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: N2L6Q

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 OptHSide
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 -944221.774785
FMO2-HF: Nuclear repulsion 897019.462265
FMO2-HF: Total energy -47202.31252
FMO2-MP2: Total energy -47338.61221


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.
0.2161.2690.0550.465-1.5730
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 : 0.152 / q_NPA : 0.019
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].
4A82ILE0-0.0950.0924.1490.0780.3940.000-0.143-0.1730.000
5A83ILE00.110-0.1103.812-0.1331.066-0.002-0.601-0.5960.001
6A83ILE0-0.0350.1324.687-0.115-0.051-0.001-0.009-0.0530.000
7A84SER00.037-0.1023.6371.8801.988-0.0020.021-0.1270.000
8A84SER0-0.0030.0952.807-1.382-2.2830.0631.275-0.437-0.001
9A85SER00.013-0.0854.1660.7260.915-0.002-0.060-0.1280.000
10A85SER0-0.0490.0774.0780.8930.971-0.001-0.018-0.0590.000
11A86VAL00.055-0.1115.5400.5480.5480.0000.0000.0000.000
12A86VAL0-0.0680.1077.6200.0460.0460.0000.0000.0000.000
13A87LEU00.096-0.1088.1250.4290.4290.0000.0000.0000.000
14A87LEU0-0.0710.1047.880-0.011-0.0110.0000.0000.0000.000
15A88GLU00.014-0.1858.4860.1060.1060.0000.0000.0000.000
16A88GLU-1-0.925-0.8166.931-0.270-0.2700.0000.0000.0000.000
17A89GLU00.046-0.0819.9880.1240.1240.0000.0000.0000.000
18A89GLU-1-0.887-0.79011.760-0.064-0.0640.0000.0000.0000.000
19A90VAL00.020-0.11912.3400.1220.1220.0000.0000.0000.000
20A90VAL0-0.0780.10212.922-0.010-0.0100.0000.0000.0000.000
21A91LYS00.192-0.05413.0690.0800.0800.0000.0000.0000.000
22A91LYS10.7931.03610.6030.9930.9930.0000.0000.0000.000
23A92ARG00.072-0.09914.2260.0270.0270.0000.0000.0000.000
24A92ARG10.7240.98710.4610.0970.0970.0000.0000.0000.000
25A93ARG00.096-0.07416.0890.0480.0480.0000.0000.0000.000
26A93ARG10.7731.00717.7420.2010.2010.0000.0000.0000.000
27A94LEU00.026-0.12717.7800.0510.0510.0000.0000.0000.000
28A94LEU0-0.0800.09116.865-0.011-0.0110.0000.0000.0000.000
29A95GLU00.072-0.10118.9250.0030.0030.0000.0000.0000.000
30A95GLU-1-1.039-0.86518.706-0.192-0.1920.0000.0000.0000.000
31A96THR0-0.060-0.11020.5060.0130.0130.0000.0000.0000.000
32A96THR0-0.0750.05021.9050.0080.0080.0000.0000.0000.000
33A97MET00.149-0.06922.6870.0310.0310.0000.0000.0000.000
34A97MET0-0.1640.09921.103-0.014-0.0140.0000.0000.0000.000
35A98SER00.011-0.08024.256-0.007-0.0070.0000.0000.0000.000
36A98SER0-0.0110.07928.2970.0030.0030.0000.0000.0000.000
37A99GLU00.142-0.08527.018-0.019-0.0190.0000.0000.0000.000
38A99GLU-1-0.893-0.77929.240-0.178-0.1780.0000.0000.0000.000
39A100ASP00.078-0.11028.969-0.018-0.0180.0000.0000.0000.000
