FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: MNV7Z

Calculation Name: 3JV1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JV1

Chain ID: A

ChEMBL ID:

UniProt ID: Q584R4

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1786761.427554
FMO2-HF: Nuclear repulsion 1714747.715195
FMO2-HF: Total energy -72013.712359
FMO2-MP2: Total energy -72224.629435


3D Structure
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:46:ALA)


Summations of interaction energy for fragment #1(A:46:ALA)
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.
-18.003-15.398.312-5.654-5.272-0.051
Interaction energy analysis for fragmet #1(A:46:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.019
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].
3A48SER0-0.048-0.0252.791-1.1951.1540.048-1.133-1.2640.002
4A49ASP-1-0.810-0.9061.906-16.601-16.6608.265-4.422-3.784-0.053
5A50GLN0-0.037-0.0184.3421.0901.413-0.001-0.099-0.2240.000
6A51ARG10.9400.9606.0550.7630.7630.0000.0000.0000.000
7A52LEU00.0020.0147.5420.2750.2750.0000.0000.0000.000
8A53SER0-0.0150.0028.3840.3360.3360.0000.0000.0000.000
9A54GLU-1-0.872-0.94610.006-0.435-0.4350.0000.0000.0000.000
10A55ALA0-0.041-0.02312.0130.1270.1270.0000.0000.0000.000
11A56THR00.004-0.01412.6380.0780.0780.0000.0000.0000.000
12A57LEU0-0.0310.00314.4400.0610.0610.0000.0000.0000.000
13A58ARG10.8790.92616.1130.2740.2740.0000.0000.0000.000
14A59GLU-1-0.766-0.81917.857-0.195-0.1950.0000.0000.0000.000
15A60LEU0-0.021-0.01018.9720.0320.0320.0000.0000.0000.000
16A61GLU-1-0.955-0.99019.489-0.260-0.2600.0000.0000.0000.000
17A62ASP-1-0.865-0.92022.085-0.172-0.1720.0000.0000.0000.000
18A63GLU-1-0.775-0.87323.531-0.166-0.1660.0000.0000.0000.000
19A64ARG10.8150.89323.5940.2570.2570.0000.0000.0000.000
20A65GLN0-0.125-0.07125.3320.0260.0260.0000.0000.0000.000
21A66ARG10.7120.82922.9350.2070.2070.0000.0000.0000.000
22A67ALA0-0.021-0.01330.2290.0000.0000.0000.0000.0000.000
23A68GLY00.006-0.00932.990-0.002-0.0020.0000.0000.0000.000
24A69LEU0-0.0230.00329.438-0.001-0.0010.0000.0000.0000.000
25A70PRO00.0070.01132.6730.0060.0060.0000.0000.0000.000
26A71GLU-1-0.936-0.96435.133-0.095-0.0950.0000.0000.0000.000
27A72LYS10.8630.93836.4740.1170.1170.0000.0000.0000.000
28A73PRO00.0220.01438.2260.0040.0040.0000.0000.0000.000
29A74GLU-1-0.965-0.97641.387-0.077-0.0770.0000.0000.0000.000
30A75ILE0-0.049-0.03242.6300.0010.0010.0000.0000.0000.000
31A76PRO0-0.008-0.00144.5790.0030.0030.0000.0000.0000.000
32A77GLU-1-0.880-0.95147.975-0.063-0.0630.0000.0000.0000.000
33A78GLY0-0.050-0.02050.7100.0010.0010.0000.0000.0000.000
34A79TRP0-0.035-0.02346.087-0.001-0.0010.0000.0000.0000.000
35A80THR0-0.037-0.01244.325-0.003-0.0030.0000.0000.0000.000
36A81ILE0-0.003-0.01638.7860.0010.0010.0000.0000.0000.000
37A82ASP-1-0.885-0.91537.299-0.119-0.1190.0000.0000.0000.000
38A83ARG10.9050.94829.5770.1640.1640.0000.0000.0000.000
