Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3Q3RL

Calculation Name: 2XDN-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XDN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9AIU0

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2307844.148643
FMO2-HF: Nuclear repulsion 2225741.477564
FMO2-HF: Total energy -82102.671079
FMO2-MP2: Total energy -82341.203226


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:4:ACE )


Summations of interaction energy for fragment #1(A:4:ACE )
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.
-0.9232.4762.21-3.193-2.417-0.02
Interaction energy analysis for fragmet #1(A:4:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / 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].
3A6LYS 10.8760.9493.6390.8002.062-0.004-0.626-0.633-0.001
4A7GLU -1-0.900-0.9665.715-0.209-0.2090.0000.0000.0000.000
5A8GLU -1-0.870-0.9202.531-0.8871.1962.214-2.551-1.746-0.019
6A9ALA 00.0090.0024.377-0.0130.0410.000-0.016-0.0380.000
7A10GLN 00.0110.0116.189-0.097-0.0970.0000.0000.0000.000
8A11GLU -1-0.868-0.9498.197-0.075-0.0750.0000.0000.0000.000
9A12THR 0-0.045-0.0306.4880.0230.0230.0000.0000.0000.000
10A13ARG 10.9931.0069.320-0.219-0.2190.0000.0000.0000.000
11A14ALA 00.0070.00611.890-0.031-0.0310.0000.0000.0000.000
12A15GLN 00.0210.01611.822-0.039-0.0390.0000.0000.0000.000
13A16ILE 0-0.023-0.00411.924-0.014-0.0140.0000.0000.0000.000
14A17ILE 00.012-0.00415.223-0.030-0.0300.0000.0000.0000.000
15A18GLU -1-0.944-0.95817.1890.0690.0690.0000.0000.0000.000
16A19ALA 00.004-0.00717.829-0.013-0.0130.0000.0000.0000.000
17A20ALA 00.003-0.01419.421-0.009-0.0090.0000.0000.0000.000
18A21GLU -1-0.773-0.86421.1590.0610.0610.0000.0000.0000.000
19A22ARG 10.9030.94317.674-0.148-0.1480.0000.0000.0000.000
20A23ALA 00.000-0.00223.247-0.008-0.0080.0000.0000.0000.000
21A24PHE 00.014-0.00823.526-0.008-0.0080.0000.0000.0000.000
22A25TYR 00.0430.03426.887-0.007-0.0070.0000.0000.0000.000
23A26LYS 10.9120.96728.097-0.072-0.0720.0000.0000.0000.000
24A27ARG 10.7750.87426.305-0.114-0.1140.0000.0000.0000.000
25A28GLY 00.0090.03730.037-0.003-0.0030.0000.0000.0000.000
26A29VAL 00.025-0.00727.2040.0070.0070.0000.0000.0000.000
27A30ALA 00.0020.00528.4070.0070.0070.0000.0000.0000.000
28A31ARG 10.9700.97230.344-0.064-0.0640.0000.0000.0000.000
29A32THR 0-0.0310.01024.1550.0040.0040.0000.0000.0000.000
30A33THR 0-0.033-0.01823.0360.0020.0020.0000.0000.0000.000
31A34LEU 00.1140.03818.6070.0040.0040.0000.0000.0000.000
32A35ALA 00.025-0.00119.4430.0140.0140.0000.0000.0000.000
33A36ASP -1-0.808-0.90120.2220.1410.1410.0000.0000.0000.000
34A37ILE 0-0.022-0.00317.898-0.004-0.0040.0000.0000.0000.000
