FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: Y9Q92

Calculation Name: 1T3U-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T3U

Chain ID: B

ChEMBL ID:

UniProt ID: Q9HTW3

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -541754.353609
FMO2-HF: Nuclear repulsion 504106.225494
FMO2-HF: Total energy -37648.128115
FMO2-MP2: Total energy -37755.735443


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(B:4:SER)


Summations of interaction energy for fragment #1(B:4:SER)
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.
-9.729-8.6459.973-4.507-6.553-0.019
Interaction energy analysis for fragmet #1(B:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.043
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].
4B5ASN0-0.0930.0542.928-2.009-0.8400.141-0.594-0.716-0.005
5B6THR00.091-0.0683.827-0.2061.807-0.019-1.221-0.7740.006
6B6THR0-0.0150.0887.959-0.138-0.1380.0000.0000.0000.000
7B7LEU00.037-0.1366.986-0.162-0.1620.0000.0000.0000.000
8B7LEU0-0.0890.1266.9150.0290.0290.0000.0000.0000.000
9B8THR0-0.035-0.0968.3400.0710.0710.0000.0000.0000.000
10B8THR00.0280.07912.579-0.046-0.0460.0000.0000.0000.000
11B9VAL0-0.017-0.12012.105-0.001-0.0010.0000.0000.0000.000
12B9VAL0-0.0120.12012.1130.0160.0160.0000.0000.0000.000
13B10GLN00.106-0.11214.597-0.017-0.0170.0000.0000.0000.000
14B10GLN0-0.0760.12217.369-0.011-0.0110.0000.0000.0000.000
15B11ILE00.097-0.10118.3580.0220.0220.0000.0000.0000.000
16B11ILE0-0.1130.08516.1180.0070.0070.0000.0000.0000.000
17B12LEU00.061-0.12420.101-0.012-0.0120.0000.0000.0000.000
18B12LEU0-0.1270.08123.7850.0010.0010.0000.0000.0000.000
19B13ASP00.003-0.12723.534-0.004-0.0040.0000.0000.0000.000
20B13ASP-1-0.987-0.85625.6820.0220.0220.0000.0000.0000.000
21B14LYS00.119-0.09221.607-0.019-0.0190.0000.0000.0000.000
22B14LYS10.8701.06220.8210.0000.0000.0000.0000.0000.000
23B15GLU00.150-0.10517.9420.0380.0380.0000.0000.0000.000
24B15GLU-1-0.996-0.82016.245-0.203-0.2030.0000.0000.0000.000
25B16TYR0-0.028-0.12514.980-0.014-0.0140.0000.0000.0000.000
26B16TYR0-0.1210.07414.1890.0180.0180.0000.0000.0000.000
27B17CYS00.124-0.12511.6870.0580.0580.0000.0000.0000.000
28B17CYS0-0.0980.14511.276-0.036-0.0360.0000.0000.0000.000
29B18ILE00.112-0.1059.001-0.078-0.0780.0000.0000.0000.000
30B18ILE0-0.0890.1017.8550.0230.0230.0000.0000.0000.000
31B19ASN00.069-0.0445.269-0.255-0.2550.0000.0000.0000.000
32B19ASN0-0.1030.0554.735-0.268-0.269-0.001-0.0040.0050.000
33B20CYS00.097-0.1124.3420.4730.701-0.001-0.074-0.1540.000
34B20CYS0-0.1680.0894.656-0.286-0.241-0.001-0.013-0.0310.000
35B21PRO00.088-0.0912.064-4.405-4.8358.538-4.826-3.281-0.016
36B22ASP00.1430.0062.590-2.986-5.7421.2092.757-1.2100.000
37B22ASP-1-0.962-0.8363.295-1.769-1.0070.101-0.496-0.368-0.004
38B23ASP00.000-0.1413.920-1.275-1.2210.006-0.036-0.0240.000
39B23ASP-1-0.944-0.8216.7833.5293.5290.0000.0000.0000.000
