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: 7GVKK

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 OptAll
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 -1851698.911561
FMO2-HF: Nuclear repulsion 1777580.001295
FMO2-HF: Total energy -74118.910266
FMO2-MP2: Total energy -74339.379409


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.
0.7342.247-0.017-0.616-0.8820.001
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 : -0.014 / q_NPA : -0.016
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-1-0.912-0.9513.8761.6913.204-0.017-0.616-0.8820.001
4Q4GLN00.0440.0296.4600.3500.3500.0000.0000.0000.000
5Q5LEU00.0080.0137.1350.2870.2870.0000.0000.0000.000
6Q6SER0-0.038-0.0499.359-0.241-0.2410.0000.0000.0000.000
7Q7ASP-1-0.800-0.91111.9140.7330.7330.0000.0000.0000.000
8Q8GLU-1-0.758-0.84513.0130.8900.8900.0000.0000.0000.000
9Q9GLN00.0050.0186.488-0.248-0.2480.0000.0000.0000.000
10Q10LYS10.8010.88811.957-0.840-0.8400.0000.0000.0000.000
11Q11GLU-1-0.846-0.92914.1440.4500.4500.0000.0000.0000.000
12Q12THR0-0.033-0.02813.438-0.081-0.0810.0000.0000.0000.000
13Q13ILE0-0.031-0.01310.474-0.068-0.0680.0000.0000.0000.000
14Q14LEU0-0.025-0.01114.949-0.091-0.0910.0000.0000.0000.000
15Q15LYN00.0360.03718.471-0.075-0.0750.0000.0000.0000.000
16Q16ALA00.0270.01816.700-0.056-0.0560.0000.0000.0000.000
17Q17LEU0-0.042-0.02717.145-0.062-0.0620.0000.0000.0000.000
18Q18ASN0-0.012-0.03319.994-0.056-0.0560.0000.0000.0000.000
19Q19ASP-1-0.808-0.87521.5300.2680.2680.0000.0000.0000.000
20Q20ALA00.0030.00220.501-0.032-0.0320.0000.0000.0000.000
21Q21ILE0-0.088-0.05222.637-0.031-0.0310.0000.0000.0000.000
22Q22GLU-1-0.981-0.98825.3890.1860.1860.0000.0000.0000.000
23Q23LYS10.8870.94023.378-0.279-0.2790.0000.0000.0000.000
24Q24GLY00.0040.01626.774-0.011-0.0110.0000.0000.0000.000
25Q25PRO00.010-0.00627.299-0.008-0.0080.0000.0000.0000.000
26Q26TRP0-0.070-0.04924.046-0.017-0.0170.0000.0000.0000.000
27Q27ASP-1-0.799-0.88430.3520.1290.1290.0000.0000.0000.000
28Q28LYS10.8620.91933.388-0.137-0.1370.0000.0000.0000.000
29Q29SER00.0250.00833.432-0.008-0.0080.0000.0000.0000.000
30Q30ASN00.0310.01033.5100.0120.0120.0000.0000.0000.000
31Q31PHE00.0360.02027.4830.0080.0080.0000.0000.0000.000
32Q32LEU00.0460.01928.0590.0100.0100.0000.0000.0000.000
33Q33ARG10.9200.96728.987-0.106-0.1060.0000.0000.0000.000
34Q34VAL0-0.012-0.00528.2980.0120.0120.0000.0000.0000.000
35Q35ILE0-0.028-0.00823.9240.0170.0170.0000.0000.0000.000
36Q36GLY00.0830.03825.0780.0220.0220.0000.0000.0000.000
37Q37LYS10.9200.95726.396-0.156-0.1560.0000.0000.0000.000
38Q38LYS10.9720.99421.749-0.219-0.2190.0000.0000.0000.000
39Q39LEU00.0300.01120.9610.0270.0270.0000.0000.0000.000
40Q40ILE0-0.0100.00122.3960.0300.0300.0000.0000.0000.000
41Q41ALA00.0010.00424.4200.0150.0150.0000.0000.0000.000
42Q42ILE0-0.015-0.01017.8360.0160.0160.0000.0000.0000.000
43Q43ARG10.9530.97019.823-0.284-0.2840.0000.0000.0000.000
