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: 534GZ

Calculation Name: 3GKU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GKU

Chain ID: B

ChEMBL ID:

UniProt ID: D0VX24

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1904380.350179
FMO2-HF: Nuclear repulsion 1826444.304218
FMO2-HF: Total energy -77936.045961
FMO2-MP2: Total energy -78163.39932


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(B:2:ASP)


Summations of interaction energy for fragment #1(B:2:ASP)
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.
-147.047-157.20638.906-16.212-12.5350.166
Interaction energy analysis for fragmet #1(B:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.775 / q_NPA : -0.848
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].
3B4VAL00.0260.0143.7065.6148.2880.032-1.396-1.3100.004
4B5THR00.0190.0066.418-0.927-0.9270.0000.0000.0000.000
5B6VAL0-0.015-0.0018.956-2.064-2.0640.0000.0000.0000.000
6B7THR0-0.036-0.03412.6400.0370.0370.0000.0000.0000.000
7B8ALA0-0.0130.00015.905-0.592-0.5920.0000.0000.0000.000
8B9LYS10.8080.89219.369-13.082-13.0820.0000.0000.0000.000
9B10THR0-0.020-0.02820.448-0.323-0.3230.0000.0000.0000.000
10B11VAL00.0390.02415.8160.6500.6500.0000.0000.0000.000
11B12GLU-1-0.797-0.88817.09516.32916.3290.0000.0000.0000.000
12B13GLU-1-0.778-0.87919.41814.01914.0190.0000.0000.0000.000
13B14ALA0-0.001-0.00115.2980.1670.1670.0000.0000.0000.000
14B15VAL00.018-0.00514.5451.1111.1110.0000.0000.0000.000
15B16THR0-0.070-0.04616.033-0.003-0.0030.0000.0000.0000.000
16B17LYS10.7780.88516.621-18.039-18.0390.0000.0000.0000.000
17B18ALA00.0740.02512.197-0.217-0.2170.0000.0000.0000.000
18B19LEU0-0.0140.00813.9680.5530.5530.0000.0000.0000.000
19B20ILE00.0230.01715.620-0.458-0.4580.0000.0000.0000.000
20B21GLU-1-0.801-0.88214.76918.70218.7020.0000.0000.0000.000
21B22LEU0-0.038-0.0129.5770.1940.1940.0000.0000.0000.000
22B23GLN0-0.035-0.01713.504-0.605-0.6050.0000.0000.0000.000
23B24THR0-0.051-0.02612.762-0.216-0.2160.0000.0000.0000.000
24B25THR00.009-0.01515.886-0.779-0.7790.0000.0000.0000.000
25B26SER00.021-0.00715.7230.9730.9730.0000.0000.0000.000
26B27ASP-1-0.877-0.91315.84316.75716.7570.0000.0000.0000.000
27B28LYS10.8630.92712.407-20.410-20.4100.0000.0000.0000.000
28B29LEU0-0.027-0.00710.9261.9701.9700.0000.0000.0000.000
29B30THR0-0.023-0.0097.828-0.997-0.9970.0000.0000.0000.000
30B31TYR0-0.007-0.0229.0762.4112.4110.0000.0000.0000.000
31B32GLU-1-0.898-0.9456.37039.70439.7040.0000.0000.0000.000
32B33ILE0-0.021-0.0149.808-0.340-0.3400.0000.0000.0000.000
33B34VAL0-0.040-0.0259.962-1.828-1.8280.0000.0000.0000.000
34B47LYS10.9800.97523.854-12.894-12.8940.0000.0000.0000.000
35B48PRO0-0.028-0.00218.673-0.076-0.0760.0000.0000.0000.000
36B49ALA00.0530.02217.987-0.271-0.2710.0000.0000.0000.000
37B50ILE0-0.003-0.00111.8980.0730.0730.0000.0000.0000.000
38B51ILE00.0070.02711.364-0.496-0.4960.0000.0000.0000.000
39B52ARG10.8090.8641.728-128.766-137.52128.442-11.539-8.1480.132
40B53ALA00.0560.0157.583-3.045-3.0450.0000.0000.0000.000
41B54LYS10.8860.9362.046-67.386-71.46410.432-3.277-3.0770.030
