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: KGLQ3

Calculation Name: 2GZQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GZQ

Chain ID: A

ChEMBL ID:

UniProt ID: A5K000

Base Structure: X-ray

Registration Date: 2023-09-23

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2256846.309938
FMO2-HF: Nuclear repulsion 2179913.405695
FMO2-HF: Total energy -76932.904243
FMO2-MP2: Total energy -77155.222621


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:2:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-12.047-13.299.991-4.019-4.728-0.045
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.027
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].
3A4PRO00.0300.0031.932-4.588-7.4669.167-3.163-3.126-0.044
4A5PRO0-0.062-0.0314.650-0.206-0.158-0.001-0.020-0.0260.000
5A6THR00.0770.0565.796-0.197-0.1970.0000.0000.0000.000
6A7ILE00.0600.0127.9330.3000.3000.0000.0000.0000.000
7A8GLU-1-0.938-0.9689.8800.3230.3230.0000.0000.0000.000
8A9GLU-1-0.776-0.8735.4271.8041.8040.0000.0000.0000.000
9A10LEU0-0.015-0.0199.6780.1430.1430.0000.0000.0000.000
10A11LYS10.8640.91511.7910.1120.1120.0000.0000.0000.000
11A12ARG10.8470.9379.096-0.881-0.8810.0000.0000.0000.000
12A13GLU-1-0.893-0.94011.6620.7340.7340.0000.0000.0000.000
13A14LYS10.8850.93114.577-0.234-0.2340.0000.0000.0000.000
14A15ILE00.0130.01312.274-0.024-0.0240.0000.0000.0000.000
15A16ILE00.0240.06814.275-0.042-0.0420.0000.0000.0000.000
16A17PRO0-0.027-0.03917.0640.0310.0310.0000.0000.0000.000
17A18HIS0-0.064-0.04319.2970.0160.0160.0000.0000.0000.000
18A19VAL0-0.018-0.00315.9970.0060.0060.0000.0000.0000.000
19A20PHE00.0270.01112.678-0.026-0.0260.0000.0000.0000.000
20A21PRO00.009-0.00718.2930.0140.0140.0000.0000.0000.000
21A22ASP-1-0.881-0.94219.959-0.119-0.1190.0000.0000.0000.000
22A23GLU-1-0.888-0.93516.707-0.128-0.1280.0000.0000.0000.000
23A24ASN0-0.033-0.00616.599-0.068-0.0680.0000.0000.0000.000
24A25VAL0-0.042-0.01413.545-0.009-0.0090.0000.0000.0000.000
25A26ASP-1-0.813-0.90214.338-0.656-0.6560.0000.0000.0000.000
26A27LEU0-0.079-0.0419.0270.0200.0200.0000.0000.0000.000
27A28THR00.0420.0129.643-0.246-0.2460.0000.0000.0000.000
28A29VAL0-0.0180.0129.565-0.202-0.2020.0000.0000.0000.000
29A30ASP-1-0.898-0.9653.727-5.042-4.6120.005-0.247-0.188-0.002
30A31MET0-0.033-0.0175.8740.5220.5220.0000.0000.0000.000
31A32TYR0-0.0380.0007.2210.3540.3540.0000.0000.0000.000
32A33ILE00.022-0.0048.146-0.122-0.1220.0000.0000.0000.000
33A34SER00.0350.02411.0310.1900.1900.0000.0000.0000.000
34A35PHE0-0.018-0.02813.320-0.094-0.0940.0000.0000.0000.000
35A36LYS10.8750.94216.266-0.361-0.3610.0000.0000.0000.000
36A37SER00.0200.01716.1510.0720.0720.0000.0000.0000.000
37A38GLY00.0790.04114.829-0.020-0.0200.0000.0000.0000.000
38A39LYS10.7800.89414.789-0.438-0.4380.0000.0000.0000.000
39A40GLU-1-0.825-0.9189.3110.8790.8790.0000.0000.0000.000
40A41VAL0-0.072-0.0289.4890.0800.0800.0000.0000.0000.000
41A42ASN0-0.011-0.0234.7391.6121.744-0.001-0.007-0.1240.000
