FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 2J7ZR

Calculation Name: 5D6H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D6H

Chain ID: A

ChEMBL ID:

UniProt ID: Q6XBY4

Base Structure: X-ray

Registration Date: 2023-06-21

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2656315.202256
FMO2-HF: Nuclear repulsion 2568085.278121
FMO2-HF: Total energy -88229.924135
FMO2-MP2: Total energy -88491.043101


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-14.066-8.767.385-5.275-7.415-0.043
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.003
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].
3A3PHE00.002-0.0062.3010.1430.8233.363-1.502-2.541-0.001
4A4LEU0-0.0050.0195.668-0.049-0.0490.0000.0000.0000.000
5A5ILE0-0.004-0.0138.6690.0480.0480.0000.0000.0000.000
6A6TRP0-0.0310.01411.1620.0150.0150.0000.0000.0000.000
7A7PRO00.0440.01214.8160.0150.0150.0000.0000.0000.000
8A8ILE00.0690.01413.043-0.022-0.0220.0000.0000.0000.000
9A9TYR0-0.025-0.02516.256-0.025-0.0250.0000.0000.0000.000
10A10PRO0-0.0030.02317.4910.0280.0280.0000.0000.0000.000
11A11LYS10.8850.91820.2710.0990.0990.0000.0000.0000.000
12A12ILE0-0.013-0.01622.9750.0060.0060.0000.0000.0000.000
13A13GLU-1-0.726-0.83025.901-0.093-0.0930.0000.0000.0000.000
14A14ALA00.0270.01129.4850.0010.0010.0000.0000.0000.000
15A15ASN0-0.050-0.02532.539-0.003-0.0030.0000.0000.0000.000
16A16GLU-1-0.860-0.90927.309-0.084-0.0840.0000.0000.0000.000
17A17LYS10.9430.94428.6950.0580.0580.0000.0000.0000.000
18A18ALA0-0.005-0.00723.871-0.006-0.0060.0000.0000.0000.000
19A19THR00.0360.04720.4600.0050.0050.0000.0000.0000.000
20A20ALA0-0.005-0.00918.350-0.001-0.0010.0000.0000.0000.000
21A21VAL0-0.0130.00113.236-0.008-0.0080.0000.0000.0000.000
22A22TRP0-0.009-0.01713.5500.0110.0110.0000.0000.0000.000
23A23LEU00.0070.0017.791-0.059-0.0590.0000.0000.0000.000
24A24GLN0-0.054-0.0368.9580.0170.0170.0000.0000.0000.000
25A25ASN00.0020.0114.734-0.0210.057-0.001-0.009-0.0670.000
26A26THR0-0.033-0.0196.0370.0460.0460.0000.0000.0000.000
27A27GLY00.0350.0254.363-0.0050.027-0.001-0.008-0.0220.000
28A28LYS10.9450.9535.424-1.261-1.2610.0000.0000.0000.000
29A29THR0-0.0020.0053.693-0.0250.1350.000-0.026-0.1350.000
30A30ASP-1-0.836-0.9024.9280.9600.994-0.001-0.002-0.0310.000
31A31ALA00.0340.0253.079-0.2890.1210.182-0.146-0.4460.000
32A32MET0-0.033-0.0204.7330.0630.064-0.001-0.0060.0060.000
33A33VAL00.0220.0185.524-0.276-0.2760.0000.0000.0000.000
34A34GLN00.0020.0017.9380.1870.1870.0000.0000.0000.000
35A35ILE0-0.033-0.01610.684-0.091-0.0910.0000.0000.0000.000
36A36ARG10.8990.93612.9240.4900.4900.0000.0000.0000.000
37A37VAL00.0080.00615.767-0.031-0.0310.0000.0000.0000.000
