FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VK7M1

Calculation Name: 3TNU-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3TNU

Chain ID: A

ChEMBL ID:

UniProt ID: P02533

Base Structure: X-ray

Registration Date: 2025-07-10

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 OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -439894.984235
FMO2-HF: Nuclear repulsion 401231.986122
FMO2-HF: Total energy -38662.998113
FMO2-MP2: Total energy -38770.314065


3D Structure Molmil
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:332:SER)


Summations of interaction energy for fragment #1(A:332: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.
-13.195-11.3530.0690.478-2.388-0.004
Interaction energy analysis for fragmet #1(A:332:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.096 / q_NPA : 0.069
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].
4A333GLU-1-0.791-0.7193.406-10.865-11.8150.0501.700-0.800-0.007
5A334LEU00.144-0.0693.460-0.3720.778-0.001-0.540-0.6090.001
6A334LEU0-0.0610.1214.2830.0460.136-0.001-0.018-0.0720.000
7A335ARG00.119-0.0673.856-1.846-1.4660.003-0.120-0.2630.000
8A335ARG10.8711.0673.579-5.782-5.4200.017-0.117-0.2610.000
9A336ARG00.125-0.0554.204-0.428-0.167-0.001-0.136-0.1230.000
10A336ARG10.7660.9803.2434.9755.5240.002-0.291-0.2600.002
11A337THR00.008-0.1085.940-0.052-0.0520.0000.0000.0000.000
12A337THR0-0.0630.0577.3110.1440.1440.0000.0000.0000.000
13A338MET00.138-0.0768.166-0.294-0.2940.0000.0000.0000.000
14A338MET0-0.1130.0928.4910.2570.2570.0000.0000.0000.000
15A339GLN00.119-0.0598.514-0.162-0.1620.0000.0000.0000.000
16A339GLN0-0.1080.0686.9380.4790.4790.0000.0000.0000.000
17A340ASN00.122-0.06710.118-0.076-0.0760.0000.0000.0000.000
18A340ASN0-0.1410.04710.9300.0000.0000.0000.0000.0000.000
19A341LEU00.077-0.09512.172-0.097-0.0970.0000.0000.0000.000
20A341LEU0-0.0880.09812.8470.0050.0050.0000.0000.0000.000
21A342GLU00.068-0.11213.165-0.076-0.0760.0000.0000.0000.000
22A342GLU-1-0.970-0.85111.5911.0911.0910.0000.0000.0000.000
23A343ILE00.096-0.06414.181-0.017-0.0170.0000.0000.0000.000
24A343ILE0-0.0980.08412.873-0.011-0.0110.0000.0000.0000.000
25A344GLU00.116-0.09416.014-0.020-0.0200.0000.0000.0000.000
26A344GLU-1-0.900-0.78417.2680.0680.0680.0000.0000.0000.000
27A345LEU00.099-0.10717.757-0.044-0.0440.0000.0000.0000.000
28A345LEU0-0.1080.10218.4030.0100.0100.0000.0000.0000.000
29A346GLN00.025-0.12719.155-0.014-0.0140.0000.0000.0000.000
30A346GLN0-0.0820.07818.103-0.023-0.0230.0000.0000.0000.000
31A347SER0-0.021-0.07320.575-0.014-0.0140.0000.0000.0000.000
32A347SER0-0.0100.05020.375-0.002-0.0020.0000.0000.0000.000
33A348GLN00.114-0.07422.365-0.019-0.0190.0000.0000.0000.000
34A348GLN0-0.1190.07622.3930.0020.0020.0000.0000.0000.000
35A349LEU00.033-0.12023.629-0.018-0.0180.0000.0000.0000.000
