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: 762RK

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 OptAll
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 -1789546.255873
FMO2-HF: Nuclear repulsion 1717532.119686
FMO2-HF: Total energy -72014.136187
FMO2-MP2: Total energy -72225.023153


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.
-15.784-13.1488.811-5.648-5.8-0.046
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 : 0.012 / q_NPA : -0.006
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].
3A48SER0-0.061-0.0532.300-0.6382.0010.429-1.444-1.6250.001
4A49ASP-1-0.827-0.8921.940-15.339-15.7578.382-4.029-3.935-0.047
5A50GLN0-0.040-0.0303.9021.1771.5920.000-0.175-0.2400.000
6A51ARG10.9480.9705.8820.7780.7780.0000.0000.0000.000
7A52LEU00.0100.0217.5530.3120.3120.0000.0000.0000.000
8A53SER0-0.0060.0138.1840.3500.3500.0000.0000.0000.000
9A54GLU-1-0.858-0.9339.834-0.397-0.3970.0000.0000.0000.000
10A55ALA0-0.045-0.02211.7480.1260.1260.0000.0000.0000.000
11A56THR0-0.014-0.03112.2470.0820.0820.0000.0000.0000.000
12A57LEU0-0.0260.00314.0480.0590.0590.0000.0000.0000.000
13A58ARG10.8770.91615.8260.2770.2770.0000.0000.0000.000
14A59GLU-1-0.775-0.82217.451-0.204-0.2040.0000.0000.0000.000
15A60LEU0-0.0070.00218.8040.0330.0330.0000.0000.0000.000
16A61GLU-1-0.954-0.99318.900-0.251-0.2510.0000.0000.0000.000
17A62ASP-1-0.861-0.90921.733-0.172-0.1720.0000.0000.0000.000
18A63GLU-1-0.789-0.88123.174-0.170-0.1700.0000.0000.0000.000
19A64ARG10.7960.87423.8390.2430.2430.0000.0000.0000.000
20A65GLN0-0.117-0.06525.1140.0260.0260.0000.0000.0000.000
21A66ARG10.7170.83322.6080.2130.2130.0000.0000.0000.000
22A67ALA0-0.025-0.01829.7910.0000.0000.0000.0000.0000.000
23A68GLY00.007-0.01033.029-0.001-0.0010.0000.0000.0000.000
24A69LEU0-0.0220.00728.8880.0010.0010.0000.0000.0000.000
25A70PRO00.0000.00632.2980.0070.0070.0000.0000.0000.000
26A71GLU-1-0.934-0.96334.518-0.095-0.0950.0000.0000.0000.000
27A72LYS10.8840.95236.0600.1120.1120.0000.0000.0000.000
28A73PRO00.0010.00337.6160.0040.0040.0000.0000.0000.000
29A74GLU-1-0.959-0.98140.891-0.076-0.0760.0000.0000.0000.000
30A75ILE0-0.047-0.02242.6080.0000.0000.0000.0000.0000.000
31A76PRO0-0.005-0.00244.4400.0030.0030.0000.0000.0000.000
32A77GLU-1-0.868-0.93747.915-0.062-0.0620.0000.0000.0000.000
33A78GLY0-0.056-0.03350.6650.0010.0010.0000.0000.0000.000
34A79TRP0-0.038-0.01446.127-0.001-0.0010.0000.0000.0000.000
35A80THR0-0.039-0.01943.901-0.003-0.0030.0000.0000.0000.000
36A81ILE0-0.004-0.00938.5610.0010.0010.0000.0000.0000.000
37A82ASP-1-0.875-0.91337.323-0.115-0.1150.0000.0000.0000.000
38A83ARG10.9000.95629.1160.1650.1650.0000.0000.0000.000
39A84LYS10.8330.90230.4610.1360.1360.0000.0000.0000.000
40A85PRO00.015-0.00426.8210.0010.0010.0000.0000.0000.000
41A86GLY00.0030.00725.816-0.004-0.0040.0000.0000.0000.000
