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: YVJY2

Calculation Name: 3A1Y-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A1Y

Chain ID: G

ChEMBL ID:

UniProt ID: O74109

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1980277.669148
FMO2-HF: Nuclear repulsion 1897229.048443
FMO2-HF: Total energy -83048.620705
FMO2-MP2: Total energy -83292.024605


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(G:1:MET)


Summations of interaction energy for fragment #1(G:1:MET)
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.
-3.510.3870.01-1.878-2.028-0.003
Interaction energy analysis for fragmet #1(G:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.051
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].
3G3HIS0-0.0180.0073.393-2.0911.385-0.029-1.765-1.682-0.004
4G4VAL00.006-0.0154.9440.3860.3860.0000.0000.0000.000
5G5ALA0-0.0560.0006.626-0.119-0.1190.0000.0000.0000.000
6G6GLU-1-0.828-0.9194.964-2.179-2.251-0.001-0.0060.0800.000
7G7TRP0-0.051-0.0247.3740.2040.2040.0000.0000.0000.000
8G8LYS10.9950.9799.0350.4280.4280.0000.0000.0000.000
9G9LYS10.9210.94412.1340.2320.2320.0000.0000.0000.000
10G10LYS11.0011.0203.152-0.0070.4860.040-0.107-0.4260.001
11G11GLU-1-0.897-0.9487.738-0.773-0.7730.0000.0000.0000.000
12G12VAL0-0.004-0.00610.0530.0710.0710.0000.0000.0000.000
13G13GLU-1-0.973-0.96410.3510.0150.0150.0000.0000.0000.000
14G14GLU-1-0.899-0.9559.5840.1740.1740.0000.0000.0000.000
15G15LEU00.019-0.00212.1340.0270.0270.0000.0000.0000.000
16G16ALA00.027-0.05514.3430.0260.0260.0000.0000.0000.000
17G17LYS10.9170.93711.998-0.084-0.0840.0000.0000.0000.000
18G18LEU0-0.0020.03114.2200.0110.0110.0000.0000.0000.000
19G19ILE00.0520.02016.9900.0120.0120.0000.0000.0000.000
20G20LYS10.8720.93619.7620.0350.0350.0000.0000.0000.000
21G21SER0-0.073-0.03419.1370.0160.0160.0000.0000.0000.000
22G22TYR0-0.065-0.02418.2010.0100.0100.0000.0000.0000.000
23G23PRO00.0110.01923.257-0.006-0.0060.0000.0000.0000.000
24G24VAL00.0170.02725.565-0.005-0.0050.0000.0000.0000.000
25G25ILE0-0.044-0.03221.881-0.006-0.0060.0000.0000.0000.000
26G26ALA00.0180.01323.2990.0010.0010.0000.0000.0000.000
27G27LEU0-0.0090.00121.598-0.016-0.0160.0000.0000.0000.000
28G28VAL0-0.004-0.00920.9390.0120.0120.0000.0000.0000.000
29G29ASP-1-0.726-0.84722.041-0.130-0.1300.0000.0000.0000.000
30G30VAL0-0.058-0.05117.7940.0080.0080.0000.0000.0000.000
31G31SER0-0.096-0.05920.9060.0070.0070.0000.0000.0000.000
32G32SER00.0250.02222.2760.0070.0070.0000.0000.0000.000
33G33MET0-0.047-0.01120.4240.0110.0110.0000.0000.0000.000
34G34PRO00.0140.01020.057-0.010-0.0100.0000.0000.0000.000
