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: 94VY2

Calculation Name: 1F6F-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F6F

Chain ID: B

ChEMBL ID:

UniProt ID: P16038

Base Structure: X-ray

Registration Date: 2023-09-19

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2145125.258349
FMO2-HF: Nuclear repulsion 2062913.685859
FMO2-HF: Total energy -82211.572489
FMO2-MP2: Total energy -82450.148659


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:5:GLY)


Summations of interaction energy for fragment #1(B:5:GLY)
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.
-9.581-10.32917.067-9.853-6.465-0.044
Interaction energy analysis for fragmet #1(B:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.018
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].
3B7PRO0-0.0100.0063.469-1.0791.0790.002-1.163-0.9980.001
4B8GLU-1-0.870-0.9455.700-2.999-3.049-0.001-0.0070.0590.000
5B9ILE00.004-0.0058.3480.5320.5320.0000.0000.0000.000
6B10HIS00.0050.0099.4210.1290.1290.0000.0000.0000.000
7B11LYS10.8940.95213.3670.6000.6000.0000.0000.0000.000
8B12CYS00.0180.03316.005-0.023-0.0230.0000.0000.0000.000
9B13ARG10.8800.92919.1820.4280.4280.0000.0000.0000.000
10B14SER00.0010.00122.9900.0100.0100.0000.0000.0000.000
11B15PRO00.0130.01126.0330.0030.0030.0000.0000.0000.000
12B16ASP-1-0.767-0.92429.502-0.178-0.1780.0000.0000.0000.000
13B17LYS10.8190.91228.8930.1680.1680.0000.0000.0000.000
14B18GLU-1-0.980-0.98229.846-0.129-0.1290.0000.0000.0000.000
15B19THR0-0.052-0.02327.1920.0010.0010.0000.0000.0000.000
16B20PHE0-0.013-0.01519.231-0.007-0.0070.0000.0000.0000.000
17B21THR00.0190.02620.5760.0210.0210.0000.0000.0000.000
18B23TRP00.020-0.00216.2690.0420.0420.0000.0000.0000.000
19B24TRP0-0.0010.01110.857-0.086-0.0860.0000.0000.0000.000
20B25ASN0-0.024-0.02011.2890.2770.2770.0000.0000.0000.000
21B26PRO00.003-0.0019.808-0.320-0.3200.0000.0000.0000.000
22B27GLY00.0470.0237.850-0.117-0.1170.0000.0000.0000.000
23B28THR0-0.076-0.0536.9620.2140.2140.0000.0000.0000.000
24B29ASP-1-0.847-0.9078.275-0.228-0.2280.0000.0000.0000.000
25B30GLY0-0.013-0.01410.8660.1080.1080.0000.0000.0000.000
26B31GLY0-0.019-0.01013.4720.0380.0380.0000.0000.0000.000
27B32LEU0-0.042-0.00913.5830.0060.0060.0000.0000.0000.000
28B33PRO0-0.022-0.00414.969-0.041-0.0410.0000.0000.0000.000
29B34THR00.006-0.00810.1540.0660.0660.0000.0000.0000.000
30B35ASN0-0.030-0.01213.291-0.073-0.0730.0000.0000.0000.000
31B36TYR00.007-0.0189.307-0.027-0.0270.0000.0000.0000.000
32B37SER0-0.0030.01511.2430.0730.0730.0000.0000.0000.000
33B38LEU0-0.046-0.01411.250-0.087-0.0870.0000.0000.0000.000
34B39THR0-0.0090.00311.9040.0860.0860.0000.0000.0000.000
35B40TYR0-0.035-0.03313.321-0.089-0.0890.0000.0000.0000.000
36B41SER00.0270.02615.5910.0680.0680.0000.0000.0000.000
37B42LYS10.9400.97217.2490.1210.1210.0000.0000.0000.000
38B43GLU-1-0.834-0.91020.271-0.158-0.1580.0000.0000.0000.000
39B44GLY0-0.055-0.03521.8490.0060.0060.0000.0000.0000.000
40B45GLU-1-0.883-0.93223.185-0.097-0.0970.0000.0000.0000.000
41B46LYS10.9050.96921.1020.0040.0040.0000.0000.0000.000
42B47THR00.012-0.01720.8690.0300.0300.0000.0000.0000.000
