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: JLR79

Calculation Name: 5CGY-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CGY

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280309.823387
FMO2-HF: Nuclear repulsion 2194772.911586
FMO2-HF: Total energy -85536.911801
FMO2-MP2: Total energy -85787.046559


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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
1.6064.0940.001-0.949-1.540.003
Interaction energy analysis for fragmet #1(H:1:GLN)
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 : 0.009
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].
3H3GLN0-0.033-0.0133.578-1.1820.688-0.009-0.695-1.1650.004
4H4LEU00.007-0.0125.4640.5330.5330.0000.0000.0000.000
5H5VAL00.0020.0018.832-0.040-0.0400.0000.0000.0000.000
6H6GLN00.009-0.01011.1970.1190.1190.0000.0000.0000.000
7H7SER00.0210.02614.860-0.029-0.0290.0000.0000.0000.000
8H8GLY00.0130.01317.9740.0020.0020.0000.0000.0000.000
9H9SER0-0.007-0.00920.4300.0160.0160.0000.0000.0000.000
10H10GLU-1-0.925-0.95323.308-0.256-0.2560.0000.0000.0000.000
11H11LEU0-0.015-0.00226.2800.0120.0120.0000.0000.0000.000
12H12LYS10.8860.94328.9340.1910.1910.0000.0000.0000.000
13H13LYS10.9991.00532.2280.1340.1340.0000.0000.0000.000
14H14PRO00.0310.01535.126-0.002-0.0020.0000.0000.0000.000
15H15GLY0-0.027-0.00936.5310.0040.0040.0000.0000.0000.000
16H16ALA0-0.036-0.00933.9280.0030.0030.0000.0000.0000.000
17H17SER00.010-0.00130.9760.0010.0010.0000.0000.0000.000
18H18VAL0-0.024-0.01525.802-0.005-0.0050.0000.0000.0000.000
19H19LYS10.9580.98023.5330.1830.1830.0000.0000.0000.000
20H20VAL00.0250.03020.362-0.016-0.0160.0000.0000.0000.000
21H21SER0-0.014-0.02417.8090.0120.0120.0000.0000.0000.000
22H22CYS0-0.0350.00113.762-0.038-0.0380.0000.0000.0000.000
23H23LYS10.8990.95310.6350.6300.6300.0000.0000.0000.000
24H24ALA00.0430.0279.381-0.212-0.2120.0000.0000.0000.000
25H25SER0-0.061-0.0386.086-0.220-0.2200.0000.0000.0000.000
26H26GLY00.0820.0364.114-0.868-0.6900.002-0.114-0.0660.000
27H27TYR0-0.0010.0073.6520.9921.4320.008-0.140-0.309-0.001
28H28SER00.000-0.0026.272-0.347-0.3470.0000.0000.0000.000
29H29PHE00.0530.0179.993-0.075-0.0750.0000.0000.0000.000
30H30THR00.0310.00111.911-0.021-0.0210.0000.0000.0000.000
31H31SER0-0.023-0.00212.1690.0010.0010.0000.0000.0000.000
32H32TYR0-0.037-0.02410.1150.0540.0540.0000.0000.0000.000
33H33SER0-0.0290.01913.442-0.046-0.0460.0000.0000.0000.000
34H34ILE0-0.037-0.00812.909-0.014-0.0140.0000.0000.0000.000
35H35ASN00.0120.00315.5770.0200.0200.0000.0000.0000.000
36H36TRP00.0210.00216.972-0.065-0.0650.0000.0000.0000.000
37H37VAL00.0210.00919.0940.0310.0310.0000.0000.0000.000
38H38ARG10.8800.95320.4990.0820.0820.0000.0000.0000.000
39H39GLN0-0.011-0.00922.4640.0030.0030.0000.0000.0000.000