40A100ASP-1-0.919-0.80631.544-0.136-0.1360.0000.0000.0000.000
41A101GLU00.116-0.10427.047-0.002-0.0020.0000.0000.0000.000
42A101GLU-1-0.933-0.82624.409-0.174-0.1740.0000.0000.0000.000
43A102TYR00.128-0.09024.579-0.009-0.0090.0000.0000.0000.000
44A102TYR0-0.0930.06921.274-0.014-0.0140.0000.0000.0000.000
45A103PHE00.068-0.09425.496-0.028-0.0280.0000.0000.0000.000
46A103PHE0-0.0680.10928.8960.0000.0000.0000.0000.0000.000
47A104GLU00.080-0.11428.111-0.006-0.0060.0000.0000.0000.000
48A104GLU-1-0.924-0.79727.840-0.162-0.1620.0000.0000.0000.000
49A105SER00.016-0.07823.2680.0070.0070.0000.0000.0000.000
50A105SER00.0050.07022.080-0.016-0.0160.0000.0000.0000.000
51A106VAL0-0.019-0.11224.477-0.021-0.0210.0000.0000.0000.000
52A106VAL0-0.0660.09724.7510.0000.0000.0000.0000.0000.000
53A107LYS00.081-0.11725.682-0.015-0.0150.0000.0000.0000.000
54A107LYS10.7050.97229.2070.1630.1630.0000.0000.0000.000
55A108ALA00.083-0.10126.1440.0090.0090.0000.0000.0000.000
56A108ALA0-0.0680.11525.2610.0000.0000.0000.0000.0000.000
57A109LEU00.064-0.12123.0170.0150.0150.0000.0000.0000.000
58A109LEU0-0.0950.10720.283-0.008-0.0080.0000.0000.0000.000
59A110LEU00.084-0.11124.268-0.020-0.0200.0000.0000.0000.000
60A110LEU0-0.0680.09726.9090.0030.0030.0000.0000.0000.000
61A111LYS00.068-0.06327.1190.0010.0010.0000.0000.0000.000
62A111LYS10.7211.00129.2360.1890.1890.0000.0000.0000.000
63A112GLU00.071-0.09725.6210.0210.0210.0000.0000.0000.000
64A112GLU-1-0.879-0.75822.813-0.357-0.3570.0000.0000.0000.000
65A113ALA00.124-0.08125.6150.0130.0130.0000.0000.0000.000
66A113ALA0-0.0780.09824.579-0.006-0.0060.0000.0000.0000.000
67A114ILE00.123-0.08926.3840.0020.0020.0000.0000.0000.000
68A114ILE0-0.1150.08129.2560.0020.0020.0000.0000.0000.000
69A115LYS00.035-0.09629.8970.0110.0110.0000.0000.0000.000
70A115LYS10.8321.03330.2610.1710.1710.0000.0000.0000.000
71A116GLU00.050-0.09827.8580.0230.0230.0000.0000.0000.000
72A116GLU-1-0.992-0.86025.236-0.288-0.2880.0000.0000.0000.000
73A117LEU00.029-0.12829.3560.0080.0080.0000.0000.0000.000
74A117LEU0-0.0910.08327.9470.0010.0010.0000.0000.0000.000
75A118ASN00.023-0.05730.5600.0080.0080.0000.0000.0000.000
76A118ASN0-0.1370.05333.6710.0060.0060.0000.0000.0000.000
77A119GLU00.046-0.14133.7630.0140.0140.0000.0000.0000.000
78A119GLU-1-0.864-0.78333.984-0.192-0.1920.0000.0000.0000.000
79A120LYS00.034-0.11035.346-0.006-0.0060.0000.0000.0000.000
80A120LYS10.8371.05738.1550.1450.1450.0000.0000.0000.000
81A121LYS00.101-0.08936.4540.0040.0040.0000.0000.0000.000
82A121LYS10.7130.96437.2070.1570.1570.0000.0000.0000.000
83A122VAL00.018-0.10831.8650.0010.0010.0000.0000.0000.000