38A38PHE0-0.0100.00816.3280.0120.0120.0000.0000.0000.000
39A39LYS10.8450.90420.5560.1420.1420.0000.0000.0000.000
40A40TRP0-0.095-0.07022.009-0.017-0.0170.0000.0000.0000.000
41A41ASN00.012-0.00324.0370.0130.0130.0000.0000.0000.000
42A42GLN00.042-0.00325.7330.0030.0030.0000.0000.0000.000
43A43ASP-1-0.866-0.91528.773-0.123-0.1230.0000.0000.0000.000
44A44GLY0-0.028-0.02330.508-0.007-0.0070.0000.0000.0000.000
45A45LEU0-0.075-0.04131.8530.0000.0000.0000.0000.0000.000
46A46LYS10.9540.97327.0770.1670.1670.0000.0000.0000.000
47A47ASP-1-0.822-0.88622.883-0.226-0.2260.0000.0000.0000.000
48A48ASN0-0.064-0.01124.441-0.014-0.0140.0000.0000.0000.000
49A49TYR00.011-0.02620.028-0.012-0.0120.0000.0000.0000.000
50A50SER0-0.040-0.01122.8550.0110.0110.0000.0000.0000.000
51A51GLU-1-0.860-0.93621.973-0.224-0.2240.0000.0000.0000.000
52A52GLN00.0170.00022.2310.0250.0250.0000.0000.0000.000
53A53SER00.0090.01124.177-0.006-0.0060.0000.0000.0000.000
54A54GLU-1-0.814-0.86126.448-0.126-0.1260.0000.0000.0000.000
55A55ILE0-0.013-0.01221.4160.0080.0080.0000.0000.0000.000
56A56ILE0-0.0010.00821.703-0.015-0.0150.0000.0000.0000.000
57A57PRO0-0.009-0.00316.5640.0130.0130.0000.0000.0000.000
58A58SER0-0.106-0.01118.1370.0110.0110.0000.0000.0000.000
59A59PRO00.0430.00513.8420.0090.0090.0000.0000.0000.000
60A60PRO00.0890.02615.019-0.020-0.0200.0000.0000.0000.000
61A61VAL00.0040.00011.973-0.053-0.0530.0000.0000.0000.000
62A62ALA00.0160.00510.5810.0460.0460.0000.0000.0000.000
63A63LYS10.9500.9819.221-0.196-0.1960.0000.0000.0000.000
64A64ILE0-0.0270.0026.592-0.010-0.0100.0000.0000.0000.000
65A65LYS10.8780.9146.952-0.231-0.2310.0000.0000.0000.000
66A66ALA00.0220.0197.382-0.009-0.0090.0000.0000.0000.000
67A67GLY0-0.016-0.0078.343-0.151-0.1510.0000.0000.0000.000
68A68GLU-1-0.861-0.9209.9090.1460.1460.0000.0000.0000.000
69A69LYS10.9460.9629.563-0.039-0.0390.0000.0000.0000.000
70A70HIS00.0360.01410.520-0.026-0.0260.0000.0000.0000.000
71A71MET0-0.037-0.02412.404-0.032-0.0320.0000.0000.0000.000
72A72LEU00.0140.01711.6270.0000.0000.0000.0000.0000.000
73A73ARG10.9620.98115.3200.0840.0840.0000.0000.0000.000
74A74LEU0-0.006-0.00717.006-0.015-0.0150.0000.0000.0000.000
75A75THR0-0.035-0.02720.4690.0150.0150.0000.0000.0000.000
76A76LYS10.8960.95524.0270.0840.0840.0000.0000.0000.000
77A77SER0-0.043-0.01726.8660.0090.0090.0000.0000.0000.000
78A78VAL00.0120.00328.8800.0090.0090.0000.0000.0000.000
79A79ASN0-0.052-0.03631.458-0.007-0.0070.0000.0000.0000.000
80A80LEU00.0290.02228.526-0.001-0.0010.0000.0000.0000.000
81A81PRO00.001-0.01333.1050.0050.0050.0000.0000.0000.000
82A82ASP-1-0.875-0.94035.552-0.069-0.0690.0000.0000.0000.000
83A83GLY0-0.039-0.02237.650-0.001-0.0010.0000.0000.0000.000