40H40ALA00.0280.02024.372-0.017-0.0170.0000.0000.0000.000
41H41PRO00.009-0.01727.6870.0030.0030.0000.0000.0000.000
42H42GLY0-0.0210.00628.9040.0100.0100.0000.0000.0000.000
43H43GLN0-0.028-0.00628.9770.0140.0140.0000.0000.0000.000
44H44GLY00.0280.02426.178-0.011-0.0110.0000.0000.0000.000
45H45PRO0-0.026-0.03321.820-0.001-0.0010.0000.0000.0000.000
46H46GLU-1-0.872-0.93924.145-0.076-0.0760.0000.0000.0000.000
47H47TRP0-0.008-0.00520.131-0.016-0.0160.0000.0000.0000.000
48H48MET0-0.033-0.01822.862-0.002-0.0020.0000.0000.0000.000
49H49GLY00.0370.00922.6970.0090.0090.0000.0000.0000.000
50H50TRP0-0.048-0.01019.434-0.014-0.0140.0000.0000.0000.000
51H51ILE0-0.037-0.02018.966-0.004-0.0040.0000.0000.0000.000
52H52ASP-1-0.774-0.89618.9630.1250.1250.0000.0000.0000.000
53H53THR0-0.056-0.03815.044-0.008-0.0080.0000.0000.0000.000
54H54ASN0-0.069-0.03018.154-0.008-0.0080.0000.0000.0000.000
55H55THR0-0.036-0.02619.802-0.020-0.0200.0000.0000.0000.000
56H56GLY00.0070.01221.921-0.013-0.0130.0000.0000.0000.000
57H57ASN0-0.012-0.01223.155-0.024-0.0240.0000.0000.0000.000
58H58PRO0-0.021-0.00423.8150.0060.0060.0000.0000.0000.000
59H59THR0-0.0020.00024.4210.0090.0090.0000.0000.0000.000
60H60TYR0-0.0030.00425.004-0.011-0.0110.0000.0000.0000.000
61H61ALA00.0280.01226.6280.0100.0100.0000.0000.0000.000
62H62GLN00.017-0.00728.244-0.001-0.0010.0000.0000.0000.000
63H63ASP-1-0.905-0.94930.797-0.044-0.0440.0000.0000.0000.000
64H64PHE0-0.071-0.04227.794-0.011-0.0110.0000.0000.0000.000
65H65ALA0-0.0040.00730.100-0.005-0.0050.0000.0000.0000.000
66H66GLY00.0140.00031.6730.0030.0030.0000.0000.0000.000
67H67ARG10.7310.84532.7150.0920.0920.0000.0000.0000.000
68H68PHE0-0.0030.00127.106-0.012-0.0120.0000.0000.0000.000
69H69VAL00.0170.01426.7350.0110.0110.0000.0000.0000.000
70H70PHE0-0.004-0.00122.235-0.024-0.0240.0000.0000.0000.000
71H71SER0-0.030-0.01522.4470.0120.0120.0000.0000.0000.000
72H72LEU00.020-0.00418.152-0.022-0.0220.0000.0000.0000.000
73H73ASP-1-0.824-0.88219.136-0.141-0.1410.0000.0000.0000.000
74H74THR00.010-0.01117.424-0.037-0.0370.0000.0000.0000.000
75H75SER0-0.047-0.02016.9110.0090.0090.0000.0000.0000.000
76H76VAL00.0120.01016.009-0.021-0.0210.0000.0000.0000.000
77H77THR0-0.054-0.01811.503-0.106-0.1060.0000.0000.0000.000
78H78THR0-0.014-0.00513.144-0.114-0.1140.0000.0000.0000.000
79H79ALA00.0040.01415.6440.0660.0660.0000.0000.0000.000
80H80TYR0-0.036-0.04617.569-0.049-0.0490.0000.0000.0000.000
81H81LEU00.0260.02520.4760.0300.0300.0000.0000.0000.000
82H82GLN0-0.044-0.02022.795-0.020-0.0200.0000.0000.0000.000
83H83ILE00.0120.02326.1910.0150.0150.0000.0000.0000.000
84H84SER00.016-0.00729.073-0.007-0.0070.0000.0000.0000.000
85H85SER0-0.038-0.02232.7080.0050.0050.0000.0000.0000.000
86H86LEU0-0.018-0.00229.7070.0050.0050.0000.0000.0000.000
87H87LYS10.9530.96333.7060.0870.0870.0000.0000.0000.000
