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: J37Z9

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1972680.563467
FMO2-HF: Nuclear repulsion 1899812.128795
FMO2-HF: Total energy -72868.434672
FMO2-MP2: Total energy -73082.379014


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.
-7.392-6.4884.456-2.348-3.0090.016
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 : -0.010 / q_NPA : -0.017
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-1-0.866-0.9263.8677.1988.667-0.012-0.684-0.7720.002
4A7LYS10.8520.9256.984-0.955-0.9550.0000.0000.0000.000
5A8VAL00.0200.0168.7310.0770.0770.0000.0000.0000.000
6A9TYR0-0.006-0.01211.098-0.138-0.1380.0000.0000.0000.000
7A10HIS00.0060.00814.326-0.082-0.0820.0000.0000.0000.000
8A11LEU00.0330.01416.329-0.051-0.0510.0000.0000.0000.000
9A12LYS10.8770.94719.328-0.115-0.1150.0000.0000.0000.000
10A13LEU00.0240.01819.921-0.019-0.0190.0000.0000.0000.000
11A14SER0-0.043-0.03924.0380.0140.0140.0000.0000.0000.000
12A15ILE00.0700.05127.816-0.010-0.0100.0000.0000.0000.000
13A16LYS10.7980.88530.0670.0040.0040.0000.0000.0000.000
14A17GLY0-0.002-0.00932.676-0.002-0.0020.0000.0000.0000.000
15A18ILE00.0520.05333.955-0.002-0.0020.0000.0000.0000.000
16A19THR0-0.139-0.06336.0200.0060.0060.0000.0000.0000.000
17A20PRO00.0780.02536.850-0.002-0.0020.0000.0000.0000.000
18A21GLN00.0150.02030.8180.0120.0120.0000.0000.0000.000
19A22ILE00.1040.08229.4740.0110.0110.0000.0000.0000.000
20A23TRP0-0.112-0.05825.5250.0090.0090.0000.0000.0000.000
21A24ARG10.8540.92723.154-0.111-0.1110.0000.0000.0000.000
22A25ARG10.7980.88320.950-0.248-0.2480.0000.0000.0000.000
23A26ILE00.0840.04816.5230.0200.0200.0000.0000.0000.000
24A27GLN0-0.043-0.02513.4660.1050.1050.0000.0000.0000.000
25A28VAL00.0690.03011.7430.0510.0510.0000.0000.0000.000
26A29PRO00.0460.0236.5450.0330.0330.0000.0000.0000.000
27A30GLU-1-0.821-0.9167.5210.4380.4380.0000.0000.0000.000
28A31ASN0-0.033-0.0253.446-0.4090.2050.016-0.267-0.3620.001
29A32TYR00.0470.0237.546-0.263-0.2630.0000.0000.0000.000
30A33THR0-0.070-0.0519.544-0.001-0.0010.0000.0000.0000.000
31A34PHE00.0430.00912.2240.1090.1090.0000.0000.0000.000
32A35LEU00.0190.01814.4950.0480.0480.0000.0000.0000.000
33A36ASP-1-0.813-0.87210.625-0.567-0.5670.0000.0000.0000.000
34A37LEU0-0.008-0.00513.2840.0950.0950.0000.0000.0000.000
35A38HIS0-0.0410.00015.5440.0540.0540.0000.0000.0000.000
36A39LYS10.8910.93712.5660.4150.4150.0000.0000.0000.000
37A40ALA0-0.022-0.01315.0300.0390.0390.0000.0000.0000.000
38A41ILE0-0.037-0.02616.9820.0310.0310.0000.0000.0000.000
39A42GLN00.0350.00520.3270.0130.0130.0000.0000.0000.000
40A43ALA00.0410.03418.8190.0080.0080.0000.0000.0000.000
41A44VAL0-0.066-0.05419.9550.0190.0190.0000.0000.0000.000
