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: 37MGL

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 OptH
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 -942624.517532
FMO2-HF: Nuclear repulsion 895423.859315
FMO2-HF: Total energy -47200.658217
FMO2-MP2: Total energy -47336.909875


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.
0.3172.5690.05-0.75-1.5510
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 : 0.168 / q_NPA : 0.005
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].
4A82ILE0-0.0730.1024.2280.1300.4480.001-0.144-0.1730.000
5A83ILE00.107-0.1103.812-0.3400.898-0.003-0.629-0.6070.001
6A83ILE00.0130.1484.600-0.196-0.130-0.001-0.013-0.0520.000
7A84SER00.001-0.0963.5801.8021.889-0.0020.042-0.1270.000
8A84SER0-0.0230.0792.8370.0890.3300.0580.089-0.387-0.001
9A85SER00.022-0.0844.0810.7630.968-0.002-0.066-0.1380.000
10A85SER0-0.0530.0803.8840.7390.836-0.001-0.029-0.0670.000
11A86VAL00.065-0.1075.4540.6270.6270.0000.0000.0000.000
12A86VAL0-0.0560.1037.5470.0560.0560.0000.0000.0000.000
13A87LEU00.077-0.1148.0850.4770.4770.0000.0000.0000.000
14A87LEU0-0.0640.1137.890-0.005-0.0050.0000.0000.0000.000
15A88GLU00.039-0.1318.4430.1770.1770.0000.0000.0000.000
16A88GLU-1-1.002-0.8586.740-0.990-0.9900.0000.0000.0000.000
17A89GLU00.056-0.1179.9490.1610.1610.0000.0000.0000.000
18A89GLU-1-0.923-0.82011.802-0.183-0.1830.0000.0000.0000.000
19A90VAL00.018-0.12212.2880.1460.1460.0000.0000.0000.000
20A90VAL0-0.0650.10612.900-0.007-0.0070.0000.0000.0000.000
21A91LYS00.180-0.07113.0410.0990.0990.0000.0000.0000.000
22A91LYS10.8181.05310.5011.1541.1540.0000.0000.0000.000
23A92ARG00.054-0.10114.1790.0460.0460.0000.0000.0000.000
24A92ARG10.7951.03210.8070.2510.2510.0000.0000.0000.000
25A93ARG00.106-0.07816.0380.0600.0600.0000.0000.0000.000
26A93ARG10.8121.06017.6240.2660.2660.0000.0000.0000.000
27A94LEU00.009-0.13717.7450.0600.0600.0000.0000.0000.000
28A94LEU0-0.0690.09716.931-0.010-0.0100.0000.0000.0000.000
29A95GLU00.075-0.09318.8800.0100.0100.0000.0000.0000.000
30A95GLU-1-1.049-0.87318.738-0.268-0.2680.0000.0000.0000.000
31A96THR0-0.056-0.10720.4800.0180.0180.0000.0000.0000.000
32A96THR0-0.0650.04221.9820.0110.0110.0000.0000.0000.000
33A97MET00.130-0.06622.6590.0340.0340.0000.0000.0000.000
34A97MET0-0.1400.10521.052-0.013-0.0130.0000.0000.0000.000
35A98SER00.026-0.06324.218-0.005-0.0050.0000.0000.0000.000
36A98SER0-0.0240.05828.972-0.002-0.0020.0000.0000.0000.000
37A99GLU00.135-0.09326.994-0.022-0.0220.0000.0000.0000.000
38A99GLU-1-0.997-0.85929.166-0.203-0.2030.0000.0000.0000.000
39A100ASP00.086-0.11828.936-0.019-0.0190.0000.0000.0000.000