84A122VAL0-0.0430.09930.834-0.001-0.0010.0000.0000.0000.000
85A123ARG00.140-0.08530.8830.0140.0140.0000.0000.0000.000
86A123ARG10.6830.98229.7290.2400.2400.0000.0000.0000.000
87A124VAL00.049-0.10427.428-0.016-0.0160.0000.0000.0000.000
88A124VAL0-0.1070.07526.5010.0010.0010.0000.0000.0000.000
89A125MET00.095-0.10425.0020.0260.0260.0000.0000.0000.000
90A125MET0-0.0670.13324.3090.0000.0000.0000.0000.0000.000
91A126SER00.012-0.09122.313-0.028-0.0280.0000.0000.0000.000
92A126SER0-0.0280.02922.3350.0010.0010.0000.0000.0000.000
93A127ASN00.129-0.02122.0570.0130.0130.0000.0000.0000.000
94A127ASN0-0.0760.07720.1050.0510.0510.0000.0000.0000.000
95A128GLU00.176-0.13323.0490.0160.0160.0000.0000.0000.000
96A128GLU-1-1.041-0.83926.352-0.267-0.2670.0000.0000.0000.000
97A129LYS00.081-0.09725.4830.0250.0250.0000.0000.0000.000
98A129LYS10.7891.02724.9110.2170.2170.0000.0000.0000.000
99A130THR0-0.004-0.12024.8140.0320.0320.0000.0000.0000.000
100A130THR0-0.0480.08623.482-0.003-0.0030.0000.0000.0000.000
101A131LEU00.055-0.10026.1160.0170.0170.0000.0000.0000.000
102A131LEU0-0.0490.13226.4390.0030.0030.0000.0000.0000.000
103A132GLY00.022-0.09828.5490.0190.0190.0000.0000.0000.000
104A133LEU00.064-0.00529.5270.0230.0230.0000.0000.0000.000
105A133LEU0-0.1150.09327.618-0.001-0.0010.0000.0000.0000.000
106A134ILE00.153-0.06830.0200.0190.0190.0000.0000.0000.000
107A134ILE0-0.0940.08427.309-0.002-0.0020.0000.0000.0000.000
108A135ALA00.061-0.11531.4180.0110.0110.0000.0000.0000.000
109A135ALA0-0.0940.09733.5830.0000.0000.0000.0000.0000.000
110A136SER0-0.016-0.10334.0350.0120.0120.0000.0000.0000.000
111A136SER0-0.0660.04434.1520.0030.0030.0000.0000.0000.000
112A137ARG0-0.046-0.10234.4260.0140.0140.0000.0000.0000.000
113A137ARG10.7270.97632.6610.1610.1610.0000.0000.0000.000
114A138ILE00.193-0.09535.349-0.002-0.0020.0000.0000.0000.000
115A138ILE0-0.0790.13034.7970.0000.0000.0000.0000.0000.000
116A139GLU00.065-0.13036.332-0.003-0.0030.0000.0000.0000.000
117A139GLU-1-0.869-0.78240.214-0.125-0.1250.0000.0000.0000.000
118A140GLU00.097-0.08336.3100.0070.0070.0000.0000.0000.000
119A140GLU-1-0.886-0.80134.150-0.154-0.1540.0000.0000.0000.000
120A141ILE00.036-0.10434.0140.0050.0050.0000.0000.0000.000
121A141ILE0-0.0820.08231.590-0.004-0.0040.0000.0000.0000.000
122A142LYS00.067-0.10434.885-0.003-0.0030.0000.0000.0000.000
123A142LYS10.7720.99937.7380.1330.1330.0000.0000.0000.000
124A143SER0-0.004-0.09837.9630.0030.0030.0000.0000.0000.000
125A143SER0-0.0680.06038.7830.0040.0040.0000.0000.0000.000
126A144GLU00.008-0.09835.4070.0090.0090.0000.0000.0000.000
127A144GLU-1-0.902-0.81933.487-0.159-0.1590.0000.0000.0000.000
