Manual

About

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: K9ZN3

Calculation Name: 5I66-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I66

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2223732.484041
FMO2-HF: Nuclear repulsion 2140279.012273
FMO2-HF: Total energy -83453.471768
FMO2-MP2: Total energy -83695.890607


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(B:21:ASP)


Summations of interaction energy for fragment #1(B:21: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.
-67.577-60.43.614-4.146-6.6430.039
Interaction energy analysis for fragmet #1(B:21:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.903 / q_NPA : -0.960
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].
3B23VAL00.0200.0163.509-0.4542.1740.016-1.192-1.4520.007
4B24MET0-0.0010.0095.499-3.460-3.4600.0000.0000.0000.000
5B25THR0-0.007-0.0178.387-0.059-0.0590.0000.0000.0000.000
6B26GLN00.0350.00211.2570.1690.1690.0000.0000.0000.000
7B27SER00.000-0.00814.4200.1460.1460.0000.0000.0000.000
8B28HIS0-0.0080.01816.444-0.490-0.4900.0000.0000.0000.000
9B29LYS10.9981.00514.498-18.565-18.5650.0000.0000.0000.000
10B30PHE00.0150.01319.2220.0430.0430.0000.0000.0000.000
11B31MET0-0.0260.00420.3780.0210.0210.0000.0000.0000.000
12B32SER00.0060.01524.712-0.073-0.0730.0000.0000.0000.000
13B33THR00.0170.01028.424-0.053-0.0530.0000.0000.0000.000
14B34SER00.0210.01930.366-0.100-0.1000.0000.0000.0000.000
15B35VAL0-0.008-0.01333.1700.1380.1380.0000.0000.0000.000
16B36GLY0-0.019-0.00834.206-0.238-0.2380.0000.0000.0000.000
17B37ASP-1-0.897-0.93732.4958.7478.7470.0000.0000.0000.000
18B38ARG10.9410.98027.714-10.216-10.2160.0000.0000.0000.000
19B39VAL0-0.039-0.01925.0870.0040.0040.0000.0000.0000.000
20B40SER0-0.022-0.03923.641-0.024-0.0240.0000.0000.0000.000
21B41ILE00.008-0.01318.1230.0210.0210.0000.0000.0000.000
22B42THR0-0.0150.00418.3490.2640.2640.0000.0000.0000.000
23B43CYS0-0.046-0.00512.1690.6380.6380.0000.0000.0000.000
24B44LYS10.9490.98912.879-17.977-17.9770.0000.0000.0000.000
25B45ALA00.014-0.0019.4251.4881.4880.0000.0000.0000.000
26B46SER0-0.028-0.0106.209-0.633-0.6330.0000.0000.0000.000
27B47GLN00.004-0.0066.1762.1912.1910.0000.0000.0000.000
28B48ASP-1-0.857-0.9289.52118.89718.8970.0000.0000.0000.000
29B49VAL0-0.015-0.0168.6661.7791.7790.0000.0000.0000.000
30B50SER0-0.0010.00911.279-0.935-0.9350.0000.0000.0000.000
31B51THR00.0590.01414.988-0.129-0.1290.0000.0000.0000.000
32B52ALA0-0.0190.01412.116-0.578-0.5780.0000.0000.0000.000
33B53VAL0-0.004-0.00812.0331.9601.9600.0000.0000.0000.000
34B54ALA0-0.032-0.01413.404-1.573-1.5730.0000.0000.0000.000
35B55TRP00.002-0.01214.4091.1151.1150.0000.0000.0000.000
