FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 98462

Calculation Name: 3JV1-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3JV1

Chain ID: A

ChEMBL ID:
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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:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1786413.395444
FMO2-HF: Nuclear repulsion 1714400.74489
FMO2-HF: Total energy -72012.650553
FMO2-MP2: Total energy -72223.609515


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.
-10.086-5.5870.154-2.004-2.649-0.005
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 : 0.027 / 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].
3A48SER0-0.041-0.0353.378-2.562-0.3110.012-1.099-1.1640.002
4A49ASP-1-0.844-0.9162.877-6.837-4.8560.143-0.815-1.309-0.007
5A50GLN0-0.0040.0124.3510.5780.845-0.001-0.090-0.1760.000
6A51ARG10.9350.9546.0610.5860.5860.0000.0000.0000.000
7A52LEU0-0.0040.0167.5890.2300.2300.0000.0000.0000.000
8A53SER0-0.0110.0028.3780.2860.2860.0000.0000.0000.000
9A54GLU-1-0.921-0.98210.024-0.404-0.4040.0000.0000.0000.000
10A55ALA0-0.047-0.02512.0600.1140.1140.0000.0000.0000.000
11A56THR00.014-0.00312.6890.0660.0660.0000.0000.0000.000
12A57LEU0-0.0150.00714.4540.0520.0520.0000.0000.0000.000
13A58ARG10.9770.98316.1270.2290.2290.0000.0000.0000.000
14A59GLU-1-0.759-0.82317.902-0.163-0.1630.0000.0000.0000.000
15A60LEU0-0.025-0.01519.0500.0270.0270.0000.0000.0000.000
16A61GLU-1-0.999-1.01219.803-0.235-0.2350.0000.0000.0000.000
17A62ASP-1-0.928-0.97222.101-0.153-0.1530.0000.0000.0000.000
18A63GLU-1-0.804-0.89123.550-0.138-0.1380.0000.0000.0000.000
19A64ARG10.9160.96022.7750.2420.2420.0000.0000.0000.000
20A65GLN0-0.112-0.05325.3820.0230.0230.0000.0000.0000.000
21A66ARG10.7400.86823.2330.1700.1700.0000.0000.0000.000
22A67ALA0-0.019-0.01230.2720.0000.0000.0000.0000.0000.000
23A68GLY00.001-0.01233.031-0.001-0.0010.0000.0000.0000.000
24A69LEU0-0.0180.00429.6890.0000.0000.0000.0000.0000.000
25A70PRO00.0150.01632.7210.0050.0050.0000.0000.0000.000
26A71GLU-1-0.925-0.96035.161-0.084-0.0840.0000.0000.0000.000
27A72LYS10.8510.92936.1920.1060.1060.0000.0000.0000.000
28A73PRO00.0240.01638.2510.0030.0030.0000.0000.0000.000
29A74GLU-1-0.962-0.97641.414-0.069-0.0690.0000.0000.0000.000
30A75ILE0-0.055-0.02842.6980.0010.0010.0000.0000.0000.000
31A76PRO0-0.0030.00344.5930.0020.0020.0000.0000.0000.000
32A77GLU-1-0.899-0.96047.989-0.056-0.0560.0000.0000.0000.000
33A78GLY0-0.053-0.02750.6430.0010.0010.0000.0000.0000.000
34A79TRP0-0.023-0.01446.022-0.001-0.0010.0000.0000.0000.000
35A80THR0-0.059-0.00944.317-0.003-0.0030.0000.0000.0000.000
36A81ILE00.009-0.02038.7540.0010.0010.0000.0000.0000.000
37A82ASP-1-0.981-0.97537.636-0.103-0.1030.0000.0000.0000.000
38A83ARG11.0000.99930.0850.1410.1410.0000.0000.0000.000
39A84LYS10.8980.94430.9790.1240.1240.0000.0000.0000.000
40A85PRO0-0.012-0.01827.6140.0020.0020.0000.0000.0000.000