84A84LYS10.8740.94433.9800.0940.0940.0000.0000.0000.000
85A85GLU-1-0.735-0.85828.671-0.131-0.1310.0000.0000.0000.000
86A86GLN00.0020.00227.927-0.008-0.0080.0000.0000.0000.000
87A87SER00.0350.01325.000-0.003-0.0030.0000.0000.0000.000
88A88TYR0-0.031-0.06421.2390.0030.0030.0000.0000.0000.000
89A89ARG10.8450.92915.9990.3590.3590.0000.0000.0000.000
90A90LEU00.0210.02013.6970.0130.0130.0000.0000.0000.000
91A91ILE0-0.049-0.03411.908-0.050-0.0500.0000.0000.0000.000
92A92VAL00.0370.0186.9610.0700.0700.0000.0000.0000.000
93A93ASP-1-0.806-0.8907.927-0.986-0.9860.0000.0000.0000.000
94A94GLU-1-0.825-0.9242.444-14.305-10.9793.831-3.395-3.761-0.042
95A95LEU0-0.068-0.0415.3590.0940.094-0.001-0.0010.0020.000
96A96PRO00.0300.0256.566-0.099-0.0990.0000.0000.0000.000
97A97ILE0-0.023-0.0146.7040.2540.2540.0000.0000.0000.000
98A108SER00.016-0.00219.182-0.003-0.0030.0000.0000.0000.000
99A109LYS10.9040.95310.521-0.195-0.1950.0000.0000.0000.000
100A110VAL00.0650.04512.596-0.024-0.0240.0000.0000.0000.000
101A111SER0-0.040-0.0268.3290.0860.0860.0000.0000.0000.000
102A112PHE00.002-0.0155.8100.0210.0210.0000.0000.0000.000
103A113GLN00.0390.0275.535-0.245-0.2450.0000.0000.0000.000
104A114MET0-0.034-0.0023.5480.8301.1870.008-0.077-0.2880.000
105A115ARG10.9030.9345.6560.9740.9740.0000.0000.0000.000
106A116TYR0-0.0070.0013.772-0.470-0.2420.006-0.103-0.1320.000
107A117SER0-0.0060.0019.2230.1320.1320.0000.0000.0000.000
108A118ILE0-0.0170.00012.6840.0080.0080.0000.0000.0000.000
109A119PRO0-0.047-0.00515.2280.0150.0150.0000.0000.0000.000
110A120LEU00.0310.00918.9950.0030.0030.0000.0000.0000.000
111A121PHE00.0120.01120.8830.0010.0010.0000.0000.0000.000
112A122ALA00.0020.00724.6640.0060.0060.0000.0000.0000.000
113A123TYR0-0.022-0.01227.132-0.001-0.0010.0000.0000.0000.000
114A124GLY00.0270.03530.8420.0020.0020.0000.0000.0000.000
115A125LYS10.9630.94934.1560.0630.0630.0000.0000.0000.000
116A126GLY00.0500.02637.134-0.001-0.0010.0000.0000.0000.000
117A127ILE0-0.036-0.00133.4960.0010.0010.0000.0000.0000.000
118A128GLY00.0340.01031.960-0.001-0.0010.0000.0000.0000.000
119A129SER0-0.024-0.04727.712-0.002-0.0020.0000.0000.0000.000
120A130GLY00.0080.00029.717-0.003-0.0030.0000.0000.0000.000
121A131LEU0-0.001-0.01325.2550.0020.0020.0000.0000.0000.000
122A132THR00.0180.02229.2100.0030.0030.0000.0000.0000.000
123A133GLU-1-0.836-0.92531.582-0.049-0.0490.0000.0000.0000.000
124A134GLU-1-0.977-0.97734.103-0.055-0.0550.0000.0000.0000.000
125A135SER0-0.018-0.02531.895-0.001-0.0010.0000.0000.0000.000
126A136GLN00.0190.01032.8140.0020.0020.0000.0000.0000.000
127A137LYS10.9550.97436.0780.0420.0420.0000.0000.0000.000
128A138LEU0-0.076-0.02535.2960.0020.0020.0000.0000.0000.000
