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: 174QZ

Calculation Name: 3ZC8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZC8

Chain ID: A

ChEMBL ID:

UniProt ID: D2YW43

Base Structure: X-ray

Registration Date: 2023-06-21

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945985.802385
FMO2-HF: Nuclear repulsion 1875550.608776
FMO2-HF: Total energy -70435.193609
FMO2-MP2: Total energy -70640.361485


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
-32.282-39.15231.156-12.881-11.4040.13
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.833 / q_NPA : -0.889
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].
3A3LEU0-0.008-0.0113.0632.0024.3210.155-1.220-1.2550.001
4A4LEU0-0.012-0.0064.971-1.983-1.9830.0000.0000.0000.000
5A5ASP-1-0.766-0.9047.31019.83319.8330.0000.0000.0000.000
6A6ILE0-0.054-0.03511.0680.7260.7260.0000.0000.0000.000
7A7ASN0-0.121-0.06713.390-1.251-1.2510.0000.0000.0000.000
8A8GLY00.0110.0209.829-0.307-0.3070.0000.0000.0000.000
9A9ASN0-0.057-0.02810.1900.9340.9340.0000.0000.0000.000
10A10VAL00.0150.0016.8370.6160.6160.0000.0000.0000.000
11A11VAL0-0.0080.0058.233-2.705-2.7050.0000.0000.0000.000
12A12GLU-1-0.882-0.94310.10919.12919.1290.0000.0000.0000.000
13A13ALA00.0250.00112.869-0.775-0.7750.0000.0000.0000.000
14A14SER0-0.052-0.01714.808-0.759-0.7590.0000.0000.0000.000
15A15ARG10.8510.91416.005-17.692-17.6920.0000.0000.0000.000
16A16ASP-1-0.813-0.85717.41113.45313.4530.0000.0000.0000.000
17A17TYR00.0580.02413.4670.2050.2050.0000.0000.0000.000
18A18TYR00.0130.01117.755-0.817-0.8170.0000.0000.0000.000
19A19LEU00.0190.01613.8230.8140.8140.0000.0000.0000.000
20A20VAL0-0.005-0.01617.104-0.985-0.9850.0000.0000.0000.000
21A21SER00.005-0.00417.5630.9240.9240.0000.0000.0000.000
22A22VAL0-0.0170.00115.911-0.495-0.4950.0000.0000.0000.000
23A23ILE0-0.0140.00015.807-0.548-0.5480.0000.0000.0000.000
24A24GLY00.0440.03419.3000.0500.0500.0000.0000.0000.000
25A25GLY00.0090.00821.677-0.249-0.2490.0000.0000.0000.000
26A26ALA0-0.006-0.01423.013-0.443-0.4430.0000.0000.0000.000
27A27GLY00.0320.00825.343-0.427-0.4270.0000.0000.0000.000
28A28GLY0-0.048-0.01624.904-0.313-0.3130.0000.0000.0000.000
29A29GLY00.0190.01923.8790.2560.2560.0000.0000.0000.000
30A30GLY0-0.011-0.00121.4110.6150.6150.0000.0000.0000.000
31A31LEU0-0.023-0.00518.787-0.430-0.4300.0000.0000.0000.000
32A32THR0-0.023-0.03422.873-0.203-0.2030.0000.0000.0000.000
33A33LEU00.0120.02525.8360.1330.1330.0000.0000.0000.000
34A34TYR0-0.014-0.01528.198-0.348-0.3480.0000.0000.0000.000
35A35ARG10.8730.92831.031-7.904-7.9040.0000.0000.0000.000
36A36GLY00.0970.06332.9290.1970.1970.0000.0000.0000.000
37A37ARG10.6600.79230.544-9.902-9.9020.0000.0000.0000.000
38A38ASN00.0030.00835.497-0.342-0.3420.0000.0000.0000.000
39A39GLU-1-0.816-0.90637.9437.3527.3520.0000.0000.0000.000