36B56TYR0-0.021-0.03513.785-1.266-1.2660.0000.0000.0000.000
37B57GLN00.000-0.00917.9080.0630.0630.0000.0000.0000.000
38B58GLN0-0.011-0.02018.4750.5070.5070.0000.0000.0000.000
39B59LYS10.9240.98421.047-11.088-11.0880.0000.0000.0000.000
40B60PRO00.0470.01324.0740.3850.3850.0000.0000.0000.000
41B61GLY00.0100.01024.727-0.375-0.3750.0000.0000.0000.000
42B62GLN0-0.0260.00024.4020.0560.0560.0000.0000.0000.000
43B63SER00.001-0.00221.1620.6510.6510.0000.0000.0000.000
44B64PRO0-0.011-0.01516.873-0.501-0.5010.0000.0000.0000.000
45B65LYS10.9771.00219.596-11.829-11.8290.0000.0000.0000.000
46B66LEU0-0.0070.00217.6360.2470.2470.0000.0000.0000.000
47B67LEU0-0.060-0.03219.936-0.777-0.7770.0000.0000.0000.000
48B68ILE00.0140.01019.410-0.540-0.5400.0000.0000.0000.000
49B69TYR00.0160.00317.7391.0291.0290.0000.0000.0000.000
50B70SER00.0200.00417.288-0.749-0.7490.0000.0000.0000.000
51B71ALA00.0110.01217.445-0.686-0.6860.0000.0000.0000.000
52B72SER0-0.063-0.04718.415-0.476-0.4760.0000.0000.0000.000
53B73TYR0-0.0160.01421.615-0.833-0.8330.0000.0000.0000.000
54B74ARG10.9050.97122.422-10.012-10.0120.0000.0000.0000.000
55B75TYR00.0030.00022.382-0.211-0.2110.0000.0000.0000.000
56B76THR00.0550.00624.412-0.363-0.3630.0000.0000.0000.000
57B77GLY0-0.0090.00227.4400.1670.1670.0000.0000.0000.000
58B78VAL0-0.093-0.02324.477-0.124-0.1240.0000.0000.0000.000
59B79PRO0-0.004-0.00527.783-0.169-0.1690.0000.0000.0000.000
60B80ASP-1-0.802-0.92228.7769.7889.7880.0000.0000.0000.000
61B81ARG10.7550.87029.076-9.827-9.8270.0000.0000.0000.000
62B82PHE0-0.0110.01224.6880.2030.2030.0000.0000.0000.000
63B83THR0-0.026-0.02525.033-0.116-0.1160.0000.0000.0000.000
64B84GLY00.0320.01521.0700.3580.3580.0000.0000.0000.000
65B85SER0-0.030-0.01220.787-0.550-0.5500.0000.0000.0000.000
66B86GLY00.0630.02419.0870.5300.5300.0000.0000.0000.000
67B87SER0-0.007-0.02517.4840.3050.3050.0000.0000.0000.000
68B88GLY00.0290.03515.156-0.460-0.4600.0000.0000.0000.000
69B89THR00.0100.00012.3871.1971.1970.0000.0000.0000.000
70B90ASP-1-0.890-0.92213.92717.35017.3500.0000.0000.0000.000
71B91PHE0-0.042-0.02213.206-0.660-0.6600.0000.0000.0000.000
72B92THR0-0.028-0.02717.127-0.071-0.0710.0000.0000.0000.000
73B93PHE00.0030.01419.332-0.237-0.2370.0000.0000.0000.000
74B94THR0-0.002-0.00820.910-0.264-0.2640.0000.0000.0000.000
75B95ILE0-0.0040.02324.603-0.020-0.0200.0000.0000.0000.000
76B96SER0-0.037-0.03627.144-0.142-0.1420.0000.0000.0000.000
77B97SER00.0240.00630.366-0.286-0.2860.0000.0000.0000.000
78B98VAL0-0.025-0.00828.6550.0510.0510.0000.0000.0000.000
79B99GLN00.0060.00330.891-0.471-0.4710.0000.0000.0000.000
80B100ALA00.0690.03031.0350.3120.3120.0000.0000.0000.000
