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: 9G6K2

Calculation Name: 4ZG0-A-Xray372

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: 2023-06-20

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 OptHSide
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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2167613.576058
FMO2-HF: Nuclear repulsion 2090491.873423
FMO2-HF: Total energy -77121.702635
FMO2-MP2: Total energy -77346.05138


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:8:GLU)


Summations of interaction energy for fragment #1(A:8:GLU)
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.
-138.081-141.91922.275-10.649-7.7880.087
Interaction energy analysis for fragmet #1(A:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.920 / q_NPA : -0.946
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].
3A10LYS10.9660.9923.718-25.644-23.877-0.008-0.773-0.9860.003
4A11GLN00.0390.0155.574-5.682-5.6820.0000.0000.0000.000
5A12ILE0-0.070-0.0367.397-1.921-1.9210.0000.0000.0000.000
6A13SER00.002-0.02011.1450.2690.2690.0000.0000.0000.000
7A14ARG10.8750.91313.815-16.799-16.7990.0000.0000.0000.000
8A15GLU-1-0.867-0.93016.26916.09416.0940.0000.0000.0000.000
9A16GLU-1-0.907-0.94914.82418.07418.0740.0000.0000.0000.000
10A17ALA00.0400.01414.909-0.547-0.5470.0000.0000.0000.000
11A18MET0-0.067-0.04016.805-0.695-0.6950.0000.0000.0000.000
12A19ARG10.9170.96618.600-16.491-16.4910.0000.0000.0000.000
13A20LEU0-0.067-0.00615.536-0.510-0.5100.0000.0000.0000.000
14A21GLY00.0360.01720.152-0.508-0.5080.0000.0000.0000.000
15A22PRO00.018-0.01522.2750.5060.5060.0000.0000.0000.000
16A23GLY0-0.045-0.01022.415-0.082-0.0820.0000.0000.0000.000
17A24TRP0-0.012-0.00713.7540.4090.4090.0000.0000.0000.000
18A25SER0-0.0030.00518.316-0.520-0.5200.0000.0000.0000.000
19A26HIS00.0540.02017.6291.3681.3680.0000.0000.0000.000
20A27SER00.0150.01515.036-0.593-0.5930.0000.0000.0000.000
21A28CYS0-0.059-0.01216.5900.9860.9860.0000.0000.0000.000
22A29HIS00.0030.00515.264-0.660-0.6600.0000.0000.0000.000
23A30ALA00.0220.01016.9620.6080.6080.0000.0000.0000.000
24A31MET0-0.018-0.00614.9270.4060.4060.0000.0000.0000.000
25A32LEU00.0210.01317.699-0.273-0.2730.0000.0000.0000.000
26A33TYR00.021-0.01018.6380.0610.0610.0000.0000.0000.000
27A34ALA00.0460.04121.576-0.480-0.4800.0000.0000.0000.000
28A35ALA00.0370.02023.9080.3950.3950.0000.0000.0000.000
29A36ASN0-0.038-0.04825.217-0.924-0.9240.0000.0000.0000.000
30A37PRO00.0120.00527.0100.2390.2390.0000.0000.0000.000
31A38GLY00.0300.02129.413-0.333-0.3330.0000.0000.0000.000
32A39GLN00.022-0.00729.1000.4590.4590.0000.0000.0000.000
33A40LEU00.0370.03327.187-0.395-0.3950.0000.0000.0000.000
34A41PHE00.028-0.00130.314-0.053-0.0530.0000.0000.0000.000
35A42GLY00.0130.00633.369-0.262-0.2620.0000.0000.0000.000
36A43ARG10.8530.92531.744-9.245-9.2450.0000.0000.0000.000
37A44ILE0-0.010-0.00225.5050.1280.1280.0000.0000.0000.000
38A45PRO00.0280.01825.5970.0610.0610.0000.0000.0000.000
39A46MET0-0.040-0.01824.8060.5300.5300.0000.0000.0000.000
40A47ARG10.8630.93518.616-15.687-15.6870.0000.0000.0000.000
41A48PHE00.0460.02020.168-0.097-0.0970.0000.0000.0000.000
