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: 9GVR2

Calculation Name: 4EYY-Q-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EYY

Chain ID: Q

ChEMBL ID:

UniProt ID: Q5ZYC9

Base Structure: X-ray

Registration Date: 2023-06-19

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1850813.339529
FMO2-HF: Nuclear repulsion 1776699.503722
FMO2-HF: Total energy -74113.835806
FMO2-MP2: Total energy -74334.697735


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(Q:1:MET)


Summations of interaction energy for fragment #1(Q: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.
-0.0971.4770.001-0.637-0.9380.003
Interaction energy analysis for fragmet #1(Q:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.006
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].
3Q3ASP-1-0.903-0.9573.8010.8782.4520.001-0.637-0.9380.003
4Q4GLN0-0.044-0.0155.8600.4320.4320.0000.0000.0000.000
5Q5LEU0-0.015-0.0177.4010.4590.4590.0000.0000.0000.000
6Q6SER0-0.021-0.0119.650-0.340-0.3400.0000.0000.0000.000
7Q7ASP-1-0.841-0.93212.0110.5780.5780.0000.0000.0000.000
8Q8GLU-1-0.841-0.93413.0820.6830.6830.0000.0000.0000.000
9Q9GLN00.0010.0096.413-0.369-0.3690.0000.0000.0000.000
10Q10LYS10.9160.95711.895-0.708-0.7080.0000.0000.0000.000
11Q11GLU-1-0.894-0.94314.2220.3990.3990.0000.0000.0000.000
12Q12THR0-0.023-0.01213.345-0.066-0.0660.0000.0000.0000.000
13Q13ILE0-0.038-0.01510.541-0.055-0.0550.0000.0000.0000.000
14Q14LEU0-0.013-0.01015.027-0.077-0.0770.0000.0000.0000.000
15Q15LYN00.0470.03818.420-0.062-0.0620.0000.0000.0000.000
16Q16ALA0-0.0030.00816.720-0.047-0.0470.0000.0000.0000.000
17Q17LEU0-0.036-0.02817.131-0.056-0.0560.0000.0000.0000.000
18Q18ASN0-0.007-0.03120.239-0.048-0.0480.0000.0000.0000.000
19Q19ASP-1-0.794-0.88322.0700.2610.2610.0000.0000.0000.000
20Q20ALA0-0.019-0.01321.411-0.028-0.0280.0000.0000.0000.000
21Q21ILE0-0.092-0.06123.390-0.028-0.0280.0000.0000.0000.000
22Q22GLU-1-0.984-0.99525.9330.1810.1810.0000.0000.0000.000
23Q23LYS10.9380.99523.740-0.277-0.2770.0000.0000.0000.000
24Q24GLY0-0.042-0.02227.235-0.011-0.0110.0000.0000.0000.000
25Q25PRO00.0200.01527.865-0.010-0.0100.0000.0000.0000.000
26Q26TRP0-0.068-0.05124.773-0.014-0.0140.0000.0000.0000.000
27Q27ASP-1-0.867-0.92930.9230.1350.1350.0000.0000.0000.000
28Q28LYS10.9250.96433.907-0.135-0.1350.0000.0000.0000.000
29Q29SER00.021-0.00433.954-0.007-0.0070.0000.0000.0000.000
30Q30ASN0-0.012-0.00834.6380.0110.0110.0000.0000.0000.000
31Q31PHE00.0610.03727.8950.0070.0070.0000.0000.0000.000
32Q32LEU00.0350.01428.6510.0100.0100.0000.0000.0000.000
33Q33ARG11.0061.00329.871-0.110-0.1100.0000.0000.0000.000
34Q34VAL0-0.041-0.01529.3370.0100.0100.0000.0000.0000.000
35Q35ILE0-0.036-0.01924.9150.0150.0150.0000.0000.0000.000
36Q36GLY00.0550.02626.1160.0200.0200.0000.0000.0000.000
37Q37LYS10.9270.95927.429-0.156-0.1560.0000.0000.0000.000
38Q38LYS10.9741.00422.693-0.233-0.2330.0000.0000.0000.000
39Q39LEU00.0590.01921.3480.0240.0240.0000.0000.0000.000
40Q40ILE0-0.0100.01022.9310.0250.0250.0000.0000.0000.000