43B48THR0-0.0240.00315.176-0.026-0.0260.0000.0000.0000.000
44B49TYR0-0.079-0.04618.0580.0360.0360.0000.0000.0000.000
45B50GLU-1-0.789-0.90916.197-0.199-0.1990.0000.0000.0000.000
46B51CYS0-0.057-0.01616.8110.0330.0330.0000.0000.0000.000
47B52PRO0-0.010-0.00818.4280.0240.0240.0000.0000.0000.000
48B53ASP-1-0.812-0.87521.255-0.178-0.1780.0000.0000.0000.000
49B54TYR00.0140.00015.639-0.041-0.0410.0000.0000.0000.000
50B55LYS10.8860.94320.7900.1300.1300.0000.0000.0000.000
51B56THR0-0.025-0.04824.022-0.002-0.0020.0000.0000.0000.000
52B57SER0-0.026-0.01522.3040.0170.0170.0000.0000.0000.000
53B58GLY00.0040.02122.823-0.021-0.0210.0000.0000.0000.000
54B59PRO0-0.0170.00919.705-0.014-0.0140.0000.0000.0000.000
55B60ASN0-0.008-0.01015.0140.0040.0040.0000.0000.0000.000
56B61SER0-0.011-0.02816.264-0.065-0.0650.0000.0000.0000.000
57B63PHE0-0.030-0.01518.972-0.011-0.0110.0000.0000.0000.000
58B64PHE00.0550.02117.8350.0190.0190.0000.0000.0000.000
59B65SER00.0440.00923.7910.0060.0060.0000.0000.0000.000
60B66LYS11.0120.98727.3780.1250.1250.0000.0000.0000.000
61B67GLN0-0.056-0.00428.6870.0010.0010.0000.0000.0000.000
62B68TYR0-0.005-0.01324.1630.0070.0070.0000.0000.0000.000
63B69THR0-0.0150.01724.647-0.026-0.0260.0000.0000.0000.000
64B70SER0-0.030-0.01625.4610.0220.0220.0000.0000.0000.000
65B71ILE00.004-0.00825.536-0.019-0.0190.0000.0000.0000.000
66B72TRP0-0.028-0.01926.6850.0180.0180.0000.0000.0000.000
67B73LYS10.9190.96423.3860.1610.1610.0000.0000.0000.000
68B74ILE00.0130.01517.883-0.027-0.0270.0000.0000.0000.000
69B75TYR0-0.033-0.01817.5960.0390.0390.0000.0000.0000.000
70B76ILE0-0.026-0.01912.212-0.048-0.0480.0000.0000.0000.000
71B77ILE00.008-0.01112.6390.0730.0730.0000.0000.0000.000
72B78THR00.0010.0107.815-0.188-0.1880.0000.0000.0000.000
73B79VAL00.0320.0087.9520.2610.2610.0000.0000.0000.000
74B80ASN0-0.035-0.0326.450-0.321-0.3210.0000.0000.0000.000
75B81ALA00.0290.0216.593-0.033-0.0330.0000.0000.0000.000
76B82THR00.008-0.0077.7650.2280.2280.0000.0000.0000.000
77B83ASN00.0900.03910.498-0.010-0.0100.0000.0000.0000.000
78B84GLN0-0.026-0.02712.8350.0750.0750.0000.0000.0000.000
79B85MET0-0.046-0.01612.6260.0080.0080.0000.0000.0000.000
80B86GLY0-0.0090.0019.6770.1450.1450.0000.0000.0000.000
81B87SER0-0.008-0.0037.596-0.335-0.3350.0000.0000.0000.000
82B88SER0-0.0110.0122.399-1.474-1.2412.577-1.441-1.368-0.009
83B89SER00.0260.0122.448-1.770-1.0910.469-0.554-0.594-0.002
84B90SER00.0060.0412.0880.932-3.23514.021-6.594-3.260-0.034
85B91ASP-1-0.899-0.9364.058-4.791-4.4130.000-0.093-0.2850.000
86B92PRO0-0.064-0.0465.1120.5240.545-0.001-0.001-0.0190.000
87B93LEU00.0290.0318.5790.0150.0150.0000.0000.0000.000
88B94TYR0-0.021-0.02011.2170.1470.1470.0000.0000.0000.000
89B95VAL00.000-0.01314.758-0.005-0.0050.0000.0000.0000.000
90B96ASP-1-0.747-0.83017.862-0.214-0.2140.0000.0000.0000.000
91B97VAL0-0.006-0.02521.550-0.003-0.0030.0000.0000.0000.000
92B98THR0-0.079-0.07723.5940.0160.0160.0000.0000.0000.000
93B99TYR0-0.040-0.02623.2570.0230.0230.0000.0000.0000.000
94B100ILE0-0.0260.01520.774-0.015-0.0150.0000.0000.0000.000