41A86GLY00.0450.02726.093-0.006-0.0060.0000.0000.0000.000
42A87VAL0-0.120-0.05426.7260.0020.0020.0000.0000.0000.000
43A88THR00.0520.02429.6130.0060.0060.0000.0000.0000.000
44A89HIS0-0.037-0.01331.2620.0050.0050.0000.0000.0000.000
45A90PHE0-0.023-0.00334.3830.0000.0000.0000.0000.0000.000
46A91THR00.000-0.01236.4340.0070.0070.0000.0000.0000.000
47A92MET0-0.006-0.00440.048-0.003-0.0030.0000.0000.0000.000
48A93ARG10.9070.95840.9870.0790.0790.0000.0000.0000.000
49A94LYS10.9731.00446.3470.0490.0490.0000.0000.0000.000
50A95SER0-0.0050.01149.8350.0010.0010.0000.0000.0000.000
51A96HIS0-0.018-0.01253.208-0.001-0.0010.0000.0000.0000.000
52A97GLY0-0.007-0.00356.2750.0020.0020.0000.0000.0000.000
53A98ASP-1-0.954-0.98857.639-0.039-0.0390.0000.0000.0000.000
54A99GLU-1-0.866-0.91755.510-0.041-0.0410.0000.0000.0000.000
55A100GLU-1-0.963-0.97348.895-0.060-0.0600.0000.0000.0000.000
56A101ILE0-0.042-0.02749.5880.0010.0010.0000.0000.0000.000
57A102ILE0-0.037-0.03044.583-0.003-0.0030.0000.0000.0000.000
58A103LEU00.0140.01343.4570.0020.0020.0000.0000.0000.000
59A104GLN00.004-0.00640.445-0.003-0.0030.0000.0000.0000.000
60A105LEU00.0150.02137.0740.0040.0040.0000.0000.0000.000
61A106THR0-0.023-0.03537.676-0.002-0.0020.0000.0000.0000.000
62A107GLY0-0.023-0.00834.954-0.001-0.0010.0000.0000.0000.000
63A108GLU-1-0.880-0.92632.635-0.094-0.0940.0000.0000.0000.000
64A109ASP-1-0.948-0.97935.198-0.056-0.0560.0000.0000.0000.000
65A110ARG10.8990.94137.1050.0450.0450.0000.0000.0000.000
66A111SER0-0.0080.01435.675-0.003-0.0030.0000.0000.0000.000
67A112ASN0-0.042-0.02436.2640.0020.0020.0000.0000.0000.000
68A113GLU-1-0.950-0.96436.682-0.046-0.0460.0000.0000.0000.000
69A114GLU-1-0.954-0.96638.117-0.051-0.0510.0000.0000.0000.000
70A115ILE00.002-0.02434.3810.0000.0000.0000.0000.0000.000
71A116THR00.0540.04237.8190.0000.0000.0000.0000.0000.000
72A117ARG10.9030.95235.2650.0790.0790.0000.0000.0000.000
73A118THR00.0100.01338.6780.0040.0040.0000.0000.0000.000
74A119LEU0-0.018-0.01439.741-0.005-0.0050.0000.0000.0000.000
75A120ASP-1-0.874-0.91242.115-0.054-0.0540.0000.0000.0000.000
76A121VAL0-0.015-0.02344.763-0.002-0.0020.0000.0000.0000.000
77A122LEU0-0.051-0.02645.5620.0030.0030.0000.0000.0000.000
78A123VAL00.0030.01149.365-0.001-0.0010.0000.0000.0000.000
79A124VAL0-0.010-0.01250.3630.0020.0020.0000.0000.0000.000
80A125ASN00.0830.01853.516-0.001-0.0010.0000.0000.0000.000
81A126GLY0-0.0040.00856.9530.0010.0010.0000.0000.0000.000
82A127GLY0-0.046-0.02555.4390.0010.0010.0000.0000.0000.000
83A128LYS10.8290.92955.4420.0340.0340.0000.0000.0000.000
84A129ALA00.0430.01451.712-0.001-0.0010.0000.0000.0000.000
85A130LEU0-0.0400.00353.7500.0020.0020.0000.0000.0000.000
86A131VAL0-0.016-0.02347.794-0.002-0.0020.0000.0000.0000.000
87A132PHE00.0230.00849.8690.0020.0020.0000.0000.0000.000
88A133GLY00.0460.04146.433-0.003-0.0030.0000.0000.0000.000