41Q41ALA00.0390.02124.5950.0090.0090.0000.0000.0000.000
42Q42ILE0-0.049-0.02418.3290.0140.0140.0000.0000.0000.000
43Q43ARG10.9520.96719.730-0.272-0.2720.0000.0000.0000.000
44Q44ASP-1-0.931-0.96820.9600.2730.2730.0000.0000.0000.000
45Q45ARG10.9280.96119.221-0.321-0.3210.0000.0000.0000.000
46Q46PHE00.000-0.00513.383-0.007-0.0070.0000.0000.0000.000
47Q47LEU00.0690.03018.0070.0150.0150.0000.0000.0000.000
48Q48LYS10.9110.96420.554-0.266-0.2660.0000.0000.0000.000
49Q49ARG10.9130.95315.450-0.436-0.4360.0000.0000.0000.000
50Q50ILE00.0160.01215.562-0.016-0.0160.0000.0000.0000.000
51Q51GLY00.0030.01518.022-0.022-0.0220.0000.0000.0000.000
52Q52ALA0-0.020-0.00920.595-0.028-0.0280.0000.0000.0000.000
53Q53ALA0-0.041-0.01317.751-0.021-0.0210.0000.0000.0000.000
54Q54SER00.0620.02119.238-0.030-0.0300.0000.0000.0000.000
55Q55GLN00.063-0.00722.203-0.016-0.0160.0000.0000.0000.000
56Q56ALA0-0.0110.00919.710-0.020-0.0200.0000.0000.0000.000
57Q57GLN0-0.034-0.00720.075-0.003-0.0030.0000.0000.0000.000
58Q58LEU00.0290.00021.417-0.022-0.0220.0000.0000.0000.000
59Q59GLN0-0.036-0.01924.283-0.020-0.0200.0000.0000.0000.000
60Q60ALA0-0.026-0.00721.095-0.015-0.0150.0000.0000.0000.000
61Q61GLU-1-0.880-0.94423.0840.0830.0830.0000.0000.0000.000
62Q62SER0-0.062-0.02225.283-0.013-0.0130.0000.0000.0000.000
63Q63HIS00.0460.01724.974-0.011-0.0110.0000.0000.0000.000
64Q64LEU00.0060.00423.962-0.007-0.0070.0000.0000.0000.000
65Q65ALA00.000-0.01628.339-0.004-0.0040.0000.0000.0000.000
66Q66ASN0-0.0200.00131.008-0.008-0.0080.0000.0000.0000.000
67Q67GLN00.0160.00728.778-0.004-0.0040.0000.0000.0000.000
68Q68ILE00.005-0.00130.053-0.003-0.0030.0000.0000.0000.000
69Q69ALA0-0.0170.02933.931-0.001-0.0010.0000.0000.0000.000
70Q70LEU00.0350.01536.165-0.001-0.0010.0000.0000.0000.000
71Q71GLN0-0.088-0.03634.366-0.002-0.0020.0000.0000.0000.000
72Q72SER0-0.057-0.06237.3400.0000.0000.0000.0000.0000.000
73Q73GLY0-0.0150.00839.8440.0020.0020.0000.0000.0000.000
74Q74GLN0-0.040-0.01837.5760.0080.0080.0000.0000.0000.000
75Q75GLN00.0250.00539.500-0.004-0.0040.0000.0000.0000.000
76Q76GLU-1-0.849-0.92835.5750.0530.0530.0000.0000.0000.000
77Q77ILE0-0.045-0.02239.224-0.003-0.0030.0000.0000.0000.000
78Q78TYR0-0.008-0.00237.0900.0040.0040.0000.0000.0000.000
79Q79VAL00.0220.00842.783-0.003-0.0030.0000.0000.0000.000
80Q80SER0-0.029-0.00344.5080.0030.0030.0000.0000.0000.000
81Q81LEU00.003-0.02043.698-0.001-0.0010.0000.0000.0000.000
82Q82TYR00.013-0.01047.3730.0000.0000.0000.0000.0000.000
83Q83SER00.0040.01447.950-0.001-0.0010.0000.0000.0000.000
84Q84SER0-0.003-0.01649.916-0.002-0.0020.0000.0000.0000.000
85Q85ASP-1-0.866-0.94349.1270.0640.0640.0000.0000.0000.000
86Q86GLY00.0260.01146.8350.0030.0030.0000.0000.0000.000
87Q87SER00.0330.01245.0600.0020.0020.0000.0000.0000.000
88Q88ASN00.0100.02043.9890.0090.0090.0000.0000.0000.000
89Q89LEU0-0.024-0.01538.251-0.001-0.0010.0000.0000.0000.000
90Q90GLN00.0260.01239.7080.0020.0020.0000.0000.0000.000
91Q91SER0-0.122-0.07343.196-0.001-0.0010.0000.0000.0000.000
