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: 5JZ5Z

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 OptAll
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 -6885695.399392
FMO2-HF: Nuclear repulsion 6722410.345509
FMO2-HF: Total energy -163285.053883
FMO2-MP2: Total energy -163756.621225


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.
-6.359-2.1590.664-1.811-3.053-0.001
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 : 0.014 / 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].
3A116ILE00.0030.0022.819-2.846-0.1010.520-1.230-2.0350.003
4A117ASN0-0.011-0.0153.092-2.512-1.0570.144-0.581-1.018-0.004
5A118GLU-1-0.931-0.9395.532-0.435-0.4350.0000.0000.0000.000
6A119LEU00.0440.0347.5470.3040.3040.0000.0000.0000.000
7A120ILE00.006-0.0088.0850.0630.0630.0000.0000.0000.000
8A121SER0-0.104-0.05810.2950.0110.0110.0000.0000.0000.000
9A122ASP-1-0.916-0.95412.194-0.144-0.1440.0000.0000.0000.000
10A123GLY0-0.048-0.02013.7370.0410.0410.0000.0000.0000.000
11A124SER0-0.069-0.03411.9550.0630.0630.0000.0000.0000.000
12A125VAL0-0.006-0.00712.9140.0100.0100.0000.0000.0000.000
13A126VAL00.0010.0158.6040.1110.1110.0000.0000.0000.000
14A127CYS0-0.037-0.02011.996-0.118-0.1180.0000.0000.0000.000
15A128ALA00.0180.00311.5280.2220.2220.0000.0000.0000.000
16A129GLU-1-0.836-0.89913.3390.3320.3320.0000.0000.0000.000
17A130ALA00.0310.03115.1870.0530.0530.0000.0000.0000.000
18A131LEU0-0.048-0.02113.568-0.007-0.0070.0000.0000.0000.000
19A132TRP0-0.059-0.05716.323-0.029-0.0290.0000.0000.0000.000
20A133ASP-1-0.801-0.90319.6290.1460.1460.0000.0000.0000.000
21A134HIS0-0.100-0.04418.884-0.011-0.0110.0000.0000.0000.000
22A135VAL00.0150.01220.999-0.005-0.0050.0000.0000.0000.000
23A136THR00.000-0.04322.251-0.008-0.0080.0000.0000.0000.000
24A137MET0-0.017-0.01124.8590.0070.0070.0000.0000.0000.000
25A138ASP-1-0.824-0.90623.758-0.046-0.0460.0000.0000.0000.000
26A139ASP-1-0.876-0.92324.992-0.019-0.0190.0000.0000.0000.000
27A140GLN0-0.065-0.04922.445-0.012-0.0120.0000.0000.0000.000
28A141GLU-1-0.847-0.89219.985-0.020-0.0200.0000.0000.0000.000
29A142LEU0-0.051-0.01117.1280.0090.0090.0000.0000.0000.000
30A143GLY00.0130.01119.9070.0070.0070.0000.0000.0000.000
31A144PHE0-0.063-0.03916.3720.0090.0090.0000.0000.0000.000
32A145LYS10.8670.91422.265-0.153-0.1530.0000.0000.0000.000
33A146ALA00.006-0.00820.7800.0210.0210.0000.0000.0000.000
34A147GLY0-0.052-0.03220.232-0.018-0.0180.0000.0000.0000.000
35A148ASP-1-0.825-0.88420.9400.1660.1660.0000.0000.0000.000
36A149VAL0-0.037-0.02817.8480.0350.0350.0000.0000.0000.000
37A150ILE0-0.024-0.00914.724-0.044-0.0440.0000.0000.0000.000
