FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YV122

Calculation Name: 2F2F-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F2F

Chain ID: B

ChEMBL ID:

UniProt ID: O87120

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 261
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3571080.613041
FMO2-HF: Nuclear repulsion 3470672.184037
FMO2-HF: Total energy -100408.429004
FMO2-MP2: Total energy -100705.878966


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:23:ASN)


Summations of interaction energy for fragment #1(B:23:ASN)
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.
-28.986-28.88829.56-14.55-15.11-0.123
Interaction energy analysis for fragmet #1(B:23:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.008
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].
3B25SER0-0.043-0.0302.978-2.7861.0870.047-1.921-2.0000.011
4B26ASP-1-0.885-0.9332.040-8.226-4.7335.399-4.306-4.586-0.054
5B27PHE0-0.120-0.0622.8551.8832.7240.050-0.312-0.5790.002
6B28LYS10.8340.9307.0790.7180.7180.0000.0000.0000.000
7B29VAL00.0200.0079.0540.2010.2010.0000.0000.0000.000
8B30ALA00.022-0.00211.8500.0860.0860.0000.0000.0000.000
9B31THR00.0250.01615.5350.0140.0140.0000.0000.0000.000
10B32TRP0-0.065-0.05518.1850.0330.0330.0000.0000.0000.000
11B33ASN00.0200.02121.9070.0340.0340.0000.0000.0000.000
12B34LEU0-0.0070.00324.7420.0160.0160.0000.0000.0000.000
13B35GLN00.011-0.00226.7230.0260.0260.0000.0000.0000.000
14B36GLY0-0.015-0.00429.1950.0170.0170.0000.0000.0000.000
15B37SER0-0.026-0.03730.8710.0080.0080.0000.0000.0000.000
16B38SER00.0260.00634.2820.0030.0030.0000.0000.0000.000
17B39ALA0-0.0040.01536.7970.0070.0070.0000.0000.0000.000
18B40VAL0-0.024-0.01734.0600.0030.0030.0000.0000.0000.000
19B41ASN00.0280.00229.122-0.015-0.0150.0000.0000.0000.000
20B42GLU-1-0.779-0.89330.355-0.143-0.1430.0000.0000.0000.000
21B43SER0-0.002-0.00330.675-0.008-0.0080.0000.0000.0000.000
22B44LYS10.9140.96028.8590.2190.2190.0000.0000.0000.000
23B45TRP00.0180.00722.295-0.026-0.0260.0000.0000.0000.000
24B46ASN0-0.065-0.07226.265-0.008-0.0080.0000.0000.0000.000
25B47ILE00.0040.02128.7180.0050.0050.0000.0000.0000.000
26B48ASN00.0380.04325.8820.0010.0010.0000.0000.0000.000
27B49VAL00.0270.02721.453-0.022-0.0220.0000.0000.0000.000
28B50ARG10.8710.94622.1380.1200.1200.0000.0000.0000.000
29B51GLN0-0.012-0.01723.054-0.013-0.0130.0000.0000.0000.000
30B52LEU00.0210.00919.668-0.014-0.0140.0000.0000.0000.000
31B53LEU00.0200.01617.128-0.050-0.0500.0000.0000.0000.000
32B54SER0-0.086-0.02418.5900.0290.0290.0000.0000.0000.000
33B55GLY00.0470.01519.938-0.036-0.0360.0000.0000.0000.000
34B56GLU-1-0.889-0.95017.795-0.202-0.2020.0000.0000.0000.000
