Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K2GY3

Calculation Name: 2ZYZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZYZ

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZVI1

Base Structure: X-ray

Registration Date: 2023-09-27

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945711.93338
FMO2-HF: Nuclear repulsion 1873992.921413
FMO2-HF: Total energy -71719.011967
FMO2-MP2: Total energy -71930.38219


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:MET)


Summations of interaction energy for fragment #1(B: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.
-8.868-0.78611.428-5.447-14.062-0.042
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.017
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].
3B3GLY0-0.0140.0003.760-1.4460.588-0.049-0.966-1.018-0.002
4B4TYR00.0090.0056.907-0.036-0.0360.0000.0000.0000.000
5B5LEU0-0.016-0.00710.408-0.060-0.0600.0000.0000.0000.000
6B6ARG10.9050.95913.277-0.362-0.3620.0000.0000.0000.000
7B7GLY00.0140.01316.351-0.017-0.0170.0000.0000.0000.000
8B8LEU0-0.031-0.02718.085-0.005-0.0050.0000.0000.0000.000
9B9ALA0-0.034-0.01415.213-0.022-0.0220.0000.0000.0000.000
10B10VAL00.0310.0238.9610.0210.0210.0000.0000.0000.000
11B11ILE0-0.023-0.01211.301-0.042-0.0420.0000.0000.0000.000
12B12VAL00.002-0.0025.8680.0620.0620.0000.0000.0000.000
13B13GLU-1-0.866-0.9508.3130.5630.5630.0000.0000.0000.000
14B14ASP-1-0.862-0.9144.4833.1703.350-0.001-0.009-0.1700.000
15B15VAL00.051-0.0017.183-0.177-0.1770.0000.0000.0000.000
16B16GLU-1-0.914-0.9567.5350.0690.0690.0000.0000.0000.000
17B17PHE0-0.061-0.0222.816-3.280-1.4462.882-1.345-3.371-0.011
18B18ALA00.000-0.0055.481-0.527-0.5270.0000.0000.0000.000
19B19ARG10.8870.9407.965-0.302-0.3020.0000.0000.0000.000
20B20ARG10.9530.9743.9930.7450.888-0.001-0.008-0.1340.000
21B21LEU00.0390.0245.145-0.007-0.0070.0000.0000.0000.000
22B22TYR0-0.082-0.0468.5260.0470.0470.0000.0000.0000.000
23B23LYS10.8720.94511.5350.2660.2660.0000.0000.0000.000
24B24GLU-1-0.967-0.9768.252-1.043-1.0430.0000.0000.0000.000
25B25GLY00.0650.02010.743-0.082-0.0820.0000.0000.0000.000
26B26PHE0-0.004-0.00113.2210.0510.0510.0000.0000.0000.000
27B27TYR0-0.038-0.01010.2010.0220.0220.0000.0000.0000.000
28B28GLY00.0360.01812.0750.0100.0100.0000.0000.0000.000
29B29ARG10.8630.91713.316-0.010-0.0100.0000.0000.0000.000
30B30PHE00.0610.04011.9750.0060.0060.0000.0000.0000.000
31B31LEU0-0.0190.00015.631-0.020-0.0200.0000.0000.0000.000
32B32GLY00.0050.00418.0730.0170.0170.0000.0000.0000.000
33B33TYR0-0.002-0.01718.703-0.008-0.0080.0000.0000.0000.000
34B34ASP-1-0.948-1.00120.626-0.015-0.0150.0000.0000.0000.000
35B35LYS10.9180.95721.7400.0250.0250.0000.0000.0000.000
36B36VAL00.0540.05717.2350.0010.0010.0000.0000.0000.000
37B37LYS10.9911.02419.7130.0330.0330.0000.0000.0000.000
38B38ARG10.9770.97016.4160.2290.2290.0000.0000.0000.000