36A349LEU0-0.0740.10622.4670.0020.0020.0000.0000.0000.000
37A350SER00.051-0.08624.938-0.004-0.0040.0000.0000.0000.000
38A350SER0-0.0560.05124.324-0.003-0.0030.0000.0000.0000.000
39A351MET00.090-0.08426.597-0.008-0.0080.0000.0000.0000.000
40A351MET0-0.1130.09826.429-0.003-0.0030.0000.0000.0000.000
41A352LYS00.128-0.06528.129-0.014-0.0140.0000.0000.0000.000
42A352LYS10.7220.99628.401-0.136-0.1360.0000.0000.0000.000
43A353ALA00.129-0.09929.417-0.008-0.0080.0000.0000.0000.000
44A353ALA0-0.0710.11229.8460.0020.0020.0000.0000.0000.000
45A354SER0-0.004-0.08630.955-0.003-0.0030.0000.0000.0000.000
46A354SER0-0.0650.05231.317-0.006-0.0060.0000.0000.0000.000
47A355LEU00.059-0.11432.670-0.008-0.0080.0000.0000.0000.000
48A355LEU0-0.0870.10231.7130.0000.0000.0000.0000.0000.000
49A356GLU00.096-0.10934.102-0.008-0.0080.0000.0000.0000.000
50A356GLU-1-0.880-0.78232.8720.1240.1240.0000.0000.0000.000
51A357ASN00.080-0.06835.526-0.003-0.0030.0000.0000.0000.000
52A357ASN0-0.1550.04034.579-0.003-0.0030.0000.0000.0000.000
53A358SER00.068-0.07637.070-0.003-0.0030.0000.0000.0000.000
54A358SER0-0.0050.09437.810-0.002-0.0020.0000.0000.0000.000
55A359LEU00.097-0.08838.568-0.007-0.0070.0000.0000.0000.000
56A359LEU0-0.1140.10439.0660.0010.0010.0000.0000.0000.000
57A360GLU00.049-0.12540.045-0.004-0.0040.0000.0000.0000.000
58A360GLU-1-0.879-0.77640.3040.0720.0720.0000.0000.0000.000
59A361GLU00.105-0.08741.433-0.002-0.0020.0000.0000.0000.000
60A361GLU-1-0.924-0.79541.5530.0360.0360.0000.0000.0000.000
61A362THR00.024-0.11042.821-0.003-0.0030.0000.0000.0000.000
62A362THR0-0.0840.05542.447-0.002-0.0020.0000.0000.0000.000
63A363LYS00.030-0.11044.433-0.004-0.0040.0000.0000.0000.000
64A363LYS10.7240.98742.158-0.068-0.0680.0000.0000.0000.000
65A364GLY00.031-0.09145.976-0.002-0.0020.0000.0000.0000.000
66A365ARG00.1340.04447.240-0.002-0.0020.0000.0000.0000.000
67A365ARG10.7170.98244.208-0.033-0.0330.0000.0000.0000.000
68A366TYR00.065-0.11848.907-0.002-0.0020.0000.0000.0000.000
69A366TYR0-0.0780.08947.2620.0000.0000.0000.0000.0000.000
70A367CYS00.160-0.09150.423-0.003-0.0030.0000.0000.0000.000
71A367CYS0-0.1280.10150.7850.0010.0010.0000.0000.0000.000
72A368MET00.057-0.10351.881-0.001-0.0010.0000.0000.0000.000
73A368MET0-0.0890.09151.3350.0010.0010.0000.0000.0000.000
74A369GLN00.115-0.06653.245-0.001-0.0010.0000.0000.0000.000
75A369GLN0-0.0990.06551.7600.0010.0010.0000.0000.0000.000
76A370LEU00.117-0.09254.825-0.002-0.0020.0000.0000.0000.000
77A370LEU0-0.1200.09755.4830.0000.0000.0000.0000.0000.000
78A371ALA00.098-0.10156.376-0.002-0.0020.0000.0000.0000.000
79A371ALA0-0.0780.10856.8780.0000.0000.0000.0000.0000.000
80A372GLN00.124-0.06357.8930.0000.0000.0000.0000.0000.000
81A372GLN0-0.1070.06455.9400.0010.0010.0000.0000.0000.000
82A373ILE00.051-0.09759.511-0.001-0.0010.0000.0000.0000.000
83A373ILE0-0.1030.08359.0660.0000.0000.0000.0000.0000.000
