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: VV2V1

Calculation Name: 1T3U-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T3U

Chain ID: A

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 OptHSide
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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -544139.473273
FMO2-HF: Nuclear repulsion 506809.253578
FMO2-HF: Total energy -37330.219694
FMO2-MP2: Total energy -37436.872571


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:6:THR)


Summations of interaction energy for fragment #1(A:6: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.
-6.198-1.2552.287-3.694-3.538-0.006
Interaction energy analysis for fragmet #1(A:6:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.082 / q_NPA : 0.025
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].
4A7LEU0-0.1170.0984.2460.0790.4630.003-0.206-0.1820.000
5A8THR00.023-0.0823.797-1.714-0.028-0.019-0.950-0.7180.003
6A8THR0-0.0330.0785.907-0.598-0.5980.0000.0000.0000.000
7A9VAL00.059-0.0926.8700.2850.2850.0000.0000.0000.000
8A9VAL0-0.0380.1058.5150.0520.0520.0000.0000.0000.000
9A10GLN00.095-0.12010.156-0.139-0.1390.0000.0000.0000.000
10A10GLN0-0.1160.09713.2380.0840.0840.0000.0000.0000.000
11A11ILE00.077-0.09113.6470.0900.0900.0000.0000.0000.000
12A11ILE0-0.1450.07212.7620.0130.0130.0000.0000.0000.000
13A12LEU00.122-0.09315.865-0.038-0.0380.0000.0000.0000.000
14A12LEU0-0.1640.05519.4940.0090.0090.0000.0000.0000.000
15A13ASP00.054-0.05919.136-0.013-0.0130.0000.0000.0000.000
16A13ASP-1-0.935-0.85820.844-0.173-0.1730.0000.0000.0000.000
17A14LYS00.107-0.10116.304-0.035-0.0350.0000.0000.0000.000
18A14LYS10.8531.05115.8420.2990.2990.0000.0000.0000.000
19A15GLU00.095-0.10612.3360.1110.1110.0000.0000.0000.000
20A15GLU-1-0.963-0.80410.308-1.089-1.0890.0000.0000.0000.000
21A16TYR00.069-0.11510.064-0.084-0.0840.0000.0000.0000.000
22A16TYR0-0.1530.0719.9750.0720.0720.0000.0000.0000.000
23A17CYS00.176-0.0986.0210.2190.2190.0000.0000.0000.000
24A17CYS0-0.1430.1284.431-0.286-0.2660.0010.046-0.0670.000
25A18ILE00.013-0.1204.914-0.186-0.1860.0000.0000.0000.000
26A18ILE0-0.0670.0934.8290.0610.0610.0000.0000.0000.000
27A19ASN00.124-0.0762.484-0.3940.8332.164-1.840-1.551-0.015
28A19ASN0-0.0760.0694.128-0.773-0.5380.000-0.080-0.1550.000
29A20CYS00.035-0.1413.266-1.802-1.7980.0100.038-0.0520.000
30A20CYS0-0.0550.1154.834-0.202-0.1200.004-0.031-0.0550.000
31A21PRO00.016-0.0684.9102.5782.685-0.002-0.004-0.1010.000
32A22ASP00.1430.0046.8900.5300.5300.0000.0000.0000.000
33A22ASP-1-0.940-0.8025.7335.6925.722-0.0010.000-0.0290.000
34A23ASP00.032-0.1377.663-0.234-0.2340.0000.0000.0000.000
35A23ASP-1-1.005-0.83911.9161.2481.2480.0000.0000.0000.000
36A24GLU00.009-0.1809.349-0.428-0.4280.0000.0000.0000.000
37A24GLU-1-0.944-0.8148.7521.7931.7930.0000.0000.0000.000
