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: J2VK9

Calculation Name: 2DM9-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DM9

Chain ID: A

ChEMBL ID:

UniProt ID: O57724

Base Structure: X-ray

Registration Date: 2025-07-08

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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -946905.242581
FMO2-HF: Nuclear repulsion 899703.070355
FMO2-HF: Total energy -47202.172226
FMO2-MP2: Total energy -47338.545784


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:81:GLU)


Summations of interaction energy for fragment #1(A:81:GLU)
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.
0.0631.9020.046-0.469-1.4140
Interaction energy analysis for fragmet #1(A:81:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.175 / q_NPA : 0.036
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].
4A82ILE0-0.1070.0934.045-0.0110.3100.001-0.148-0.1740.000
5A83ILE00.116-0.0983.8720.1231.1310.002-0.519-0.4900.001
6A83ILE0-0.0420.1234.656-0.086-0.025-0.001-0.008-0.0520.000
7A84SER0-0.010-0.0903.9921.5511.678-0.002-0.019-0.1070.000
8A84SER0-0.0420.0582.901-1.292-1.2000.0500.266-0.408-0.001
9A85SER00.071-0.0704.5870.4710.612-0.002-0.029-0.1100.000
10A85SER0-0.0740.0554.7280.7670.813-0.001-0.006-0.0380.000
11A86VAL00.056-0.1066.1260.3540.3540.0000.0000.0000.000
12A86VAL0-0.0590.0977.7180.0260.0260.0000.0000.0000.000
13A87LEU00.080-0.0978.4530.3270.3270.0000.0000.0000.000
14A87LEU0-0.0870.1018.155-0.014-0.0140.0000.0000.0000.000
15A88GLU00.055-0.1709.154-0.027-0.0270.0000.0000.0000.000
16A88GLU-1-0.909-0.7977.7630.3240.3240.0000.0000.0000.000
17A89GLU00.052-0.07010.6990.0540.0540.0000.0000.0000.000
18A89GLU-1-0.893-0.78812.2470.1600.1600.0000.0000.0000.000
19A90VAL00.044-0.11612.9740.0800.0800.0000.0000.0000.000
20A90VAL0-0.0800.09613.178-0.013-0.0130.0000.0000.0000.000
21A91LYS00.169-0.05713.6390.0380.0380.0000.0000.0000.000
22A91LYS10.7921.01411.1040.6950.6950.0000.0000.0000.000
23A92ARG00.070-0.10414.8240.0040.0040.0000.0000.0000.000
24A92ARG10.7070.95810.878-0.166-0.1660.0000.0000.0000.000
25A93ARG00.124-0.05916.7300.0330.0330.0000.0000.0000.000
26A93ARG10.7320.98318.4830.1170.1170.0000.0000.0000.000
27A94LEU00.044-0.12018.2930.0370.0370.0000.0000.0000.000
28A94LEU0-0.0850.08417.160-0.011-0.0110.0000.0000.0000.000
29A95GLU00.085-0.10519.196-0.006-0.0060.0000.0000.0000.000
30A95GLU-1-1.051-0.86418.991-0.080-0.0800.0000.0000.0000.000
31A96THR0-0.094-0.12920.8450.0120.0120.0000.0000.0000.000
32A96THR0-0.0690.05221.8190.0080.0080.0000.0000.0000.000
33A97MET00.159-0.05622.8380.0240.0240.0000.0000.0000.000
34A97MET0-0.1800.09421.298-0.015-0.0150.0000.0000.0000.000
35A98SER00.004-0.07724.388-0.005-0.0050.0000.0000.0000.000