84A374GLN00.096-0.08460.914-0.002-0.0020.0000.0000.0000.000
85A374GLN0-0.0970.06660.073-0.001-0.0010.0000.0000.0000.000
86A375GLU00.140-0.07662.347-0.001-0.0010.0000.0000.0000.000
87A375GLU-1-1.038-0.85162.2530.0260.0260.0000.0000.0000.000
88A376MET00.084-0.09664.0160.0000.0000.0000.0000.0000.000
89A376MET0-0.1180.06962.829-0.001-0.0010.0000.0000.0000.000
90A377ILE00.045-0.09065.483-0.001-0.0010.0000.0000.0000.000
91A377ILE0-0.1100.08864.0990.0000.0000.0000.0000.0000.000
92A378GLY00.066-0.08466.849-0.001-0.0010.0000.0000.0000.000
93A379SER00.0630.01968.3850.0000.0000.0000.0000.0000.000
94A379SER0-0.0570.05367.8310.0000.0000.0000.0000.0000.000
95A380VAL00.086-0.07970.132-0.001-0.0010.0000.0000.0000.000
96A380VAL0-0.1250.08570.1970.0000.0000.0000.0000.0000.000
97A381GLU00.037-0.13971.390-0.001-0.0010.0000.0000.0000.000
98A381GLU-1-1.003-0.85069.7190.0220.0220.0000.0000.0000.000
99A382GLU00.078-0.12372.846-0.001-0.0010.0000.0000.0000.000
100A382GLU-1-0.993-0.82872.3700.0220.0220.0000.0000.0000.000
101A383GLN00.090-0.09874.4120.0000.0000.0000.0000.0000.000
102A383GLN0-0.1170.08774.5010.0000.0000.0000.0000.0000.000
103A384LEU00.070-0.11575.912-0.001-0.0010.0000.0000.0000.000
104A384LEU0-0.1370.08476.2290.0000.0000.0000.0000.0000.000
105A385ALA00.074-0.12577.180-0.001-0.0010.0000.0000.0000.000
106A385ALA0-0.0720.11377.3090.0000.0000.0000.0000.0000.000
107A386GLN00.095-0.09578.8260.0000.0000.0000.0000.0000.000
108A386GLN0-0.1390.06879.4180.0010.0010.0000.0000.0000.000
109A387LEU00.142-0.08580.5300.0000.0000.0000.0000.0000.000
110A387LEU0-0.1110.09880.9740.0000.0000.0000.0000.0000.000
111A388ARG00.045-0.11781.728-0.001-0.0010.0000.0000.0000.000
112A388ARG10.8601.05879.104-0.015-0.0150.0000.0000.0000.000
113A389CYS00.138-0.10883.2280.0000.0000.0000.0000.0000.000
114A389CYS0-0.1220.11683.4930.0000.0000.0000.0000.0000.000
115A390GLU00.050-0.13284.9480.0000.0000.0000.0000.0000.000
116A390GLU-1-0.947-0.79784.2030.0140.0140.0000.0000.0000.000
117A391MET00.068-0.09886.3360.0000.0000.0000.0000.0000.000
118A391MET0-0.1340.06385.3620.0000.0000.0000.0000.0000.000
119A392GLU00.093-0.08387.736-0.001-0.0010.0000.0000.0000.000
120A392GLU-1-0.910-0.79288.1700.0130.0130.0000.0000.0000.000
121A393GLN00.078-0.11489.3170.0000.0000.0000.0000.0000.000
122A393GLN0-0.1620.06289.5800.0000.0000.0000.0000.0000.000
123A394GLN00.167-0.07290.9450.0000.0000.0000.0000.0000.000
124A394GLN0-0.1480.08091.4710.0000.0000.0000.0000.0000.000
125A395ASN00.066-0.11692.198-0.001-0.0010.0000.0000.0000.000
126A395ASN0-0.1520.04990.4750.0000.0000.0000.0000.0000.000
127A396GLN00.091-0.10093.907-0.001-0.0010.0000.0000.0000.000
128A396GLN0-0.1310.07592.1440.0000.0000.0000.0000.0000.000
129A397GLU00.037-0.14095.3990.0000.0000.0000.0000.0000.000
130A397GLU-1-0.903-0.79193.4210.0120.0120.0000.0000.0000.000
