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: MNYQZ

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2476916.984783
FMO2-HF: Nuclear repulsion 2395464.172662
FMO2-HF: Total energy -81452.812121
FMO2-MP2: Total energy -81690.242705


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.
29.26637.8491.266-4.29-5.561-0.022
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 : 1.004 / q_NPA : 0.999
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].
3A250VAL00.0940.0303.790-2.2960.250-0.031-1.264-1.2500.007
4A251GLU-1-0.848-0.9346.113-23.465-23.4650.0000.0000.0000.000
5A252ASN00.003-0.0074.1973.4533.582-0.001-0.018-0.1110.000
6A253GLN00.0040.0123.3070.0430.8560.033-0.261-0.585-0.002
7A254MET0-0.0130.0076.1972.4432.4430.0000.0000.0000.000
8A255ARG10.9790.9949.32619.66419.6640.0000.0000.0000.000
9A256TYR00.0050.0028.1031.3521.3520.0000.0000.0000.000
10A257ALA00.0340.01310.1851.4611.4610.0000.0000.0000.000
11A258GLN0-0.028-0.01812.2380.9610.9610.0000.0000.0000.000
12A259THR0-0.024-0.00113.3711.4351.4350.0000.0000.0000.000
13A260GLN0-0.006-0.00914.5730.4520.4520.0000.0000.0000.000
14A261LEU0-0.012-0.01316.0611.0551.0550.0000.0000.0000.000
15A262ASP-1-0.835-0.91518.251-14.033-14.0330.0000.0000.0000.000
16A263LYS10.8510.93217.59616.73216.7320.0000.0000.0000.000
17A264LEU0-0.0290.02119.4580.5280.5280.0000.0000.0000.000
18A265LYS10.9120.91823.10712.51012.5100.0000.0000.0000.000
19A266LYS10.8820.93826.73310.53410.5340.0000.0000.0000.000
20A267THR00.0790.06623.8240.3420.3420.0000.0000.0000.000
21A268ASN00.0290.00422.2470.0380.0380.0000.0000.0000.000
22A269VAL0-0.022-0.01224.2680.4130.4130.0000.0000.0000.000
23A270PHE0-0.005-0.01122.751-0.149-0.1490.0000.0000.0000.000
24A271ASN0-0.0120.00727.7830.0900.0900.0000.0000.0000.000
25A272ALA00.0230.02127.9190.2070.2070.0000.0000.0000.000
26A273THR00.0200.00823.827-0.380-0.3800.0000.0000.0000.000
27A274PHE00.015-0.00621.3700.1620.1620.0000.0000.0000.000
28A275HIS00.0040.00617.911-0.702-0.7020.0000.0000.0000.000
29A276ILE00.0000.01414.3080.2700.2700.0000.0000.0000.000
30A277TRP00.002-0.00813.273-0.970-0.9700.0000.0000.0000.000
31A278HIS00.0290.00512.260-0.155-0.1550.0000.0000.0000.000
32A279SER00.0000.00514.7820.8160.8160.0000.0000.0000.000
33A280GLY00.0430.02715.5100.3400.3400.0000.0000.0000.000
34A281GLN00.038-0.00213.958-1.510-1.5100.0000.0000.0000.000
35A282PHE00.0050.02314.695-0.616-0.6160.0000.0000.0000.000
36A283GLY00.0260.01714.643-0.704-0.7040.0000.0000.0000.000
37A284THR0-0.019-0.02515.2860.6760.6760.0000.0000.0000.000
38A285ILE00.0360.00817.583-0.643-0.6430.0000.0000.0000.000
39A286ASN0-0.039-0.02920.1040.2200.2200.0000.0000.0000.000
40A287ASN0-0.041-0.02821.7750.2240.2240.0000.0000.0000.000
41A288PHE00.0080.03922.9340.2860.2860.0000.0000.0000.000
42A289ARG10.8280.87120.26010.99810.9980.0000.0000.0000.000
43A290LEU0-0.0030.00118.1010.5120.5120.0000.0000.0000.000
44A291GLY00.005-0.00718.743-0.834-0.8340.0000.0000.0000.000
45A292ARG10.7910.87720.73111.29611.2960.0000.0000.0000.000
46A293LEU00.0260.01418.385-0.568-0.5680.0000.0000.0000.000
47A294PRO00.0920.04821.7740.4390.4390.0000.0000.0000.000