42A43HIS10.8740.9282.378-2.954-1.9290.821-0.582-1.2640.001
43A44GLY0-0.0020.0087.120-0.222-0.2220.0000.0000.0000.000
44A45ASN00.0370.0329.986-0.146-0.1460.0000.0000.0000.000
45A46ILE0-0.015-0.01511.630-0.187-0.1870.0000.0000.0000.000
46A47LEU0-0.0040.00413.499-0.024-0.0240.0000.0000.0000.000
47A48ASP-1-0.922-0.96216.4490.3920.3920.0000.0000.0000.000
48A49LEU00.0350.00319.813-0.003-0.0030.0000.0000.0000.000
49A50ALA00.0150.03222.053-0.024-0.0240.0000.0000.0000.000
50A51GLY0-0.002-0.01821.4870.0340.0340.0000.0000.0000.000
51A52THR00.002-0.02418.841-0.001-0.0010.0000.0000.0000.000
52A53GLY00.0100.01521.142-0.012-0.0120.0000.0000.0000.000
53A54SER0-0.031-0.01322.811-0.021-0.0210.0000.0000.0000.000
54A55VAL00.0320.02819.7540.0310.0310.0000.0000.0000.000
55A56PRO0-0.012-0.00415.5790.0030.0030.0000.0000.0000.000
56A57ARG10.9470.98617.748-0.176-0.1760.0000.0000.0000.000
57A58ASN0-0.009-0.01314.793-0.010-0.0100.0000.0000.0000.000
58A59ILE00.0170.01311.9750.0910.0910.0000.0000.0000.000
59A60LYS10.9200.96610.5750.0780.0780.0000.0000.0000.000
60A61PHE00.0290.0139.971-0.008-0.0080.0000.0000.0000.000
61A62SER00.0120.0048.245-0.002-0.0020.0000.0000.0000.000
62A63GLU-1-0.976-0.98710.273-0.806-0.8060.0000.0000.0000.000
63A64GLU-1-0.959-0.97113.709-0.289-0.2890.0000.0000.0000.000
64A65PRO0-0.059-0.00116.898-0.035-0.0350.0000.0000.0000.000
65A66PRO00.0400.00718.1470.0170.0170.0000.0000.0000.000
66A67GLU-1-0.899-0.95021.022-0.185-0.1850.0000.0000.0000.000
67A68ASP-1-0.903-0.95024.497-0.170-0.1700.0000.0000.0000.000
68A69TYR0-0.049-0.01521.5770.0180.0180.0000.0000.0000.000
69A70CYS0-0.077-0.01920.8790.0030.0030.0000.0000.0000.000
70A71TYR00.002-0.03114.295-0.002-0.0020.0000.0000.0000.000
71A72ILE0-0.011-0.00618.4420.0360.0360.0000.0000.0000.000
72A73LEU0-0.032-0.01213.977-0.015-0.0150.0000.0000.0000.000
73A74PHE00.0250.01216.9050.0260.0260.0000.0000.0000.000
74A75MET0-0.055-0.01716.4240.0160.0160.0000.0000.0000.000
75A76ILE00.020-0.00117.379-0.017-0.0170.0000.0000.0000.000
76A77ASP-1-0.775-0.87518.1230.3210.3210.0000.0000.0000.000
77A78PRO00.0440.04417.949-0.033-0.0330.0000.0000.0000.000
78A79ASP-1-0.799-0.87719.7970.2860.2860.0000.0000.0000.000
79A80PHE00.0130.03122.7970.0060.0060.0000.0000.0000.000
80A81PRO00.0360.01625.548-0.013-0.0130.0000.0000.0000.000
81A82SER0-0.066-0.05726.3260.0170.0170.0000.0000.0000.000
82A83ARG10.9570.98118.552-0.369-0.3690.0000.0000.0000.000
83A84ARG10.9120.94524.721-0.200-0.2000.0000.0000.0000.000
84A85ARG10.9890.99827.763-0.142-0.1420.0000.0000.0000.000
85A86PRO00.0140.03025.245-0.001-0.0010.0000.0000.0000.000
86A87ASP-1-0.871-0.94527.2020.0940.0940.0000.0000.0000.000
87A88GLY0-0.076-0.05428.561-0.013-0.0130.0000.0000.0000.000
88A89ARG10.8380.94322.879-0.146-0.1460.0000.0000.0000.000
89A90ASP-1-0.794-0.91221.6270.0860.0860.0000.0000.0000.000
90A91TYR0-0.045-0.03623.510-0.015-0.0150.0000.0000.0000.000
91A92VAL00.0220.01522.0690.0210.0210.0000.0000.0000.000
92A93HIS0-0.049-0.03220.5820.0100.0100.0000.0000.0000.000