42A49SER0-0.038-0.00421.988-0.205-0.2050.0000.0000.0000.000
43A50VAL00.0360.01417.035-0.166-0.1660.0000.0000.0000.000
44A51LEU00.0140.01720.429-0.238-0.2380.0000.0000.0000.000
45A52MET0-0.044-0.01614.1121.1691.1690.0000.0000.0000.000
46A53GLN00.0260.01019.412-1.214-1.2140.0000.0000.0000.000
47A54MET00.0110.02320.1441.0001.0000.0000.0000.0000.000
48A55ARG10.8140.89018.046-16.367-16.3670.0000.0000.0000.000
49A56PHE00.0730.03022.166-0.031-0.0310.0000.0000.0000.000
50A57ASP-1-0.848-0.89319.50515.12715.1270.0000.0000.0000.000
51A58GLY0-0.0020.00221.2250.1700.1700.0000.0000.0000.000
52A59LEU0-0.047-0.01515.4900.5170.5170.0000.0000.0000.000
53A60LEU00.015-0.00616.596-0.455-0.4550.0000.0000.0000.000
54A61GLY0-0.009-0.02315.4291.3971.3970.0000.0000.0000.000
55A62PHE00.000-0.00412.541-0.547-0.5470.0000.0000.0000.000
56A63PRO00.0540.03317.335-0.164-0.1640.0000.0000.0000.000
57A64GLY00.017-0.00119.2350.8170.8170.0000.0000.0000.000
58A65GLY00.0280.01819.349-0.435-0.4350.0000.0000.0000.000
59A66PHE0-0.010-0.01217.8330.4460.4460.0000.0000.0000.000
60A67VAL0-0.047-0.01321.039-0.742-0.7420.0000.0000.0000.000
61A68ASP-1-0.777-0.87022.67311.89811.8980.0000.0000.0000.000
62A69ARG10.9310.94721.523-14.120-14.1200.0000.0000.0000.000
63A70ARG10.8150.89625.730-11.150-11.1500.0000.0000.0000.000
64A71PHE0-0.043-0.02528.646-0.384-0.3840.0000.0000.0000.000
65A72TRP00.0320.01726.745-0.192-0.1920.0000.0000.0000.000
66A73SER00.0300.00926.0640.5310.5310.0000.0000.0000.000
67A74LEU00.0450.00319.124-0.038-0.0380.0000.0000.0000.000
68A75GLU-1-0.726-0.82621.87114.65214.6520.0000.0000.0000.000
69A76ASP-1-0.799-0.86724.22110.94310.9430.0000.0000.0000.000
70A77GLY0-0.020-0.01325.150-0.258-0.2580.0000.0000.0000.000
71A78LEU0-0.002-0.00120.016-0.057-0.0570.0000.0000.0000.000
72A79ASN0-0.055-0.06023.507-0.225-0.2250.0000.0000.0000.000
73A80ARG10.8860.97426.063-12.003-12.0030.0000.0000.0000.000
74A81VAL0-0.027-0.01723.298-0.312-0.3120.0000.0000.0000.000
75A82LEU00.000-0.01722.178-0.135-0.1350.0000.0000.0000.000
76A83GLY00.0150.03026.054-0.258-0.2580.0000.0000.0000.000
77A84LEU0-0.086-0.06029.822-0.172-0.1720.0000.0000.0000.000
78A85GLY00.1170.06928.005-0.365-0.3650.0000.0000.0000.000
79A86LEU0-0.095-0.05224.4790.3200.3200.0000.0000.0000.000
80A87GLY00.0410.04328.112-0.510-0.5100.0000.0000.0000.000
81A88GLY0-0.005-0.00927.6400.5120.5120.0000.0000.0000.000
82A89LEU0-0.022-0.02527.762-0.332-0.3320.0000.0000.0000.000
83A90ARG10.8400.92527.134-10.452-10.4520.0000.0000.0000.000
84A91LEU0-0.0020.00021.2430.0630.0630.0000.0000.0000.000
85A92THR0-0.036-0.04323.863-0.475-0.4750.0000.0000.0000.000
86A93GLU-1-0.853-0.93221.12015.63115.6310.0000.0000.0000.000
87A94ALA00.0510.02820.8020.6920.6920.0000.0000.0000.000
88A95ASP-1-0.774-0.83320.19314.35914.3590.0000.0000.0000.000
89A96TYR0-0.009-0.02413.8591.1821.1820.0000.0000.0000.000
90A97LEU0-0.027-0.01412.4210.3180.3180.0000.0000.0000.000
91A98SER0-0.023-0.0169.5452.1992.1990.0000.0000.0000.000
92A99SER00.0030.00710.852-2.050-2.0500.0000.0000.0000.000
93A100HIS00.0030.0095.7474.2824.2820.0000.0000.0000.000
94A101LEU0-0.024-0.0038.825-3.312-3.3120.0000.0000.0000.000
