Manual

About

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: NNN5Q

Calculation Name: 2IQI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IQI

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PCT0

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1732446.645679
FMO2-HF: Nuclear repulsion 1666545.000467
FMO2-HF: Total energy -65901.645212
FMO2-MP2: Total energy -66098.33825


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:32:ALA)


Summations of interaction energy for fragment #1(A:32: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.
-2.6210.3741.957-2.247-2.705-0.013
Interaction energy analysis for fragmet #1(A:32:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.029
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].
3A34ILE0-0.028-0.0133.316-0.9210.7080.057-0.611-1.0750.002
4A35TYR0-0.018-0.0305.5730.4620.4620.0000.0000.0000.000
5A36ALA00.018-0.0158.740-0.001-0.0010.0000.0000.0000.000
6A37PRO0-0.039-0.00711.9170.0500.0500.0000.0000.0000.000
7A38THR0-0.054-0.02415.044-0.011-0.0110.0000.0000.0000.000
8A39VAL00.0080.00518.4110.0260.0260.0000.0000.0000.000
9A40ARG10.9480.96821.1050.2190.2190.0000.0000.0000.000
10A41VAL00.0330.01524.6380.0080.0080.0000.0000.0000.000
11A42THR0-0.030-0.00727.3110.0030.0030.0000.0000.0000.000
12A43PRO00.0120.01430.6710.0040.0040.0000.0000.0000.000
13A44ASN00.0190.02433.6010.0070.0070.0000.0000.0000.000
14A45PRO0-0.015-0.02536.0720.0000.0000.0000.0000.0000.000
15A46ALA0-0.002-0.01039.3250.0020.0020.0000.0000.0000.000
16A47TRP0-0.0290.00331.3300.0010.0010.0000.0000.0000.000
17A48PRO00.0280.01538.9690.0000.0000.0000.0000.0000.000
18A49GLN0-0.026-0.01839.688-0.001-0.0010.0000.0000.0000.000
19A50VAL0-0.033-0.01338.9210.0040.0040.0000.0000.0000.000
20A51SER0-0.009-0.02041.704-0.001-0.0010.0000.0000.0000.000
21A52TRP0-0.0240.01236.433-0.001-0.0010.0000.0000.0000.000
22A53GLN0-0.029-0.03237.932-0.005-0.0050.0000.0000.0000.000
23A54LEU0-0.034-0.01432.1160.0030.0030.0000.0000.0000.000
24A55LEU00.0040.01330.899-0.005-0.0050.0000.0000.0000.000
25A56VAL0-0.018-0.01326.5360.0060.0060.0000.0000.0000.000
26A57ALA0-0.045-0.03628.077-0.005-0.0050.0000.0000.0000.000
27A58LYS10.9900.99221.9840.1820.1820.0000.0000.0000.000
28A59PRO0-0.031-0.00321.6030.0150.0150.0000.0000.0000.000
29A60SER0-0.040-0.02322.664-0.006-0.0060.0000.0000.0000.000
30A61ALA00.0470.00719.7450.0010.0010.0000.0000.0000.000
31A62ALA00.0280.02420.3460.0000.0000.0000.0000.0000.000
32A63ARG11.0130.97617.4140.0980.0980.0000.0000.0000.000
33A64ILE0-0.0050.00414.941-0.019-0.0190.0000.0000.0000.000
34A65ILE0-0.0290.00014.311-0.012-0.0120.0000.0000.0000.000
35A66ASP-1-0.877-0.89314.762-0.257-0.2570.0000.0000.0000.000
36A67SER0-0.0060.02411.168-0.017-0.0170.0000.0000.0000.000
37A68PRO00.0560.0207.5810.0180.0180.0000.0000.0000.000