93A94TRP0-0.030-0.02516.5960.0100.0100.0000.0000.0000.000
94A95ALA00.0480.03020.7970.0010.0010.0000.0000.0000.000
95A96VAL0-0.039-0.00219.6410.0010.0010.0000.0000.0000.000
96A97SER00.0360.00120.693-0.024-0.0240.0000.0000.0000.000
97A98GLY00.0940.02022.1790.0140.0140.0000.0000.0000.000
98A99ILE0-0.050-0.00917.1580.0010.0010.0000.0000.0000.000
99A100LYS10.9630.97320.1290.1920.1920.0000.0000.0000.000
100A101SER00.0490.04719.190-0.036-0.0360.0000.0000.0000.000
101A102LYS10.9950.99213.5670.5770.5770.0000.0000.0000.000
102A103GLU-1-0.951-0.97714.285-0.118-0.1180.0000.0000.0000.000
103A104LEU0-0.0140.00416.0720.0130.0130.0000.0000.0000.000
104A105VAL00.022-0.00217.2570.0390.0390.0000.0000.0000.000
105A106LYS10.8990.92519.776-0.083-0.0830.0000.0000.0000.000
106A107GLY00.0080.00019.8270.0000.0000.0000.0000.0000.000
107A108THR00.0290.00720.820-0.010-0.0100.0000.0000.0000.000
108A109ASP-1-0.826-0.90822.413-0.099-0.0990.0000.0000.0000.000
109A110LYS10.9530.96724.8410.0980.0980.0000.0000.0000.000
110A111ASN0-0.0120.00324.0460.0090.0090.0000.0000.0000.000
111A112CYS0-0.084-0.02222.488-0.007-0.0070.0000.0000.0000.000
112A113ILE00.0520.03124.9880.0120.0120.0000.0000.0000.000
113A114THR0-0.026-0.02525.1230.0020.0020.0000.0000.0000.000
114A115LEU0-0.0050.00624.8330.0050.0050.0000.0000.0000.000
115A116LEU00.0270.00825.0030.0070.0070.0000.0000.0000.000
116A117PRO00.0320.02524.7050.0060.0060.0000.0000.0000.000
117A118TYR00.002-0.02419.1760.0200.0200.0000.0000.0000.000
118A119VAL0-0.0080.01223.855-0.002-0.0020.0000.0000.0000.000
119A120GLY00.0200.00922.3980.0130.0130.0000.0000.0000.000
120A121PRO0-0.012-0.01720.008-0.015-0.0150.0000.0000.0000.000
121A122SER00.0240.02822.759-0.008-0.0080.0000.0000.0000.000
122A123ILE00.0270.01821.331-0.004-0.0040.0000.0000.0000.000
123A124LYS10.9791.00425.984-0.168-0.1680.0000.0000.0000.000
124A125LYS11.0110.99528.072-0.177-0.1770.0000.0000.0000.000
125A126GLY0-0.056-0.02628.695-0.014-0.0140.0000.0000.0000.000
126A127THR00.0040.01026.7140.0000.0000.0000.0000.0000.000
127A128GLY00.0170.01124.7340.0010.0010.0000.0000.0000.000
128A129LEU0-0.020-0.00918.672-0.013-0.0130.0000.0000.0000.000
129A130HIS10.7710.85019.945-0.297-0.2970.0000.0000.0000.000
130A131ARG10.7890.86315.415-0.265-0.2650.0000.0000.0000.000
131A132ILE0-0.0310.00015.886-0.059-0.0590.0000.0000.0000.000
132A133SER00.012-0.01213.2970.1260.1260.0000.0000.0000.000
133A134PHE0-0.026-0.01711.567-0.042-0.0420.0000.0000.0000.000
134A135ILE00.0260.00911.991-0.017-0.0170.0000.0000.0000.000
135A136LEU00.0190.01611.7160.0370.0370.0000.0000.0000.000
136A137SER00.0220.00614.195-0.059-0.0590.0000.0000.0000.000
137A138LEU0-0.0060.00916.9990.0070.0070.0000.0000.0000.000
138A139VAL00.011-0.00419.3910.0190.0190.0000.0000.0000.000
139A140LYS11.0251.01222.9930.1310.1310.0000.0000.0000.000
140A141GLU-1-0.819-0.92825.920-0.118-0.1180.0000.0000.0000.000
141A142GLU-1-0.973-0.98926.992-0.102-0.1020.0000.0000.0000.000
142A143ASN00.000-0.00827.7340.0160.0160.0000.0000.0000.000