36A98SER0-0.0230.07528.3370.0020.0020.0000.0000.0000.000
37A99GLU00.113-0.09127.299-0.015-0.0150.0000.0000.0000.000
38A99GLU-1-0.877-0.78829.529-0.136-0.1360.0000.0000.0000.000
39A100ASP00.078-0.08728.954-0.019-0.0190.0000.0000.0000.000
40A100ASP-1-0.905-0.81531.831-0.102-0.1020.0000.0000.0000.000
41A101GLU00.095-0.10827.212-0.006-0.0060.0000.0000.0000.000
42A101GLU-1-0.883-0.79924.617-0.108-0.1080.0000.0000.0000.000
43A102TYR00.139-0.09524.664-0.010-0.0100.0000.0000.0000.000
44A102TYR0-0.0990.06821.591-0.012-0.0120.0000.0000.0000.000
45A103PHE00.054-0.09425.599-0.026-0.0260.0000.0000.0000.000
46A103PHE0-0.0710.10928.9680.0000.0000.0000.0000.0000.000
47A104GLU00.088-0.11428.333-0.010-0.0100.0000.0000.0000.000
48A104GLU-1-0.918-0.80028.074-0.129-0.1290.0000.0000.0000.000
49A105SER00.019-0.07323.4740.0020.0020.0000.0000.0000.000
50A105SER00.0080.07222.267-0.011-0.0110.0000.0000.0000.000
51A106VAL0-0.009-0.10624.463-0.026-0.0260.0000.0000.0000.000
52A106VAL0-0.0590.09624.7770.0000.0000.0000.0000.0000.000
53A107LYS00.067-0.12725.863-0.015-0.0150.0000.0000.0000.000
54A107LYS10.6900.97629.4370.1320.1320.0000.0000.0000.000
55A108ALA00.101-0.09826.3280.0080.0080.0000.0000.0000.000
56A108ALA0-0.0720.10925.4750.0010.0010.0000.0000.0000.000
57A109LEU00.065-0.11723.2070.0100.0100.0000.0000.0000.000
58A109LEU0-0.1070.10320.590-0.008-0.0080.0000.0000.0000.000
59A110LEU00.091-0.09824.364-0.025-0.0250.0000.0000.0000.000
60A110LEU0-0.0760.09227.1170.0030.0030.0000.0000.0000.000
61A111LYS00.067-0.07227.333-0.004-0.0040.0000.0000.0000.000
62A111LYS10.7200.99729.6310.1640.1640.0000.0000.0000.000
63A112GLU00.078-0.09025.5300.0210.0210.0000.0000.0000.000
64A112GLU-1-0.897-0.77322.705-0.338-0.3380.0000.0000.0000.000
65A113ALA00.142-0.09225.6030.0130.0130.0000.0000.0000.000
66A113ALA0-0.0800.10824.555-0.005-0.0050.0000.0000.0000.000
67A114ILE00.105-0.08726.3990.0000.0000.0000.0000.0000.000
68A114ILE0-0.0970.08929.2770.0020.0020.0000.0000.0000.000
69A115LYS00.033-0.09429.9440.0100.0100.0000.0000.0000.000
70A115LYS10.8401.04130.3380.1530.1530.0000.0000.0000.000
71A116GLU00.052-0.09727.9160.0210.0210.0000.0000.0000.000
72A116GLU-1-1.001-0.86625.239-0.280-0.2800.0000.0000.0000.000
73A117LEU00.052-0.11529.3270.0050.0050.0000.0000.0000.000
74A117LEU0-0.0870.09527.6310.0010.0010.0000.0000.0000.000
75A118ASN00.050-0.06030.5180.0070.0070.0000.0000.0000.000
76A118ASN0-0.1190.05233.7390.0070.0070.0000.0000.0000.000
77A119GLU00.089-0.14733.6570.0160.0160.0000.0000.0000.000
78A119GLU-1-0.863-0.76433.893-0.187-0.1870.0000.0000.0000.000
79A120LYS00.011-0.10335.046-0.008-0.0080.0000.0000.0000.000
80A120LYS10.7711.03537.5700.1390.1390.0000.0000.0000.000