38A69ARG10.9160.9587.158-0.041-0.0410.0000.0000.0000.000
39A70ILE00.0190.0257.5020.0200.0200.0000.0000.0000.000
40A71ASN00.003-0.0139.8570.0910.0910.0000.0000.0000.000
41A72VAL00.0030.01112.765-0.020-0.0200.0000.0000.0000.000
42A73ARG10.8190.88714.9580.0220.0220.0000.0000.0000.000
43A74PRO0-0.022-0.00316.955-0.007-0.0070.0000.0000.0000.000
44A75THR00.0280.00119.464-0.004-0.0040.0000.0000.0000.000
45A76PRO00.0350.00522.526-0.005-0.0050.0000.0000.0000.000
46A77GLY0-0.019-0.00924.420-0.010-0.0100.0000.0000.0000.000
47A78GLU-1-0.934-0.96120.1550.1080.1080.0000.0000.0000.000
48A79LEU0-0.013-0.00916.737-0.007-0.0070.0000.0000.0000.000
49A80GLN0-0.025-0.00613.8850.0420.0420.0000.0000.0000.000
50A81VAL0-0.033-0.0239.216-0.055-0.0550.0000.0000.0000.000
51A82TYR00.0420.0268.1970.0720.0720.0000.0000.0000.000
52A83HIS00.010-0.0026.7820.0430.0430.0000.0000.0000.000
53A84GLY00.003-0.0012.507-0.0520.1640.703-0.436-0.4830.000
54A85ALA0-0.026-0.0102.705-2.057-1.1131.196-1.156-0.985-0.015
55A86GLY0-0.0080.0004.1370.1690.4120.002-0.042-0.2030.000
56A87TRP0-0.017-0.0114.987-0.213-0.250-0.001-0.0020.0410.000
57A88ALA0-0.011-0.0178.021-0.059-0.0590.0000.0000.0000.000
58A89GLN0-0.070-0.0339.5200.0320.0320.0000.0000.0000.000
59A90PRO00.024-0.00311.437-0.036-0.0360.0000.0000.0000.000
60A91ALA00.0390.02112.9370.0110.0110.0000.0000.0000.000
61A92THR0-0.046-0.07314.7770.0110.0110.0000.0000.0000.000
62A93ASP-1-0.798-0.90015.883-0.292-0.2920.0000.0000.0000.000
63A94MET0-0.046-0.00213.365-0.003-0.0030.0000.0000.0000.000
64A95LEU0-0.033-0.01216.8050.0250.0250.0000.0000.0000.000
65A96GLU-1-0.909-0.97919.943-0.188-0.1880.0000.0000.0000.000
66A97ASP-1-0.853-0.92919.086-0.288-0.2880.0000.0000.0000.000
67A98SER0-0.029-0.01619.7760.0110.0110.0000.0000.0000.000
68A99VAL00.0030.00022.1670.0170.0170.0000.0000.0000.000
69A100VAL0-0.013-0.00124.9280.0120.0120.0000.0000.0000.000
70A101ARG10.9350.97919.2750.2870.2870.0000.0000.0000.000
71A102ALA00.0230.01425.8820.0100.0100.0000.0000.0000.000
72A103PHE0-0.060-0.03627.6220.0130.0130.0000.0000.0000.000
73A104GLU-1-0.933-0.95427.686-0.158-0.1580.0000.0000.0000.000
74A105ASP-1-0.934-0.96727.322-0.155-0.1550.0000.0000.0000.000
75A106SER0-0.083-0.04630.7010.0100.0100.0000.0000.0000.000
76A107GLY00.0160.00333.2000.0070.0070.0000.0000.0000.000
77A108LYS10.8240.91435.7180.0800.0800.0000.0000.0000.000
78A109ILE00.0440.01834.1920.0050.0050.0000.0000.0000.000
79A110ALA00.0120.02035.582-0.005-0.0050.0000.0000.0000.000
80A111ALA0-0.008-0.00735.910-0.003-0.0030.0000.0000.0000.000
81A112VAL00.0500.02630.4220.0030.0030.0000.0000.0000.000
82A113ALA00.0060.01230.591-0.004-0.0040.0000.0000.0000.000
83A114ARG10.9580.98322.5330.2090.2090.0000.0000.0000.000
84A115ILE00.0250.00627.3120.0090.0090.0000.0000.0000.000
85A116GLY0-0.010-0.01927.4750.0060.0060.0000.0000.0000.000