81B101GLU-1-0.929-0.96830.4569.7939.7930.0000.0000.0000.000
82B102ASP-1-0.798-0.88427.09210.79510.7950.0000.0000.0000.000
83B103LEU0-0.0110.02726.1560.5490.5490.0000.0000.0000.000
84B104ALA0-0.010-0.01822.8150.0170.0170.0000.0000.0000.000
85B105VAL0-0.0260.00217.632-0.114-0.1140.0000.0000.0000.000
86B106TYR0-0.013-0.02418.6920.0280.0280.0000.0000.0000.000
87B107TYR00.0030.01513.3110.4440.4440.0000.0000.0000.000
88B109GLN00.0380.0179.595-0.429-0.4290.0000.0000.0000.000
89B110GLN00.0840.0475.035-6.114-6.1140.0000.0000.0000.000
90B111HIS0-0.037-0.0368.6622.7762.7760.0000.0000.0000.000
91B112TYR00.0090.0028.188-1.872-1.8720.0000.0000.0000.000
92B113SER0-0.038-0.0144.9741.1961.276-0.001-0.002-0.0760.000
93B114ILE0-0.051-0.0026.289-1.044-1.0440.0000.0000.0000.000
94B115PRO00.0880.0412.583-10.384-6.5833.111-2.682-4.2290.032
95B116ARG10.8940.9424.679-30.307-30.211-0.001-0.005-0.0900.000
96B117THR0-0.016-0.0132.4550.1720.7440.489-0.265-0.7960.000
97B118PHE00.019-0.0045.777-4.056-4.0560.0000.0000.0000.000
98B119GLY00.0360.0088.1951.6441.6440.0000.0000.0000.000
99B120GLY0-0.072-0.04410.532-0.102-0.1020.0000.0000.0000.000
100B121GLY0-0.002-0.00512.426-0.860-0.8600.0000.0000.0000.000
101B122THR0-0.057-0.04915.4680.0540.0540.0000.0000.0000.000
102B123LYS10.8810.94818.738-12.328-12.3280.0000.0000.0000.000
103B124LEU0-0.024-0.00721.894-0.212-0.2120.0000.0000.0000.000
104B125GLU-1-0.937-0.97324.90110.98510.9850.0000.0000.0000.000
105B126ILE00.0000.00227.996-0.094-0.0940.0000.0000.0000.000
106B127LYS10.9650.99231.274-8.522-8.5220.0000.0000.0000.000
107B128ARG10.8680.92034.102-7.983-7.9830.0000.0000.0000.000
108B129ALA0-0.004-0.00737.382-0.005-0.0050.0000.0000.0000.000
109B130ASP-1-0.815-0.89840.4877.6517.6510.0000.0000.0000.000
110B131ALA0-0.040-0.02441.551-0.138-0.1380.0000.0000.0000.000
111B132ALA00.0410.02142.6780.1350.1350.0000.0000.0000.000
112B133PRO0-0.0360.00442.9250.0300.0300.0000.0000.0000.000
113B134THR00.0260.00544.433-0.241-0.2410.0000.0000.0000.000
114B135VAL0-0.028-0.02245.4890.1330.1330.0000.0000.0000.000
115B136SER0-0.036-0.01346.908-0.204-0.2040.0000.0000.0000.000
116B137ILE0-0.0030.00247.3510.1550.1550.0000.0000.0000.000
117B138PHE0-0.021-0.01046.547-0.099-0.0990.0000.0000.0000.000
118B139PRO00.0220.01449.5410.0930.0930.0000.0000.0000.000
119B140PRO00.0060.00249.6880.0860.0860.0000.0000.0000.000
120B141SER00.0310.02849.211-0.128-0.1280.0000.0000.0000.000
121B142SER00.0480.01451.494-0.032-0.0320.0000.0000.0000.000
122B143GLU-1-0.869-0.94250.0716.2266.2260.0000.0000.0000.000
123B144GLN00.037-0.00545.761-0.045-0.0450.0000.0000.0000.000
124B145LEU00.0310.01549.771-0.007-0.0070.0000.0000.0000.000