48A295SER0-0.030-0.01222.2600.3070.3070.0000.0000.0000.000
49A296VAL0-0.034-0.01922.2930.1780.1780.0000.0000.0000.000
50A297PRO00.0520.03724.667-0.374-0.3740.0000.0000.0000.000
51A298VAL0-0.035-0.01723.1190.3840.3840.0000.0000.0000.000
52A299GLU-1-0.859-0.91426.426-9.246-9.2460.0000.0000.0000.000
53A300TRP00.1000.02426.424-0.303-0.3030.0000.0000.0000.000
54A301ASN0-0.034-0.01229.065-0.107-0.1070.0000.0000.0000.000
55A302GLU-1-0.749-0.83624.613-11.437-11.4370.0000.0000.0000.000
56A303ILE0-0.008-0.00223.722-0.327-0.3270.0000.0000.0000.000
57A304ASN0-0.012-0.01525.139-0.527-0.5270.0000.0000.0000.000
58A305ALA00.0070.00627.361-0.033-0.0330.0000.0000.0000.000
59A306ALA00.0180.01121.807-0.141-0.1410.0000.0000.0000.000
60A307TRP00.0450.02021.067-0.517-0.5170.0000.0000.0000.000
61A308GLY00.0000.00324.352-0.108-0.1080.0000.0000.0000.000
62A309GLN0-0.014-0.01223.749-0.057-0.0570.0000.0000.0000.000
63A310THR0-0.033-0.02919.703-0.454-0.4540.0000.0000.0000.000
64A311VAL00.0080.00222.232-0.280-0.2800.0000.0000.0000.000
65A312LEU0-0.020-0.00225.0980.0750.0750.0000.0000.0000.000
66A313LEU00.0110.01318.8190.0720.0720.0000.0000.0000.000
67A314LEU0-0.006-0.00520.543-0.092-0.0920.0000.0000.0000.000
68A315HIS00.0070.00022.990-0.098-0.0980.0000.0000.0000.000
69A316ALA0-0.009-0.00625.3420.2510.2510.0000.0000.0000.000
70A317LEU0-0.043-0.01819.4830.1050.1050.0000.0000.0000.000
71A318ALA00.0350.01623.634-0.020-0.0200.0000.0000.0000.000
72A319ASN0-0.019-0.01425.4540.3210.3210.0000.0000.0000.000
73A320LYS10.8290.93324.51812.49412.4940.0000.0000.0000.000
74A321MET0-0.059-0.02920.860-0.113-0.1130.0000.0000.0000.000
75A322GLY00.0110.02725.9030.0680.0680.0000.0000.0000.000
76A323LEU0-0.0270.00623.1410.1390.1390.0000.0000.0000.000
77A324LYS10.9470.97127.1829.7369.7360.0000.0000.0000.000
78A325PHE0-0.011-0.01423.285-0.007-0.0070.0000.0000.0000.000
79A326GLN00.013-0.00826.6120.7790.7790.0000.0000.0000.000
80A327ARG10.8610.90024.97911.95611.9560.0000.0000.0000.000
81A328TYR00.002-0.01027.4310.4180.4180.0000.0000.0000.000
82A329ARG10.8430.92930.1748.7848.7840.0000.0000.0000.000
83A330LEU00.0330.00725.4230.0760.0760.0000.0000.0000.000
84A331VAL0-0.0040.00629.7460.2150.2150.0000.0000.0000.000
85A332PRO0-0.016-0.01229.577-0.064-0.0640.0000.0000.0000.000
86A333TYR00.0130.00231.1370.3380.3380.0000.0000.0000.000
87A334GLY00.0550.03231.3790.1060.1060.0000.0000.0000.000
88A335ASN0-0.011-0.01229.796-0.188-0.1880.0000.0000.0000.000
89A336HIS10.8910.95030.8808.8528.8520.0000.0000.0000.000
90A337SER00.0640.03628.6200.2050.2050.0000.0000.0000.000
91A338TYR0-0.021-0.00830.146-0.133-0.1330.0000.0000.0000.000
92A339LEU00.0060.01026.507-0.154-0.1540.0000.0000.0000.000
93A340GLU-1-0.818-0.89930.910-8.384-8.3840.0000.0000.0000.000
94A341SER00.0340.01032.777-0.318-0.3180.0000.0000.0000.000
95A342LEU0-0.075-0.04332.6030.3130.3130.0000.0000.0000.000
96A343THR00.002-0.00334.9690.0930.0930.0000.0000.0000.000
97A344ASP-1-0.888-0.94036.653-8.180-8.1800.0000.0000.0000.000
98A345LYS10.9380.95337.7717.4087.4080.0000.0000.0000.000
99A346SER00.0110.01540.1000.0730.0730.0000.0000.0000.000