95A102THR0-0.007-0.0077.9692.9012.9010.0000.0000.0000.000
96A103GLU-1-0.948-0.9725.66431.04031.0400.0000.0000.0000.000
97A104GLY00.0060.0188.435-1.333-1.3330.0000.0000.0000.000
98A105PRO00.016-0.01211.5200.4360.4360.0000.0000.0000.000
99A106HIS00.0170.00014.9550.3260.3260.0000.0000.0000.000
100A107ARG10.9220.97414.411-13.692-13.6920.0000.0000.0000.000
101A108VAL00.0220.02013.862-1.080-1.0800.0000.0000.0000.000
102A109VAL0-0.0110.00612.7691.6811.6810.0000.0000.0000.000
103A110ALA0-0.017-0.01510.980-1.508-1.5080.0000.0000.0000.000
104A111HIS00.017-0.00212.0702.9032.9030.0000.0000.0000.000
105A112LEU0-0.058-0.02210.873-0.597-0.5970.0000.0000.0000.000
106A113TYR0-0.004-0.03913.9710.0380.0380.0000.0000.0000.000
107A114ALA0-0.017-0.01115.8310.3970.3970.0000.0000.0000.000
108A115ARG10.8070.88217.889-13.548-13.5480.0000.0000.0000.000
109A116GLN0-0.008-0.00421.2910.0050.0050.0000.0000.0000.000
110A117LEU0-0.025-0.01022.974-0.537-0.5370.0000.0000.0000.000
111A118THR00.0370.00026.3660.2030.2030.0000.0000.0000.000
112A119LEU00.036-0.00127.4670.1850.1850.0000.0000.0000.000
113A120GLU-1-0.940-0.96529.4499.2359.2350.0000.0000.0000.000
114A121GLN00.0420.01529.5290.2580.2580.0000.0000.0000.000
115A122LEU0-0.021-0.00423.9220.0640.0640.0000.0000.0000.000
116A123HIS0-0.027-0.02928.047-0.189-0.1890.0000.0000.0000.000
117A124ALA00.0250.01630.907-0.143-0.1430.0000.0000.0000.000
118A125VAL0-0.009-0.00226.112-0.113-0.1130.0000.0000.0000.000
119A126GLU-1-0.753-0.83027.46511.76311.7630.0000.0000.0000.000
120A127ILE0-0.019-0.00729.581-0.183-0.1830.0000.0000.0000.000
121A128SER0-0.075-0.04230.863-0.139-0.1390.0000.0000.0000.000
122A129ALA00.022-0.00328.270-0.120-0.1200.0000.0000.0000.000
123A130VAL0-0.024-0.00230.1960.0100.0100.0000.0000.0000.000
124A131HIS0-0.040-0.01532.578-0.296-0.2960.0000.0000.0000.000
125A132SER0-0.061-0.02629.407-0.262-0.2620.0000.0000.0000.000
126A133ARG10.9260.95032.618-9.242-9.2420.0000.0000.0000.000
127A134ASP-1-0.826-0.90627.13911.33811.3380.0000.0000.0000.000
128A135HIS0-0.063-0.01329.3660.4810.4810.0000.0000.0000.000
129A136GLY0-0.025-0.01229.937-0.375-0.3750.0000.0000.0000.000
130A137LEU0-0.055-0.02230.160-0.250-0.2500.0000.0000.0000.000
131A138GLU-1-0.900-0.95625.32911.21911.2190.0000.0000.0000.000
132A139VAL0-0.044-0.03124.0820.7660.7660.0000.0000.0000.000
133A140LEU0-0.002-0.00525.376-0.494-0.4940.0000.0000.0000.000
134A141GLY00.0360.02026.005-0.386-0.3860.0000.0000.0000.000
135A142LEU0-0.027-0.01224.0770.6340.6340.0000.0000.0000.000
136A143VAL0-0.014-0.00821.037-0.359-0.3590.0000.0000.0000.000
137A144ARG10.8180.86522.324-11.466-11.4660.0000.0000.0000.000
138A145VAL0-0.030-0.01316.943-0.020-0.0200.0000.0000.0000.000
139A146PRO0-0.064-0.00419.968-0.413-0.4130.0000.0000.0000.000
140A147LEU00.0550.00016.3090.7750.7750.0000.0000.0000.000
141A148TYR0-0.0090.01419.1020.4000.4000.0000.0000.0000.000
142A149THR0-0.009-0.01819.5320.6640.6640.0000.0000.0000.000
143A150GLN0-0.011-0.00321.882-0.248-0.2480.0000.0000.0000.000
144A151LYS10.9860.97324.533-10.248-10.2480.0000.0000.0000.000
145A152ASP-1-0.814-0.88925.23512.60012.6000.0000.0000.0000.000