40A40LEU0-0.049-0.01437.731-0.014-0.0140.0000.0000.0000.000
41A41CYS0-0.0370.00333.081-0.106-0.1060.0000.0000.0000.000
42A42PRO00.0280.02630.000-0.198-0.1980.0000.0000.0000.000
43A43LEU0-0.033-0.02130.037-0.068-0.0680.0000.0000.0000.000
44A44ASP-1-0.738-0.82428.25210.12110.1210.0000.0000.0000.000
45A45VAL00.0230.01522.328-0.096-0.0960.0000.0000.0000.000
46A46ILE0-0.056-0.02225.712-0.070-0.0700.0000.0000.0000.000
47A47GLN00.0160.02022.459-0.132-0.1320.0000.0000.0000.000
48A48LEU0-0.022-0.01724.709-0.571-0.5710.0000.0000.0000.000
49A49SER00.018-0.00726.2130.3480.3480.0000.0000.0000.000
50A50PRO00.0080.02928.5720.0540.0540.0000.0000.0000.000
51A51ASP-1-0.749-0.89523.43212.82412.8240.0000.0000.0000.000
52A52LEU0-0.034-0.01125.3390.2720.2720.0000.0000.0000.000
53A53HIS0-0.0130.00327.3440.0820.0820.0000.0000.0000.000
54A54LYS10.8980.94321.714-12.628-12.6280.0000.0000.0000.000
55A55GLY0-0.0040.01322.8170.4800.4800.0000.0000.0000.000
56A56THR0-0.040-0.00724.592-0.287-0.2870.0000.0000.0000.000
57A57ARG10.9060.95221.645-11.603-11.6030.0000.0000.0000.000
58A58LEU0-0.006-0.00316.690-0.507-0.5070.0000.0000.0000.000
59A59ARG10.8320.90317.576-13.457-13.4570.0000.0000.0000.000
60A60PHE00.0340.01112.993-0.060-0.0600.0000.0000.0000.000
61A61ALA00.0390.02014.924-0.034-0.0340.0000.0000.0000.000
62A62ALA00.0280.01610.796-0.126-0.1260.0000.0000.0000.000
63A63TYR00.020-0.01110.441-1.802-1.8020.0000.0000.0000.000
64A64ASN0-0.049-0.02610.372-0.794-0.7940.0000.0000.0000.000
65A65ASN0-0.068-0.03014.219-0.255-0.2550.0000.0000.0000.000
66A66THR00.0090.0029.979-0.680-0.6800.0000.0000.0000.000
67A67SER00.019-0.00412.648-0.261-0.2610.0000.0000.0000.000
68A68ILE0-0.0110.0086.928-0.626-0.6260.0000.0000.0000.000
69A69ILE0-0.0040.0128.8380.0900.0900.0000.0000.0000.000
70A70HIS00.0020.0033.8105.1065.4660.002-0.100-0.2620.000
71A71GLU-1-0.768-0.8562.78150.57152.6370.240-0.892-1.413-0.002
72A72ALA0-0.013-0.0034.0661.1221.315-0.001-0.054-0.1390.000
73A73VAL0-0.055-0.0215.337-1.594-1.5940.0000.0000.0000.000
74A74ASP-1-0.809-0.9047.94718.41118.4110.0000.0000.0000.000
75A75LEU0-0.022-0.02210.120-0.045-0.0450.0000.0000.0000.000
76A76ASN00.0060.00913.251-0.964-0.9640.0000.0000.0000.000
77A77VAL00.0630.02615.5340.6390.6390.0000.0000.0000.000
78A78LYS10.8820.94217.911-13.123-13.1230.0000.0000.0000.000
79A79PHE00.0420.01721.1650.2990.2990.0000.0000.0000.000
80A80SER0-0.071-0.06022.418-0.229-0.2290.0000.0000.0000.000
81A81THR0-0.064-0.04324.873-0.335-0.3350.0000.0000.0000.000
82A82GLU-1-0.911-0.93228.4399.3149.3140.0000.0000.0000.000
83A83THR00.009-0.01530.289-0.090-0.0900.0000.0000.0000.000
84A84SER00.0150.00133.075-0.027-0.0270.0000.0000.0000.000
85A86ASN0-0.068-0.02034.400-0.020-0.0200.0000.0000.0000.000
86A87GLU-1-0.826-0.92230.3069.3459.3450.0000.0000.0000.000