89A134MET0-0.050-0.04245.6760.0040.0040.0000.0000.0000.000
90A135SER00.0690.03143.267-0.003-0.0030.0000.0000.0000.000
91A136VAL0-0.081-0.02342.2400.0020.0020.0000.0000.0000.000
92A137GLU-1-0.875-0.96042.736-0.046-0.0460.0000.0000.0000.000
93A138ASP-1-0.928-0.96243.919-0.045-0.0450.0000.0000.0000.000
94A139GLY0-0.035-0.00944.5900.0020.0020.0000.0000.0000.000
95A140GLU-1-0.922-0.95546.314-0.039-0.0390.0000.0000.0000.000
96A141PHE0-0.073-0.05245.401-0.002-0.0020.0000.0000.0000.000
97A142VAL00.0530.04647.7320.0030.0030.0000.0000.0000.000
98A143ILE0-0.057-0.05048.429-0.002-0.0020.0000.0000.0000.000
99A144ASN00.0120.00145.7890.0030.0030.0000.0000.0000.000
100A145ASN0-0.036-0.02948.2180.0000.0000.0000.0000.0000.000
101A146VAL00.0390.03150.843-0.002-0.0020.0000.0000.0000.000
102A147CYS0-0.037-0.00350.6110.0020.0020.0000.0000.0000.000
103A148PHE00.013-0.00153.108-0.001-0.0010.0000.0000.0000.000
104A149ARG10.8700.93149.1950.0420.0420.0000.0000.0000.000
105A150HIS00.0580.01253.874-0.001-0.0010.0000.0000.0000.000
106A151ASP-1-0.846-0.91952.401-0.043-0.0430.0000.0000.0000.000
107A152GLY00.0720.02151.745-0.002-0.0020.0000.0000.0000.000
108A153LYS10.9280.96949.1470.0450.0450.0000.0000.0000.000
109A154LEU00.0180.01446.792-0.003-0.0030.0000.0000.0000.000
110A155ALA0-0.041-0.03346.876-0.002-0.0020.0000.0000.0000.000
111A156LEU0-0.008-0.00746.209-0.002-0.0020.0000.0000.0000.000
112A157ASP-1-0.890-0.92642.668-0.068-0.0680.0000.0000.0000.000
113A158THR00.0450.02439.1240.0020.0020.0000.0000.0000.000
114A159SER0-0.0190.01538.393-0.003-0.0030.0000.0000.0000.000
115A160ALA00.0340.00136.1540.0020.0020.0000.0000.0000.000
116A161GLU-1-0.871-0.92638.265-0.048-0.0480.0000.0000.0000.000
117A162ALA00.0000.00841.3880.0040.0040.0000.0000.0000.000
118A163GLN0-0.009-0.04738.1240.0050.0050.0000.0000.0000.000
119A164PHE0-0.0100.00741.6090.0030.0030.0000.0000.0000.000
120A165GLN0-0.045-0.02443.2030.0040.0040.0000.0000.0000.000
121A166LYS10.8460.91144.0450.0600.0600.0000.0000.0000.000
122A167SER0-0.075-0.03144.1440.0020.0020.0000.0000.0000.000
123A168GLN0-0.039-0.01746.2930.0010.0010.0000.0000.0000.000
124A169LEU0-0.074-0.02149.3760.0020.0020.0000.0000.0000.000
125A170TYR0-0.008-0.00351.3660.0000.0000.0000.0000.0000.000
126A171MET00.035-0.00347.335-0.002-0.0020.0000.0000.0000.000
127A172GLY00.0080.01452.046-0.001-0.0010.0000.0000.0000.000
128A173PRO0-0.072-0.03754.8440.0000.0000.0000.0000.0000.000
129A174ASP-1-0.820-0.89654.287-0.030-0.0300.0000.0000.0000.000
130A175LEU00.006-0.01753.2810.0010.0010.0000.0000.0000.000
131A176ALA0-0.0220.00255.9130.0010.0010.0000.0000.0000.000
132A177ASP-1-0.978-0.98757.558-0.022-0.0220.0000.0000.0000.000
133A178LEU0-0.120-0.06557.9210.0010.0010.0000.0000.0000.000
134A179GLU-1-0.939-0.97361.398-0.021-0.0210.0000.0000.0000.000
135A180ASP-1-0.824-0.91861.943-0.026-0.0260.0000.0000.0000.000