81A121LYS00.077-0.10736.3910.0060.0060.0000.0000.0000.000
82A121LYS10.7210.96037.4070.1460.1460.0000.0000.0000.000
83A122VAL00.011-0.09231.9720.0000.0000.0000.0000.0000.000
84A122VAL0-0.0410.09930.931-0.001-0.0010.0000.0000.0000.000
85A123ARG00.125-0.07830.9160.0150.0150.0000.0000.0000.000
86A123ARG10.6810.96429.6330.2270.2270.0000.0000.0000.000
87A124VAL00.046-0.10527.365-0.016-0.0160.0000.0000.0000.000
88A124VAL0-0.0970.08126.4990.0010.0010.0000.0000.0000.000
89A125MET00.084-0.09925.2500.0270.0270.0000.0000.0000.000
90A125MET0-0.0660.12424.454-0.001-0.0010.0000.0000.0000.000
91A126SER00.025-0.08222.253-0.032-0.0320.0000.0000.0000.000
92A126SER0-0.0350.02922.3430.0040.0040.0000.0000.0000.000
93A127ASN00.109-0.02622.2980.0120.0120.0000.0000.0000.000
94A127ASN0-0.0970.06020.6050.0400.0400.0000.0000.0000.000
95A128GLU00.188-0.12623.3570.0110.0110.0000.0000.0000.000
96A128GLU-1-1.045-0.83927.009-0.214-0.2140.0000.0000.0000.000
97A129LYS00.076-0.09625.9740.0180.0180.0000.0000.0000.000
98A129LYS10.7921.02825.4640.1660.1660.0000.0000.0000.000
99A130THR0-0.012-0.11225.1700.0280.0280.0000.0000.0000.000
100A130THR0-0.0090.10323.3430.0040.0040.0000.0000.0000.000
101A131LEU00.078-0.07626.4270.0150.0150.0000.0000.0000.000
102A131LEU0-0.0560.12826.7890.0030.0030.0000.0000.0000.000
103A132GLY00.026-0.10528.9800.0160.0160.0000.0000.0000.000
104A133LEU00.0360.00029.8490.0200.0200.0000.0000.0000.000
105A133LEU0-0.1000.09127.805-0.001-0.0010.0000.0000.0000.000
106A134ILE00.159-0.06730.2720.0170.0170.0000.0000.0000.000
107A134ILE0-0.0950.08527.638-0.002-0.0020.0000.0000.0000.000
108A135ALA00.082-0.11731.7240.0090.0090.0000.0000.0000.000
109A135ALA0-0.1040.09234.0880.0000.0000.0000.0000.0000.000
110A136SER0-0.021-0.11034.2980.0090.0090.0000.0000.0000.000
111A136SER0-0.0680.04334.4370.0030.0030.0000.0000.0000.000
112A137ARG0-0.047-0.10334.7250.0120.0120.0000.0000.0000.000
113A137ARG10.7230.96432.7350.1250.1250.0000.0000.0000.000
114A138ILE00.170-0.08935.405-0.001-0.0010.0000.0000.0000.000
115A138ILE0-0.0770.12734.8370.0000.0000.0000.0000.0000.000
116A139GLU00.063-0.13336.392-0.003-0.0030.0000.0000.0000.000
117A139GLU-1-0.853-0.77940.293-0.110-0.1100.0000.0000.0000.000
118A140GLU00.069-0.06936.2260.0060.0060.0000.0000.0000.000
119A140GLU-1-0.854-0.79734.297-0.125-0.1250.0000.0000.0000.000
120A141ILE00.058-0.09033.9590.0040.0040.0000.0000.0000.000
121A141ILE0-0.0870.07931.846-0.003-0.0030.0000.0000.0000.000
122A142LYS00.075-0.09734.764-0.002-0.0020.0000.0000.0000.000
123A142LYS10.7580.99137.6530.1180.1180.0000.0000.0000.000
124A143SER00.001-0.11237.9340.0020.0020.0000.0000.0000.000
125A143SER0-0.0660.05838.6700.0040.0040.0000.0000.0000.000