42A45MET0-0.112-0.05022.4610.0130.0130.0000.0000.0000.000
43A46ASP-1-0.911-0.93124.5430.0500.0500.0000.0000.0000.000
44A47TRP0-0.063-0.03624.780-0.011-0.0110.0000.0000.0000.000
45A48GLU-1-0.838-0.90624.423-0.022-0.0220.0000.0000.0000.000
46A49ASP-1-0.849-0.93521.967-0.149-0.1490.0000.0000.0000.000
47A50TYR0-0.094-0.05624.942-0.018-0.0180.0000.0000.0000.000
48A51HIS10.7680.90027.5350.0430.0430.0000.0000.0000.000
49A52LEU0-0.019-0.00526.744-0.010-0.0100.0000.0000.0000.000
50A53HIS10.8380.89620.7350.1720.1720.0000.0000.0000.000
51A54GLU-1-0.910-0.92923.783-0.124-0.1240.0000.0000.0000.000
52A55PHE0-0.016-0.01418.8430.0230.0230.0000.0000.0000.000
53A56GLU-1-0.853-0.91223.890-0.084-0.0840.0000.0000.0000.000
54A57MET0-0.071-0.02420.1210.0120.0120.0000.0000.0000.000
55A58VAL00.0230.02424.684-0.014-0.0140.0000.0000.0000.000
56A59ASN00.0210.00622.3130.0040.0040.0000.0000.0000.000
57A60PRO0-0.013-0.00120.1690.0090.0090.0000.0000.0000.000
58A61LYS10.7810.86717.0980.2860.2860.0000.0000.0000.000
59A62THR0-0.036-0.02323.6040.0030.0030.0000.0000.0000.000
60A63GLY0-0.0020.01026.5520.0090.0090.0000.0000.0000.000
61A64MET0-0.024-0.00527.8210.0130.0130.0000.0000.0000.000
62A65LEU00.0000.00027.1080.0000.0000.0000.0000.0000.000
63A66ASP-1-0.788-0.86423.128-0.187-0.1870.0000.0000.0000.000
64A67LYS10.8160.88325.2140.1060.1060.0000.0000.0000.000
65A68ILE0-0.048-0.02419.332-0.026-0.0260.0000.0000.0000.000
66A69GLY00.0840.02621.9870.0260.0260.0000.0000.0000.000
67A70ALA00.0270.02521.273-0.037-0.0370.0000.0000.0000.000
68A71GLU-1-0.832-0.87619.108-0.463-0.4630.0000.0000.0000.000
69A72GLY00.0490.02722.6590.0090.0090.0000.0000.0000.000
70A73ASP-1-0.998-0.98425.950-0.206-0.2060.0000.0000.0000.000
71A81PRO00.0190.00228.0710.0020.0020.0000.0000.0000.000
72A82LEU0-0.027-0.01124.6340.0120.0120.0000.0000.0000.000
73A83VAL0-0.022-0.00219.842-0.025-0.0250.0000.0000.0000.000
74A84SER0-0.024-0.04818.523-0.005-0.0050.0000.0000.0000.000
75A85GLU-1-0.793-0.89617.837-0.279-0.2790.0000.0000.0000.000
76A86LYS10.8850.93214.5160.4090.4090.0000.0000.0000.000
77A87LYS10.8660.90713.5220.3610.3610.0000.0000.0000.000
78A88ALA00.0420.03914.132-0.079-0.0790.0000.0000.0000.000
79A89LYS10.8520.9229.3020.8470.8470.0000.0000.0000.000
80A90LEU00.0450.02112.4000.0830.0830.0000.0000.0000.000
81A91SER00.0390.01511.1080.0120.0120.0000.0000.0000.000
82A92ASP-1-0.923-0.92813.061-0.477-0.4770.0000.0000.0000.000
83A93TYR0-0.061-0.07415.5680.0070.0070.0000.0000.0000.000
84A94PHE00.0010.00916.4910.0400.0400.0000.0000.0000.000
85A95THR0-0.020-0.03217.1010.0130.0130.0000.0000.0000.000
86A96LEU0-0.033-0.03319.3940.0160.0160.0000.0000.0000.000
87A97GLU-1-0.867-0.92121.8460.0650.0650.0000.0000.0000.000
88A98ASN0-0.058-0.03721.599-0.006-0.0060.0000.0000.0000.000