39A84LYS10.8250.89530.9920.1340.1340.0000.0000.0000.000
40A85PRO0-0.006-0.01427.4510.0010.0010.0000.0000.0000.000
41A86GLY00.0180.01026.083-0.006-0.0060.0000.0000.0000.000
42A87VAL0-0.109-0.04826.7210.0000.0000.0000.0000.0000.000
43A88THR00.0270.01529.6110.0070.0070.0000.0000.0000.000
44A89HIS0-0.045-0.03131.2540.0060.0060.0000.0000.0000.000
45A90PHE0-0.0130.00134.3780.0010.0010.0000.0000.0000.000
46A91THR00.013-0.01236.4290.0080.0080.0000.0000.0000.000
47A92MET0-0.016-0.00340.045-0.003-0.0030.0000.0000.0000.000
48A93ARG10.8620.94641.0830.0900.0900.0000.0000.0000.000
49A94LYS10.9180.97846.3450.0560.0560.0000.0000.0000.000
50A95SER00.0000.01149.8320.0010.0010.0000.0000.0000.000
51A96HIS00.013-0.00653.207-0.001-0.0010.0000.0000.0000.000
52A97GLY0-0.019-0.00156.2730.0020.0020.0000.0000.0000.000
53A98ASP-1-0.946-0.98457.640-0.045-0.0450.0000.0000.0000.000
54A99GLU-1-0.869-0.89755.647-0.048-0.0480.0000.0000.0000.000
55A100GLU-1-0.927-0.96448.501-0.069-0.0690.0000.0000.0000.000
56A101ILE0-0.034-0.02749.5550.0010.0010.0000.0000.0000.000
57A102ILE0-0.043-0.03044.464-0.003-0.0030.0000.0000.0000.000
58A103LEU00.0220.02043.4750.0020.0020.0000.0000.0000.000
59A104GLN0-0.004-0.01040.476-0.003-0.0030.0000.0000.0000.000
60A105LEU00.0250.02636.9980.0040.0040.0000.0000.0000.000
61A106THR0-0.035-0.03737.654-0.004-0.0040.0000.0000.0000.000
62A107GLY00.0040.01034.945-0.002-0.0020.0000.0000.0000.000
63A108GLU-1-0.850-0.89632.941-0.116-0.1160.0000.0000.0000.000
64A109ASP-1-0.855-0.93735.184-0.070-0.0700.0000.0000.0000.000
65A110ARG10.8230.89837.0880.0630.0630.0000.0000.0000.000
66A111SER0-0.0220.00635.654-0.003-0.0030.0000.0000.0000.000
67A112ASN0-0.050-0.03436.2400.0010.0010.0000.0000.0000.000
68A113GLU-1-0.951-0.95936.651-0.064-0.0640.0000.0000.0000.000
69A114GLU-1-0.983-0.98238.084-0.064-0.0640.0000.0000.0000.000
70A115ILE0-0.012-0.02134.0750.0000.0000.0000.0000.0000.000
71A116THR00.0660.05137.7930.0010.0010.0000.0000.0000.000
72A117ARG10.8780.92334.6610.0980.0980.0000.0000.0000.000
73A118THR00.0170.00038.8370.0050.0050.0000.0000.0000.000
74A119LEU0-0.045-0.02239.730-0.006-0.0060.0000.0000.0000.000
75A120ASP-1-0.879-0.92142.106-0.068-0.0680.0000.0000.0000.000
76A121VAL0-0.005-0.01544.758-0.002-0.0020.0000.0000.0000.000
77A122LEU0-0.046-0.02245.3490.0040.0040.0000.0000.0000.000
78A123VAL00.0120.01249.364-0.001-0.0010.0000.0000.0000.000
79A124VAL0-0.012-0.01450.3200.0020.0020.0000.0000.0000.000
80A125ASN00.0810.01653.5190.0000.0000.0000.0000.0000.000
81A126GLY00.0080.01656.9580.0010.0010.0000.0000.0000.000
82A127GLY0-0.047-0.02655.4490.0010.0010.0000.0000.0000.000
83A128LYS10.8050.91055.4460.0410.0410.0000.0000.0000.000
84A129ALA00.0400.01251.680-0.001-0.0010.0000.0000.0000.000
85A130LEU0-0.0390.00653.7540.0020.0020.0000.0000.0000.000
86A131VAL0-0.016-0.02447.773-0.002-0.0020.0000.0000.0000.000
87A132PHE00.0310.00949.8760.0030.0030.0000.0000.0000.000