44Q44ASP-1-0.823-0.88321.1680.3090.3090.0000.0000.0000.000
45Q45ARG10.9540.96818.992-0.360-0.3600.0000.0000.0000.000
46Q46PHE0-0.009-0.00713.3720.0020.0020.0000.0000.0000.000
47Q47LEU00.0390.01218.2150.0200.0200.0000.0000.0000.000
48Q48LYS10.7910.87120.781-0.303-0.3030.0000.0000.0000.000
49Q49ARG10.9060.95814.681-0.617-0.6170.0000.0000.0000.000
50Q50ILE00.0190.01115.507-0.004-0.0040.0000.0000.0000.000
51Q51GLY00.0080.01418.071-0.021-0.0210.0000.0000.0000.000
52Q52ALA0-0.022-0.01320.720-0.029-0.0290.0000.0000.0000.000
53Q53ALA00.0040.01317.710-0.023-0.0230.0000.0000.0000.000
54Q54SER00.0620.02519.277-0.024-0.0240.0000.0000.0000.000
55Q55GLN00.0130.01922.188-0.032-0.0320.0000.0000.0000.000
56Q56ALA0-0.034-0.02019.784-0.025-0.0250.0000.0000.0000.000
57Q57GLN0-0.069-0.03420.0700.0090.0090.0000.0000.0000.000
58Q58LEU00.0350.01021.404-0.027-0.0270.0000.0000.0000.000
59Q59GLN0-0.030-0.00724.400-0.023-0.0230.0000.0000.0000.000
60Q60ALA00.0100.01521.285-0.020-0.0200.0000.0000.0000.000
61Q61GLU-1-0.840-0.92023.2210.1560.1560.0000.0000.0000.000
62Q62SER0-0.071-0.04425.405-0.018-0.0180.0000.0000.0000.000
63Q63HIS00.0120.00325.490-0.020-0.0200.0000.0000.0000.000
64Q64LEU00.0060.00423.653-0.011-0.0110.0000.0000.0000.000
65Q65ALA00.011-0.00428.246-0.007-0.0070.0000.0000.0000.000
66Q66ASN0-0.031-0.00830.997-0.011-0.0110.0000.0000.0000.000
67Q67GLN00.0080.00329.284-0.006-0.0060.0000.0000.0000.000
68Q68ILE00.0040.00229.511-0.005-0.0050.0000.0000.0000.000
69Q69ALA0-0.0110.01533.670-0.003-0.0030.0000.0000.0000.000
70Q70LEU00.0350.01935.869-0.004-0.0040.0000.0000.0000.000
71Q71GLN0-0.069-0.03333.424-0.001-0.0010.0000.0000.0000.000
72Q72SER0-0.054-0.04737.334-0.001-0.0010.0000.0000.0000.000
73Q73GLY00.0050.01939.5540.0010.0010.0000.0000.0000.000
74Q74GLN0-0.079-0.04337.8510.0060.0060.0000.0000.0000.000
75Q75GLN00.0110.00439.062-0.005-0.0050.0000.0000.0000.000
76Q76GLU-1-0.733-0.81935.3380.0850.0850.0000.0000.0000.000
77Q77ILE0-0.029-0.00239.150-0.005-0.0050.0000.0000.0000.000
78Q78TYR0-0.015-0.03237.2820.0040.0040.0000.0000.0000.000
79Q79VAL00.0270.01343.011-0.004-0.0040.0000.0000.0000.000
80Q80SER00.0350.03844.7460.0040.0040.0000.0000.0000.000
81Q81LEU0-0.017-0.01043.738-0.002-0.0020.0000.0000.0000.000
82Q82TYR00.028-0.00447.4620.0000.0000.0000.0000.0000.000
83Q83SER0-0.007-0.01048.165-0.001-0.0010.0000.0000.0000.000
84Q84SER0-0.015-0.02550.0790.0000.0000.0000.0000.0000.000
85Q85ASP-1-0.825-0.90749.4210.0770.0770.0000.0000.0000.000
86Q86GLY00.0160.02446.8140.0030.0030.0000.0000.0000.000
87Q87SER00.0240.01345.1040.0040.0040.0000.0000.0000.000
88Q88ASN0-0.015-0.00244.3500.0100.0100.0000.0000.0000.000
89Q89LEU00.0400.02038.695-0.002-0.0020.0000.0000.0000.000
90Q90GLN0-0.082-0.03540.0480.0090.0090.0000.0000.0000.000
91Q91SER0-0.068-0.04043.538-0.002-0.0020.0000.0000.0000.000
92Q92TRP00.0240.01042.597-0.003-0.0030.0000.0000.0000.000
93Q93GLU-1-0.730-0.84739.3960.1160.1160.0000.0000.0000.000