38A151GLU-1-0.832-0.88914.7590.2170.2170.0000.0000.0000.000
39A152VAL0-0.036-0.0278.982-0.043-0.0430.0000.0000.0000.000
40A153MET0-0.049-0.03411.9440.0060.0060.0000.0000.0000.000
41A154ASP-1-0.809-0.88210.687-0.617-0.6170.0000.0000.0000.000
42A155ALA00.008-0.0065.6350.1610.1610.0000.0000.0000.000
43A156THR0-0.046-0.0366.475-0.522-0.5220.0000.0000.0000.000
44A157ASN0-0.062-0.0238.103-0.130-0.1300.0000.0000.0000.000
45A158ARG10.8590.8956.5070.2710.2710.0000.0000.0000.000
46A159GLU-1-0.812-0.8697.5850.1270.1270.0000.0000.0000.000
47A160TRP00.0460.03210.2890.0810.0810.0000.0000.0000.000
48A161TRP00.0410.0395.3070.1540.1540.0000.0000.0000.000
49A162TRP00.0000.00411.3920.0320.0320.0000.0000.0000.000
50A163GLY00.027-0.00213.0770.0310.0310.0000.0000.0000.000
51A164ARG10.7840.87315.316-0.095-0.0950.0000.0000.0000.000
52A165VAL00.0150.00918.3210.0390.0390.0000.0000.0000.000
53A166ALA0-0.020-0.01921.183-0.017-0.0170.0000.0000.0000.000
54A167ASP-1-0.862-0.91924.7350.0660.0660.0000.0000.0000.000
55A168GLY0-0.019-0.01124.004-0.013-0.0130.0000.0000.0000.000
56A169GLU-1-0.832-0.91219.1370.0200.0200.0000.0000.0000.000
57A170GLY00.0410.03018.601-0.011-0.0110.0000.0000.0000.000
58A171TRP0-0.010-0.00813.6000.0090.0090.0000.0000.0000.000
59A172PHE0-0.020-0.01711.7980.0280.0280.0000.0000.0000.000
60A173PRO00.0200.02113.297-0.023-0.0230.0000.0000.0000.000
61A174ALA00.0380.0158.3950.0680.0680.0000.0000.0000.000
62A175SER0-0.074-0.06710.5010.1340.1340.0000.0000.0000.000
63A176PHE00.0310.00511.6040.0140.0140.0000.0000.0000.000
64A177VAL0-0.020-0.00711.035-0.007-0.0070.0000.0000.0000.000
65A178ARG10.7580.86811.026-0.674-0.6740.0000.0000.0000.000
66A179LEU00.0230.0106.305-0.060-0.0600.0000.0000.0000.000
67A180ARG10.7830.87910.231-0.511-0.5110.0000.0000.0000.000
68A181VAL0-0.024-0.01410.6320.2390.2390.0000.0000.0000.000
69A182ASN0-0.081-0.05611.6920.0450.0450.0000.0000.0000.000
70A183GLN0-0.033-0.02210.378-0.250-0.2500.0000.0000.0000.000
71A184ASP-1-0.932-0.95213.8300.2450.2450.0000.0000.0000.000
72A206ALA00.0550.01626.861-0.002-0.0020.0000.0000.0000.000
73A207GLN0-0.030-0.02426.0750.0120.0120.0000.0000.0000.000
74A208SER00.0400.00724.1920.0080.0080.0000.0000.0000.000
75A209SER00.0150.00722.0180.0120.0120.0000.0000.0000.000
76A210LYS10.8520.93721.381-0.202-0.2020.0000.0000.0000.000
77A211ASP-1-0.756-0.87622.3880.2180.2180.0000.0000.0000.000
78A212GLN00.0080.00817.7410.0280.0280.0000.0000.0000.000
79A213MET00.0200.01817.4970.0580.0580.0000.0000.0000.000
80A214ARG10.7750.84917.653-0.200-0.2000.0000.0000.0000.000
81A215THR0-0.026-0.01617.5950.0080.0080.0000.0000.0000.000
82A216ASN00.0080.00713.571-0.001-0.0010.0000.0000.0000.000