129A139ASN00.041-0.01633.5450.0020.0020.0000.0000.0000.000
130A140ALA0-0.0110.00937.8990.0000.0000.0000.0000.0000.000
131A141LYS10.8900.95341.0610.0470.0470.0000.0000.0000.000
132A142ASN0-0.011-0.00439.1020.0010.0010.0000.0000.0000.000
133A143ALA00.0400.01740.627-0.002-0.0020.0000.0000.0000.000
134A144LEU00.0200.00039.322-0.001-0.0010.0000.0000.0000.000
135A145ALA0-0.0290.02036.237-0.006-0.0060.0000.0000.0000.000
136A146LYS10.9250.92734.6120.0680.0680.0000.0000.0000.000
137A147PRO00.0430.04732.3310.0010.0010.0000.0000.0000.000
138A148VAL0-0.007-0.00634.6590.0060.0060.0000.0000.0000.000
139A149LEU00.0180.01833.113-0.002-0.0020.0000.0000.0000.000
140A150GLN00.019-0.00937.2880.0040.0040.0000.0000.0000.000
141A151TRP0-0.024-0.01737.848-0.007-0.0070.0000.0000.0000.000
142A152SER0-0.030-0.02338.6270.0060.0060.0000.0000.0000.000
143A153VAL00.0520.03138.772-0.005-0.0050.0000.0000.0000.000
144A154ARG10.9390.97439.6060.0790.0790.0000.0000.0000.000
145A155ASN00.0520.03439.372-0.005-0.0050.0000.0000.0000.000
146A156ASN0-0.0030.00639.3620.0050.0050.0000.0000.0000.000
147A157GLN0-0.004-0.00241.545-0.002-0.0020.0000.0000.0000.000
148A158GLN00.0070.01041.6690.0010.0010.0000.0000.0000.000
149A159GLY00.0340.00737.875-0.005-0.0050.0000.0000.0000.000
150A160GLN0-0.018-0.00634.8270.0000.0000.0000.0000.0000.000
151A161SER0-0.031-0.04437.9430.0010.0010.0000.0000.0000.000
152A162GLU-1-0.871-0.94334.280-0.119-0.1190.0000.0000.0000.000
153A163LEU0-0.012-0.00933.9850.0080.0080.0000.0000.0000.000
154A164TYR0-0.034-0.02234.152-0.008-0.0080.0000.0000.0000.000
155A165LEU00.014-0.01031.7220.0060.0060.0000.0000.0000.000
156A166LYS10.9200.98234.0760.0750.0750.0000.0000.0000.000
157A167ASN0-0.013-0.01831.8560.0130.0130.0000.0000.0000.000
158A168ASN0-0.035-0.03235.350-0.002-0.0020.0000.0000.0000.000
159A169GLY0-0.0090.01036.3140.0040.0040.0000.0000.0000.000
160A170GLN0-0.006-0.02035.012-0.008-0.0080.0000.0000.0000.000
161A171LYS10.8130.92829.2390.1110.1110.0000.0000.0000.000
162A172PHE0-0.047-0.01925.5710.0010.0010.0000.0000.0000.000
163A173ALA00.0200.01829.5400.0060.0060.0000.0000.0000.000
164A174ARG10.8330.88722.0900.1800.1800.0000.0000.0000.000
165A175LEU0-0.010-0.01726.6530.0090.0090.0000.0000.0000.000
166A176SER00.0160.00825.721-0.009-0.0090.0000.0000.0000.000
167A177ALA00.0210.01227.1960.0010.0010.0000.0000.0000.000
168A178LEU00.0150.00730.6840.0020.0020.0000.0000.0000.000
169A179LYS10.9160.98434.1940.0760.0760.0000.0000.0000.000
170A180THR00.0420.02137.5070.0000.0000.0000.0000.0000.000
171A181SER00.020-0.00940.7910.0020.0020.0000.0000.0000.000
172A182LYN00.0410.01440.527-0.003-0.0030.0000.0000.0000.000
173A183THR0-0.014-0.00240.282-0.002-0.0020.0000.0000.0000.000
