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

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FMODB ID: RKNV8

Calculation Name: 2JWP-A-Other549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2JWP

Chain ID: A

ChEMBL ID:

UniProt ID: Q6INX3

Base Structure: SolutionNMR

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1851348.520425
FMO2-HF: Nuclear repulsion 1783663.08303
FMO2-HF: Total energy -67685.437395
FMO2-MP2: Total energy -67885.998953


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:5:GLY)


Summations of interaction energy for fragment #1(A:5:GLY)
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.
-72.366-70.403-0.007-0.76-1.196-0.003
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.912
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].
3A7ALA00.0360.0163.8196.8178.269-0.012-0.636-0.805-0.003
4A8ASP-1-0.945-0.9673.763-40.443-40.1100.007-0.085-0.2550.000
5A9LYS10.9400.9804.43160.68560.831-0.001-0.025-0.1190.000
22A26GLY00.003-0.0124.427-9.351-9.319-0.001-0.014-0.0170.000
6A10VAL0-0.0300.0097.4564.4424.4420.0000.0000.0000.000
7A11ILE0-0.0040.0089.6421.1061.1060.0000.0000.0000.000
8A12TRP0-0.079-0.04813.1591.1681.1680.0000.0000.0000.000
9A13ALA00.0500.01413.022-1.132-1.1320.0000.0000.0000.000
10A14VAL0-0.067-0.03915.1480.6700.6700.0000.0000.0000.000
11A15ASN00.0460.01918.140-0.159-0.1590.0000.0000.0000.000
12A16ALA0-0.030-0.00419.5710.3510.3510.0000.0000.0000.000
13A17GLY00.0600.02123.3270.2560.2560.0000.0000.0000.000
14A18GLY00.0240.03421.5850.3820.3820.0000.0000.0000.000
15A19GLU-1-0.734-0.87321.492-11.559-11.5590.0000.0000.0000.000
16A20SER0-0.082-0.02618.2560.1280.1280.0000.0000.0000.000
17A21HIS00.0590.03814.1330.1260.1260.0000.0000.0000.000
18A22VAL0-0.024-0.01710.096-0.727-0.7270.0000.0000.0000.000
19A23ASP-1-0.766-0.8948.758-32.216-32.2160.0000.0000.0000.000
20A24VAL00.0340.0319.134-2.669-2.6690.0000.0000.0000.000
21A25HIS10.8340.9195.09633.68233.6820.0000.0000.0000.000
23A27ILE0-0.023-0.0106.8760.6210.6210.0000.0000.0000.000
24A28HIS0-0.0090.0049.2503.1123.1120.0000.0000.0000.000
25A29TYR0-0.017-0.02012.384-0.099-0.0990.0000.0000.0000.000
26A30ARG10.8490.91412.61021.95621.9560.0000.0000.0000.000
27A31LYS10.8340.89218.36513.67313.6730.0000.0000.0000.000
28A32ASP-1-0.720-0.82321.341-12.679-12.6790.0000.0000.0000.000
29A33PRO00.0090.02021.0870.5920.5920.0000.0000.0000.000
30A34LEU0-0.024-0.02124.2680.1510.1510.0000.0000.0000.000
31A35GLU-1-0.742-0.85426.895-10.444-10.4440.0000.0000.0000.000
32A36GLY0-0.009-0.00429.7590.0430.0430.0000.0000.0000.000
33A37ARG10.8170.91326.72111.39711.3970.0000.0000.0000.000
34A38VAL00.0190.02727.214-0.187-0.1870.0000.0000.0000.000
35A39GLY00.0030.00425.487-0.036-0.0360.0000.0000.0000.000
36A40ARG10.8060.86626.24011.12811.1280.0000.0000.0000.000
