FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: KG7V3

Calculation Name: 2DX1-A-Xray372

Preferred Name: APC/Asef

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 2DX1

Chain ID: A

ChEMBL ID: CHEMBL4296093

UniProt ID: Q9NR80

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

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. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 391
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6871145.294393
FMO2-HF: Nuclear repulsion 6707865.756868
FMO2-HF: Total energy -163279.537525
FMO2-MP2: Total energy -163751.584301


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:114:LEU)


Summations of interaction energy for fragment #1(A:114:LEU)
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.
-4.671-1.2822.793-1.898-4.284-0.004
Interaction energy analysis for fragmet #1(A:114:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : -0.006
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].
3A116ILE00.0180.0032.476-2.545-0.9812.441-1.115-2.8890.002
4A117ASN0-0.012-0.0092.587-1.6290.1960.352-0.783-1.395-0.006
5A118GLU-1-0.903-0.9425.5480.0820.0820.0000.0000.0000.000
6A119LEU00.0090.0397.8820.1230.1230.0000.0000.0000.000
7A120ILE00.0170.0038.220-0.005-0.0050.0000.0000.0000.000
8A121SER0-0.107-0.06610.351-0.038-0.0380.0000.0000.0000.000
9A122ASP-1-0.917-0.96212.2140.0570.0570.0000.0000.0000.000
10A123GLY0-0.047-0.02013.7080.0180.0180.0000.0000.0000.000
11A124SER0-0.072-0.03312.3920.0380.0380.0000.0000.0000.000
12A125VAL00.002-0.00313.393-0.015-0.0150.0000.0000.0000.000
13A126VAL00.0040.0148.4890.1040.1040.0000.0000.0000.000
14A127CYS0-0.037-0.02011.862-0.124-0.1240.0000.0000.0000.000
15A128ALA00.008-0.00610.7900.1750.1750.0000.0000.0000.000
16A129GLU-1-0.971-0.98612.4040.2630.2630.0000.0000.0000.000
17A130ALA00.0410.04314.1340.0180.0180.0000.0000.0000.000
18A131LEU0-0.036-0.01913.2310.0140.0140.0000.0000.0000.000
19A132TRP0-0.030-0.02816.123-0.017-0.0170.0000.0000.0000.000
20A133ASP-1-0.799-0.89918.9570.0540.0540.0000.0000.0000.000
21A134HIS0-0.083-0.05818.651-0.023-0.0230.0000.0000.0000.000
22A135VAL00.010-0.00520.7020.0040.0040.0000.0000.0000.000
23A136THR0-0.021-0.06422.469-0.009-0.0090.0000.0000.0000.000
24A137MET0-0.0100.00324.8930.0110.0110.0000.0000.0000.000
25A138ASP-1-0.811-0.88323.706-0.100-0.1000.0000.0000.0000.000
26A139ASP-1-0.964-1.00124.599-0.066-0.0660.0000.0000.0000.000
27A140GLN0-0.089-0.04522.061-0.006-0.0060.0000.0000.0000.000
28A141GLU-1-0.892-0.90319.971-0.131-0.1310.0000.0000.0000.000
29A142LEU0-0.044-0.00517.3490.0180.0180.0000.0000.0000.000
30A143GLY0-0.0020.01919.761-0.003-0.0030.0000.0000.0000.000
31A144PHE0-0.057-0.04216.0360.0140.0140.0000.0000.0000.000