42B55ARG10.8880.9537.249-24.274-24.2740.0000.0000.0000.000
43B56LYS10.9400.9698.000-22.464-22.4640.0000.0000.0000.000
44B57GLU-1-0.802-0.8918.98821.03321.0330.0000.0000.0000.000
45B58THR0-0.070-0.04810.243-1.034-1.0340.0000.0000.0000.000
46B59LEU00.0250.02113.8550.1860.1860.0000.0000.0000.000
47B60GLN00.0710.02216.861-0.114-0.1140.0000.0000.0000.000
48B61ASP-1-0.779-0.87011.85320.19720.1970.0000.0000.0000.000
49B62LYS10.8430.91312.378-20.003-20.0030.0000.0000.0000.000
50B63ALA0-0.017-0.01215.079-0.560-0.5600.0000.0000.0000.000
51B64ILE0-0.016-0.01216.103-0.618-0.6180.0000.0000.0000.000
52B65GLU-1-0.840-0.90213.18617.39417.3940.0000.0000.0000.000
53B66PHE0-0.009-0.01315.614-0.716-0.7160.0000.0000.0000.000
54B67LEU0-0.013-0.02018.435-0.609-0.6090.0000.0000.0000.000
55B68GLU-1-0.913-0.95816.95614.45714.4570.0000.0000.0000.000
56B69GLN0-0.049-0.02715.403-0.887-0.8870.0000.0000.0000.000
57B70VAL0-0.050-0.02919.130-0.559-0.5590.0000.0000.0000.000
58B71PHE0-0.024-0.03822.596-0.655-0.6550.0000.0000.0000.000
59B72ASP-1-0.882-0.92520.83112.40812.4080.0000.0000.0000.000
60B73ALA00.0110.01122.836-0.440-0.4400.0000.0000.0000.000
61B74MET0-0.156-0.08924.586-0.474-0.4740.0000.0000.0000.000
62B75ASN0-0.107-0.04526.277-0.472-0.4720.0000.0000.0000.000
63B76MET0-0.069-0.02526.323-0.387-0.3870.0000.0000.0000.000
64B77ALA00.0190.00824.7200.4650.4650.0000.0000.0000.000
65B78VAL0-0.059-0.04224.466-0.420-0.4200.0000.0000.0000.000
66B79ASP-1-0.877-0.93623.45211.44311.4430.0000.0000.0000.000
67B80ILE0-0.034-0.02120.537-0.433-0.4330.0000.0000.0000.000
68B81SER0-0.066-0.03721.5960.2520.2520.0000.0000.0000.000
69B82VAL00.004-0.02419.614-0.232-0.2320.0000.0000.0000.000
70B83GLU-1-0.892-0.92922.08411.17511.1750.0000.0000.0000.000
71B84TYR0-0.034-0.07020.6380.0240.0240.0000.0000.0000.000
72B85ASN00.0540.06023.5570.3580.3580.0000.0000.0000.000
73B86GLU-1-0.767-0.87620.58113.54113.5410.0000.0000.0000.000
74B87THR0-0.048-0.03324.249-0.050-0.0500.0000.0000.0000.000
75B88GLU-1-0.879-0.92227.6798.9698.9690.0000.0000.0000.000
76B89LYS10.8110.91323.077-12.664-12.6640.0000.0000.0000.000
77B90GLU-1-0.787-0.86526.5789.3949.3940.0000.0000.0000.000
78B91MET0-0.034-0.01020.0880.3380.3380.0000.0000.0000.000
79B92ASN0-0.059-0.03425.343-0.626-0.6260.0000.0000.0000.000
80B93VAL00.0120.00523.3360.2660.2660.0000.0000.0000.000
81B94ASN0-0.032-0.03325.640-0.565-0.5650.0000.0000.0000.000
82B95LEU00.0180.03525.7560.3600.3600.0000.0000.0000.000
83B96LYS10.8250.89327.093-10.241-10.2410.0000.0000.0000.000
84B97GLY00.1490.07928.0180.2890.2890.0000.0000.0000.000
85B98ASP-1-0.923-0.97430.1058.5838.5830.0000.0000.0000.000
86B99ASP-1-0.776-0.88029.3699.3229.3220.0000.0000.0000.000
87B100MET0-0.0150.00128.974-0.147-0.1470.0000.0000.0000.000
88B101GLY0-0.040-0.02032.770-0.259-0.2590.0000.0000.0000.000
89B102ILE00.0230.02033.506-0.332-0.3320.0000.0000.0000.000
90B103LEU00.011-0.00130.930-0.180-0.1800.0000.0000.0000.000
91B104ILE0-0.0050.01135.566-0.141-0.1410.0000.0000.0000.000
92B105GLY0-0.016-0.01638.835-0.066-0.0660.0000.0000.0000.000