92Q92TRP00.0280.01242.439-0.004-0.0040.0000.0000.0000.000
93Q93GLU-1-0.863-0.93540.0150.0900.0900.0000.0000.0000.000
94Q94LYS10.8850.94142.839-0.069-0.0690.0000.0000.0000.000
95Q95ILE00.0080.01546.076-0.003-0.0030.0000.0000.0000.000
96Q96VAL00.0080.00941.219-0.003-0.0030.0000.0000.0000.000
97Q97GLY00.0150.01444.549-0.001-0.0010.0000.0000.0000.000
98Q98SER0-0.090-0.05545.760-0.002-0.0020.0000.0000.0000.000
99Q99LEU00.0410.00143.980-0.003-0.0030.0000.0000.0000.000
100Q100PRO0-0.093-0.08046.892-0.003-0.0030.0000.0000.0000.000
101Q101ARG11.0411.10749.474-0.041-0.0410.0000.0000.0000.000
102Q102GLN00.019-0.06349.536-0.001-0.0010.0000.0000.0000.000
103Q103MET00.0170.00545.4860.0000.0000.0000.0000.0000.000
104Q104ILE0-0.0490.02249.471-0.001-0.0010.0000.0000.0000.000
105Q105SER00.0340.02353.039-0.001-0.0010.0000.0000.0000.000
106Q106ARG10.7790.91349.642-0.042-0.0420.0000.0000.0000.000
107Q107PRO00.0300.01050.128-0.001-0.0010.0000.0000.0000.000
108Q108ILE00.0340.01846.4970.0030.0030.0000.0000.0000.000
109Q109TYR0-0.011-0.02045.150-0.001-0.0010.0000.0000.0000.000
110Q110ALA00.026-0.01044.2770.0020.0020.0000.0000.0000.000
111Q111ASP-1-0.820-0.89641.6880.0230.0230.0000.0000.0000.000
112Q112GLU-1-0.769-0.86636.8240.0520.0520.0000.0000.0000.000
113Q113GLU-1-0.835-0.93338.8570.0370.0370.0000.0000.0000.000
114Q114ASP-1-0.847-0.94441.7480.0240.0240.0000.0000.0000.000
115Q115ILE0-0.017-0.00342.5500.0010.0010.0000.0000.0000.000
116Q116LYS10.8260.92940.474-0.031-0.0310.0000.0000.0000.000
117Q117ALA0-0.046-0.02543.0870.0010.0010.0000.0000.0000.000
118Q118ILE00.0040.00345.7270.0000.0000.0000.0000.0000.000
119Q119LEU0-0.0060.00843.2420.0000.0000.0000.0000.0000.000
120Q120LYS10.9150.94843.140-0.040-0.0400.0000.0000.0000.000
121Q121THR0-0.090-0.04746.7220.0000.0000.0000.0000.0000.000
122Q122LYS10.8880.97249.202-0.040-0.0400.0000.0000.0000.000
123Q123GLU-1-0.881-0.94450.3940.0370.0370.0000.0000.0000.000
124Q124ASN0-0.0330.00050.1780.0030.0030.0000.0000.0000.000
125Q125LYS10.9110.96644.999-0.046-0.0460.0000.0000.0000.000
126Q126GLN00.0190.00043.8870.0060.0060.0000.0000.0000.000
127Q127ASN0-0.015-0.02346.1020.0040.0040.0000.0000.0000.000
128Q128GLU-1-0.877-0.94846.3300.0430.0430.0000.0000.0000.000
129Q129ALA0-0.017-0.00342.0120.0030.0030.0000.0000.0000.000
130Q130TYR0-0.054-0.04338.140-0.004-0.0040.0000.0000.0000.000
131Q131VAL0-0.0220.00339.5120.0050.0050.0000.0000.0000.000
132Q132ALA00.0290.01536.849-0.004-0.0040.0000.0000.0000.000
133Q133ILE0-0.028-0.01738.4920.0040.0040.0000.0000.0000.000
134Q134TYR00.0460.04233.225-0.006-0.0060.0000.0000.0000.000
135Q135ILE0-0.045-0.02139.2370.0010.0010.0000.0000.0000.000
136Q136SER00.0930.02541.973-0.002-0.0020.0000.0000.0000.000
137Q137GLN0-0.0050.01642.699-0.003-0.0030.0000.0000.0000.000
138Q138SER0-0.018-0.01245.888-0.003-0.0030.0000.0000.0000.000
139Q139ASP-1-0.857-0.97347.3120.0270.0270.0000.0000.0000.000
140Q140ILE0-0.051-0.00846.0930.0010.0010.0000.0000.0000.000
141Q141LEU0-0.034-0.01350.286-0.002-0.0020.0000.0000.0000.000
