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

tag_button

FMODB ID: 2NQVR

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2483716.019704
FMO2-HF: Nuclear repulsion 2402262.321862
FMO2-HF: Total energy -81453.697842
FMO2-MP2: Total energy -81691.186659


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.
-24.397-16.42115.738-11.047-12.667-0.119
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 : 0.920 / q_NPA : 0.957
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].
3A250VAL00.0390.0143.853-2.678-0.803-0.006-0.873-0.9950.005
4A251GLU-1-0.811-0.9145.484-26.204-26.2040.0000.0000.0000.000
5A252ASN00.0150.0054.3942.4972.577-0.001-0.005-0.0740.000
6A253GLN00.0050.0153.002-9.451-7.5770.279-0.768-1.385-0.008
7A254MET0-0.0020.0165.9062.6942.6940.0000.0000.0000.000
8A255ARG10.8880.9339.31620.26820.2680.0000.0000.0000.000
9A256TYR00.0050.0208.1151.8361.8360.0000.0000.0000.000
10A257ALA00.0420.0239.9921.6661.6660.0000.0000.0000.000
11A258GLN0-0.033-0.03511.7561.1681.1680.0000.0000.0000.000
12A259THR0-0.014-0.02113.0771.7391.7390.0000.0000.0000.000
13A260GLN00.0240.02514.4790.8870.8870.0000.0000.0000.000
14A261LEU00.0100.00016.1241.1711.1710.0000.0000.0000.000
15A262ASP-1-0.797-0.88917.600-15.245-15.2450.0000.0000.0000.000
16A263LYS10.8530.92317.52817.32817.3280.0000.0000.0000.000
17A264LEU0-0.0270.02218.9120.7440.7440.0000.0000.0000.000
18A265LYS10.8820.91622.72712.94812.9480.0000.0000.0000.000
19A266LYS10.8890.93425.96010.92410.9240.0000.0000.0000.000
20A267THR00.0790.05322.5140.4320.4320.0000.0000.0000.000
21A268ASN0-0.014-0.00321.632-0.139-0.1390.0000.0000.0000.000
22A269VAL0-0.013-0.00323.4280.4610.4610.0000.0000.0000.000
23A270PHE00.001-0.00321.589-0.263-0.2630.0000.0000.0000.000
24A271ASN0-0.002-0.00326.884-0.057-0.0570.0000.0000.0000.000
25A272ALA00.0180.02227.4800.3430.3430.0000.0000.0000.000
26A273THR00.0000.00723.360-0.379-0.3790.0000.0000.0000.000
27A274PHE00.0560.02020.9220.1850.1850.0000.0000.0000.000
28A275HIS00.0240.01716.692-1.062-1.0620.0000.0000.0000.000
29A276ILE0-0.0060.00513.9190.3970.3970.0000.0000.0000.000
30A277TRP0-0.017-0.00212.941-1.026-1.0260.0000.0000.0000.000
31A278HIS00.0390.00211.710-0.283-0.2830.0000.0000.0000.000
32A279SER0-0.0130.00014.3011.0401.0400.0000.0000.0000.000
33A280GLY00.0730.04414.7960.3530.3530.0000.0000.0000.000
34A281GLN00.029-0.00713.597-1.798-1.7980.0000.0000.0000.000
35A282PHE00.0140.02014.030-0.805-0.8050.0000.0000.0000.000
36A283GLY00.0380.01814.123-1.037-1.0370.0000.0000.0000.000
37A284THR0-0.032-0.02914.7150.8290.8290.0000.0000.0000.000
38A285ILE00.0380.01316.971-0.840-0.8400.0000.0000.0000.000
39A286ASN0-0.051-0.04719.6300.3110.3110.0000.0000.0000.000
40A287ASN0-0.024-0.01521.1930.3800.3800.0000.0000.0000.000
41A288PHE0-0.0160.01722.2260.0380.0380.0000.0000.0000.000
42A289ARG10.8410.86719.73611.56211.5620.0000.0000.0000.000
43A290LEU0-0.019-0.00917.2610.5450.5450.0000.0000.0000.000
44A291GLY00.000-0.00818.206-0.930-0.9300.0000.0000.0000.000
45A292ARG10.7410.84120.11312.28512.2850.0000.0000.0000.000
46A293LEU00.0170.00717.789-0.702-0.7020.0000.0000.0000.000
