Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 824ZY

Calculation Name: 2I1S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I1S

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PRU3

Base Structure: X-ray

Registration Date: 2023-06-19

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 -1969365.381039
FMO2-HF: Nuclear repulsion 1896500.501117
FMO2-HF: Total energy -72864.879921
FMO2-MP2: Total energy -73079.01369


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:4:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-10.227-6.7150.183-1.672-2.0240.01
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.021
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].
3A6GLU-1-0.888-0.9413.8320.4912.141-0.010-0.743-0.8980.001
4A7LYS10.8700.9276.126-0.402-0.4020.0000.0000.0000.000
5A8VAL00.0010.0049.1890.3870.3870.0000.0000.0000.000
6A9TYR00.0230.00111.608-0.259-0.2590.0000.0000.0000.000
7A10HIS0-0.007-0.01414.366-0.028-0.0280.0000.0000.0000.000
8A11LEU00.0380.02215.853-0.076-0.0760.0000.0000.0000.000
9A12LYS10.8660.93019.210-0.240-0.2400.0000.0000.0000.000
10A13LEU00.0480.02119.764-0.011-0.0110.0000.0000.0000.000
11A14SER0-0.083-0.05223.743-0.009-0.0090.0000.0000.0000.000
12A15ILE00.1300.08327.500-0.002-0.0020.0000.0000.0000.000
13A16LYS10.8370.90229.742-0.130-0.1300.0000.0000.0000.000
14A17GLY00.010-0.00132.312-0.003-0.0030.0000.0000.0000.000
15A18ILE00.0950.08234.329-0.005-0.0050.0000.0000.0000.000
16A19THR0-0.153-0.07635.4340.0080.0080.0000.0000.0000.000
17A20PRO00.1160.03236.752-0.004-0.0040.0000.0000.0000.000
18A21GLN0-0.0120.01730.8880.0120.0120.0000.0000.0000.000
19A22ILE00.1090.08729.1850.0070.0070.0000.0000.0000.000
20A23TRP0-0.081-0.05025.4210.0150.0150.0000.0000.0000.000
21A24ARG10.8900.94222.822-0.257-0.2570.0000.0000.0000.000
22A25ARG10.7620.87821.628-0.334-0.3340.0000.0000.0000.000
23A26ILE00.0780.04516.1760.0120.0120.0000.0000.0000.000
24A27GLN0-0.065-0.04014.1780.0830.0830.0000.0000.0000.000
25A28VAL00.0570.02211.6160.0720.0720.0000.0000.0000.000
26A29PRO00.0450.0196.162-0.076-0.0760.0000.0000.0000.000
27A30GLU-1-0.814-0.9167.7170.4040.4040.0000.0000.0000.000
28A31ASN0-0.049-0.0293.246-1.300-0.5710.038-0.337-0.4300.003
29A32TYR00.0480.0237.484-0.308-0.3080.0000.0000.0000.000
30A33THR0-0.048-0.0099.550-0.163-0.1630.0000.0000.0000.000
31A34PHE00.036-0.00112.2070.0870.0870.0000.0000.0000.000
32A35LEU0-0.0200.01014.2900.0080.0080.0000.0000.0000.000
33A36ASP-1-0.847-0.9379.7060.4500.4500.0000.0000.0000.000
34A37LEU0-0.025-0.01512.9570.0560.0560.0000.0000.0000.000
35A38HIS0-0.0510.00615.3820.0110.0110.0000.0000.0000.000
36A39LYS10.9840.98014.253-0.164-0.1640.0000.0000.0000.000
37A40ALA0-0.0110.01114.8040.0110.0110.0000.0000.0000.000
38A41ILE0-0.037-0.03416.815-0.007-0.0070.0000.0000.0000.000