143A144LYS10.8280.93225.5120.1060.1060.0000.0000.0000.000
144A145GLY0-0.006-0.01226.8060.0090.0090.0000.0000.0000.000
145A146ASN0-0.075-0.03429.2930.0150.0150.0000.0000.0000.000
146A147VAL00.0440.03825.719-0.006-0.0060.0000.0000.0000.000
147A148THR00.0560.02128.6640.0140.0140.0000.0000.0000.000
148A149GLY00.0330.00029.011-0.001-0.0010.0000.0000.0000.000
149A150VAL0-0.063-0.03925.7530.0130.0130.0000.0000.0000.000
150A151PRO0-0.0010.00929.075-0.006-0.0060.0000.0000.0000.000
151A152LEU00.0550.02630.6650.0050.0050.0000.0000.0000.000
152A153TYR0-0.056-0.05230.1330.0050.0050.0000.0000.0000.000
153A154ARG10.9520.97232.151-0.007-0.0070.0000.0000.0000.000
154A155GLY00.0330.01133.7930.0010.0010.0000.0000.0000.000
155A156GLU-1-0.767-0.86630.7250.0630.0630.0000.0000.0000.000
156A157HIS0-0.0340.00034.0910.0020.0020.0000.0000.0000.000
157A158TYR0-0.054-0.02935.906-0.003-0.0030.0000.0000.0000.000
158A159ILE0-0.0240.01230.248-0.005-0.0050.0000.0000.0000.000
159A160THR00.0160.01031.4350.0090.0090.0000.0000.0000.000
160A161ARG10.7840.85925.355-0.088-0.0880.0000.0000.0000.000
161A162VAL0-0.023-0.00827.0220.0110.0110.0000.0000.0000.000
162A163LYS10.9610.99127.629-0.071-0.0710.0000.0000.0000.000
163A164PHE00.022-0.00121.537-0.010-0.0100.0000.0000.0000.000
164A165ASN00.0310.00826.659-0.006-0.0060.0000.0000.0000.000
165A166ASN0-0.033-0.00929.905-0.003-0.0030.0000.0000.0000.000
166A167CYS0-0.0180.01928.000-0.010-0.0100.0000.0000.0000.000
167A168GLN0-0.026-0.00928.0590.0000.0000.0000.0000.0000.000
168A169SER00.0320.00122.8790.0100.0100.0000.0000.0000.000
169A170ALA00.0360.01019.804-0.013-0.0130.0000.0000.0000.000
170A171TYR00.0310.01319.252-0.009-0.0090.0000.0000.0000.000
171A172ASN0-0.021-0.01621.351-0.026-0.0260.0000.0000.0000.000
172A173VAL00.0210.00523.923-0.009-0.0090.0000.0000.0000.000
173A174ILE00.0160.00318.461-0.007-0.0070.0000.0000.0000.000
174A175GLN0-0.0140.00222.687-0.020-0.0200.0000.0000.0000.000
175A176MET0-0.048-0.01624.5380.0000.0000.0000.0000.0000.000
176A177ASN0-0.096-0.06625.5640.0070.0070.0000.0000.0000.000
177A178ASP-1-0.891-0.92025.769-0.121-0.1210.0000.0000.0000.000
178A179MET0-0.098-0.03521.219-0.013-0.0130.0000.0000.0000.000
179A180LYS10.8760.93516.8560.4210.4210.0000.0000.0000.000
180A181ILE0-0.033-0.02113.936-0.013-0.0130.0000.0000.0000.000
181A182VAL00.018-0.00613.186-0.022-0.0220.0000.0000.0000.000
182A183GLY00.0690.0449.633-0.212-0.2120.0000.0000.0000.000
183A184PHE00.002-0.0168.4930.2170.2170.0000.0000.0000.000
184A185ASN00.0300.0206.0150.3970.3970.0000.0000.0000.000
185A186TRP00.0270.0157.607-0.158-0.1580.0000.0000.0000.000
186A187CYS0-0.0210.0199.8690.3050.3050.0000.0000.0000.000
187A188GLN0-0.021-0.03412.552-0.295-0.2950.0000.0000.0000.000
188A189MET00.0090.02415.830-0.007-0.0070.0000.0000.0000.000
189A190ARG11.0020.99018.936-0.386-0.3860.0000.0000.0000.000
190A191ARG10.8980.93022.502-0.215-0.2150.0000.0000.0000.000
191A192LYS10.9840.99423.144-0.389-0.3890.0000.0000.0000.000