142Q142HIS0-0.003-0.00348.5480.0000.0000.0000.0000.0000.000
143Q143LEU0-0.0230.00653.832-0.001-0.0010.0000.0000.0000.000
144Q144SER00.0180.00755.2150.0000.0000.0000.0000.0000.000
145Q145ALA00.0660.00555.2300.0010.0010.0000.0000.0000.000
146Q146ASP-1-0.911-0.94956.7780.0080.0080.0000.0000.0000.000
147Q147LYS10.8590.92259.178-0.011-0.0110.0000.0000.0000.000
148Q148ALA0-0.0400.00654.8370.0010.0010.0000.0000.0000.000
149Q149PRO00.0150.01555.5020.0000.0000.0000.0000.0000.000
150Q150VAL00.0220.02354.6500.0000.0000.0000.0000.0000.000
151Q151ASP-1-0.743-0.87550.7220.0270.0270.0000.0000.0000.000
152Q152LYS10.9310.94754.077-0.030-0.0300.0000.0000.0000.000
153Q153LEU0-0.073-0.02450.1140.0000.0000.0000.0000.0000.000
154Q154GLY00.0560.02953.8400.0000.0000.0000.0000.0000.000
155Q155LYS10.7870.90047.832-0.029-0.0290.0000.0000.0000.000
156Q156PRO00.0340.00650.6770.0010.0010.0000.0000.0000.000
157Q157LEU0-0.049-0.00950.3440.0020.0020.0000.0000.0000.000
158Q158LEU0-0.029-0.01746.550-0.002-0.0020.0000.0000.0000.000
159Q159THR00.009-0.00750.7970.0010.0010.0000.0000.0000.000
160Q160LEU0-0.027-0.01447.837-0.001-0.0010.0000.0000.0000.000
161Q161LYS10.9430.96451.958-0.019-0.0190.0000.0000.0000.000
162Q162ASP-1-0.859-0.93753.0290.0260.0260.0000.0000.0000.000
163Q163LYS10.8400.91653.359-0.031-0.0310.0000.0000.0000.000
164Q164SER00.0740.05149.1690.0000.0000.0000.0000.0000.000
165Q165ILE0-0.030-0.01346.0640.0010.0010.0000.0000.0000.000
166Q166SER0-0.078-0.03646.5060.0020.0020.0000.0000.0000.000
167Q167LEU00.0000.01239.7360.0020.0020.0000.0000.0000.000
168Q168GLU-1-0.900-0.95239.3610.0540.0540.0000.0000.0000.000
169Q169ASN0-0.036-0.01334.4730.0110.0110.0000.0000.0000.000
170Q170ILE0-0.036-0.01636.441-0.002-0.0020.0000.0000.0000.000
171Q171SER00.1320.04333.046-0.003-0.0030.0000.0000.0000.000
172Q172ARG10.7460.88232.751-0.054-0.0540.0000.0000.0000.000
173Q173PHE00.0060.00234.699-0.005-0.0050.0000.0000.0000.000
174Q174VAL0-0.010-0.00136.0870.0070.0070.0000.0000.0000.000
175Q175HIS00.0540.07238.0020.0000.0000.0000.0000.0000.000
176Q176VAL00.0100.00538.5340.0020.0020.0000.0000.0000.000
177Q177SER0-0.066-0.05337.6310.0040.0040.0000.0000.0000.000
178Q178GLY00.0170.00734.5130.0070.0070.0000.0000.0000.000
179Q179VAL0-0.0080.00331.780-0.005-0.0050.0000.0000.0000.000
180Q180TYR0-0.023-0.03332.4040.0140.0140.0000.0000.0000.000
181Q181ARG10.9290.96126.389-0.150-0.1500.0000.0000.0000.000
182Q182TYR00.0080.00233.3080.0040.0040.0000.0000.0000.000
183Q183SER0-0.112-0.10733.2160.0010.0010.0000.0000.0000.000
184Q184ASN0-0.121-0.25734.234-0.001-0.0010.0000.0000.0000.000
185Q185GLY00.1760.12236.6200.0000.0000.0000.0000.0000.000
186Q186ARG10.9581.17537.617-0.076-0.0760.0000.0000.0000.000
187Q187LEU00.0470.03337.148-0.003-0.0030.0000.0000.0000.000
188Q188ILE00.0360.04135.5130.0020.0020.0000.0000.0000.000
189Q189LYS10.9490.95432.496-0.126-0.1260.0000.0000.0000.000
190Q190ASN0-0.0330.00028.1870.0140.0140.0000.0000.0000.000
191Q191ALA00.0010.02426.7450.0000.0000.0000.0000.0000.000