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: N137Q

Calculation Name: 4ZG0-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZG0

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VHN8

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 199
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2165599.182823
FMO2-HF: Nuclear repulsion 2088307.377617
FMO2-HF: Total energy -77291.805206
FMO2-MP2: Total energy -77516.600168


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:7:ACE )


Summations of interaction energy for fragment #1(A:7: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.
3.764.832-0.006-0.383-0.682-0.001
Interaction energy analysis for fragmet #1(A:7:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.009
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].
3A9LEU 0-0.0200.0133.8211.2092.006-0.006-0.349-0.442-0.001
4A10LYS 10.9870.9966.4010.5100.5100.0000.0000.0000.000
5A11GLN 00.002-0.0069.9520.1450.1450.0000.0000.0000.000
6A12ILE 0-0.058-0.01512.4120.0240.0240.0000.0000.0000.000
7A13SER 00.0660.02915.8520.0030.0030.0000.0000.0000.000
8A14ARG 10.9330.95419.1430.1180.1180.0000.0000.0000.000
9A15GLU -1-0.953-0.98420.945-0.106-0.1060.0000.0000.0000.000
10A16GLU -1-0.935-0.97419.664-0.156-0.1560.0000.0000.0000.000
11A17ALA 00.0340.00618.3930.0140.0140.0000.0000.0000.000
12A18MET 0-0.088-0.04920.1160.0170.0170.0000.0000.0000.000
13A19ARG 10.9670.98423.3740.1150.1150.0000.0000.0000.000
14A20LEU 0-0.062-0.00318.2550.0080.0080.0000.0000.0000.000
15A21GLY 00.0290.01422.8190.0060.0060.0000.0000.0000.000
16A22PRO 00.018-0.01623.7270.0000.0000.0000.0000.0000.000
17A23GLY 0-0.046-0.00923.3150.0060.0060.0000.0000.0000.000
18A24TRP 0-0.032-0.01215.0920.0090.0090.0000.0000.0000.000
19A25SER 0-0.0080.00518.2310.0020.0020.0000.0000.0000.000
20A26HIS 00.0850.03718.314-0.016-0.0160.0000.0000.0000.000
21A27SER 00.0070.01015.2580.0070.0070.0000.0000.0000.000
22A28CYS 0-0.051-0.01217.727-0.025-0.0250.0000.0000.0000.000
23A29HIS 00.0090.01015.9620.0220.0220.0000.0000.0000.000
24A30ALA 00.0260.01318.185-0.022-0.0220.0000.0000.0000.000
25A31MET 0-0.010-0.00316.9610.0060.0060.0000.0000.0000.000
26A32LEU 00.0240.01019.141-0.007-0.0070.0000.0000.0000.000
27A33TYR 00.009-0.01421.3830.0060.0060.0000.0000.0000.000
28A34ALA 00.0520.04223.4540.0000.0000.0000.0000.0000.000
29A35ALA 00.0370.01825.930-0.002-0.0020.0000.0000.0000.000
30A36ASN 0-0.033-0.04627.2200.0080.0080.0000.0000.0000.000
31A37PRO 0-0.006-0.00128.827-0.002-0.0020.0000.0000.0000.000
32A38GLY 00.0180.01330.9120.0020.0020.0000.0000.0000.000
33A39GLN 00.0510.01030.424-0.003-0.0030.0000.0000.0000.000
34A40LEU 00.0310.03327.0370.0040.0040.0000.0000.0000.000
35A41PHE 00.015-0.00529.922-0.001-0.0010.0000.0000.0000.000
36A42GLY 00.0250.01033.6330.0010.0010.0000.0000.0000.000
37A43ARG 10.8460.92231.9170.0020.0020.0000.0000.0000.000
38A44ILE 0-0.029-0.00725.980-0.003-0.0030.0000.0000.0000.000
39A45PRO 00.0480.02027.3420.0020.0020.0000.0000.0000.000
40A46MET 0-0.025-0.01625.754-0.002-0.0020.0000.0000.0000.000
41A47ARG 10.8700.95521.3540.0890.0890.0000.0000.0000.000
42A48PHE 00.0490.01922.282-0.004-0.0040.0000.0000.0000.000