174A184GLY00.0160.02840.9390.0020.0020.0000.0000.0000.000
175A185ASN00.017-0.00837.094-0.003-0.0030.0000.0000.0000.000
176A186ASP-1-0.962-0.99031.965-0.088-0.0880.0000.0000.0000.000
177A187ILE0-0.014-0.01135.0640.0020.0020.0000.0000.0000.000
178A188SER0-0.029-0.02633.503-0.004-0.0040.0000.0000.0000.000
179A189LEU0-0.0220.00230.399-0.006-0.0060.0000.0000.0000.000
180A190GLY00.0810.04729.447-0.006-0.0060.0000.0000.0000.000
181A191LYS10.7490.87028.0350.1030.1030.0000.0000.0000.000
182A192ALA0-0.007-0.02928.323-0.005-0.0050.0000.0000.0000.000
183A193ALA00.0030.03024.110-0.006-0.0060.0000.0000.0000.000
184A194PHE0-0.004-0.01525.1590.0030.0030.0000.0000.0000.000
185A195GLY00.0660.02724.411-0.007-0.0070.0000.0000.0000.000
186A196TYR0-0.0150.02720.2140.0130.0130.0000.0000.0000.000
187A197VAL00.0030.02625.9250.0000.0000.0000.0000.0000.000
188A198LEU00.0420.00725.1560.0070.0070.0000.0000.0000.000
189A199SER00.0450.03129.1410.0070.0070.0000.0000.0000.000
190A200ASN0-0.0420.01832.337-0.005-0.0050.0000.0000.0000.000
191A201SER00.022-0.01531.227-0.003-0.0030.0000.0000.0000.000
192A202THR0-0.084-0.06533.2050.0070.0070.0000.0000.0000.000
193A203VAL00.0520.02528.171-0.004-0.0040.0000.0000.0000.000
194A204LYS10.8770.95030.9850.1310.1310.0000.0000.0000.000
195A205PHE0-0.0060.01129.199-0.010-0.0100.0000.0000.0000.000
196A206ALA00.0360.03030.5820.0110.0110.0000.0000.0000.000
197A207ILE00.0250.00031.510-0.004-0.0040.0000.0000.0000.000
198A208ASP-1-0.825-0.90433.493-0.098-0.0980.0000.0000.0000.000
199A209GLN00.0610.03035.786-0.002-0.0020.0000.0000.0000.000
200A210SER00.0150.00438.2790.0010.0010.0000.0000.0000.000
201A211THR00.0780.03535.3720.0000.0000.0000.0000.0000.000
202A212ALA00.0300.01138.2030.0020.0020.0000.0000.0000.000
203A213HIS0-0.006-0.01740.2490.0010.0010.0000.0000.0000.000
204A214GLU-1-0.971-0.99139.745-0.063-0.0630.0000.0000.0000.000
205A215LEU00.0060.00037.4490.0020.0020.0000.0000.0000.000
206A216ALA0-0.032-0.01442.0220.0010.0010.0000.0000.0000.000
207A217LYS10.8760.96444.4450.0570.0570.0000.0000.0000.000
208A218THR00.0500.02443.3890.0030.0030.0000.0000.0000.000
209A219SER0-0.010-0.02145.502-0.002-0.0020.0000.0000.0000.000
210A220LYS10.8650.93143.2240.0560.0560.0000.0000.0000.000
211A221ILE0-0.0090.00837.4380.0020.0020.0000.0000.0000.000
212A222TYR00.002-0.00237.6340.0010.0010.0000.0000.0000.000
213A223GLY00.0440.03933.588-0.003-0.0030.0000.0000.0000.000
214A224VAL0-0.020-0.00929.9680.0060.0060.0000.0000.0000.000
215A225ASP-1-0.770-0.89329.477-0.131-0.1310.0000.0000.0000.000
216A226SER00.0100.00725.3460.0010.0010.0000.0000.0000.000
217A227SER0-0.078-0.04526.263-0.006-0.0060.0000.0000.0000.000
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