42A87VAL0-0.113-0.05126.4610.0020.0020.0000.0000.0000.000
43A88THR00.0510.02829.6590.0090.0090.0000.0000.0000.000
44A89HIS0-0.033-0.03331.4100.0060.0060.0000.0000.0000.000
45A90PHE0-0.027-0.01534.3270.0010.0010.0000.0000.0000.000
46A91THR00.0110.00036.2960.0070.0070.0000.0000.0000.000
47A92MET0-0.020-0.01239.936-0.003-0.0030.0000.0000.0000.000
48A93ARG10.8290.92640.6420.0920.0920.0000.0000.0000.000
49A94LYS10.9030.95246.3160.0570.0570.0000.0000.0000.000
50A95SER0-0.0010.01349.8310.0000.0000.0000.0000.0000.000
51A96HIS00.0180.00353.259-0.002-0.0020.0000.0000.0000.000
52A97GLY0-0.0060.00756.2580.0020.0020.0000.0000.0000.000
53A98ASP-1-0.950-0.98957.341-0.045-0.0450.0000.0000.0000.000
54A99GLU-1-0.846-0.88755.505-0.049-0.0490.0000.0000.0000.000
55A100GLU-1-0.908-0.96148.127-0.070-0.0700.0000.0000.0000.000
56A101ILE0-0.027-0.01949.9430.0010.0010.0000.0000.0000.000
57A102ILE0-0.040-0.02844.715-0.003-0.0030.0000.0000.0000.000
58A103LEU00.0270.02343.5680.0020.0020.0000.0000.0000.000
59A104GLN0-0.009-0.02440.747-0.003-0.0030.0000.0000.0000.000
60A105LEU00.0330.03436.8510.0040.0040.0000.0000.0000.000
61A106THR0-0.037-0.02437.535-0.004-0.0040.0000.0000.0000.000
62A107GLY00.0030.01134.854-0.002-0.0020.0000.0000.0000.000
63A108GLU-1-0.845-0.88832.944-0.123-0.1230.0000.0000.0000.000
64A109ASP-1-0.799-0.87134.963-0.079-0.0790.0000.0000.0000.000
65A110ARG10.7820.84437.3960.0730.0730.0000.0000.0000.000
66A111SER0-0.038-0.00635.540-0.006-0.0060.0000.0000.0000.000
67A112ASN0-0.072-0.04236.2010.0030.0030.0000.0000.0000.000
68A113GLU-1-0.921-0.95736.577-0.072-0.0720.0000.0000.0000.000
69A114GLU-1-0.946-0.96638.537-0.068-0.0680.0000.0000.0000.000
70A115ILE0-0.013-0.01933.7000.0000.0000.0000.0000.0000.000
71A116THR00.0460.03937.4030.0000.0000.0000.0000.0000.000
72A117ARG10.8420.91034.1620.1060.1060.0000.0000.0000.000
73A118THR00.000-0.02038.7810.0050.0050.0000.0000.0000.000
74A119LEU0-0.042-0.03239.712-0.006-0.0060.0000.0000.0000.000
75A120ASP-1-0.886-0.92442.150-0.072-0.0720.0000.0000.0000.000
76A121VAL0-0.018-0.02344.716-0.002-0.0020.0000.0000.0000.000
77A122LEU0-0.037-0.01245.4350.0040.0040.0000.0000.0000.000
78A123VAL00.0080.00249.464-0.001-0.0010.0000.0000.0000.000
79A124VAL0-0.013-0.00650.1350.0020.0020.0000.0000.0000.000
80A125ASN00.0740.02353.4930.0000.0000.0000.0000.0000.000
81A126GLY0-0.0040.00356.9040.0000.0000.0000.0000.0000.000
82A127GLY0-0.038-0.01855.8330.0010.0010.0000.0000.0000.000
83A128LYS10.7700.87955.4300.0430.0430.0000.0000.0000.000
84A129ALA00.0560.01951.748-0.001-0.0010.0000.0000.0000.000
85A130LEU0-0.0200.00753.8290.0010.0010.0000.0000.0000.000
86A131VAL0-0.025-0.02248.057-0.002-0.0020.0000.0000.0000.000
87A132PHE00.0350.01450.2690.0020.0020.0000.0000.0000.000
88A133GLY00.0360.03246.574-0.003-0.0030.0000.0000.0000.000
89A134MET0-0.060-0.03945.6810.0050.0050.0000.0000.0000.000