83A217VAL0-0.019-0.00714.2610.0690.0690.0000.0000.0000.000
84A218ILE0-0.0050.00015.9650.0120.0120.0000.0000.0000.000
85A219ASN0-0.029-0.02513.916-0.048-0.0480.0000.0000.0000.000
86A220GLU-1-0.726-0.83210.6070.9080.9080.0000.0000.0000.000
87A221ILE0-0.006-0.00412.848-0.013-0.0130.0000.0000.0000.000
88A222LEU00.0290.01115.844-0.017-0.0170.0000.0000.0000.000
89A223SER0-0.041-0.01510.998-0.044-0.0440.0000.0000.0000.000
90A224THR0-0.028-0.02711.192-0.050-0.0500.0000.0000.0000.000
91A225GLU-1-0.743-0.83213.2210.2580.2580.0000.0000.0000.000
92A226ARG10.8650.91214.934-0.324-0.3240.0000.0000.0000.000
93A227ASP-1-0.830-0.90110.5700.4540.4540.0000.0000.0000.000
94A228TYR00.0220.00312.955-0.049-0.0490.0000.0000.0000.000
95A229ILE0-0.009-0.01015.302-0.041-0.0410.0000.0000.0000.000
96A230LYS10.8200.90711.787-0.293-0.2930.0000.0000.0000.000
97A231HIS00.0740.03610.637-0.061-0.0610.0000.0000.0000.000
98A232LEU00.0230.01415.874-0.026-0.0260.0000.0000.0000.000
99A233ARG10.8530.91116.704-0.092-0.0920.0000.0000.0000.000
100A234ASP-1-0.784-0.86616.4020.0470.0470.0000.0000.0000.000
101A235ILE00.0150.01217.872-0.017-0.0170.0000.0000.0000.000
102A236CYS0-0.034-0.01120.743-0.012-0.0120.0000.0000.0000.000
103A237GLU-1-0.850-0.90622.9960.0540.0540.0000.0000.0000.000
104A238GLY00.0280.02021.851-0.007-0.0070.0000.0000.0000.000
105A239TYR0-0.0020.00117.859-0.013-0.0130.0000.0000.0000.000
106A240VAL00.0050.01023.806-0.005-0.0050.0000.0000.0000.000
107A241ARG10.8170.90326.604-0.043-0.0430.0000.0000.0000.000
108A242GLN00.0130.01126.201-0.003-0.0030.0000.0000.0000.000
109A243CYS0-0.058-0.02026.805-0.004-0.0040.0000.0000.0000.000
110A244ARG10.8040.87229.734-0.041-0.0410.0000.0000.0000.000
111A245LYS10.9130.95631.976-0.014-0.0140.0000.0000.0000.000
112A246ARG10.8020.86431.9620.0050.0050.0000.0000.0000.000
113A247ALA00.1100.05034.2680.0000.0000.0000.0000.0000.000
114A248ASP-1-0.840-0.87136.364-0.005-0.0050.0000.0000.0000.000
115A249MET0-0.143-0.06831.117-0.004-0.0040.0000.0000.0000.000
116A250PHE00.0580.04228.3710.0000.0000.0000.0000.0000.000
117A251SER00.0500.03933.7930.0020.0020.0000.0000.0000.000
118A252GLU-1-0.763-0.89934.6070.0340.0340.0000.0000.0000.000
119A253GLU-1-0.871-0.92134.6900.0230.0230.0000.0000.0000.000
120A254GLN00.0350.02031.9840.0030.0030.0000.0000.0000.000
121A255LEU0-0.036-0.01630.2710.0020.0020.0000.0000.0000.000
122A256ARG10.8500.91029.705-0.031-0.0310.0000.0000.0000.000
123A257THR0-0.013-0.02530.1830.0070.0070.0000.0000.0000.000
124A258ILE0-0.033-0.02025.3660.0030.0030.0000.0000.0000.000
125A259PHE00.003-0.01223.4390.0030.0030.0000.0000.0000.000
126A260GLY00.0380.02326.2890.0090.0090.0000.0000.0000.000