32A145LYS10.8590.91321.557-0.074-0.0740.0000.0000.0000.000
33A146ALA00.006-0.01119.8970.0120.0120.0000.0000.0000.000
34A147GLY0-0.059-0.04619.224-0.004-0.0040.0000.0000.0000.000
35A148ASP-1-0.840-0.88420.0060.0950.0950.0000.0000.0000.000
36A149VAL0-0.019-0.02616.7300.0190.0190.0000.0000.0000.000
37A150ILE0-0.033-0.01714.471-0.032-0.0320.0000.0000.0000.000
38A151GLU-1-0.829-0.89314.1490.1800.1800.0000.0000.0000.000
39A152VAL0-0.024-0.0238.878-0.063-0.0630.0000.0000.0000.000
40A153MET0-0.046-0.02811.8010.0370.0370.0000.0000.0000.000
41A154ASP-1-0.839-0.88110.766-0.531-0.5310.0000.0000.0000.000
42A155ALA00.020-0.0115.9870.0860.0860.0000.0000.0000.000
43A156THR0-0.038-0.0316.542-0.393-0.3930.0000.0000.0000.000
44A157ASN0-0.079-0.0358.360-0.167-0.1670.0000.0000.0000.000
45A158ARG10.9520.9716.5440.4880.4880.0000.0000.0000.000
46A159GLU-1-0.850-0.9357.622-0.348-0.3480.0000.0000.0000.000
47A160TRP00.0460.03610.3940.0580.0580.0000.0000.0000.000
48A161TRP00.0070.0135.3080.0880.0880.0000.0000.0000.000
49A162TRP00.0100.01911.5010.0440.0440.0000.0000.0000.000
50A163GLY00.017-0.00513.3820.0210.0210.0000.0000.0000.000
51A164ARG10.8690.91915.491-0.071-0.0710.0000.0000.0000.000
52A165VAL0-0.006-0.00218.3530.0280.0280.0000.0000.0000.000
53A166ALA0-0.059-0.03620.8560.0000.0000.0000.0000.0000.000
54A167ASP-1-0.982-1.02124.5910.0070.0070.0000.0000.0000.000
55A168GLY00.0240.01323.915-0.008-0.0080.0000.0000.0000.000
56A169GLU-1-0.877-0.94819.314-0.020-0.0200.0000.0000.0000.000
57A170GLY00.0430.02818.518-0.001-0.0010.0000.0000.0000.000
58A171TRP0-0.019-0.01613.360-0.002-0.0020.0000.0000.0000.000
59A172PHE0-0.029-0.00911.4090.0340.0340.0000.0000.0000.000
60A173PRO00.0190.02213.590-0.047-0.0470.0000.0000.0000.000
61A174ALA00.0650.0338.1780.0690.0690.0000.0000.0000.000
62A175SER0-0.110-0.06410.3240.1360.1360.0000.0000.0000.000
63A176PHE00.015-0.00511.2450.0520.0520.0000.0000.0000.000
64A177VAL0-0.021-0.0059.9290.0400.0400.0000.0000.0000.000
65A178ARG10.7370.84910.064-0.565-0.5650.0000.0000.0000.000
66A179LEU00.0110.0005.413-0.013-0.0130.0000.0000.0000.000
67A180ARG10.9040.9679.454-0.368-0.3680.0000.0000.0000.000
68A181VAL0-0.035-0.02610.6940.1900.1900.0000.0000.0000.000
69A182ASN0-0.063-0.05511.7980.1420.1420.0000.0000.0000.000
70A183GLN0-0.0310.00610.562-0.201-0.2010.0000.0000.0000.000
71A184ASP-1-0.919-0.96214.1820.3060.3060.0000.0000.0000.000
72A206ALA00.0320.00526.9740.0010.0010.0000.0000.0000.000
73A207GLN00.0400.00227.2360.0170.0170.0000.0000.0000.000
74A208SER00.0120.01825.6140.0140.0140.0000.0000.0000.000
75A209SER00.0400.00122.4200.0140.0140.0000.0000.0000.000
76A210LYS10.9570.98621.805-0.211-0.2110.0000.0000.0000.000
77A211ASP-1-0.844-0.91823.2020.2250.2250.0000.0000.0000.000
