FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5N3ZZ

Calculation Name: 2IF4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IF4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9LDC0

Base Structure: X-ray

Registration Date: 2023-09-26

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 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 258
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3321002.625879
FMO2-HF: Nuclear repulsion 3216532.987601
FMO2-HF: Total energy -104469.638279
FMO2-MP2: Total energy -104769.300815


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:35:ASN)


Summations of interaction energy for fragment #1(A:35:ASN)
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.
-8.662-4.5925.325-3.523-5.8680.013
Interaction energy analysis for fragmet #1(A:35:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.007
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].
3A37PRO00.0060.0223.824-1.7330.521-0.021-1.157-1.076-0.001
4A38PRO00.0060.0044.775-0.327-0.214-0.001-0.002-0.1090.000
5A39LYS10.8610.9326.7332.4172.4170.0000.0000.0000.000
6A40VAL00.0230.01810.133-0.025-0.0250.0000.0000.0000.000
7A41ASP-1-0.925-0.96312.702-0.793-0.7930.0000.0000.0000.000
8A42SER0-0.067-0.03915.9580.0500.0500.0000.0000.0000.000
9A43GLU-1-0.850-0.91917.921-0.262-0.2620.0000.0000.0000.000
10A44ALA0-0.058-0.04718.9510.0030.0030.0000.0000.0000.000
11A45GLU-1-0.885-0.94720.148-0.026-0.0260.0000.0000.0000.000
12A46VAL00.005-0.02521.444-0.001-0.0010.0000.0000.0000.000
13A47LEU0-0.089-0.03319.9670.0100.0100.0000.0000.0000.000
14A48ASP-1-0.792-0.91623.9260.0950.0950.0000.0000.0000.000
15A49GLU-1-0.974-0.95424.332-0.014-0.0140.0000.0000.0000.000
16A50LYS10.7470.85322.653-0.054-0.0540.0000.0000.0000.000
17A51VAL00.004-0.01419.4200.0330.0330.0000.0000.0000.000
18A52SER0-0.0030.02018.743-0.035-0.0350.0000.0000.0000.000
19A53LYS10.7870.89116.1370.0320.0320.0000.0000.0000.000
20A54GLN0-0.027-0.00314.503-0.013-0.0130.0000.0000.0000.000
21A55ILE00.0280.00914.259-0.036-0.0360.0000.0000.0000.000
22A56ILE0-0.016-0.0029.478-0.065-0.0650.0000.0000.0000.000
23A57LYS10.8410.92113.663-0.029-0.0290.0000.0000.0000.000
24A58GLU-1-0.774-0.88415.436-0.010-0.0100.0000.0000.0000.000
25A59GLY0-0.036-0.01318.8980.0200.0200.0000.0000.0000.000
26A60HIS0-0.026-0.00220.352-0.023-0.0230.0000.0000.0000.000
27A61GLY00.016-0.00123.6120.0280.0280.0000.0000.0000.000
28A62SER00.010-0.00326.052-0.018-0.0180.0000.0000.0000.000
29A63LYS10.8500.91923.428-0.016-0.0160.0000.0000.0000.000
30A64PRO00.0100.01222.660-0.004-0.0040.0000.0000.0000.000
31A65SER0-0.037-0.03125.845-0.016-0.0160.0000.0000.0000.000
32A66LYS10.8120.88328.456-0.097-0.0970.0000.0000.0000.000