127A261ASN0-0.043-0.03327.7530.0030.0030.0000.0000.0000.000
128A262ILE00.0230.01221.3890.0070.0070.0000.0000.0000.000
129A263GLU-1-0.824-0.89925.0380.0570.0570.0000.0000.0000.000
130A264ASP-1-0.818-0.90027.3130.0760.0760.0000.0000.0000.000
131A265ILE0-0.0120.00822.7790.0070.0070.0000.0000.0000.000
132A266TYR0-0.032-0.05222.0990.0130.0130.0000.0000.0000.000
133A267ARG10.7860.88824.401-0.072-0.0720.0000.0000.0000.000
134A268CYS0-0.016-0.02227.1890.0010.0010.0000.0000.0000.000
135A269GLN0-0.015-0.01620.433-0.009-0.0090.0000.0000.0000.000
136A270LYS10.8670.93823.331-0.086-0.0860.0000.0000.0000.000
137A271ALA0-0.0160.01024.5950.0000.0000.0000.0000.0000.000
138A272PHE00.0370.01321.2290.0050.0050.0000.0000.0000.000
139A273VAL00.009-0.00319.7960.0110.0110.0000.0000.0000.000
140A274LYS10.8520.93022.497-0.137-0.1370.0000.0000.0000.000
141A275ALA00.0310.01025.315-0.002-0.0020.0000.0000.0000.000
142A276LEU00.0320.00320.6530.0040.0040.0000.0000.0000.000
143A277GLU-1-0.871-0.91921.1180.1970.1970.0000.0000.0000.000
144A278GLN0-0.057-0.03023.797-0.002-0.0020.0000.0000.0000.000
145A279ARG10.8550.93725.571-0.158-0.1580.0000.0000.0000.000
146A280PHE0-0.002-0.00519.3990.0060.0060.0000.0000.0000.000
147A281ASN00.002-0.00423.983-0.018-0.0180.0000.0000.0000.000
148A282ARG10.8840.91622.729-0.133-0.1330.0000.0000.0000.000
149A283GLU-1-0.834-0.90323.1790.1460.1460.0000.0000.0000.000
150A284ARG10.9050.96024.793-0.142-0.1420.0000.0000.0000.000
151A285PRO00.0620.05120.2100.0000.0000.0000.0000.0000.000
152A286HIS00.0040.00922.437-0.005-0.0050.0000.0000.0000.000
153A287LEU0-0.025-0.01523.492-0.006-0.0060.0000.0000.0000.000
154A288SER0-0.029-0.02123.247-0.015-0.0150.0000.0000.0000.000
155A289GLU-1-0.894-0.92625.4700.1490.1490.0000.0000.0000.000
156A290LEU00.0210.00020.728-0.004-0.0040.0000.0000.0000.000
157A291GLY00.018-0.00425.0460.0000.0000.0000.0000.0000.000
158A292ALA00.0330.01626.914-0.005-0.0050.0000.0000.0000.000
159A293CYS0-0.0020.01225.848-0.008-0.0080.0000.0000.0000.000
160A294PHE0-0.007-0.00620.6890.0020.0020.0000.0000.0000.000
161A295LEU0-0.033-0.01026.851-0.009-0.0090.0000.0000.0000.000
162A296GLU-1-0.887-0.94030.4040.1280.1280.0000.0000.0000.000
163A297HIS0-0.016-0.00627.713-0.010-0.0100.0000.0000.0000.000
164A298GLN0-0.011-0.00329.1750.0060.0060.0000.0000.0000.000
165A299ALA0-0.006-0.01230.520-0.002-0.0020.0000.0000.0000.000
166A300ASP-1-0.816-0.90428.4550.1160.1160.0000.0000.0000.000
167A301PHE00.014-0.01023.1100.0000.0000.0000.0000.0000.000
168A302GLN0-0.0100.00227.3820.0070.0070.0000.0000.0000.000
169A303ILE00.0280.01727.895-0.005-0.0050.0000.0000.0000.000
