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: 8986Y

Calculation Name: 2IAI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IAI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9XA31

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2140581.515927
FMO2-HF: Nuclear repulsion 2060182.987797
FMO2-HF: Total energy -80398.528131
FMO2-MP2: Total energy -80634.950635


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:-8:GLY)


Summations of interaction energy for fragment #1(A:-8:GLY)
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.
-12.549-14.3268.806-3.366-3.6630.015
Interaction energy analysis for fragmet #1(A:-8:GLY)
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 : 0.017
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].
3A-6GLU-1-0.922-0.9583.790-2.202-1.086-0.005-0.359-0.7520.001
4A-5ASN00.0180.0026.1410.6000.6000.0000.0000.0000.000
5A-4LEU00.0300.0049.5090.0400.0400.0000.0000.0000.000
6A-3TYR0-0.064-0.02511.6330.0470.0470.0000.0000.0000.000
7A-2PHE00.0570.01414.9910.0630.0630.0000.0000.0000.000
8A-1GLN0-0.019-0.01016.323-0.013-0.0130.0000.0000.0000.000
9A0GLY00.0180.01314.6110.0160.0160.0000.0000.0000.000
10A1MET0-0.0390.00513.148-0.037-0.0370.0000.0000.0000.000
11A2THR00.002-0.0187.646-0.064-0.0640.0000.0000.0000.000
12A3THR00.0450.0366.015-0.019-0.0190.0000.0000.0000.000
13A4ALA00.0040.0096.611-0.435-0.4350.0000.0000.0000.000
14A5LYS10.8020.8732.603-2.438-1.9330.571-0.450-0.6270.000
15A6ARG10.9080.9422.089-11.440-14.8388.240-2.557-2.2840.014
16A7ASP-1-0.809-0.8895.4933.2733.2730.0000.0000.0000.000
17A8THR00.000-0.0047.890-0.194-0.1940.0000.0000.0000.000
18A9TYR0-0.024-0.0139.0070.0020.0020.0000.0000.0000.000
19A10THR0-0.002-0.00813.6370.0810.0810.0000.0000.0000.000
20A11PRO0-0.0050.00615.692-0.049-0.0490.0000.0000.0000.000
21A12GLU-1-0.895-0.92618.4650.3070.3070.0000.0000.0000.000
22A13THR00.0070.01121.045-0.006-0.0060.0000.0000.0000.000
23A14LEU00.0430.00223.4490.0040.0040.0000.0000.0000.000
24A15LEU0-0.014-0.01124.536-0.002-0.0020.0000.0000.0000.000
25A16SER00.0410.02022.883-0.007-0.0070.0000.0000.0000.000
26A17VAL00.0520.02619.885-0.001-0.0010.0000.0000.0000.000
27A18ALA0-0.019-0.02622.379-0.006-0.0060.0000.0000.0000.000
28A19VAL0-0.002-0.00425.156-0.011-0.0110.0000.0000.0000.000
29A20GLN00.0180.01419.628-0.013-0.0130.0000.0000.0000.000
30A21VAL00.0210.01221.199-0.008-0.0080.0000.0000.0000.000
31A22PHE0-0.056-0.03823.701-0.015-0.0150.0000.0000.0000.000
32A23ILE0-0.033-0.01026.401-0.013-0.0130.0000.0000.0000.000
33A24GLU-1-0.973-0.98020.7670.1880.1880.0000.0000.0000.000
34A25ARG10.8970.95020.438-0.151-0.1510.0000.0000.0000.000
35A26GLY00.0480.03926.592-0.011-0.0110.0000.0000.0000.000
36A27TYR00.024-0.00529.3210.0050.0050.0000.0000.0000.000
37A28ASP-1-0.866-0.93530.9800.0700.0700.0000.0000.0000.000
38A29GLY0-0.015-0.00529.631-0.001-0.0010.0000.0000.0000.000
39A30THR0-0.0210.00225.5200.0100.0100.0000.0000.0000.000
40A31SER00.000-0.01025.177-0.005-0.0050.0000.0000.0000.000
41A32MET00.0540.00725.5710.0090.0090.0000.0000.0000.000
42A33GLU-1-0.876-0.93220.7240.1820.1820.0000.0000.0000.000
43A34HIS00.0170.01721.1920.0210.0210.0000.0000.0000.000
44A35LEU00.0490.02820.6710.0210.0210.0000.0000.0000.000