35A38ALA 0-0.0020.00615.6820.0090.0090.0000.0000.0000.000
36A39GLU -1-0.765-0.85816.3300.2480.2480.0000.0000.0000.000
37A40LEU 0-0.099-0.03218.748-0.011-0.0110.0000.0000.0000.000
38A41ALA 0-0.036-0.02614.601-0.014-0.0140.0000.0000.0000.000
39A42GLY 0-0.0100.01714.3510.0160.0160.0000.0000.0000.000
40A43VAL 0-0.018-0.00910.8180.0630.0630.0000.0000.0000.000
41A44THR 0-0.032-0.01610.3520.0100.0100.0000.0000.0000.000
42A45ARG 10.8830.87912.505-0.201-0.2010.0000.0000.0000.000
43A46GLY 0-0.009-0.01713.568-0.001-0.0010.0000.0000.0000.000
44A47ALA 00.0190.0229.826-0.004-0.0040.0000.0000.0000.000
45A48ILE 0-0.008-0.00411.071-0.016-0.0160.0000.0000.0000.000
46A49TYR 0-0.011-0.01813.875-0.035-0.0350.0000.0000.0000.000
47A50TRP 0-0.052-0.0029.3470.0040.0040.0000.0000.0000.000
48A51HIS 0-0.071-0.0317.908-0.160-0.1600.0000.0000.0000.000
49A52PHE 0-0.021-0.01912.863-0.048-0.0480.0000.0000.0000.000
50A53ASN 00.0400.03216.6350.0270.0270.0000.0000.0000.000
51A54ASN 0-0.017-0.01119.1600.0020.0020.0000.0000.0000.000
52A55LYS 10.8610.93020.944-0.099-0.0990.0000.0000.0000.000
53A56ALA 00.0270.01223.194-0.002-0.0020.0000.0000.0000.000
54A57GLU -1-0.805-0.88719.0740.1400.1400.0000.0000.0000.000
55A58LEU 0-0.040-0.02718.292-0.002-0.0020.0000.0000.0000.000
56A59VAL 0-0.052-0.03320.912-0.006-0.0060.0000.0000.0000.000
57A60GLN 0-0.004-0.01723.638-0.008-0.0080.0000.0000.0000.000
58A61ALA 00.0000.01419.521-0.006-0.0060.0000.0000.0000.000
59A62LEU 0-0.036-0.02621.543-0.008-0.0080.0000.0000.0000.000
60A63LEU 0-0.007-0.00123.448-0.008-0.0080.0000.0000.0000.000
61A64ASP -1-0.837-0.91923.0540.0480.0480.0000.0000.0000.000
62A65SER 0-0.067-0.03921.982-0.008-0.0080.0000.0000.0000.000
63A66LEU 0-0.027-0.01423.710-0.006-0.0060.0000.0000.0000.000
64A67ALA 0-0.015-0.00926.856-0.005-0.0050.0000.0000.0000.000
65A68GLU -1-0.954-0.97621.2950.0200.0200.0000.0000.0000.000
66A69THR 0-0.042-0.02725.948-0.007-0.0070.0000.0000.0000.000
67A70HIS 0-0.024-0.01828.315-0.007-0.0070.0000.0000.0000.000
68A71ASP -1-0.852-0.89928.384-0.008-0.0080.0000.0000.0000.000
69A72HIS 00.0380.01930.479-0.002-0.0020.0000.0000.0000.000
70A73LEU 00.001-0.00732.6070.0000.0000.0000.0000.0000.000
71A74ALA 00.0120.00533.2970.0000.0000.0000.0000.0000.000
72A75ARG 10.8460.91830.8340.0010.0010.0000.0000.0000.000
73A76ALA 00.0030.00734.902-0.001-0.0010.0000.0000.0000.000
74A77SER 0-0.095-0.06637.8690.0010.0010.0000.0000.0000.000
75A78GLU -1-0.859-0.94935.7890.0050.0050.0000.0000.0000.000
76A79SER 0-0.0120.01138.5310.0000.0000.0000.0000.0000.000
77A80GLU -1-0.918-0.98340.201-0.006-0.0060.0000.0000.0000.000