90A135SER0-0.012-0.03543.325-0.003-0.0030.0000.0000.0000.000
91A136VAL0-0.038-0.00542.4600.0030.0030.0000.0000.0000.000
92A137GLU-1-0.781-0.87742.642-0.068-0.0680.0000.0000.0000.000
93A138ASP-1-0.952-0.97344.203-0.060-0.0600.0000.0000.0000.000
94A139GLY0-0.044-0.01144.6200.0020.0020.0000.0000.0000.000
95A140GLU-1-0.943-0.96445.899-0.050-0.0500.0000.0000.0000.000
96A141PHE0-0.062-0.05045.490-0.003-0.0030.0000.0000.0000.000
97A142VAL00.0000.02147.4600.0040.0040.0000.0000.0000.000
98A143ILE0-0.032-0.03748.324-0.002-0.0020.0000.0000.0000.000
99A144ASN00.0080.00545.9620.0040.0040.0000.0000.0000.000
100A145ASN0-0.033-0.02348.3790.0000.0000.0000.0000.0000.000
101A146VAL0-0.0010.00350.918-0.001-0.0010.0000.0000.0000.000
102A147CYS0-0.0210.01750.7320.0020.0020.0000.0000.0000.000
103A148PHE00.013-0.00553.1830.0000.0000.0000.0000.0000.000
104A149ARG10.8270.89849.4730.0550.0550.0000.0000.0000.000
105A150HIS00.0710.02553.896-0.001-0.0010.0000.0000.0000.000
106A151ASP-1-0.838-0.90652.026-0.054-0.0540.0000.0000.0000.000
107A152GLY00.0550.01752.136-0.002-0.0020.0000.0000.0000.000
108A153LYS10.9100.95949.0740.0530.0530.0000.0000.0000.000
109A154LEU00.0140.01146.912-0.003-0.0030.0000.0000.0000.000
110A155ALA0-0.038-0.01947.105-0.003-0.0030.0000.0000.0000.000
111A156LEU00.0030.00146.434-0.003-0.0030.0000.0000.0000.000
112A157ASP-1-0.878-0.90542.780-0.084-0.0840.0000.0000.0000.000
113A158THR00.0620.02938.9270.0020.0020.0000.0000.0000.000
114A159SER0-0.071-0.04238.577-0.005-0.0050.0000.0000.0000.000
115A160ALA00.0350.00136.4640.0030.0030.0000.0000.0000.000
116A161GLU-1-0.864-0.91438.599-0.065-0.0650.0000.0000.0000.000
117A162ALA00.0190.01741.7930.0040.0040.0000.0000.0000.000
118A163GLN00.038-0.01538.8510.0070.0070.0000.0000.0000.000
119A164PHE0-0.0350.00141.7670.0040.0040.0000.0000.0000.000
120A165GLN0-0.037-0.03343.4060.0050.0050.0000.0000.0000.000
121A166LYS10.8290.90943.9780.0780.0780.0000.0000.0000.000
122A167SER0-0.037-0.02444.4120.0020.0020.0000.0000.0000.000
123A168GLN0-0.058-0.02146.5650.0020.0020.0000.0000.0000.000
124A169LEU0-0.056-0.02049.4550.0030.0030.0000.0000.0000.000
125A170TYR00.001-0.00951.183-0.001-0.0010.0000.0000.0000.000
126A171MET00.0350.01147.253-0.001-0.0010.0000.0000.0000.000
127A172GLY00.0520.04051.871-0.001-0.0010.0000.0000.0000.000
128A173PRO0-0.088-0.04654.9910.0000.0000.0000.0000.0000.000
129A174ASP-1-0.815-0.89853.752-0.045-0.0450.0000.0000.0000.000
130A175LEU0-0.014-0.01753.1650.0010.0010.0000.0000.0000.000
131A176ALA0-0.030-0.01255.7900.0010.0010.0000.0000.0000.000
132A177ASP-1-0.981-0.98657.591-0.034-0.0340.0000.0000.0000.000
133A178LEU0-0.106-0.05958.2440.0010.0010.0000.0000.0000.000
134A179GLU-1-0.879-0.92961.291-0.030-0.0300.0000.0000.0000.000
135A180ASP-1-0.843-0.92661.771-0.035-0.0350.0000.0000.0000.000
136A181HIS0-0.068-0.04162.560-0.001-0.0010.0000.0000.0000.000