38A25ARG00.140-0.0527.775-0.384-0.3840.0000.0000.0000.000
39A25ARG10.7881.0303.237-9.387-8.2190.127-0.667-0.6280.006
40A26ALA00.162-0.0908.563-0.297-0.2970.0000.0000.0000.000
41A26ALA0-0.0620.10812.957-0.028-0.0280.0000.0000.0000.000
42A27ASN00.039-0.10612.116-0.215-0.2150.0000.0000.0000.000
43A27ASN0-0.0820.08712.657-0.125-0.1250.0000.0000.0000.000
44A28LEU00.121-0.1039.413-0.297-0.2970.0000.0000.0000.000
45A28LEU0-0.0390.1417.576-0.003-0.0030.0000.0000.0000.000
46A29GLU00.062-0.17910.840-0.216-0.2160.0000.0000.0000.000
47A29GLU-1-0.967-0.8189.7350.7590.7590.0000.0000.0000.000
48A30SER0-0.015-0.09411.715-0.176-0.1760.0000.0000.0000.000
49A30SER0-0.0650.07314.878-0.032-0.0320.0000.0000.0000.000
50A31ALA00.081-0.09613.864-0.117-0.1170.0000.0000.0000.000
51A31ALA0-0.0650.12113.0970.0110.0110.0000.0000.0000.000
52A32ALA00.075-0.11212.762-0.074-0.0740.0000.0000.0000.000
53A32ALA0-0.0500.11211.846-0.010-0.0100.0000.0000.0000.000
54A33ARG00.063-0.08813.978-0.091-0.0910.0000.0000.0000.000
55A33ARG10.8141.03614.028-0.416-0.4160.0000.0000.0000.000
56A34TYR00.118-0.07016.930-0.051-0.0510.0000.0000.0000.000
57A34TYR0-0.1390.05618.0920.0010.0010.0000.0000.0000.000
58A35LEU00.060-0.08817.226-0.026-0.0260.0000.0000.0000.000
59A35LEU0-0.0800.09014.910-0.009-0.0090.0000.0000.0000.000
60A36ASP00.060-0.12317.572-0.024-0.0240.0000.0000.0000.000
61A36ASP-1-0.846-0.76417.330-0.082-0.0820.0000.0000.0000.000
62A37GLY0-0.002-0.09219.081-0.022-0.0220.0000.0000.0000.000
63A38LYS00.1360.01021.809-0.019-0.0190.0000.0000.0000.000
64A38LYS10.7761.03122.435-0.078-0.0780.0000.0000.0000.000
65A39MET00.063-0.11921.841-0.001-0.0010.0000.0000.0000.000
66A39MET0-0.0870.09318.016-0.017-0.0170.0000.0000.0000.000
67A40ARG00.037-0.11023.089-0.015-0.0150.0000.0000.0000.000
68A40ARG10.7340.99220.3800.1030.1030.0000.0000.0000.000
69A41GLU00.126-0.07825.021-0.013-0.0130.0000.0000.0000.000
70A41GLU-1-0.949-0.80026.7940.0650.0650.0000.0000.0000.000
71A42ILE00.080-0.09726.625-0.003-0.0030.0000.0000.0000.000
72A42ILE0-0.0910.09725.0750.0000.0000.0000.0000.0000.000
73A43ARG00.090-0.05126.8710.0000.0000.0000.0000.0000.000
74A43ARG10.8521.04324.1930.1020.1020.0000.0000.0000.000
75A44SER0-0.033-0.12128.225-0.008-0.0080.0000.0000.0000.000
76A44SER0-0.0610.06929.1770.0030.0030.0000.0000.0000.000
77A45SER0-0.018-0.09930.8110.0000.0000.0000.0000.0000.000
78A45SER0-0.0670.04631.0460.0030.0030.0000.0000.0000.000
79A46GLY0-0.007-0.09432.1950.0020.0020.0000.0000.0000.000
80A47LYS00.0680.00232.967-0.003-0.0030.0000.0000.0000.000
81A47LYS10.8701.06133.551-0.009-0.0090.0000.0000.0000.000
82A48VAL00.012-0.12330.1700.0040.0040.0000.0000.0000.000
83A48VAL0-0.0800.11528.3890.0010.0010.0000.0000.0000.000
84A49ILE00.055-0.11930.424-0.006-0.0060.0000.0000.0000.000
85A49ILE0-0.0410.12932.664-0.001-0.0010.0000.0000.0000.000