88A133GLY00.0380.03746.426-0.003-0.0030.0000.0000.0000.000
89A134MET0-0.059-0.04145.6620.0040.0040.0000.0000.0000.000
90A135SER00.0560.00143.282-0.003-0.0030.0000.0000.0000.000
91A136VAL0-0.082-0.02742.2610.0030.0030.0000.0000.0000.000
92A137GLU-1-0.828-0.90942.715-0.061-0.0610.0000.0000.0000.000
93A138ASP-1-0.929-0.96043.883-0.057-0.0570.0000.0000.0000.000
94A139GLY0-0.042-0.01744.5650.0020.0020.0000.0000.0000.000
95A140GLU-1-0.925-0.95546.290-0.048-0.0480.0000.0000.0000.000
96A141PHE0-0.054-0.04445.384-0.003-0.0030.0000.0000.0000.000
97A142VAL00.0470.04447.7050.0030.0030.0000.0000.0000.000
98A143ILE0-0.048-0.04748.415-0.002-0.0020.0000.0000.0000.000
99A144ASN00.000-0.00545.8080.0040.0040.0000.0000.0000.000
100A145ASN0-0.039-0.03248.1560.0000.0000.0000.0000.0000.000
101A146VAL00.0330.02650.836-0.002-0.0020.0000.0000.0000.000
102A147CYS0-0.0360.00850.9440.0020.0020.0000.0000.0000.000
103A148PHE00.0210.00053.1070.0000.0000.0000.0000.0000.000
104A149ARG10.8500.90949.6740.0510.0510.0000.0000.0000.000
105A150HIS00.0680.02753.880-0.001-0.0010.0000.0000.0000.000
106A151ASP-1-0.847-0.92452.424-0.051-0.0510.0000.0000.0000.000
107A152GLY00.0690.02151.756-0.002-0.0020.0000.0000.0000.000
108A153LYS10.9310.97049.0260.0520.0520.0000.0000.0000.000
109A154LEU00.0180.01646.725-0.003-0.0030.0000.0000.0000.000
110A155ALA0-0.038-0.02646.887-0.003-0.0030.0000.0000.0000.000
111A156LEU0-0.002-0.00246.240-0.002-0.0020.0000.0000.0000.000
112A157ASP-1-0.881-0.90442.676-0.080-0.0800.0000.0000.0000.000
113A158THR00.0700.03138.7880.0020.0020.0000.0000.0000.000
114A159SER0-0.073-0.03338.406-0.005-0.0050.0000.0000.0000.000
115A160ALA00.0360.00136.1440.0030.0030.0000.0000.0000.000
116A161GLU-1-0.875-0.92438.279-0.060-0.0600.0000.0000.0000.000
117A162ALA00.0150.01241.4050.0040.0040.0000.0000.0000.000
118A163GLN00.010-0.02838.3860.0070.0070.0000.0000.0000.000
119A164PHE0-0.0220.00241.5850.0040.0040.0000.0000.0000.000
120A165GLN0-0.043-0.02643.2150.0050.0050.0000.0000.0000.000
121A166LYS10.8450.91044.0560.0720.0720.0000.0000.0000.000
122A167SER0-0.074-0.03744.1450.0020.0020.0000.0000.0000.000
123A168GLN0-0.043-0.01746.2990.0020.0020.0000.0000.0000.000
124A169LEU0-0.073-0.02249.3840.0030.0030.0000.0000.0000.000
125A170TYR00.0050.00251.370-0.001-0.0010.0000.0000.0000.000
126A171MET00.0390.00447.425-0.002-0.0020.0000.0000.0000.000
127A172GLY00.0210.02452.046-0.001-0.0010.0000.0000.0000.000
128A173PRO0-0.072-0.04254.8400.0000.0000.0000.0000.0000.000
129A174ASP-1-0.821-0.89754.094-0.040-0.0400.0000.0000.0000.000
130A175LEU00.004-0.00953.3410.0020.0020.0000.0000.0000.000
131A176ALA0-0.0160.00155.8810.0010.0010.0000.0000.0000.000
132A177ASP-1-0.995-0.99457.544-0.030-0.0300.0000.0000.0000.000
133A178LEU0-0.117-0.06358.3340.0010.0010.0000.0000.0000.000
134A179GLU-1-0.901-0.95061.386-0.027-0.0270.0000.0000.0000.000
135A180ASP-1-0.838-0.93062.130-0.033-0.0330.0000.0000.0000.000
