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: QY5GY

Calculation Name: 3GHE-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHE

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2242162.669341
FMO2-HF: Nuclear repulsion 2156614.994618
FMO2-HF: Total energy -85547.674723
FMO2-MP2: Total energy -85796.983734


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.
-13.966-7.9395.924-4.907-7.044-0.014
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 : 0.031 / q_NPA : 0.021
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].
3H3GLN00.002-0.0152.416-15.041-9.1825.927-4.842-6.943-0.014
4H4LEU00.0110.0064.5771.2761.351-0.001-0.012-0.0620.000
5H5VAL0-0.026-0.0068.1260.4090.4090.0000.0000.0000.000
6H6GLN00.0390.03210.5400.0800.0800.0000.0000.0000.000
7H7SER0-0.074-0.04414.2430.1380.1380.0000.0000.0000.000
8H8GLY00.0700.02917.332-0.054-0.0540.0000.0000.0000.000
9H9GLY0-0.044-0.00720.3970.0170.0170.0000.0000.0000.000
10H10GLY00.0360.01122.2280.0350.0350.0000.0000.0000.000
11H11LEU0-0.034-0.00925.409-0.014-0.0140.0000.0000.0000.000
12H12VAL0-0.0100.00128.7370.0080.0080.0000.0000.0000.000
13H13GLN00.0170.00931.5340.0030.0030.0000.0000.0000.000
14H14PRO0-0.004-0.01934.355-0.014-0.0140.0000.0000.0000.000
15H15GLY0-0.031-0.01234.9230.0110.0110.0000.0000.0000.000
16H16GLY0-0.0160.00333.372-0.002-0.0020.0000.0000.0000.000
17H17SER0-0.044-0.04230.352-0.014-0.0140.0000.0000.0000.000
18H18LEU00.0250.01525.2060.0130.0130.0000.0000.0000.000
19H19ARG10.9450.97520.9260.4940.4940.0000.0000.0000.000
20H20LEU0-0.043-0.00719.3730.0040.0040.0000.0000.0000.000
21H21SER00.000-0.01217.2710.0190.0190.0000.0000.0000.000
22H22CYS0-0.066-0.01113.143-0.046-0.0460.0000.0000.0000.000
23H23VAL00.0130.02710.6290.0460.0460.0000.0000.0000.000
24H24ALA00.0230.0128.967-0.303-0.3030.0000.0000.0000.000
25H25SER0-0.004-0.0195.3041.0401.0400.0000.0000.0000.000
26H26GLY00.0300.0194.099-2.058-2.059-0.001-0.0470.0490.000
27H27PHE0-0.005-0.0114.8450.4500.544-0.001-0.006-0.0880.000
28H28THR00.0330.0208.2150.1190.1190.0000.0000.0000.000
29H29PHE00.0490.02411.7920.1330.1330.0000.0000.0000.000
30H30ASN0-0.013-0.01413.324-0.029-0.0290.0000.0000.0000.000
31H31ASN00.0320.01614.4450.2130.2130.0000.0000.0000.000
32H32TYR0-0.054-0.02011.548-0.055-0.0550.0000.0000.0000.000
33H33TRP00.0920.07816.2700.0510.0510.0000.0000.0000.000
34H34MET0-0.062-0.02912.331-0.233-0.2330.0000.0000.0000.000
35H35SER00.042-0.02215.9850.2110.2110.0000.0000.0000.000
36H36TRP0-0.048-0.01816.476-0.161-0.1610.0000.0000.0000.000
37H37VAL00.0060.00317.0260.0860.0860.0000.0000.0000.000
38H38ARG10.8010.90818.3700.4130.4130.0000.0000.0000.000
39H39GLN0-0.003-0.00518.429-0.029-0.0290.0000.0000.0000.000