86A117ALA0-0.042-0.01828.487-0.006-0.0060.0000.0000.0000.000
87A118GLY00.0110.02330.8690.0040.0040.0000.0000.0000.000
88A119ILE0-0.023-0.01733.7000.0010.0010.0000.0000.0000.000
89A120ARG10.8510.91437.5320.0740.0740.0000.0000.0000.000
90A121SER00.020-0.01136.671-0.005-0.0050.0000.0000.0000.000
91A122ASP-1-0.801-0.86038.688-0.065-0.0650.0000.0000.0000.000
92A123TYR0-0.055-0.04537.0850.0020.0020.0000.0000.0000.000
93A124LYS10.9850.99631.8150.0850.0850.0000.0000.0000.000
94A125LEU0-0.0030.00129.0850.0050.0050.0000.0000.0000.000
95A126ALA0-0.026-0.02329.159-0.008-0.0080.0000.0000.0000.000
96A127ILE00.0170.00724.5880.0070.0070.0000.0000.0000.000
97A128ASP-1-0.857-0.90125.403-0.095-0.0950.0000.0000.0000.000
98A129VAL00.007-0.01519.5930.0040.0040.0000.0000.0000.000
99A130ARG10.8450.91422.5880.0640.0640.0000.0000.0000.000
100A131ARG10.8680.93920.4410.0520.0520.0000.0000.0000.000
101A132PHE00.0570.02314.116-0.004-0.0040.0000.0000.0000.000
102A133GLU-1-0.842-0.89715.475-0.046-0.0460.0000.0000.0000.000
103A134SER00.000-0.01114.464-0.008-0.0080.0000.0000.0000.000
104A135ASP-1-0.837-0.94516.3750.0200.0200.0000.0000.0000.000
105A136TYR00.0250.01715.8500.0000.0000.0000.0000.0000.000
106A137ALA0-0.0070.01021.3970.0020.0020.0000.0000.0000.000
107A138GLY0-0.045-0.02324.780-0.001-0.0010.0000.0000.0000.000
108A139GLN00.0090.02024.4350.0050.0050.0000.0000.0000.000
109A140SER00.001-0.01423.5990.0120.0120.0000.0000.0000.000
110A141LEU0-0.053-0.02520.0110.0160.0160.0000.0000.0000.000
111A142PRO00.0030.02516.912-0.007-0.0070.0000.0000.0000.000
112A143ALA00.005-0.02120.070-0.011-0.0110.0000.0000.0000.000
113A144ALA0-0.0140.02117.1280.0010.0010.0000.0000.0000.000
114A145THR0-0.025-0.02218.5150.0040.0040.0000.0000.0000.000
115A146ILE0-0.013-0.00418.742-0.011-0.0110.0000.0000.0000.000
116A147GLU-1-0.840-0.92021.318-0.042-0.0420.0000.0000.0000.000
117A148LEU00.0180.02122.985-0.006-0.0060.0000.0000.0000.000
118A149ASN0-0.078-0.04825.5820.0080.0080.0000.0000.0000.000
119A150ALA00.0410.04128.646-0.006-0.0060.0000.0000.0000.000
120A151LYS10.9330.96330.4340.0740.0740.0000.0000.0000.000
121A152LEU00.0210.02332.888-0.007-0.0070.0000.0000.0000.000
122A153LEU0-0.030-0.01434.9080.0050.0050.0000.0000.0000.000
123A154HIS00.0350.02237.661-0.002-0.0020.0000.0000.0000.000
124A155SER0-0.044-0.06538.4930.0000.0000.0000.0000.0000.000
125A156SER0-0.0050.00539.9790.0000.0000.0000.0000.0000.000
126A157ASP-1-0.833-0.91843.693-0.049-0.0490.0000.0000.0000.000
127A158GLN0-0.086-0.03639.393-0.002-0.0020.0000.0000.0000.000
128A159ARG10.8450.92541.1320.0520.0520.0000.0000.0000.000
129A160VAL0-0.036-0.05137.814-0.003-0.0030.0000.0000.0000.000
130A161VAL0-0.0180.01939.2300.0030.0030.0000.0000.0000.000
131A162ALA00.0210.00238.2330.0030.0030.0000.0000.0000.000