89A99LYS10.8520.93321.770-0.173-0.1730.0000.0000.0000.000
90A100GLU-1-0.789-0.88922.8410.0790.0790.0000.0000.0000.000
91A101ALA00.0230.01222.479-0.018-0.0180.0000.0000.0000.000
92A102LEU0-0.057-0.02024.4590.0240.0240.0000.0000.0000.000
93A103TYR00.017-0.02421.725-0.009-0.0090.0000.0000.0000.000
94A104THR00.004-0.00325.0870.0190.0190.0000.0000.0000.000
95A105TYR0-0.073-0.07525.982-0.024-0.0240.0000.0000.0000.000
96A106ASP-1-0.697-0.85227.762-0.040-0.0400.0000.0000.0000.000
97A107PHE0-0.107-0.06728.4220.0010.0010.0000.0000.0000.000
98A108GLY0-0.035-0.00433.4020.0000.0000.0000.0000.0000.000
99A109ASP-1-0.767-0.90034.170-0.012-0.0120.0000.0000.0000.000
100A110ASN0-0.104-0.04632.8920.0010.0010.0000.0000.0000.000
101A111TRP00.0810.06629.8720.0110.0110.0000.0000.0000.000
102A112GLN0-0.010-0.01228.929-0.001-0.0010.0000.0000.0000.000
103A113VAL00.0030.00924.3700.0140.0140.0000.0000.0000.000
104A114LYS10.8290.91326.122-0.056-0.0560.0000.0000.0000.000
105A115VAL00.0300.01420.3530.0220.0220.0000.0000.0000.000
106A116ARG10.8310.89122.995-0.109-0.1090.0000.0000.0000.000
107A117LEU00.0130.02217.3530.0350.0350.0000.0000.0000.000
108A118GLU-1-0.893-0.93220.4580.2230.2230.0000.0000.0000.000
109A119LYS10.8620.91018.729-0.420-0.4200.0000.0000.0000.000
110A120ILE00.0480.03613.6210.0270.0270.0000.0000.0000.000
111A121LEU0-0.048-0.02114.331-0.048-0.0480.0000.0000.0000.000
112A122PRO00.023-0.00211.1340.0590.0590.0000.0000.0000.000
113A123ARG10.8750.9542.279-15.357-16.5364.452-1.397-1.8750.013
114A124LYS10.9090.9559.973-0.792-0.7920.0000.0000.0000.000
115A125GLU-1-0.825-0.92910.3411.9801.9800.0000.0000.0000.000
116A126GLY0-0.042-0.02610.899-0.256-0.2560.0000.0000.0000.000
117A127VAL0-0.100-0.03711.230-0.215-0.2150.0000.0000.0000.000
118A128GLU-1-0.922-0.9489.3791.1101.1100.0000.0000.0000.000
119A129TYR0-0.062-0.0298.306-0.088-0.0880.0000.0000.0000.000
120A130PRO00.002-0.0059.4420.0520.0520.0000.0000.0000.000
121A131ILE0-0.0050.00912.193-0.029-0.0290.0000.0000.0000.000
122A132CYS00.0000.00115.371-0.034-0.0340.0000.0000.0000.000
123A133THR0-0.065-0.03718.3650.0100.0100.0000.0000.0000.000
124A134ALA0-0.008-0.01620.967-0.014-0.0140.0000.0000.0000.000
125A135GLY00.0430.00224.0640.0020.0020.0000.0000.0000.000
126A136LYS10.8510.93126.839-0.121-0.1210.0000.0000.0000.000
127A137ARG10.8470.90530.540-0.068-0.0680.0000.0000.0000.000
128A138ALA00.1090.08330.9490.0100.0100.0000.0000.0000.000
129A139ALA0-0.059-0.04028.4350.0010.0010.0000.0000.0000.000
130A140VAL0-0.028-0.00130.528-0.001-0.0010.0000.0000.0000.000
131A141PRO00.0830.04331.234-0.003-0.0030.0000.0000.0000.000
132A142GLU-1-0.713-0.83028.328-0.032-0.0320.0000.0000.0000.000
133A143ASP-1-0.897-0.95232.333-0.028-0.0280.0000.0000.0000.000