33A67TYR00.015-0.02528.222-0.012-0.0120.0000.0000.0000.000
34A68SER0-0.019-0.00225.8600.0070.0070.0000.0000.0000.000
35A69THR0-0.020-0.02423.9220.0160.0160.0000.0000.0000.000
36A70CYS0-0.044-0.02519.950-0.023-0.0230.0000.0000.0000.000
37A71PHE00.0450.03819.2770.0440.0440.0000.0000.0000.000
38A72LEU0-0.083-0.06513.761-0.052-0.0520.0000.0000.0000.000
39A73HIS00.1160.06910.3460.2800.2800.0000.0000.0000.000
40A74TYR0-0.044-0.0709.249-0.295-0.2950.0000.0000.0000.000
41A75ARG10.7690.9033.000-6.629-5.2980.182-0.330-1.182-0.001
42A76ALA00.0270.0227.035-0.727-0.7270.0000.0000.0000.000
43A77TRP0-0.006-0.0112.5670.1140.9330.331-0.207-0.942-0.001
44A78THR00.0640.0499.219-0.195-0.1950.0000.0000.0000.000
45A79LYS10.8860.92911.7330.2090.2090.0000.0000.0000.000
46A80ASN0-0.022-0.02813.067-0.210-0.2100.0000.0000.0000.000
47A81SER00.0400.01512.588-0.086-0.0860.0000.0000.0000.000
48A82GLN0-0.056-0.0308.225-0.192-0.1920.0000.0000.0000.000
49A83HIS00.0110.0067.527-0.291-0.2910.0000.0000.0000.000
50A84LYS10.8140.8882.276-13.359-14.0444.836-1.823-2.3290.016
51A85PHE0-0.037-0.0236.523-0.059-0.0590.0000.0000.0000.000
52A86GLU-1-0.723-0.8398.4340.9860.9860.0000.0000.0000.000
53A87ASP-1-0.779-0.9114.86510.74710.894-0.001-0.004-0.1410.000
54A88THR00.0800.0427.9980.0770.0770.0000.0000.0000.000
55A89TRP0-0.038-0.0216.465-0.143-0.1430.0000.0000.0000.000
56A90HIS0-0.077-0.0166.5990.2440.2440.0000.0000.0000.000
57A91GLU-1-0.916-0.9648.2411.3651.3650.0000.0000.0000.000
58A92GLN0-0.103-0.03910.710-0.405-0.4050.0000.0000.0000.000
59A93GLN0-0.033-0.02912.219-0.336-0.3360.0000.0000.0000.000
60A94PRO0-0.058-0.01314.0630.0890.0890.0000.0000.0000.000
61A95ILE00.0130.01014.992-0.074-0.0740.0000.0000.0000.000
62A96GLU-1-0.888-0.93717.1880.4490.4490.0000.0000.0000.000
63A97LEU0-0.040-0.02917.7460.0070.0070.0000.0000.0000.000
64A98VAL0-0.0040.00420.907-0.034-0.0340.0000.0000.0000.000
65A99LEU00.0110.00721.819-0.003-0.0030.0000.0000.0000.000
66A100GLY00.0770.01325.204-0.026-0.0260.0000.0000.0000.000
67A101LYS10.7930.89726.766-0.246-0.2460.0000.0000.0000.000
68A102GLU-1-0.780-0.86022.1170.2900.2900.0000.0000.0000.000
69A103LYS10.9150.94321.568-0.437-0.4370.0000.0000.0000.000
70A104LYS10.8910.93322.175-0.233-0.2330.0000.0000.0000.000
71A105GLU-1-0.870-0.93519.4880.4620.4620.0000.0000.0000.000
72A106LEU0-0.016-0.00216.184-0.005-0.0050.0000.0000.0000.000
73A107ALA0-0.0030.00819.337-0.013-0.0130.0000.0000.0000.000
74A108GLY00.0650.00418.993-0.021-0.0210.0000.0000.0000.000
75A109LEU0-0.0090.00013.972-0.039-0.0390.0000.0000.0000.000
76A110ALA00.0140.01817.246-0.017-0.0170.0000.0000.0000.000
77A111ILE00.0080.00820.416-0.026-0.0260.0000.0000.0000.000