37A41ALA0-0.0070.02724.900-0.024-0.0240.0000.0000.0000.000
38A42SER0-0.018-0.01226.2760.6480.6480.0000.0000.0000.000
39A43ASP-1-0.861-0.93125.225-11.456-11.4560.0000.0000.0000.000
40A44TYR0-0.004-0.00327.0470.2500.2500.0000.0000.0000.000
41A45GLY0-0.030-0.01430.0180.2420.2420.0000.0000.0000.000
42A46MET00.029-0.00824.304-0.199-0.1990.0000.0000.0000.000
43A47LYS10.9120.95726.9238.8928.8920.0000.0000.0000.000
44A48LEU0-0.025-0.00628.1600.3520.3520.0000.0000.0000.000
45A49PRO0-0.018-0.00824.518-0.334-0.3340.0000.0000.0000.000
46A50ILE00.0550.03419.8640.2450.2450.0000.0000.0000.000
47A51LEU0-0.0120.01222.141-0.259-0.2590.0000.0000.0000.000
48A52ARG10.8800.92218.19815.82215.8220.0000.0000.0000.000
49A53SER0-0.009-0.02515.188-1.054-1.0540.0000.0000.0000.000
50A54ASN0-0.061-0.02714.5201.8711.8710.0000.0000.0000.000
51A55PRO00.013-0.01816.965-0.109-0.1090.0000.0000.0000.000
52A56GLU-1-0.896-0.93214.197-20.127-20.1270.0000.0000.0000.000
53A57ASP-1-0.765-0.88213.011-21.445-21.4450.0000.0000.0000.000
54A58GLN00.0290.03015.1290.4370.4370.0000.0000.0000.000
55A59VAL00.000-0.00218.6950.6400.6400.0000.0000.0000.000
56A60LEU0-0.070-0.03013.5070.5050.5050.0000.0000.0000.000
57A61TYR00.018-0.01812.680-0.463-0.4630.0000.0000.0000.000
58A62GLN0-0.018-0.00419.2000.0820.0820.0000.0000.0000.000
59A63THR0-0.069-0.02721.7250.6320.6320.0000.0000.0000.000
60A64GLU-1-0.788-0.88823.687-11.000-11.0000.0000.0000.0000.000
61A65ARG10.7540.82826.02811.41411.4140.0000.0000.0000.000
62A66TYR0-0.058-0.02828.3410.2530.2530.0000.0000.0000.000
63A67ASN0-0.022-0.02730.164-0.114-0.1140.0000.0000.0000.000
64A68GLU-1-0.951-0.96932.631-8.358-8.3580.0000.0000.0000.000
65A69ASP-1-0.807-0.88634.313-8.452-8.4520.0000.0000.0000.000
66A70SER0-0.047-0.03732.426-0.377-0.3770.0000.0000.0000.000
67A71PHE0-0.0200.01727.6700.0560.0560.0000.0000.0000.000
68A72GLY00.0470.00426.920-0.169-0.1690.0000.0000.0000.000
69A73TYR0-0.064-0.04422.0180.1560.1560.0000.0000.0000.000
70A74ASP-1-0.853-0.92623.779-12.255-12.2550.0000.0000.0000.000
71A75ILE00.0280.01918.017-0.478-0.4780.0000.0000.0000.000
72A76PRO0-0.022-0.01720.5090.0800.0800.0000.0000.0000.000
73A77ILE00.0000.01118.487-0.863-0.8630.0000.0000.0000.000
74A78LYS10.9260.95119.79415.71315.7130.0000.0000.0000.000
75A79GLU-1-0.809-0.87916.488-19.203-19.2030.0000.0000.0000.000
76A80GLU-1-0.838-0.89619.712-14.148-14.1480.0000.0000.0000.000
77A81GLY0-0.005-0.00316.393-0.831-0.8310.0000.0000.0000.000
78A82GLU-1-0.880-0.94114.592-18.646-18.6460.0000.0000.0000.000
79A83TYR0-0.050-0.05714.146-1.821-1.8210.0000.0000.0000.000
80A84VAL00.0330.03012.5461.5221.5220.0000.0000.0000.000
81A85LEU0-0.015-0.00913.865-1.344-1.3440.0000.0000.0000.000
82A86VAL00.0160.00912.0860.7980.7980.0000.0000.0000.000