40A100ASP-1-0.921-0.81231.498-0.159-0.1590.0000.0000.0000.000
41A101GLU00.107-0.10327.0010.0000.0000.0000.0000.0000.000
42A101GLU-1-0.975-0.84325.096-0.211-0.2110.0000.0000.0000.000
43A102TYR00.122-0.09824.505-0.011-0.0110.0000.0000.0000.000
44A102TYR0-0.0900.06521.208-0.017-0.0170.0000.0000.0000.000
45A103PHE00.064-0.10125.429-0.030-0.0300.0000.0000.0000.000
46A103PHE0-0.0620.10829.0290.0010.0010.0000.0000.0000.000
47A104GLU00.067-0.11628.033-0.004-0.0040.0000.0000.0000.000
48A104GLU-1-0.944-0.82427.514-0.187-0.1870.0000.0000.0000.000
49A105SER00.024-0.06423.2210.0080.0080.0000.0000.0000.000
50A105SER0-0.0520.04521.350-0.011-0.0110.0000.0000.0000.000
51A106VAL00.025-0.09324.398-0.020-0.0200.0000.0000.0000.000
52A106VAL0-0.0550.09324.7330.0010.0010.0000.0000.0000.000
53A107LYS00.072-0.11725.607-0.014-0.0140.0000.0000.0000.000
54A107LYS10.7341.02029.2270.1870.1870.0000.0000.0000.000
55A108ALA00.107-0.11826.0520.0120.0120.0000.0000.0000.000
56A108ALA0-0.0770.12725.1590.0000.0000.0000.0000.0000.000
57A109LEU00.056-0.12822.9110.0180.0180.0000.0000.0000.000
58A109LEU0-0.1030.11120.170-0.011-0.0110.0000.0000.0000.000
59A110LEU00.089-0.11124.183-0.019-0.0190.0000.0000.0000.000
60A110LEU0-0.0800.10227.0140.0030.0030.0000.0000.0000.000
61A111LYS00.061-0.06827.0380.0040.0040.0000.0000.0000.000
62A111LYS10.7771.03429.0280.2090.2090.0000.0000.0000.000
63A112GLU00.090-0.11125.5200.0240.0240.0000.0000.0000.000
64A112GLU-1-0.919-0.80322.650-0.368-0.3680.0000.0000.0000.000
65A113ALA00.104-0.08825.5660.0140.0140.0000.0000.0000.000
66A113ALA0-0.0770.10324.526-0.006-0.0060.0000.0000.0000.000
67A114ILE00.102-0.07826.2980.0040.0040.0000.0000.0000.000
68A114ILE0-0.1070.07129.2770.0020.0020.0000.0000.0000.000
69A115LYS00.035-0.09829.8100.0120.0120.0000.0000.0000.000
70A115LYS10.8291.03030.1650.1920.1920.0000.0000.0000.000
71A116GLU00.049-0.10327.7590.0240.0240.0000.0000.0000.000
72A116GLU-1-0.997-0.86325.280-0.300-0.3000.0000.0000.0000.000
73A117LEU00.034-0.12729.2680.0090.0090.0000.0000.0000.000
74A117LEU0-0.1040.08827.8870.0010.0010.0000.0000.0000.000
75A118ASN00.031-0.06630.4770.0090.0090.0000.0000.0000.000
76A118ASN0-0.1320.05733.5660.0040.0040.0000.0000.0000.000
77A119GLU00.059-0.14233.6940.0150.0150.0000.0000.0000.000
78A119GLU-1-0.919-0.81933.159-0.197-0.1970.0000.0000.0000.000
79A120LYS00.033-0.11835.266-0.007-0.0070.0000.0000.0000.000
80A120LYS10.8491.05638.5960.1460.1460.0000.0000.0000.000
81A121LYS00.062-0.09136.3830.0030.0030.0000.0000.0000.000
82A121LYS10.8171.04337.0650.1610.1610.0000.0000.0000.000
83A122VAL00.028-0.09731.7900.0020.0020.0000.0000.0000.000