136A181HIS0-0.062-0.02462.921-0.001-0.0010.0000.0000.0000.000
137A182LEU0-0.037-0.00261.197-0.001-0.0010.0000.0000.0000.000
138A183VAL00.0610.02457.234-0.001-0.0010.0000.0000.0000.000
139A184ASP-1-0.829-0.94458.775-0.030-0.0300.0000.0000.0000.000
140A185SER0-0.073-0.04960.606-0.001-0.0010.0000.0000.0000.000
141A186PHE0-0.028-0.01856.573-0.001-0.0010.0000.0000.0000.000
142A187THR00.0320.04355.877-0.002-0.0020.0000.0000.0000.000
143A188SER0-0.008-0.01356.805-0.001-0.0010.0000.0000.0000.000
144A189TYR0-0.076-0.03456.0390.0000.0000.0000.0000.0000.000
145A190LEU00.0220.00552.169-0.001-0.0010.0000.0000.0000.000
146A191SER00.0410.02954.501-0.002-0.0020.0000.0000.0000.000
147A192ALA0-0.063-0.02856.064-0.001-0.0010.0000.0000.0000.000
148A193ARG10.7610.86154.2660.0400.0400.0000.0000.0000.000
149A194GLY0-0.041-0.02652.774-0.002-0.0020.0000.0000.0000.000
150A195VAL0-0.0210.00649.123-0.002-0.0020.0000.0000.0000.000
151A196ASN00.028-0.00150.9710.0000.0000.0000.0000.0000.000
152A197ASP-1-0.711-0.87649.743-0.045-0.0450.0000.0000.0000.000
153A198THR0-0.079-0.03148.634-0.002-0.0020.0000.0000.0000.000
154A199LEU0-0.036-0.00445.967-0.003-0.0030.0000.0000.0000.000
155A200ALA00.0330.02545.242-0.004-0.0040.0000.0000.0000.000
156A201ASN00.0310.00644.008-0.005-0.0050.0000.0000.0000.000
157A202PHE0-0.003-0.01441.135-0.004-0.0040.0000.0000.0000.000
158A203ILE00.0080.00240.002-0.006-0.0060.0000.0000.0000.000
159A204ASP-1-0.850-0.91539.147-0.073-0.0730.0000.0000.0000.000
160A205GLN0-0.029-0.02338.095-0.007-0.0070.0000.0000.0000.000
161A206PHE0-0.045-0.03436.112-0.008-0.0080.0000.0000.0000.000
162A207SER0-0.012-0.02535.078-0.009-0.0090.0000.0000.0000.000
163A208LEU00.0310.03033.442-0.007-0.0070.0000.0000.0000.000
164A209TRP0-0.0010.00132.630-0.010-0.0100.0000.0000.0000.000
165A210SER0-0.093-0.05631.794-0.009-0.0090.0000.0000.0000.000
166A211GLU-1-0.896-0.93428.875-0.130-0.1300.0000.0000.0000.000
167A212GLN0-0.068-0.07227.434-0.008-0.0080.0000.0000.0000.000
168A213ALA0-0.025-0.02527.213-0.015-0.0150.0000.0000.0000.000
169A214ASP-1-0.852-0.93025.988-0.187-0.1870.0000.0000.0000.000
170A215TYR0-0.049-0.03621.409-0.036-0.0360.0000.0000.0000.000
171A216GLU-1-0.862-0.92922.168-0.214-0.2140.0000.0000.0000.000
172A217GLU-1-1.008-1.00521.656-0.313-0.3130.0000.0000.0000.000
173A218TRP00.0060.01317.862-0.051-0.0510.0000.0000.0000.000
174A219LEU0-0.0150.00217.634-0.058-0.0580.0000.0000.0000.000
175A220SER0-0.022-0.01316.561-0.081-0.0810.0000.0000.0000.000
176A221SER0-0.011-0.01616.505-0.068-0.0680.0000.0000.0000.000
177A222ILE00.0050.00312.579-0.081-0.0810.0000.0000.0000.000
178A223ASN0-0.064-0.01612.358-0.109-0.1090.0000.0000.0000.000
179A224LYS10.9100.94411.5820.2920.2920.0000.0000.0000.000
180A225PHE0-0.069-0.01511.030-0.064-0.0640.0000.0000.0000.000
181A226VAL0-0.044-0.0166.802-0.105-0.1050.0000.0000.0000.000
182A227SER0-0.053-0.0196.963-0.472-0.4720.0000.0000.0000.000