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: 2KZ2R

Calculation Name: 3GKU-B-Xray312

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: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1918013.068271
FMO2-HF: Nuclear repulsion 1839739.362081
FMO2-HF: Total energy -78273.70619
FMO2-MP2: Total energy -78502.533679


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:1:ACE )


Summations of interaction energy for fragment #1(B:1:ACE )
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.
3.8644.557-0.005-0.334-0.3550
Interaction energy analysis for fragmet #1(B:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.001
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].
3B3MET 0-0.057-0.0133.8171.6722.288-0.005-0.311-0.3000.000
4B4VAL 00.0130.0067.3780.0900.0900.0000.0000.0000.000
5B5THR 0-0.024-0.01010.571-0.005-0.0050.0000.0000.0000.000
6B6VAL 0-0.0060.00214.1990.0490.0490.0000.0000.0000.000
7B7THR 00.004-0.00817.508-0.014-0.0140.0000.0000.0000.000
8B8ALA 0-0.037-0.01721.0930.0160.0160.0000.0000.0000.000
9B9LYS 10.8210.90424.3150.0780.0780.0000.0000.0000.000
10B10THR 00.0010.00426.121-0.006-0.0060.0000.0000.0000.000
11B11VAL 00.0600.02620.482-0.014-0.0140.0000.0000.0000.000
12B12GLU -1-0.831-0.93321.365-0.137-0.1370.0000.0000.0000.000
13B13GLU -1-0.813-0.88523.151-0.082-0.0820.0000.0000.0000.000
14B14ALA 0-0.007-0.02120.6060.0030.0030.0000.0000.0000.000
15B15VAL 00.0600.02318.305-0.010-0.0100.0000.0000.0000.000
16B16THR 0-0.072-0.04418.9520.0040.0040.0000.0000.0000.000
17B17LYS 10.8380.92819.3280.1120.1120.0000.0000.0000.000
18B18ALA 00.007-0.00415.5200.0150.0150.0000.0000.0000.000
19B19LEU 0-0.0240.00215.9610.0070.0070.0000.0000.0000.000
20B20ILE 00.0270.01417.5490.0230.0230.0000.0000.0000.000
21B21GLU -1-0.851-0.91517.025-0.080-0.0800.0000.0000.0000.000
22B22LEU 0-0.031-0.01511.2650.0190.0190.0000.0000.0000.000
23B23GLN 0-0.037-0.03514.6290.0270.0270.0000.0000.0000.000
24B24THR 0-0.081-0.00813.6470.0350.0350.0000.0000.0000.000
25B25THR 00.0520.01815.992-0.016-0.0160.0000.0000.0000.000
26B26SER 00.024-0.01416.545-0.007-0.0070.0000.0000.0000.000
27B27ASP -1-0.893-0.92917.429-0.026-0.0260.0000.0000.0000.000
28B28LYS 10.8810.94711.453-0.191-0.1910.0000.0000.0000.000
29B29LEU 0-0.033-0.01912.1500.0010.0010.0000.0000.0000.000
30B30THR 0-0.021-0.0139.5000.0030.0030.0000.0000.0000.000
31B31TYR 0-0.019-0.02711.930-0.033-0.0330.0000.0000.0000.000
32B32GLU -1-0.908-0.94511.414-0.660-0.6600.0000.0000.0000.000
33B33ILE 00.002-0.02214.4300.0320.0320.0000.0000.0000.000
34B34VAL 0-0.036-0.00816.348-0.001-0.0010.0000.0000.0000.000
35B35NME 0-0.0150.00318.9210.0260.0260.0000.0000.0000.000
36B46ACE 00.0360.00631.239-0.001-0.0010.0000.0000.0000.000
37B47LYS 10.9120.94929.9070.0870.0870.0000.0000.0000.000
38B48PRO 0-0.0110.00725.0330.0030.0030.0000.0000.0000.000
39B49ALA 00.0600.01623.6270.0020.0020.0000.0000.0000.000
40B50ILE 0-0.0050.01016.8600.0020.0020.0000.0000.0000.000
41B51ILE 00.0190.02116.358-0.009-0.0090.0000.0000.0000.000
42B52ARG 10.9230.9619.1110.7730.7730.0000.0000.0000.000
43B53ALA 00.0750.02211.1960.0050.0050.0000.0000.0000.000