125B146THR0-0.073-0.03252.967-0.114-0.1140.0000.0000.0000.000
126B147SER0-0.073-0.03849.0180.0050.0050.0000.0000.0000.000
127B148GLY0-0.014-0.00850.4280.0560.0560.0000.0000.0000.000
128B149GLY0-0.019-0.00548.2980.0590.0590.0000.0000.0000.000
129B150ALA00.014-0.01048.687-0.117-0.1170.0000.0000.0000.000
130B151SER0-0.0220.01544.4430.0610.0610.0000.0000.0000.000
131B152VAL0-0.0160.01046.823-0.092-0.0920.0000.0000.0000.000
132B153VAL00.0170.01543.5760.1500.1500.0000.0000.0000.000
133B154CYS0-0.063-0.01644.438-0.118-0.1180.0000.0000.0000.000
134B155PHE0-0.022-0.00841.0310.2280.2280.0000.0000.0000.000
135B156LEU00.005-0.00641.576-0.215-0.2150.0000.0000.0000.000
136B157ASN00.043-0.00540.7740.3780.3780.0000.0000.0000.000
137B158ASN0-0.022-0.02739.662-0.265-0.2650.0000.0000.0000.000
138B159PHE0-0.0110.00637.891-0.157-0.1570.0000.0000.0000.000
139B160TYR00.0430.02433.4550.2520.2520.0000.0000.0000.000
140B161PRO00.0050.00336.336-0.221-0.2210.0000.0000.0000.000
141B162LYS11.0161.00029.684-10.387-10.3870.0000.0000.0000.000
142B163ASP-1-0.910-0.93835.5808.7298.7290.0000.0000.0000.000
143B164ILE0-0.045-0.02837.403-0.230-0.2300.0000.0000.0000.000
144B165ASN0-0.038-0.01339.887-0.006-0.0060.0000.0000.0000.000
145B166VAL00.0340.01141.813-0.135-0.1350.0000.0000.0000.000
146B167LYS10.8710.95644.239-6.461-6.4610.0000.0000.0000.000
147B168TRP00.0320.00144.213-0.174-0.1740.0000.0000.0000.000
148B169LYS10.8010.88548.714-6.029-6.0290.0000.0000.0000.000
149B170ILE00.009-0.00450.7980.0140.0140.0000.0000.0000.000
150B171ASP-1-0.767-0.88654.3985.4165.4160.0000.0000.0000.000
151B172GLY0-0.018-0.00656.984-0.057-0.0570.0000.0000.0000.000
152B173SER0-0.015-0.00653.9740.0100.0100.0000.0000.0000.000
153B174GLU-1-0.899-0.94947.9276.6466.6460.0000.0000.0000.000
154B175ARG10.8020.87847.291-6.603-6.6030.0000.0000.0000.000
155B176GLN00.0420.00544.6340.1990.1990.0000.0000.0000.000
156B177ASN00.0140.00744.0130.2560.2560.0000.0000.0000.000
157B178GLY00.0510.03642.979-0.147-0.1470.0000.0000.0000.000
158B179VAL0-0.0110.01241.390-0.004-0.0040.0000.0000.0000.000
159B180LEU0-0.0150.00436.2500.2010.2010.0000.0000.0000.000
160B181ASN00.0530.04037.260-0.295-0.2950.0000.0000.0000.000
161B182SER0-0.015-0.00133.7880.3540.3540.0000.0000.0000.000
162B183TRP0-0.018-0.01332.775-0.165-0.1650.0000.0000.0000.000
163B184THR00.007-0.00332.2580.1670.1670.0000.0000.0000.000
164B185ASP-1-0.892-0.96027.14911.50911.5090.0000.0000.0000.000
165B186GLN0-0.057-0.05429.922-0.020-0.0200.0000.0000.0000.000
166B187ASP-1-0.791-0.89231.2698.9008.9000.0000.0000.0000.000
167B188SER0-0.025-0.01631.208-0.089-0.0890.0000.0000.0000.000