39A42GLN00.0300.00520.125-0.019-0.0190.0000.0000.0000.000
40A43ALA00.0280.03618.604-0.013-0.0130.0000.0000.0000.000
41A44VAL0-0.065-0.05219.563-0.005-0.0050.0000.0000.0000.000
42A45MET0-0.111-0.05922.080-0.011-0.0110.0000.0000.0000.000
43A46ASP-1-0.913-0.93824.1260.1750.1750.0000.0000.0000.000
44A47TRP0-0.086-0.04024.695-0.008-0.0080.0000.0000.0000.000
45A48GLU-1-0.894-0.97624.7890.1440.1440.0000.0000.0000.000
46A49ASP-1-0.949-0.96221.8810.1210.1210.0000.0000.0000.000
47A50TYR00.0200.02624.935-0.016-0.0160.0000.0000.0000.000
48A51HIS10.7770.90627.691-0.103-0.1030.0000.0000.0000.000
49A52LEU0-0.020-0.00526.7770.0030.0030.0000.0000.0000.000
50A53HIS10.8560.91120.517-0.122-0.1220.0000.0000.0000.000
51A54GLU-1-0.938-0.97123.9350.0590.0590.0000.0000.0000.000
52A55PHE0-0.026-0.01918.8930.0220.0220.0000.0000.0000.000
53A56GLU-1-0.910-0.94523.6780.0710.0710.0000.0000.0000.000
54A57MET0-0.038-0.01820.4070.0260.0260.0000.0000.0000.000
55A58VAL00.0300.02924.618-0.017-0.0170.0000.0000.0000.000
56A59ASN00.0210.01022.6030.0220.0220.0000.0000.0000.000
57A60PRO0-0.0070.01420.881-0.014-0.0140.0000.0000.0000.000
58A61LYS10.8920.94117.900-0.001-0.0010.0000.0000.0000.000
59A62THR0-0.015-0.01624.145-0.007-0.0070.0000.0000.0000.000
60A63GLY0-0.0100.00226.866-0.003-0.0030.0000.0000.0000.000
61A64MET0-0.033-0.01128.3470.0020.0020.0000.0000.0000.000
62A65LEU0-0.029-0.01027.4590.0070.0070.0000.0000.0000.000
63A66ASP-1-0.786-0.87223.9100.0290.0290.0000.0000.0000.000
64A67LYS10.9310.97025.581-0.042-0.0420.0000.0000.0000.000
65A68ILE0-0.045-0.02119.260-0.014-0.0140.0000.0000.0000.000
66A69GLY00.0880.03022.0200.0210.0210.0000.0000.0000.000
67A70ALA00.0130.00721.430-0.015-0.0150.0000.0000.0000.000
68A71GLU-1-0.906-0.96219.196-0.103-0.1030.0000.0000.0000.000
69A72GLY00.0450.05122.916-0.001-0.0010.0000.0000.0000.000
70A73ASP-1-1.029-1.01325.930-0.047-0.0470.0000.0000.0000.000
71A81PRO00.0190.00428.515-0.002-0.0020.0000.0000.0000.000
72A82LEU0-0.037-0.01224.6500.0090.0090.0000.0000.0000.000
73A83VAL0-0.0100.00220.342-0.019-0.0190.0000.0000.0000.000
74A84SER0-0.038-0.03919.1650.0210.0210.0000.0000.0000.000
75A85GLU-1-0.753-0.88717.8010.1140.1140.0000.0000.0000.000
76A86LYS10.9320.97014.8230.0960.0960.0000.0000.0000.000
77A87LYS10.9010.94813.7270.1000.1000.0000.0000.0000.000
78A88ALA00.0040.01014.484-0.013-0.0130.0000.0000.0000.000
79A89LYS10.9550.9828.4990.1450.1450.0000.0000.0000.000
80A90LEU00.0410.00912.558-0.033-0.0330.0000.0000.0000.000
81A91SER00.0000.00011.560-0.043-0.0430.0000.0000.0000.000
82A92ASP-1-0.978-0.97213.635-0.073-0.0730.0000.0000.0000.000
83A93TYR0-0.097-0.09716.266-0.033-0.0330.0000.0000.0000.000
84A94PHE0-0.009-0.00216.641-0.007-0.0070.0000.0000.0000.000
85A95THR0-0.001-0.00317.4530.0150.0150.0000.0000.0000.000
86A96LEU0-0.011-0.03219.6650.0160.0160.0000.0000.0000.000