45A36SER0-0.066-0.04620.9060.0190.0190.0000.0000.0000.000
46A37LYS10.8150.88615.519-0.214-0.2140.0000.0000.0000.000
47A38ALA00.0330.01616.2590.0440.0440.0000.0000.0000.000
48A39ALA0-0.0020.01017.2160.0350.0350.0000.0000.0000.000
49A40GLY00.0050.00716.0430.0290.0290.0000.0000.0000.000
50A41ILE00.0040.01516.758-0.003-0.0030.0000.0000.0000.000
51A42SER00.0250.03419.922-0.016-0.0160.0000.0000.0000.000
52A43LYS11.0000.97622.335-0.128-0.1280.0000.0000.0000.000
53A44SER0-0.0080.00425.439-0.005-0.0050.0000.0000.0000.000
54A45SER00.0310.00923.434-0.011-0.0110.0000.0000.0000.000
55A46ILE00.0380.01023.402-0.002-0.0020.0000.0000.0000.000
56A47TYR00.0080.00826.828-0.006-0.0060.0000.0000.0000.000
57A48HIS0-0.053-0.00627.521-0.011-0.0110.0000.0000.0000.000
58A49HIS0-0.047-0.01226.174-0.007-0.0070.0000.0000.0000.000
59A50VAL0-0.031-0.02829.290-0.008-0.0080.0000.0000.0000.000
60A51THR00.0380.01631.5680.0040.0040.0000.0000.0000.000
61A52GLY00.0300.00030.775-0.002-0.0020.0000.0000.0000.000
62A53LYS10.8530.91229.447-0.089-0.0890.0000.0000.0000.000
63A54GLU-1-0.843-0.88730.9450.0710.0710.0000.0000.0000.000
64A55GLU-1-0.722-0.82333.7030.0900.0900.0000.0000.0000.000
65A56LEU0-0.013-0.01027.5300.0010.0010.0000.0000.0000.000
66A57LEU00.0190.01231.4970.0010.0010.0000.0000.0000.000
67A58ARG10.8800.90833.255-0.086-0.0860.0000.0000.0000.000
68A59ARG10.8250.90131.773-0.115-0.1150.0000.0000.0000.000
69A60ALA00.0160.01731.423-0.001-0.0010.0000.0000.0000.000
70A61VAL0-0.005-0.01933.355-0.003-0.0030.0000.0000.0000.000
71A62SER0-0.012-0.00836.656-0.004-0.0040.0000.0000.0000.000
72A63ARG10.8680.94133.007-0.104-0.1040.0000.0000.0000.000
73A64ALA00.0160.01236.084-0.002-0.0020.0000.0000.0000.000
74A65LEU0-0.048-0.03937.614-0.005-0.0050.0000.0000.0000.000
75A66ASP-1-0.901-0.95440.0510.0660.0660.0000.0000.0000.000
76A67GLU-1-0.924-0.95737.6140.0700.0700.0000.0000.0000.000
77A68LEU0-0.038-0.01740.677-0.004-0.0040.0000.0000.0000.000
78A69PHE0-0.077-0.07043.086-0.004-0.0040.0000.0000.0000.000
79A70GLY00.0380.04044.426-0.003-0.0030.0000.0000.0000.000
80A71ILE00.0050.00743.236-0.002-0.0020.0000.0000.0000.000
81A72LEU0-0.078-0.05046.664-0.003-0.0030.0000.0000.0000.000
82A73ASP-1-0.906-0.95249.4880.0390.0390.0000.0000.0000.000
83A74GLU-1-0.773-0.82545.4320.0500.0500.0000.0000.0000.000
84A75GLU-1-0.931-0.97450.2160.0330.0330.0000.0000.0000.000
85A76HIS00.0420.00651.399-0.002-0.0020.0000.0000.0000.000
86A77ALA00.0010.01050.852-0.001-0.0010.0000.0000.0000.000
87A78ARG10.7810.88852.968-0.036-0.0360.0000.0000.0000.000
88A79VAL0-0.038-0.00756.066-0.001-0.0010.0000.0000.0000.000
89A80GLY00.0450.02857.6990.0000.0000.0000.0000.0000.000
90A81THR00.0470.01560.2040.0010.0010.0000.0000.0000.000
91A82ALA00.0190.01958.9120.0010.0010.0000.0000.0000.000
92A83ALA00.005-0.00857.3940.0010.0010.0000.0000.0000.000
93A84GLU-1-0.868-0.92156.1060.0260.0260.0000.0000.0000.000
94A85ARG10.8260.92854.468-0.027-0.0270.0000.0000.0000.000
95A86LEU0-0.035-0.02152.4420.0020.0020.0000.0000.0000.000
96A87GLU-1-0.848-0.93251.5500.0300.0300.0000.0000.0000.000
97A88TYR0-0.059-0.05447.7720.0010.0010.0000.0000.0000.000
98A89VAL00.022-0.00248.3300.0030.0030.0000.0000.0000.000
99A90VAL0-0.021-0.01446.9940.0030.0030.0000.0000.0000.000