78A112GLY00.0270.00217.984-0.036-0.0360.0000.0000.0000.000
79A113VAL00.008-0.01416.744-0.031-0.0310.0000.0000.0000.000
80A114ALA0-0.0120.01118.800-0.032-0.0320.0000.0000.0000.000
81A115SER0-0.024-0.00920.556-0.031-0.0310.0000.0000.0000.000
82A116MET0-0.147-0.06714.368-0.027-0.0270.0000.0000.0000.000
83A117LYS10.8340.89420.0520.0450.0450.0000.0000.0000.000
84A118SER0-0.009-0.00319.1940.0230.0230.0000.0000.0000.000
85A119GLY00.0060.00017.464-0.051-0.0510.0000.0000.0000.000
86A120GLU-1-0.768-0.87416.381-0.033-0.0330.0000.0000.0000.000
87A121ARG10.8020.8816.6050.0310.0310.0000.0000.0000.000
88A122ALA0-0.005-0.00712.231-0.144-0.1440.0000.0000.0000.000
89A123LEU0-0.0020.0099.0070.1180.1180.0000.0000.0000.000
90A124VAL00.0250.01012.240-0.026-0.0260.0000.0000.0000.000
91A125HIS10.8220.90613.7700.3180.3180.0000.0000.0000.000
92A126VAL00.0240.02515.7870.0040.0040.0000.0000.0000.000
93A127GLY00.0680.04417.702-0.005-0.0050.0000.0000.0000.000
94A128TRP00.0230.01419.8560.0350.0350.0000.0000.0000.000
95A129GLU-1-0.848-0.89820.7230.0800.0800.0000.0000.0000.000
96A130LEU0-0.055-0.02521.4170.0110.0110.0000.0000.0000.000
97A131ALA00.0380.02217.7860.0390.0390.0000.0000.0000.000
98A132TYR0-0.047-0.05815.514-0.089-0.0890.0000.0000.0000.000
99A133GLY0-0.004-0.02319.928-0.013-0.0130.0000.0000.0000.000
100A134LYN00.0180.01522.530-0.009-0.0090.0000.0000.0000.000
101A135GLU-1-0.888-0.94524.9310.1440.1440.0000.0000.0000.000
102A136GLY0-0.074-0.01620.7220.0030.0030.0000.0000.0000.000
103A137ASN00.0040.00518.178-0.023-0.0230.0000.0000.0000.000
104A138PHE00.0470.01719.395-0.008-0.0080.0000.0000.0000.000
105A139SER0-0.058-0.03518.879-0.012-0.0120.0000.0000.0000.000
106A140PHE00.0210.00917.0430.0340.0340.0000.0000.0000.000
107A141PRO0-0.0110.04114.1580.0970.0970.0000.0000.0000.000
108A142ASN0-0.014-0.02414.195-0.146-0.1460.0000.0000.0000.000
109A143VAL0-0.006-0.01614.0840.0380.0380.0000.0000.0000.000
110A144PRO0-0.0060.00515.148-0.045-0.0450.0000.0000.0000.000
111A145PRO00.0230.00118.1000.0010.0010.0000.0000.0000.000
112A146MET0-0.059-0.03620.799-0.031-0.0310.0000.0000.0000.000
113A147ALA00.0300.03116.333-0.044-0.0440.0000.0000.0000.000
114A148ASP-1-0.855-0.91817.3510.0710.0710.0000.0000.0000.000
115A149LEU00.0000.01013.180-0.015-0.0150.0000.0000.0000.000
116A150LEU0-0.055-0.0339.984-0.135-0.1350.0000.0000.0000.000
117A151TYR00.0430.0139.5910.1250.1250.0000.0000.0000.000
118A152GLU-1-0.779-0.8504.984-0.255-0.164-0.0010.000-0.0890.000
119A153VAL0-0.016-0.0218.5350.4420.4420.0000.0000.0000.000
120A154GLU-1-0.805-0.91410.9320.2250.2250.0000.0000.0000.000
121A155VAL00.0090.01612.5630.1320.1320.0000.0000.0000.000
122A156ILE0-0.0080.01015.288-0.061-0.0610.0000.0000.0000.000
