.504-0.5040.0000.0000.0000.000
125A146SER00.0490.0286.884-1.916-1.9160.0000.0000.0000.000
126A147SER0-0.015-0.0209.0363.5763.5760.0000.0000.0000.000
127A148GLY00.0120.01711.3830.2540.2540.0000.0000.0000.000
128A149SER00.003-0.0068.713-3.841-3.8410.0000.0000.0000.000
129A150SER00.005-0.0157.5465.1695.1690.0000.0000.0000.000
130A151TYR00.0220.0245.924-8.550-8.5500.0000.0000.0000.000
132A153SER00.0670.0036.957-1.039-1.0390.0000.0000.0000.000
133A154LEU0-0.050-0.0199.1260.7910.7910.0000.0000.0000.000
134A155LEU0-0.0080.0155.419-5.215-5.2150.0000.0000.0000.000
138A160ALA00.0310.0096.932-0.932-0.9320.0000.0000.0000.000
139A161PRO00.0720.0598.9260.4320.4320.0000.0000.0000.000
140A162VAL0-0.009-0.01211.971-0.972-0.9720.0000.0000.0000.000
141A163LEU0-0.021-0.00312.7661.2401.2400.0000.0000.0000.000
142A164SER00.0280.01015.5580.2350.2350.0000.0000.0000.000
143A165ASP-1-0.860-0.93319.001-13.528-13.5280.0000.0000.0000.000
144A166SER0-0.0010.00120.939-0.271-0.2710.0000.0000.0000.000
145A167SER00.0290.02517.5040.1200.1200.0000.0000.0000.000
146A168CYS0-0.0060.03012.545-1.290-1.2900.0000.0000.0000.000
147A169LYS10.9800.97117.93312.40312.4030.0000.0000.0000.000
148A170SER0-0.062-0.03821.1700.1730.1730.0000.0000.0000.000
149A171SER0-0.006-0.00816.610-0.109-0.1090.0000.0000.0000.000
150A172TYR0-0.060-0.04412.7270.0160.0160.0000.0000.0000.000
151A173PRO00.0380.01619.4630.3070.3070.0000.0000.0000.000
152A174GLY0-0.017-0.00923.2730.0820.0820.0000.0000.0000.000
153A175GLN0-0.014-0.00719.2360.0350.0350.0000.0000.0000.000
154A176ILE0-0.019-0.00416.621-0.279-0.2790.0000.0000.0000.000
155A177THR00.021-0.02319.7920.6010.6010.0000.0000.0000.000
156A178GLY0-0.009-0.01220.625-0.287-0.2870.0000.0000.0000.000
157A179ASN0-0.036-0.02419.5050.2270.2270.0000.0000.0000.000
158A180MET0-0.0310.03616.161-0.885-0.8850.0000.0000.0000.000
159A181ILE0-0.010-0.00512.7080.9140.9140.0000.0000.0000.000
160A183VAL0-0.015-0.0108.9541.1151.1150.0000.0000.0000.000
161A184GLY00.0230.0178.667-2.300-2.3000.0000.0000.0000.000
162A184PHE0-0.018-0.0197.3401.6891.6890.0000.0000.0000.000
163A185LEU00.0300.01611.340-0.168-0.1680.0000.0000.0000.000
164A186GLU-1-0.868-0.94212.908-17.912-17.9120.0000.0000.0000.000
165A187GLY0-0.021-0.00711.961-1.173-1.1730.0000.0000.0000.000
166A188GLY0-0.032-0.0269.2330.6630.6630.0000.0000.0000.000
167A188LYS10.9010.9545.56424.00024.0000.0000.0000.0000.000
175A196GLY00.011-0.0137.9620.6460.6460.0000.0000.0000.000
176A197GLY0-0.0210.0015.3382.0602.0600.0000.0000.0000.000
177A198PRO0-0.017-0.0085.5182.2102.2100.0000.0000.0000.000
178A199VAL00.0220.0155.667-3.116-3.1160.0000.0000.0000.000
179A200VAL0-0.028-0.0148.1572.3692.3690.0000.0000.0000.000
180A202ASN00.0230.00513.1360.5950.5950.0000.0000.0000.000
181A203GLY00.0160.01315.1900.7470.7470.0000.0000.0000.000
182A204GLN0-0.041-0.02415.3760.8800.8800.0000.0000.0000.000
183A209LEU00.0120.01110.511-0.828-0.8280.0000.0000.0000.000
184A210GLN00.013-0.02112.6730.9290.9290.0000.0000.0000.000
185A211GLY0-0.0020.00211.0210.8560.8560.0000.0000.0000.000
186A212ILE0-0.011-0.0019.169-0.596-0.5960.0000.0000.0000.000
188A214SER0-0.030-0.0317.6330.8500.8500.0000.0000.0000.000
189A215TRP00.000-0.03110.799-0.424-0.4240.0000.0000.0000.000
190A216GLY00.0800.03510.542-1.190-1.1900.0000.0000.0000.000
191A217TYR0-0.036-0.01412.0151.2651.2650.0000.0000.0000.000
192A219GLY0-0.014-0.00111.546-0.029-0.0290.0000.0000.0000.000
193A221ALA0-0.025-0.0106.7001.4341.4340.0000.0000.0000.000
194A221GLN00.0570.0278.6113.0483.0480.0000.0000.0000.000
195A222LYS10.9510.96512.40515.72615.7260.0000.0000.0000.000
196A223ASN0-0.070-0.04215.1580.7340.7340.0000.0000.0000.000
197A224LYS10.8500.93313.44118.12318.1230.0000.0000.0000.000
198A225PRO00.0210.03710.413-1.653-1.6530.0000.0000.0000.000
199A226GLY00.0820.0638.1400.9960.9960.0000.0000.0000.000
200A227VAL0-0.020-0.0309.1602.1072.1070.0000.0000.0000.000
201A228TYR0-0.038-0.0385.734-0.437-0.4370.0000.0000.0000.000
202A229THR0-0.013-0.02211.5401.4121.4120.0000.0000.0000.000
203A230LYS10.9370.96913.63213.38713.3870.0000.0000.0000.000
204A231VAL00.0250.00913.5441.0871.0870.0000.0000.0000.000
205A233ASN0-0.021-0.01819.4670.5970.5970.0000.0000.0000.000
206A234TYR0-0.033-0.04018.0650.2500.2500.0000.0000.0000.000
207A235VAL0-0.0050.00720.1170.1300.1300.0000.0000.0000.000
208A236ASN00.0360.01721.9430.0420.0420.0000.0000.0000.000
209A237TRP00.0450.02219.1350.0660.0660.0000.0000.0000.000
210A238ILE00.0240.01617.9850.0750.0750.0000.0000.0000.000
211A239GLN00.0030.00222.1110.2180.2180.0000.0000.0000.000
212A240GLN0-0.003-0.01625.0480.2230.2230.0000.0000.0000.000
213A241THR0-0.022-0.01023.6450.3070.3070.0000.0000.0000.000
214A242ILE0-0.036-0.02521.1910.1200.1200.0000.0000.0000.000
215A243ALA0-0.021-0.01525.4650.2000.2000.0000.0000.0000.000
216A244ALA0-0.0170.00828.7810.3490.3490.0000.0000.0000.000
217A245ASN-1-0.842-0.87327.161-10.258-10.2580.0000.0000.0000.000