39B39ASP-1-0.966-0.98717.696-0.094-0.0940.0000.0000.0000.000
40B40GLU-1-0.864-0.94620.081-0.022-0.0220.0000.0000.0000.000
41B41VAL0-0.0010.01113.6390.0180.0180.0000.0000.0000.000
42B42GLU-1-0.891-0.97514.097-0.045-0.0450.0000.0000.0000.000
43B43LYS10.9300.97816.5880.0150.0150.0000.0000.0000.000
44B44ILE0-0.0230.01215.6160.0120.0120.0000.0000.0000.000
45B45ASN00.000-0.01114.7500.0250.0250.0000.0000.0000.000
46B46ALA0-0.0180.00114.361-0.010-0.0100.0000.0000.0000.000
47B47PRO00.0480.02712.0320.0120.0120.0000.0000.0000.000
48B48LEU0-0.038-0.0079.040-0.072-0.0720.0000.0000.0000.000
49B49ILE0-0.027-0.01511.2040.0220.0220.0000.0000.0000.000
50B50LEU0-0.0090.0007.978-0.047-0.0470.0000.0000.0000.000
51B51GLY00.010-0.00212.5350.0380.0380.0000.0000.0000.000
52B52LEU00.0580.01413.527-0.031-0.0310.0000.0000.0000.000
53B53TYR00.0120.00314.006-0.009-0.0090.0000.0000.0000.000
54B54GLU-1-0.811-0.90211.696-0.208-0.2080.0000.0000.0000.000
55B55ALA00.0140.0029.230-0.062-0.0620.0000.0000.0000.000
56B56LEU00.0330.0249.3220.0060.0060.0000.0000.0000.000
57B57TYR0-0.017-0.01811.205-0.010-0.0100.0000.0000.0000.000
58B58LEU0-0.037-0.0326.193-0.037-0.0370.0000.0000.0000.000
59B59ALA00.0060.0096.7230.0930.0930.0000.0000.0000.000
60B60GLU-1-0.862-0.9007.7130.0070.0070.0000.0000.0000.000
61B61LYS10.8480.9257.6460.3340.3340.0000.0000.0000.000
62B62GLY00.0470.0695.078-0.225-0.2250.0000.0000.0000.000
63B63ARG10.8150.8822.352-2.111-0.1821.774-1.262-2.441-0.011
64B64LEU0-0.015-0.0212.378-4.070-2.9743.770-1.286-3.580-0.017
65B65LYS10.9620.9922.002-1.132-0.2753.054-0.551-3.360-0.001
66B66VAL00.0020.0074.546-0.522-0.513-0.001-0.0200.0120.000
67B67MET0-0.0010.0077.3390.0870.0870.0000.0000.0000.000
68B68GLY00.010-0.0139.739-0.025-0.0250.0000.0000.0000.000
69B69GLU-1-0.937-0.99213.4870.2210.2210.0000.0000.0000.000
70B70ASP-1-0.865-0.92916.1520.2390.2390.0000.0000.0000.000
71B71GLY0-0.044-0.01713.1630.0010.0010.0000.0000.0000.000
72B72ARG10.9010.98613.023-0.167-0.1670.0000.0000.0000.000
73B73GLU-1-0.898-0.9797.8150.7720.7720.0000.0000.0000.000
74B74VAL0-0.075-0.03510.100-0.040-0.0400.0000.0000.0000.000
75B75ALA00.0110.01210.6520.0160.0160.0000.0000.0000.000
76B76PRO00.018-0.01410.170-0.041-0.0410.0000.0000.0000.000
77B77GLU-1-0.876-0.96012.695-0.016-0.0160.0000.0000.0000.000
78B78GLU-1-0.890-0.93114.7810.1450.1450.0000.0000.0000.000
79B79LEU0-0.040-0.02110.702-0.015-0.0150.0000.0000.0000.000
80B80ALA00.017-0.00215.300-0.013-0.0130.0000.0000.0000.000
81B81ALA0-0.043-0.00917.875-0.006-0.0060.0000.0000.0000.000
82B82LEU00.0140.01417.051-0.002-0.0020.0000.0000.0000.000
83B83GLY00.013-0.01518.941-0.003-0.0030.0000.0000.0000.000
84B84ARG10.8450.89420.304-0.003-0.0030.0000.0000.0000.000
85B85GLU-1-0.962-0.96823.0640.0480.0480.0000.0000.0000.000
86B86ARG10.9180.95322.056-0.054-0.0540.0000.0000.0000.000
87B87MET0-0.082-0.02519.580-0.005-0.0050.0000.0000.0000.000