44B54LYS 10.9580.9873.826-0.275-0.1980.000-0.023-0.0550.000
45B55ARG 10.9640.9688.513-0.069-0.0690.0000.0000.0000.000
46B56LYS 10.9020.9538.2470.2750.2750.0000.0000.0000.000
47B57GLU -1-0.939-0.9747.4530.7310.7310.0000.0000.0000.000
48B58THR 0-0.0360.0139.014-0.131-0.1310.0000.0000.0000.000
49B59LEU 00.0440.02912.1870.0410.0410.0000.0000.0000.000
50B60GLN 00.0950.02914.7640.0110.0110.0000.0000.0000.000
51B61ASP -1-0.845-0.9389.5040.5810.5810.0000.0000.0000.000
52B62LYS 10.9520.97810.556-0.193-0.1930.0000.0000.0000.000
53B63ALA 0-0.054-0.02312.836-0.026-0.0260.0000.0000.0000.000
54B64ILE 0-0.030-0.04013.559-0.028-0.0280.0000.0000.0000.000
55B65GLU -1-0.872-0.91310.2070.5910.5910.0000.0000.0000.000
56B66PHE 0-0.008-0.01012.863-0.050-0.0500.0000.0000.0000.000
57B67LEU 0-0.022-0.03215.899-0.025-0.0250.0000.0000.0000.000
58B68GLU -1-0.898-0.94213.9160.4120.4120.0000.0000.0000.000
59B69GLN 00.0360.02113.9930.0010.0010.0000.0000.0000.000
60B70VAL 0-0.069-0.03616.626-0.035-0.0350.0000.0000.0000.000
61B71PHE 0-0.047-0.05420.053-0.026-0.0260.0000.0000.0000.000
62B72ASP -1-0.903-0.92117.9230.2100.2100.0000.0000.0000.000
63B73ALA 0-0.014-0.01120.011-0.020-0.0200.0000.0000.0000.000
64B74MET 0-0.156-0.07821.930-0.018-0.0180.0000.0000.0000.000
65B75ASN 0-0.045-0.01823.635-0.003-0.0030.0000.0000.0000.000
66B76MET 0-0.078-0.03623.751-0.010-0.0100.0000.0000.0000.000
67B77ALA 00.0410.01221.9920.0170.0170.0000.0000.0000.000
68B78VAL 0-0.056-0.03321.935-0.015-0.0150.0000.0000.0000.000
69B79ASP -1-0.903-0.94920.8580.2190.2190.0000.0000.0000.000
70B80ILE 0-0.019-0.01317.730-0.027-0.0270.0000.0000.0000.000
71B81SER 0-0.048-0.02119.4030.0100.0100.0000.0000.0000.000
72B82VAL 0-0.009-0.02517.350-0.016-0.0160.0000.0000.0000.000
73B83GLU -1-0.928-0.94219.7260.1180.1180.0000.0000.0000.000
74B84TYR 0-0.001-0.03319.045-0.004-0.0040.0000.0000.0000.000
75B85ASN 00.0460.03721.780-0.002-0.0020.0000.0000.0000.000
76B86GLU -1-0.859-0.95220.4680.0660.0660.0000.0000.0000.000
77B87THR 0-0.060-0.02223.011-0.008-0.0080.0000.0000.0000.000
78B88GLU -1-0.953-0.98626.4630.0440.0440.0000.0000.0000.000
79B89LYS 10.8470.95422.724-0.051-0.0510.0000.0000.0000.000
80B90GLU -1-0.922-0.97024.5390.0710.0710.0000.0000.0000.000
81B91MET 0-0.066-0.00717.8470.0100.0100.0000.0000.0000.000
82B92ASN 0-0.015-0.01623.079-0.008-0.0080.0000.0000.0000.000
83B93VAL 00.0320.00520.3450.0110.0110.0000.0000.0000.000
84B94ASN 00.0030.00323.130-0.021-0.0210.0000.0000.0000.000
85B95LEU 0-0.0140.01323.0490.0150.0150.0000.0000.0000.000
86B96LYS 10.9050.93424.498-0.147-0.1470.0000.0000.0000.000
87B97GLY 00.1230.06325.9050.0090.0090.0000.0000.0000.000
88B98ASP -1-0.902-0.95127.6520.1060.1060.0000.0000.0000.000
89B99ASP -1-0.750-0.86426.3390.1240.1240.0000.0000.0000.000
90B100MET 0-0.064-0.01526.164-0.006-0.0060.0000.0000.0000.000
91B101GLY 0-0.036-0.02629.856-0.009-0.0090.0000.0000.0000.000
92B102ILE 00.0160.00630.953-0.009-0.0090.0000.0000.0000.000
93B103LEU 00.029-0.00528.611-0.006-0.0060.0000.0000.0000.000
94B104ILE 0-0.044-0.00232.995-0.004-0.0040.0000.0000.0000.000
95B105GLY 0-0.064-0.04536.424-0.001-0.0010.0000.0000.0000.000