35G35ALA00.0400.00415.2020.0000.0000.0000.0000.0000.000
36G36TYR0-0.004-0.00116.431-0.005-0.0050.0000.0000.0000.000
37G37PRO00.0540.01418.2820.0030.0030.0000.0000.0000.000
38G38LEU00.0830.05115.513-0.003-0.0030.0000.0000.0000.000
39G39SER0-0.064-0.03114.943-0.012-0.0120.0000.0000.0000.000
40G40GLN0-0.019-0.01716.3040.0150.0150.0000.0000.0000.000
41G41MET00.0830.05119.6380.0050.0050.0000.0000.0000.000
42G42ARG10.8610.93012.0950.2260.2260.0000.0000.0000.000
43G43ARG10.8360.89816.921-0.062-0.0620.0000.0000.0000.000
44G44LEU00.0870.05118.4010.0070.0070.0000.0000.0000.000
45G45ILE0-0.0180.00519.3700.0020.0020.0000.0000.0000.000
46G46ARG10.9040.94712.4790.0160.0160.0000.0000.0000.000
47G47GLU-1-0.926-0.93919.3150.0550.0550.0000.0000.0000.000
48G48ASN0-0.072-0.03322.4140.0040.0040.0000.0000.0000.000
49G49GLY00.0230.02522.910-0.005-0.0050.0000.0000.0000.000
50G50GLY00.0490.01420.757-0.002-0.0020.0000.0000.0000.000
51G51LEU0-0.096-0.05414.9820.0030.0030.0000.0000.0000.000
52G52LEU00.0500.03415.963-0.007-0.0070.0000.0000.0000.000
53G53ARG10.8380.91711.0980.1330.1330.0000.0000.0000.000
54G54VAL00.0600.03712.0920.0330.0330.0000.0000.0000.000
55G55SER00.0240.00112.387-0.096-0.0960.0000.0000.0000.000
56G56ARG10.9370.96314.4310.2730.2730.0000.0000.0000.000
57G57ASN00.013-0.01117.4170.0270.0270.0000.0000.0000.000
58G58THR00.006-0.00513.6090.0110.0110.0000.0000.0000.000
59G59LEU00.0470.03516.3190.0070.0070.0000.0000.0000.000
60G60ILE00.0290.02917.6870.0230.0230.0000.0000.0000.000
61G61GLU-1-0.908-0.98416.458-0.210-0.2100.0000.0000.0000.000
62G62LEU00.1310.04220.4810.0140.0140.0000.0000.0000.000
63G63ALA00.0130.01722.3470.0150.0150.0000.0000.0000.000
64G64ILE0-0.021-0.01418.6760.0080.0080.0000.0000.0000.000
65G65LYN0-0.0880.04717.1160.0230.0230.0000.0000.0000.000
66G66LYS10.8970.95222.4970.0770.0770.0000.0000.0000.000
67G67ALA0-0.0160.00524.7350.0070.0070.0000.0000.0000.000
68G68ALA0-0.088-0.04622.3840.0070.0070.0000.0000.0000.000
69G69LYN0-0.023-0.02123.3870.0060.0060.0000.0000.0000.000
70G70GLU-1-0.917-0.96127.450-0.029-0.0290.0000.0000.0000.000
71G71LEU00.0070.01727.551-0.001-0.0010.0000.0000.0000.000
72G72GLY00.0450.00031.144-0.002-0.0020.0000.0000.0000.000
73G73LYS10.8370.95523.7590.0680.0680.0000.0000.0000.000
74G74PRO0-0.104-0.04726.069-0.006-0.0060.0000.0000.0000.000
75G75GLU-1-0.808-0.91125.730-0.128-0.1280.0000.0000.0000.000
76G76LEU0-0.160-0.11928.1310.0070.0070.0000.0000.0000.000
77G77GLU-1-0.916-0.94831.004-0.051-0.0510.0000.0000.0000.000
78G78LYN0-0.0110.03528.3030.0060.0060.0000.0000.0000.000
79G79LEU0-0.0060.00332.2520.0020.0020.0000.0000.0000.000
80G80VAL00.006-0.01732.3350.0000.0000.0000.0000.0000.000