88H88ALA00.0690.02133.691-0.007-0.0070.0000.0000.0000.000
89H89GLY00.004-0.01033.336-0.007-0.0070.0000.0000.0000.000
90H90ASP-1-0.735-0.82729.996-0.109-0.1090.0000.0000.0000.000
91H91THR0-0.0240.01928.595-0.016-0.0160.0000.0000.0000.000
92H92ALA0-0.0050.00225.4940.0110.0110.0000.0000.0000.000
93H93VAL0-0.0030.02019.902-0.016-0.0160.0000.0000.0000.000
94H94TYR0-0.012-0.04821.0340.0320.0320.0000.0000.0000.000
95H95TYR00.0320.02515.748-0.048-0.0480.0000.0000.0000.000
96H97ALA00.0460.01112.774-0.067-0.0670.0000.0000.0000.000
97H98THR00.0120.0098.9940.0680.0680.0000.0000.0000.000
98H99TYR00.003-0.02910.321-0.022-0.0220.0000.0000.0000.000
99H100TYR00.0230.0085.712-0.030-0.0300.0000.0000.0000.000
100H101VAL0-0.010-0.0135.5410.0640.0640.0000.0000.0000.000
101H102ASP-1-0.902-0.9435.8532.4022.4020.0000.0000.0000.000
102H103LEU0-0.096-0.0498.233-0.093-0.0930.0000.0000.0000.000
103H104TRP0-0.061-0.04311.016-0.128-0.1280.0000.0000.0000.000
104H105GLY0-0.034-0.01813.122-0.042-0.0420.0000.0000.0000.000
105H106SER00.001-0.00111.9160.0670.0670.0000.0000.0000.000
106H107TYR00.0620.03013.305-0.005-0.0050.0000.0000.0000.000
107H108ARG10.8490.93314.861-0.363-0.3630.0000.0000.0000.000
108H109GLN00.0530.03015.690-0.038-0.0380.0000.0000.0000.000
109H110ASP-1-0.799-0.86918.0610.1620.1620.0000.0000.0000.000
110H111TYR00.0340.00318.469-0.008-0.0080.0000.0000.0000.000
111H112TYR0-0.024-0.01416.779-0.021-0.0210.0000.0000.0000.000
112H113GLY0-0.0050.01913.8080.0240.0240.0000.0000.0000.000
113H114MET0-0.049-0.05214.409-0.074-0.0740.0000.0000.0000.000
114H115ASP-1-0.783-0.86110.2680.2430.2430.0000.0000.0000.000
115H116VAL0-0.032-0.0166.536-0.047-0.0470.0000.0000.0000.000
116H117TRP0-0.027-0.0279.827-0.011-0.0110.0000.0000.0000.000
117H118GLY0-0.002-0.00310.723-0.135-0.1350.0000.0000.0000.000
118H119HIS0-0.011-0.02410.2140.1780.1780.0000.0000.0000.000
119H120GLY0-0.0090.00814.0300.0640.0640.0000.0000.0000.000
120H121THR0-0.038-0.03017.199-0.037-0.0370.0000.0000.0000.000
121H122LEU0-0.033-0.01020.0190.0390.0390.0000.0000.0000.000
122H123VAL00.0150.01123.419-0.004-0.0040.0000.0000.0000.000
123H124THR0-0.002-0.01226.3080.0160.0160.0000.0000.0000.000
124H125VAL0-0.030-0.02229.7140.0000.0000.0000.0000.0000.000
125H126SER00.0310.01132.8100.0090.0090.0000.0000.0000.000
126H127SER0-0.022-0.02135.402-0.001-0.0010.0000.0000.0000.000
127H128ALA0-0.0320.00237.1820.0060.0060.0000.0000.0000.000
128H129SER0-0.016-0.01237.678-0.005-0.0050.0000.0000.0000.000
129H130THR0-0.028-0.02538.8260.0000.0000.0000.0000.0000.000
130H131LYS10.9360.97240.1860.1020.1020.0000.0000.0000.000
131H132GLY00.0400.02942.234-0.005-0.0050.0000.0000.0000.000
132H133PRO0-0.049-0.01143.5130.0030.0030.0000.0000.0000.000
133H134SER0-0.015-0.01045.3650.0050.0050.0000.0000.0000.000