84A122VAL0-0.0350.10130.763-0.001-0.0010.0000.0000.0000.000
85A123ARG00.143-0.09130.8090.0140.0140.0000.0000.0000.000
86A123ARG10.7671.04529.6460.2560.2560.0000.0000.0000.000
87A124VAL00.047-0.11627.365-0.016-0.0160.0000.0000.0000.000
88A124VAL0-0.1050.09126.4500.0010.0010.0000.0000.0000.000
89A125MET00.098-0.11824.8480.0270.0270.0000.0000.0000.000
90A125MET0-0.0850.13624.1520.0010.0010.0000.0000.0000.000
91A126SER00.008-0.09022.259-0.029-0.0290.0000.0000.0000.000
92A126SER0-0.0200.03722.3130.0010.0010.0000.0000.0000.000
93A127ASN00.116-0.02222.0440.0150.0150.0000.0000.0000.000
94A127ASN0-0.0710.07520.0870.0530.0530.0000.0000.0000.000
95A128GLU00.170-0.12623.0070.0170.0170.0000.0000.0000.000
96A128GLU-1-1.037-0.84526.258-0.289-0.2890.0000.0000.0000.000
97A129LYS00.099-0.10125.4420.0280.0280.0000.0000.0000.000
98A129LYS10.8501.07324.8550.2570.2570.0000.0000.0000.000
99A130THR0-0.022-0.11124.7550.0340.0340.0000.0000.0000.000
100A130THR0-0.0450.09123.397-0.005-0.0050.0000.0000.0000.000
101A131LEU00.060-0.10126.0620.0180.0180.0000.0000.0000.000
102A131LEU0-0.0500.13326.4480.0030.0030.0000.0000.0000.000
103A132GLY00.016-0.09728.4970.0210.0210.0000.0000.0000.000
104A133LEU00.041-0.02929.4770.0240.0240.0000.0000.0000.000
105A133LEU0-0.0700.10927.314-0.002-0.0020.0000.0000.0000.000
106A134ILE00.116-0.07229.9570.0200.0200.0000.0000.0000.000
107A134ILE0-0.0790.08327.315-0.002-0.0020.0000.0000.0000.000
108A135ALA00.083-0.12831.3550.0120.0120.0000.0000.0000.000
109A135ALA0-0.1040.11333.4890.0000.0000.0000.0000.0000.000
110A136SER0-0.016-0.10133.9850.0130.0130.0000.0000.0000.000
111A136SER0-0.0490.06634.1430.0040.0040.0000.0000.0000.000
112A137ARG0-0.021-0.11734.3580.0160.0160.0000.0000.0000.000
113A137ARG10.7741.03032.4310.1840.1840.0000.0000.0000.000
114A138ILE00.150-0.09935.281-0.003-0.0030.0000.0000.0000.000
115A138ILE0-0.0620.12934.8530.0010.0010.0000.0000.0000.000
116A139GLU00.071-0.13536.263-0.003-0.0030.0000.0000.0000.000
117A139GLU-1-0.936-0.82140.082-0.133-0.1330.0000.0000.0000.000
118A140GLU00.094-0.10136.2330.0080.0080.0000.0000.0000.000
119A140GLU-1-0.898-0.79934.294-0.172-0.1720.0000.0000.0000.000
120A141ILE00.021-0.10933.9960.0040.0040.0000.0000.0000.000
121A141ILE0-0.0680.08631.577-0.004-0.0040.0000.0000.0000.000
122A142LYS00.054-0.10934.807-0.004-0.0040.0000.0000.0000.000
123A142LYS10.8321.04937.7960.1440.1440.0000.0000.0000.000
124A143SER00.014-0.09537.8840.0040.0040.0000.0000.0000.000
125A143SER0-0.0540.07938.7480.0040.0040.0000.0000.0000.000
126A144GLU00.001-0.09535.3320.0100.0100.0000.0000.0000.000
127A144GLU-1-0.950-0.86833.574-0.176-0.1760.0000.0000.0000.000