81G81GLU-1-0.895-0.94524.786-0.124-0.1240.0000.0000.0000.000
82G82TYR00.0260.02428.412-0.005-0.0050.0000.0000.0000.000
83G83ILE0-0.069-0.02821.205-0.006-0.0060.0000.0000.0000.000
84G84ASP-1-0.770-0.89424.599-0.114-0.1140.0000.0000.0000.000
85G85ARG10.8710.90822.6400.1270.1270.0000.0000.0000.000
86G86GLY0-0.017-0.00719.4160.0050.0050.0000.0000.0000.000
87G87ALA00.0840.05720.4720.0100.0100.0000.0000.0000.000
88G88GLY0-0.090-0.04817.778-0.037-0.0370.0000.0000.0000.000
89G89ILE0-0.011-0.01216.6300.0190.0190.0000.0000.0000.000
90G90LEU0-0.011-0.01317.712-0.012-0.0120.0000.0000.0000.000
91G91VAL0-0.0100.01917.9030.0070.0070.0000.0000.0000.000
92G92THR00.0540.00120.6370.0100.0100.0000.0000.0000.000
93G93ASN00.014-0.00223.258-0.001-0.0010.0000.0000.0000.000
94G94MET0-0.060-0.01526.0260.0010.0010.0000.0000.0000.000
95G95ASN00.0940.04728.054-0.007-0.0070.0000.0000.0000.000
96G96PRO00.0990.04629.727-0.001-0.0010.0000.0000.0000.000
97G97PHE00.0520.03130.798-0.002-0.0020.0000.0000.0000.000
98G98LYS10.8420.92930.4500.0090.0090.0000.0000.0000.000
99G99LEU00.0270.00724.5870.0010.0010.0000.0000.0000.000
100G100TYR00.0600.03328.473-0.001-0.0010.0000.0000.0000.000
101G101LYN00.0580.03330.549-0.001-0.0010.0000.0000.0000.000
102G102PHE0-0.049-0.03624.2420.0020.0020.0000.0000.0000.000
103G103LEU00.0270.01923.9570.0020.0020.0000.0000.0000.000
104G104GLN0-0.060-0.03327.705-0.002-0.0020.0000.0000.0000.000
105G105GLN0-0.008-0.01131.0080.0030.0030.0000.0000.0000.000
106G106ASN0-0.094-0.04926.7580.0090.0090.0000.0000.0000.000
107G107ARG10.9320.98626.5610.0300.0300.0000.0000.0000.000
108G108GLN00.0260.01626.455-0.002-0.0020.0000.0000.0000.000
109G109PRO0-0.064-0.03322.942-0.001-0.0010.0000.0000.0000.000
110G183GLN0-0.005-0.03331.8210.0020.0020.0000.0000.0000.000
111G184PRO0-0.0040.01932.212-0.001-0.0010.0000.0000.0000.000
112G185LEU0-0.031-0.01329.045-0.002-0.0020.0000.0000.0000.000
113G186GLU-1-0.892-0.95129.706-0.006-0.0060.0000.0000.0000.000
114G187VAL0-0.059-0.02824.714-0.004-0.0040.0000.0000.0000.000
115G188GLY00.013-0.01925.0070.0050.0050.0000.0000.0000.000
116G189LEU0-0.024-0.00420.426-0.008-0.0080.0000.0000.0000.000
117G190ASP-1-0.853-0.90924.554-0.052-0.0520.0000.0000.0000.000
118G191VAL0-0.047-0.02725.963-0.010-0.0100.0000.0000.0000.000
119G192LEU0-0.024-0.00224.8840.0040.0040.0000.0000.0000.000
120G193ALA00.018-0.00527.5160.0050.0050.0000.0000.0000.000
121G194VAL0-0.045-0.02227.146-0.006-0.0060.0000.0000.0000.000
122G195TYR00.0120.01826.9930.0030.0030.0000.0000.0000.000
123G196GLU-1-0.899-0.98028.008-0.019-0.0190.0000.0000.0000.000