40B24GLU00.056-0.1365.879-0.494-0.4940.0000.0000.0000.000
41B24GLU-1-0.930-0.8165.9831.9871.9870.0000.0000.0000.000
42B25ARG00.042-0.1076.346-0.338-0.3380.0000.0000.0000.000
43B25ARG10.8501.0514.8510.4160.4160.0000.0000.0000.000
44B26ALA00.177-0.0667.646-0.129-0.1290.0000.0000.0000.000
45B26ALA0-0.0590.12211.694-0.008-0.0080.0000.0000.0000.000
46B27ASN00.074-0.09810.436-0.174-0.1740.0000.0000.0000.000
47B27ASN0-0.1020.10310.723-0.179-0.1790.0000.0000.0000.000
48B28LEU00.101-0.1279.950-0.124-0.1240.0000.0000.0000.000
49B28LEU0-0.0720.1328.071-0.013-0.0130.0000.0000.0000.000
50B29GLU00.113-0.12911.191-0.094-0.0940.0000.0000.0000.000
51B29GLU-1-1.019-0.83911.1110.1660.1660.0000.0000.0000.000
52B30SER0-0.052-0.10713.165-0.087-0.0870.0000.0000.0000.000
53B30SER0-0.0740.03414.333-0.018-0.0180.0000.0000.0000.000
54B31ALA00.090-0.08714.599-0.077-0.0770.0000.0000.0000.000
55B31ALA0-0.0640.11514.2440.0140.0140.0000.0000.0000.000
56B32ALA00.073-0.12014.841-0.035-0.0350.0000.0000.0000.000
57B32ALA0-0.0550.12614.554-0.006-0.0060.0000.0000.0000.000
58B33ARG00.084-0.08316.366-0.045-0.0450.0000.0000.0000.000
59B33ARG10.8451.06616.301-0.238-0.2380.0000.0000.0000.000
60B34TYR00.111-0.11218.840-0.039-0.0390.0000.0000.0000.000
61B34TYR0-0.1400.08919.6280.0070.0070.0000.0000.0000.000
62B35LEU00.095-0.11219.354-0.024-0.0240.0000.0000.0000.000
63B35LEU0-0.1060.09518.238-0.001-0.0010.0000.0000.0000.000
64B36ASP00.049-0.11120.262-0.016-0.0160.0000.0000.0000.000
65B36ASP-1-0.858-0.76920.5940.0870.0870.0000.0000.0000.000
66B37GLY0-0.008-0.09822.077-0.018-0.0180.0000.0000.0000.000
67B38LYS00.1750.00624.060-0.019-0.0190.0000.0000.0000.000
68B38LYS10.7271.05124.389-0.164-0.1640.0000.0000.0000.000
69B39MET00.092-0.12424.613-0.008-0.0080.0000.0000.0000.000
70B39MET0-0.0950.10821.571-0.007-0.0070.0000.0000.0000.000
71B40ARG0-0.010-0.12126.114-0.013-0.0130.0000.0000.0000.000
72B40ARG10.7551.01624.384-0.066-0.0660.0000.0000.0000.000
73B41GLU00.090-0.12127.979-0.013-0.0130.0000.0000.0000.000
74B41GLU-1-0.955-0.82028.9470.1250.1250.0000.0000.0000.000
75B42ILE00.032-0.13429.460-0.006-0.0060.0000.0000.0000.000
76B42ILE0-0.0490.12527.9390.0000.0000.0000.0000.0000.000
77B43ARG00.107-0.08130.256-0.004-0.0040.0000.0000.0000.000
78B43ARG10.8391.06128.758-0.046-0.0460.0000.0000.0000.000
79B44SER0-0.017-0.08631.764-0.008-0.0080.0000.0000.0000.000
80B44SER0-0.0420.06333.105-0.002-0.0020.0000.0000.0000.000
81B45SER0-0.016-0.09234.117-0.006-0.0060.0000.0000.0000.000
82B45SER0-0.0490.07534.1940.0010.0010.0000.0000.0000.000
83B46GLY0-0.017-0.09235.326-0.003-0.0030.0000.0000.0000.000
84B47LYS00.093-0.01136.349-0.005-0.0050.0000.0000.0000.000
85B47LYS10.8751.08635.834-0.067-0.0670.0000.0000.0000.000
86B48VAL0-0.013-0.13633.446-0.002-0.0020.0000.0000.0000.000
87B48VAL0-0.0680.10731.6480.0010.0010.0000.0000.0000.000