78A81ASP -1-0.892-0.94441.924-0.013-0.0130.0000.0000.0000.000
79A82GLU -1-0.871-0.92041.376-0.011-0.0110.0000.0000.0000.000
80A83VAL 0-0.0070.01843.3070.0010.0010.0000.0000.0000.000
81A84ASP -1-0.855-0.93444.955-0.004-0.0040.0000.0000.0000.000
82A85PRO 00.0330.04243.1350.0000.0000.0000.0000.0000.000
83A86LEU 00.016-0.01643.2520.0010.0010.0000.0000.0000.000
84A87GLY 00.0490.02945.0300.0010.0010.0000.0000.0000.000
85A88CYS 0-0.132-0.06139.5270.0000.0000.0000.0000.0000.000
86A89MET 00.0600.03340.1890.0010.0010.0000.0000.0000.000
87A90ARG 10.8350.90541.0160.0000.0000.0000.0000.0000.000
88A91LYS 10.8990.93939.6510.0070.0070.0000.0000.0000.000
89A92LEU 00.0040.02335.7750.0000.0000.0000.0000.0000.000
90A93LEU 00.006-0.00437.2980.0020.0020.0000.0000.0000.000
91A94LEU 00.0250.00939.0940.0010.0010.0000.0000.0000.000
92A95GLN 0-0.039-0.00632.806-0.001-0.0010.0000.0000.0000.000
93A96VAL 00.0170.00534.2840.0020.0020.0000.0000.0000.000
94A97PHE 00.001-0.01435.3650.0030.0030.0000.0000.0000.000
95A98ASN 0-0.002-0.01236.4240.0020.0020.0000.0000.0000.000
96A99GLU -1-0.815-0.90928.8050.0170.0170.0000.0000.0000.000
97A100LEU 0-0.0080.00532.5030.0030.0030.0000.0000.0000.000
98A101VAL 0-0.023-0.01234.0490.0030.0030.0000.0000.0000.000
99A102LEU 0-0.069-0.03633.4510.0000.0000.0000.0000.0000.000
100A103ASP -1-0.814-0.89527.6600.0260.0260.0000.0000.0000.000
101A104ALA 0-0.044-0.02628.0020.0040.0040.0000.0000.0000.000
102A105ARG 10.8800.94519.229-0.057-0.0570.0000.0000.0000.000
103A106THR 00.0700.02026.4960.0060.0060.0000.0000.0000.000
104A107ARG 10.9381.00028.853-0.026-0.0260.0000.0000.0000.000
105A108ARG 10.8330.89725.008-0.060-0.0600.0000.0000.0000.000
106A109ILE 00.0180.01024.2580.0050.0050.0000.0000.0000.000
107A110ASN 0-0.021-0.01928.2330.0000.0000.0000.0000.0000.000
108A111GLU -1-0.804-0.90831.8080.0430.0430.0000.0000.0000.000
109A112ILE 0-0.109-0.05626.4200.0020.0020.0000.0000.0000.000
110A113LEU 0-0.039-0.02927.8590.0010.0010.0000.0000.0000.000
111A114HIS 0-0.053-0.03031.4900.0010.0010.0000.0000.0000.000
112A115HIS 0-0.081-0.04034.535-0.002-0.0020.0000.0000.0000.000
113A116LYS 10.8120.90631.350-0.054-0.0540.0000.0000.0000.000
114A117CYS 0-0.029-0.00730.3250.0070.0070.0000.0000.0000.000
115A118GLU -1-0.923-0.95032.0730.0540.0540.0000.0000.0000.000
116A119PHE 0-0.034-0.02733.0650.0030.0030.0000.0000.0000.000
117A120THR 00.0470.02333.275-0.002-0.0020.0000.0000.0000.000
118A121ASP -1-0.918-0.96334.7850.0470.0470.0000.0000.0000.000
119A122ASP -1-0.999-0.98932.7130.0760.0760.0000.0000.0000.000
120A123MET 0-0.003-0.00726.2860.0050.0050.0000.0000.0000.000
121A124CYS 00.0260.00131.3690.0000.0000.0000.0000.0000.000