87A97GLU-1-0.941-0.96122.0770.1290.1290.0000.0000.0000.000
88A98ASN0-0.060-0.03422.090-0.025-0.0250.0000.0000.0000.000
89A99LYS10.9370.97021.759-0.228-0.2280.0000.0000.0000.000
90A100GLU-1-0.895-0.94522.1950.2220.2220.0000.0000.0000.000
91A101ALA00.0240.02221.684-0.014-0.0140.0000.0000.0000.000
92A102LEU0-0.045-0.02523.7600.0110.0110.0000.0000.0000.000
93A103TYR0-0.006-0.03221.659-0.006-0.0060.0000.0000.0000.000
94A104THR00.0420.01924.9330.0030.0030.0000.0000.0000.000
95A105TYR0-0.054-0.08325.624-0.003-0.0030.0000.0000.0000.000
96A106ASP-1-0.761-0.89227.5360.0870.0870.0000.0000.0000.000
97A107PHE0-0.099-0.06228.160-0.001-0.0010.0000.0000.0000.000
98A108GLY0-0.046-0.01032.938-0.006-0.0060.0000.0000.0000.000
99A109ASP-1-0.799-0.89733.8890.0870.0870.0000.0000.0000.000
100A110ASN0-0.125-0.06732.6870.0050.0050.0000.0000.0000.000
101A111TRP00.0610.05929.4680.0090.0090.0000.0000.0000.000
102A112GLN0-0.022-0.02728.7990.0040.0040.0000.0000.0000.000
103A113VAL00.0180.00623.9550.0050.0050.0000.0000.0000.000
104A114LYS10.8770.94125.802-0.159-0.1590.0000.0000.0000.000
105A115VAL00.0420.02519.5830.0240.0240.0000.0000.0000.000
106A116ARG10.8700.92922.712-0.237-0.2370.0000.0000.0000.000
107A117LEU0-0.019-0.00216.9130.0390.0390.0000.0000.0000.000
108A118GLU-1-0.931-0.97520.4350.2920.2920.0000.0000.0000.000
109A119LYS10.8840.94318.856-0.473-0.4730.0000.0000.0000.000
110A120ILE00.0490.04813.7170.0680.0680.0000.0000.0000.000
111A121LEU0-0.060-0.03914.166-0.097-0.0970.0000.0000.0000.000
112A122PRO0-0.020-0.00510.6110.1470.1470.0000.0000.0000.000
113A123ARG10.9250.9863.231-11.303-10.1700.155-0.592-0.6960.006
114A124LYS10.9340.9589.975-0.873-0.8730.0000.0000.0000.000
115A125GLU-1-0.919-0.97410.4601.1771.1770.0000.0000.0000.000
116A126GLY00.0110.00810.707-0.168-0.1680.0000.0000.0000.000
117A127VAL0-0.081-0.03012.020-0.146-0.1460.0000.0000.0000.000
118A128GLU-1-0.922-0.95310.3831.3501.3500.0000.0000.0000.000
119A129TYR0-0.075-0.0229.022-0.180-0.1800.0000.0000.0000.000
120A130PRO00.0310.0029.7110.1660.1660.0000.0000.0000.000
121A131ILE0-0.0240.00612.524-0.080-0.0800.0000.0000.0000.000
122A132CYS00.0290.02115.809-0.028-0.0280.0000.0000.0000.000
123A133THR0-0.069-0.03818.802-0.019-0.0190.0000.0000.0000.000
124A134ALA00.003-0.00721.295-0.036-0.0360.0000.0000.0000.000
125A135GLY00.027-0.00424.1490.0220.0220.0000.0000.0000.000
126A136LYS10.8720.94026.766-0.202-0.2020.0000.0000.0000.000
127A137ARG10.8690.91030.332-0.138-0.1380.0000.0000.0000.000
128A138ALA00.0990.06430.4960.0200.0200.0000.0000.0000.000
129A139ALA0-0.054-0.03727.9730.0000.0000.0000.0000.0000.000
130A140VAL0-0.047-0.00430.067-0.006-0.0060.0000.0000.0000.000
131A141PRO00.0940.04431.0020.0070.0070.0000.0000.0000.000
132A142GLU-1-0.716-0.82628.1360.1270.1270.0000.0000.0000.000