100A347LYS10.8320.93732.8029.4549.4540.0000.0000.0000.000
101A348GLU-1-0.873-0.93735.603-8.338-8.3380.0000.0000.0000.000
102A349LEU0-0.045-0.03230.026-0.211-0.2110.0000.0000.0000.000
103A350PRO00.0310.02730.852-0.196-0.1960.0000.0000.0000.000
104A351LEU0-0.010-0.02424.868-0.281-0.2810.0000.0000.0000.000
105A352TYR0-0.010-0.01527.854-0.094-0.0940.0000.0000.0000.000
106A353CYS0-0.0350.00229.5880.1570.1570.0000.0000.0000.000
107A354SER0-0.034-0.02031.1800.1280.1280.0000.0000.0000.000
108A355GLY00.033-0.00232.177-0.169-0.1690.0000.0000.0000.000
109A356GLY00.0130.01533.2430.0170.0170.0000.0000.0000.000
110A357LEU00.0370.01532.260-0.290-0.2900.0000.0000.0000.000
111A358ARG10.8720.92828.55710.34210.3420.0000.0000.0000.000
112A359PHE00.001-0.00931.3670.0080.0080.0000.0000.0000.000
113A360PHE0-0.014-0.00434.4740.1190.1190.0000.0000.0000.000
114A361TRP00.0060.03032.7360.1360.1360.0000.0000.0000.000
115A362ASP-1-0.791-0.89734.472-8.880-8.8800.0000.0000.0000.000
116A363ASN0-0.002-0.02330.632-0.203-0.2030.0000.0000.0000.000
117A364LYS10.8750.96430.4578.0798.0790.0000.0000.0000.000
118A365PHE00.0710.02925.397-0.276-0.2760.0000.0000.0000.000
119A366ASP-1-0.702-0.85026.054-11.991-11.9910.0000.0000.0000.000
120A367HIS0-0.014-0.03126.036-0.292-0.2920.0000.0000.0000.000
121A368ALA00.0140.02227.493-0.235-0.2350.0000.0000.0000.000
122A369MET0-0.0110.01422.509-0.533-0.5330.0000.0000.0000.000
123A370VAL0-0.023-0.00522.598-0.646-0.6460.0000.0000.0000.000
124A371ALA00.0170.01823.557-0.364-0.3640.0000.0000.0000.000
125A372PHE00.030-0.00419.999-0.181-0.1810.0000.0000.0000.000
126A373LEU00.0200.00616.795-0.398-0.3980.0000.0000.0000.000
127A374ASP-1-0.795-0.86620.089-13.623-13.6230.0000.0000.0000.000
128A375CYS0-0.018-0.00722.163-0.006-0.0060.0000.0000.0000.000
129A376VAL0-0.027-0.01616.657-0.317-0.3170.0000.0000.0000.000
130A377GLN00.0330.00216.188-1.637-1.6370.0000.0000.0000.000
131A378GLN0-0.0020.00318.5850.0710.0710.0000.0000.0000.000
132A379PHE0-0.0010.00016.670-0.033-0.0330.0000.0000.0000.000
133A380LYS10.8820.94513.02521.76221.7620.0000.0000.0000.000
134A381GLU-1-0.954-0.99016.434-16.247-16.2470.0000.0000.0000.000
135A382GLU-1-0.930-0.96918.353-13.211-13.2110.0000.0000.0000.000
136A383VAL0-0.077-0.04115.2170.1550.1550.0000.0000.0000.000
137A384GLU-1-0.803-0.88912.101-25.285-25.2850.0000.0000.0000.000
138A385LYS10.8840.97115.89913.53913.5390.0000.0000.0000.000
139A386GLY00.0150.00819.2080.3620.3620.0000.0000.0000.000
140A387GLU-1-0.825-0.90417.827-17.440-17.4400.0000.0000.0000.000
141A388THR0-0.0390.00015.189-0.591-0.5910.0000.0000.0000.000
142A389ARG10.8160.86911.28319.35719.3570.0000.0000.0000.000
143A390PHE0-0.032-0.01110.488-2.979-2.9790.0000.0000.0000.000
144A391CYS0-0.046-0.0287.9970.2400.2400.0000.0000.0000.000
145A392LEU0-0.073-0.0318.716-1.757-1.7570.0000.0000.0000.000
146A393PRO00.0040.0045.736-1.226-1.2260.0000.0000.0000.000
147A394TYR0-0.053-0.0224.552-3.569-3.439-0.001-0.004-0.1250.000
148A395ARG10.9690.9928.81434.69834.6980.0000.0000.0000.000
149A396MET00.0000.00211.0600.7780.7780.0000.0000.0000.000
