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: GNQQ1

Calculation Name: 4DQZ-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DQZ

Chain ID: A

ChEMBL ID:

UniProt ID: A3DJ37

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1870710.813752
FMO2-HF: Nuclear repulsion 1801582.708879
FMO2-HF: Total energy -69128.104874
FMO2-MP2: Total energy -69328.655735


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(A:1:MET )


Summations of interaction energy for fragment #1(A: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.
-24.965-12.54816.938-10.228-19.128-0.046
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.012
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].
3A3LEU 00.0160.0223.794-0.1132.094-0.015-1.059-1.1330.002
4A4THR 0-0.028-0.0245.514-0.292-0.2920.0000.0000.0000.000
5A5ILE 0-0.016-0.0099.2340.2210.2210.0000.0000.0000.000
6A6THR 0-0.025-0.02112.276-0.092-0.0920.0000.0000.0000.000
7A7TYR 0-0.016-0.01415.7180.0520.0520.0000.0000.0000.000
8A8THR 00.008-0.02219.157-0.029-0.0290.0000.0000.0000.000
9A9GLN 00.0030.02222.520-0.013-0.0130.0000.0000.0000.000
10A10PRO 00.0070.00825.3180.0040.0040.0000.0000.0000.000
11A11PRO 0-0.0180.01527.1300.0000.0000.0000.0000.0000.000
12A12ALA 00.0730.04421.9720.0110.0110.0000.0000.0000.000
13A13THR 0-0.017-0.03121.7410.0070.0070.0000.0000.0000.000
14A14ASP -1-0.864-0.95022.7140.0760.0760.0000.0000.0000.000
15A15LEU 0-0.045-0.02515.4280.0250.0250.0000.0000.0000.000
16A16GLY 00.005-0.00218.8100.0240.0240.0000.0000.0000.000
17A17TYR 0-0.034-0.02320.1310.0140.0140.0000.0000.0000.000
18A18LEU 00.002-0.00119.6130.0250.0250.0000.0000.0000.000
19A19LEU 0-0.030-0.01613.8030.0550.0550.0000.0000.0000.000
20A20HIS 0-0.075-0.02917.164-0.002-0.0020.0000.0000.0000.000
21A21LYS 10.8720.94815.100-0.225-0.2250.0000.0000.0000.000
22A22ASN 00.0100.00818.400-0.030-0.0300.0000.0000.0000.000
23A23PRO 00.0930.03418.761-0.022-0.0220.0000.0000.0000.000
24A24SER 0-0.044-0.02019.686-0.038-0.0380.0000.0000.0000.000
25A25ARG 10.8660.92320.1670.0340.0340.0000.0000.0000.000
26A26PRO 00.0450.03815.4360.0200.0200.0000.0000.0000.000
27A27GLN 0-0.0110.00114.5900.0420.0420.0000.0000.0000.000
28A28THR 00.010-0.00111.557-0.099-0.0990.0000.0000.0000.000
29A29PHE 0-0.072-0.03911.9450.0910.0910.0000.0000.0000.000
30A30GLU -1-0.848-0.92011.684-0.071-0.0710.0000.0000.0000.000
31A31LEU 0-0.068-0.0519.0120.0940.0940.0000.0000.0000.000
32A32ASN 0-0.037-0.01812.825-0.149-0.1490.0000.0000.0000.000
33A33HIS 00.0600.01611.7320.1450.1450.0000.0000.0000.000
34A34GLY 00.1290.0718.9140.0720.0720.0000.0000.0000.000
35A35LYS 10.8860.9478.3410.3490.3490.0000.0000.0000.000
36A36ALA 00.0270.0207.059-0.065-0.0650.0000.0000.0000.000
37A37HIS 0-0.025-0.0087.4930.1020.1020.0000.0000.0000.000
38A38ILE 0-0.0010.0028.937-0.113-0.1130.0000.0000.0000.000