47A294PRO00.0500.02521.7620.5330.5330.0000.0000.0000.000
48A295SER0-0.0060.00321.9570.3440.3440.0000.0000.0000.000
49A296VAL0-0.031-0.01722.1870.2210.2210.0000.0000.0000.000
50A297PRO00.0490.03423.942-0.464-0.4640.0000.0000.0000.000
51A298VAL0-0.033-0.02422.5910.4120.4120.0000.0000.0000.000
52A299GLU-1-0.836-0.90025.857-9.710-9.7100.0000.0000.0000.000
53A300TRP00.0840.01525.471-0.414-0.4140.0000.0000.0000.000
54A301ASN0-0.052-0.02728.431-0.188-0.1880.0000.0000.0000.000
55A302GLU-1-0.739-0.82323.960-12.229-12.2290.0000.0000.0000.000
56A303ILE00.0140.01422.981-0.354-0.3540.0000.0000.0000.000
57A304ASN00.010-0.01424.434-0.677-0.6770.0000.0000.0000.000
58A305ALA00.0030.00426.9340.0080.0080.0000.0000.0000.000
59A306ALA00.0030.00721.239-0.138-0.1380.0000.0000.0000.000
60A307TRP00.0580.01920.273-0.625-0.6250.0000.0000.0000.000
61A308GLY00.0040.00323.790-0.113-0.1130.0000.0000.0000.000
62A309GLN0-0.037-0.01322.982-0.030-0.0300.0000.0000.0000.000
63A310THR0-0.023-0.02519.312-0.502-0.5020.0000.0000.0000.000
64A311VAL0-0.005-0.00521.709-0.376-0.3760.0000.0000.0000.000
65A312LEU00.0000.00624.2610.0410.0410.0000.0000.0000.000
66A313LEU00.0110.01318.0950.0940.0940.0000.0000.0000.000
67A314LEU0-0.009-0.00218.503-0.087-0.0870.0000.0000.0000.000
68A315HIS00.0300.00821.332-0.096-0.0960.0000.0000.0000.000
69A316ALA0-0.016-0.00924.0440.2900.2900.0000.0000.0000.000
70A317LEU0-0.033-0.02017.8380.1710.1710.0000.0000.0000.000
71A318ALA00.0220.01121.8570.0250.0250.0000.0000.0000.000
72A319ASN0-0.027-0.01423.3740.4650.4650.0000.0000.0000.000
73A320LYS10.8000.90823.25713.32713.3270.0000.0000.0000.000
74A321MET0-0.040-0.01318.956-0.269-0.2690.0000.0000.0000.000
75A322GLY00.0100.02124.0620.1140.1140.0000.0000.0000.000
76A323LEU0-0.037-0.00321.0290.2000.2000.0000.0000.0000.000
77A324LYS10.9060.94825.08410.66710.6670.0000.0000.0000.000
78A325PHE0-0.009-0.00721.0070.1050.1050.0000.0000.0000.000
79A326GLN00.0570.02523.9630.7790.7790.0000.0000.0000.000
80A327ARG10.8370.87822.91612.90412.9040.0000.0000.0000.000
81A328TYR0-0.004-0.01524.7700.5590.5590.0000.0000.0000.000
82A329ARG10.8430.91628.1249.4059.4050.0000.0000.0000.000
83A330LEU00.0290.01223.3530.0610.0610.0000.0000.0000.000
84A331VAL00.0060.00627.7700.2930.2930.0000.0000.0000.000
85A332PRO0-0.014-0.01227.855-0.061-0.0610.0000.0000.0000.000
86A333TYR00.0150.00529.8950.3740.3740.0000.0000.0000.000
87A334GLY00.0790.04330.8820.1250.1250.0000.0000.0000.000
88A335ASN0-0.019-0.00929.156-0.237-0.2370.0000.0000.0000.000
89A336HIS10.8720.93130.2339.6139.6130.0000.0000.0000.000
90A337SER00.0350.02528.0260.2110.2110.0000.0000.0000.000
91A338TYR0-0.080-0.05129.000-0.174-0.1740.0000.0000.0000.000
92A339LEU00.0000.00824.665-0.260-0.2600.0000.0000.0000.000
93A340GLU-1-0.779-0.85429.296-8.883-8.8830.0000.0000.0000.000
94A341SER00.0210.00330.821-0.325-0.3250.0000.0000.0000.000
95A342LEU0-0.087-0.05029.9420.3520.3520.0000.0000.0000.000
96A343THR00.000-0.00532.9800.1340.1340.0000.0000.0000.000
97A344ASP-1-0.844-0.92134.253-8.797-8.7970.0000.0000.0000.000
98A345LYS10.9370.95935.5287.6507.6500.0000.0000.0000.000
