FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: JL359

Calculation Name: 3QLL-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3QLL

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9ZC38

Base Structure: X-ray

Registration Date: 2023-06-21

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2401734.070181
FMO2-HF: Nuclear repulsion 2321071.557641
FMO2-HF: Total energy -80662.512539
FMO2-MP2: Total energy -80898.502545


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:5:ASP)


Summations of interaction energy for fragment #1(A:5:ASP)
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.
41.61646.79518.694-11.489-12.3860.116
Interaction energy analysis for fragmet #1(A:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.807 / q_NPA : -0.906
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].
3A7TYR0-0.021-0.0042.188-30.069-23.1503.263-4.835-5.3480.053
4A8GLN0-0.090-0.0431.822-41.816-44.01715.428-6.537-6.6900.063
5A9THR0-0.082-0.0244.672-10.716-10.4960.000-0.062-0.1580.000
6A10ARG10.8410.8887.212-25.526-25.5260.0000.0000.0000.000
7A11SER0-0.024-0.04110.969-1.969-1.9690.0000.0000.0000.000
8A12TRP00.0070.0007.212-0.696-0.6960.0000.0000.0000.000
9A13LEU0-0.020-0.01812.865-1.236-1.2360.0000.0000.0000.000
10A14PHE00.0290.02915.7700.2100.2100.0000.0000.0000.000
11A15THR0-0.039-0.03318.001-0.692-0.6920.0000.0000.0000.000
12A16PRO00.0870.05920.0210.2920.2920.0000.0000.0000.000
13A17ALA00.0240.03422.064-0.015-0.0150.0000.0000.0000.000
14A18THR0-0.033-0.01422.961-0.213-0.2130.0000.0000.0000.000
15A19ARG10.8540.92119.085-13.126-13.1260.0000.0000.0000.000
16A30GLY0-0.020-0.02715.728-0.327-0.3270.0000.0000.0000.000
17A31ALA0-0.029-0.01913.6770.7020.7020.0000.0000.0000.000
18A32ASP-1-0.730-0.8218.25526.54526.5450.0000.0000.0000.000
19A33VAL00.0150.0127.1460.9310.9310.0000.0000.0000.000
20A34ALA0-0.038-0.0039.924-1.249-1.2490.0000.0000.0000.000
21A35ILE00.019-0.00912.6210.6010.6010.0000.0000.0000.000
22A36ILE0-0.026-0.00514.646-1.084-1.0840.0000.0000.0000.000
23A37ASP-1-0.760-0.84917.51713.71013.7100.0000.0000.0000.000
24A38LEU00.006-0.00319.986-0.649-0.6490.0000.0000.0000.000
25A39GLU-1-0.810-0.93022.29712.19112.1910.0000.0000.0000.000
26A40ASP-1-0.809-0.88624.07511.75911.7590.0000.0000.0000.000
27A41SER0-0.102-0.07123.090-0.431-0.4310.0000.0000.0000.000
28A42VAL0-0.072-0.02224.623-0.392-0.3920.0000.0000.0000.000
29A43SER00.001-0.03327.312-0.135-0.1350.0000.0000.0000.000
30A44GLN00.0760.00930.3360.3200.3200.0000.0000.0000.000
31A45ALA0-0.049-0.02632.191-0.028-0.0280.0000.0000.0000.000
32A46ASP-1-0.872-0.90229.7389.0939.0930.0000.0000.0000.000
33A47LYS10.7780.91426.421-10.644-10.6440.0000.0000.0000.000
34A48GLU-1-0.801-0.87627.6499.9599.9590.0000.0000.0000.000
35A49GLN00.0250.00528.7460.2910.2910.0000.0000.0000.000
36A50ALA0-0.049-0.03525.0370.1680.1680.0000.0000.0000.000
37A51ARG10.7960.87124.102-10.017-10.0170.0000.0000.0000.000
38A52GLN0-0.029-0.03023.7370.3150.3150.0000.0000.0000.000
39A53LYS10.8630.91924.385-9.842-9.8420.0000.0000.0000.000
40A54ALA00.0110.02119.7270.2100.2100.0000.0000.0000.000
41A55ILE0-0.032-0.00619.9230.4090.4090.0000.0000.0000.000