94Q94LYS10.8960.93942.703-0.088-0.0880.0000.0000.0000.000
95Q95ILE00.0060.02646.172-0.003-0.0030.0000.0000.0000.000
96Q96VAL00.0380.02741.114-0.003-0.0030.0000.0000.0000.000
97Q97GLY0-0.0030.00244.526-0.001-0.0010.0000.0000.0000.000
98Q98SER0-0.078-0.05345.429-0.003-0.0030.0000.0000.0000.000
99Q99LEU00.0750.04143.796-0.004-0.0040.0000.0000.0000.000
100Q100PRO00.0540.01946.709-0.003-0.0030.0000.0000.0000.000
101Q101ARG10.8400.91049.720-0.054-0.0540.0000.0000.0000.000
102Q102GLN0-0.035-0.01150.354-0.002-0.0020.0000.0000.0000.000
103Q103MET00.0040.00246.064-0.001-0.0010.0000.0000.0000.000
104Q104ILE0-0.006-0.00750.014-0.001-0.0010.0000.0000.0000.000
105Q105SER00.0030.02153.432-0.002-0.0020.0000.0000.0000.000
106Q106ARG10.7820.89149.677-0.057-0.0570.0000.0000.0000.000
107Q107PRO00.0040.01350.298-0.001-0.0010.0000.0000.0000.000
108Q108ILE00.025-0.00446.8510.0040.0040.0000.0000.0000.000
109Q109TYR0-0.032-0.05345.204-0.002-0.0020.0000.0000.0000.000
110Q110ALA00.0380.00444.4030.0020.0020.0000.0000.0000.000
111Q111ASP-1-0.851-0.92041.4470.0440.0440.0000.0000.0000.000
112Q112GLU-1-0.730-0.82336.5280.0830.0830.0000.0000.0000.000
113Q113GLU-1-0.797-0.88139.3670.0580.0580.0000.0000.0000.000
114Q114ASP-1-0.803-0.89341.5350.0400.0400.0000.0000.0000.000
115Q115ILE00.0100.02442.5110.0000.0000.0000.0000.0000.000
116Q116LYS10.7690.86140.008-0.054-0.0540.0000.0000.0000.000
117Q117ALA0-0.033-0.01743.0220.0010.0010.0000.0000.0000.000
118Q118ILE0-0.0030.00245.7620.0000.0000.0000.0000.0000.000
119Q119LEU0-0.0030.01244.1080.0000.0000.0000.0000.0000.000
120Q120LYS10.9460.97744.291-0.055-0.0550.0000.0000.0000.000
121Q121THR0-0.065-0.04546.714-0.001-0.0010.0000.0000.0000.000
122Q122LYS10.8320.93249.572-0.055-0.0550.0000.0000.0000.000
123Q123GLU-1-0.852-0.94150.5200.0490.0490.0000.0000.0000.000
124Q124ASN00.0260.00850.4530.0040.0040.0000.0000.0000.000
125Q125LYS10.8190.91545.579-0.059-0.0590.0000.0000.0000.000
126Q126GLN00.0510.02944.2470.0070.0070.0000.0000.0000.000
127Q127ASN0-0.025-0.01946.3790.0060.0060.0000.0000.0000.000
128Q128GLU-1-0.785-0.90347.1520.0560.0560.0000.0000.0000.000
129Q129ALA00.0020.00742.4600.0040.0040.0000.0000.0000.000
130Q130TYR0-0.088-0.07038.299-0.006-0.0060.0000.0000.0000.000
131Q131VAL0-0.0170.00139.8810.0070.0070.0000.0000.0000.000
132Q132ALA00.0340.02737.148-0.006-0.0060.0000.0000.0000.000
133Q133ILE00.000-0.02239.2900.0030.0030.0000.0000.0000.000
134Q134TYR0-0.0210.00734.299-0.006-0.0060.0000.0000.0000.000
135Q135ILE00.003-0.00239.4370.0000.0000.0000.0000.0000.000
136Q136SER00.0560.00842.381-0.002-0.0020.0000.0000.0000.000
137Q137GLN0-0.0140.00442.867-0.004-0.0040.0000.0000.0000.000
138Q138SER00.023-0.00545.580-0.002-0.0020.0000.0000.0000.000
139Q139ASP-1-0.819-0.92347.3190.0410.0410.0000.0000.0000.000
140Q140ILE0-0.053-0.01245.8140.0010.0010.0000.0000.0000.000
141Q141LEU0-0.042-0.02550.241-0.002-0.0020.0000.0000.0000.000
142Q142HIS00.001-0.00848.2300.0000.0000.0000.0000.0000.000