100A91ARG10.8360.90945.568-0.031-0.0310.0000.0000.0000.000
101A92ARG10.8270.88841.548-0.051-0.0510.0000.0000.0000.000
102A93MET0-0.055-0.02042.5100.0030.0030.0000.0000.0000.000
103A94VAL0-0.017-0.00640.3110.0030.0030.0000.0000.0000.000
104A95GLU-1-0.879-0.93639.1730.0540.0540.0000.0000.0000.000
105A96VAL0-0.003-0.00237.9030.0050.0050.0000.0000.0000.000
106A97LEU0-0.068-0.01535.6000.0060.0060.0000.0000.0000.000
107A98MET0-0.050-0.01834.5580.0040.0040.0000.0000.0000.000
108A99ALA0-0.0170.00433.1120.0070.0070.0000.0000.0000.000
109A100GLU-1-0.823-0.90832.5620.1070.1070.0000.0000.0000.000
110A101LEU00.0500.04829.3880.0030.0030.0000.0000.0000.000
111A102PRO0-0.011-0.00227.875-0.003-0.0030.0000.0000.0000.000
112A103TYR00.0060.00029.1860.0020.0020.0000.0000.0000.000
113A104VAL00.0640.01932.856-0.005-0.0050.0000.0000.0000.000
114A105THR0-0.007-0.01731.332-0.006-0.0060.0000.0000.0000.000
115A106LEU0-0.059-0.03929.615-0.004-0.0040.0000.0000.0000.000
116A107LEU0-0.0080.01133.664-0.005-0.0050.0000.0000.0000.000
117A108LEU0-0.065-0.04237.025-0.005-0.0050.0000.0000.0000.000
118A109ARG10.8960.95629.515-0.086-0.0860.0000.0000.0000.000
119A110VAL0-0.0550.00536.651-0.002-0.0020.0000.0000.0000.000
120A111ARG10.8790.93838.274-0.054-0.0540.0000.0000.0000.000
121A112GLY00.1020.06339.446-0.001-0.0010.0000.0000.0000.000
122A113ASN0-0.063-0.04240.381-0.002-0.0020.0000.0000.0000.000
123A114THR00.012-0.01137.639-0.002-0.0020.0000.0000.0000.000
124A115GLY00.003-0.00641.003-0.002-0.0020.0000.0000.0000.000
125A116THR00.002-0.02037.396-0.001-0.0010.0000.0000.0000.000
126A117GLU-1-0.831-0.91237.5880.0660.0660.0000.0000.0000.000
127A118ARG10.9100.96140.646-0.050-0.0500.0000.0000.0000.000
128A119TRP00.0320.03040.264-0.001-0.0010.0000.0000.0000.000
129A120ALA00.0660.02440.425-0.001-0.0010.0000.0000.0000.000
130A121LEU0-0.059-0.04642.395-0.002-0.0020.0000.0000.0000.000
131A122GLU-1-0.956-0.98944.5990.0430.0430.0000.0000.0000.000
132A123ARG10.9460.98344.388-0.053-0.0530.0000.0000.0000.000
133A124ARG11.0170.99841.484-0.052-0.0520.0000.0000.0000.000
134A125ARG10.8830.96245.624-0.043-0.0430.0000.0000.0000.000
135A126GLU-1-0.930-0.95449.0870.0360.0360.0000.0000.0000.000
136A127PHE00.011-0.00146.281-0.001-0.0010.0000.0000.0000.000
137A128ASP-1-0.922-0.98048.7780.0340.0340.0000.0000.0000.000
138A129HIS00.0250.00950.023-0.002-0.0020.0000.0000.0000.000
139A130ARG10.9050.97151.381-0.041-0.0410.0000.0000.0000.000
140A131VAL00.0530.02949.080-0.001-0.0010.0000.0000.0000.000
141A132ALA0-0.014-0.01452.438-0.002-0.0020.0000.0000.0000.000
142A133ALA0-0.066-0.03554.956-0.002-0.0020.0000.0000.0000.000
143A134LEU00.0570.03852.920-0.001-0.0010.0000.0000.0000.000
144A135LEU00.0120.02054.236-0.001-0.0010.0000.0000.0000.000
145A136LYS10.9070.93857.231-0.025-0.0250.0000.0000.0000.000
146A137ASP-1-0.922-0.95560.0910.0250.0250.0000.0000.0000.000
147A138ALA00.0290.00158.945-0.001-0.0010.0000.0000.0000.000
148A139ALA0-0.051-0.02460.953-0.001-0.0010.0000.0000.0000.000
149A140ALA0-0.082-0.03962.847-0.001-0.0010.0000.0000.0000.000
150A141GLU-1-0.890-0.95263.2460.0230.0230.0000.0000.0000.000
151A142GLY0-0.045-0.00465.365-0.001-0.0010.0000.0000.0000.000
152A143ASP-1-0.900-0.94461.2430.0210.0210.0000.0000.0000.000