170A304TYR00.0490.02320.513-0.007-0.0070.0000.0000.0000.000
171A305SER0-0.012-0.00726.361-0.002-0.0020.0000.0000.0000.000
172A306GLU-1-0.902-0.92628.9490.0680.0680.0000.0000.0000.000
173A307TYR0-0.007-0.01721.217-0.006-0.0060.0000.0000.0000.000
174A308CYS0-0.033-0.02624.104-0.001-0.0010.0000.0000.0000.000
175A309ASN0-0.060-0.03825.977-0.009-0.0090.0000.0000.0000.000
176A310ASN00.0060.01228.092-0.010-0.0100.0000.0000.0000.000
177A311HIS00.0440.02220.622-0.003-0.0030.0000.0000.0000.000
178A312PRO00.0140.00325.383-0.007-0.0070.0000.0000.0000.000
179A313ASN00.004-0.00327.290-0.009-0.0090.0000.0000.0000.000
180A314ALA00.0140.02925.077-0.007-0.0070.0000.0000.0000.000
181A315CYS0-0.035-0.02223.259-0.007-0.0070.0000.0000.0000.000
182A316VAL00.0070.01225.090-0.010-0.0100.0000.0000.0000.000
183A317GLU-1-0.736-0.83728.597-0.001-0.0010.0000.0000.0000.000
184A318LEU00.0120.00222.044-0.006-0.0060.0000.0000.0000.000
185A319SER00.0370.03425.649-0.011-0.0110.0000.0000.0000.000
186A320ARG10.8110.88826.459-0.007-0.0070.0000.0000.0000.000
187A321LEU0-0.003-0.01327.439-0.005-0.0050.0000.0000.0000.000
188A322THR0-0.014-0.02423.444-0.006-0.0060.0000.0000.0000.000
189A323LYS10.8240.90826.2520.0140.0140.0000.0000.0000.000
190A324LEU0-0.032-0.00829.3630.0000.0000.0000.0000.0000.000
191A325SER00.0420.01429.2330.0030.0030.0000.0000.0000.000
192A326LYS10.9360.97829.2790.0090.0090.0000.0000.0000.000
193A327TYR0-0.028-0.04027.9780.0000.0000.0000.0000.0000.000
194A328VAL00.0050.02324.0290.0010.0010.0000.0000.0000.000
195A329TYR00.012-0.00924.716-0.004-0.0040.0000.0000.0000.000
196A330PHE00.0100.00926.250-0.001-0.0010.0000.0000.0000.000
197A331PHE00.059-0.00222.3930.0040.0040.0000.0000.0000.000
198A332GLU-1-0.868-0.92420.134-0.079-0.0790.0000.0000.0000.000
199A333ALA00.0070.00122.2240.0000.0000.0000.0000.0000.000
200A334CYS0-0.060-0.02722.7380.0050.0050.0000.0000.0000.000
201A335ARG10.8960.93016.5170.0660.0660.0000.0000.0000.000
202A336LEU0-0.043-0.01919.7280.0000.0000.0000.0000.0000.000
203A337LEU0-0.048-0.01621.5000.0000.0000.0000.0000.0000.000
204A338GLN0-0.037-0.02519.655-0.001-0.0010.0000.0000.0000.000
205A339LYS10.8950.95715.1060.0910.0910.0000.0000.0000.000
206A340MET0-0.0480.00015.9950.0020.0020.0000.0000.0000.000
207A341ILE0-0.017-0.0089.819-0.019-0.0190.0000.0000.0000.000
208A342ASP-1-0.931-0.96410.207-0.183-0.1830.0000.0000.0000.000
209A343ILE0-0.023-0.0069.623-0.025-0.0250.0000.0000.0000.000
210A344SER0-0.011-0.03012.5720.0080.0080.0000.0000.0000.000
211A345LEU00.003-0.00215.9780.0200.0200.0000.0000.0000.000
212A346ASP-1-0.771-0.88218.396-0.001-0.0010.0000.0000.0000.000
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