96B106LYS 10.8890.97634.214-0.072-0.0720.0000.0000.0000.000
97B107ARG 10.9930.96932.287-0.077-0.0770.0000.0000.0000.000
98B108GLY 00.0680.03932.3650.0030.0030.0000.0000.0000.000
99B109GLN 00.0490.03333.2020.0020.0020.0000.0000.0000.000
100B110THR 00.0220.03328.9460.0020.0020.0000.0000.0000.000
101B111LEU 0-0.015-0.00827.6620.0050.0050.0000.0000.0000.000
102B112ASP -1-0.837-0.91328.4000.0750.0750.0000.0000.0000.000
103B113SER 0-0.074-0.05129.026-0.001-0.0010.0000.0000.0000.000
104B114LEU 00.0180.01323.5930.0000.0000.0000.0000.0000.000
105B115GLN 00.0170.01824.4860.0070.0070.0000.0000.0000.000
106B116TYR 0-0.0280.00025.2480.0000.0000.0000.0000.0000.000
107B117LEU 00.0450.01323.007-0.001-0.0010.0000.0000.0000.000
108B118VAL 00.0420.02219.2790.0030.0030.0000.0000.0000.000
109B119SER 0-0.0030.00820.6390.0030.0030.0000.0000.0000.000
110B120LEU 0-0.038-0.01422.191-0.005-0.0050.0000.0000.0000.000
111B121VAL 0-0.026-0.01516.449-0.013-0.0130.0000.0000.0000.000
112B122VAL 0-0.023-0.02517.476-0.003-0.0030.0000.0000.0000.000
113B123ASN 0-0.029-0.02718.767-0.013-0.0130.0000.0000.0000.000
114B124LYS 10.9690.99418.347-0.070-0.0700.0000.0000.0000.000
115B125SER 0-0.095-0.03915.004-0.011-0.0110.0000.0000.0000.000
116B126SER 0-0.001-0.02216.8420.0080.0080.0000.0000.0000.000
117B127SER 00.0080.02319.605-0.007-0.0070.0000.0000.0000.000
118B128ASP -1-0.943-0.97222.5220.0330.0330.0000.0000.0000.000
119B129TYR 0-0.0210.00023.3390.0080.0080.0000.0000.0000.000
120B130ILE 00.0260.01620.6470.0020.0020.0000.0000.0000.000
121B131ARG 10.9050.95624.098-0.052-0.0520.0000.0000.0000.000
122B132VAL 00.0180.00922.1390.0040.0040.0000.0000.0000.000
123B133LYS 10.8930.94424.851-0.080-0.0800.0000.0000.0000.000
124B134LEU 0-0.011-0.00323.3180.0090.0090.0000.0000.0000.000
125B135ASP -1-0.858-0.97026.3060.0790.0790.0000.0000.0000.000
126B136THR 00.0680.04827.5550.0050.0050.0000.0000.0000.000
127B137GLU -1-0.843-0.94029.0180.1010.1010.0000.0000.0000.000
128B138ASN 00.035-0.00131.035-0.007-0.0070.0000.0000.0000.000
129B139TYR 0-0.048-0.04032.877-0.008-0.0080.0000.0000.0000.000
130B140ARG 10.7890.89329.860-0.087-0.0870.0000.0000.0000.000
131B141GLU -1-0.851-0.92534.6780.0490.0490.0000.0000.0000.000
132B142ARG 10.9440.99334.504-0.077-0.0770.0000.0000.0000.000
133B143ARG 10.8600.94537.687-0.055-0.0550.0000.0000.0000.000
134B144LYS 10.8830.93138.772-0.054-0.0540.0000.0000.0000.000
135B145GLU -1-0.872-0.92141.0820.0450.0450.0000.0000.0000.000
136B146THR 0-0.047-0.03742.553-0.003-0.0030.0000.0000.0000.000
137B147LEU 00.0070.00541.757-0.003-0.0030.0000.0000.0000.000
138B148GLU -1-0.903-0.95744.4570.0390.0390.0000.0000.0000.000
139B149THR 0-0.081-0.03147.294-0.003-0.0030.0000.0000.0000.000
140B150LEU 00.0020.00547.795-0.002-0.0020.0000.0000.0000.000
141B151ALA 00.0190.00549.347-0.002-0.0020.0000.0000.0000.000
142B152LYS 10.9960.98850.468-0.035-0.0350.0000.0000.0000.000
143B153ASN 00.0220.02453.041-0.002-0.0020.0000.0000.0000.000
144B154ILE 0-0.044-0.02853.291-0.002-0.0020.0000.0000.0000.000
145B155ALA 00.0470.04055.250-0.001-0.0010.0000.0000.0000.000
146B156TYR 00.016-0.00657.082-0.002-0.0020.0000.0000.0000.000