35B57GLN0-0.053-0.03116.015-0.076-0.0760.0000.0000.0000.000
36B58GLY0-0.0010.02916.615-0.060-0.0600.0000.0000.0000.000
37B59ALA0-0.036-0.02813.988-0.051-0.0510.0000.0000.0000.000
38B60ASP-1-0.872-0.9339.716-0.934-0.9340.0000.0000.0000.000
39B61ILE0-0.019-0.0218.3760.1610.1610.0000.0000.0000.000
40B62LEU0-0.026-0.01012.298-0.067-0.0670.0000.0000.0000.000
41B63MET0-0.016-0.01613.6700.0360.0360.0000.0000.0000.000
42B64VAL0-0.015-0.01217.1180.0160.0160.0000.0000.0000.000
43B65GLN0-0.011-0.01719.6510.0370.0370.0000.0000.0000.000
44B66GLU-1-0.852-0.93123.528-0.259-0.2590.0000.0000.0000.000
45B67ALA00.0540.01324.0840.0110.0110.0000.0000.0000.000
46B68GLY00.0250.05026.1770.0170.0170.0000.0000.0000.000
47B69SER0-0.0240.03228.3820.0060.0060.0000.0000.0000.000
48B70LEU00.0170.00823.644-0.017-0.0170.0000.0000.0000.000
49B71PRO00.0210.00925.3010.0120.0120.0000.0000.0000.000
50B72SER00.0060.00428.2810.0140.0140.0000.0000.0000.000
51B73SER0-0.037-0.02028.5620.0070.0070.0000.0000.0000.000
52B74ALA0-0.039-0.01625.2710.0110.0110.0000.0000.0000.000
53B75VAL00.001-0.00125.8570.0080.0080.0000.0000.0000.000
54B76ARG10.9380.99224.5020.0180.0180.0000.0000.0000.000
55B77THR0-0.065-0.06022.0300.0100.0100.0000.0000.0000.000
56B78SER00.036-0.00825.120-0.005-0.0050.0000.0000.0000.000
57B79ARG10.8060.92215.820-0.134-0.1340.0000.0000.0000.000
58B80VAL00.0160.00323.535-0.028-0.0280.0000.0000.0000.000
59B81ILE0-0.040-0.01818.9810.0250.0250.0000.0000.0000.000
60B82GLN00.0070.00321.232-0.023-0.0230.0000.0000.0000.000
61B83HIS00.0330.01821.0760.0010.0010.0000.0000.0000.000
62B84GLY00.0130.01225.2000.0000.0000.0000.0000.0000.000
63B85GLY00.001-0.00226.4150.0070.0070.0000.0000.0000.000
64B86THR0-0.026-0.01524.873-0.001-0.0010.0000.0000.0000.000
65B87PRO00.0030.01225.3170.0070.0070.0000.0000.0000.000
66B88ILE00.0020.00119.025-0.030-0.0300.0000.0000.0000.000
67B89GLU-1-0.896-0.95722.840-0.048-0.0480.0000.0000.0000.000
68B90GLU-1-0.733-0.80518.3170.0230.0230.0000.0000.0000.000
69B91TYR0-0.038-0.01920.9690.0240.0240.0000.0000.0000.000
70B92THR0-0.026-0.00220.777-0.012-0.0120.0000.0000.0000.000
71B93TRP00.020-0.00321.752-0.008-0.0080.0000.0000.0000.000
72B94ASN00.0380.00322.510-0.015-0.0150.0000.0000.0000.000
73B95LEU0-0.010-0.00120.747-0.003-0.0030.0000.0000.0000.000
74B96GLY0-0.014-0.00924.730-0.005-0.0050.0000.0000.0000.000
75B97THR00.0150.00826.9010.0050.0050.0000.0000.0000.000
76B98ARG11.0070.98828.799-0.008-0.0080.0000.0000.0000.000
77B99SER0-0.017-0.01229.9060.0090.0090.0000.0000.0000.000
78B100ARG10.9530.98225.911-0.027-0.0270.0000.0000.0000.000
79B101PRO00.0130.01124.525-0.018-0.0180.0000.0000.0000.000
80B102ASN00.0350.02820.813-0.015-0.0150.0000.0000.0000.000
81B103MET0-0.0050.01020.013-0.023-0.0230.0000.0000.0000.000