93B106LYS10.8650.92235.882-8.072-8.0720.0000.0000.0000.000
94B107ARG10.9300.97134.879-7.683-7.6830.0000.0000.0000.000
95B108GLY00.0630.04134.7140.2010.2010.0000.0000.0000.000
96B109GLN00.0530.02535.3060.2550.2550.0000.0000.0000.000
97B110THR0-0.0110.00131.9950.1170.1170.0000.0000.0000.000
98B111LEU00.0170.02030.3060.2740.2740.0000.0000.0000.000
99B112ASP-1-0.809-0.90130.5848.7288.7280.0000.0000.0000.000
100B113SER0-0.055-0.03831.3100.1050.1050.0000.0000.0000.000
101B114LEU00.0230.01225.7780.2140.2140.0000.0000.0000.000
102B115GLN00.0210.02426.4560.4440.4440.0000.0000.0000.000
103B116TYR0-0.025-0.01227.4760.2960.2960.0000.0000.0000.000
104B117LEU00.0030.00025.1080.2470.2470.0000.0000.0000.000
105B118VAL00.0500.02521.1900.4100.4100.0000.0000.0000.000
106B119SER00.0070.00722.6440.5310.5310.0000.0000.0000.000
107B120LEU0-0.014-0.00324.3620.2720.2720.0000.0000.0000.000
108B121VAL0-0.023-0.01218.5340.3140.3140.0000.0000.0000.000
109B122VAL00.0130.00419.4320.6580.6580.0000.0000.0000.000
110B123ASN0-0.023-0.02220.4430.3290.3290.0000.0000.0000.000
111B124LYS10.8840.95120.492-13.333-13.3330.0000.0000.0000.000
112B125SER0-0.070-0.03216.4810.8020.8020.0000.0000.0000.000
113B126SER0-0.007-0.01717.8780.8440.8440.0000.0000.0000.000
114B127SER0-0.027-0.02220.585-0.066-0.0660.0000.0000.0000.000
115B128ASP-1-0.875-0.91923.10412.06312.0630.0000.0000.0000.000
116B129TYR0-0.034-0.01424.4560.2110.2110.0000.0000.0000.000
117B130ILE00.0410.02821.933-0.153-0.1530.0000.0000.0000.000
118B131ARG10.7470.86225.442-9.650-9.6500.0000.0000.0000.000
119B132VAL0-0.008-0.00723.591-0.073-0.0730.0000.0000.0000.000
120B133LYS10.7540.86226.772-9.911-9.9110.0000.0000.0000.000
121B134LEU00.0050.01125.9060.2820.2820.0000.0000.0000.000
122B135ASP-1-0.835-0.92428.9308.1708.1700.0000.0000.0000.000
123B136THR00.0260.01629.8800.2400.2400.0000.0000.0000.000
124B137GLU-1-0.786-0.87831.5708.9078.9070.0000.0000.0000.000
125B138ASN00.0260.01333.564-0.226-0.2260.0000.0000.0000.000
126B139TYR0-0.022-0.01235.374-0.339-0.3390.0000.0000.0000.000
127B140ARG10.8010.86832.479-8.952-8.9520.0000.0000.0000.000
128B141GLU-1-0.829-0.90137.4306.9966.9960.0000.0000.0000.000
129B142ARG10.8970.95236.878-7.912-7.9120.0000.0000.0000.000
130B143ARG10.8130.90540.516-6.980-6.9800.0000.0000.0000.000
131B144LYS10.8350.91441.974-7.091-7.0910.0000.0000.0000.000
132B145GLU-1-0.873-0.93543.7816.5256.5250.0000.0000.0000.000
133B146THR0-0.010-0.01744.794-0.195-0.1950.0000.0000.0000.000
134B147LEU0-0.014-0.01044.645-0.188-0.1880.0000.0000.0000.000
135B148GLU-1-0.873-0.95446.7166.2416.2410.0000.0000.0000.000
136B149THR0-0.068-0.03549.679-0.188-0.1880.0000.0000.0000.000
137B150LEU0-0.033-0.01549.887-0.164-0.1640.0000.0000.0000.000
138B151ALA00.0150.00451.820-0.138-0.1380.0000.0000.0000.000
139B152LYS10.9480.98051.672-6.004-6.0040.0000.0000.0000.000
140B153ASN00.0080.00555.123-0.174-0.1740.0000.0000.0000.000
141B154ILE0-0.032-0.01555.548-0.140-0.1400.0000.0000.0000.000
142B155ALA00.0460.03557.847-0.108-0.1080.0000.0000.0000.000
143B156TYR00.0760.03259.728-0.155-0.1550.0000.0000.0000.000