40H40ALA00.0410.02921.4530.0270.0270.0000.0000.0000.000
41H41PRO00.010-0.01623.953-0.003-0.0030.0000.0000.0000.000
42H42GLY00.0110.00823.8690.0120.0120.0000.0000.0000.000
43H43LYS10.9290.97724.4000.2570.2570.0000.0000.0000.000
44H44GLY00.0400.01822.622-0.018-0.0180.0000.0000.0000.000
45H45LEU0-0.025-0.01817.4140.0030.0030.0000.0000.0000.000
46H46GLU-1-0.812-0.89921.406-0.399-0.3990.0000.0000.0000.000
47H47TRP0-0.028-0.00220.0160.0020.0020.0000.0000.0000.000
48H48VAL0-0.020-0.01821.5420.0630.0630.0000.0000.0000.000
49H49ALA00.013-0.01721.8410.0600.0600.0000.0000.0000.000
50H50ASN0-0.017-0.00220.441-0.033-0.0330.0000.0000.0000.000
51H51ILE0-0.058-0.01120.1980.0800.0800.0000.0000.0000.000
52H52LYS11.0231.03320.8240.5270.5270.0000.0000.0000.000
53H52GLN00.018-0.01718.7670.0360.0360.0000.0000.0000.000
54H53ASP-1-0.884-0.95920.949-0.623-0.6230.0000.0000.0000.000
55H54GLY0-0.082-0.04423.2670.0370.0370.0000.0000.0000.000
56H55ASN00.0130.01124.2890.0180.0180.0000.0000.0000.000
57H56ASP-1-0.897-0.94926.681-0.502-0.5020.0000.0000.0000.000
58H57LYS10.8550.92925.5860.4800.4800.0000.0000.0000.000
59H58TYR0-0.0010.01925.4010.0640.0640.0000.0000.0000.000
60H59TYR00.0200.00125.429-0.049-0.0490.0000.0000.0000.000
61H60VAL00.0520.04326.6360.0250.0250.0000.0000.0000.000
62H61ASP-1-0.787-0.91728.343-0.338-0.3380.0000.0000.0000.000
63H62SER0-0.027-0.00830.0840.0070.0070.0000.0000.0000.000
64H63VAL0-0.003-0.00427.0760.0160.0160.0000.0000.0000.000
65H64LYS10.8690.94830.4360.3720.3720.0000.0000.0000.000
66H65GLY00.0060.00832.0640.0230.0230.0000.0000.0000.000
67H66ARG10.7240.85430.4770.3300.3300.0000.0000.0000.000
68H67PHE0-0.007-0.01525.932-0.003-0.0030.0000.0000.0000.000
69H68THR0-0.0080.00027.3720.0090.0090.0000.0000.0000.000
70H69ILE00.0060.01520.467-0.011-0.0110.0000.0000.0000.000
71H70SER0-0.039-0.02822.5150.0420.0420.0000.0000.0000.000
72H71ARG10.8360.91017.1591.0761.0760.0000.0000.0000.000
73H72ASP-1-0.830-0.91419.182-0.624-0.6240.0000.0000.0000.000
74H73ASN0-0.009-0.03417.539-0.178-0.1780.0000.0000.0000.000
75H74ALA0-0.0080.02017.097-0.063-0.0630.0000.0000.0000.000
76H75LYS10.9370.96016.4210.5550.5550.0000.0000.0000.000
77H76ASN0-0.0030.01311.741-0.073-0.0730.0000.0000.0000.000
78H77SER0-0.002-0.00713.552-0.151-0.1510.0000.0000.0000.000
79H78LEU0-0.0190.00015.8260.0730.0730.0000.0000.0000.000
80H79PHE0-0.033-0.04017.3690.0180.0180.0000.0000.0000.000
81H80LEU00.0340.00820.293-0.006-0.0060.0000.0000.0000.000
82H81GLN0-0.0280.00022.7570.0120.0120.0000.0000.0000.000
83H82MET0-0.017-0.00623.284-0.001-0.0010.0000.0000.0000.000
84H82ASN00.0650.02127.8930.0330.0330.0000.0000.0000.000
85H82SER00.0140.00231.678-0.001-0.0010.0000.0000.0000.000