95B101VAL00.007-0.00324.123-0.006-0.0060.0000.0000.0000.000
96B102GLU-1-0.948-0.97826.014-0.305-0.3050.0000.0000.0000.000
97B103PRO0-0.013-0.00328.6520.0000.0000.0000.0000.0000.000
98B104GLU-1-0.912-0.95532.079-0.190-0.1900.0000.0000.0000.000
99B105PRO0-0.017-0.02434.3060.0040.0040.0000.0000.0000.000
100B106PRO0-0.028-0.00337.3910.0040.0040.0000.0000.0000.000
101B107ARG10.9280.96340.6780.1070.1070.0000.0000.0000.000
102B108ASN0-0.043-0.03043.4120.0000.0000.0000.0000.0000.000
103B109LEU00.0120.01945.4630.0020.0020.0000.0000.0000.000
104B110THR0-0.013-0.01348.0080.0030.0030.0000.0000.0000.000
105B111LEU0-0.036-0.02150.702-0.001-0.0010.0000.0000.0000.000
106B112GLU-1-0.807-0.89254.010-0.059-0.0590.0000.0000.0000.000
107B113VAL00.011-0.00957.486-0.001-0.0010.0000.0000.0000.000
108B114LYS10.8700.97259.9890.0540.0540.0000.0000.0000.000
109B115GLN0-0.068-0.05160.3740.0010.0010.0000.0000.0000.000
110B116LEU0-0.024-0.02563.4500.0020.0020.0000.0000.0000.000
111B117LYS10.8930.92866.3280.0450.0450.0000.0000.0000.000
112B118ASP-1-0.823-0.89067.831-0.045-0.0450.0000.0000.0000.000
113B119LYS10.9920.97567.9970.0450.0450.0000.0000.0000.000
114B120LYS10.9470.99161.2220.0560.0560.0000.0000.0000.000
115B121THR0-0.004-0.00962.221-0.001-0.0010.0000.0000.0000.000
116B122TYR00.0150.00457.4600.0000.0000.0000.0000.0000.000
117B123LEU00.0460.03653.0940.0010.0010.0000.0000.0000.000
118B124TRP0-0.055-0.01654.022-0.002-0.0020.0000.0000.0000.000
119B125VAL00.0460.02948.7220.0000.0000.0000.0000.0000.000
120B126LYS10.9890.98149.9040.0720.0720.0000.0000.0000.000
121B127TRP0-0.0210.00343.5130.0010.0010.0000.0000.0000.000
122B128SER0-0.024-0.01444.9830.0030.0030.0000.0000.0000.000
123B129PRO00.0320.02340.101-0.003-0.0030.0000.0000.0000.000
124B130PRO00.0730.03936.5800.0070.0070.0000.0000.0000.000
125B131THR0-0.053-0.03839.2650.0000.0000.0000.0000.0000.000
126B132ILE00.0290.01134.1190.0040.0040.0000.0000.0000.000
127B133THR0-0.0060.02034.416-0.004-0.0040.0000.0000.0000.000
128B134ASP-1-0.797-0.90236.887-0.100-0.1000.0000.0000.0000.000
129B135VAL00.012-0.00539.0090.0010.0010.0000.0000.0000.000
130B136LYS10.8790.94740.8630.0920.0920.0000.0000.0000.000
131B137THR0-0.052-0.04340.6560.0040.0040.0000.0000.0000.000
132B138GLY00.0200.02041.2460.0030.0030.0000.0000.0000.000
133B139TRP00.0020.02432.0740.0010.0010.0000.0000.0000.000
134B140PHE0-0.026-0.01332.464-0.009-0.0090.0000.0000.0000.000
135B141THR00.0130.00435.9730.0080.0080.0000.0000.0000.000
136B142MET0-0.021-0.01735.952-0.012-0.0120.0000.0000.0000.000
137B143GLU-1-0.884-0.92737.153-0.136-0.1360.0000.0000.0000.000
138B144TYR0-0.023-0.02938.397-0.007-0.0070.0000.0000.0000.000
139B145GLU-1-0.829-0.90138.429-0.142-0.1420.0000.0000.0000.000
140B146ILE0-0.043-0.02141.398-0.001-0.0010.0000.0000.0000.000
141B147ARG10.8430.91439.7840.1310.1310.0000.0000.0000.000
142B148LEU0-0.017-0.01944.7320.0010.0010.0000.0000.0000.000
143B149LYS10.9300.96346.8020.0930.0930.0000.0000.0000.000
144B150PRO00.0310.02650.023-0.001-0.0010.0000.0000.0000.000
145B151GLU-1-0.889-0.97751.372-0.078-0.0780.0000.0000.0000.000
146B152GLU-1-0.979-0.97651.659-0.067-0.0670.0000.0000.0000.000