128A145LEU00.020-0.12635.023-0.001-0.0010.0000.0000.0000.000
129A145LEU0-0.0980.08532.788-0.002-0.0020.0000.0000.0000.000
130A146GLY00.052-0.08336.493-0.005-0.0050.0000.0000.0000.000
131A147ASP00.1130.00738.9750.0030.0030.0000.0000.0000.000
132A147ASP-1-1.007-0.86938.674-0.126-0.1260.0000.0000.0000.000
133A148VAL0-0.029-0.10335.6350.0040.0040.0000.0000.0000.000
134A148VAL0-0.0760.09233.743-0.002-0.0020.0000.0000.0000.000
135A149SER00.056-0.10037.1350.0030.0030.0000.0000.0000.000
136A149SER0-0.0500.07038.4590.0040.0040.0000.0000.0000.000
137A150ILE00.072-0.08033.698-0.004-0.0040.0000.0000.0000.000
138A150ILE0-0.1010.07431.767-0.001-0.0010.0000.0000.0000.000
139A151GLU00.079-0.12133.6510.0120.0120.0000.0000.0000.000
140A151GLU-1-0.933-0.78933.926-0.200-0.2000.0000.0000.0000.000
141A152LEU00.012-0.13930.931-0.015-0.0150.0000.0000.0000.000
142A152LEU0-0.0540.10130.8200.0010.0010.0000.0000.0000.000
143A153GLY00.037-0.07929.2260.0130.0130.0000.0000.0000.000
144A154GLU00.010-0.04827.7500.0120.0120.0000.0000.0000.000
145A154GLU-1-0.931-0.81626.119-0.320-0.3200.0000.0000.0000.000
146A155THR00.044-0.06825.472-0.017-0.0170.0000.0000.0000.000
147A155THR0-0.0460.04825.1760.0020.0020.0000.0000.0000.000
148A156VAL0-0.064-0.10621.4320.0140.0140.0000.0000.0000.000
149A156VAL0-0.0690.08420.497-0.010-0.0100.0000.0000.0000.000
150A157ASP00.131-0.13018.4360.0470.0470.0000.0000.0000.000
151A157ASP-1-1.025-0.83516.578-0.768-0.7680.0000.0000.0000.000
152A158THR00.036-0.10216.375-0.096-0.0960.0000.0000.0000.000
153A158THR0-0.0770.05916.3260.0310.0310.0000.0000.0000.000
154A159MET00.137-0.07915.4520.1090.1090.0000.0000.0000.000
155A159MET0-0.1500.09611.9520.0140.0140.0000.0000.0000.000
156A160GLY0-0.061-0.14516.7520.0860.0860.0000.0000.0000.000
157A161GLY00.0270.02818.256-0.064-0.0640.0000.0000.0000.000
158A162VAL00.015-0.00120.5240.0080.0080.0000.0000.0000.000
159A162VAL0-0.0230.10423.5600.0070.0070.0000.0000.0000.000
160A163ILE00.083-0.09821.580-0.026-0.0260.0000.0000.0000.000
161A163ILE0-0.0850.10719.749-0.003-0.0030.0000.0000.0000.000
162A164VAL00.096-0.08822.9000.0180.0180.0000.0000.0000.000
163A164VAL0-0.0880.10025.2780.0030.0030.0000.0000.0000.000
164A165GLU00.078-0.10426.074-0.015-0.0150.0000.0000.0000.000
165A165GLU-1-0.917-0.80026.845-0.312-0.3120.0000.0000.0000.000
166A166THR00.092-0.05928.2380.0120.0120.0000.0000.0000.000
167A166THR0-0.1090.03030.946-0.005-0.0050.0000.0000.0000.000
168A167GLU00.177-0.06831.683-0.013-0.0130.0000.0000.0000.000
169A167GLU-1-0.922-0.79535.727-0.162-0.1620.0000.0000.0000.000
170A168ASP00.011-0.10734.199-0.003-0.0030.0000.0000.0000.000