39A39PHE 0-0.001-0.01410.4380.0530.0530.0000.0000.0000.000
40A40TYR 00.0540.01713.347-0.001-0.0010.0000.0000.0000.000
41A41PRO 0-0.049-0.00613.2770.0140.0140.0000.0000.0000.000
42A42GLU -1-0.840-0.91916.371-0.158-0.1580.0000.0000.0000.000
43A43ALA 00.0120.00118.7210.0300.0300.0000.0000.0000.000
44A44THR 00.0170.01121.3230.0130.0130.0000.0000.0000.000
45A45SER 00.038-0.00824.0480.0130.0130.0000.0000.0000.000
46A46GLU -1-0.885-0.93325.809-0.017-0.0170.0000.0000.0000.000
47A47ARG 10.8780.93118.5580.1320.1320.0000.0000.0000.000
48A48CYS 0-0.075-0.00619.184-0.021-0.0210.0000.0000.0000.000
49A49THR 00.0360.01513.4620.0430.0430.0000.0000.0000.000
50A50VAL 0-0.0290.00911.201-0.052-0.0520.0000.0000.0000.000
51A51ALA 00.005-0.0179.451-0.008-0.0080.0000.0000.0000.000
52A52LEU 0-0.017-0.0196.4600.1590.1590.0000.0000.0000.000
53A53LEU 0-0.010-0.0024.715-0.460-0.4070.000-0.029-0.0240.000
54A54LEU 0-0.047-0.0282.131-0.5441.5931.902-1.433-2.6050.006
55A55ASP -1-0.917-0.9562.908-5.097-3.3580.168-0.988-0.919-0.011
56A56ILE 0-0.037-0.0254.5000.5690.7830.000-0.021-0.1930.000
57A57ASP -1-0.873-0.9327.088-0.307-0.3070.0000.0000.0000.000
58A58NME 0-0.068-0.02710.8080.0590.0590.0000.0000.0000.000
59A86ACE 00.1050.0473.226-0.287-0.1220.027-0.061-0.1320.000
60A87SER 0-0.050-0.0424.095-0.242-0.1490.001-0.010-0.0840.000
61A88PHE 00.0280.0254.8780.1400.1400.0000.0000.0000.000
62A89MET 00.0920.0422.080-1.742-2.8875.913-1.184-3.5840.010
63A90SER 0-0.0030.0034.866-1.188-1.0990.001-0.038-0.0510.000
64A91VAL 0-0.021-0.0108.064-0.594-0.5940.0000.0000.0000.000
65A92ALA 00.0240.0136.691-0.427-0.4270.0000.0000.0000.000
66A93ILE 00.017-0.0036.547-0.456-0.4560.0000.0000.0000.000
67A94SER 0-0.060-0.0249.531-0.380-0.3800.0000.0000.0000.000
68A95ARG 10.8890.95512.073-0.566-0.5660.0000.0000.0000.000
69A96VAL 0-0.085-0.03610.726-0.174-0.1740.0000.0000.0000.000
70A97PHE 00.031-0.0039.457-0.139-0.1390.0000.0000.0000.000
71A98GLY 00.0730.04014.0930.0190.0190.0000.0000.0000.000
72A99THR 0-0.013-0.01916.673-0.002-0.0020.0000.0000.0000.000
73A100ALA 00.0970.10416.184-0.013-0.0130.0000.0000.0000.000
74A101MET 0-0.032-0.00913.2710.0150.0150.0000.0000.0000.000
75A102SER 0-0.132-0.10117.363-0.037-0.0370.0000.0000.0000.000
76A103GLY 00.0360.00820.512-0.026-0.0260.0000.0000.0000.000
77A104LYS 10.8790.94922.112-0.289-0.2890.0000.0000.0000.000
78A105CYS 00.0420.02022.6460.0050.0050.0000.0000.0000.000
79A106LYS 10.9260.96724.699-0.130-0.1300.0000.0000.0000.000
80A107GLU -1-0.903-0.96225.7750.1120.1120.0000.0000.0000.000
81A108LYS 10.9450.97025.736-0.088-0.0880.0000.0000.0000.000
82A109PRO 0-0.0060.01526.6460.0170.0170.0000.0000.0000.000
83A110GLU -1-0.826-0.93927.8620.1330.1330.0000.0000.0000.000
84A111LEU 0-0.004-0.00224.2390.0100.0100.0000.0000.0000.000
85A112ALA 0-0.0050.00522.8360.0210.0210.0000.0000.0000.000