153A144VAL0-0.070-0.03558.0310.0000.0000.0000.0000.0000.000
154A145ARG10.7870.87658.697-0.019-0.0190.0000.0000.0000.000
155A146ALA00.0560.00661.8720.0010.0010.0000.0000.0000.000
156A147ASP-1-0.844-0.88962.6810.0170.0170.0000.0000.0000.000
157A148VAL0-0.039-0.02456.9990.0000.0000.0000.0000.0000.000
158A149GLU-1-0.898-0.94459.4370.0210.0210.0000.0000.0000.000
159A150VAL00.0850.04357.5330.0010.0010.0000.0000.0000.000
160A151ARG10.9340.95455.452-0.027-0.0270.0000.0000.0000.000
161A152LEU0-0.0220.01153.6180.0010.0010.0000.0000.0000.000
162A153ALA00.0480.00753.3080.0010.0010.0000.0000.0000.000
163A154THR00.0380.01151.0460.0010.0010.0000.0000.0000.000
164A155ARG10.8520.93848.276-0.032-0.0320.0000.0000.0000.000
165A156LEU0-0.011-0.01748.4080.0010.0010.0000.0000.0000.000
166A157VAL00.0500.04448.0260.0010.0010.0000.0000.0000.000
167A158PHE00.010-0.01445.7780.0020.0020.0000.0000.0000.000
168A159GLY0-0.038-0.00344.1550.0020.0020.0000.0000.0000.000
169A160MET0-0.008-0.00543.1230.0010.0010.0000.0000.0000.000
170A161ILE00.0510.02542.0090.0010.0010.0000.0000.0000.000
171A162ASN0-0.018-0.03840.0910.0040.0040.0000.0000.0000.000
172A163SER0-0.021-0.00538.5370.0030.0030.0000.0000.0000.000
173A164ILE00.0370.01836.2580.0010.0010.0000.0000.0000.000
174A165VAL0-0.051-0.02533.7940.0030.0030.0000.0000.0000.000
175A166GLU-1-1.029-1.01532.6180.0500.0500.0000.0000.0000.000
176A167TRP0-0.041-0.02032.4080.0010.0010.0000.0000.0000.000
177A168TYR0-0.075-0.07432.2650.0010.0010.0000.0000.0000.000
178A169ARG10.9430.96924.768-0.066-0.0660.0000.0000.0000.000
179A170PRO0-0.0170.01127.829-0.006-0.0060.0000.0000.0000.000
180A171GLU-1-0.978-0.99427.7200.0680.0680.0000.0000.0000.000
181A183SER00.010-0.00341.1690.0010.0010.0000.0000.0000.000
182A184GLY0-0.0110.00040.9400.0000.0000.0000.0000.0000.000
183A185VAL00.010-0.00436.5800.0000.0000.0000.0000.0000.000
184A186SER00.0210.00834.5140.0010.0010.0000.0000.0000.000
185A187GLY00.0750.03235.349-0.003-0.0030.0000.0000.0000.000
186A188ALA0-0.030-0.01037.017-0.002-0.0020.0000.0000.0000.000
187A189GLY00.0750.03736.132-0.002-0.0020.0000.0000.0000.000
188A190GLU-1-0.774-0.86733.7680.0630.0630.0000.0000.0000.000
189A191ARG10.8790.93137.903-0.046-0.0460.0000.0000.0000.000
190A192GLU-1-0.948-0.95139.6290.0290.0290.0000.0000.0000.000
191A193VAL00.010-0.00137.703-0.002-0.0020.0000.0000.0000.000
192A194VAL00.0220.00741.070-0.002-0.0020.0000.0000.0000.000
193A195ASP-1-0.901-0.94943.3320.0310.0310.0000.0000.0000.000
194A196ALA0-0.064-0.02543.850-0.002-0.0020.0000.0000.0000.000
195A197VAL00.0180.00742.994-0.002-0.0020.0000.0000.0000.000
196A198ALA00.0160.01445.992-0.001-0.0010.0000.0000.0000.000
197A199ARG10.9450.96347.913-0.027-0.0270.0000.0000.0000.000
198A200LEU0-0.023-0.00846.696-0.002-0.0020.0000.0000.0000.000
199A201VAL0-0.036-0.01648.422-0.001-0.0010.0000.0000.0000.000
200A202PHE0-0.012-0.00551.080-0.001-0.0010.0000.0000.0000.000
201A203GLY00.0000.01353.661-0.001-0.0010.0000.0000.0000.000
202A204GLY0-0.064-0.02052.796-0.001-0.0010.0000.0000.0000.000
203A205LEU00.005-0.01949.3840.0000.0000.0000.0000.0000.000
204A206ARG10.9040.95953.152-0.014-0.0140.0000.0000.0000.000
205A207LYS11.0221.02055.936-0.010-0.0100.0000.0000.0000.000