128A145LEU0-0.007-0.14534.961-0.001-0.0010.0000.0000.0000.000
129A145LEU0-0.1090.08532.434-0.003-0.0030.0000.0000.0000.000
130A146GLY00.065-0.07336.408-0.005-0.0050.0000.0000.0000.000
131A147ASP00.139-0.00238.8900.0030.0030.0000.0000.0000.000
132A147ASP-1-1.038-0.86738.671-0.135-0.1350.0000.0000.0000.000
133A148VAL0-0.043-0.11435.5580.0050.0050.0000.0000.0000.000
134A148VAL0-0.0600.09733.661-0.003-0.0030.0000.0000.0000.000
135A149SER00.046-0.10037.0560.0030.0030.0000.0000.0000.000
136A149SER0-0.0470.07338.3910.0040.0040.0000.0000.0000.000
137A150ILE00.070-0.09133.634-0.003-0.0030.0000.0000.0000.000
138A150ILE0-0.0930.08131.867-0.001-0.0010.0000.0000.0000.000
139A151GLU00.069-0.12733.5930.0110.0110.0000.0000.0000.000
140A151GLU-1-0.997-0.82534.158-0.201-0.2010.0000.0000.0000.000
141A152LEU0-0.002-0.15330.873-0.016-0.0160.0000.0000.0000.000
142A152LEU0-0.0670.11730.4540.0000.0000.0000.0000.0000.000
143A153GLY00.040-0.08429.1700.0140.0140.0000.0000.0000.000
144A154GLU00.014-0.04527.6880.0110.0110.0000.0000.0000.000
145A154GLU-1-0.943-0.82526.117-0.332-0.3320.0000.0000.0000.000
146A155THR00.059-0.06225.432-0.018-0.0180.0000.0000.0000.000
147A155THR0-0.0520.04425.2030.0020.0020.0000.0000.0000.000
148A156VAL0-0.060-0.11821.3480.0170.0170.0000.0000.0000.000
149A156VAL0-0.0600.09120.373-0.010-0.0100.0000.0000.0000.000
150A157ASP00.090-0.12518.3780.0480.0480.0000.0000.0000.000
151A157ASP-1-1.028-0.85016.131-0.874-0.8740.0000.0000.0000.000
152A158THR00.084-0.08316.334-0.091-0.0910.0000.0000.0000.000
153A158THR0-0.1010.04516.2410.0300.0300.0000.0000.0000.000
154A159MET00.127-0.09615.4360.1130.1130.0000.0000.0000.000
155A159MET0-0.1380.10411.7920.0120.0120.0000.0000.0000.000
156A160GLY0-0.049-0.13416.7060.0870.0870.0000.0000.0000.000
157A161GLY00.0260.03118.190-0.067-0.0670.0000.0000.0000.000
158A162VAL00.003-0.00420.4520.0090.0090.0000.0000.0000.000
159A162VAL0-0.0090.10223.3380.0080.0080.0000.0000.0000.000
160A163ILE00.110-0.08321.507-0.028-0.0280.0000.0000.0000.000
161A163ILE0-0.1050.10119.582-0.001-0.0010.0000.0000.0000.000
162A164VAL00.094-0.10722.8330.0190.0190.0000.0000.0000.000
163A164VAL0-0.0790.11225.2410.0030.0030.0000.0000.0000.000
164A165GLU00.068-0.09626.003-0.015-0.0150.0000.0000.0000.000
165A165GLU-1-0.932-0.81526.777-0.330-0.3300.0000.0000.0000.000
166A166THR00.093-0.06428.1710.0110.0110.0000.0000.0000.000
167A166THR0-0.0790.04430.977-0.005-0.0050.0000.0000.0000.000
168A167GLU00.159-0.08531.621-0.014-0.0140.0000.0000.0000.000
169A167GLU-1-0.978-0.83435.668-0.174-0.1740.0000.0000.0000.000
170A168ASP0-0.013-0.11934.142-0.003-0.0030.0000.0000.0000.000
