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: 7671K

Calculation Name: 4DDP-A-Xray372

Preferred Name: Beclin-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DDP

Chain ID: A

ChEMBL ID: CHEMBL4296010

UniProt ID: Q14457

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptHSide
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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2478266.526025
FMO2-HF: Nuclear repulsion 2396813.103185
FMO2-HF: Total energy -81453.422841
FMO2-MP2: Total energy -81690.881624


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:248:LYS)


Summations of interaction energy for fragment #1(A:248:LYS)
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.
26.63335.9941.703-4.608-6.457-0.023
Interaction energy analysis for fragmet #1(A:248:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.003 / q_NPA : 1.005
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].
3A250VAL00.0740.0253.790-2.4660.165-0.031-1.328-1.2720.008
4A251GLU-1-0.817-0.9146.189-24.492-24.4920.0000.0000.0000.000
5A252ASN00.000-0.0114.2302.9483.053-0.001-0.011-0.0930.000
6A253GLN00.0030.0143.522-2.478-1.6150.039-0.279-0.623-0.002
7A254MET0-0.0050.0116.2022.4812.4810.0000.0000.0000.000
8A255ARG10.9790.9949.31719.79019.7900.0000.0000.0000.000
9A256TYR00.0130.0188.1251.4791.4790.0000.0000.0000.000
10A257ALA00.0320.01310.1461.5071.5070.0000.0000.0000.000
11A258GLN0-0.038-0.03712.2220.9690.9690.0000.0000.0000.000
12A259THR0-0.037-0.02213.2321.5091.5090.0000.0000.0000.000
13A260GLN00.011-0.00214.5630.7280.7280.0000.0000.0000.000
14A261LEU0-0.008-0.00816.1211.0851.0850.0000.0000.0000.000
15A262ASP-1-0.830-0.90018.225-14.364-14.3640.0000.0000.0000.000
16A263LYS10.8430.93017.88516.99816.9980.0000.0000.0000.000
17A264LEU0-0.0280.01919.5490.5530.5530.0000.0000.0000.000
18A265LYS10.9100.91923.08012.58112.5810.0000.0000.0000.000
19A266LYS10.8780.93626.64810.61610.6160.0000.0000.0000.000
20A267THR00.0900.06823.5770.3600.3600.0000.0000.0000.000
21A268ASN00.0340.00922.1500.0410.0410.0000.0000.0000.000
22A269VAL0-0.040-0.01224.2290.4090.4090.0000.0000.0000.000
23A270PHE00.001-0.00922.834-0.167-0.1670.0000.0000.0000.000
24A271ASN0-0.0150.00627.7950.0100.0100.0000.0000.0000.000
25A272ALA00.0320.02728.0080.2130.2130.0000.0000.0000.000
26A273THR00.0150.00623.864-0.329-0.3290.0000.0000.0000.000
27A274PHE00.0240.00321.5620.1700.1700.0000.0000.0000.000
28A275HIS00.0110.00817.419-0.775-0.7750.0000.0000.0000.000
29A276ILE00.0040.01614.3760.2680.2680.0000.0000.0000.000
30A277TRP0-0.004-0.00312.814-0.992-0.9920.0000.0000.0000.000
31A278HIS00.0340.00111.854-0.068-0.0680.0000.0000.0000.000
32A279SER0-0.0060.00614.8430.8340.8340.0000.0000.0000.000
33A280GLY00.0530.02815.5110.3300.3300.0000.0000.0000.000
34A281GLN00.039-0.00113.958-1.624-1.6240.0000.0000.0000.000
35A282PHE00.0080.02314.789-0.632-0.6320.0000.0000.0000.000
36A283GLY00.0250.01414.719-0.699-0.6990.0000.0000.0000.000
37A284THR0-0.025-0.02815.3670.7010.7010.0000.0000.0000.000
38A285ILE00.0330.01117.644-0.667-0.6670.0000.0000.0000.000
39A286ASN0-0.046-0.04420.1650.2470.2470.0000.0000.0000.000
40A287ASN0-0.048-0.02721.8300.1720.1720.0000.0000.0000.000
41A288PHE00.0060.03122.9900.3020.3020.0000.0000.0000.000