43A49SER 0-0.032-0.00223.2310.0070.0070.0000.0000.0000.000
44A50VAL 00.0350.01817.894-0.005-0.0050.0000.0000.0000.000
45A51LEU 00.0080.01321.1300.0120.0120.0000.0000.0000.000
46A52MET 0-0.039-0.01213.491-0.011-0.0110.0000.0000.0000.000
47A53GLN 00.0270.01518.511-0.007-0.0070.0000.0000.0000.000
48A54MET 00.0180.02318.7350.0170.0170.0000.0000.0000.000
49A55ARG 10.8160.89816.488-0.128-0.1280.0000.0000.0000.000
50A56PHE 00.0600.02820.5110.0110.0110.0000.0000.0000.000
51A57ASP -1-0.846-0.90217.4110.1600.1600.0000.0000.0000.000
52A58GLY 0-0.004-0.00118.9890.0200.0200.0000.0000.0000.000
53A59LEU 0-0.051-0.01713.2710.0210.0210.0000.0000.0000.000
54A60LEU 00.018-0.00614.834-0.032-0.0320.0000.0000.0000.000
55A61GLY 0-0.014-0.02614.0680.0290.0290.0000.0000.0000.000
56A62PHE 0-0.008-0.00513.097-0.010-0.0100.0000.0000.0000.000
57A63PRO 00.0450.02717.1460.0110.0110.0000.0000.0000.000
58A64GLY 00.025-0.00119.564-0.016-0.0160.0000.0000.0000.000
59A65GLY 00.0220.01419.0940.0150.0150.0000.0000.0000.000
60A66PHE 0-0.007-0.00917.139-0.014-0.0140.0000.0000.0000.000
61A67VAL 0-0.039-0.01121.0870.0010.0010.0000.0000.0000.000
62A68ASP -1-0.777-0.87923.424-0.009-0.0090.0000.0000.0000.000
63A69ARG 10.9450.96423.4450.0560.0560.0000.0000.0000.000
64A70ARG 10.8070.90026.9440.0010.0010.0000.0000.0000.000
65A71PHE 0-0.040-0.02229.5680.0010.0010.0000.0000.0000.000
66A72TRP 00.0300.01827.7930.0000.0000.0000.0000.0000.000
67A73SER 00.0540.03427.970-0.004-0.0040.0000.0000.0000.000
68A74LEU 00.039-0.00121.9340.0050.0050.0000.0000.0000.000
69A75GLU -1-0.742-0.85124.736-0.071-0.0710.0000.0000.0000.000
70A76ASP -1-0.911-0.95926.586-0.030-0.0300.0000.0000.0000.000
71A77GLY 0-0.040-0.03026.1760.0060.0060.0000.0000.0000.000
72A78LEU 00.0080.00521.5070.0060.0060.0000.0000.0000.000
73A79ASN 0-0.021-0.03424.5270.0060.0060.0000.0000.0000.000
74A80ARG 10.8830.96326.3280.0100.0100.0000.0000.0000.000
75A81VAL 0-0.052-0.01723.0830.0040.0040.0000.0000.0000.000
76A82LEU 0-0.026-0.02022.8550.0030.0030.0000.0000.0000.000
77A83GLY 0-0.0190.02626.4590.0010.0010.0000.0000.0000.000
78A84LEU 00.0480.02230.2370.0040.0040.0000.0000.0000.000
79A85GLY 0-0.045-0.03832.155-0.003-0.0030.0000.0000.0000.000
80A86LEU 0-0.060-0.03332.2960.0030.0030.0000.0000.0000.000
81A87GLY 00.0800.05231.021-0.001-0.0010.0000.0000.0000.000
82A88GLY 0-0.0110.00632.078-0.002-0.0020.0000.0000.0000.000
83A89LEU 0-0.038-0.03830.318-0.003-0.0030.0000.0000.0000.000
84A90ARG 10.9330.98329.6810.0300.0300.0000.0000.0000.000
85A91LEU 0-0.026-0.01223.634-0.004-0.0040.0000.0000.0000.000
86A92THR 0-0.026-0.02427.1150.0040.0040.0000.0000.0000.000
87A93GLU -1-0.910-0.96725.772-0.108-0.1080.0000.0000.0000.000
88A94ALA 00.0550.03025.257-0.009-0.0090.0000.0000.0000.000
89A95ASP -1-0.802-0.88923.834-0.082-0.0820.0000.0000.0000.000
90A96TYR 0-0.036-0.05618.163-0.014-0.0140.0000.0000.0000.000
91A97LEU 0-0.023-0.01416.579-0.008-0.0080.0000.0000.0000.000
92A98SER 00.005-0.00413.772-0.020-0.0200.0000.0000.0000.000
93A99SER 0-0.013-0.00115.1570.0400.0400.0000.0000.0000.000
94A100HIS 0-0.0130.0069.6660.0230.0230.0000.0000.0000.000
95A101LEU 0-0.027-0.00311.3490.0870.0870.0000.0000.0000.000