86A113ALA 0-0.062-0.01823.6440.0310.0310.0000.0000.0000.000
87A114ILE 0-0.0170.00725.5740.0060.0060.0000.0000.0000.000
88A115LYS 10.8950.94623.069-0.173-0.1730.0000.0000.0000.000
89A116LEU 0-0.012-0.00820.883-0.029-0.0290.0000.0000.0000.000
90A117PRO 00.0420.02121.1190.0260.0260.0000.0000.0000.000
91A118LEU 0-0.056-0.02516.266-0.015-0.0150.0000.0000.0000.000
92A119LYS 10.9970.99715.247-0.013-0.0130.0000.0000.0000.000
93A120ALA 0-0.0050.00210.352-0.011-0.0110.0000.0000.0000.000
94A121LYS 10.9370.9708.5750.4920.4920.0000.0000.0000.000
95A122ILE 00.0430.0193.672-0.4830.0680.292-0.147-0.6960.000
96A123MET 0-0.028-0.0144.286-0.3630.0370.000-0.090-0.3110.000
97A124MET 0-0.001-0.0012.226-4.785-3.9255.014-2.475-3.400-0.029
98A125LEU 00.0310.0172.507-5.905-2.2972.559-2.313-3.854-0.023
99A126PRO 0-0.0180.0012.633-0.2380.1070.812-0.084-1.073-0.001
100A127CYS 00.0300.0265.4140.2560.2560.0000.0000.0000.000
101A128LYS 10.9730.9668.0560.0900.0900.0000.0000.0000.000
102A129GLY 00.0120.00911.314-0.016-0.0160.0000.0000.0000.000
103A130GLY 00.1150.01712.2140.0190.0190.0000.0000.0000.000
104A131GLU -1-0.878-0.96112.2340.0420.0420.0000.0000.0000.000
105A132GLU -1-0.893-0.95013.7410.1500.1500.0000.0000.0000.000
106A133ILE 0-0.052-0.02411.6100.0340.0340.0000.0000.0000.000
107A134ILE 00.009-0.0039.4760.0950.0950.0000.0000.0000.000
108A135TYR 00.0250.00712.2410.0840.0840.0000.0000.0000.000
109A136ARG 10.8620.91015.732-0.217-0.2170.0000.0000.0000.000
110A137LEU 0-0.029-0.00910.9350.0130.0130.0000.0000.0000.000
111A138PHE 0-0.010-0.0118.9260.0660.0660.0000.0000.0000.000
112A139GLU -1-0.853-0.93014.8510.1780.1780.0000.0000.0000.000
113A140PRO 0-0.054-0.01917.711-0.022-0.0220.0000.0000.0000.000
114A141LEU 0-0.076-0.03115.404-0.007-0.0070.0000.0000.0000.000
115A142GLY 0-0.027-0.00619.000-0.004-0.0040.0000.0000.0000.000
116A143TYR 0-0.118-0.07315.026-0.017-0.0170.0000.0000.0000.000
117A144LYS 10.9930.99517.985-0.084-0.0840.0000.0000.0000.000
118A145VAL 0-0.024-0.03113.5950.0310.0310.0000.0000.0000.000
119A146ASP -1-0.969-0.97314.408-0.096-0.0960.0000.0000.0000.000
120A147VAL 0-0.0040.00311.4100.0570.0570.0000.0000.0000.000
121A148GLU -1-0.871-0.92111.356-0.515-0.5150.0000.0000.0000.000
122A149GLY 0-0.001-0.01410.604-0.056-0.0560.0000.0000.0000.000
123A150TYR 0-0.026-0.0396.987-0.207-0.2070.0000.0000.0000.000
124A151NME 0-0.0750.04810.411-0.026-0.0260.0000.0000.0000.000
125A162ACE 00.000-0.01111.8140.0050.0050.0000.0000.0000.000
126A163ARG 00.0890.06410.2430.0590.0590.0000.0000.0000.000
127A164TYR 0-0.096-0.0414.756-0.0660.0670.000-0.007-0.1260.000
128A165TYR 0-0.109-0.1226.5120.1450.1450.0000.0000.0000.000
129A166THR 0-0.0220.0035.967-0.342-0.3420.0000.0000.0000.000
130A167VAL 00.0420.0427.4860.0640.0640.0000.0000.0000.000
131A168SER 0-0.034-0.0209.1970.0200.0200.0000.0000.0000.000
132A169LEU 0-0.0090.00710.4860.0290.0290.0000.0000.0000.000
