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: G6NM1

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 OptAll
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 -1946195.386075
FMO2-HF: Nuclear repulsion 1875759.908718
FMO2-HF: Total energy -70435.477356
FMO2-MP2: Total energy -70640.636389


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.
-33.263-41.64332.055-12.778-10.90.125
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 : -0.816 / q_NPA : -0.882
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].
3A3LEU0-0.023-0.0133.1512.6504.7370.099-1.088-1.0990.000
4A4LEU0-0.013-0.0095.222-1.994-1.9940.0000.0000.0000.000
5A5ASP-1-0.727-0.8897.47019.43019.4300.0000.0000.0000.000
6A6ILE0-0.048-0.02311.1800.9060.9060.0000.0000.0000.000
7A7ASN0-0.116-0.07213.656-1.030-1.0300.0000.0000.0000.000
8A8GLY00.0160.02110.476-0.475-0.4750.0000.0000.0000.000
9A9ASN0-0.091-0.04210.1931.4031.4030.0000.0000.0000.000
10A10VAL00.0150.0046.8271.0071.0070.0000.0000.0000.000
11A11VAL00.0050.0098.430-2.762-2.7620.0000.0000.0000.000
12A12GLU-1-0.807-0.89610.38519.09119.0910.0000.0000.0000.000
13A13ALA00.0240.00413.201-0.816-0.8160.0000.0000.0000.000
14A14SER0-0.042-0.01515.201-0.898-0.8980.0000.0000.0000.000
15A15ARG10.8200.88615.855-17.914-17.9140.0000.0000.0000.000
16A16ASP-1-0.795-0.84417.52113.54413.5440.0000.0000.0000.000
17A17TYR00.0300.01313.9520.3360.3360.0000.0000.0000.000
18A18TYR00.0110.01117.586-0.766-0.7660.0000.0000.0000.000
19A19LEU00.0070.02013.4830.7290.7290.0000.0000.0000.000
20A20VAL0-0.009-0.02316.777-1.151-1.1510.0000.0000.0000.000
21A21SER0-0.020-0.01717.3290.9450.9450.0000.0000.0000.000
22A22VAL0-0.0140.00315.476-0.383-0.3830.0000.0000.0000.000
23A23ILE0-0.0080.00215.805-0.566-0.5660.0000.0000.0000.000
24A24GLY00.0790.06119.1600.0610.0610.0000.0000.0000.000
25A25GLY0-0.022-0.01421.104-0.655-0.6550.0000.0000.0000.000
26A26ALA00.004-0.00122.745-0.401-0.4010.0000.0000.0000.000
27A27GLY00.0330.01825.242-0.434-0.4340.0000.0000.0000.000
28A28GLY0-0.013-0.00725.108-0.281-0.2810.0000.0000.0000.000
29A29GLY00.0270.03123.1800.3840.3840.0000.0000.0000.000
30A30GLY00.0000.01421.1170.6820.6820.0000.0000.0000.000
31A31LEU0-0.036-0.00918.570-0.539-0.5390.0000.0000.0000.000
32A32THR0-0.023-0.04122.609-0.286-0.2860.0000.0000.0000.000
33A33LEU00.0010.01625.6410.1900.1900.0000.0000.0000.000
34A34TYR0-0.013-0.01228.258-0.365-0.3650.0000.0000.0000.000
35A35ARG10.8320.88831.377-7.853-7.8530.0000.0000.0000.000
36A36GLY00.0890.05632.9160.1700.1700.0000.0000.0000.000
37A37ARG10.6510.77130.409-9.931-9.9310.0000.0000.0000.000
38A38ASN0-0.0370.00835.148-0.352-0.3520.0000.0000.0000.000
39A39GLU-1-0.806-0.89337.7997.3207.3200.0000.0000.0000.000
40A40LEU0-0.0270.00237.720-0.025-0.0250.0000.0000.0000.000
41A41CYS0-0.0220.00533.488-0.085-0.0850.0000.0000.0000.000
42A42PRO00.0290.02830.028-0.189-0.1890.0000.0000.0000.000
43A43LEU0-0.043-0.01730.013-0.119-0.1190.0000.0000.0000.000
44A44ASP-1-0.714-0.80628.25910.18410.1840.0000.0000.0000.000
45A45VAL00.0110.00522.179-0.121-0.1210.0000.0000.0000.000
46A46ILE0-0.044-0.01625.613-0.101-0.1010.0000.0000.0000.000
47A47GLN0-0.0030.00022.183-0.116-0.1160.0000.0000.0000.000
48A48LEU0-0.028-0.01824.703-0.542-0.5420.0000.0000.0000.000