134H135VAL00.0020.00047.539-0.002-0.0020.0000.0000.0000.000
135H136PHE0-0.028-0.02149.4230.0040.0040.0000.0000.0000.000
136H137PRO00.0140.01150.506-0.003-0.0030.0000.0000.0000.000
137H138LEU0-0.022-0.00147.2100.0010.0010.0000.0000.0000.000
138H139ALA00.0490.01951.8470.0000.0000.0000.0000.0000.000
139H140PRO00.0010.02554.4600.0010.0010.0000.0000.0000.000
140H141SER0-0.021-0.02953.6760.0010.0010.0000.0000.0000.000
141H142SER00.021-0.00454.6700.0000.0000.0000.0000.0000.000
142H143LYS10.9280.97357.1010.0320.0320.0000.0000.0000.000
143H144SER00.0410.03360.5460.0000.0000.0000.0000.0000.000
144H145THR0-0.072-0.06062.4220.0020.0020.0000.0000.0000.000
145H146SER00.0510.04761.1940.0010.0010.0000.0000.0000.000
146H147GLY00.0530.01561.182-0.001-0.0010.0000.0000.0000.000
147H148GLY00.0000.01057.632-0.001-0.0010.0000.0000.0000.000
148H149THR0-0.029-0.01452.1190.0000.0000.0000.0000.0000.000
149H150ALA00.008-0.00253.8870.0010.0010.0000.0000.0000.000
150H151ALA00.0130.01649.653-0.002-0.0020.0000.0000.0000.000
151H152LEU00.0020.01551.4290.0020.0020.0000.0000.0000.000
152H153GLY00.0360.00248.823-0.003-0.0030.0000.0000.0000.000
153H154CYS0-0.084-0.00447.8190.0020.0020.0000.0000.0000.000
154H155LEU00.0240.02144.871-0.003-0.0030.0000.0000.0000.000
155H156VAL0-0.028-0.01743.0660.0020.0020.0000.0000.0000.000
156H157LYS10.9750.97443.1670.0730.0730.0000.0000.0000.000
157H158ASP-1-0.881-0.94942.369-0.092-0.0920.0000.0000.0000.000
158H159TYR0-0.051-0.06537.2690.0060.0060.0000.0000.0000.000
159H160PHE00.0270.03733.976-0.005-0.0050.0000.0000.0000.000
160H161PRO00.0130.00733.9980.0070.0070.0000.0000.0000.000
161H162GLU-1-0.757-0.85732.980-0.148-0.1480.0000.0000.0000.000
162H163PRO0-0.022-0.01334.154-0.006-0.0060.0000.0000.0000.000
163H164VAL00.014-0.00535.9620.0050.0050.0000.0000.0000.000
164H165THR0-0.040-0.01938.632-0.003-0.0030.0000.0000.0000.000
165H166VAL0-0.005-0.02040.8010.0040.0040.0000.0000.0000.000
166H167SER0-0.0200.00343.506-0.003-0.0030.0000.0000.0000.000
167H168TRP00.0230.00146.1200.0040.0040.0000.0000.0000.000
168H169ASN00.003-0.00549.5190.0000.0000.0000.0000.0000.000
169H170SER0-0.002-0.01450.4810.0010.0010.0000.0000.0000.000
170H171GLY0-0.019-0.00647.683-0.002-0.0020.0000.0000.0000.000
171H172ALA0-0.026-0.00248.5320.0000.0000.0000.0000.0000.000
172H173LEU0-0.047-0.01050.2220.0020.0020.0000.0000.0000.000
173H174THR00.0330.00145.819-0.002-0.0020.0000.0000.0000.000
174H175SER00.006-0.00346.456-0.001-0.0010.0000.0000.0000.000
175H176GLY00.0350.01746.9690.0020.0020.0000.0000.0000.000
176H177VAL0-0.037-0.00744.0910.0010.0010.0000.0000.0000.000
177H178HIS00.0030.00438.359-0.005-0.0050.0000.0000.0000.000
178H179THR00.003-0.01339.4610.0050.0050.0000.0000.0000.000
179H180PHE0-0.023-0.00838.493-0.004-0.0040.0000.0000.0000.000