82B104VAL00.0250.03117.341-0.017-0.0170.0000.0000.0000.000
83B105TYR00.000-0.00415.8080.0560.0560.0000.0000.0000.000
84B106ILE0-0.032-0.01917.466-0.066-0.0660.0000.0000.0000.000
85B107TYR0-0.009-0.04115.0530.0530.0530.0000.0000.0000.000
86B108TYR0-0.052-0.07518.982-0.041-0.0410.0000.0000.0000.000
87B109SER00.0350.01622.1750.0230.0230.0000.0000.0000.000
88B110ARG10.9350.96723.9060.1010.1010.0000.0000.0000.000
89B111LEU00.0200.00024.6980.0160.0160.0000.0000.0000.000
90B112ASP-1-0.789-0.86728.604-0.154-0.1540.0000.0000.0000.000
91B113VAL0-0.018-0.01331.6080.0080.0080.0000.0000.0000.000
92B114GLY0-0.0140.00734.1820.0090.0090.0000.0000.0000.000
93B115ALA0-0.016-0.02835.4230.0070.0070.0000.0000.0000.000
94B116ASN0-0.042-0.02031.400-0.005-0.0050.0000.0000.0000.000
95B117ARG10.9720.96531.2780.1840.1840.0000.0000.0000.000
96B118VAL0-0.040-0.02028.229-0.019-0.0190.0000.0000.0000.000
97B119ASN0-0.050-0.03426.3250.0020.0020.0000.0000.0000.000
98B120LEU0-0.0030.00821.130-0.018-0.0180.0000.0000.0000.000
99B121ALA00.006-0.00820.3790.0410.0410.0000.0000.0000.000
100B122ILE00.0060.03113.685-0.048-0.0480.0000.0000.0000.000
101B123VAL0-0.040-0.01416.6250.0780.0780.0000.0000.0000.000
102B124SER00.037-0.00111.969-0.175-0.1750.0000.0000.0000.000
103B125ARG10.8800.93412.9940.3880.3880.0000.0000.0000.000
104B126ARG10.9490.9845.905-0.265-0.2650.0000.0000.0000.000
105B127GLN0-0.019-0.00512.385-0.056-0.0560.0000.0000.0000.000
106B128ALA0-0.0020.00411.6820.0440.0440.0000.0000.0000.000
107B129ASP-1-0.815-0.9019.7800.9020.9020.0000.0000.0000.000
108B130GLU-1-0.964-0.99212.7010.2430.2430.0000.0000.0000.000
109B131ALA0-0.0040.00513.521-0.092-0.0920.0000.0000.0000.000
110B132PHE0-0.007-0.01812.3240.0280.0280.0000.0000.0000.000
111B133ILE00.007-0.00517.220-0.043-0.0430.0000.0000.0000.000
112B134VAL0-0.022-0.00217.0450.0310.0310.0000.0000.0000.000
113B135HIS00.0270.00620.191-0.036-0.0360.0000.0000.0000.000
114B136SER00.0560.01023.029-0.010-0.0100.0000.0000.0000.000
115B137ASP-1-0.894-0.98124.796-0.241-0.2410.0000.0000.0000.000
116B138SER0-0.011-0.01327.9730.0140.0140.0000.0000.0000.000
117B139SER0-0.0110.04225.4910.0050.0050.0000.0000.0000.000
118B140VAL00.0180.02127.8460.0080.0080.0000.0000.0000.000
119B141LEU0-0.090-0.03430.7220.0130.0130.0000.0000.0000.000
120B142GLN00.040-0.00731.8260.0050.0050.0000.0000.0000.000
121B143SER0-0.0440.00727.793-0.002-0.0020.0000.0000.0000.000
122B144ARG10.8680.91925.4000.3000.3000.0000.0000.0000.000
123B145PRO0-0.0040.00822.749-0.019-0.0190.0000.0000.0000.000
124B146ALA0-0.0080.01117.618-0.021-0.0210.0000.0000.0000.000
125B147VAL00.0150.00117.9710.0500.0500.0000.0000.0000.000
126B148GLY00.039-0.00114.494-0.092-0.0920.0000.0000.0000.000