132A163SER0-0.017-0.02634.684-0.006-0.0060.0000.0000.0000.000
133A164ARG10.9360.98132.7730.0640.0640.0000.0000.0000.000
134A165THR0-0.032-0.01029.268-0.006-0.0060.0000.0000.0000.000
135A166PHE00.0060.01627.6420.0040.0040.0000.0000.0000.000
136A167THR0-0.002-0.01225.848-0.003-0.0030.0000.0000.0000.000
137A168VAL0-0.0030.00623.6250.0040.0040.0000.0000.0000.000
138A169ALA00.0240.00922.873-0.005-0.0050.0000.0000.0000.000
139A170ARG10.8760.94221.5520.0940.0940.0000.0000.0000.000
140A171PRO0-0.0030.00921.158-0.004-0.0040.0000.0000.0000.000
141A172SER00.0330.01117.391-0.021-0.0210.0000.0000.0000.000
142A173SER00.001-0.01319.4110.0120.0120.0000.0000.0000.000
143A174SER0-0.022-0.01216.4570.0090.0090.0000.0000.0000.000
144A175THR00.0460.01215.822-0.022-0.0220.0000.0000.0000.000
145A176ASP-1-0.895-0.92911.8800.2040.2040.0000.0000.0000.000
146A177THR00.0090.0017.483-0.143-0.1430.0000.0000.0000.000
147A178ALA00.0440.02110.481-0.097-0.0970.0000.0000.0000.000
148A179ALA00.0060.01711.808-0.036-0.0360.0000.0000.0000.000
149A180VAL00.0250.00712.624-0.024-0.0240.0000.0000.0000.000
150A181ALA0-0.006-0.01211.021-0.020-0.0200.0000.0000.0000.000
151A182ALA00.0190.01313.096-0.009-0.0090.0000.0000.0000.000
152A183ALA0-0.013-0.00416.3770.0080.0080.0000.0000.0000.000
153A184PHE00.025-0.00613.6090.0040.0040.0000.0000.0000.000
154A185GLU-1-0.830-0.88816.681-0.275-0.2750.0000.0000.0000.000
155A186GLN0-0.0180.00018.0250.0320.0320.0000.0000.0000.000
156A187ALA0-0.001-0.00619.6210.0110.0110.0000.0000.0000.000
157A188LEU00.0030.00216.4110.0100.0100.0000.0000.0000.000
158A189THR0-0.007-0.00120.5540.0080.0080.0000.0000.0000.000
159A190GLN0-0.017-0.01223.2010.0080.0080.0000.0000.0000.000
160A191VAL00.0260.00922.8070.0080.0080.0000.0000.0000.000
161A192THR00.011-0.00122.9290.0040.0040.0000.0000.0000.000
162A193THR0-0.037-0.02825.6320.0070.0070.0000.0000.0000.000
163A194GLU-1-0.932-0.97828.436-0.071-0.0710.0000.0000.0000.000
164A195LEU0-0.0010.00225.7380.0060.0060.0000.0000.0000.000
165A196VAL00.0590.04228.5530.0070.0070.0000.0000.0000.000
166A197GLY00.0060.00531.0830.0050.0050.0000.0000.0000.000
167A198TRP0-0.009-0.01332.9920.0050.0050.0000.0000.0000.000
168A199THR0-0.008-0.01032.1040.0040.0040.0000.0000.0000.000
169A200LEU0-0.015-0.00334.6790.0040.0040.0000.0000.0000.000
170A201ILE0-0.006-0.00737.0210.0040.0040.0000.0000.0000.000
171A202THR0-0.035-0.03637.2500.0050.0050.0000.0000.0000.000
172A203GLY00.0290.00838.4260.0030.0030.0000.0000.0000.000
173A204GLN00.0070.00439.7880.0010.0010.0000.0000.0000.000
174A205GLN0-0.031-0.02242.5470.0020.0020.0000.0000.0000.000
175A206ASP-1-0.786-0.83842.660-0.051-0.0510.0000.0000.0000.000
176A207SER0-0.003-0.00843.8900.0020.0020.0000.0000.0000.000
177A208GLN0-0.094-0.04445.4190.0010.0010.0000.0000.0000.000
178A209THR0-0.0400.00447.8700.0030.0030.0000.0000.0000.000