122A125GLU -1-0.871-0.94826.1220.0870.0870.0000.0000.0000.000
123A126ILE 00.0060.01628.579-0.002-0.0020.0000.0000.0000.000
124A127ARG 10.9590.97630.365-0.042-0.0420.0000.0000.0000.000
125A128GLN 0-0.012-0.00431.750-0.002-0.0020.0000.0000.0000.000
126A129GLN 00.0500.02526.9420.0020.0020.0000.0000.0000.000
127A130ARG 10.9040.96029.760-0.058-0.0580.0000.0000.0000.000
128A131GLN 0-0.033-0.02632.584-0.003-0.0030.0000.0000.0000.000
129A132SER 00.0240.01231.343-0.004-0.0040.0000.0000.0000.000
130A133ALA 00.0660.05230.328-0.003-0.0030.0000.0000.0000.000
131A134VAL 0-0.032-0.02832.072-0.003-0.0030.0000.0000.0000.000
132A135LEU 0-0.036-0.02535.622-0.003-0.0030.0000.0000.0000.000
133A136ASP -1-0.903-0.94031.3010.0220.0220.0000.0000.0000.000
134A137CYS 0-0.024-0.03534.231-0.003-0.0030.0000.0000.0000.000
135A138HIS 0-0.0550.00235.493-0.002-0.0020.0000.0000.0000.000
136A139LYS 10.9580.97837.090-0.013-0.0130.0000.0000.0000.000
137A140GLY 00.0510.03436.859-0.002-0.0020.0000.0000.0000.000
138A141ILE 0-0.020-0.00937.743-0.002-0.0020.0000.0000.0000.000
139A142THR 0-0.020-0.02140.497-0.001-0.0010.0000.0000.0000.000
140A143LEU 0-0.0120.00539.292-0.001-0.0010.0000.0000.0000.000
141A144ALA 00.0640.03840.661-0.001-0.0010.0000.0000.0000.000
142A145LEU 0-0.036-0.01342.583-0.001-0.0010.0000.0000.0000.000
143A146ALA 0-0.002-0.00845.408-0.001-0.0010.0000.0000.0000.000
144A147ASN 0-0.071-0.04442.143-0.001-0.0010.0000.0000.0000.000
145A148ALA 00.0020.00646.333-0.001-0.0010.0000.0000.0000.000
146A149VAL 0-0.044-0.00248.1500.0000.0000.0000.0000.0000.000
147A150ARG 10.9180.97546.2820.0010.0010.0000.0000.0000.000
148A151ARG 10.7370.84046.2430.0060.0060.0000.0000.0000.000
149A152GLY 0-0.027-0.00551.2890.0000.0000.0000.0000.0000.000
150A153GLN 0-0.042-0.03948.1660.0000.0000.0000.0000.0000.000
151A154LEU 0-0.035-0.01548.2640.0010.0010.0000.0000.0000.000
152A155PRO 0-0.055-0.02352.4800.0000.0000.0000.0000.0000.000
153A156GLY 00.0430.01654.2610.0000.0000.0000.0000.0000.000
154A157GLU -1-0.911-0.95555.6180.0030.0030.0000.0000.0000.000
155A158LEU 0-0.056-0.02749.8260.0010.0010.0000.0000.0000.000
156A159ASP -1-0.859-0.92251.1750.0080.0080.0000.0000.0000.000
157A160ALA 0-0.003-0.01447.1410.0010.0010.0000.0000.0000.000
158A161GLU -1-0.861-0.93944.9160.0120.0120.0000.0000.0000.000
159A162ARG 10.8740.92346.415-0.008-0.0080.0000.0000.0000.000
160A163ALA 00.0100.00248.2760.0010.0010.0000.0000.0000.000
161A164ALA 00.0700.03243.0590.0000.0000.0000.0000.0000.000
162A165VAL 00.0030.01043.6490.0010.0010.0000.0000.0000.000
163A166ALA 0-0.039-0.02144.8910.0010.0010.0000.0000.0000.000
164A167MET 0-0.0100.00743.0590.0000.0000.0000.0000.0000.000
