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: 2NQQR

Calculation Name: 4B89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B89

Chain ID: A

ChEMBL ID:

UniProt ID: P25655

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2957397.992694
FMO2-HF: Nuclear repulsion 2866139.973601
FMO2-HF: Total energy -91258.019094
FMO2-MP2: Total energy -91528.091318


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:770:GLU)


Summations of interaction energy for fragment #1(A:770:GLU)
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.
-210.745-214.29831.81-15.568-12.6880.168
Interaction energy analysis for fragmet #1(A:770:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.816 / q_NPA : -0.902
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].
3A772ILE0-0.0050.0053.4074.7187.551-0.004-1.430-1.399-0.001
4A773PRO00.017-0.0036.065-3.256-3.2560.0000.0000.0000.000
5A774LEU0-0.013-0.0059.388-0.826-0.8260.0000.0000.0000.000
6A775LYS10.8590.90912.527-19.485-19.4850.0000.0000.0000.000
7A776PHE0-0.007-0.00115.490-0.849-0.8490.0000.0000.0000.000
8A777PHE00.014-0.00815.427-0.895-0.8950.0000.0000.0000.000
9A778ALA00.0020.01116.2320.8210.8210.0000.0000.0000.000
10A779VAL0-0.034-0.02116.396-0.712-0.7120.0000.0000.0000.000
11A780ASP-1-0.823-0.88418.95212.17412.1740.0000.0000.0000.000
12A781GLU-1-0.761-0.85519.81213.92113.9210.0000.0000.0000.000
13A782VAL0-0.034-0.01823.199-0.349-0.3490.0000.0000.0000.000
14A783SER0-0.023-0.00226.063-0.048-0.0480.0000.0000.0000.000
15A784CYS0-0.028-0.02129.228-0.245-0.2450.0000.0000.0000.000
16A785GLN00.0380.02530.9770.0750.0750.0000.0000.0000.000
17A786ILE0-0.019-0.00233.452-0.130-0.1300.0000.0000.0000.000
18A787ASN00.0490.01931.6000.4330.4330.0000.0000.0000.000
19A788GLN0-0.050-0.03027.8620.0020.0020.0000.0000.0000.000
20A789GLU-1-0.850-0.90729.1908.5648.5640.0000.0000.0000.000
21A790GLY0-0.037-0.02527.8960.1550.1550.0000.0000.0000.000
22A791ALA00.0060.00128.551-0.269-0.2690.0000.0000.0000.000
23A792PRO00.0350.03230.8150.1730.1730.0000.0000.0000.000
24A793LYS10.9850.96232.373-8.265-8.2650.0000.0000.0000.000
25A794ASP-1-0.741-0.87133.9597.6087.6080.0000.0000.0000.000
26A795VAL0-0.032-0.00433.484-0.072-0.0720.0000.0000.0000.000
27A796VAL0-0.032-0.01829.8570.0570.0570.0000.0000.0000.000
28A797GLU-1-0.934-0.96032.4907.5677.5670.0000.0000.0000.000
29A798LYS10.8950.94735.086-7.441-7.4410.0000.0000.0000.000
30A799VAL0-0.014-0.00931.185-0.021-0.0210.0000.0000.0000.000
31A800LEU0-0.023-0.01628.9770.0680.0680.0000.0000.0000.000
32A801PHE00.0080.01732.894-0.033-0.0330.0000.0000.0000.000
33A802VAL00.0170.00635.628-0.105-0.1050.0000.0000.0000.000