127B149ILE0-0.055-0.00910.9160.1330.1330.0000.0000.0000.000
128B150ARG10.8870.9368.597-0.936-0.9360.0000.0000.0000.000
129B151ILE0-0.0150.0156.2570.1580.1580.0000.0000.0000.000
130B152GLY00.018-0.0025.532-0.037-0.0370.0000.0000.0000.000
131B153THR0-0.0100.0024.163-0.222-0.072-0.001-0.016-0.1330.000
132B154ASP-1-0.797-0.8721.772-5.746-15.50521.345-6.416-5.170-0.068
133B155VAL0-0.044-0.0355.1480.2100.264-0.001-0.004-0.0490.000
134B156PHE00.0260.0125.184-0.142-0.1420.0000.0000.0000.000
135B157PHE00.029-0.01010.5350.2370.2370.0000.0000.0000.000
136B158THR0-0.0260.00514.080-0.089-0.0890.0000.0000.0000.000
137B159VAL00.025-0.00417.0990.0660.0660.0000.0000.0000.000
138B160HIS0-0.015-0.02120.005-0.026-0.0260.0000.0000.0000.000
139B161ALA00.0240.04523.5330.0330.0330.0000.0000.0000.000
140B162LEU0-0.058-0.04125.0830.0180.0180.0000.0000.0000.000
141B163ALA00.0480.01328.824-0.014-0.0140.0000.0000.0000.000
142B164THR0-0.031-0.00730.7790.0010.0010.0000.0000.0000.000
143B165GLY00.0240.00530.2390.0060.0060.0000.0000.0000.000
144B166GLY00.0500.02926.578-0.017-0.0170.0000.0000.0000.000
145B167SER0-0.089-0.05626.320-0.018-0.0180.0000.0000.0000.000
146B168ASP-1-0.749-0.87225.854-0.336-0.3360.0000.0000.0000.000
147B169ALA0-0.0020.00322.160-0.013-0.0130.0000.0000.0000.000
148B170VAL00.0200.00521.604-0.033-0.0330.0000.0000.0000.000
149B171SER00.0040.01822.284-0.017-0.0170.0000.0000.0000.000
150B172LEU00.0400.00120.3810.0000.0000.0000.0000.0000.000
151B173ILE0-0.023-0.00416.464-0.023-0.0230.0000.0000.0000.000
152B174ARG10.8440.92717.5970.3080.3080.0000.0000.0000.000
153B175ASN00.025-0.00919.4930.0020.0020.0000.0000.0000.000
154B176ILE0-0.0010.05113.9110.0440.0440.0000.0000.0000.000
155B177PHE00.018-0.00114.8950.0290.0290.0000.0000.0000.000
156B178THR0-0.020-0.02716.0840.0230.0230.0000.0000.0000.000
157B179THR0-0.045-0.04816.7150.0620.0620.0000.0000.0000.000
158B180PHE0-0.056-0.03712.0770.0860.0860.0000.0000.0000.000
159B181THR00.0650.04412.0610.0620.0620.0000.0000.0000.000
160B182SER0-0.042-0.02814.4270.0540.0540.0000.0000.0000.000
161B183SER0-0.073-0.03718.0670.0470.0470.0000.0000.0000.000
162B184PRO0-0.0140.02215.6820.0190.0190.0000.0000.0000.000
163B185SER0-0.005-0.01617.8010.0160.0160.0000.0000.0000.000
164B186SER0-0.040-0.01716.087-0.007-0.0070.0000.0000.0000.000
165B187PRO00.022-0.00716.209-0.052-0.0520.0000.0000.0000.000
166B188GLU-1-0.834-0.92312.4030.5190.5190.0000.0000.0000.000
167B189ARG10.9010.97211.424-0.053-0.0530.0000.0000.0000.000
168B190ARG10.9450.99411.283-0.010-0.0100.0000.0000.0000.000
169B191GLY0-0.036-0.0228.785-0.261-0.2610.0000.0000.0000.000
170B192TYR0-0.055-0.0286.9480.4320.4320.0000.0000.0000.000