86A50GLY00.074-0.07628.9600.0020.0020.0000.0000.0000.000
87A51ALA00.1550.01624.7030.0170.0170.0000.0000.0000.000
88A51ALA0-0.0940.09523.676-0.006-0.0060.0000.0000.0000.000
89A52ASP00.012-0.13423.2480.0030.0030.0000.0000.0000.000
90A52ASP-1-0.883-0.82724.608-0.083-0.0830.0000.0000.0000.000
91A53ARG00.106-0.08224.2100.0140.0140.0000.0000.0000.000
92A53ARG10.8651.08928.2500.0200.0200.0000.0000.0000.000
93A54VAL00.064-0.12625.3930.0210.0210.0000.0000.0000.000
94A54VAL0-0.0680.10423.788-0.001-0.0010.0000.0000.0000.000
95A55ALA00.129-0.08121.0620.0240.0240.0000.0000.0000.000
96A55ALA0-0.0710.11020.054-0.006-0.0060.0000.0000.0000.000
97A56VAL00.077-0.11421.3150.0260.0260.0000.0000.0000.000
98A56VAL0-0.0780.11922.8820.0000.0000.0000.0000.0000.000
99A57MET00.096-0.09523.2420.0240.0240.0000.0000.0000.000
100A57MET0-0.1180.09226.2320.0000.0000.0000.0000.0000.000
101A58ALA00.093-0.08521.8640.0210.0210.0000.0000.0000.000
102A58ALA0-0.0560.09921.248-0.003-0.0030.0000.0000.0000.000
103A59ALA00.077-0.11919.7590.0340.0340.0000.0000.0000.000
104A59ALA0-0.0660.10919.429-0.003-0.0030.0000.0000.0000.000
105A60LEU00.072-0.11120.5870.0380.0380.0000.0000.0000.000
106A60LEU0-0.0840.11724.909-0.003-0.0030.0000.0000.0000.000
107A61ASN00.118-0.07723.7600.0180.0180.0000.0000.0000.000
108A61ASN0-0.1210.07223.805-0.018-0.0180.0000.0000.0000.000
109A62ILE00.064-0.09019.8610.0040.0040.0000.0000.0000.000
110A62ILE0-0.0540.10617.0610.0040.0040.0000.0000.0000.000
111A63THR00.047-0.11120.7820.0440.0440.0000.0000.0000.000
112A63THR0-0.0560.05920.6210.0060.0060.0000.0000.0000.000
113A64HIS00.079-0.07921.6140.0180.0180.0000.0000.0000.000
114A64HIS0-0.0930.09425.873-0.005-0.0050.0000.0000.0000.000
115A65ASP00.104-0.10323.518-0.003-0.0030.0000.0000.0000.000
116A65ASP-1-0.967-0.83222.6130.2070.2070.0000.0000.0000.000
117A66LEU0-0.006-0.12120.2940.0040.0040.0000.0000.0000.000
118A66LEU0-0.0530.11917.3250.0090.0090.0000.0000.0000.000
119A67LEU00.089-0.10621.5970.0330.0330.0000.0000.0000.000
120A67LEU0-0.0550.12423.527-0.002-0.0020.0000.0000.0000.000
121A68HIS00.172-0.05824.3370.0040.0040.0000.0000.0000.000
122A68HIS0-0.1280.09126.6380.0050.0050.0000.0000.0000.000
123A69ARG00.070-0.07923.263-0.010-0.0100.0000.0000.0000.000
124A69ARG10.8030.99621.570-0.283-0.2830.0000.0000.0000.000
125A70LYS00.099-0.07323.2970.0160.0160.0000.0000.0000.000
126A70LYS10.7420.97922.236-0.303-0.3030.0000.0000.0000.000
127A71GLU00.070-0.12623.9710.0120.0120.0000.0000.0000.000
128A71GLU-1-1.016-0.84428.0880.1780.1780.0000.0000.0000.000
129A72ARG00.107-0.08427.430-0.011-0.0110.0000.0000.0000.000
130A72ARG10.7640.96826.618-0.283-0.2830.0000.0000.0000.000
131A73LEU00.075-0.12424.561-0.016-0.0160.0000.0000.0000.000
132A73LEU0-0.1090.11321.8740.0070.0070.0000.0000.0000.000
133A74ASP00.118-0.12626.0690.0080.0080.0000.0000.0000.000