49A49SER00.025-0.00526.1720.3350.3350.0000.0000.0000.000
50A50PRO0-0.0170.01728.5050.0330.0330.0000.0000.0000.000
51A51ASP-1-0.741-0.89423.10612.96812.9680.0000.0000.0000.000
52A52LEU0-0.018-0.00825.0410.2420.2420.0000.0000.0000.000
53A53HIS00.0000.00927.2580.1470.1470.0000.0000.0000.000
54A54LYS10.8650.91621.870-12.687-12.6870.0000.0000.0000.000
55A55GLY00.0060.02322.5800.4770.4770.0000.0000.0000.000
56A56THR0-0.042-0.00524.620-0.251-0.2510.0000.0000.0000.000
57A57ARG10.8950.95021.448-11.759-11.7590.0000.0000.0000.000
58A58LEU0-0.004-0.00216.551-0.568-0.5680.0000.0000.0000.000
59A59ARG10.8010.88317.426-13.607-13.6070.0000.0000.0000.000
60A60PHE00.0380.00813.633-0.084-0.0840.0000.0000.0000.000
61A61ALA00.0280.01515.418-0.088-0.0880.0000.0000.0000.000
62A62ALA00.0390.02611.047-0.185-0.1850.0000.0000.0000.000
63A63TYR00.002-0.01510.618-1.616-1.6160.0000.0000.0000.000
64A64ASN0-0.028-0.01510.052-0.996-0.9960.0000.0000.0000.000
65A65ASN0-0.056-0.03214.227-0.335-0.3350.0000.0000.0000.000
66A66THR0-0.012-0.00210.252-0.480-0.4800.0000.0000.0000.000
67A67SER00.013-0.00812.8470.1120.1120.0000.0000.0000.000
68A68ILE0-0.0240.0077.455-0.664-0.6640.0000.0000.0000.000
69A69ILE0-0.0160.0009.006-0.169-0.1690.0000.0000.0000.000
70A70HIS00.0110.0024.2365.4635.649-0.001-0.048-0.1380.000
71A71GLU-1-0.741-0.8462.82650.70752.4260.239-0.690-1.268-0.002
72A72ALA0-0.014-0.0054.4740.5310.644-0.001-0.014-0.0990.000
73A73VAL0-0.058-0.0215.451-2.422-2.4220.0000.0000.0000.000
74A74ASP-1-0.840-0.9188.03518.14518.1450.0000.0000.0000.000
75A75LEU0-0.009-0.02010.299-0.012-0.0120.0000.0000.0000.000
76A76ASN00.0070.00913.453-0.807-0.8070.0000.0000.0000.000
77A77VAL00.0480.01815.5630.7950.7950.0000.0000.0000.000
78A78LYS10.8610.92418.109-13.355-13.3550.0000.0000.0000.000
79A79PHE00.0390.01820.8770.3440.3440.0000.0000.0000.000
80A80SER0-0.075-0.04922.210-0.227-0.2270.0000.0000.0000.000
81A81THR0-0.067-0.04424.510-0.336-0.3360.0000.0000.0000.000
82A82GLU-1-0.895-0.92728.1469.3329.3320.0000.0000.0000.000
83A83THR0-0.007-0.02530.140-0.041-0.0410.0000.0000.0000.000
84A84SER00.0290.00932.888-0.042-0.0420.0000.0000.0000.000
85A86ASN0-0.058-0.01934.909-0.113-0.1130.0000.0000.0000.000
86A87GLU-1-0.828-0.91830.6869.3489.3480.0000.0000.0000.000
87A88PRO00.016-0.00326.7800.1280.1280.0000.0000.0000.000
88A89THR0-0.007-0.02025.2610.0730.0730.0000.0000.0000.000
89A90VAL0-0.034-0.02121.3280.4370.4370.0000.0000.0000.000
90A91TRP0-0.004-0.01217.860-0.256-0.2560.0000.0000.0000.000
91A92ARG10.8750.92821.853-10.153-10.1530.0000.0000.0000.000
92A93VAL00.0150.02021.376-0.272-0.2720.0000.0000.0000.000
93A94ASP-1-0.778-0.87124.0299.4719.4710.0000.0000.0000.000
94A95ASN0-0.049-0.03327.4460.5130.5130.0000.0000.0000.000
95A96TYR00.0120.01430.0510.0450.0450.0000.0000.0000.000
96A97ASP-1-0.728-0.84931.0668.5558.5550.0000.0000.0000.000
97A98PRO00.018-0.00433.3150.0310.0310.0000.0000.0000.000
98A99SER0-0.083-0.04335.882-0.147-0.1470.0000.0000.0000.000
99A100ARG10.8260.89033.273-8.570-8.5700.0000.0000.0000.000
100A101GLY00.0170.02632.9250.1400.1400.0000.0000.0000.000
101A102LYS10.8060.88927.964-10.066-10.0660.0000.0000.0000.000
102A103TRP00.0530.02025.426-0.326-0.3260.0000.0000.0000.000