124G197ASP-1-0.956-0.96330.366-0.021-0.0210.0000.0000.0000.000
125G198GLY00.0250.01231.6560.0010.0010.0000.0000.0000.000
126G199ILE0-0.011-0.00733.178-0.002-0.0020.0000.0000.0000.000
127G200VAL0-0.048-0.03330.197-0.003-0.0030.0000.0000.0000.000
128G201TYR0-0.005-0.00131.8560.0030.0030.0000.0000.0000.000
129G202THR00.018-0.02331.880-0.005-0.0050.0000.0000.0000.000
130G203PRO0-0.005-0.02631.4460.0040.0040.0000.0000.0000.000
131G204ASP-1-0.884-0.92533.768-0.037-0.0370.0000.0000.0000.000
132G205VAL00.0030.02036.4960.0030.0030.0000.0000.0000.000
133G206LEU0-0.052-0.03831.2940.0030.0030.0000.0000.0000.000
134G207ALA0-0.057-0.01935.4450.0030.0030.0000.0000.0000.000
135G208ILE0-0.0110.00437.0890.0010.0010.0000.0000.0000.000
136G209ASP-1-0.851-0.92639.800-0.013-0.0130.0000.0000.0000.000
137G210GLU-1-0.919-0.98241.710-0.006-0.0060.0000.0000.0000.000
138G211GLN0-0.064-0.03843.5770.0020.0020.0000.0000.0000.000
139G212GLU-1-0.907-0.93346.455-0.015-0.0150.0000.0000.0000.000
140G213TYR00.016-0.00543.0730.0010.0010.0000.0000.0000.000
141G214ILE0-0.055-0.01646.4680.0010.0010.0000.0000.0000.000
142G215ASP-1-0.833-0.92549.295-0.006-0.0060.0000.0000.0000.000
143G216MET0-0.077-0.04150.0420.0000.0000.0000.0000.0000.000
144G217LEU0-0.0020.00949.4320.0000.0000.0000.0000.0000.000
145G218GLN0-0.003-0.00452.4810.0000.0000.0000.0000.0000.000
146G219LYS10.9310.96655.1890.0080.0080.0000.0000.0000.000
147G220ALA00.0030.00455.0720.0000.0000.0000.0000.0000.000
148G221TYR00.0170.00956.5340.0000.0000.0000.0000.0000.000
149G222MET0-0.007-0.00958.2670.0010.0010.0000.0000.0000.000
150G223HIS0-0.036-0.01459.0400.0000.0000.0000.0000.0000.000
151G224ALA00.0170.01260.6220.0000.0000.0000.0000.0000.000
152G225PHE00.0120.01462.4250.0000.0000.0000.0000.0000.000
153G226ASN00.010-0.01664.3770.0010.0010.0000.0000.0000.000
154G227LEU00.0100.02665.0840.0000.0000.0000.0000.0000.000
155G228ALA00.0410.01866.4970.0000.0000.0000.0000.0000.000
156G229VAL00.0050.00068.2040.0000.0000.0000.0000.0000.000
157G230ASN0-0.128-0.09969.4770.0000.0000.0000.0000.0000.000
158G231ILE0-0.040-0.00969.3790.0000.0000.0000.0000.0000.000
159G232ALA0-0.028-0.01172.7900.0000.0000.0000.0000.0000.000
160G233TYR0-0.0070.00066.5050.0000.0000.0000.0000.0000.000
161G234PRO0-0.017-0.00869.9960.0000.0000.0000.0000.0000.000
162G235THR00.017-0.00366.1900.0000.0000.0000.0000.0000.000
163G236PRO00.014-0.01466.1150.0000.0000.0000.0000.0000.000
164G237GLU-1-0.883-0.93162.0960.0010.0010.0000.0000.0000.000
165G238THR0-0.022-0.01066.0150.0000.0000.0000.0000.0000.000
166G239ILE00.0070.00368.8660.0000.0000.0000.0000.0000.000
167G240GLU-1-0.903-0.95971.5240.0020.0020.0000.0000.0000.000