34A803LEU0-0.038-0.02929.373-0.017-0.0170.0000.0000.0000.000
35A804ASN00.0070.01832.2040.2600.2600.0000.0000.0000.000
36A805ASN0-0.034-0.02034.532-0.229-0.2290.0000.0000.0000.000
37A806VAL0-0.048-0.00634.954-0.236-0.2360.0000.0000.0000.000
38A807THR00.010-0.00537.1190.0580.0580.0000.0000.0000.000
39A808LEU00.038-0.00537.991-0.034-0.0340.0000.0000.0000.000
40A809ALA00.0140.01740.634-0.079-0.0790.0000.0000.0000.000
41A810ASN00.0060.00641.1160.0030.0030.0000.0000.0000.000
42A811LEU00.0390.03037.5350.0200.0200.0000.0000.0000.000
43A812ASN00.0360.00440.8110.1960.1960.0000.0000.0000.000
44A813ASN00.0530.02843.1640.0080.0080.0000.0000.0000.000
45A814LYS10.8610.94138.983-7.133-7.1330.0000.0000.0000.000
46A815VAL00.001-0.00737.3870.1260.1260.0000.0000.0000.000
47A816ASP-1-0.842-0.91439.6366.7796.7790.0000.0000.0000.000
48A817GLU-1-0.875-0.92340.9726.6376.6370.0000.0000.0000.000
49A818LEU0-0.007-0.01033.9580.0760.0760.0000.0000.0000.000
50A819LYS10.8560.92537.871-6.952-6.9520.0000.0000.0000.000
51A820LYS10.8210.91839.561-6.533-6.5330.0000.0000.0000.000
52A821SER0-0.005-0.00537.025-0.060-0.0600.0000.0000.0000.000
53A822LEU0-0.067-0.03531.6260.1480.1480.0000.0000.0000.000
54A823THR00.0420.00835.642-0.049-0.0490.0000.0000.0000.000
55A824PRO00.051-0.01334.2270.2180.2180.0000.0000.0000.000
56A825ASN0-0.0120.01432.6710.1990.1990.0000.0000.0000.000
57A826TYR00.0480.02930.6550.1890.1890.0000.0000.0000.000
58A827PHE00.0540.02229.7920.1870.1870.0000.0000.0000.000
59A828SER00.0560.03624.3480.3270.3270.0000.0000.0000.000
60A829TRP00.0220.01624.9420.3370.3370.0000.0000.0000.000
61A830PHE00.0550.01225.5100.2610.2610.0000.0000.0000.000
62A831SER00.009-0.02224.6760.0680.0680.0000.0000.0000.000
63A832THR00.004-0.01019.7800.4810.4810.0000.0000.0000.000
64A833TYR00.0140.03421.4720.3210.3210.0000.0000.0000.000
65A834LEU00.0160.00523.4180.1780.1780.0000.0000.0000.000
66A835VAL0-0.007-0.00819.6110.1170.1170.0000.0000.0000.000
67A836THR0-0.090-0.06917.5840.3350.3350.0000.0000.0000.000
68A837GLN0-0.030-0.02319.2420.1180.1180.0000.0000.0000.000
69A838ARG10.8360.91422.004-9.962-9.9620.0000.0000.0000.000
70A839ALA00.0180.01322.5990.0250.0250.0000.0000.0000.000
71A840LYS10.9130.96814.600-15.603-15.6030.0000.0000.0000.000
72A841THR00.0170.00419.6310.4740.4740.0000.0000.0000.000
73A842GLU-1-0.809-0.86421.8989.7739.7730.0000.0000.0000.000
74A843PRO00.009-0.00924.083-0.219-0.2190.0000.0000.0000.000
75A844ASN0-0.028-0.01826.374-0.018-0.0180.0000.0000.0000.000
76A845TYR00.0410.02428.825-0.286-0.2860.0000.0000.0000.000
77A846HIS0-0.084-0.02923.875-0.267-0.2670.0000.0000.0000.000
78A847ASP-1-0.798-0.88528.8908.2348.2340.0000.0000.0000.000