126A144GLU0-0.011-0.10235.4740.0090.0090.0000.0000.0000.000
127A144GLU-1-0.897-0.81833.588-0.132-0.1320.0000.0000.0000.000
128A145LEU00.024-0.13535.0750.0000.0000.0000.0000.0000.000
129A145LEU0-0.0960.08432.950-0.002-0.0020.0000.0000.0000.000
130A146GLY00.044-0.07736.523-0.005-0.0050.0000.0000.0000.000
131A147ASP00.0550.00539.0390.0020.0020.0000.0000.0000.000
132A147ASP-1-0.992-0.88038.389-0.117-0.1170.0000.0000.0000.000
133A148VAL00.026-0.10435.6290.0020.0020.0000.0000.0000.000
134A148VAL0-0.0850.10433.715-0.002-0.0020.0000.0000.0000.000
135A149SER00.079-0.09937.1060.0030.0030.0000.0000.0000.000
136A149SER0-0.0540.06638.3540.0030.0030.0000.0000.0000.000
137A150ILE00.062-0.08433.852-0.005-0.0050.0000.0000.0000.000
138A150ILE0-0.1010.07831.893-0.001-0.0010.0000.0000.0000.000
139A151GLU00.092-0.11533.9330.0110.0110.0000.0000.0000.000
140A151GLU-1-0.921-0.78833.764-0.189-0.1890.0000.0000.0000.000
141A152LEU0-0.015-0.14231.177-0.016-0.0160.0000.0000.0000.000
142A152LEU0-0.0710.09931.1560.0010.0010.0000.0000.0000.000
143A153GLY00.036-0.09229.3890.0110.0110.0000.0000.0000.000
144A154GLU00.029-0.04227.6460.0150.0150.0000.0000.0000.000
145A154GLU-1-0.937-0.81726.008-0.304-0.3040.0000.0000.0000.000
146A155THR00.051-0.07125.786-0.015-0.0150.0000.0000.0000.000
147A155THR0-0.0460.05525.7320.0020.0020.0000.0000.0000.000
148A156VAL0-0.077-0.13121.8110.0120.0120.0000.0000.0000.000
149A156VAL0-0.0590.09620.860-0.008-0.0080.0000.0000.0000.000
150A157ASP00.142-0.12018.5590.0400.0400.0000.0000.0000.000
151A157ASP-1-1.009-0.83516.893-0.650-0.6500.0000.0000.0000.000
152A158THR00.012-0.12416.500-0.075-0.0750.0000.0000.0000.000
153A158THR0-0.0800.05716.6460.0280.0280.0000.0000.0000.000
154A159MET00.133-0.07615.9320.0980.0980.0000.0000.0000.000
155A159MET0-0.1700.10912.2870.0250.0250.0000.0000.0000.000
156A160GLY0-0.049-0.13717.2200.0760.0760.0000.0000.0000.000
157A161GLY00.0430.02918.449-0.060-0.0600.0000.0000.0000.000
158A162VAL00.024-0.01520.7810.0060.0060.0000.0000.0000.000
159A162VAL0-0.0320.11023.6660.0060.0060.0000.0000.0000.000
160A163ILE00.097-0.10221.901-0.023-0.0230.0000.0000.0000.000
161A163ILE0-0.0840.11320.351-0.002-0.0020.0000.0000.0000.000
162A164VAL00.042-0.10722.8150.0240.0240.0000.0000.0000.000
163A164VAL0-0.0570.09824.9350.0040.0040.0000.0000.0000.000
164A165GLU00.077-0.09425.831-0.018-0.0180.0000.0000.0000.000
165A165GLU-1-0.909-0.80526.730-0.302-0.3020.0000.0000.0000.000
166A166THR00.088-0.06928.2030.0140.0140.0000.0000.0000.000
167A166THR0-0.1110.03830.800-0.005-0.0050.0000.0000.0000.000
168A167GLU00.176-0.05631.786-0.012-0.0120.0000.0000.0000.000
169A167GLU-1-0.905-0.79335.888-0.151-0.1510.0000.0000.0000.000
170A168ASP00.013-0.10434.342-0.001-0.0010.0000.0000.0000.000