168B189LYS10.8980.93932.590-8.246-8.2460.0000.0000.0000.000
169B190ASP-1-0.795-0.88336.1828.0668.0660.0000.0000.0000.000
170B191SER0-0.007-0.00933.776-0.125-0.1250.0000.0000.0000.000
171B192THR0-0.114-0.05234.7750.0420.0420.0000.0000.0000.000
172B193TYR00.005-0.00230.4570.2400.2400.0000.0000.0000.000
173B194SER00.0480.04235.906-0.388-0.3880.0000.0000.0000.000
174B195MET0-0.067-0.00236.2990.2950.2950.0000.0000.0000.000
175B196SER00.0090.00637.973-0.217-0.2170.0000.0000.0000.000
176B197SER0-0.002-0.02539.0600.1250.1250.0000.0000.0000.000
177B198THR00.0270.00340.765-0.218-0.2180.0000.0000.0000.000
178B199LEU00.0110.01742.4960.1190.1190.0000.0000.0000.000
179B200THR0-0.013-0.01242.840-0.106-0.1060.0000.0000.0000.000
180B201LEU0-0.062-0.02645.392-0.003-0.0030.0000.0000.0000.000
181B202THR00.0600.02148.5600.0390.0390.0000.0000.0000.000
182B203LYS10.9270.97650.498-5.753-5.7530.0000.0000.0000.000
183B204ASP-1-0.864-0.93353.2625.6695.6690.0000.0000.0000.000
184B205GLU-1-0.955-0.98651.1356.1236.1230.0000.0000.0000.000
185B206TYR00.0620.01652.401-0.071-0.0710.0000.0000.0000.000
186B207GLU-1-0.837-0.92154.2475.5505.5500.0000.0000.0000.000
187B208ARG10.8300.94354.547-5.851-5.8510.0000.0000.0000.000
188B209HIS10.8340.92155.772-5.692-5.6920.0000.0000.0000.000
189B210ASN00.0400.03058.4820.0260.0260.0000.0000.0000.000
190B211SER00.0370.03557.0010.0300.0300.0000.0000.0000.000
191B212TYR0-0.060-0.05351.9910.1180.1180.0000.0000.0000.000
192B213THR00.002-0.05452.267-0.059-0.0590.0000.0000.0000.000
193B215GLU-1-0.815-0.91648.6736.0096.0090.0000.0000.0000.000
194B216ALA00.0210.00945.2630.1510.1510.0000.0000.0000.000
195B217THR0-0.003-0.00245.407-0.196-0.1960.0000.0000.0000.000
196B218HIS00.0670.01239.958-0.003-0.0030.0000.0000.0000.000
197B219LYS10.8920.93840.769-7.550-7.5500.0000.0000.0000.000
198B220THR0-0.066-0.04743.863-0.149-0.1490.0000.0000.0000.000
199B221SER00.0040.00346.227-0.173-0.1730.0000.0000.0000.000
200B222THR00.0060.01148.7800.0820.0820.0000.0000.0000.000
201B223SER0-0.045-0.01651.072-0.085-0.0850.0000.0000.0000.000
202B224PRO00.0050.00149.6620.0740.0740.0000.0000.0000.000
203B225ILE00.0020.00647.461-0.141-0.1410.0000.0000.0000.000
204B226VAL00.0020.01049.9470.1140.1140.0000.0000.0000.000
205B227LYS10.8970.95550.567-6.231-6.2310.0000.0000.0000.000
206B228SER00.0540.04352.4000.0680.0680.0000.0000.0000.000
207B229PHE0-0.0140.01451.782-0.022-0.0220.0000.0000.0000.000
208B230ASN0-0.010-0.01556.5890.0570.0570.0000.0000.0000.000
209B231ARG10.8650.92757.060-5.428-5.4280.0000.0000.0000.000
210B232ASN0-0.057-0.01758.9140.0120.0120.0000.0000.0000.000
211B233GLU-1-0.933-0.95861.7204.8304.8300.0000.0000.0000.000