42A56SER0-0.074-0.01720.3710.0460.0460.0000.0000.0000.000
43A66LEU0-0.014-0.0099.389-0.184-0.1840.0000.0000.0000.000
44A67PRO0-0.032-0.0105.830-0.909-0.9090.0000.0000.0000.000
45A68LEU0-0.015-0.0198.046-0.890-0.8900.0000.0000.0000.000
46A69ALA00.002-0.01010.2440.8450.8450.0000.0000.0000.000
47A70LEU0-0.028-0.01811.798-1.158-1.1580.0000.0000.0000.000
48A71ARG10.7660.87015.268-13.254-13.2540.0000.0000.0000.000
49A72ILE0-0.021-0.00317.467-0.747-0.7470.0000.0000.0000.000
50A73ASN0-0.015-0.04520.381-0.131-0.1310.0000.0000.0000.000
51A74GLY00.0720.04823.0390.2860.2860.0000.0000.0000.000
52A75LEU00.0280.00022.235-0.410-0.4100.0000.0000.0000.000
53A76ASP-1-0.967-0.96425.33810.69910.6990.0000.0000.0000.000
54A77THR0-0.016-0.01926.963-0.487-0.4870.0000.0000.0000.000
55A78ARG10.8510.88828.635-8.575-8.5750.0000.0000.0000.000
56A79ALA0-0.006-0.00427.5220.0030.0030.0000.0000.0000.000
57A80GLY00.0750.05424.6660.1450.1450.0000.0000.0000.000
58A81ILE0-0.026-0.01924.7660.2590.2590.0000.0000.0000.000
59A82GLU-1-0.786-0.87926.6739.4709.4700.0000.0000.0000.000
60A83ASP-1-0.736-0.85022.52111.81011.8100.0000.0000.0000.000
61A84ILE0-0.009-0.00321.4520.3330.3330.0000.0000.0000.000
62A85HIS0-0.079-0.04023.2790.2030.2030.0000.0000.0000.000
63A86ALA00.002-0.01324.653-0.037-0.0370.0000.0000.0000.000
64A87LEU0-0.047-0.02718.1780.1090.1090.0000.0000.0000.000
65A88LEU0-0.058-0.02521.1140.1450.1450.0000.0000.0000.000
66A89GLU-1-0.934-0.93923.1069.5549.5540.0000.0000.0000.000
67A90CYS0-0.063-0.03823.541-0.201-0.2010.0000.0000.0000.000
68A91GLY00.0140.00821.7540.1690.1690.0000.0000.0000.000
69A92SER0-0.051-0.01618.2770.6240.6240.0000.0000.0000.000
70A93LEU00.000-0.01114.864-0.216-0.2160.0000.0000.0000.000
71A94PRO0-0.0400.00612.3380.2990.2990.0000.0000.0000.000
72A95ASP-1-0.775-0.8917.12024.06724.0670.0000.0000.0000.000
73A96TYR0-0.027-0.0143.2523.6113.8520.003-0.055-0.1900.000
74A97LEU00.0140.0109.981-1.488-1.4880.0000.0000.0000.000
75A98VAL0-0.027-0.03312.6750.6600.6600.0000.0000.0000.000
76A99LEU00.010-0.00314.909-1.125-1.1250.0000.0000.0000.000
77A100PRO00.0350.02018.1480.5500.5500.0000.0000.0000.000
78A101LYS10.8760.91620.867-11.580-11.5800.0000.0000.0000.000
79A102THR0-0.0200.00218.298-0.029-0.0290.0000.0000.0000.000
80A103GLU-1-0.789-0.88321.18011.37211.3720.0000.0000.0000.000
81A104SER0-0.046-0.02522.510-0.318-0.3180.0000.0000.0000.000
82A105ALA00.1060.05020.3640.4550.4550.0000.0000.0000.000
83A106ALA0-0.008-0.01120.5910.4110.4110.0000.0000.0000.000
84A107HIS0-0.022-0.01421.181-0.192-0.1920.0000.0000.0000.000
85A108LEU00.0740.03515.4300.0020.0020.0000.0000.0000.000
86A109GLN0-0.048-0.03818.010-0.506-0.5060.0000.0000.0000.000
87A110ILE0-0.047-0.01819.900-0.126-0.1260.0000.0000.0000.000
88A111LEU00.0750.03617.368-0.256-0.2560.0000.0000.0000.000
89A112ASP-1-0.828-0.87716.40418.16218.1620.0000.0000.0000.000
90A113ARG10.8840.91917.479-13.429-13.4290.0000.0000.0000.000
91A114LEU0-0.029-0.00920.808-0.362-0.3620.0000.0000.0000.000
92A115MET00.0050.03414.901-0.294-0.2940.0000.0000.0000.000
93A116MET0-0.054-0.02417.1230.6520.6520.0000.0000.0000.000
94A117PHE0-0.049-0.02519.294-0.300-0.3000.0000.0000.0000.000
95A118ALA00.0350.01219.3730.0400.0400.0000.0000.0000.000