42A289ARG10.8300.86220.34011.05611.0560.0000.0000.0000.000
43A290LEU0-0.013-0.00518.0640.5170.5170.0000.0000.0000.000
44A291GLY00.005-0.00718.838-0.871-0.8710.0000.0000.0000.000
45A292ARG10.7660.86220.81511.67911.6790.0000.0000.0000.000
46A293LEU00.0160.01018.260-0.582-0.5820.0000.0000.0000.000
47A294PRO00.0780.04222.0140.4700.4700.0000.0000.0000.000
48A295SER0-0.019-0.00522.2440.3190.3190.0000.0000.0000.000
49A296VAL0-0.041-0.02422.4440.1860.1860.0000.0000.0000.000
50A297PRO00.0450.02724.667-0.385-0.3850.0000.0000.0000.000
51A298VAL0-0.041-0.01823.1270.3900.3900.0000.0000.0000.000
52A299GLU-1-0.853-0.90626.519-9.275-9.2750.0000.0000.0000.000
53A300TRP00.0980.02126.194-0.321-0.3210.0000.0000.0000.000
54A301ASN0-0.038-0.02329.157-0.133-0.1330.0000.0000.0000.000
55A302GLU-1-0.739-0.82624.621-11.642-11.6420.0000.0000.0000.000
56A303ILE00.0010.00423.802-0.346-0.3460.0000.0000.0000.000
57A304ASN0-0.017-0.01925.226-0.540-0.5400.0000.0000.0000.000
58A305ALA00.0180.00827.502-0.038-0.0380.0000.0000.0000.000
59A306ALA00.0160.01321.894-0.145-0.1450.0000.0000.0000.000
60A307TRP00.0510.01721.180-0.550-0.5500.0000.0000.0000.000
61A308GLY0-0.0010.00424.432-0.114-0.1140.0000.0000.0000.000
62A309GLN0-0.017-0.00823.685-0.051-0.0510.0000.0000.0000.000
63A310THR0-0.032-0.02919.690-0.474-0.4740.0000.0000.0000.000
64A311VAL00.0050.00122.297-0.296-0.2960.0000.0000.0000.000
65A312LEU0-0.020-0.00225.1620.0680.0680.0000.0000.0000.000
66A313LEU00.0180.01218.8720.0720.0720.0000.0000.0000.000
67A314LEU0-0.008-0.00320.447-0.094-0.0940.0000.0000.0000.000
68A315HIS00.0200.00223.005-0.094-0.0940.0000.0000.0000.000
69A316ALA0-0.019-0.00825.3950.2680.2680.0000.0000.0000.000
70A317LEU0-0.033-0.01419.4800.1220.1220.0000.0000.0000.000
71A318ALA00.0280.01323.576-0.012-0.0120.0000.0000.0000.000
72A319ASN0-0.027-0.01325.1620.3950.3950.0000.0000.0000.000
73A320LYS10.8120.91324.76912.56712.5670.0000.0000.0000.000
74A321MET0-0.050-0.02020.434-0.143-0.1430.0000.0000.0000.000
75A322GLY00.0040.02425.5160.0740.0740.0000.0000.0000.000
76A323LEU0-0.039-0.00222.7440.1320.1320.0000.0000.0000.000
77A324LYS10.9170.95726.78610.19710.1970.0000.0000.0000.000
78A325PHE0-0.003-0.00822.7680.0060.0060.0000.0000.0000.000
79A326GLN00.0420.00925.9580.7150.7150.0000.0000.0000.000
80A327ARG10.8400.87824.10912.19612.1960.0000.0000.0000.000
81A328TYR00.003-0.01126.3160.4460.4460.0000.0000.0000.000
82A329ARG10.8260.90829.6618.8528.8520.0000.0000.0000.000
83A330LEU00.0360.01125.3450.0790.0790.0000.0000.0000.000
84A331VAL0-0.0020.00529.8090.2190.2190.0000.0000.0000.000
85A332PRO0-0.022-0.01429.513-0.054-0.0540.0000.0000.0000.000
86A333TYR00.0120.00131.2000.3440.3440.0000.0000.0000.000
87A334GLY00.0540.03231.4460.1090.1090.0000.0000.0000.000
88A335ASN0-0.009-0.01329.875-0.199-0.1990.0000.0000.0000.000
89A336HIS10.8810.94030.9579.0089.0080.0000.0000.0000.000
90A337SER00.0540.03428.7100.2120.2120.0000.0000.0000.000
91A338TYR0-0.052-0.03230.228-0.145-0.1450.0000.0000.0000.000
92A339LEU00.0090.01426.387-0.156-0.1560.0000.0000.0000.000
93A340GLU-1-0.782-0.86330.984-8.476-8.4760.0000.0000.0000.000
94A341SER00.0360.00932.327-0.343-0.3430.0000.0000.0000.000
95A342LEU0-0.072-0.04231.8720.3020.3020.0000.0000.0000.000