87A88PRO00.000-0.00126.2750.1370.1370.0000.0000.0000.000
88A89THR0-0.015-0.01725.3000.0590.0590.0000.0000.0000.000
89A90VAL0-0.038-0.02920.7790.3990.3990.0000.0000.0000.000
90A91TRP00.011-0.01018.012-0.222-0.2220.0000.0000.0000.000
91A92ARG10.9110.96021.427-10.257-10.2570.0000.0000.0000.000
92A93VAL00.0130.02621.029-0.358-0.3580.0000.0000.0000.000
93A94ASP-1-0.786-0.87923.7539.5669.5660.0000.0000.0000.000
94A95ASN0-0.071-0.05427.4100.4600.4600.0000.0000.0000.000
95A96TYR00.0170.01429.9180.0000.0000.0000.0000.0000.000
96A97ASP-1-0.742-0.86230.8668.5068.5060.0000.0000.0000.000
97A98PRO00.027-0.00333.4230.0700.0700.0000.0000.0000.000
98A99SER0-0.089-0.04135.884-0.139-0.1390.0000.0000.0000.000
99A100ARG10.8180.88733.437-8.551-8.5510.0000.0000.0000.000
100A101GLY0-0.0030.01932.9240.1610.1610.0000.0000.0000.000
101A102LYS10.8140.89828.380-9.890-9.8900.0000.0000.0000.000
102A103TRP00.0500.02525.500-0.320-0.3200.0000.0000.0000.000
103A104PHE0-0.003-0.00525.4960.3600.3600.0000.0000.0000.000
104A105ILE0-0.0030.00621.1570.0590.0590.0000.0000.0000.000
105A106THR0-0.024-0.02324.298-0.300-0.3000.0000.0000.0000.000
106A107THR0-0.034-0.02224.7550.4180.4180.0000.0000.0000.000
107A108GLY00.0980.03826.596-0.211-0.2110.0000.0000.0000.000
108A109GLY0-0.090-0.02824.173-0.182-0.1820.0000.0000.0000.000
109A110VAL0-0.005-0.01624.012-0.188-0.1880.0000.0000.0000.000
110A111GLU-1-0.837-0.92020.15813.60813.6080.0000.0000.0000.000
111A112GLY00.0150.00919.408-0.396-0.3960.0000.0000.0000.000
112A113ASN0-0.029-0.03520.453-0.038-0.0380.0000.0000.0000.000
113A114PRO00.0140.03617.245-0.196-0.1960.0000.0000.0000.000
114A115GLY00.0510.01819.289-0.178-0.1780.0000.0000.0000.000
115A116ALA00.001-0.01721.2490.0630.0630.0000.0000.0000.000
116A117GLN0-0.010-0.00524.0560.0030.0030.0000.0000.0000.000
117A118THR00.0150.00121.441-0.073-0.0730.0000.0000.0000.000
118A119LEU00.0000.01519.5980.4700.4700.0000.0000.0000.000
119A120LYS10.8590.91420.033-10.518-10.5180.0000.0000.0000.000
120A121ASN0-0.004-0.00820.512-0.236-0.2360.0000.0000.0000.000
121A122TRP0-0.073-0.00314.9180.6370.6370.0000.0000.0000.000
122A123PHE0-0.023-0.01414.638-0.563-0.5630.0000.0000.0000.000
123A124LYS10.8860.9559.647-21.284-21.2840.0000.0000.0000.000
124A125LEU0-0.010-0.0049.099-1.353-1.3530.0000.0000.0000.000
125A126GLU-1-0.845-0.9477.03829.18129.1810.0000.0000.0000.000
126A127ARG10.7580.8411.680-94.707-101.81517.694-6.006-4.5790.075
127A128VAL00.0000.0038.268-1.475-1.4750.0000.0000.0000.000
128A129GLY0-0.017-0.00611.018-1.766-1.7660.0000.0000.0000.000
129A130THR0-0.023-0.0178.5260.6070.6070.0000.0000.0000.000
130A131ASP-1-0.938-0.9617.24032.57732.5770.0000.0000.0000.000
131A132GLN0-0.042-0.0421.783-26.411-31.11113.066-4.609-3.7560.056
132A133GLY00.0150.0066.645-4.054-4.0540.0000.0000.0000.000
133A134THR0-0.049-0.0319.011-3.852-3.8520.0000.0000.0000.000