147B153ALA0-0.029-0.02450.8110.0020.0020.0000.0000.0000.000
148B154GLU-1-0.949-0.96946.559-0.093-0.0930.0000.0000.0000.000
149B155GLU-1-0.887-0.92545.625-0.098-0.0980.0000.0000.0000.000
150B156TRP0-0.071-0.04043.1960.0030.0030.0000.0000.0000.000
151B157GLH0-0.020-0.01145.631-0.001-0.0010.0000.0000.0000.000
152B158ILE0-0.035-0.03040.623-0.001-0.0010.0000.0000.0000.000
153B159HIS00.0510.02744.3580.0020.0020.0000.0000.0000.000
154B160PHE00.0120.00339.124-0.002-0.0020.0000.0000.0000.000
155B161THR0-0.020-0.01343.3220.0030.0030.0000.0000.0000.000
156B162GLY00.0260.01642.2720.0040.0040.0000.0000.0000.000
157B163HIS0-0.014-0.03839.242-0.001-0.0010.0000.0000.0000.000
158B164GLN0-0.048-0.00343.3840.0030.0030.0000.0000.0000.000
159B165THR00.0080.01044.439-0.003-0.0030.0000.0000.0000.000
160B166GLN00.001-0.01346.7240.0050.0050.0000.0000.0000.000
161B167PHE0-0.002-0.00448.641-0.001-0.0010.0000.0000.0000.000
162B168LYS10.8950.95350.7650.0700.0700.0000.0000.0000.000
163B169VAL00.0380.02151.1500.0000.0000.0000.0000.0000.000
164B170PHE0-0.054-0.06253.9130.0040.0040.0000.0000.0000.000
165B171ASP-1-0.935-0.95053.932-0.072-0.0720.0000.0000.0000.000
166B172LEU0-0.0120.00553.266-0.001-0.0010.0000.0000.0000.000
167B173TYR00.0010.00056.9180.0030.0030.0000.0000.0000.000
168B174PRO0-0.032-0.03859.298-0.001-0.0010.0000.0000.0000.000
169B175GLY00.0230.02362.1540.0010.0010.0000.0000.0000.000
170B176GLN00.0280.02556.9230.0000.0000.0000.0000.0000.000
171B177LYS10.9420.98154.3560.0720.0720.0000.0000.0000.000
172B178TYR0-0.019-0.01652.245-0.001-0.0010.0000.0000.0000.000
173B179LEU00.0330.02448.1920.0010.0010.0000.0000.0000.000
174B180VAL0-0.015-0.02247.053-0.001-0.0010.0000.0000.0000.000
175B181GLN00.0570.06041.351-0.003-0.0030.0000.0000.0000.000
176B182THR00.022-0.00142.1430.0010.0010.0000.0000.0000.000
177B183ARG10.8610.93334.0060.1630.1630.0000.0000.0000.000
178B184CYS0-0.007-0.00835.7570.0090.0090.0000.0000.0000.000
179B185LYS10.9570.99932.2460.1710.1710.0000.0000.0000.000
180B186PRO00.0240.01930.6760.0110.0110.0000.0000.0000.000
181B187ASP-1-0.872-0.95433.598-0.159-0.1590.0000.0000.0000.000
182B188HIS10.8510.92529.0940.1730.1730.0000.0000.0000.000
183B189GLY00.0050.02427.773-0.015-0.0150.0000.0000.0000.000
184B190TYR0-0.020-0.01122.411-0.007-0.0070.0000.0000.0000.000
185B191TRP0-0.014-0.01228.8780.0100.0100.0000.0000.0000.000
186B192SER00.0560.04230.965-0.009-0.0090.0000.0000.0000.000
187B193ARG10.9460.96029.7190.2170.2170.0000.0000.0000.000
188B194TRP00.008-0.00734.2690.0060.0060.0000.0000.0000.000
189B195SER00.0090.00937.994-0.001-0.0010.0000.0000.0000.000
190B196GLN0-0.008-0.00640.417-0.001-0.0010.0000.0000.0000.000
191B197GLU-1-0.917-0.97642.864-0.107-0.1070.0000.0000.0000.000
192B198SER0-0.0220.00445.7970.0030.0030.0000.0000.0000.000
193B199SER0-0.006-0.01649.2470.0000.0000.0000.0000.0000.000
194B200VAL0-0.024-0.01652.4630.0010.0010.0000.0000.0000.000
195B201GLU-1-0.894-0.93155.603-0.064-0.0640.0000.0000.0000.000
196B202MET0-0.050-0.00857.6260.0010.0010.0000.0000.0000.000
197B203PRO00.002-0.00160.1130.0010.0010.0000.0000.0000.000