171A168ASP-1-0.834-0.76133.597-0.201-0.2010.0000.0000.0000.000
172A169GLY00.025-0.09329.9420.0000.0000.0000.0000.0000.000
173A170ARG00.075-0.01129.134-0.020-0.0200.0000.0000.0000.000
174A170ARG10.6430.93732.0220.1980.1980.0000.0000.0000.000
175A171ILE00.033-0.12327.945-0.010-0.0100.0000.0000.0000.000
176A171ILE0-0.0910.08827.6570.0030.0030.0000.0000.0000.000
177A172ARG00.164-0.06724.9510.0200.0200.0000.0000.0000.000
178A172ARG10.7941.03620.0290.4740.4740.0000.0000.0000.000
179A173ILE00.009-0.12022.622-0.018-0.0180.0000.0000.0000.000
180A173ILE0-0.0610.12222.3520.0000.0000.0000.0000.0000.000
181A174ASP00.088-0.09019.0360.0320.0320.0000.0000.0000.000
182A174ASP-1-0.894-0.79018.117-0.628-0.6280.0000.0000.0000.000
183A175ASN00.097-0.07018.609-0.060-0.0600.0000.0000.0000.000
184A175ASN0-0.1160.04020.476-0.030-0.0300.0000.0000.0000.000
185A176THR00.099-0.07717.1570.0700.0700.0000.0000.0000.000
186A176THR0-0.0250.08316.458-0.050-0.0500.0000.0000.0000.000
187A177PHE00.052-0.09415.412-0.029-0.0290.0000.0000.0000.000
188A177PHE0-0.0700.08714.8020.0120.0120.0000.0000.0000.000
189A178GLU00.029-0.11611.578-0.059-0.0590.0000.0000.0000.000
190A178GLU-1-0.817-0.76511.924-0.835-0.8350.0000.0000.0000.000
191A179ALA00.209-0.06211.579-0.207-0.2070.0000.0000.0000.000
192A179ALA0-0.0630.11515.0650.0260.0260.0000.0000.0000.000
193A180ARG00.067-0.10313.7880.0050.0050.0000.0000.0000.000
194A180ARG10.7000.95215.5480.4370.4370.0000.0000.0000.000
195A181MET00.083-0.10110.5620.1510.1510.0000.0000.0000.000
196A181MET0-0.1290.1039.1340.0620.0620.0000.0000.0000.000
197A182GLU00.046-0.1479.456-0.022-0.0220.0000.0000.0000.000
198A182GLU-1-0.989-0.8468.672-1.756-1.7560.0000.0000.0000.000
199A183ARG00.014-0.08610.4210.0450.0450.0000.0000.0000.000
200A183ARG10.7701.00114.7530.6280.6280.0000.0000.0000.000
201A184PHE00.049-0.09512.8760.1020.1020.0000.0000.0000.000
202A184PHE0-0.0810.10513.7160.0110.0110.0000.0000.0000.000
203A185GLU00.099-0.1109.2960.2200.2200.0000.0000.0000.000
204A185GLU-1-0.884-0.7667.227-0.973-0.9730.0000.0000.0000.000
205A186GLY00.078-0.08310.1660.2150.2150.0000.0000.0000.000
206A187GLU00.067-0.04012.4030.1480.1480.0000.0000.0000.000
207A187GLU-1-0.930-0.79914.324-0.240-0.2400.0000.0000.0000.000
208A188ILE00.025-0.10410.0770.1430.1430.0000.0000.0000.000
209A188ILE0-0.0540.1268.9340.0240.0240.0000.0000.0000.000
210A189ARG00.089-0.09510.0460.2430.2430.0000.0000.0000.000
211A189ARG10.7460.9844.5050.4250.468-0.001-0.006-0.0350.000
212A190SER00.045-0.10910.5830.1360.1360.0000.0000.0000.000
213A190SER0-0.0450.06314.693-0.003-0.0030.0000.0000.0000.000
214A191THR0-0.055-0.11413.4740.0140.0140.0000.0000.0000.000
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