150A397ASP-1-0.801-0.89014.668-16.608-16.6080.0000.0000.0000.000
151A398VAL00.029-0.00517.3880.5250.5250.0000.0000.0000.000
152A399GLU-1-0.926-0.94520.685-12.822-12.8220.0000.0000.0000.000
153A400LYS10.8390.90019.29916.47016.4700.0000.0000.0000.000
154A401GLY0-0.048-0.00620.8160.2980.2980.0000.0000.0000.000
155A402LYS10.8980.94216.15315.79815.7980.0000.0000.0000.000
156A403ILE0-0.0050.01511.487-0.096-0.0960.0000.0000.0000.000
157A404GLU-1-0.799-0.8998.996-30.890-30.8900.0000.0000.0000.000
158A405ASP-1-0.834-0.9155.194-41.510-41.508-0.001-0.0020.0010.000
159A406THR0-0.008-0.0284.842-1.267-1.2670.0000.0000.0000.000
160A407GLY0-0.064-0.0332.548-10.446-9.4440.498-0.546-0.954-0.003
161A408GLY00.0110.0162.832-12.329-8.5840.766-2.171-2.341-0.024
162A409SER0-0.073-0.0313.9254.2114.4270.003-0.024-0.1960.000
163A410GLY00.0290.0197.0851.9961.9960.0000.0000.0000.000
164A411GLY0-0.0010.0128.8432.4242.4240.0000.0000.0000.000
165A412SER0-0.010-0.01310.887-1.326-1.3260.0000.0000.0000.000
166A413TYR0-0.041-0.04710.0372.0922.0920.0000.0000.0000.000
167A414SER0-0.023-0.01215.023-0.168-0.1680.0000.0000.0000.000
168A415ILE00.0550.02218.449-0.044-0.0440.0000.0000.0000.000
169A416LYS10.9420.97619.57313.34313.3430.0000.0000.0000.000
170A417THR00.002-0.02622.374-0.168-0.1680.0000.0000.0000.000
171A418GLN0-0.035-0.02224.680-0.007-0.0070.0000.0000.0000.000
172A419PHE0-0.056-0.03425.226-0.302-0.3020.0000.0000.0000.000
173A420ASN0-0.0220.00119.280-0.651-0.6510.0000.0000.0000.000
174A421SER00.0130.00619.9540.4160.4160.0000.0000.0000.000
175A422GLU-1-0.852-0.93120.765-11.907-11.9070.0000.0000.0000.000
176A423GLU-1-0.853-0.94017.331-13.957-13.9570.0000.0000.0000.000
177A424GLN0-0.016-0.00415.852-0.433-0.4330.0000.0000.0000.000
178A425TRP0-0.0070.00516.106-0.804-0.8040.0000.0000.0000.000
179A426THR00.000-0.01016.166-0.300-0.3000.0000.0000.0000.000
180A427LYS10.9100.9819.49423.50323.5030.0000.0000.0000.000
181A428ALA00.0160.00312.655-1.316-1.3160.0000.0000.0000.000
182A429LEU00.0390.01414.167-0.735-0.7350.0000.0000.0000.000
183A430LYS10.8000.91610.75820.67220.6720.0000.0000.0000.000
184A431PHE0-0.0050.0017.276-1.025-1.0250.0000.0000.0000.000
185A432MET00.0030.01710.809-0.510-0.5100.0000.0000.0000.000
186A433LEU00.008-0.00813.9610.0010.0010.0000.0000.0000.000
187A434THR0-0.034-0.0267.7620.1930.1930.0000.0000.0000.000
188A435ASN00.0370.00310.540-2.115-2.1150.0000.0000.0000.000
189A436LEU00.0300.01412.1930.5890.5890.0000.0000.0000.000
190A437LYS10.7810.89912.35118.79518.7950.0000.0000.0000.000
191A438TRP0-0.018-0.0236.6820.5160.5160.0000.0000.0000.000
192A439GLY00.0340.01412.7680.4300.4300.0000.0000.0000.000
193A440LEU00.0110.01115.8040.8510.8510.0000.0000.0000.000
194A441ALA0-0.0130.00414.4870.8700.8700.0000.0000.0000.000
195A442TRP00.0420.04014.5490.3600.3600.0000.0000.0000.000
196A443VAL00.0370.00416.9220.7740.7740.0000.0000.0000.000
197A444SER0-0.103-0.06819.9511.0061.0060.0000.0000.0000.000
198A445SER0-0.056-0.04918.2600.4720.4720.0000.0000.0000.000
199A446GLN0-0.0120.00017.6430.9700.9700.0000.0000.0000.000
200A447PHE0-0.0110.01521.8050.5130.5130.0000.0000.0000.000