131A398TYR00.123-0.08696.7280.0000.0000.0000.0000.0000.000
132A398TYR0-0.1030.09796.9700.0000.0000.0000.0000.0000.000
133A399LYS00.093-0.11098.2140.0000.0000.0000.0000.0000.000
134A399LYS10.6900.98598.360-0.010-0.0100.0000.0000.0000.000
135A400ILE00.074-0.10299.9610.0000.0000.0000.0000.0000.000
136A400ILE0-0.0830.10798.8530.0000.0000.0000.0000.0000.000
137A401LEU00.091-0.111101.3990.0000.0000.0000.0000.0000.000
138A401LEU0-0.0910.110101.5650.0000.0000.0000.0000.0000.000
139A402LEU00.092-0.109102.6330.0000.0000.0000.0000.0000.000
140A402LEU0-0.0900.109102.2980.0000.0000.0000.0000.0000.000
141A403ASP00.115-0.099104.3780.0000.0000.0000.0000.0000.000
142A403ASP-1-0.892-0.772104.2190.0100.0100.0000.0000.0000.000
143A404VAL00.046-0.108106.1500.0000.0000.0000.0000.0000.000
144A404VAL0-0.0880.095106.3370.0000.0000.0000.0000.0000.000
145A405LYS00.113-0.084107.1400.0000.0000.0000.0000.0000.000
146A405LYS10.7320.990106.952-0.007-0.0070.0000.0000.0000.000
147A406THR0-0.010-0.117108.4630.0000.0000.0000.0000.0000.000
148A406THR0-0.0710.060107.8060.0000.0000.0000.0000.0000.000
149A407ARG00.135-0.078110.2430.0000.0000.0000.0000.0000.000
150A407ARG10.8131.042110.026-0.009-0.0090.0000.0000.0000.000
151A408LEU00.059-0.107111.9820.0000.0000.0000.0000.0000.000
152A408LEU0-0.0860.107110.7580.0000.0000.0000.0000.0000.000
153A409GLU00.101-0.105113.1200.0000.0000.0000.0000.0000.000
154A409GLU-1-0.879-0.780111.1960.0070.0070.0000.0000.0000.000
155A410GLN00.051-0.117114.7840.0000.0000.0000.0000.0000.000
156A410GLN0-0.0810.099114.2790.0000.0000.0000.0000.0000.000
157A411GLU00.101-0.095116.4800.0000.0000.0000.0000.0000.000
158A411GLU-1-0.936-0.798115.5180.0080.0080.0000.0000.0000.000
159A412ILE00.115-0.069117.7090.0000.0000.0000.0000.0000.000
160A412ILE0-0.0940.089115.8720.0000.0000.0000.0000.0000.000
161A413ALA00.087-0.120118.9580.0000.0000.0000.0000.0000.000
162A413ALA0-0.0800.111119.1480.0000.0000.0000.0000.0000.000
163A414THR0-0.052-0.123120.7890.0000.0000.0000.0000.0000.000
164A414THR0-0.0890.041120.8310.0000.0000.0000.0000.0000.000
165A415TYR00.082-0.088122.4060.0000.0000.0000.0000.0000.000
166A415TYR0-0.0720.095119.9950.0000.0000.0000.0000.0000.000
167A416ARG00.105-0.064123.4360.0000.0000.0000.0000.0000.000
168A416ARG10.8791.049119.112-0.006-0.0060.0000.0000.0000.000
169A417ARG00.160-0.061124.9450.0000.0000.0000.0000.0000.000
170A417ARG10.7781.032125.254-0.007-0.0070.0000.0000.0000.000
171A418LEU00.038-0.112126.8570.0000.0000.0000.0000.0000.000
172A418LEU0-0.1210.079126.3320.0000.0000.0000.0000.0000.000
173A419LEU00.039-0.085128.4390.0000.0000.0000.0000.0000.000
174A419LEU0-0.0870.080126.7830.0000.0000.0000.0000.0000.000
175A420GLU00.039-0.114130.2200.0000.0000.0000.0000.0000.000
176A420GLU-1-1.004-0.847129.6810.0050.0050.0000.0000.0000.000
177A421GLY0-0.068-0.130132.0980.0000.0000.0000.0000.0000.000