78A212GLN0-0.015-0.01418.1690.0520.0520.0000.0000.0000.000
79A213MET00.0160.01617.9670.0590.0590.0000.0000.0000.000
80A214ARG10.8220.88718.033-0.194-0.1940.0000.0000.0000.000
81A215THR0-0.015-0.01718.006-0.007-0.0070.0000.0000.0000.000
82A216ASN0-0.020-0.00614.0730.0170.0170.0000.0000.0000.000
83A217VAL00.0070.00114.6200.0480.0480.0000.0000.0000.000
84A218ILE0-0.0180.00015.9170.0060.0060.0000.0000.0000.000
85A219ASN0-0.022-0.02314.210-0.060-0.0600.0000.0000.0000.000
86A220GLU-1-0.764-0.85610.7350.6760.6760.0000.0000.0000.000
87A221ILE00.0020.00312.915-0.040-0.0400.0000.0000.0000.000
88A222LEU00.0180.00215.860-0.032-0.0320.0000.0000.0000.000
89A223SER0-0.031-0.00510.415-0.026-0.0260.0000.0000.0000.000
90A224THR0-0.050-0.04910.839-0.056-0.0560.0000.0000.0000.000
91A225GLU-1-0.803-0.90212.7600.1590.1590.0000.0000.0000.000
92A226ARG10.9160.96214.041-0.334-0.3340.0000.0000.0000.000
93A227ASP-1-0.931-0.9679.6080.3570.3570.0000.0000.0000.000
94A228TYR0-0.028-0.05612.499-0.059-0.0590.0000.0000.0000.000
95A229ILE00.0060.01414.704-0.037-0.0370.0000.0000.0000.000
96A230LYS10.9300.95912.801-0.162-0.1620.0000.0000.0000.000
97A231HIS00.0790.04810.195-0.039-0.0390.0000.0000.0000.000
98A232LEU00.0240.01115.258-0.019-0.0190.0000.0000.0000.000
99A233ARG10.8670.96116.669-0.030-0.0300.0000.0000.0000.000
100A234ASP-1-0.825-0.92315.335-0.038-0.0380.0000.0000.0000.000
101A235ILE0-0.0050.00617.634-0.011-0.0110.0000.0000.0000.000
102A236CYS0-0.036-0.02220.321-0.005-0.0050.0000.0000.0000.000
103A237GLU-1-0.944-1.00322.4770.0140.0140.0000.0000.0000.000
104A238GLY00.0190.01421.338-0.003-0.0030.0000.0000.0000.000
105A239TYR0-0.019-0.01318.168-0.010-0.0100.0000.0000.0000.000
106A240VAL00.0190.02723.6530.0000.0000.0000.0000.0000.000
107A241ARG10.9190.96926.3820.0010.0010.0000.0000.0000.000
108A242GLN00.0190.01325.7580.0040.0040.0000.0000.0000.000
109A243CYS0-0.0090.00326.716-0.001-0.0010.0000.0000.0000.000
110A244ARG10.8140.88129.6290.0030.0030.0000.0000.0000.000
111A245LYS10.8980.94831.7400.0150.0150.0000.0000.0000.000
112A246ARG10.8010.89132.0060.0380.0380.0000.0000.0000.000
113A247ALA00.0820.04334.314-0.002-0.0020.0000.0000.0000.000
114A248ASP-1-0.841-0.90636.525-0.034-0.0340.0000.0000.0000.000
115A249MET0-0.120-0.05531.341-0.004-0.0040.0000.0000.0000.000
116A250PHE00.0350.02828.342-0.003-0.0030.0000.0000.0000.000
117A251SER00.0510.04633.6670.0030.0030.0000.0000.0000.000
118A252GLU-1-0.869-0.97334.462-0.008-0.0080.0000.0000.0000.000
119A253GLU-1-0.983-0.99234.528-0.017-0.0170.0000.0000.0000.000
120A254GLN00.0460.02431.7980.0020.0020.0000.0000.0000.000
121A255LEU0-0.0070.00329.953-0.001-0.0010.0000.0000.0000.000
122A256ARG10.9480.96729.5040.0030.0030.0000.0000.0000.000