79A848LEU00.0430.03032.399-0.123-0.1230.0000.0000.0000.000
80A849TYR0-0.024-0.04827.549-0.220-0.2200.0000.0000.0000.000
81A850SER0-0.053-0.03330.427-0.061-0.0610.0000.0000.0000.000
82A851LYS10.8510.90331.580-8.151-8.1510.0000.0000.0000.000
83A852VAL00.0260.01833.132-0.191-0.1910.0000.0000.0000.000
84A853ILE0-0.037-0.01528.558-0.084-0.0840.0000.0000.0000.000
85A854VAL0-0.044-0.02933.093-0.099-0.0990.0000.0000.0000.000
86A855ALA0-0.0030.00435.871-0.152-0.1520.0000.0000.0000.000
87A856MET0-0.040-0.01734.489-0.210-0.2100.0000.0000.0000.000
88A857GLY0-0.0130.01537.224-0.098-0.0980.0000.0000.0000.000
89A858SER0-0.0120.00734.421-0.040-0.0400.0000.0000.0000.000
90A859GLY00.029-0.00233.8590.2040.2040.0000.0000.0000.000
91A860LEU00.0340.01730.5020.2700.2700.0000.0000.0000.000
92A861LEU00.0040.01029.2990.3340.3340.0000.0000.0000.000
93A862HIS0-0.046-0.03528.8390.2590.2590.0000.0000.0000.000
94A863GLN0-0.003-0.01127.8690.4720.4720.0000.0000.0000.000
95A864PHE00.0610.01924.9200.4700.4700.0000.0000.0000.000
96A865MET0-0.0130.02423.9820.6220.6220.0000.0000.0000.000
97A866VAL00.0120.01123.4050.4930.4930.0000.0000.0000.000
98A867ASN0-0.0120.01121.3890.8200.8200.0000.0000.0000.000
99A868VAL00.0440.02119.1600.7410.7410.0000.0000.0000.000
100A869THR0-0.034-0.03318.2420.6890.6890.0000.0000.0000.000
101A870LEU0-0.016-0.01017.9340.6310.6310.0000.0000.0000.000
102A871ARG10.8120.86415.484-13.451-13.4510.0000.0000.0000.000
103A872GLN0-0.001-0.00313.7330.9810.9810.0000.0000.0000.000
104A873LEU0-0.008-0.01213.1670.8770.8770.0000.0000.0000.000
105A874PHE00.0210.01910.3970.8250.8250.0000.0000.0000.000
106A875VAL00.0130.0198.1091.6061.6060.0000.0000.0000.000
107A876LEU0-0.0080.0038.2161.8611.8610.0000.0000.0000.000
108A877LEU0-0.010-0.0119.3921.3321.3320.0000.0000.0000.000
109A878SER0-0.0040.0007.8000.5660.5660.0000.0000.0000.000
110A879THR0-0.006-0.0074.2804.1434.196-0.001-0.021-0.0300.000
111A880LYS10.8110.8941.755-151.665-158.44431.816-14.100-10.9370.169
112A881ASP-1-0.820-0.9114.36730.28430.624-0.001-0.017-0.3220.000
113A882GLU-1-0.786-0.9156.02921.26221.2620.0000.0000.0000.000
114A883GLN0-0.064-0.0319.476-3.303-3.3030.0000.0000.0000.000
115A884ALA0-0.0040.0136.267-1.743-1.7430.0000.0000.0000.000
116A885ILE0-0.046-0.0028.326-1.311-1.3110.0000.0000.0000.000
117A886ASP-1-0.789-0.88510.21514.68114.6810.0000.0000.0000.000
118A887LYS10.8810.90212.690-20.779-20.7790.0000.0000.0000.000
119A888LYS10.8840.95215.984-12.569-12.5690.0000.0000.0000.000
120A889HIS00.0440.01214.961-0.174-0.1740.0000.0000.0000.000
121A890LEU00.0090.01513.910-0.493-0.4930.0000.0000.0000.000