99A346SER00.0260.02137.9010.1990.1990.0000.0000.0000.000
100A347LYS10.8150.91330.70510.18410.1840.0000.0000.0000.000
101A348GLU-1-0.838-0.92033.642-9.016-9.0160.0000.0000.0000.000
102A349LEU0-0.051-0.02728.204-0.283-0.2830.0000.0000.0000.000
103A350PRO00.0370.02529.572-0.220-0.2200.0000.0000.0000.000
104A351LEU0-0.024-0.02123.989-0.278-0.2780.0000.0000.0000.000
105A352TYR0-0.002-0.01127.087-0.020-0.0200.0000.0000.0000.000
106A353CYS0-0.0190.01428.7360.2040.2040.0000.0000.0000.000
107A354SER0-0.008-0.00530.3660.1660.1660.0000.0000.0000.000
108A355GLY00.0300.00731.548-0.232-0.2320.0000.0000.0000.000
109A356GLY00.0150.01932.9270.1260.1260.0000.0000.0000.000
110A357LEU00.0360.00731.514-0.280-0.2800.0000.0000.0000.000
111A358ARG10.8080.87627.58611.20311.2030.0000.0000.0000.000
112A359PHE0-0.0030.00430.586-0.061-0.0610.0000.0000.0000.000
113A360PHE0-0.013-0.00633.6100.1400.1400.0000.0000.0000.000
114A361TRP00.0070.01432.0550.1330.1330.0000.0000.0000.000
115A362ASP-1-0.788-0.89033.308-9.544-9.5440.0000.0000.0000.000
116A363ASN0-0.023-0.03229.026-0.048-0.0480.0000.0000.0000.000
117A364LYS10.8590.93829.1888.5688.5680.0000.0000.0000.000
118A365PHE00.0530.02924.609-0.310-0.3100.0000.0000.0000.000
119A366ASP-1-0.712-0.83224.919-13.063-13.0630.0000.0000.0000.000
120A367HIS00.016-0.00724.585-0.383-0.3830.0000.0000.0000.000
121A368ALA00.0130.02525.700-0.306-0.3060.0000.0000.0000.000
122A369MET00.0040.01021.393-0.601-0.6010.0000.0000.0000.000
123A370VAL0-0.020-0.00320.919-0.846-0.8460.0000.0000.0000.000
124A371ALA00.0170.01421.577-0.428-0.4280.0000.0000.0000.000
125A372PHE00.0330.00218.649-0.112-0.1120.0000.0000.0000.000
126A373LEU0-0.009-0.00214.888-0.447-0.4470.0000.0000.0000.000
127A374ASP-1-0.762-0.84017.823-15.006-15.0060.0000.0000.0000.000
128A375CYS0-0.045-0.01219.795-0.052-0.0520.0000.0000.0000.000
129A376VAL0-0.005-0.01614.411-0.291-0.2910.0000.0000.0000.000
130A377GLN00.002-0.00114.210-2.041-2.0410.0000.0000.0000.000
131A378GLN00.008-0.00716.4260.1670.1670.0000.0000.0000.000
132A379PHE00.015-0.00314.760-0.042-0.0420.0000.0000.0000.000
133A380LYS10.7860.88411.05123.42923.4290.0000.0000.0000.000
134A381GLU-1-0.847-0.93014.500-19.627-19.6270.0000.0000.0000.000
135A382GLU-1-0.845-0.89016.706-13.800-13.8000.0000.0000.0000.000
136A383VAL0-0.067-0.03713.4630.1080.1080.0000.0000.0000.000
137A384GLU-1-0.789-0.89410.551-28.046-28.0460.0000.0000.0000.000
138A385LYS10.7770.88614.50714.78714.7870.0000.0000.0000.000
139A386GLY00.013-0.00317.4320.9760.9760.0000.0000.0000.000
140A387GLU-1-0.836-0.88117.066-17.674-17.6740.0000.0000.0000.000
141A388THR0-0.026-0.00214.843-0.866-0.8660.0000.0000.0000.000
142A389ARG10.8090.85711.06019.68419.6840.0000.0000.0000.000
143A390PHE0-0.0150.0029.941-3.510-3.5100.0000.0000.0000.000
144A391CYS0-0.043-0.0337.062-0.345-0.3450.0000.0000.0000.000
145A392LEU0-0.045-0.0097.398-1.926-1.9260.0000.0000.0000.000
146A393PRO0-0.033-0.0083.939-2.255-2.066-0.001-0.023-0.1650.000
147A394TYR0-0.034-0.0143.441-15.246-14.0920.020-0.399-0.775-0.002
148A395ARG10.9410.9616.30641.79541.7950.0000.0000.0000.000
149A396MET0-0.0010.0128.6931.0961.0960.0000.0000.0000.000