171A168ASP-1-0.840-0.77733.669-0.207-0.2070.0000.0000.0000.000
172A169GLY00.017-0.08130.1620.0020.0020.0000.0000.0000.000
173A170ARG00.1020.01029.379-0.018-0.0180.0000.0000.0000.000
174A170ARG10.6410.93631.7990.2030.2030.0000.0000.0000.000
175A171ILE00.042-0.11827.907-0.012-0.0120.0000.0000.0000.000
176A171ILE0-0.0900.09127.4880.0030.0030.0000.0000.0000.000
177A172ARG00.177-0.07324.8760.0160.0160.0000.0000.0000.000
178A172ARG10.7951.04719.6590.5130.5130.0000.0000.0000.000
179A173ILE00.026-0.12522.888-0.020-0.0200.0000.0000.0000.000
180A173ILE0-0.0880.12022.6560.0000.0000.0000.0000.0000.000
181A174ASP00.101-0.09318.9880.0290.0290.0000.0000.0000.000
182A174ASP-1-0.905-0.78917.936-0.695-0.6950.0000.0000.0000.000
183A175ASN00.100-0.06318.835-0.050-0.0500.0000.0000.0000.000
184A175ASN0-0.1310.03420.513-0.029-0.0290.0000.0000.0000.000
185A176THR00.096-0.08717.0030.0690.0690.0000.0000.0000.000
186A176THR0-0.0180.08316.232-0.054-0.0540.0000.0000.0000.000
187A177PHE00.036-0.09215.287-0.011-0.0110.0000.0000.0000.000
188A177PHE0-0.0480.09314.5990.0070.0070.0000.0000.0000.000
189A178GLU00.003-0.13411.423-0.047-0.0470.0000.0000.0000.000
190A178GLU-1-0.768-0.75011.517-0.999-0.9990.0000.0000.0000.000
191A179ALA00.185-0.05211.340-0.240-0.2400.0000.0000.0000.000
192A179ALA0-0.0830.10315.1800.0310.0310.0000.0000.0000.000
193A180ARG00.054-0.11513.695-0.014-0.0140.0000.0000.0000.000
194A180ARG10.7140.94515.6370.4670.4670.0000.0000.0000.000
195A181MET00.084-0.09410.8020.1740.1740.0000.0000.0000.000
196A181MET0-0.1070.0939.3760.0610.0610.0000.0000.0000.000
197A182GLU00.023-0.1479.605-0.020-0.0200.0000.0000.0000.000
198A182GLU-1-1.006-0.8488.706-1.744-1.7440.0000.0000.0000.000
199A183ARG00.043-0.07710.5780.0700.0700.0000.0000.0000.000
200A183ARG10.7921.01114.9880.6300.6300.0000.0000.0000.000
201A184PHE00.002-0.09613.1940.1150.1150.0000.0000.0000.000
202A184PHE0-0.0790.09713.8770.0120.0120.0000.0000.0000.000
203A185GLU00.120-0.1179.7740.1530.1530.0000.0000.0000.000
204A185GLU-1-0.870-0.7497.725-0.623-0.6230.0000.0000.0000.000
205A186GLY00.050-0.10310.5870.2020.2020.0000.0000.0000.000
206A187GLU00.075-0.05213.0510.1450.1450.0000.0000.0000.000
207A187GLU-1-0.949-0.79414.661-0.258-0.2580.0000.0000.0000.000
208A188ILE00.026-0.12710.3430.1320.1320.0000.0000.0000.000
209A188ILE0-0.0510.1328.9430.0250.0250.0000.0000.0000.000
210A189ARG00.085-0.10610.7950.2160.2160.0000.0000.0000.000
211A189ARG10.7811.0095.298-0.147-0.1470.0000.0000.0000.000
212A190SER00.024-0.10011.4050.1260.1260.0000.0000.0000.000
213A190SER0-0.0610.06215.384-0.005-0.0050.0000.0000.0000.000
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