96A119GLY00.0590.01715.3390.4410.4410.0000.0000.0000.000
97A120SER0-0.028-0.02214.4590.2990.2990.0000.0000.0000.000
98A121ASP-1-0.967-0.97010.33721.53421.5340.0000.0000.0000.000
99A122THR0-0.024-0.0019.5461.6931.6930.0000.0000.0000.000
100A123ARG10.8620.9255.715-35.198-35.1980.0000.0000.0000.000
101A124LEU0-0.013-0.0109.776-1.448-1.4480.0000.0000.0000.000
102A125ILE00.0030.0078.4782.3512.3510.0000.0000.0000.000
103A126GLY00.0270.02112.339-1.601-1.6010.0000.0000.0000.000
104A127ILE0-0.014-0.00215.5251.0331.0330.0000.0000.0000.000
105A128ILE0-0.034-0.01717.725-0.881-0.8810.0000.0000.0000.000
106A129GLU-1-0.793-0.90220.12314.09314.0930.0000.0000.0000.000
107A130SER0-0.019-0.03023.295-0.415-0.4150.0000.0000.0000.000
108A131VAL00.041-0.00125.3670.4290.4290.0000.0000.0000.000
109A132ARG10.8470.93227.177-10.314-10.3140.0000.0000.0000.000
110A133GLY00.0550.02923.3960.1450.1450.0000.0000.0000.000
111A134LEU0-0.021-0.00722.2630.4870.4870.0000.0000.0000.000
112A135ASN0-0.043-0.03523.5560.3040.3040.0000.0000.0000.000
113A136ALA00.0070.02223.962-0.176-0.1760.0000.0000.0000.000
114A137VAL00.0420.02118.1680.5380.5380.0000.0000.0000.000
115A138GLU-1-0.783-0.86018.69314.94114.9410.0000.0000.0000.000
116A139SER0-0.094-0.05019.0330.3630.3630.0000.0000.0000.000
117A140ILE0-0.031-0.02617.0920.2310.2310.0000.0000.0000.000
118A141ALA00.0190.00514.5270.7250.7250.0000.0000.0000.000
119A142ALA00.0250.03314.2131.2711.2710.0000.0000.0000.000
120A143ALA0-0.087-0.02716.590-0.560-0.5600.0000.0000.0000.000
121A144THR0-0.006-0.04414.365-0.496-0.4960.0000.0000.0000.000
122A145PRO00.0490.02612.1651.0981.0980.0000.0000.0000.000
123A146LYS10.8680.93510.176-15.793-15.7930.0000.0000.0000.000
124A147LEU0-0.0680.00010.0360.9690.9690.0000.0000.0000.000
125A148ALA0-0.043-0.0295.9571.9001.9000.0000.0000.0000.000
126A149GLY00.0800.0347.0794.6944.6940.0000.0000.0000.000
127A150LEU0-0.044-0.0119.629-2.468-2.4680.0000.0000.0000.000
128A151ILE00.0250.02513.1850.6420.6420.0000.0000.0000.000
129A152PHE0-0.007-0.01115.211-1.064-1.0640.0000.0000.0000.000
130A153GLY00.0600.01518.4280.0460.0460.0000.0000.0000.000
131A154ALA0-0.029-0.02821.499-0.627-0.6270.0000.0000.0000.000
132A155ALA0-0.010-0.00823.878-0.505-0.5050.0000.0000.0000.000
133A156ASP-1-0.831-0.91725.54111.13611.1360.0000.0000.0000.000
134A157MET0-0.0390.00923.186-0.524-0.5240.0000.0000.0000.000
135A158ALA0-0.050-0.03426.628-0.358-0.3580.0000.0000.0000.000
136A159ALA00.0160.01829.360-0.441-0.4410.0000.0000.0000.000
137A160ASP-1-0.872-0.93329.29210.29710.2970.0000.0000.0000.000
138A161ILE0-0.080-0.03928.041-0.252-0.2520.0000.0000.0000.000
139A162GLY0-0.0190.00132.103-0.332-0.3320.0000.0000.0000.000
140A163ALA0-0.085-0.03831.266-0.257-0.2570.0000.0000.0000.000
141A164ALA00.001-0.00732.5630.0470.0470.0000.0000.0000.000
142A165SER00.038-0.00628.0860.0960.0960.0000.0000.0000.000
143A166THR0-0.020-0.00427.5870.3810.3810.0000.0000.0000.000
144A167TRP00.0410.00820.466-0.076-0.0760.0000.0000.0000.000
145A168GLU-1-0.801-0.89726.84211.11711.1170.0000.0000.0000.000
146A169PRO0-0.050-0.02629.1990.0660.0660.0000.0000.0000.000
147A170LEU00.0170.02224.9800.0340.0340.0000.0000.0000.000