134A74ASP-1-0.909-0.77225.8560.2900.2900.0000.0000.0000.000
135A75GLN00.059-0.09727.938-0.010-0.0100.0000.0000.0000.000
136A75GLN0-0.0890.10931.064-0.002-0.0020.0000.0000.0000.000
137A76GLU00.094-0.09729.642-0.016-0.0160.0000.0000.0000.000
138A76GLU-1-0.879-0.76328.2940.2810.2810.0000.0000.0000.000
139A77SER00.063-0.08228.005-0.008-0.0080.0000.0000.0000.000
140A77SER0-0.0410.07927.0320.0000.0000.0000.0000.0000.000
141A78SER00.006-0.10329.189-0.001-0.0010.0000.0000.0000.000
142A78SER0-0.0090.09032.062-0.005-0.0050.0000.0000.0000.000
143A79SER00.006-0.09532.426-0.013-0.0130.0000.0000.0000.000
144A79SER0-0.0600.07133.644-0.005-0.0050.0000.0000.0000.000
145A80THR0-0.014-0.10131.859-0.016-0.0160.0000.0000.0000.000
146A80THR0-0.0620.07430.8710.0020.0020.0000.0000.0000.000
147A81ARG00.136-0.08132.410-0.007-0.0070.0000.0000.0000.000
148A81ARG10.8291.05031.885-0.193-0.1930.0000.0000.0000.000
149A82GLU00.000-0.11833.604-0.004-0.0040.0000.0000.0000.000
150A82GLU-1-0.854-0.75636.3350.1630.1630.0000.0000.0000.000
151A83ARG00.176-0.04436.597-0.012-0.0120.0000.0000.0000.000
152A83ARG10.7921.02336.685-0.157-0.1570.0000.0000.0000.000
153A84VAL00.039-0.14235.514-0.012-0.0120.0000.0000.0000.000
154A84VAL0-0.0840.11633.6820.0020.0020.0000.0000.0000.000
155A85ARG00.119-0.07236.967-0.005-0.0050.0000.0000.0000.000
156A85ARG10.7720.99337.514-0.152-0.1520.0000.0000.0000.000
157A86GLU00.104-0.09438.829-0.007-0.0070.0000.0000.0000.000
158A86GLU-1-0.905-0.78340.9950.1420.1420.0000.0000.0000.000
159A87LEU00.022-0.12840.498-0.010-0.0100.0000.0000.0000.000
160A87LEU0-0.0900.08438.8160.0010.0010.0000.0000.0000.000
161A88LEU00.069-0.11040.008-0.007-0.0070.0000.0000.0000.000
162A88LEU0-0.0630.10236.6660.0010.0010.0000.0000.0000.000
163A89ASP00.102-0.07541.228-0.004-0.0040.0000.0000.0000.000
164A89ASP-1-0.898-0.78943.5840.1160.1160.0000.0000.0000.000
165A90ARG00.069-0.11044.156-0.007-0.0070.0000.0000.0000.000
166A90ARG10.8070.99644.821-0.125-0.1250.0000.0000.0000.000
167A91VAL00.047-0.07844.021-0.007-0.0070.0000.0000.0000.000
168A91VAL0-0.1120.09142.3900.0010.0010.0000.0000.0000.000
169A92ASP00.082-0.10045.050-0.004-0.0040.0000.0000.0000.000
170A92ASP-1-0.991-0.84944.9480.1130.1130.0000.0000.0000.000
171A93ARG00.110-0.08346.568-0.004-0.0040.0000.0000.0000.000
172A93ARG10.7150.94447.799-0.106-0.1060.0000.0000.0000.000
173A94ALA00.065-0.08249.044-0.006-0.0060.0000.0000.0000.000
174A94ALA0-0.0840.08348.6720.0010.0010.0000.0000.0000.000
175A95LEU00.010-0.13948.976-0.004-0.0040.0000.0000.0000.000
176A95LEU0-0.1060.09945.8960.0010.0010.0000.0000.0000.000
177A96ALA00.078-0.08350.274-0.003-0.0030.0000.0000.0000.000
178A96ALA0-0.0960.09851.3580.0000.0000.0000.0000.0000.000
179A97ASN0-0.104-0.12052.601-0.005-0.0050.0000.0000.0000.000
180A97ASN0-0.004-0.01254.280-0.003-0.0030.0000.0000.0000.000