171A168ASP-1-0.881-0.81433.698-0.211-0.2110.0000.0000.0000.000
172A169GLY00.022-0.08930.1050.0020.0020.0000.0000.0000.000
173A170ARG00.0910.00229.325-0.018-0.0180.0000.0000.0000.000
174A170ARG10.7361.00831.4530.2090.2090.0000.0000.0000.000
175A171ILE00.033-0.12527.853-0.011-0.0110.0000.0000.0000.000
176A171ILE0-0.0800.10127.2280.0030.0030.0000.0000.0000.000
177A172ARG00.189-0.07924.7470.0160.0160.0000.0000.0000.000
178A172ARG10.8501.09420.0880.5050.5050.0000.0000.0000.000
179A173ILE00.012-0.12822.817-0.019-0.0190.0000.0000.0000.000
180A173ILE0-0.0770.12822.5610.0000.0000.0000.0000.0000.000
181A174ASP00.113-0.12418.8680.0310.0310.0000.0000.0000.000
182A174ASP-1-0.933-0.78717.169-0.796-0.7960.0000.0000.0000.000
183A175ASN00.070-0.07718.755-0.049-0.0490.0000.0000.0000.000
184A175ASN0-0.1260.04320.458-0.029-0.0290.0000.0000.0000.000
185A176THR00.096-0.08316.9580.0700.0700.0000.0000.0000.000
186A176THR0-0.0190.07416.104-0.060-0.0600.0000.0000.0000.000
187A177PHE00.035-0.09915.210-0.009-0.0090.0000.0000.0000.000
188A177PHE0-0.0520.09214.5640.0140.0140.0000.0000.0000.000
189A178GLU0-0.011-0.13411.355-0.054-0.0540.0000.0000.0000.000
190A178GLU-1-0.754-0.74311.416-1.090-1.0900.0000.0000.0000.000
191A179ALA00.184-0.07711.260-0.263-0.2630.0000.0000.0000.000
192A179ALA0-0.0790.12715.1080.0340.0340.0000.0000.0000.000
193A180ARG00.048-0.10313.607-0.009-0.0090.0000.0000.0000.000
194A180ARG10.7521.00115.5130.5280.5280.0000.0000.0000.000
195A181MET00.096-0.08910.7150.1880.1880.0000.0000.0000.000
196A181MET0-0.1160.0869.2140.0600.0600.0000.0000.0000.000
197A182GLU00.033-0.1529.503-0.034-0.0340.0000.0000.0000.000
198A182GLU-1-1.025-0.8528.741-1.752-1.7520.0000.0000.0000.000
199A183ARG00.061-0.08310.4860.0850.0850.0000.0000.0000.000
200A183ARG10.8081.03415.0620.6620.6620.0000.0000.0000.000
201A184PHE0-0.004-0.09913.0850.1310.1310.0000.0000.0000.000
202A184PHE0-0.0770.10213.7500.0140.0140.0000.0000.0000.000
203A185GLU00.125-0.1239.7510.1420.1420.0000.0000.0000.000
204A185GLU-1-0.975-0.8197.705-0.738-0.7380.0000.0000.0000.000
205A186GLY00.033-0.10210.5650.2210.2210.0000.0000.0000.000
206A187GLU00.058-0.07713.0310.1540.1540.0000.0000.0000.000
207A187GLU-1-0.958-0.79114.628-0.292-0.2920.0000.0000.0000.000
208A188ILE00.036-0.12010.3030.1390.1390.0000.0000.0000.000
209A188ILE0-0.0410.1298.7870.0270.0270.0000.0000.0000.000
210A189ARG00.062-0.11610.7700.2220.2220.0000.0000.0000.000
211A189ARG10.8901.0825.158-0.593-0.5930.0000.0000.0000.000
212A190SER00.033-0.09311.3930.1360.1360.0000.0000.0000.000
213A190SER0-0.0500.08315.655-0.003-0.0030.0000.0000.0000.000
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