86H82LEU0-0.0200.00727.905-0.004-0.0040.0000.0000.0000.000
87H83ARG10.9810.98531.5110.2490.2490.0000.0000.0000.000
88H84ALA00.0730.04131.342-0.012-0.0120.0000.0000.0000.000
89H85GLU-1-0.909-0.97230.877-0.222-0.2220.0000.0000.0000.000
90H86ASP-1-0.810-0.87327.911-0.350-0.3500.0000.0000.0000.000
91H87THR0-0.028-0.00326.468-0.029-0.0290.0000.0000.0000.000
92H88ALA0-0.010-0.01522.7060.0010.0010.0000.0000.0000.000
93H89VAL0-0.0210.01916.9470.0120.0120.0000.0000.0000.000
94H90TYR0-0.024-0.04618.800-0.051-0.0510.0000.0000.0000.000
95H91PHE00.024-0.00813.083-0.037-0.0370.0000.0000.0000.000
96H93ALA00.028-0.00211.881-0.261-0.2610.0000.0000.0000.000
97H94ARG10.8000.8828.6323.2043.2040.0000.0000.0000.000
98H95GLU-1-0.836-0.89012.823-1.014-1.0140.0000.0000.0000.000
99H96PHE0-0.039-0.03413.489-0.056-0.0560.0000.0000.0000.000
100H97SER00.002-0.00515.4800.1020.1020.0000.0000.0000.000
101H98SER0-0.027-0.01918.145-0.028-0.0280.0000.0000.0000.000
102H99TYR0-0.028-0.01320.0860.0570.0570.0000.0000.0000.000
103H100THR0-0.024-0.01122.6520.0220.0220.0000.0000.0000.000
104H100ASP-1-0.879-0.96025.562-0.329-0.3290.0000.0000.0000.000
105H100HIS0-0.046-0.02128.4740.0100.0100.0000.0000.0000.000
106H100LEU00.0170.01031.8240.0220.0220.0000.0000.0000.000
107H100GLU-1-0.954-0.96833.815-0.223-0.2230.0000.0000.0000.000
108H100TYR0-0.088-0.04132.0350.0020.0020.0000.0000.0000.000
109H100TYR00.0260.01427.7030.0010.0010.0000.0000.0000.000
110H100TYR0-0.052-0.01626.6030.0000.0000.0000.0000.0000.000
111H100ASP-1-0.804-0.90923.058-0.704-0.7040.0000.0000.0000.000
112H100TYR0-0.040-0.01322.4930.0110.0110.0000.0000.0000.000
113H100TYR00.002-0.00118.761-0.093-0.0930.0000.0000.0000.000
114H100TYR0-0.0060.00316.5660.0690.0690.0000.0000.0000.000
115H100MET0-0.020-0.01813.523-0.080-0.0800.0000.0000.0000.000
116H101ASP-1-0.745-0.83910.540-2.585-2.5850.0000.0000.0000.000
117H102VAL0-0.052-0.0135.992-0.639-0.6390.0000.0000.0000.000
118H103TRP00.019-0.0077.9220.7290.7290.0000.0000.0000.000
119H104GLY00.0080.0037.917-0.543-0.5430.0000.0000.0000.000
120H105LYS10.9580.9719.7320.2720.2720.0000.0000.0000.000
121H106GLY0-0.0070.00210.9550.1430.1430.0000.0000.0000.000
122H107THR0-0.024-0.01614.5500.1490.1490.0000.0000.0000.000
123H108THR00.007-0.00617.673-0.046-0.0460.0000.0000.0000.000
124H109VAL0-0.0140.01220.9200.0190.0190.0000.0000.0000.000
125H110THR0-0.015-0.01224.2170.0110.0110.0000.0000.0000.000
126H111VAL00.0040.01127.4380.0090.0090.0000.0000.0000.000
127H112SER00.022-0.00330.7680.0060.0060.0000.0000.0000.000
128H113SER00.0230.00333.819-0.001-0.0010.0000.0000.0000.000
129H114ALA0-0.0040.02035.8810.0090.0090.0000.0000.0000.000