133A170GLU -1-0.937-0.98313.9770.0430.0430.0000.0000.0000.000
134A171GLY 00.0500.02517.2980.0050.0050.0000.0000.0000.000
135A172GLU -1-0.942-0.96719.5970.1400.1400.0000.0000.0000.000
136A173VAL 00.0150.01716.9740.0010.0010.0000.0000.0000.000
137A174ARG 10.8780.91820.394-0.350-0.3500.0000.0000.0000.000
138A175VAL 00.0650.02216.2560.0510.0510.0000.0000.0000.000
139A176ARG 10.8820.94116.061-0.249-0.2490.0000.0000.0000.000
140A177ASP -1-0.806-0.88916.5090.4990.4990.0000.0000.0000.000
141A178LEU 00.0250.03712.4590.0740.0740.0000.0000.0000.000
142A179LEU 0-0.032-0.03211.4370.1910.1910.0000.0000.0000.000
143A180ASN 00.0360.01611.5810.3080.3080.0000.0000.0000.000
144A181HIS 00.0970.07712.7810.1330.1330.0000.0000.0000.000
145A182ILE 00.0200.0216.6590.1420.1420.0000.0000.0000.000
146A183TYR 0-0.061-0.0308.0030.4180.4180.0000.0000.0000.000
147A184VAL 00.0040.0019.6880.0700.0700.0000.0000.0000.000
148A185LEU 00.0200.0069.920-0.026-0.0260.0000.0000.0000.000
149A186ILE 0-0.0060.0043.423-0.7100.0570.263-0.220-0.8100.000
150A187PRO 0-0.059-0.0435.553-0.495-0.4950.0000.0000.0000.000
151A188VAL 00.0140.0237.169-0.278-0.2780.0000.0000.0000.000
152A189LEU 0-0.031-0.0066.315-0.143-0.1430.0000.0000.0000.000
153A190ASP -1-0.912-0.9484.155-0.903-0.7020.001-0.069-0.1330.000
154A191NME 0-0.077-0.0467.007-0.085-0.0850.0000.0000.0000.000
155A201ACE 0-0.010-0.01817.4630.0030.0030.0000.0000.0000.000
156A202ILE 00.0240.00718.317-0.005-0.0050.0000.0000.0000.000
157A203ASP -1-0.780-0.89719.7420.4380.4380.0000.0000.0000.000
158A204LYS 10.9060.96612.149-0.974-0.9740.0000.0000.0000.000
159A205LEU 00.0450.03015.7640.0370.0370.0000.0000.0000.000
160A206PHE 0-0.029-0.00317.417-0.024-0.0240.0000.0000.0000.000
161A207GLN 0-0.032-0.03119.1370.0290.0290.0000.0000.0000.000
162A208HIS 10.8360.90815.444-0.759-0.7590.0000.0000.0000.000
163A209GLY 00.0720.04916.9990.0460.0460.0000.0000.0000.000
164A210GLU -1-0.973-0.99418.6300.3250.3250.0000.0000.0000.000
165A211GLY 0-0.028-0.01121.2230.0080.0080.0000.0000.0000.000
166A212TRP 0-0.008-0.02414.9310.0100.0100.0000.0000.0000.000
167A213LEU 00.0040.02617.927-0.015-0.0150.0000.0000.0000.000
168A214VAL 0-0.022-0.02120.430-0.020-0.0200.0000.0000.0000.000
169A215ASP -1-0.913-0.96823.9500.2400.2400.0000.0000.0000.000
170A216HIS 0-0.0040.00116.603-0.035-0.0350.0000.0000.0000.000
171A217PRO 00.0130.00320.794-0.006-0.0060.0000.0000.0000.000
172A218GLU -1-0.786-0.87517.3680.2650.2650.0000.0000.0000.000
173A219LYS 10.8430.92018.184-0.252-0.2520.0000.0000.0000.000
174A220GLU -1-0.971-0.97719.5730.2920.2920.0000.0000.0000.000
175A221LEU 0-0.0200.00714.663-0.001-0.0010.0000.0000.0000.000
176A222ILE 0-0.061-0.03414.1670.0430.0430.0000.0000.0000.000
177A223THR 0-0.047-0.04615.4850.0510.0510.0000.0000.0000.000
178A224NME 0-0.0190.01017.377-0.021-0.0210.0000.0000.0000.000