123A257THR00.0270.01929.8880.0040.0040.0000.0000.0000.000
124A258ILE0-0.061-0.03325.210-0.002-0.0020.0000.0000.0000.000
125A259PHE00.002-0.02923.128-0.002-0.0020.0000.0000.0000.000
126A260GLY00.0380.04425.8780.0060.0060.0000.0000.0000.000
127A261ASN00.0180.00827.498-0.003-0.0030.0000.0000.0000.000
128A262ILE00.0270.00820.7470.0080.0080.0000.0000.0000.000
129A263GLU-1-0.806-0.88924.4130.0110.0110.0000.0000.0000.000
130A264ASP-1-0.898-0.94526.7300.0340.0340.0000.0000.0000.000
131A265ILE0-0.018-0.01222.1770.0080.0080.0000.0000.0000.000
132A266TYR0-0.015-0.00621.1670.0130.0130.0000.0000.0000.000
133A267ARG10.9070.94923.783-0.036-0.0360.0000.0000.0000.000
134A268CYS00.0100.00126.3610.0040.0040.0000.0000.0000.000
135A269GLN00.0540.03319.982-0.007-0.0070.0000.0000.0000.000
136A270LYS10.9160.94922.770-0.041-0.0410.0000.0000.0000.000
137A271ALA0-0.036-0.00524.0190.0070.0070.0000.0000.0000.000
138A272PHE00.0530.01821.2460.0070.0070.0000.0000.0000.000
139A273VAL00.0210.01519.5790.0120.0120.0000.0000.0000.000
140A274LYS10.8920.95822.141-0.102-0.1020.0000.0000.0000.000
141A275ALA00.022-0.00425.1000.0020.0020.0000.0000.0000.000
142A276LEU00.000-0.00320.4710.0070.0070.0000.0000.0000.000
143A277GLU-1-0.938-0.98020.1940.1870.1870.0000.0000.0000.000
144A278GLN0-0.087-0.04023.2640.0000.0000.0000.0000.0000.000
145A279ARG10.9250.97425.546-0.139-0.1390.0000.0000.0000.000
146A280PHE0-0.036-0.01819.8460.0070.0070.0000.0000.0000.000
147A281ASN0-0.010-0.01024.190-0.013-0.0130.0000.0000.0000.000
148A282ARG10.9820.97422.782-0.165-0.1650.0000.0000.0000.000
149A283GLU-1-0.908-0.94023.7070.1650.1650.0000.0000.0000.000
150A284ARG10.9070.95325.131-0.147-0.1470.0000.0000.0000.000
151A285PRO00.0690.04520.635-0.005-0.0050.0000.0000.0000.000
152A286HIS00.0210.01422.796-0.012-0.0120.0000.0000.0000.000
153A287LEU0-0.030-0.02823.590-0.012-0.0120.0000.0000.0000.000
154A288SER0-0.031-0.00423.324-0.016-0.0160.0000.0000.0000.000
155A289GLU-1-0.881-0.93625.4590.1470.1470.0000.0000.0000.000
156A290LEU0-0.001-0.02521.121-0.004-0.0040.0000.0000.0000.000
157A291GLY00.0480.02325.308-0.005-0.0050.0000.0000.0000.000
158A292ALA00.0220.01026.998-0.007-0.0070.0000.0000.0000.000
159A293CYS0-0.0080.01026.020-0.008-0.0080.0000.0000.0000.000
160A294PHE0-0.010-0.00820.548-0.003-0.0030.0000.0000.0000.000
161A295LEU0-0.039-0.02426.658-0.010-0.0100.0000.0000.0000.000
162A296GLU-1-0.979-0.99230.2180.0980.0980.0000.0000.0000.000
163A297HIS0-0.027-0.00827.567-0.008-0.0080.0000.0000.0000.000
164A298GLN00.0070.01529.0720.0010.0010.0000.0000.0000.000
165A299ALA00.022-0.01029.900-0.002-0.0020.0000.0000.0000.000
166A300ASP-1-0.841-0.91828.3330.0730.0730.0000.0000.0000.000
167A301PHE0-0.011-0.01723.036-0.003-0.0030.0000.0000.0000.000