165A168PHE 00.0370.01236.8860.0010.0010.0000.0000.0000.000
166A169ALA 00.0080.00841.6460.0010.0010.0000.0000.0000.000
167A170TYR 0-0.058-0.03243.8730.0010.0010.0000.0000.0000.000
168A171VAL 00.0170.00539.1760.0000.0000.0000.0000.0000.000
169A172ASP -1-0.900-0.94038.0630.0290.0290.0000.0000.0000.000
170A173GLY 0-0.006-0.01640.1250.0010.0010.0000.0000.0000.000
171A174LEU 0-0.042-0.02142.8390.0010.0010.0000.0000.0000.000
172A175ILE 00.0280.01436.2380.0000.0000.0000.0000.0000.000
173A176ARG 10.9570.98838.575-0.032-0.0320.0000.0000.0000.000
174A177ARG 10.9190.95040.131-0.018-0.0180.0000.0000.0000.000
175A178TRP 0-0.0110.00435.9880.0010.0010.0000.0000.0000.000
176A179LEU 0-0.018-0.01434.9400.0000.0000.0000.0000.0000.000
177A180LEU 0-0.062-0.01038.8720.0020.0020.0000.0000.0000.000
178A181LEU 0-0.071-0.05041.5390.0000.0000.0000.0000.0000.000
179A182PRO 00.0920.06740.334-0.002-0.0020.0000.0000.0000.000
180A183ASP -1-0.928-0.96342.5750.0180.0180.0000.0000.0000.000
181A184SER 0-0.149-0.08845.652-0.001-0.0010.0000.0000.0000.000
182A185VAL 0-0.034-0.02544.419-0.001-0.0010.0000.0000.0000.000
183A186ASP -1-0.790-0.85144.3830.0100.0100.0000.0000.0000.000
184A187LEU 0-0.023-0.02639.466-0.001-0.0010.0000.0000.0000.000
185A188LEU 0-0.004-0.00638.867-0.001-0.0010.0000.0000.0000.000
186A189GLY 00.011-0.01641.970-0.002-0.0020.0000.0000.0000.000
187A190ASP -1-0.914-0.96445.3800.0060.0060.0000.0000.0000.000
188A191VAL 00.0040.00341.0700.0000.0000.0000.0000.0000.000
189A192GLU -1-0.940-0.96644.3570.0010.0010.0000.0000.0000.000
190A193LYS 10.9470.98946.722-0.005-0.0050.0000.0000.0000.000
191A194TRP 0-0.0140.01944.9640.0010.0010.0000.0000.0000.000
192A195VAL 00.006-0.00742.5610.0010.0010.0000.0000.0000.000
193A196ASP -1-0.817-0.91145.4710.0020.0020.0000.0000.0000.000
194A197THR 0-0.034-0.01449.0350.0000.0000.0000.0000.0000.000
195A198GLY 0-0.015-0.00847.2770.0000.0000.0000.0000.0000.000
196A199LEU 00.016-0.01045.1080.0000.0000.0000.0000.0000.000
197A200ASP -1-0.895-0.93848.7360.0040.0040.0000.0000.0000.000
198A201MET 0-0.079-0.03148.2350.0000.0000.0000.0000.0000.000
199A202LEU 0-0.025-0.02946.3410.0000.0000.0000.0000.0000.000
200A203ARG 10.9430.95051.084-0.003-0.0030.0000.0000.0000.000
201A204LEU 0-0.035-0.01553.643-0.001-0.0010.0000.0000.0000.000
202A205SER 0-0.0060.01054.6250.0000.0000.0000.0000.0000.000
203A206PRO 0-0.004-0.01756.5730.0000.0000.0000.0000.0000.000
204A207ALA 00.0260.02756.5700.0000.0000.0000.0000.0000.000
205A208LEU 0-0.057-0.02551.0840.0000.0000.0000.0000.0000.000
206A209ARG 10.8500.92954.002-0.004-0.0040.0000.0000.0000.000
207A210LYS 00.0310.03953.2290.0010.0010.0000.0000.0000.000