150A397ASP-1-0.781-0.87512.327-17.982-17.9820.0000.0000.0000.000
151A398VAL00.0330.00815.3940.6470.6470.0000.0000.0000.000
152A399GLU-1-0.869-0.91518.626-14.279-14.2790.0000.0000.0000.000
153A400LYS10.8010.88017.38417.80717.8070.0000.0000.0000.000
154A401GLY0-0.058-0.02519.1570.4010.4010.0000.0000.0000.000
155A402LYS10.8910.93414.71317.08717.0870.0000.0000.0000.000
156A403ILE00.0060.01710.099-0.067-0.0670.0000.0000.0000.000
157A404GLU-1-0.747-0.8267.042-37.576-37.5760.0000.0000.0000.000
158A405ASP-1-0.723-0.8324.993-44.967-44.934-0.001-0.003-0.0300.000
159A406THR0-0.012-0.0393.296-0.1870.5890.009-0.350-0.434-0.002
160A407GLY0-0.006-0.0041.757-46.804-48.16512.015-6.022-4.632-0.073
161A408GLY00.0020.0122.232-7.726-4.6403.412-2.592-3.907-0.039
162A409SER0-0.052-0.0623.6094.9105.1800.012-0.012-0.2700.000
163A410GLY00.0060.0126.7552.8322.8320.0000.0000.0000.000
164A411GLY00.0160.0208.5202.1902.1900.0000.0000.0000.000
165A412SER0-0.018-0.02510.291-2.571-2.5710.0000.0000.0000.000
166A413TYR0-0.035-0.0289.9522.7442.7440.0000.0000.0000.000
167A414SER0-0.026-0.01814.368-0.340-0.3400.0000.0000.0000.000
168A415ILE00.0470.01217.158-0.006-0.0060.0000.0000.0000.000
169A416LYS10.9030.97318.70314.91414.9140.0000.0000.0000.000
170A417THR00.019-0.02321.618-0.199-0.1990.0000.0000.0000.000
171A418GLN00.0070.01023.8190.0240.0240.0000.0000.0000.000
172A419PHE0-0.042-0.02624.215-0.433-0.4330.0000.0000.0000.000
173A420ASN0-0.020-0.00318.679-0.867-0.8670.0000.0000.0000.000
174A421SER00.023-0.00319.3610.4590.4590.0000.0000.0000.000
175A422GLU-1-0.805-0.87119.813-12.701-12.7010.0000.0000.0000.000
176A423GLU-1-0.814-0.91716.693-14.817-14.8170.0000.0000.0000.000
177A424GLN0-0.0160.01215.098-0.541-0.5410.0000.0000.0000.000
178A425TRP0-0.033-0.01515.225-1.067-1.0670.0000.0000.0000.000
179A426THR00.000-0.00815.713-0.486-0.4860.0000.0000.0000.000
180A427LYS10.8090.9177.75628.77728.7770.0000.0000.0000.000
181A428ALA00.0060.00011.691-1.956-1.9560.0000.0000.0000.000
182A429LEU00.0280.01013.468-1.110-1.1100.0000.0000.0000.000
183A430LYS10.8000.91010.00822.60822.6080.0000.0000.0000.000
184A431PHE0-0.0170.0046.025-1.253-1.2530.0000.0000.0000.000
185A432MET00.0140.02210.232-0.928-0.9280.0000.0000.0000.000
186A433LEU00.0030.00413.2480.0820.0820.0000.0000.0000.000
187A434THR0-0.033-0.0337.0780.2460.2460.0000.0000.0000.000
188A435ASN00.000-0.0388.350-3.046-3.0460.0000.0000.0000.000
189A436LEU00.0380.01910.5451.0051.0050.0000.0000.0000.000
190A437LYS10.7810.89812.06720.26820.2680.0000.0000.0000.000
191A438TRP0-0.013-0.0255.818-0.016-0.0160.0000.0000.0000.000
192A439GLY00.0360.01611.3450.8760.8760.0000.0000.0000.000
193A440LEU0-0.0020.00314.0361.0821.0820.0000.0000.0000.000
194A441ALA0-0.021-0.00913.4291.1221.1220.0000.0000.0000.000
195A442TRP00.0360.03313.4550.6500.6500.0000.0000.0000.000
196A443VAL00.0320.00615.4141.0051.0050.0000.0000.0000.000
197A444SER0-0.049-0.03918.5391.2231.2230.0000.0000.0000.000
198A445SER0-0.060-0.03317.1630.5090.5090.0000.0000.0000.000
199A446GLN00.010-0.00116.6451.1131.1130.0000.0000.0000.000
200A447PHE0-0.0100.01320.0910.5870.5870.0000.0000.0000.000