130H115SER00.016-0.00436.846-0.007-0.0070.0000.0000.0000.000
131H116THR0-0.037-0.02636.4610.0010.0010.0000.0000.0000.000
132H117LYS10.8240.89837.8340.0300.0300.0000.0000.0000.000
133H118GLY00.0680.04939.0490.0020.0020.0000.0000.0000.000
134H119PRO0-0.023-0.01839.174-0.006-0.0060.0000.0000.0000.000
135H120SER0-0.0260.00341.4280.0020.0020.0000.0000.0000.000
136H121VAL00.009-0.00542.3930.0000.0000.0000.0000.0000.000
137H122PHE00.000-0.00744.7360.0000.0000.0000.0000.0000.000
138H123PRO0-0.0120.00345.8060.0030.0030.0000.0000.0000.000
139H124LEU0-0.036-0.01843.504-0.004-0.0040.0000.0000.0000.000
140H125ALA00.0380.00947.6720.0050.0050.0000.0000.0000.000
141H126PRO00.0060.02050.222-0.003-0.0030.0000.0000.0000.000
142H134GLY00.0500.01752.799-0.001-0.0010.0000.0000.0000.000
143H135THR0-0.084-0.01747.4020.0000.0000.0000.0000.0000.000
144H136ALA00.0490.02549.073-0.005-0.0050.0000.0000.0000.000
145H137ALA00.0040.01445.1580.0060.0060.0000.0000.0000.000
146H138LEU00.0250.02345.285-0.005-0.0050.0000.0000.0000.000
147H139GLY00.050-0.00643.4350.0060.0060.0000.0000.0000.000
148H140CYS0-0.094-0.00741.7490.0020.0020.0000.0000.0000.000
149H141LEU00.0170.02041.4200.0010.0010.0000.0000.0000.000
150H142VAL0-0.029-0.01638.172-0.001-0.0010.0000.0000.0000.000
151H143LYS10.9710.96939.4210.0190.0190.0000.0000.0000.000
152H144ASP-1-0.820-0.90840.087-0.035-0.0350.0000.0000.0000.000
153H145TYR0-0.015-0.00832.9810.0020.0020.0000.0000.0000.000
154H146PHE00.0240.02432.688-0.007-0.0070.0000.0000.0000.000
155H147PRO00.0080.00330.9590.0050.0050.0000.0000.0000.000
156H148GLU-1-0.780-0.87528.9420.0070.0070.0000.0000.0000.000
157H149PRO0-0.034-0.02428.410-0.005-0.0050.0000.0000.0000.000
158H150VAL00.019-0.00630.696-0.001-0.0010.0000.0000.0000.000
159H151THR0-0.046-0.01831.2180.0100.0100.0000.0000.0000.000
160H152VAL0-0.009-0.01733.805-0.009-0.0090.0000.0000.0000.000
161H153SER00.0000.00535.7680.0130.0130.0000.0000.0000.000
162H154TRP00.0160.02338.090-0.012-0.0120.0000.0000.0000.000
163H155ASN00.0150.00941.5070.0030.0030.0000.0000.0000.000
164H156SER0-0.003-0.01241.5590.0020.0020.0000.0000.0000.000
165H157GLY0-0.021-0.00838.8690.0070.0070.0000.0000.0000.000
166H158ALA0-0.027-0.00939.6980.0080.0080.0000.0000.0000.000
167H159LEU0-0.0210.00641.5220.0000.0000.0000.0000.0000.000
168H160THR00.011-0.01036.516-0.003-0.0030.0000.0000.0000.000
169H161SER00.0040.00337.2360.0070.0070.0000.0000.0000.000
170H162GLY00.0300.01538.701-0.008-0.0080.0000.0000.0000.000
171H163VAL0-0.0110.00736.364-0.011-0.0110.0000.0000.0000.000
172H164HIS00.0040.00032.9060.0130.0130.0000.0000.0000.000
173H165THR00.0060.00033.486-0.014-0.0140.0000.0000.0000.000
174H166PHE0-0.008-0.00332.9070.0060.0060.0000.0000.0000.000