143Q143LEU0-0.039-0.00753.421-0.002-0.0020.0000.0000.0000.000
144Q144SER0-0.004-0.02154.9170.0000.0000.0000.0000.0000.000
145Q145ALA00.028-0.00755.3650.0010.0010.0000.0000.0000.000
146Q146ASP-1-0.862-0.90056.7330.0180.0180.0000.0000.0000.000
147Q147LYS10.8590.91959.088-0.021-0.0210.0000.0000.0000.000
148Q148ALA0-0.0010.01654.7900.0010.0010.0000.0000.0000.000
149Q149PRO0-0.0020.00655.5780.0000.0000.0000.0000.0000.000
150Q150VAL00.0220.02254.8350.0000.0000.0000.0000.0000.000
151Q151ASP-1-0.702-0.83551.0740.0420.0420.0000.0000.0000.000
152Q152LYS10.8830.93854.262-0.044-0.0440.0000.0000.0000.000
153Q153LEU0-0.035-0.00650.706-0.001-0.0010.0000.0000.0000.000
154Q154GLY00.0310.02254.4670.0000.0000.0000.0000.0000.000
155Q155LYS10.7020.82548.304-0.043-0.0430.0000.0000.0000.000
156Q156PRO00.011-0.00451.2600.0010.0010.0000.0000.0000.000
157Q157LEU0-0.057-0.01150.6730.0020.0020.0000.0000.0000.000
158Q158LEU0-0.013-0.00946.646-0.002-0.0020.0000.0000.0000.000
159Q159THR0-0.010-0.00351.0930.0010.0010.0000.0000.0000.000
160Q160LEU0-0.016-0.00648.4420.0000.0000.0000.0000.0000.000
161Q161LYS10.8810.93351.246-0.036-0.0360.0000.0000.0000.000
162Q162ASP-1-0.807-0.90553.0210.0400.0400.0000.0000.0000.000
163Q163LYS10.8310.91153.709-0.043-0.0430.0000.0000.0000.000
164Q164SER00.0300.02249.9120.0000.0000.0000.0000.0000.000
165Q165ILE0-0.014-0.01246.5740.0020.0020.0000.0000.0000.000
166Q166SER0-0.090-0.03646.2000.0030.0030.0000.0000.0000.000
167Q167LEU0-0.033-0.00639.9680.0020.0020.0000.0000.0000.000
168Q168GLU-1-0.833-0.93039.0630.0760.0760.0000.0000.0000.000
169Q169ASN0-0.051-0.01534.6460.0130.0130.0000.0000.0000.000
170Q170ILE00.002-0.00836.788-0.003-0.0030.0000.0000.0000.000
171Q171SER0-0.021-0.00733.3430.0000.0000.0000.0000.0000.000
172Q172ARG10.7240.81532.841-0.078-0.0780.0000.0000.0000.000
173Q173PHE00.0350.01035.029-0.008-0.0080.0000.0000.0000.000
174Q174VAL0-0.0040.00436.2760.0090.0090.0000.0000.0000.000
175Q175HIS00.0480.04138.395-0.001-0.0010.0000.0000.0000.000
176Q176VAL00.0000.00538.9660.0040.0040.0000.0000.0000.000
177Q177SER0-0.045-0.02638.5090.0050.0050.0000.0000.0000.000
178Q178GLY00.0060.00235.0450.0090.0090.0000.0000.0000.000
179Q179VAL00.0050.01232.317-0.007-0.0070.0000.0000.0000.000
180Q180TYR0-0.046-0.04932.6180.0170.0170.0000.0000.0000.000
181Q181ARG10.9460.95727.888-0.188-0.1880.0000.0000.0000.000
182Q182TYR00.015-0.00633.4100.0020.0020.0000.0000.0000.000
183Q183SER0-0.030-0.04433.5580.0020.0020.0000.0000.0000.000
184Q184ASN0-0.080-0.02634.6140.0030.0030.0000.0000.0000.000
185Q185GLY00.1090.05636.9530.0010.0010.0000.0000.0000.000
186Q186ARG10.8750.93337.816-0.096-0.0960.0000.0000.0000.000
187Q187LEU00.0280.02537.337-0.003-0.0030.0000.0000.0000.000
188Q188ILE00.0060.01635.9070.0030.0030.0000.0000.0000.000
189Q189LYS10.8610.91132.359-0.137-0.1370.0000.0000.0000.000
190Q190ASN0-0.010-0.00228.4870.0170.0170.0000.0000.0000.000
191Q191ALA0-0.0050.00426.511-0.003-0.0030.0000.0000.0000.000