134A144SER0-0.027-0.02234.7570.0020.0020.0000.0000.0000.000
135A145GLY00.0460.02037.2210.0030.0030.0000.0000.0000.000
136A146GLY0-0.003-0.00635.8170.0000.0000.0000.0000.0000.000
137A147VAL0-0.094-0.05934.9660.0040.0040.0000.0000.0000.000
138A148TRP0-0.048-0.02237.3210.0050.0050.0000.0000.0000.000
139A149GLY00.1070.07340.4720.0030.0030.0000.0000.0000.000
140A150TYR00.0520.01635.6270.0030.0030.0000.0000.0000.000
141A151GLU-1-0.801-0.93238.9480.0460.0460.0000.0000.0000.000
142A152GLU-1-0.965-0.98441.0960.0090.0090.0000.0000.0000.000
143A153MET00.0310.02439.5870.0010.0010.0000.0000.0000.000
144A154LEU0-0.020-0.01538.2990.0040.0040.0000.0000.0000.000
145A155GLU-1-0.889-0.92842.7540.0380.0380.0000.0000.0000.000
146A156VAL00.0220.02646.2550.0010.0010.0000.0000.0000.000
147A157LEU00.003-0.00942.1240.0010.0010.0000.0000.0000.000
148A158LYS10.6550.81445.219-0.036-0.0360.0000.0000.0000.000
149A159ASP-1-0.943-0.97648.4360.0250.0250.0000.0000.0000.000
150A160SER0-0.038-0.04751.644-0.001-0.0010.0000.0000.0000.000
151A161GLU-1-0.969-0.96352.5300.0220.0220.0000.0000.0000.000
152A162HIS0-0.063-0.01051.584-0.001-0.0010.0000.0000.0000.000
153A163GLU-1-0.928-0.98353.4860.0130.0130.0000.0000.0000.000
154A164GLU-1-0.933-0.95748.8540.0060.0060.0000.0000.0000.000
155A165TYR0-0.0140.01248.0440.0010.0010.0000.0000.0000.000
156A166GLU-1-0.949-0.98448.1480.0170.0170.0000.0000.0000.000
157A167ASP-1-0.929-0.96347.7920.0070.0070.0000.0000.0000.000
158A168THR0-0.017-0.02243.938-0.001-0.0010.0000.0000.0000.000
159A169VAL0-0.016-0.01043.4500.0020.0020.0000.0000.0000.000
160A170LEU0-0.066-0.02943.2120.0010.0010.0000.0000.0000.000
161A171TRP0-0.078-0.03336.844-0.001-0.0010.0000.0000.0000.000
162A172LEU0-0.034-0.01938.129-0.001-0.0010.0000.0000.0000.000
163A173GLY00.0100.02138.3040.0030.0030.0000.0000.0000.000
164A174ASP-1-0.958-0.99340.4940.0310.0310.0000.0000.0000.000
165A175ASP-1-1.006-1.00036.8500.0500.0500.0000.0000.0000.000
166A176PHE00.0040.00434.4150.0080.0080.0000.0000.0000.000
167A177ASP-1-0.844-0.92336.7680.0790.0790.0000.0000.0000.000
168A178PRO00.0340.01636.1610.0050.0050.0000.0000.0000.000
169A179GLU-1-0.861-0.92735.6560.0790.0790.0000.0000.0000.000
170A180TYR0-0.118-0.06429.7930.0130.0130.0000.0000.0000.000
171A181PHE0-0.008-0.02424.0190.0040.0040.0000.0000.0000.000
172A182ASP-1-0.785-0.85826.4320.2160.2160.0000.0000.0000.000
173A183PRO0-0.045-0.03022.2180.0010.0010.0000.0000.0000.000
174A184LYS10.7500.83622.010-0.191-0.1910.0000.0000.0000.000
175A185ASP-1-0.794-0.86523.1220.1540.1540.0000.0000.0000.000
176A186VAL0-0.045-0.02019.531-0.015-0.0150.0000.0000.0000.000
177A187SER0-0.0220.00119.6170.0330.0330.0000.0000.0000.000
178A188PHE0-0.015-0.01014.781-0.024-0.0240.0000.0000.0000.000