168G241ALA00.0330.01570.2080.0000.0000.0000.0000.0000.000
169G242ILE0-0.0410.00271.5220.0000.0000.0000.0000.0000.000
170G243ILE0-0.029-0.00774.2870.0000.0000.0000.0000.0000.000
171G244GLN0-0.003-0.00773.5640.0000.0000.0000.0000.0000.000
172G245LYS10.9510.99273.2550.0020.0020.0000.0000.0000.000
173G246ALA00.0220.01176.6730.0000.0000.0000.0000.0000.000
174G247PHE00.0100.00579.7570.0000.0000.0000.0000.0000.000
175G248LEU0-0.0080.00378.1030.0000.0000.0000.0000.0000.000
176G249ASN00.0000.01178.5920.0000.0000.0000.0000.0000.000
177G250ALA00.0090.00881.5930.0000.0000.0000.0000.0000.000
178G251LYS10.9440.97683.3920.0000.0000.0000.0000.0000.000
179G252THR0-0.037-0.05181.9990.0000.0000.0000.0000.0000.000
180G253VAL00.0150.01084.5350.0000.0000.0000.0000.0000.000
181G254ALA00.0010.00286.7930.0000.0000.0000.0000.0000.000
182G255ILE0-0.043-0.03086.1480.0000.0000.0000.0000.0000.000
183G256GLU-1-0.942-0.96186.742-0.002-0.0020.0000.0000.0000.000
184G257ALA0-0.028-0.01189.1850.0000.0000.0000.0000.0000.000
185G258GLY0-0.0240.00092.1030.0000.0000.0000.0000.0000.000
186G259TYR0-0.020-0.01493.0150.0000.0000.0000.0000.0000.000
187G260ILE00.0000.00193.3600.0000.0000.0000.0000.0000.000
188G261THR00.0200.00191.5050.0000.0000.0000.0000.0000.000
189G262LYS10.9660.96890.665-0.001-0.0010.0000.0000.0000.000
190G263GLU-1-0.891-0.95587.4000.0010.0010.0000.0000.0000.000
191G264THR0-0.036-0.01388.3010.0000.0000.0000.0000.0000.000
192G265ILE00.0080.00990.3010.0000.0000.0000.0000.0000.000
193G266GLN00.008-0.00289.7690.0000.0000.0000.0000.0000.000
194G267ASP-1-0.853-0.92385.789-0.001-0.0010.0000.0000.0000.000
195G268ILE0-0.047-0.02289.3440.0000.0000.0000.0000.0000.000
196G269ILE00.0140.00092.4970.0000.0000.0000.0000.0000.000
197G270GLY00.0220.02090.7620.0000.0000.0000.0000.0000.000
198G271ARG10.8670.93086.3580.0020.0020.0000.0000.0000.000
199G272ALA00.0200.01792.0990.0000.0000.0000.0000.0000.000
200G273PHE0-0.004-0.00793.0100.0000.0000.0000.0000.0000.000
201G274ARG10.9750.97688.2770.0010.0010.0000.0000.0000.000
202G275ALA00.0110.01893.5010.0000.0000.0000.0000.0000.000
203G276MET0-0.0210.00995.7880.0000.0000.0000.0000.0000.000
204G277LEU00.009-0.00793.1870.0000.0000.0000.0000.0000.000
205G278LEU0-0.003-0.01092.4530.0000.0000.0000.0000.0000.000
206G279LEU0-0.016-0.00695.9230.0000.0000.0000.0000.0000.000
207G280ALA00.009-0.01199.4350.0000.0000.0000.0000.0000.000
208G281GLN0-0.038-0.01594.3540.0000.0000.0000.0000.0000.000
209G282GLN0-0.062-0.02198.1490.0000.0000.0000.0000.0000.000
210G283LEU0-0.066-0.019101.5520.0000.0000.0000.0000.0000.000
211G284PRO0-0.0080.008103.0020.0000.0000.0000.0000.0000.000