133A143ASP-1-0.862-0.92632.2560.0840.0840.0000.0000.0000.000
134A144SER0-0.056-0.02934.964-0.006-0.0060.0000.0000.0000.000
135A145GLY00.0770.03137.184-0.002-0.0020.0000.0000.0000.000
136A146GLY00.0060.00635.629-0.003-0.0030.0000.0000.0000.000
137A147VAL0-0.090-0.06834.9130.0020.0020.0000.0000.0000.000
138A148TRP0-0.055-0.03037.3110.0000.0000.0000.0000.0000.000
139A149GLY00.0830.05840.229-0.001-0.0010.0000.0000.0000.000
140A150TYR00.0460.01735.6890.0010.0010.0000.0000.0000.000
141A151GLU-1-0.888-0.98338.9830.1100.1100.0000.0000.0000.000
142A152GLU-1-0.979-0.97741.1360.0680.0680.0000.0000.0000.000
143A153MET00.0250.02338.788-0.002-0.0020.0000.0000.0000.000
144A154LEU0-0.020-0.01738.2300.0010.0010.0000.0000.0000.000
145A155GLU-1-0.929-0.95842.6500.0830.0830.0000.0000.0000.000
146A156VAL00.0250.03346.088-0.002-0.0020.0000.0000.0000.000
147A157LEU00.001-0.00741.813-0.001-0.0010.0000.0000.0000.000
148A158LYS10.7020.85244.323-0.091-0.0910.0000.0000.0000.000
149A159ASP-1-0.877-0.94548.0550.0600.0600.0000.0000.0000.000
150A160SER0-0.011-0.02250.9010.0000.0000.0000.0000.0000.000
151A161GLU-1-1.041-1.01351.8850.0510.0510.0000.0000.0000.000
152A162HIS0-0.0170.00751.317-0.002-0.0020.0000.0000.0000.000
153A163GLU-1-0.972-0.99953.4300.0530.0530.0000.0000.0000.000
154A164GLU-1-0.913-0.95648.9200.0580.0580.0000.0000.0000.000
155A165TYR0-0.0370.01647.6120.0030.0030.0000.0000.0000.000
156A166GLU-1-0.910-0.96547.9560.0590.0590.0000.0000.0000.000
157A167ASP-1-0.938-0.96947.9170.0570.0570.0000.0000.0000.000
158A168THR0-0.073-0.06243.7210.0030.0030.0000.0000.0000.000
159A169VAL0-0.010-0.00743.3200.0040.0040.0000.0000.0000.000
160A170LEU0-0.053-0.01543.0970.0030.0030.0000.0000.0000.000
161A171TRP0-0.072-0.02137.0220.0040.0040.0000.0000.0000.000
162A172LEU0-0.059-0.04337.7720.0040.0040.0000.0000.0000.000
163A173GLY00.0140.02138.3330.0060.0060.0000.0000.0000.000
164A174ASP-1-0.933-0.98240.4630.0810.0810.0000.0000.0000.000
165A175ASP-1-1.014-1.00236.9500.1120.1120.0000.0000.0000.000
166A176PHE0-0.026-0.00434.5120.0100.0100.0000.0000.0000.000
167A177ASP-1-0.829-0.92536.6570.1320.1320.0000.0000.0000.000
168A178PRO00.0160.00535.8040.0110.0110.0000.0000.0000.000
169A179GLU-1-0.860-0.91735.2910.1530.1530.0000.0000.0000.000
170A180TYR0-0.101-0.05330.0580.0080.0080.0000.0000.0000.000
171A181PHE0-0.014-0.02024.1400.0160.0160.0000.0000.0000.000
172A182ASP-1-0.826-0.90627.3640.2700.2700.0000.0000.0000.000
173A183PRO0-0.062-0.04523.1710.0110.0110.0000.0000.0000.000
174A184LYS10.8050.89222.539-0.258-0.2580.0000.0000.0000.000
175A185ASP-1-0.769-0.85823.8110.2380.2380.0000.0000.0000.000
176A186VAL0-0.067-0.02319.391-0.003-0.0030.0000.0000.0000.000
177A187SER00.0160.00919.1160.0510.0510.0000.0000.0000.000
178A188PHE0-0.037-0.01614.393-0.006-0.0060.0000.0000.0000.000