175H167PRO0-0.012-0.00629.354-0.003-0.0030.0000.0000.0000.000
176H168ALA00.0210.00731.270-0.005-0.0050.0000.0000.0000.000
177H169VAL0-0.027-0.00332.111-0.008-0.0080.0000.0000.0000.000
178H170LEU0-0.035-0.01931.2520.0020.0020.0000.0000.0000.000
179H171GLN0-0.048-0.03534.232-0.001-0.0010.0000.0000.0000.000
180H172SER00.0380.00737.139-0.007-0.0070.0000.0000.0000.000
181H173SER0-0.017-0.00439.150-0.007-0.0070.0000.0000.0000.000
182H174GLY00.0120.01136.076-0.002-0.0020.0000.0000.0000.000
183H175LEU0-0.050-0.02335.7650.0010.0010.0000.0000.0000.000
184H176TYR00.009-0.00229.705-0.006-0.0060.0000.0000.0000.000
185H177SER00.0210.00135.9140.0070.0070.0000.0000.0000.000
186H178LEU00.0190.04533.777-0.003-0.0030.0000.0000.0000.000
187H179SER0-0.010-0.01636.823-0.002-0.0020.0000.0000.0000.000
188H180SER0-0.024-0.00437.2910.0060.0060.0000.0000.0000.000
189H181VAL00.007-0.00738.760-0.004-0.0040.0000.0000.0000.000
190H182VAL00.0430.00639.8450.0090.0090.0000.0000.0000.000
191H183THR0-0.046-0.01642.211-0.008-0.0080.0000.0000.0000.000
192H184VAL0-0.003-0.00144.5250.0070.0070.0000.0000.0000.000
193H185PRO00.0310.00347.334-0.005-0.0050.0000.0000.0000.000
194H186SER00.058-0.00450.668-0.002-0.0020.0000.0000.0000.000
195H187SER0-0.014-0.00653.420-0.002-0.0020.0000.0000.0000.000
196H188SER0-0.024-0.01351.741-0.001-0.0010.0000.0000.0000.000
197H189LEU00.0170.01051.3150.0000.0000.0000.0000.0000.000
198H190GLY00.0130.01854.251-0.002-0.0020.0000.0000.0000.000
199H191THR0-0.045-0.02255.858-0.001-0.0010.0000.0000.0000.000
200H192GLN0-0.043-0.01749.7380.0030.0030.0000.0000.0000.000
201H193THR0-0.0170.00251.536-0.002-0.0020.0000.0000.0000.000
202H194TYR00.0520.01346.6650.0070.0070.0000.0000.0000.000
203H195THR00.002-0.00645.632-0.008-0.0080.0000.0000.0000.000
204H197ASN00.016-0.01839.9860.0000.0000.0000.0000.0000.000
205H198VAL00.0130.00538.3640.0060.0060.0000.0000.0000.000
206H199ASN0-0.031-0.02635.090-0.010-0.0100.0000.0000.0000.000
207H200HIS00.0590.04334.8100.0070.0070.0000.0000.0000.000
208H201LYS10.9870.97331.178-0.110-0.1100.0000.0000.0000.000
209H202PRO00.0040.02932.023-0.003-0.0030.0000.0000.0000.000
210H203SER00.001-0.02534.454-0.007-0.0070.0000.0000.0000.000
211H204ASN0-0.096-0.04237.1760.0110.0110.0000.0000.0000.000
212H205THR00.0280.02138.7950.0000.0000.0000.0000.0000.000
213H206LYS10.9270.95638.017-0.070-0.0700.0000.0000.0000.000
214H207VAL00.001-0.00141.437-0.005-0.0050.0000.0000.0000.000
215H208ASP-1-0.829-0.89042.9900.0670.0670.0000.0000.0000.000
216H209LYS10.8960.94845.206-0.028-0.0280.0000.0000.0000.000
217H210ARG10.9660.98446.948-0.038-0.0380.0000.0000.0000.000
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