83A87LEU0-0.023-0.01015.357-0.643-0.6430.0000.0000.0000.000
84A88LYS10.8120.91214.85920.01220.0120.0000.0000.0000.000
85A89PHE00.003-0.02118.4550.3780.3780.0000.0000.0000.000
86A90ALA00.0550.01222.224-0.134-0.1340.0000.0000.0000.000
87A91GLU-1-0.780-0.89924.702-10.142-10.1420.0000.0000.0000.000
88A92VAL0-0.031-0.01828.3750.1220.1220.0000.0000.0000.000
89A93TYR0-0.038-0.01131.0540.1880.1880.0000.0000.0000.000
90A94PHE00.0010.00234.4450.2920.2920.0000.0000.0000.000
91A95ALA0-0.0010.00035.288-0.202-0.2020.0000.0000.0000.000
92A96GLN0-0.056-0.03135.6250.3720.3720.0000.0000.0000.000
93A97SER00.0010.00034.271-0.191-0.1910.0000.0000.0000.000
94A98GLN0-0.084-0.05633.2630.5070.5070.0000.0000.0000.000
95A99GLN0-0.0110.00136.3260.1870.1870.0000.0000.0000.000
96A100LYS10.7420.85733.2649.6149.6140.0000.0000.0000.000
97A101VAL0-0.0040.01932.734-0.282-0.2820.0000.0000.0000.000
98A102PHE00.008-0.00128.7600.2160.2160.0000.0000.0000.000
99A103ASP-1-0.822-0.88630.435-9.799-9.7990.0000.0000.0000.000
100A104VAL00.0340.00723.619-0.208-0.2080.0000.0000.0000.000
101A105ARG10.8430.91526.84610.16310.1630.0000.0000.0000.000
102A106VAL00.0220.00621.757-0.506-0.5060.0000.0000.0000.000
103A107ASN0-0.041-0.03724.5970.1090.1090.0000.0000.0000.000
104A108GLY00.0210.02626.1460.3410.3410.0000.0000.0000.000
105A109HIS00.0000.00326.4670.6440.6440.0000.0000.0000.000
106A110THR0-0.018-0.01127.446-0.338-0.3380.0000.0000.0000.000
107A111VAL0-0.0080.00723.5830.1750.1750.0000.0000.0000.000
108A112VAL00.0440.03424.4070.0160.0160.0000.0000.0000.000
109A113LYS10.7940.88427.5559.4849.4840.0000.0000.0000.000
110A114ASP-1-0.838-0.94029.856-10.508-10.5080.0000.0000.0000.000
111A115LEU00.0040.01125.4320.0460.0460.0000.0000.0000.000
112A116ASP-1-0.743-0.87129.124-9.992-9.9920.0000.0000.0000.000
113A117ILE0-0.010-0.00225.477-0.087-0.0870.0000.0000.0000.000
114A118PHE00.023-0.00127.976-0.115-0.1150.0000.0000.0000.000
115A119ASP-1-0.873-0.93030.540-9.827-9.8270.0000.0000.0000.000
116A120ARG10.8200.91625.97010.77210.7720.0000.0000.0000.000
117A121VAL0-0.0230.00224.526-0.304-0.3040.0000.0000.0000.000
118A122GLY0-0.0060.02127.0670.0560.0560.0000.0000.0000.000
119A123HIS0-0.067-0.05329.0730.2990.2990.0000.0000.0000.000
120A124SER0-0.006-0.02627.595-0.336-0.3360.0000.0000.0000.000
121A125THR0-0.037-0.00523.217-0.326-0.3260.0000.0000.0000.000
122A126ALA0-0.016-0.00819.2470.0860.0860.0000.0000.0000.000
123A127HIS00.005-0.00920.531-0.398-0.3980.0000.0000.0000.000
124A128ASP-1-0.874-0.94516.991-19.005-19.0050.0000.0000.0000.000
125A129GLU-1-0.832-0.87619.118-13.205-13.2050.0000.0000.0000.000
126A130ILE0-0.016-0.02214.468-0.831-0.8310.0000.0000.0000.000
127A131ILE00.008-0.00417.3070.6540.6540.0000.0000.0000.000
128A132PRO00.0080.00316.376-0.651-0.6510.0000.0000.0000.000