148A171ALA00.0000.01324.5420.5890.5890.0000.0000.0000.000
149A172LEU00.009-0.00423.9730.4880.4880.0000.0000.0000.000
150A173ALA00.008-0.00423.7480.3460.3460.0000.0000.0000.000
151A174ARG10.8310.90120.168-14.111-14.1110.0000.0000.0000.000
152A175ALA00.0320.01819.1330.9100.9100.0000.0000.0000.000
153A176ARG10.7530.84519.691-12.462-12.4620.0000.0000.0000.000
154A177LEU00.0260.01615.9370.2910.2910.0000.0000.0000.000
155A178VAL00.0370.02014.3801.1011.1010.0000.0000.0000.000
156A179SER0-0.035-0.01614.8531.3701.3700.0000.0000.0000.000
157A180ALA00.0080.01016.3410.4520.4520.0000.0000.0000.000
158A181CYS0-0.045-0.02011.4840.3300.3300.0000.0000.0000.000
159A182ALA00.0410.02011.6171.8601.8600.0000.0000.0000.000
160A183MET0-0.063-0.02212.7320.5170.5170.0000.0000.0000.000
161A184ASN0-0.071-0.05512.662-1.245-1.2450.0000.0000.0000.000
162A185GLY0-0.0200.0159.2561.0141.0140.0000.0000.0000.000
163A186ILE0-0.025-0.0076.9925.6825.6820.0000.0000.0000.000
164A187PRO00.0170.0125.586-3.937-3.9370.0000.0000.0000.000
165A188ALA00.0080.0058.310-2.204-2.2040.0000.0000.0000.000
166A189ILE0-0.025-0.0279.6570.5720.5720.0000.0000.0000.000
167A190ASP-1-0.735-0.86512.91614.75914.7590.0000.0000.0000.000
168A191ALA00.0290.01916.4540.3240.3240.0000.0000.0000.000
169A192PRO0-0.0140.01919.3770.2310.2310.0000.0000.0000.000
170A193PHE0-0.021-0.00120.735-0.492-0.4920.0000.0000.0000.000
171A194PHE00.015-0.00623.804-0.016-0.0160.0000.0000.0000.000
172A195ASP-1-0.854-0.92826.6299.9729.9720.0000.0000.0000.000
173A196VAL0-0.046-0.03325.9140.2860.2860.0000.0000.0000.000
174A197HIS0-0.023-0.01227.7340.1150.1150.0000.0000.0000.000
175A198ASP-1-0.863-0.91830.20710.46410.4640.0000.0000.0000.000
176A199VAL00.017-0.00526.0330.3980.3980.0000.0000.0000.000
177A200SER00.0180.00726.7300.3920.3920.0000.0000.0000.000
178A201GLY0-0.007-0.00327.4160.3080.3080.0000.0000.0000.000
179A202LEU0-0.0200.00321.3580.4370.4370.0000.0000.0000.000
180A203GLN0-0.002-0.00322.7880.5060.5060.0000.0000.0000.000
181A204SER00.0050.00922.8820.5640.5640.0000.0000.0000.000
182A205GLU-1-0.808-0.89121.63614.12614.1260.0000.0000.0000.000
183A206THR0-0.032-0.04117.6980.7510.7510.0000.0000.0000.000
184A207LEU0-0.0010.00818.6950.8500.8500.0000.0000.0000.000
185A208ARG10.8620.93520.166-11.763-11.7630.0000.0000.0000.000
186A209ALA0-0.009-0.00317.3240.2350.2350.0000.0000.0000.000
187A210SER00.0190.00015.6851.2801.2800.0000.0000.0000.000
188A211ASP-1-0.973-0.97716.51415.89715.8970.0000.0000.0000.000
189A212PHE0-0.116-0.07218.660-0.441-0.4410.0000.0000.0000.000
190A213GLY0-0.0080.01114.927-0.137-0.1370.0000.0000.0000.000
191A214PHE0-0.065-0.03913.0341.3551.3550.0000.0000.0000.000
192A215SER0-0.033-0.0128.5960.5630.5630.0000.0000.0000.000
193A216ALA00.0140.0149.8521.0291.0290.0000.0000.0000.000
194A217LYS10.7490.86011.841-17.276-17.2760.0000.0000.0000.000
195A218ALA00.0100.00715.0790.3440.3440.0000.0000.0000.000
196A219ALA0-0.020-0.01716.282-0.751-0.7510.0000.0000.0000.000
197A220ILE00.0160.00018.7260.1910.1910.0000.0000.0000.000
198A221HIS00.0470.02021.185-0.297-0.2970.0000.0000.0000.000
199A222PRO00.0430.00620.0120.4380.4380.0000.0000.0000.000
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