88B88ARG10.9910.98824.726-0.001-0.0010.0000.0000.0000.000
89B89ASN0-0.019-0.02226.433-0.002-0.0020.0000.0000.0000.000
90B90PHE00.0250.04417.062-0.007-0.0070.0000.0000.0000.000
91B91ASP-1-0.760-0.86621.885-0.028-0.0280.0000.0000.0000.000
92B92GLU-1-0.888-0.95722.706-0.040-0.0400.0000.0000.0000.000
93B93ILE0-0.005-0.00121.522-0.009-0.0090.0000.0000.0000.000
94B94TYR0-0.039-0.07114.497-0.021-0.0210.0000.0000.0000.000
95B95LYS10.9490.98519.3690.0480.0480.0000.0000.0000.000
96B96ILE00.0100.00521.412-0.011-0.0110.0000.0000.0000.000
97B97TYR0-0.011-0.01014.219-0.023-0.0230.0000.0000.0000.000
98B98LYS10.9000.93315.2580.1620.1620.0000.0000.0000.000
99B99TYR0-0.0100.00517.781-0.017-0.0170.0000.0000.0000.000
100B100PHE00.0230.00320.501-0.004-0.0040.0000.0000.0000.000
101B101ARG10.8390.91914.2650.2820.2820.0000.0000.0000.000
102B102ASP-1-0.820-0.89515.292-0.272-0.2720.0000.0000.0000.000
103B103LEU0-0.057-0.02316.837-0.006-0.0060.0000.0000.0000.000
104B104GLY00.0030.01317.0740.0060.0060.0000.0000.0000.000
105B105TYR0-0.0270.00018.1410.0020.0020.0000.0000.0000.000
106B106VAL0-0.025-0.01517.278-0.018-0.0180.0000.0000.0000.000
107B107VAL0-0.0030.00917.5690.0260.0260.0000.0000.0000.000
108B108LYS10.8240.91715.6800.1610.1610.0000.0000.0000.000
109B109SER00.0450.01719.8360.0070.0070.0000.0000.0000.000
110B110GLY00.0730.03121.812-0.002-0.0020.0000.0000.0000.000
111B111LEU00.0210.01924.9510.0040.0040.0000.0000.0000.000
112B112LYS10.9350.96726.0630.0410.0410.0000.0000.0000.000
113B113PHE0-0.033-0.02426.0570.0010.0010.0000.0000.0000.000
114B114GLY0-0.0020.01429.9730.0010.0010.0000.0000.0000.000
115B115ALA0-0.050-0.03328.5300.0000.0000.0000.0000.0000.000
116B116LEU00.0020.02024.3030.0030.0030.0000.0000.0000.000
117B117PHE0-0.015-0.02020.539-0.004-0.0040.0000.0000.0000.000
118B118SER0-0.033-0.01323.2170.0040.0040.0000.0000.0000.000
119B119VAL00.0090.00022.312-0.010-0.0100.0000.0000.0000.000
120B120TYR0-0.0400.00421.7340.0150.0150.0000.0000.0000.000
121B121GLU-1-0.883-0.95221.979-0.130-0.1300.0000.0000.0000.000
122B122LYS10.9450.98121.6710.1020.1020.0000.0000.0000.000
123B123GLY00.0600.00820.818-0.017-0.0170.0000.0000.0000.000
124B124PRO0-0.059-0.03820.2910.0120.0120.0000.0000.0000.000
125B125GLY0-0.0040.03023.0410.0080.0080.0000.0000.0000.000
126B126ILE0-0.013-0.01523.1610.0000.0000.0000.0000.0000.000
127B127ASP-1-0.951-1.00224.940-0.077-0.0770.0000.0000.0000.000
128B128HIS0-0.021-0.00727.006-0.009-0.0090.0000.0000.0000.000
129B129ALA00.0270.01826.962-0.007-0.0070.0000.0000.0000.000
130B130PRO0-0.052-0.01726.536-0.002-0.0020.0000.0000.0000.000
131B131MET00.0160.01326.9170.0080.0080.0000.0000.0000.000
132B132VAL0-0.010-0.01727.289-0.003-0.0030.0000.0000.0000.000
133B133VAL0-0.008-0.00425.8780.0010.0010.0000.0000.0000.000
134B134VAL00.011-0.00128.1240.0030.0030.0000.0000.0000.000
135B135PHE00.0090.00327.879-0.004-0.0040.0000.0000.0000.000