96A343THR00.001-0.00434.3440.1010.1010.0000.0000.0000.000
97A344ASP-1-0.857-0.92335.940-8.325-8.3250.0000.0000.0000.000
98A345LYS10.9360.95337.1747.4217.4210.0000.0000.0000.000
99A346SER00.0190.01739.5890.1200.1200.0000.0000.0000.000
100A347LYS10.8230.93132.5089.6599.6590.0000.0000.0000.000
101A348GLU-1-0.859-0.93435.592-8.455-8.4550.0000.0000.0000.000
102A349LEU0-0.055-0.04129.903-0.218-0.2180.0000.0000.0000.000
103A350PRO00.0320.02630.936-0.196-0.1960.0000.0000.0000.000
104A351LEU0-0.015-0.02424.941-0.283-0.2830.0000.0000.0000.000
105A352TYR00.002-0.00527.941-0.030-0.0300.0000.0000.0000.000
106A353CYS0-0.034-0.00229.6180.1560.1560.0000.0000.0000.000
107A354SER00.0040.00131.2280.0840.0840.0000.0000.0000.000
108A355GLY00.0080.00032.123-0.170-0.1700.0000.0000.0000.000
109A356GLY00.0150.01733.1830.0190.0190.0000.0000.0000.000
110A357LEU00.0390.01532.039-0.291-0.2910.0000.0000.0000.000
111A358ARG10.8320.89228.38710.48910.4890.0000.0000.0000.000
112A359PHE0-0.005-0.00731.1580.0130.0130.0000.0000.0000.000
113A360PHE0-0.010-0.00334.2720.1200.1200.0000.0000.0000.000
114A361TRP0-0.0010.01332.4690.1670.1670.0000.0000.0000.000
115A362ASP-1-0.772-0.87534.273-9.011-9.0110.0000.0000.0000.000
116A363ASN0-0.019-0.03530.383-0.061-0.0610.0000.0000.0000.000
117A364LYS10.8540.95130.2688.1478.1470.0000.0000.0000.000
118A365PHE00.0590.02325.267-0.298-0.2980.0000.0000.0000.000
119A366ASP-1-0.705-0.83225.863-12.125-12.1250.0000.0000.0000.000
120A367HIS0-0.002-0.02125.852-0.326-0.3260.0000.0000.0000.000
121A368ALA00.0110.02227.236-0.250-0.2500.0000.0000.0000.000
122A369MET00.0020.01822.385-0.538-0.5380.0000.0000.0000.000
123A370VAL0-0.036-0.01222.406-0.672-0.6720.0000.0000.0000.000
124A371ALA00.0200.01823.094-0.384-0.3840.0000.0000.0000.000
125A372PHE00.0400.00620.128-0.181-0.1810.0000.0000.0000.000
126A373LEU00.0210.00516.318-0.403-0.4030.0000.0000.0000.000
127A374ASP-1-0.788-0.85019.424-13.924-13.9240.0000.0000.0000.000
128A375CYS0-0.028-0.01421.3620.0030.0030.0000.0000.0000.000
129A376VAL0-0.023-0.01616.368-0.315-0.3150.0000.0000.0000.000
130A377GLN00.015-0.00615.363-1.738-1.7380.0000.0000.0000.000
131A378GLN00.002-0.00317.8450.1480.1480.0000.0000.0000.000
132A379PHE00.0030.00016.2700.0030.0030.0000.0000.0000.000
133A380LYS10.8550.92212.46321.77821.7780.0000.0000.0000.000
134A381GLU-1-0.948-0.98516.086-16.964-16.9640.0000.0000.0000.000
135A382GLU-1-0.835-0.89318.026-13.479-13.4790.0000.0000.0000.000
136A383VAL0-0.073-0.04314.9530.1780.1780.0000.0000.0000.000
137A384GLU-1-0.784-0.87111.879-25.547-25.5470.0000.0000.0000.000
138A385LYS10.7870.89515.62813.79013.7900.0000.0000.0000.000
139A386GLY00.0130.00418.9820.3640.3640.0000.0000.0000.000
140A387GLU-1-0.827-0.90517.696-17.506-17.5060.0000.0000.0000.000
141A388THR0-0.0360.00015.331-0.940-0.9400.0000.0000.0000.000
142A389ARG10.8320.87811.28319.52819.5280.0000.0000.0000.000
143A390PHE0-0.035-0.01010.385-3.228-3.2280.0000.0000.0000.000
144A391CYS0-0.051-0.0317.7910.3360.3360.0000.0000.0000.000
145A392LEU0-0.052-0.0198.350-1.923-1.9230.0000.0000.0000.000
146A393PRO0-0.0070.0035.712-1.391-1.3910.0000.0000.0000.000
147A394TYR0-0.051-0.0244.407-4.319-4.141-0.001-0.007-0.1700.000