144B157LYS11.0211.00459.894-5.216-5.2160.0000.0000.0000.000
145B158VAL0-0.0340.00960.646-0.103-0.1030.0000.0000.0000.000
146B159LYS10.8510.92963.464-4.862-4.8620.0000.0000.0000.000
147B160ARG10.8710.93765.683-4.602-4.6020.0000.0000.0000.000
148B161THR0-0.039-0.04165.496-0.066-0.0660.0000.0000.0000.000
149B162LYS10.9180.96868.032-4.412-4.4120.0000.0000.0000.000
150B163ARG11.0041.01665.649-4.666-4.6660.0000.0000.0000.000
151B164SER0-0.035-0.04861.5450.0290.0290.0000.0000.0000.000
152B165VAL0-0.022-0.01058.113-0.058-0.0580.0000.0000.0000.000
153B166SER00.0190.01255.9870.0520.0520.0000.0000.0000.000
154B167LEU0-0.032-0.01751.922-0.042-0.0420.0000.0000.0000.000
155B168GLU-1-0.823-0.91547.8096.2466.2460.0000.0000.0000.000
156B169PRO0-0.039-0.01647.928-0.002-0.0020.0000.0000.0000.000
157B170MET00.0000.01545.1960.0700.0700.0000.0000.0000.000
158B171ASN00.0400.02240.124-0.040-0.0400.0000.0000.0000.000
159B172PRO00.028-0.00141.633-0.108-0.1080.0000.0000.0000.000
160B173TYR00.0110.00236.111-0.180-0.1800.0000.0000.0000.000
161B174GLU-1-0.766-0.86741.9576.9786.9780.0000.0000.0000.000
162B175ARG10.8040.85944.123-6.698-6.6980.0000.0000.0000.000
163B176ARG10.9660.98841.688-7.133-7.1330.0000.0000.0000.000
164B177ILE00.0310.03142.330-0.078-0.0780.0000.0000.0000.000
165B178ILE0-0.0070.00046.618-0.135-0.1350.0000.0000.0000.000
166B179HIS0-0.030-0.02349.277-0.056-0.0560.0000.0000.0000.000
167B180ALA00.0330.01248.194-0.104-0.1040.0000.0000.0000.000
168B181ALA0-0.019-0.00550.204-0.095-0.0950.0000.0000.0000.000
169B182LEU0-0.073-0.04151.861-0.115-0.1150.0000.0000.0000.000
170B183GLN0-0.0220.00851.354-0.026-0.0260.0000.0000.0000.000
171B184ASN00.0380.01454.814-0.017-0.0170.0000.0000.0000.000
172B185ASP-1-0.791-0.87157.2225.0355.0350.0000.0000.0000.000
173B186LYS10.8540.89959.451-5.131-5.1310.0000.0000.0000.000
174B187TYR0-0.075-0.04460.319-0.124-0.1240.0000.0000.0000.000
175B188VAL0-0.058-0.02359.417-0.064-0.0640.0000.0000.0000.000
176B189VAL00.0320.03459.3940.0400.0400.0000.0000.0000.000
177B190THR00.0120.00154.4380.0400.0400.0000.0000.0000.000
178B191ARG10.8990.93755.562-5.228-5.2280.0000.0000.0000.000
179B192SER00.025-0.02150.4200.0600.0600.0000.0000.0000.000
180B193ASP-1-0.848-0.90252.7595.3645.3640.0000.0000.0000.000
181B194GLY0-0.019-0.00652.5490.0860.0860.0000.0000.0000.000
182B195GLU-1-0.789-0.89450.1166.0476.0470.0000.0000.0000.000
183B196GLU-1-0.785-0.86044.3326.6766.6760.0000.0000.0000.000
184B197PRO0-0.0020.00844.094-0.015-0.0150.0000.0000.0000.000
185B198PHE00.017-0.01345.9680.0020.0020.0000.0000.0000.000
186B199ARG10.7840.90247.883-6.172-6.1720.0000.0000.0000.000
187B200HIS10.8700.93148.594-5.622-5.6220.0000.0000.0000.000
188B201VAL00.0190.01750.270-0.046-0.0460.0000.0000.0000.000
189B202ILE0-0.043-0.01952.857-0.056-0.0560.0000.0000.0000.000
190B203ILE00.0370.02254.9290.0170.0170.0000.0000.0000.000
191B204SER00.0070.00358.653-0.053-0.0530.0000.0000.0000.000
192B205LEU00.0260.02262.3910.0180.0180.0000.0000.0000.000
193B206LYS10.9240.96564.184-4.545-4.5450.0000.0000.0000.000