146A153ARG10.9270.96021.534-13.180-13.1800.0000.0000.0000.000
147A154VAL00.0410.02020.4960.8570.8570.0000.0000.0000.000
148A155GLY0-0.0110.00121.2890.4540.4540.0000.0000.0000.000
149A156GLY00.015-0.00322.1820.1440.1440.0000.0000.0000.000
150A157PHE00.0310.00413.0090.4140.4140.0000.0000.0000.000
151A158PRO00.0150.01116.3800.8980.8980.0000.0000.0000.000
152A159ASN00.0470.00516.8070.6390.6390.0000.0000.0000.000
153A160PHE00.0330.02416.1600.1680.1680.0000.0000.0000.000
154A161LEU00.0020.00111.9100.6930.6930.0000.0000.0000.000
155A162SER0-0.068-0.04213.5430.7070.7070.0000.0000.0000.000
156A163ASN0-0.040-0.00615.957-0.492-0.4920.0000.0000.0000.000
157A164ALA00.0400.03015.0171.0571.0570.0000.0000.0000.000
158A165PHE0-0.013-0.01312.043-0.094-0.0940.0000.0000.0000.000
159A166VAL00.0690.04412.4360.1810.1810.0000.0000.0000.000
160A167SER00.0200.0127.7460.6190.6190.0000.0000.0000.000
161A168THR00.0500.0108.1553.6263.6260.0000.0000.0000.000
162A169ALA00.0030.0149.0191.8461.8460.0000.0000.0000.000
163A170LYS10.9230.9698.884-25.975-25.9750.0000.0000.0000.000
164A171TYR0-0.031-0.0471.593-37.433-43.19222.284-9.871-6.6550.084
165A172GLN00.0310.0006.5411.2891.2890.0000.0000.0000.000
166A173LEU00.0110.0079.135-0.858-0.8580.0000.0000.0000.000
167A174LEU0-0.032-0.0197.310-1.576-1.5760.0000.0000.0000.000
168A175PHE0-0.003-0.0024.860-1.961-1.807-0.001-0.005-0.1470.000
169A176ALA00.0310.0057.448-2.564-2.5640.0000.0000.0000.000
170A177LEU00.004-0.01411.079-2.162-2.1620.0000.0000.0000.000
171A178LYS10.9210.9675.937-50.221-50.2210.0000.0000.0000.000
172A179VAL00.0110.0189.826-2.336-2.3360.0000.0000.0000.000
173A180LEU0-0.027-0.00911.611-2.078-2.0780.0000.0000.0000.000
174A181ASN0-0.061-0.02314.061-1.204-1.2040.0000.0000.0000.000
175A182MET0-0.0010.02315.185-1.180-1.1800.0000.0000.0000.000
176A183MET0-0.052-0.02213.700-2.006-2.0060.0000.0000.0000.000
177A184PRO00.0600.03513.5321.5871.5870.0000.0000.0000.000
178A185SER00.0710.0128.9482.2112.2110.0000.0000.0000.000
179A186GLU-1-0.919-0.95110.41822.16822.1680.0000.0000.0000.000
180A187LYS10.8570.90112.786-17.704-17.7040.0000.0000.0000.000
181A188LEU0-0.041-0.0169.514-0.286-0.2860.0000.0000.0000.000
182A189ALA0-0.0010.0069.5180.4660.4660.0000.0000.0000.000
183A190GLU-1-0.805-0.88210.56017.22817.2280.0000.0000.0000.000
184A191ALA00.0020.00713.559-1.028-1.0280.0000.0000.0000.000
185A192LEU00.0300.0157.347-1.008-1.0080.0000.0000.0000.000
186A193ALA00.0010.01011.997-0.714-0.7140.0000.0000.0000.000
187A194SER0-0.024-0.01913.486-1.342-1.3420.0000.0000.0000.000
188A195ALA0-0.012-0.01113.384-0.899-0.8990.0000.0000.0000.000
189A196THR0-0.025-0.02411.626-0.589-0.5890.0000.0000.0000.000
190A197GLU-1-0.902-0.95613.95514.70714.7070.0000.0000.0000.000
191A198LYS10.9150.96217.287-16.052-16.0520.0000.0000.0000.000
192A199GLN0-0.085-0.06213.5490.0930.0930.0000.0000.0000.000
193A200LYS10.9130.96713.789-18.907-18.9070.0000.0000.0000.000
194A201LYS10.8050.89418.581-13.185-13.1850.0000.0000.0000.000
195A202ALA0-0.035-0.01921.273-0.504-0.5040.0000.0000.0000.000
196A203LEU0-0.046-0.00318.887-0.371-0.3710.0000.0000.0000.000
197A204GLU-1-0.848-0.89622.30311.64211.6420.0000.0000.0000.000