136A181HIS0-0.074-0.03262.907-0.001-0.0010.0000.0000.0000.000
137A182LEU0-0.038-0.00160.885-0.001-0.0010.0000.0000.0000.000
138A183VAL00.0600.02157.128-0.001-0.0010.0000.0000.0000.000
139A184ASP-1-0.843-0.92758.761-0.037-0.0370.0000.0000.0000.000
140A185SER0-0.084-0.04860.592-0.001-0.0010.0000.0000.0000.000
141A186PHE0-0.028-0.02256.566-0.001-0.0010.0000.0000.0000.000
142A187THR00.0600.03355.679-0.002-0.0020.0000.0000.0000.000
143A188SER0-0.020-0.01856.792-0.001-0.0010.0000.0000.0000.000
144A189TYR0-0.066-0.03555.940-0.001-0.0010.0000.0000.0000.000
145A190LEU00.0230.00851.983-0.001-0.0010.0000.0000.0000.000
146A191SER00.0410.02854.490-0.002-0.0020.0000.0000.0000.000
147A192ALA0-0.057-0.02256.051-0.001-0.0010.0000.0000.0000.000
148A193ARG10.7200.82754.1590.0470.0470.0000.0000.0000.000
149A194GLY0-0.011-0.00752.763-0.002-0.0020.0000.0000.0000.000
150A195VAL0-0.030-0.00349.114-0.002-0.0020.0000.0000.0000.000
151A196ASN00.024-0.00150.9420.0000.0000.0000.0000.0000.000
152A197ASP-1-0.737-0.88649.725-0.055-0.0550.0000.0000.0000.000
153A198THR0-0.067-0.02348.612-0.002-0.0020.0000.0000.0000.000
154A199LEU0-0.032-0.00845.885-0.003-0.0030.0000.0000.0000.000
155A200ALA00.0280.02745.225-0.004-0.0040.0000.0000.0000.000
156A201ASN00.0350.01543.988-0.005-0.0050.0000.0000.0000.000
157A202PHE0-0.008-0.01641.221-0.004-0.0040.0000.0000.0000.000
158A203ILE00.0190.00440.050-0.006-0.0060.0000.0000.0000.000
159A204ASP-1-0.810-0.86839.128-0.089-0.0890.0000.0000.0000.000
160A205GLN0-0.045-0.03538.072-0.009-0.0090.0000.0000.0000.000
161A206PHE0-0.045-0.04036.172-0.009-0.0090.0000.0000.0000.000
162A207SER0-0.011-0.02735.068-0.009-0.0090.0000.0000.0000.000
163A208LEU00.0400.02933.421-0.009-0.0090.0000.0000.0000.000
164A209TRP0-0.005-0.00332.605-0.011-0.0110.0000.0000.0000.000
165A210SER0-0.060-0.04031.791-0.008-0.0080.0000.0000.0000.000
166A211GLU-1-0.926-0.95129.006-0.154-0.1540.0000.0000.0000.000
167A212GLN0-0.022-0.02627.370-0.007-0.0070.0000.0000.0000.000
168A213ALA0-0.021-0.02027.188-0.016-0.0160.0000.0000.0000.000
169A214ASP-1-0.778-0.89025.929-0.215-0.2150.0000.0000.0000.000
170A215TYR0-0.053-0.03321.267-0.041-0.0410.0000.0000.0000.000
171A216GLU-1-0.789-0.89322.144-0.252-0.2520.0000.0000.0000.000
172A217GLU-1-0.991-1.00321.631-0.367-0.3670.0000.0000.0000.000
173A218TRP00.0180.01717.789-0.055-0.0550.0000.0000.0000.000
174A219LEU0-0.0070.00517.610-0.065-0.0650.0000.0000.0000.000
175A220SER00.0160.01316.534-0.088-0.0880.0000.0000.0000.000
176A221SER0-0.035-0.02016.484-0.076-0.0760.0000.0000.0000.000
177A222ILE00.0030.00412.667-0.090-0.0900.0000.0000.0000.000
178A223ASN0-0.039-0.00812.327-0.113-0.1130.0000.0000.0000.000
179A224LYS10.8670.92111.5640.3600.3600.0000.0000.0000.000
180A225PHE0-0.071-0.01510.847-0.062-0.0620.0000.0000.0000.000
181A226VAL0-0.051-0.0226.829-0.134-0.1340.0000.0000.0000.000
182A227SER0-0.043-0.0146.943-0.499-0.4990.0000.0000.0000.000