129A133ILE0-0.0230.00717.8921.2761.2760.0000.0000.0000.000
130A134SER00.0220.00418.218-0.789-0.7890.0000.0000.0000.000
131A135ILE0-0.043-0.00919.8070.9360.9360.0000.0000.0000.000
132A136LYS10.8960.91619.52015.09515.0950.0000.0000.0000.000
133A137LYS10.9410.97123.84811.59311.5930.0000.0000.0000.000
134A138GLY00.0370.02325.2740.5530.5530.0000.0000.0000.000
135A139LYS10.8370.92026.39611.19411.1940.0000.0000.0000.000
136A140LEU00.0030.00122.714-0.596-0.5960.0000.0000.0000.000
137A141SER00.0330.01423.7810.7880.7880.0000.0000.0000.000
138A142VAL00.008-0.00822.116-0.862-0.8620.0000.0000.0000.000
139A143GLN00.0500.02521.5760.2180.2180.0000.0000.0000.000
140A144GLY0-0.020-0.00824.5020.0870.0870.0000.0000.0000.000
141A145GLU-1-0.952-0.94727.690-10.034-10.0340.0000.0000.0000.000
142A146VAL0-0.024-0.02227.352-0.505-0.5050.0000.0000.0000.000
143A147SER00.0300.01228.4810.6490.6490.0000.0000.0000.000
144A148THR0-0.080-0.05228.571-0.306-0.3060.0000.0000.0000.000
145A149PHE0-0.0070.00723.3900.1000.1000.0000.0000.0000.000
146A150THR0-0.016-0.01327.4520.3460.3460.0000.0000.0000.000
147A151GLY00.0180.02427.375-0.023-0.0230.0000.0000.0000.000
148A152LYS10.8020.87023.63411.32811.3280.0000.0000.0000.000
149A153LEU00.0230.01219.3370.4110.4110.0000.0000.0000.000
150A154SER00.010-0.00123.002-0.366-0.3660.0000.0000.0000.000
151A155VAL0-0.0020.01621.327-0.026-0.0260.0000.0000.0000.000
152A156GLU-1-0.853-0.94124.699-11.501-11.5010.0000.0000.0000.000
153A157PHE00.0140.00125.022-0.213-0.2130.0000.0000.0000.000
154A158VAL0-0.020-0.00928.6470.2390.2390.0000.0000.0000.000
155A159LYS10.8640.90932.1238.3278.3270.0000.0000.0000.000
156A160GLY00.0440.03334.4330.1290.1290.0000.0000.0000.000
157A161TYR0-0.064-0.04035.9140.3010.3010.0000.0000.0000.000
158A162TYR0-0.034-0.00835.639-0.014-0.0140.0000.0000.0000.000
159A163ASP-1-0.765-0.86232.221-9.656-9.6560.0000.0000.0000.000
160A164ASN00.0080.00730.4780.1870.1870.0000.0000.0000.000
161A165PRO0-0.036-0.03225.794-0.015-0.0150.0000.0000.0000.000
162A166LYS10.8120.92626.8059.9069.9060.0000.0000.0000.000
163A167VAL0-0.0100.01721.850-0.030-0.0300.0000.0000.0000.000
164A168CYS0-0.043-0.00522.368-0.366-0.3660.0000.0000.0000.000
165A169ALA00.0490.02917.218-0.211-0.2110.0000.0000.0000.000
166A170LEU0-0.0280.00116.984-1.039-1.0390.0000.0000.0000.000
167A171PHE00.030-0.0048.550-1.054-1.0540.0000.0000.0000.000
168A172ILE0-0.0020.00713.8520.5890.5890.0000.0000.0000.000
169A173MET0-0.056-0.0197.900-0.381-0.3810.0000.0000.0000.000
170A174LYS10.8370.88710.47924.68124.6810.0000.0000.0000.000
171A175GLY0-0.049-0.02610.048-3.108-3.1080.0000.0000.0000.000
172A176THR0-0.049-0.0359.2922.2972.2970.0000.0000.0000.000
173A177ALA00.006-0.01911.234-1.249-1.2490.0000.0000.0000.000
174A178ASP-2-1.892-1.9138.139-65.821-65.8210.0000.0000.0000.000