168A302GLN0-0.051-0.02727.0460.0020.0020.0000.0000.0000.000
169A303ILE0-0.013-0.00427.032-0.007-0.0070.0000.0000.0000.000
170A304TYR00.0340.05220.725-0.005-0.0050.0000.0000.0000.000
171A305SER00.001-0.00326.102-0.006-0.0060.0000.0000.0000.000
172A306GLU-1-0.953-0.96328.6710.0160.0160.0000.0000.0000.000
173A307TYR0-0.024-0.02921.267-0.005-0.0050.0000.0000.0000.000
174A308CYS0-0.037-0.02123.738-0.006-0.0060.0000.0000.0000.000
175A309ASN0-0.0070.00325.554-0.007-0.0070.0000.0000.0000.000
176A310ASN0-0.016-0.01228.046-0.006-0.0060.0000.0000.0000.000
177A311HIS00.0460.03220.9450.0000.0000.0000.0000.0000.000
178A312PRO00.010-0.00125.622-0.008-0.0080.0000.0000.0000.000
179A313ASN00.0060.00127.281-0.008-0.0080.0000.0000.0000.000
180A314ALA00.0270.03725.097-0.005-0.0050.0000.0000.0000.000
181A315CYS0-0.019-0.01023.319-0.009-0.0090.0000.0000.0000.000
182A316VAL00.0140.02225.199-0.009-0.0090.0000.0000.0000.000
183A317GLU-1-0.752-0.87528.638-0.045-0.0450.0000.0000.0000.000
184A318LEU00.0310.00622.382-0.003-0.0030.0000.0000.0000.000
185A319SER0-0.0070.01125.773-0.006-0.0060.0000.0000.0000.000
186A320ARG10.8200.89226.6190.0410.0410.0000.0000.0000.000
187A321LEU0-0.012-0.01527.588-0.003-0.0030.0000.0000.0000.000
188A322THR0-0.025-0.00224.219-0.006-0.0060.0000.0000.0000.000
189A323LYS10.8840.94226.4960.0660.0660.0000.0000.0000.000
190A324LEU0-0.056-0.02629.4290.0050.0050.0000.0000.0000.000
191A325SER00.0430.02329.4390.0010.0010.0000.0000.0000.000
192A326LYS10.9840.99829.4040.0460.0460.0000.0000.0000.000
193A327TYR0-0.021-0.05328.2010.0010.0010.0000.0000.0000.000
194A328VAL00.0010.01724.357-0.002-0.0020.0000.0000.0000.000
195A329TYR0-0.006-0.01224.832-0.007-0.0070.0000.0000.0000.000
196A330PHE00.0140.01525.958-0.002-0.0020.0000.0000.0000.000
197A331PHE00.065-0.00122.7320.0020.0020.0000.0000.0000.000
198A332GLU-1-0.974-0.98721.029-0.132-0.1320.0000.0000.0000.000
199A333ALA0-0.004-0.01722.009-0.002-0.0020.0000.0000.0000.000
200A334CYS0-0.055-0.01822.6310.0070.0070.0000.0000.0000.000
201A335ARG10.9720.97616.7080.1460.1460.0000.0000.0000.000
202A336LEU0-0.063-0.02119.436-0.001-0.0010.0000.0000.0000.000
203A337LEU0-0.046-0.02421.1580.0070.0070.0000.0000.0000.000
204A338GLN0-0.0100.00618.8660.0060.0060.0000.0000.0000.000
205A339LYS10.8730.95214.9400.1250.1250.0000.0000.0000.000
206A340MET0-0.0420.00515.5020.0100.0100.0000.0000.0000.000
207A341ILE00.0060.0009.176-0.022-0.0220.0000.0000.0000.000
208A342ASP-1-0.965-0.9779.698-0.311-0.3110.0000.0000.0000.000
209A343ILE0-0.0040.0149.051-0.066-0.0660.0000.0000.0000.000
210A344SER00.0160.01012.2330.0260.0260.0000.0000.0000.000
211A345LEU0-0.004-0.01015.8440.0110.0110.0000.0000.0000.000
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