123A157GLY00.0160.00217.831-0.071-0.0710.0000.0000.0000.000
124A158PHE0-0.031-0.00721.0230.0470.0470.0000.0000.0000.000
125A159ASP-1-0.815-0.89623.5930.2170.2170.0000.0000.0000.000
126A160GLU-1-0.825-0.86026.9440.1520.1520.0000.0000.0000.000
127A161THR00.0240.01329.5920.0010.0010.0000.0000.0000.000
128A162LYS10.8330.89930.990-0.218-0.2180.0000.0000.0000.000
129A163GLU-1-0.779-0.88235.8430.1040.1040.0000.0000.0000.000
130A164GLY00.0640.04239.3910.0000.0000.0000.0000.0000.000
131A165LYS10.9330.95343.127-0.080-0.0800.0000.0000.0000.000
132A166ALA0-0.0010.00444.7970.0020.0020.0000.0000.0000.000
133A167ARG10.8440.89444.460-0.073-0.0730.0000.0000.0000.000
134A168SER0-0.075-0.05145.8410.0010.0010.0000.0000.0000.000
135A169ASP-1-0.873-0.90943.8340.1120.1120.0000.0000.0000.000
136A170MET0-0.068-0.01739.1960.0040.0040.0000.0000.0000.000
137A171THR0-0.001-0.01737.675-0.003-0.0030.0000.0000.0000.000
138A172VAL00.010-0.01136.565-0.004-0.0040.0000.0000.0000.000
139A173GLU-1-0.757-0.86133.0010.1820.1820.0000.0000.0000.000
140A174GLU-1-0.840-0.89634.7960.1640.1640.0000.0000.0000.000
141A175ARG10.9060.96636.410-0.108-0.1080.0000.0000.0000.000
142A176ILE00.0060.00033.904-0.008-0.0080.0000.0000.0000.000
143A177GLY00.0580.03932.909-0.006-0.0060.0000.0000.0000.000
144A178ALA00.0400.03333.692-0.006-0.0060.0000.0000.0000.000
145A179ALA0-0.027-0.00636.604-0.009-0.0090.0000.0000.0000.000
146A180ASP-1-0.790-0.90730.8570.1030.1030.0000.0000.0000.000
147A181ARG10.8660.92732.331-0.146-0.1460.0000.0000.0000.000
148A182ARG10.8430.89534.413-0.093-0.0930.0000.0000.0000.000
149A183LYS10.8840.96734.469-0.055-0.0550.0000.0000.0000.000
150A184MET0-0.075-0.05528.499-0.013-0.0130.0000.0000.0000.000
151A185ASP-1-0.902-0.93634.5710.0470.0470.0000.0000.0000.000
152A186GLY00.0760.02637.090-0.007-0.0070.0000.0000.0000.000
153A187ASN0-0.048-0.02533.581-0.010-0.0100.0000.0000.0000.000
154A188SER0-0.0010.00735.478-0.010-0.0100.0000.0000.0000.000
155A189LEU0-0.0320.01436.857-0.008-0.0080.0000.0000.0000.000
156A190PHE00.0340.00139.208-0.003-0.0030.0000.0000.0000.000
157A191LYS10.8340.91534.9650.0020.0020.0000.0000.0000.000
158A192GLU-1-0.916-0.94439.310-0.038-0.0380.0000.0000.0000.000
159A193GLU-1-0.910-0.95041.824-0.006-0.0060.0000.0000.0000.000
160A194LYS10.7840.85543.4330.0170.0170.0000.0000.0000.000
161A195LEU00.0530.04643.9430.0030.0030.0000.0000.0000.000
162A196GLU-1-0.860-0.94845.7070.0220.0220.0000.0000.0000.000
163A197GLU-1-0.819-0.91045.4020.0220.0220.0000.0000.0000.000
164A198ALA00.0420.01941.8550.0040.0040.0000.0000.0000.000
165A199MET0-0.026-0.01743.0990.0040.0040.0000.0000.0000.000
166A200GLN0-0.064-0.02245.2170.0070.0070.0000.0000.0000.000