122A891LYS10.8500.91016.230-14.033-14.0330.0000.0000.0000.000
123A892ASN0-0.031-0.02519.738-0.916-0.9160.0000.0000.0000.000
124A893LEU00.0480.01615.828-0.555-0.5550.0000.0000.0000.000
125A894ALA00.0010.01619.398-0.323-0.3230.0000.0000.0000.000
126A895SER00.0250.00420.872-0.651-0.6510.0000.0000.0000.000
127A896TRP00.0170.01922.197-0.634-0.6340.0000.0000.0000.000
128A897LEU00.0410.01621.036-0.353-0.3530.0000.0000.0000.000
129A898GLY00.0130.01923.904-0.352-0.3520.0000.0000.0000.000
130A899CYS0-0.081-0.04326.709-0.480-0.4800.0000.0000.0000.000
131A900ILE00.0270.01724.980-0.428-0.4280.0000.0000.0000.000
132A901THR0-0.053-0.04026.538-0.062-0.0620.0000.0000.0000.000
133A902LEU00.0280.02027.831-0.361-0.3610.0000.0000.0000.000
134A903ALA00.0400.02430.775-0.314-0.3140.0000.0000.0000.000
135A904LEU0-0.063-0.01931.890-0.328-0.3280.0000.0000.0000.000
136A905ASN0-0.071-0.04734.272-0.154-0.1540.0000.0000.0000.000
137A906LYS10.9330.98231.541-8.726-8.7260.0000.0000.0000.000
138A907PRO00.0580.02430.6810.2090.2090.0000.0000.0000.000
139A908ILE00.0310.02324.1000.0840.0840.0000.0000.0000.000
140A909LYS10.8640.92326.253-10.632-10.6320.0000.0000.0000.000
141A910HIS00.0990.04225.0730.3210.3210.0000.0000.0000.000
142A911LYS10.8750.93324.063-10.976-10.9760.0000.0000.0000.000
143A912ASN0-0.108-0.06021.423-0.188-0.1880.0000.0000.0000.000
144A913ILE00.0380.01719.6870.7470.7470.0000.0000.0000.000
145A914ALA00.0180.03321.135-0.733-0.7330.0000.0000.0000.000
146A915PHE00.047-0.00421.7990.4310.4310.0000.0000.0000.000
147A916ARG10.9600.97522.676-10.398-10.3980.0000.0000.0000.000
148A917GLU-1-0.872-0.93221.19813.49113.4910.0000.0000.0000.000
149A918MET0-0.027-0.00316.1040.4700.4700.0000.0000.0000.000
150A919LEU0-0.024-0.00818.4140.7080.7080.0000.0000.0000.000
151A920ILE00.0170.00920.4350.3380.3380.0000.0000.0000.000
152A921GLU-1-0.756-0.86415.54318.22418.2240.0000.0000.0000.000
153A922ALA00.006-0.00215.7090.9820.9820.0000.0000.0000.000
154A923TYR0-0.013-0.01816.7940.5900.5900.0000.0000.0000.000
155A924LYS10.8710.93617.413-15.768-15.7680.0000.0000.0000.000
156A925GLU-1-0.936-0.96611.93425.20325.2030.0000.0000.0000.000
157A926ASN0-0.072-0.02113.0620.6900.6900.0000.0000.0000.000
158A927ARG10.8600.9248.263-28.343-28.3430.0000.0000.0000.000
159A928LEU0-0.013-0.01214.172-0.740-0.7400.0000.0000.0000.000
160A929GLU-1-0.816-0.89215.61416.17316.1730.0000.0000.0000.000
161A930ILE0-0.0190.00911.663-0.733-0.7330.0000.0000.0000.000
162A931VAL00.013-0.01015.009-0.975-0.9750.0000.0000.0000.000
163A932VAL00.0110.01117.249-0.896-0.8960.0000.0000.0000.000
164A933PRO0-0.014-0.00918.386-0.760-0.7600.0000.0000.0000.000