180H181PRO00.011-0.00733.536-0.002-0.0020.0000.0000.0000.000
181H182ALA0-0.0040.00435.5040.0070.0070.0000.0000.0000.000
182H183VAL0-0.0090.00534.806-0.005-0.0050.0000.0000.0000.000
183H184LEU0-0.004-0.00531.487-0.002-0.0020.0000.0000.0000.000
184H185GLN0-0.036-0.02235.1930.0060.0060.0000.0000.0000.000
185H186SER00.022-0.01236.317-0.006-0.0060.0000.0000.0000.000
186H187SER0-0.0050.00037.406-0.004-0.0040.0000.0000.0000.000
187H188GLY00.0440.00835.484-0.002-0.0020.0000.0000.0000.000
188H189LEU0-0.118-0.04536.340-0.006-0.0060.0000.0000.0000.000
189H190TYR00.0430.01031.484-0.002-0.0020.0000.0000.0000.000
190H191SER00.0090.01438.1670.0080.0080.0000.0000.0000.000
191H192LEU00.0200.04538.337-0.002-0.0020.0000.0000.0000.000
192H193SER00.014-0.00440.7330.0070.0070.0000.0000.0000.000
193H194SER0-0.0090.02542.206-0.002-0.0020.0000.0000.0000.000
194H195VAL00.041-0.00144.3720.0040.0040.0000.0000.0000.000
195H196VAL00.0000.01146.418-0.002-0.0020.0000.0000.0000.000
196H197THR0-0.027-0.01547.7680.0030.0030.0000.0000.0000.000
197H198VAL0-0.010-0.01550.2370.0000.0000.0000.0000.0000.000
198H199PRO00.0690.02753.8200.0010.0010.0000.0000.0000.000
199H200SER0-0.002-0.01257.0280.0000.0000.0000.0000.0000.000
200H201SER00.0230.00958.7370.0000.0000.0000.0000.0000.000
201H202SER00.0150.02057.9050.0010.0010.0000.0000.0000.000
202H203LEU0-0.031-0.02355.920-0.001-0.0010.0000.0000.0000.000
203H204GLY00.0110.00459.5710.0020.0020.0000.0000.0000.000
204H205THR0-0.090-0.03961.7200.0010.0010.0000.0000.0000.000
205H206GLN00.0170.01258.1560.0020.0020.0000.0000.0000.000
206H207THR0-0.015-0.00657.9100.0000.0000.0000.0000.0000.000
207H208TYR00.0240.01153.687-0.001-0.0010.0000.0000.0000.000
208H209ILE00.0250.00053.1580.0010.0010.0000.0000.0000.000
209H211ASN00.034-0.01548.1430.0010.0010.0000.0000.0000.000
210H212VAL00.0160.01144.366-0.005-0.0050.0000.0000.0000.000
211H213ASN0-0.012-0.01642.7880.0050.0050.0000.0000.0000.000
212H214HIS00.0330.05138.7960.0010.0010.0000.0000.0000.000
213H215LYS10.9710.97939.0020.1460.1460.0000.0000.0000.000
214H216PRO00.0160.01337.2730.0030.0030.0000.0000.0000.000
215H217SER0-0.013-0.03939.7770.0030.0030.0000.0000.0000.000
216H218ASN0-0.057-0.02443.2250.0010.0010.0000.0000.0000.000
217H219THR00.0170.00644.7970.0070.0070.0000.0000.0000.000
218H220LYS10.9250.95945.8930.1020.1020.0000.0000.0000.000
219H221VAL00.0040.00348.4550.0040.0040.0000.0000.0000.000
220H222ASP-1-0.818-0.87649.882-0.083-0.0830.0000.0000.0000.000
221H223LYS10.9250.95052.0290.0700.0700.0000.0000.0000.000
222H224ARG10.8490.90753.5710.0540.0540.0000.0000.0000.000
223H225VAL0-0.040-0.02152.3290.0010.0010.0000.0000.0000.000
224H226GLU-1-0.826-0.90255.790-0.051-0.0510.0000.0000.0000.000
225H227PRO0-0.016-0.01158.147-0.001-0.0010.0000.0000.0000.000
226H228LYS10.9500.99259.4820.0440.0440.0000.0000.0000.000