171B193SER00.0570.0443.725-0.384-0.2130.001-0.056-0.1170.000
172B194TRP0-0.041-0.0285.9450.2490.2490.0000.0000.0000.000
173B195MET0-0.005-0.0088.186-0.286-0.2860.0000.0000.0000.000
174B196VAL0-0.0210.0059.9560.1930.1930.0000.0000.0000.000
175B197VAL00.018-0.01112.534-0.017-0.0170.0000.0000.0000.000
176B198GLY00.000-0.00615.3390.0800.0800.0000.0000.0000.000
177B199ASP-1-0.818-0.90019.065-0.422-0.4220.0000.0000.0000.000
178B200PHE0-0.012-0.01917.1500.0390.0390.0000.0000.0000.000
179B201ASN0-0.033-0.01822.9880.0400.0400.0000.0000.0000.000
180B202ARG10.8630.92324.3070.4320.4320.0000.0000.0000.000
181B203ALA00.0460.03624.842-0.034-0.0340.0000.0000.0000.000
182B204PRO00.0740.03920.6880.0080.0080.0000.0000.0000.000
183B205VAL00.0760.03522.545-0.012-0.0120.0000.0000.0000.000
184B206ASN0-0.0220.00324.6900.0100.0100.0000.0000.0000.000
185B207LEU00.0170.00619.9260.0240.0240.0000.0000.0000.000
186B208GLU-1-0.933-0.98320.667-0.634-0.6340.0000.0000.0000.000
187B209ALA0-0.042-0.02322.5520.0080.0080.0000.0000.0000.000
188B210ALA0-0.012-0.01225.3870.0190.0190.0000.0000.0000.000
189B211LEU00.0610.01718.9800.0190.0190.0000.0000.0000.000
190B212ARG10.8880.96922.0830.5200.5200.0000.0000.0000.000
191B213GLN0-0.0080.01223.8960.0200.0200.0000.0000.0000.000
192B214GLU-1-0.863-0.93222.880-0.352-0.3520.0000.0000.0000.000
193B215PRO00.0470.01121.671-0.051-0.0510.0000.0000.0000.000
194B216ALA0-0.022-0.00319.490-0.050-0.0500.0000.0000.0000.000
195B217VAL00.0620.04517.656-0.066-0.0660.0000.0000.0000.000
196B218SER00.0250.00316.822-0.093-0.0930.0000.0000.0000.000
197B219GLU-1-0.916-0.93916.992-0.599-0.5990.0000.0000.0000.000
198B220ASN0-0.074-0.04313.313-0.145-0.1450.0000.0000.0000.000
199B221THR0-0.025-0.00412.260-0.142-0.1420.0000.0000.0000.000
200B222ILE00.0290.01610.7300.0920.0920.0000.0000.0000.000
201B223ILE0-0.0130.00613.323-0.086-0.0860.0000.0000.0000.000
202B224ILE00.006-0.00410.5900.0170.0170.0000.0000.0000.000
203B225ALA00.039-0.01314.8790.0200.0200.0000.0000.0000.000
204B226PRO0-0.0220.00418.080-0.002-0.0020.0000.0000.0000.000
205B227THR00.0290.00420.3600.0080.0080.0000.0000.0000.000
206B228GLU-1-0.939-0.95923.587-0.338-0.3380.0000.0000.0000.000
207B229PRO0-0.020-0.00624.748-0.028-0.0280.0000.0000.0000.000
208B230THR0-0.012-0.04222.449-0.004-0.0040.0000.0000.0000.000
209B231HIS00.0790.09425.5090.0030.0030.0000.0000.0000.000
210B232ARG10.9550.97928.8260.2540.2540.0000.0000.0000.000
211B233SER0-0.066-0.08331.8890.0090.0090.0000.0000.0000.000
212B234GLY0-0.001-0.01231.2370.0090.0090.0000.0000.0000.000
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214B236ILE0-0.0050.00622.898-0.004-0.0040.0000.0000.0000.000
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