147B157LYS 10.9750.97657.080-0.028-0.0280.0000.0000.0000.000
148B158VAL 0-0.0300.00158.633-0.001-0.0010.0000.0000.0000.000
149B159LYS 10.9280.98061.106-0.022-0.0220.0000.0000.0000.000
150B160ARG 10.8610.92863.168-0.021-0.0210.0000.0000.0000.000
151B161THR 0-0.016-0.00563.081-0.001-0.0010.0000.0000.0000.000
152B162LYS 10.8900.95265.249-0.018-0.0180.0000.0000.0000.000
153B163ARG 10.9981.00363.140-0.020-0.0200.0000.0000.0000.000
154B164SER 0-0.075-0.07559.4490.0000.0000.0000.0000.0000.000
155B165VAL 0-0.015-0.01055.6110.0000.0000.0000.0000.0000.000
156B166SER 00.0330.02753.9950.0000.0000.0000.0000.0000.000
157B167LEU 0-0.062-0.02149.3540.0000.0000.0000.0000.0000.000
158B168GLU -1-0.868-0.95146.3900.0390.0390.0000.0000.0000.000
159B169PRO 0-0.044-0.01145.3760.0000.0000.0000.0000.0000.000
160B170MET 0-0.0040.00742.8110.0020.0020.0000.0000.0000.000
161B171ASN 00.0620.05937.933-0.003-0.0030.0000.0000.0000.000
162B172PRO 00.050-0.00239.317-0.001-0.0010.0000.0000.0000.000
163B173TYR 00.0160.01535.017-0.002-0.0020.0000.0000.0000.000
164B174GLU -1-0.831-0.92639.5050.0510.0510.0000.0000.0000.000
165B175ARG 10.8030.89641.768-0.037-0.0370.0000.0000.0000.000
166B176ARG 10.9490.97039.836-0.039-0.0390.0000.0000.0000.000
167B177ILE 00.0300.02439.780-0.002-0.0020.0000.0000.0000.000
168B178ILE 0-0.0040.00444.045-0.002-0.0020.0000.0000.0000.000
169B179HIS 0-0.045-0.05246.936-0.001-0.0010.0000.0000.0000.000
170B180ALA 00.001-0.00645.771-0.001-0.0010.0000.0000.0000.000
171B181ALA 00.0220.02847.821-0.001-0.0010.0000.0000.0000.000
172B182LEU 0-0.065-0.04749.403-0.001-0.0010.0000.0000.0000.000
173B183GLN 0-0.0250.01349.3070.0000.0000.0000.0000.0000.000
174B184ASN 00.001-0.01752.501-0.001-0.0010.0000.0000.0000.000
175B185ASP -1-0.790-0.88655.1420.0230.0230.0000.0000.0000.000
176B186LYS 10.8870.93757.028-0.021-0.0210.0000.0000.0000.000
177B187TYR 0-0.121-0.06857.861-0.001-0.0010.0000.0000.0000.000
178B188VAL 0-0.027-0.01857.158-0.001-0.0010.0000.0000.0000.000
179B189VAL 00.0060.00957.1800.0000.0000.0000.0000.0000.000
180B190THR 00.0070.01051.5480.0010.0010.0000.0000.0000.000
181B191ARG 10.9570.97453.437-0.022-0.0220.0000.0000.0000.000
182B192SER 0-0.006-0.00748.2050.0010.0010.0000.0000.0000.000
183B193ASP -1-0.896-0.95050.5250.0220.0220.0000.0000.0000.000
184B194GLY 00.0540.05550.2830.0020.0020.0000.0000.0000.000
185B195GLU -1-0.867-0.95247.7910.0240.0240.0000.0000.0000.000
186B196GLU -1-0.851-0.89341.6920.0370.0370.0000.0000.0000.000
187B197PRO 0-0.016-0.00541.813-0.001-0.0010.0000.0000.0000.000
188B198PHE 00.003-0.05043.6760.0010.0010.0000.0000.0000.000
189B199ARG 10.8830.95645.607-0.029-0.0290.0000.0000.0000.000
190B200HIS 0-0.015-0.01246.5780.0010.0010.0000.0000.0000.000
191B201VAL 0-0.003-0.00948.065-0.001-0.0010.0000.0000.0000.000
192B202ILE 0-0.013-0.01150.6410.0000.0000.0000.0000.0000.000
193B203ILE 00.0080.02352.740-0.001-0.0010.0000.0000.0000.000
194B204SER 00.0360.01156.085-0.001-0.0010.0000.0000.0000.000
195B205LEU 00.0090.00459.7470.0000.0000.0000.0000.0000.000
196B206LYS 10.9480.98462.614-0.016-0.0160.0000.0000.0000.000
197B207NME 0-0.0080.01959.3180.0000.0000.0000.0000.0000.000