137A182LEU0-0.036-0.00260.9590.0000.0000.0000.0000.0000.000
138A183VAL00.0370.02156.887-0.002-0.0020.0000.0000.0000.000
139A184ASP-1-0.836-0.92358.504-0.040-0.0400.0000.0000.0000.000
140A185SER0-0.086-0.04660.584-0.001-0.0010.0000.0000.0000.000
141A186PHE0-0.018-0.01956.355-0.001-0.0010.0000.0000.0000.000
142A187THR00.0640.03155.493-0.002-0.0020.0000.0000.0000.000
143A188SER0-0.040-0.02756.731-0.001-0.0010.0000.0000.0000.000
144A189TYR0-0.108-0.05856.0960.0000.0000.0000.0000.0000.000
145A190LEU00.0400.02851.846-0.001-0.0010.0000.0000.0000.000
146A191SER00.0590.03454.543-0.002-0.0020.0000.0000.0000.000
147A192ALA0-0.048-0.02555.852-0.001-0.0010.0000.0000.0000.000
148A193ARG10.7230.82754.0230.0490.0490.0000.0000.0000.000
149A194GLY0-0.016-0.00152.716-0.002-0.0020.0000.0000.0000.000
150A195VAL0-0.024-0.00749.081-0.003-0.0030.0000.0000.0000.000
151A196ASN00.013-0.00650.9670.0000.0000.0000.0000.0000.000
152A197ASP-1-0.744-0.89149.551-0.058-0.0580.0000.0000.0000.000
153A198THR0-0.058-0.02048.474-0.002-0.0020.0000.0000.0000.000
154A199LEU0-0.033-0.00645.821-0.003-0.0030.0000.0000.0000.000
155A200ALA00.0390.03045.109-0.005-0.0050.0000.0000.0000.000
156A201ASN00.0580.02843.749-0.006-0.0060.0000.0000.0000.000
157A202PHE0-0.004-0.01141.134-0.004-0.0040.0000.0000.0000.000
158A203ILE00.0180.00240.132-0.006-0.0060.0000.0000.0000.000
159A204ASP-1-0.793-0.86539.166-0.095-0.0950.0000.0000.0000.000
160A205GLN0-0.066-0.04038.049-0.008-0.0080.0000.0000.0000.000
161A206PHE0-0.029-0.03036.213-0.009-0.0090.0000.0000.0000.000
162A207SER0-0.031-0.02535.164-0.009-0.0090.0000.0000.0000.000
163A208LEU00.0450.03633.515-0.010-0.0100.0000.0000.0000.000
164A209TRP0-0.018-0.00632.568-0.010-0.0100.0000.0000.0000.000
165A210SER0-0.099-0.06831.531-0.010-0.0100.0000.0000.0000.000
166A211GLU-1-0.866-0.93629.307-0.155-0.1550.0000.0000.0000.000
167A212GLN0-0.018-0.02327.171-0.005-0.0050.0000.0000.0000.000
168A213ALA0-0.007-0.01326.962-0.016-0.0160.0000.0000.0000.000
169A214ASP-1-0.780-0.89425.448-0.221-0.2210.0000.0000.0000.000
170A215TYR0-0.059-0.03421.154-0.040-0.0400.0000.0000.0000.000
171A216GLU-1-0.799-0.89421.883-0.244-0.2440.0000.0000.0000.000
172A217GLU-1-0.925-0.94821.248-0.376-0.3760.0000.0000.0000.000
173A218TRP00.0190.01317.706-0.054-0.0540.0000.0000.0000.000
174A219LEU00.0040.00917.380-0.067-0.0670.0000.0000.0000.000
175A220SER00.0090.01016.253-0.082-0.0820.0000.0000.0000.000
176A221SER0-0.068-0.06516.243-0.073-0.0730.0000.0000.0000.000
177A222ILE0-0.0040.00212.605-0.088-0.0880.0000.0000.0000.000
178A223ASN0-0.007-0.00212.066-0.086-0.0860.0000.0000.0000.000
179A224LYS10.8310.92011.3740.3650.3650.0000.0000.0000.000
180A225PHE0-0.046-0.00911.445-0.044-0.0440.0000.0000.0000.000
181A226VAL0-0.054-0.0166.429-0.149-0.1490.0000.0000.0000.000
182A227SER0-0.053-0.0297.253-0.279-0.2790.0000.0000.0000.000