167A201GLN0-0.039-0.03340.9120.0060.0060.0000.0000.0000.000
168A202TYR0-0.093-0.07837.9740.0030.0030.0000.0000.0000.000
169A203GLU-1-0.874-0.96342.3780.0380.0380.0000.0000.0000.000
170A204MET0-0.0110.00043.3390.0050.0050.0000.0000.0000.000
171A205ALA0-0.0060.01039.2710.0070.0070.0000.0000.0000.000
172A206ILE0-0.026-0.04241.0110.0050.0050.0000.0000.0000.000
173A207ALA0-0.021-0.00943.4800.0030.0030.0000.0000.0000.000
174A208TYR0-0.053-0.01541.1880.0010.0010.0000.0000.0000.000
175A209MET0-0.093-0.03137.3650.0030.0030.0000.0000.0000.000
176A210GLY00.0590.02642.817-0.004-0.0040.0000.0000.0000.000
177A211ASP-1-0.911-0.96346.0840.0630.0630.0000.0000.0000.000
178A212ASP-1-0.809-0.87748.0590.0770.0770.0000.0000.0000.000
179A213PHE0-0.025-0.03239.0720.0040.0040.0000.0000.0000.000
180A214MET0-0.044-0.03940.3030.0050.0050.0000.0000.0000.000
181A215PHE0-0.0220.01343.8510.0020.0020.0000.0000.0000.000
182A216GLN0-0.078-0.02345.033-0.001-0.0010.0000.0000.0000.000
183A217LEU00.0030.00838.8580.0080.0080.0000.0000.0000.000
184A218TYR00.016-0.00537.810-0.007-0.0070.0000.0000.0000.000
185A219GLY00.0480.01536.3350.0090.0090.0000.0000.0000.000
186A220LYS10.8680.91927.190-0.223-0.2230.0000.0000.0000.000
187A221TYR0-0.062-0.04833.3400.0030.0030.0000.0000.0000.000
188A222GLN00.000-0.00535.517-0.007-0.0070.0000.0000.0000.000
189A223ASP-1-0.882-0.94733.2440.1140.1140.0000.0000.0000.000
190A224MET0-0.058-0.00829.063-0.006-0.0060.0000.0000.0000.000
191A225ALA00.0450.02433.446-0.006-0.0060.0000.0000.0000.000
192A226LEU00.0460.03836.773-0.009-0.0090.0000.0000.0000.000
193A227ALA00.0030.00532.281-0.010-0.0100.0000.0000.0000.000
194A228VAL0-0.062-0.03833.708-0.007-0.0070.0000.0000.0000.000
195A229LYS10.9300.94335.728-0.067-0.0670.0000.0000.0000.000
196A230ASN00.012-0.00538.619-0.007-0.0070.0000.0000.0000.000
197A231PRO0-0.023-0.02035.081-0.009-0.0090.0000.0000.0000.000
198A232CYS0-0.0540.00238.151-0.007-0.0070.0000.0000.0000.000
199A233HIS00.0830.05939.7230.0000.0000.0000.0000.0000.000
200A234LEU00.001-0.00739.744-0.006-0.0060.0000.0000.0000.000
201A235ASN0-0.041-0.03238.125-0.004-0.0040.0000.0000.0000.000
202A236ILE00.1090.06641.570-0.002-0.0020.0000.0000.0000.000
203A237ALA0-0.049-0.02344.705-0.003-0.0030.0000.0000.0000.000
204A238ALA00.0110.00543.351-0.003-0.0030.0000.0000.0000.000
205A239CYS0-0.059-0.00444.027-0.003-0.0030.0000.0000.0000.000
206A240LEU00.0050.01145.8750.0000.0000.0000.0000.0000.000
207A241ILE0-0.080-0.04346.895-0.003-0.0030.0000.0000.0000.000
208A242LYS10.8160.88847.8180.0130.0130.0000.0000.0000.000
209A243LEU00.0420.03249.380-0.001-0.0010.0000.0000.0000.000
210A244LYS10.8480.93251.9720.0110.0110.0000.0000.0000.000
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