88B49ILE00.108-0.11533.9270.0010.0010.0000.0000.0000.000
89B49ILE0-0.0330.14835.000-0.001-0.0010.0000.0000.0000.000
90B50GLY00.014-0.09331.4560.0010.0010.0000.0000.0000.000
91B51ALA00.139-0.00227.4350.0100.0100.0000.0000.0000.000
92B51ALA0-0.0770.11426.461-0.002-0.0020.0000.0000.0000.000
93B52ASP00.049-0.10225.4740.0120.0120.0000.0000.0000.000
94B52ASP-1-0.886-0.82226.2060.0700.0700.0000.0000.0000.000
95B53ARG00.060-0.13126.3340.0170.0170.0000.0000.0000.000
96B53ARG10.8731.08230.503-0.076-0.0760.0000.0000.0000.000
97B54VAL00.074-0.09928.2480.0110.0110.0000.0000.0000.000
98B54VAL0-0.0660.10526.993-0.001-0.0010.0000.0000.0000.000
99B55ALA00.136-0.10523.6360.0090.0090.0000.0000.0000.000
100B55ALA0-0.0820.11622.6350.0000.0000.0000.0000.0000.000
101B56VAL00.054-0.10524.2000.0250.0250.0000.0000.0000.000
102B56VAL0-0.0870.09725.132-0.001-0.0010.0000.0000.0000.000
103B57MET00.095-0.10125.7620.0180.0180.0000.0000.0000.000
104B57MET0-0.0940.10029.426-0.002-0.0020.0000.0000.0000.000
105B58ALA00.074-0.11625.1730.0010.0010.0000.0000.0000.000
106B58ALA0-0.0400.11624.4610.0000.0000.0000.0000.0000.000
107B59ALA00.098-0.09723.2110.0110.0110.0000.0000.0000.000
108B59ALA0-0.0520.10822.5480.0030.0030.0000.0000.0000.000
109B60LEU00.018-0.13323.9190.0230.0230.0000.0000.0000.000
110B60LEU0-0.0950.12526.608-0.002-0.0020.0000.0000.0000.000
111B61ASN00.208-0.05327.2130.0080.0080.0000.0000.0000.000
112B61ASN0-0.0950.06127.943-0.001-0.0010.0000.0000.0000.000
113B62ILE00.122-0.09223.844-0.009-0.0090.0000.0000.0000.000
114B62ILE0-0.0950.13221.8480.0010.0010.0000.0000.0000.000
115B63THR0-0.014-0.10025.0140.0160.0160.0000.0000.0000.000
116B63THR0-0.0630.05124.6120.0080.0080.0000.0000.0000.000
117B64HIS00.079-0.11125.7970.0060.0060.0000.0000.0000.000
118B64HIS0-0.1100.08829.876-0.006-0.0060.0000.0000.0000.000
119B65ASP00.092-0.10127.701-0.009-0.0090.0000.0000.0000.000
120B65ASP-1-0.951-0.82526.7460.1790.1790.0000.0000.0000.000
121B66LEU00.129-0.10825.452-0.009-0.0090.0000.0000.0000.000
122B66LEU0-0.1130.11523.7370.0020.0020.0000.0000.0000.000
123B67LEU00.016-0.12926.7440.0010.0010.0000.0000.0000.000
124B67LEU0-0.0610.11928.210-0.001-0.0010.0000.0000.0000.000
125B68HIS00.157-0.08429.603-0.004-0.0040.0000.0000.0000.000
126B68HIS0-0.1000.10631.632-0.005-0.0050.0000.0000.0000.000
127B69ARG00.064-0.10729.084-0.015-0.0150.0000.0000.0000.000
128B69ARG10.8351.07127.111-0.217-0.2170.0000.0000.0000.000
129B70LYS00.103-0.08430.005-0.006-0.0060.0000.0000.0000.000
130B70LYS10.8291.04328.714-0.209-0.2090.0000.0000.0000.000
131B71GLU00.115-0.09430.911-0.002-0.0020.0000.0000.0000.000
132B71GLU-1-1.045-0.86034.1860.1540.1540.0000.0000.0000.000
133B72ARG00.067-0.12834.023-0.009-0.0090.0000.0000.0000.000
134B72ARG10.8571.08033.880-0.128-0.1280.0000.0000.0000.000
135B73LEU00.086-0.12132.752-0.011-0.0110.0000.0000.0000.000