96A102THR 00.001-0.0048.826-0.095-0.0950.0000.0000.0000.000
97A103GLU -1-0.974-0.9854.8461.6071.8030.000-0.010-0.1850.000
98A104GLY 00.0070.0238.532-0.031-0.0310.0000.0000.0000.000
99A105PRO 00.005-0.01511.1050.0650.0650.0000.0000.0000.000
100A106HIS 00.0360.00314.720-0.023-0.0230.0000.0000.0000.000
101A107ARG 10.9450.98314.562-0.005-0.0050.0000.0000.0000.000
102A108VAL 00.0080.01613.860-0.011-0.0110.0000.0000.0000.000
103A109VAL 0-0.0070.01013.627-0.024-0.0240.0000.0000.0000.000
104A110ALA 0-0.021-0.02012.1560.0250.0250.0000.0000.0000.000
105A111HIS 00.0030.00614.064-0.068-0.0680.0000.0000.0000.000
106A112LEU 0-0.044-0.01613.6150.0230.0230.0000.0000.0000.000
107A113TYR 0-0.004-0.02116.495-0.008-0.0080.0000.0000.0000.000
108A114ALA 0-0.011-0.00719.0000.0040.0040.0000.0000.0000.000
109A115ARG 10.8630.92920.9280.0630.0630.0000.0000.0000.000
110A116GLN 0-0.039-0.01024.4020.0090.0090.0000.0000.0000.000
111A117LEU 0-0.020-0.01126.1150.0050.0050.0000.0000.0000.000
112A118THR 00.0370.00028.9360.0000.0000.0000.0000.0000.000
113A119LEU 00.026-0.00728.8620.0010.0010.0000.0000.0000.000
114A120GLU -1-0.921-0.95331.083-0.017-0.0170.0000.0000.0000.000
115A121GLN 00.0430.01731.282-0.001-0.0010.0000.0000.0000.000
116A122LEU 0-0.024-0.00724.8530.0020.0020.0000.0000.0000.000
117A123HIS 0-0.010-0.00829.0410.0040.0040.0000.0000.0000.000
118A124ALA 00.0220.01531.2900.0040.0040.0000.0000.0000.000
119A125VAL 0-0.011-0.00226.5630.0020.0020.0000.0000.0000.000
120A126GLU -1-0.782-0.89627.226-0.003-0.0030.0000.0000.0000.000
121A127ILE 0-0.032-0.00729.4820.0040.0040.0000.0000.0000.000
122A128SER 0-0.062-0.03431.0850.0020.0020.0000.0000.0000.000
123A129ALA 00.0240.00527.7960.0020.0020.0000.0000.0000.000
124A130VAL 0-0.015-0.00629.8300.0040.0040.0000.0000.0000.000
125A131HIS 0-0.036-0.01231.7890.0030.0030.0000.0000.0000.000
126A132SER 0-0.050-0.01429.6790.0000.0000.0000.0000.0000.000
127A133ARG 10.9480.94632.064-0.005-0.0050.0000.0000.0000.000
128A134ASP -1-0.824-0.90126.3410.0240.0240.0000.0000.0000.000
129A135HIS 0-0.060-0.01728.0700.0060.0060.0000.0000.0000.000
130A136GLY 0-0.034-0.01828.396-0.001-0.0010.0000.0000.0000.000
131A137LEU 0-0.054-0.02328.5120.0030.0030.0000.0000.0000.000
132A138GLU -1-0.901-0.95523.9890.0480.0480.0000.0000.0000.000
133A139VAL 0-0.033-0.02423.1010.0090.0090.0000.0000.0000.000
134A140LEU 0-0.009-0.01023.665-0.003-0.0030.0000.0000.0000.000
135A141GLY 00.0320.01824.547-0.002-0.0020.0000.0000.0000.000
136A142LEU 0-0.015-0.00623.2670.0050.0050.0000.0000.0000.000
137A143VAL 0-0.017-0.00919.9260.0030.0030.0000.0000.0000.000
138A144ARG 10.8440.90521.8130.0040.0040.0000.0000.0000.000
139A145VAL 0-0.026-0.01017.1630.0080.0080.0000.0000.0000.000
140A146PRO 0-0.058-0.00119.009-0.010-0.0100.0000.0000.0000.000
141A147LEU 00.058-0.00217.473-0.001-0.0010.0000.0000.0000.000
142A148TYR 0-0.0200.00719.975-0.010-0.0100.0000.0000.0000.000
143A149THR 00.006-0.00819.4960.0070.0070.0000.0000.0000.000
144A150GLN 0-0.037-0.01321.7480.0000.0000.0000.0000.0000.000
145A151LYS 10.9850.97124.0000.0090.0090.0000.0000.0000.000
146A152ASP -1-0.802-0.88623.7930.0240.0240.0000.0000.0000.000
147A153ARG 10.9280.95920.6790.0160.0160.0000.0000.0000.000