134A135TYR0-0.0130.0054.827-0.070-0.0700.0000.0000.0000.000
135A136GLU-1-0.832-0.91610.71118.17318.1730.0000.0000.0000.000
136A137ILE0-0.058-0.03611.6501.0821.0820.0000.0000.0000.000
137A138VAL00.0720.04112.403-1.150-1.1500.0000.0000.0000.000
138A139HIS0-0.072-0.03914.578-0.351-0.3510.0000.0000.0000.000
139A140CYS00.014-0.01314.3120.1460.1460.0000.0000.0000.000
140A141PRO00.0080.03314.4280.9930.9930.0000.0000.0000.000
141A142SER0-0.009-0.01412.8200.2460.2460.0000.0000.0000.000
142A143VAL0-0.0020.00714.923-0.104-0.1040.0000.0000.0000.000
143A144CYS0-0.083-0.02516.892-1.376-1.3760.0000.0000.0000.000
144A145LYS10.9260.94414.482-17.443-17.4430.0000.0000.0000.000
145A146SER00.0030.01519.8410.0200.0200.0000.0000.0000.000
146A148VAL00.0380.02422.8430.3210.3210.0000.0000.0000.000
147A149PHE0-0.041-0.03117.918-0.195-0.1950.0000.0000.0000.000
148A150LEU0-0.0100.00121.899-0.063-0.0630.0000.0000.0000.000
149A152ASN0-0.019-0.00818.640-0.393-0.3930.0000.0000.0000.000
150A153ASP-1-0.781-0.88315.89517.92417.9240.0000.0000.0000.000
151A154VAL0-0.053-0.03017.033-1.219-1.2190.0000.0000.0000.000
152A155GLY00.0250.00418.4650.5510.5510.0000.0000.0000.000
153A156VAL0-0.033-0.00921.194-0.361-0.3610.0000.0000.0000.000
154A157SER0-0.003-0.01124.074-0.235-0.2350.0000.0000.0000.000
155A158TYR0-0.010-0.03324.362-0.465-0.4650.0000.0000.0000.000
156A159ASP-1-0.782-0.86629.8209.6199.6190.0000.0000.0000.000
157A160TYR0-0.012-0.01630.986-0.416-0.4160.0000.0000.0000.000
158A161ARG10.9140.93831.166-8.301-8.3010.0000.0000.0000.000
159A162ARG10.8820.93926.573-11.007-11.0070.0000.0000.0000.000
160A163ARG10.8310.91226.374-9.159-9.1590.0000.0000.0000.000
161A164LEU00.0170.01320.1380.0650.0650.0000.0000.0000.000
162A165ALA0-0.014-0.01623.225-0.462-0.4620.0000.0000.0000.000
163A166LEU0-0.0160.01120.2060.4030.4030.0000.0000.0000.000
164A167THR0-0.017-0.01320.550-0.809-0.8090.0000.0000.0000.000
165A168ALA0-0.027-0.02321.7500.3780.3780.0000.0000.0000.000
166A169GLY00.0580.03920.8590.2240.2240.0000.0000.0000.000
167A170ASN0-0.040-0.02121.6580.3300.3300.0000.0000.0000.000
168A171GLU-1-0.963-0.97523.74510.67810.6780.0000.0000.0000.000
169A172ARG10.8850.93120.803-13.401-13.4010.0000.0000.0000.000
170A173VAL00.0680.04715.464-0.563-0.5630.0000.0000.0000.000
171A174PHE0-0.046-0.02618.019-0.317-0.3170.0000.0000.0000.000
172A175GLY00.0490.01914.9040.8740.8740.0000.0000.0000.000
173A176VAL0-0.041-0.03213.610-1.184-1.1840.0000.0000.0000.000
174A177VAL00.0560.03312.9431.5411.5410.0000.0000.0000.000
175A178ILE00.018-0.0029.583-1.557-1.5570.0000.0000.0000.000
176A179VAL00.0090.00913.5690.3180.3180.0000.0000.0000.000
177A180PRO00.0070.01015.309-0.667-0.6670.0000.0000.0000.000
178A181ALA0-0.016-0.00917.668-0.601-0.6010.0000.0000.0000.000
179A182ASN00.0100.02120.568-0.559-0.5590.0000.0000.0000.000