136B73LEU0-0.1110.11530.2320.0030.0030.0000.0000.0000.000
137B74ASP00.153-0.12134.186-0.005-0.0050.0000.0000.0000.000
138B74ASP-1-0.981-0.81633.9490.1840.1840.0000.0000.0000.000
139B75GLN00.040-0.12036.076-0.006-0.0060.0000.0000.0000.000
140B75GLN0-0.0940.09738.448-0.005-0.0050.0000.0000.0000.000
141B76GLU00.055-0.11637.686-0.010-0.0100.0000.0000.0000.000
142B76GLU-1-0.961-0.82837.0930.1320.1320.0000.0000.0000.000
143B77SER00.103-0.06737.481-0.007-0.0070.0000.0000.0000.000
144B77SER0-0.0710.06836.579-0.001-0.0010.0000.0000.0000.000
145B78SER0-0.044-0.13038.656-0.004-0.0040.0000.0000.0000.000
146B78SER0-0.0200.10140.9450.0000.0000.0000.0000.0000.000
147B79SER00.080-0.09041.548-0.005-0.0050.0000.0000.0000.000
148B79SER0-0.0580.09841.878-0.001-0.0010.0000.0000.0000.000
149B80THR0-0.038-0.11641.803-0.008-0.0080.0000.0000.0000.000
150B80THR0-0.0100.09540.618-0.001-0.0010.0000.0000.0000.000
151B81ARG00.102-0.08342.833-0.004-0.0040.0000.0000.0000.000
152B81ARG10.8571.05841.329-0.123-0.1230.0000.0000.0000.000
153B82GLU00.002-0.16244.197-0.003-0.0030.0000.0000.0000.000
154B82GLU-1-0.978-0.82145.8780.0940.0940.0000.0000.0000.000
155B83ARG00.128-0.07246.704-0.005-0.0050.0000.0000.0000.000
156B83ARG10.8721.06845.739-0.088-0.0880.0000.0000.0000.000
157B84VAL00.100-0.09846.563-0.005-0.0050.0000.0000.0000.000
158B84VAL0-0.0850.11144.4900.0010.0010.0000.0000.0000.000
159B85ARG00.023-0.12747.816-0.002-0.0020.0000.0000.0000.000
160B85ARG10.8751.07146.531-0.096-0.0960.0000.0000.0000.000
161B86GLU00.149-0.08250.204-0.003-0.0030.0000.0000.0000.000
162B86GLU-1-1.065-0.84951.5770.0750.0750.0000.0000.0000.000
163B87LEU00.081-0.12551.101-0.004-0.0040.0000.0000.0000.000
164B87LEU0-0.1230.10149.6010.0000.0000.0000.0000.0000.000
165B88LEU00.019-0.13251.686-0.003-0.0030.0000.0000.0000.000
166B88LEU0-0.0730.08649.7870.0010.0010.0000.0000.0000.000
167B89ASP00.144-0.08653.057-0.002-0.0020.0000.0000.0000.000
168B89ASP-1-0.984-0.84054.9710.0660.0660.0000.0000.0000.000
169B90ARG00.080-0.08255.511-0.003-0.0030.0000.0000.0000.000
170B90ARG10.8331.04255.941-0.063-0.0630.0000.0000.0000.000
171B91VAL0-0.037-0.13556.036-0.003-0.0030.0000.0000.0000.000
172B91VAL0-0.0770.09254.6270.0000.0000.0000.0000.0000.000
173B92ASP00.127-0.09857.460-0.001-0.0010.0000.0000.0000.000
174B92ASP-1-0.992-0.83357.0370.0650.0650.0000.0000.0000.000
175B93ARG00.048-0.12358.935-0.002-0.0020.0000.0000.0000.000
176B93ARG10.8071.04959.636-0.060-0.0600.0000.0000.0000.000
177B94ALA00.026-0.09161.311-0.002-0.0020.0000.0000.0000.000
178B94ALA0-0.0910.08661.7220.0000.0000.0000.0000.0000.000
179B95LEU00.058-0.11462.7590.0000.0000.0000.0000.0000.000
180B95LEU0-0.0830.10462.5540.0000.0000.0000.0000.0000.000
181B96ALA0-0.098-0.13863.581-0.001-0.0010.0000.0000.0000.000
182B96ALA00.0650.03965.1720.0000.0000.0000.0000.0000.000