148A395ARG10.9620.9838.14336.47136.4710.0000.0000.0000.000
149A396MET0-0.0010.00710.2550.8210.8210.0000.0000.0000.000
150A397ASP-1-0.784-0.88113.895-16.898-16.8980.0000.0000.0000.000
151A398VAL00.024-0.00316.6510.5810.5810.0000.0000.0000.000
152A399GLU-1-0.885-0.91919.896-13.462-13.4620.0000.0000.0000.000
153A400LYS10.7900.87418.91216.58516.5850.0000.0000.0000.000
154A401GLY0-0.054-0.01420.4210.3260.3260.0000.0000.0000.000
155A402LYS10.8970.94215.95115.91115.9110.0000.0000.0000.000
156A403ILE00.0010.01311.322-0.128-0.1280.0000.0000.0000.000
157A404GLU-1-0.767-0.8498.218-33.372-33.3720.0000.0000.0000.000
158A405ASP-1-0.744-0.8555.307-40.196-40.1960.0000.0000.0000.000
159A406THR00.000-0.0444.084-1.367-1.228-0.001-0.014-0.1240.000
160A407GLY0-0.076-0.0402.493-13.268-11.7830.841-0.975-1.352-0.006
161A408GLY00.0020.0132.903-10.143-6.4290.852-1.967-2.599-0.023
162A409SER0-0.068-0.0683.8614.1824.4280.005-0.027-0.2240.000
163A410GLY00.0180.0197.0252.1642.1640.0000.0000.0000.000
164A411GLY0-0.0050.0128.8042.5132.5130.0000.0000.0000.000
165A412SER0-0.006-0.01310.769-1.586-1.5860.0000.0000.0000.000
166A413TYR0-0.030-0.03010.1432.1392.1390.0000.0000.0000.000
167A414SER0-0.023-0.00914.854-0.178-0.1780.0000.0000.0000.000
168A415ILE00.0500.01618.266-0.023-0.0230.0000.0000.0000.000
169A416LYS10.9460.98119.37913.67913.6790.0000.0000.0000.000
170A417THR00.006-0.03522.178-0.175-0.1750.0000.0000.0000.000
171A418GLN00.0050.00324.477-0.043-0.0430.0000.0000.0000.000
172A419PHE0-0.044-0.02725.046-0.334-0.3340.0000.0000.0000.000
173A420ASN0-0.034-0.00619.112-0.710-0.7100.0000.0000.0000.000
174A421SER00.0180.00219.8290.3950.3950.0000.0000.0000.000
175A422GLU-1-0.819-0.89820.560-12.016-12.0160.0000.0000.0000.000
176A423GLU-1-0.828-0.92917.334-14.103-14.1030.0000.0000.0000.000
177A424GLN0-0.0220.00515.651-0.492-0.4920.0000.0000.0000.000
178A425TRP0-0.022-0.00515.898-0.834-0.8340.0000.0000.0000.000
179A426THR00.001-0.00916.254-0.324-0.3240.0000.0000.0000.000
180A427LYS10.8450.9498.14526.70326.7030.0000.0000.0000.000
181A428ALA00.0130.00312.493-1.398-1.3980.0000.0000.0000.000
182A429LEU00.0350.01314.115-0.809-0.8090.0000.0000.0000.000
183A430LYS10.7990.90910.80221.04321.0430.0000.0000.0000.000
184A431PHE0-0.034-0.0046.792-1.123-1.1230.0000.0000.0000.000
185A432MET00.0050.01510.901-0.566-0.5660.0000.0000.0000.000
186A433LEU00.003-0.00614.0410.0020.0020.0000.0000.0000.000
187A434THR0-0.034-0.0297.7910.1710.1710.0000.0000.0000.000
188A435ASN00.022-0.01610.332-2.366-2.3660.0000.0000.0000.000
189A436LEU00.0400.02012.1960.6510.6510.0000.0000.0000.000
190A437LYS10.7780.89212.45119.05219.0520.0000.0000.0000.000
191A438TRP0-0.019-0.0266.4460.4610.4610.0000.0000.0000.000
192A439GLY00.0390.01612.7090.4720.4720.0000.0000.0000.000
193A440LEU00.0050.00815.7420.9100.9100.0000.0000.0000.000
194A441ALA0-0.017-0.00714.4220.9060.9060.0000.0000.0000.000
195A442TRP00.0380.03814.2460.4060.4060.0000.0000.0000.000
196A443VAL00.0370.00116.5610.8160.8160.0000.0000.0000.000
197A444SER0-0.081-0.04819.8811.0571.0570.0000.0000.0000.000
198A445SER0-0.050-0.04318.0740.5000.5000.0000.0000.0000.000
199A446GLN0-0.016-0.00317.1780.9330.9330.0000.0000.0000.000
200A447PHE0-0.0070.01721.2760.4950.4950.0000.0000.0000.000