136B136LEU0-0.016-0.00329.8670.0040.0040.0000.0000.0000.000
137B137GLU-1-0.887-0.94631.234-0.027-0.0270.0000.0000.0000.000
138B138PRO00.002-0.02030.6980.0000.0000.0000.0000.0000.000
139B139ASP-1-0.866-0.91633.757-0.017-0.0170.0000.0000.0000.000
140B140LYS10.9130.98336.3280.0230.0230.0000.0000.0000.000
141B141GLY00.0170.00838.101-0.002-0.0020.0000.0000.0000.000
142B142ILE0-0.003-0.01038.0090.0000.0000.0000.0000.0000.000
143B143SER0-0.028-0.01840.7540.0020.0020.0000.0000.0000.000
144B144ALA00.0780.02042.656-0.001-0.0010.0000.0000.0000.000
145B145THR0-0.009-0.01442.501-0.001-0.0010.0000.0000.0000.000
146B146ASP-1-0.814-0.89838.445-0.025-0.0250.0000.0000.0000.000
147B147ILE00.0120.01638.766-0.002-0.0020.0000.0000.0000.000
148B148THR0-0.019-0.01140.088-0.002-0.0020.0000.0000.0000.000
149B149ARG10.8990.94936.7670.0240.0240.0000.0000.0000.000
150B150GLY00.0450.01535.848-0.001-0.0010.0000.0000.0000.000
151B151GLY0-0.006-0.00436.375-0.002-0.0020.0000.0000.0000.000
152B152ARG10.8830.93138.6640.0200.0200.0000.0000.0000.000
153B153LEU0-0.004-0.00232.8450.0010.0010.0000.0000.0000.000
154B154SER0-0.0350.00333.927-0.002-0.0020.0000.0000.0000.000
155B155HIS00.004-0.00532.5350.0030.0030.0000.0000.0000.000
156B156SER00.0200.02334.9220.0010.0010.0000.0000.0000.000
157B157VAL00.0520.02136.8660.0020.0020.0000.0000.0000.000
158B158ARG10.9190.93838.0230.0520.0520.0000.0000.0000.000
159B159LYS10.9200.97438.4550.0290.0290.0000.0000.0000.000
160B160THR00.0360.01434.7430.0010.0010.0000.0000.0000.000
161B161TRP0-0.0130.01232.937-0.001-0.0010.0000.0000.0000.000
162B162THR00.0230.00629.2690.0010.0010.0000.0000.0000.000
163B163LEU0-0.0330.00931.2290.0010.0010.0000.0000.0000.000
164B164ALA00.018-0.00527.363-0.004-0.0040.0000.0000.0000.000
165B165THR0-0.008-0.00829.4350.0050.0050.0000.0000.0000.000
166B166VAL0-0.004-0.00326.190-0.006-0.0060.0000.0000.0000.000
167B167LEU00.0070.01629.3650.0050.0050.0000.0000.0000.000
168B168ARG10.8810.93031.5630.0220.0220.0000.0000.0000.000
169B169GLN0-0.029-0.00932.666-0.001-0.0010.0000.0000.0000.000
170B170THR00.0480.00731.6870.0010.0010.0000.0000.0000.000
171B171GLY0-0.0120.00928.180-0.003-0.0030.0000.0000.0000.000
172B172GLU-1-0.939-0.97127.315-0.072-0.0720.0000.0000.0000.000
173B173VAL0-0.044-0.02524.1450.0040.0040.0000.0000.0000.000
174B174VAL00.0420.03227.497-0.002-0.0020.0000.0000.0000.000
175B175LEU0-0.042-0.02826.2030.0020.0020.0000.0000.0000.000
176B176LEU0-0.0010.00430.5730.0010.0010.0000.0000.0000.000
177B177GLY00.0220.01733.570-0.001-0.0010.0000.0000.0000.000
178B178PHE00.0140.00634.8080.0040.0040.0000.0000.0000.000
179B179GLY00.043-0.01237.228-0.003-0.0030.0000.0000.0000.000
180B180TRP0-0.078-0.02739.7940.0020.0020.0000.0000.0000.000
181B181ALA00.0470.01843.174-0.001-0.0010.0000.0000.0000.000
182B182ARG10.8920.94846.0170.0340.0340.0000.0000.0000.000
183B183LEU00.0740.05348.3850.0010.0010.0000.0000.0000.000