148A154VAL 00.0380.02018.4540.0010.0010.0000.0000.0000.000
149A155GLY 00.0010.00719.6160.0050.0050.0000.0000.0000.000
150A156GLY 0-0.016-0.02121.102-0.013-0.0130.0000.0000.0000.000
151A157PHE 00.0410.01013.7770.0140.0140.0000.0000.0000.000
152A158PRO 00.0150.01114.8550.0110.0110.0000.0000.0000.000
153A159ASN 00.0570.01115.0170.0410.0410.0000.0000.0000.000
154A160PHE 00.0260.02115.2260.0230.0230.0000.0000.0000.000
155A161LEU 0-0.028-0.01310.8390.0230.0230.0000.0000.0000.000
156A162SER 0-0.064-0.04011.6280.0740.0740.0000.0000.0000.000
157A163ASN 0-0.056-0.01413.8600.0130.0130.0000.0000.0000.000
158A164ALA 00.0420.02912.9860.0500.0500.0000.0000.0000.000
159A165PHE 0-0.015-0.01010.025-0.057-0.0570.0000.0000.0000.000
160A166VAL 00.0640.04010.9380.0810.0810.0000.0000.0000.000
161A167SER 00.0280.0105.738-0.151-0.1510.0000.0000.0000.000
162A168THR 00.0430.0066.763-0.093-0.0930.0000.0000.0000.000
163A169ALA 00.0090.0208.437-0.130-0.1300.0000.0000.0000.000
164A170LYS 10.9490.9887.306-0.530-0.5300.0000.0000.0000.000
165A171TYR 0-0.012-0.0084.4870.0520.1310.000-0.024-0.0550.000
166A172GLN 00.0420.0046.991-0.058-0.0580.0000.0000.0000.000
167A173LEU 00.0090.00710.520-0.007-0.0070.0000.0000.0000.000
168A174LEU 0-0.024-0.0157.1930.0090.0090.0000.0000.0000.000
169A175PHE 00.0010.0019.811-0.001-0.0010.0000.0000.0000.000
170A176ALA 00.0390.00711.3410.0480.0480.0000.0000.0000.000
171A177LEU 0-0.005-0.01713.8360.0310.0310.0000.0000.0000.000
172A178LYS 10.9300.97611.2340.6250.6250.0000.0000.0000.000
173A179VAL 00.0080.01915.3600.0340.0340.0000.0000.0000.000
174A180LEU 0-0.022-0.01017.2180.0310.0310.0000.0000.0000.000
175A181ASN 0-0.045-0.01318.9980.0090.0090.0000.0000.0000.000
176A182MET 0-0.0190.00918.8010.0210.0210.0000.0000.0000.000
177A183MET 0-0.067-0.04015.7810.0340.0340.0000.0000.0000.000
178A184PRO 00.0400.02917.235-0.028-0.0280.0000.0000.0000.000
179A185SER 00.0660.00313.329-0.034-0.0340.0000.0000.0000.000
180A186GLU -1-0.914-0.94513.407-0.205-0.2050.0000.0000.0000.000
181A187LYS 10.9960.99515.1520.1120.1120.0000.0000.0000.000
182A188LEU 0-0.042-0.01211.5300.0240.0240.0000.0000.0000.000
183A189ALA 00.0000.00610.5480.0160.0160.0000.0000.0000.000
184A190GLU -1-0.919-0.96311.613-0.038-0.0380.0000.0000.0000.000
185A191ALA 00.0000.00413.5320.0410.0410.0000.0000.0000.000
186A192LEU 00.0290.0125.7840.0560.0560.0000.0000.0000.000
187A193ALA 00.0040.00610.5360.0930.0930.0000.0000.0000.000
188A194SER 0-0.025-0.01611.8420.0490.0490.0000.0000.0000.000
189A195ALA 0-0.016-0.01511.4230.0210.0210.0000.0000.0000.000
190A196THR 0-0.031-0.0219.3420.0870.0870.0000.0000.0000.000
191A197GLU -1-0.932-0.96211.6490.1660.1660.0000.0000.0000.000
192A198LYS 10.9280.96715.024-0.146-0.1460.0000.0000.0000.000
193A199GLN 0-0.090-0.06711.1120.0430.0430.0000.0000.0000.000
194A200LYS 10.9260.96711.397-0.360-0.3600.0000.0000.0000.000
195A201LYS 10.9800.99116.032-0.108-0.1080.0000.0000.0000.000
196A202ALA 0-0.080-0.03718.774-0.009-0.0090.0000.0000.0000.000
197A203LEU 0-0.0360.00016.037-0.002-0.0020.0000.0000.0000.000
198A204GLU -1-0.947-0.96219.6760.1330.1330.0000.0000.0000.000
199A205NME 0-0.0040.00022.269-0.007-0.0070.0000.0000.0000.000