165A934PHE00.0170.01017.336-0.555-0.5550.0000.0000.0000.000
166A935VAL00.0290.00919.402-0.663-0.6630.0000.0000.0000.000
167A936THR0-0.010-0.01522.419-0.491-0.4910.0000.0000.0000.000
168A937LYS10.8350.91122.233-12.168-12.1680.0000.0000.0000.000
169A938ILE0-0.0090.01220.849-0.430-0.4300.0000.0000.0000.000
170A939LEU00.002-0.01124.768-0.490-0.4900.0000.0000.0000.000
171A940GLN00.0500.02227.570-0.087-0.0870.0000.0000.0000.000
172A941ARG10.8740.94927.623-10.349-10.3490.0000.0000.0000.000
173A942ALA0-0.023-0.01730.274-0.229-0.2290.0000.0000.0000.000
174A943SER0-0.069-0.04332.518-0.321-0.3210.0000.0000.0000.000
175A944GLU-1-0.843-0.92634.0428.5498.5490.0000.0000.0000.000
176A945SER0-0.067-0.01734.445-0.184-0.1840.0000.0000.0000.000
177A946LYS10.9830.98836.415-7.302-7.3020.0000.0000.0000.000
178A947ILE0-0.036-0.01236.511-0.135-0.1350.0000.0000.0000.000
179A948PHE00.006-0.00733.2210.0660.0660.0000.0000.0000.000
180A949LYS10.9811.03834.799-7.388-7.3880.0000.0000.0000.000
181A950PRO00.0130.03035.559-0.072-0.0720.0000.0000.0000.000
182A951PRO00.0030.00038.065-0.122-0.1220.0000.0000.0000.000
183A952ASN00.007-0.01835.1490.2220.2220.0000.0000.0000.000
184A953PRO00.0720.01336.0290.2190.2190.0000.0000.0000.000
185A954TRP0-0.0190.00727.2080.1280.1280.0000.0000.0000.000
186A955THR0-0.002-0.02531.3330.3900.3900.0000.0000.0000.000
187A956VAL00.0320.00831.9360.2090.2090.0000.0000.0000.000
188A957GLY0-0.035-0.01731.8940.0850.0850.0000.0000.0000.000
189A958ILE0-0.010-0.00526.4510.2580.2580.0000.0000.0000.000
190A959LEU00.0070.00928.6110.2450.2450.0000.0000.0000.000
191A960LYS10.8690.91930.893-8.985-8.9850.0000.0000.0000.000
192A961LEU00.0200.02724.694-0.033-0.0330.0000.0000.0000.000
193A962LEU0-0.013-0.01024.3440.2810.2810.0000.0000.0000.000
194A963ILE0-0.008-0.00827.5390.0980.0980.0000.0000.0000.000
195A964GLU-1-0.692-0.80028.60810.95410.9540.0000.0000.0000.000
196A965LEU0-0.017-0.01623.0760.1100.1100.0000.0000.0000.000
197A966ASN00.0130.00626.5010.4120.4120.0000.0000.0000.000
198A967GLU-1-0.958-0.96728.1669.5169.5160.0000.0000.0000.000
199A968LYS10.8040.88427.753-10.686-10.6860.0000.0000.0000.000
200A969ALA0-0.044-0.02222.8040.2570.2570.0000.0000.0000.000
201A970ASN0-0.0310.00223.5380.0600.0600.0000.0000.0000.000
202A971TRP00.0190.01221.9500.7510.7510.0000.0000.0000.000
203A972LYS10.8980.91518.294-17.006-17.0060.0000.0000.0000.000
204A973LEU00.0900.03523.203-0.093-0.0930.0000.0000.0000.000
205A974SER00.011-0.00621.861-0.267-0.2670.0000.0000.0000.000
206A975LEU0-0.022-0.00919.760-0.129-0.1290.0000.0000.0000.000
207A976THR00.0440.02723.965-0.126-0.1260.0000.0000.0000.000
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