103A104PHE00.0040.00225.2190.4120.4120.0000.0000.0000.000
104A105ILE00.0040.01621.0440.0790.0790.0000.0000.0000.000
105A106THR0-0.015-0.02324.236-0.315-0.3150.0000.0000.0000.000
106A107THR0-0.030-0.01925.1660.3300.3300.0000.0000.0000.000
107A108GLY00.0740.02927.053-0.179-0.1790.0000.0000.0000.000
108A109GLY0-0.058-0.00624.456-0.174-0.1740.0000.0000.0000.000
109A110VAL0-0.027-0.03724.335-0.252-0.2520.0000.0000.0000.000
110A111GLU-1-0.811-0.89520.40313.41613.4160.0000.0000.0000.000
111A112GLY00.0280.01919.622-0.379-0.3790.0000.0000.0000.000
112A113ASN0-0.030-0.03420.657-0.057-0.0570.0000.0000.0000.000
113A114PRO00.0060.03217.635-0.184-0.1840.0000.0000.0000.000
114A115GLY00.0600.02319.621-0.090-0.0900.0000.0000.0000.000
115A116ALA00.004-0.01821.5990.0240.0240.0000.0000.0000.000
116A117GLN0-0.016-0.00424.3060.0690.0690.0000.0000.0000.000
117A118THR00.0170.00121.742-0.072-0.0720.0000.0000.0000.000
118A119LEU0-0.0110.00519.4700.3860.3860.0000.0000.0000.000
119A120LYS10.8530.90120.239-10.442-10.4420.0000.0000.0000.000
120A121ASN00.0040.00020.984-0.237-0.2370.0000.0000.0000.000
121A122TRP0-0.078-0.00715.1920.6680.6680.0000.0000.0000.000
122A123PHE0-0.022-0.01315.088-0.603-0.6030.0000.0000.0000.000
123A124LYS10.8640.95110.016-21.194-21.1940.0000.0000.0000.000
124A125LEU00.0020.0009.358-1.490-1.4900.0000.0000.0000.000
125A126GLU-1-0.852-0.9497.07027.98627.9860.0000.0000.0000.000
126A127ARG10.7680.8381.689-92.559-99.73017.711-5.981-4.5600.070
127A128VAL0-0.021-0.0028.388-1.152-1.1520.0000.0000.0000.000
128A129GLY0-0.023-0.02210.467-2.441-2.4410.0000.0000.0000.000
129A130THR0-0.041-0.0358.5750.8090.8090.0000.0000.0000.000
130A131ASP-1-0.893-0.9126.72236.10236.1020.0000.0000.0000.000
131A132GLN0-0.036-0.0391.733-27.572-32.95914.009-4.956-3.6650.057
132A133GLY00.0020.0006.269-4.646-4.6460.0000.0000.0000.000
133A134THR0-0.052-0.0358.795-4.181-4.1810.0000.0000.0000.000
134A135TYR0-0.0050.0104.506-0.194-0.121-0.001-0.001-0.0710.000
135A136GLU-1-0.852-0.92210.58418.13818.1380.0000.0000.0000.000
136A137ILE0-0.040-0.03611.7411.1391.1390.0000.0000.0000.000
137A138VAL00.0380.01812.316-1.140-1.1400.0000.0000.0000.000
138A139HIS0-0.061-0.04814.530-0.305-0.3050.0000.0000.0000.000
139A140CYS00.0190.00014.421-0.018-0.0180.0000.0000.0000.000
140A141PRO00.0130.03614.2601.1121.1120.0000.0000.0000.000
141A142SER0-0.017-0.02412.9580.3260.3260.0000.0000.0000.000
142A143VAL00.0140.01915.065-0.110-0.1100.0000.0000.0000.000
143A144CYS0-0.064-0.01117.068-1.359-1.3590.0000.0000.0000.000
144A145LYS10.9080.93814.246-17.419-17.4190.0000.0000.0000.000
145A146SER00.0070.01219.5540.0100.0100.0000.0000.0000.000
146A148VAL00.0300.01723.0980.3030.3030.0000.0000.0000.000
147A149PHE0-0.053-0.03217.987-0.171-0.1710.0000.0000.0000.000
148A150LEU0-0.0060.00421.987-0.133-0.1330.0000.0000.0000.000
149A152ASN0-0.024-0.02218.420-0.210-0.2100.0000.0000.0000.000
150A153ASP-1-0.745-0.86816.05616.23116.2310.0000.0000.0000.000
151A154VAL0-0.032-0.01517.042-1.208-1.2080.0000.0000.0000.000
152A155GLY00.0250.00318.5500.5530.5530.0000.0000.0000.000
153A156VAL0-0.036-0.00821.312-0.415-0.4150.0000.0000.0000.000
154A157SER0-0.007-0.01924.180-0.262-0.2620.0000.0000.0000.000
155A158TYR0-0.014-0.03924.668-0.447-0.4470.0000.0000.0000.000
156A159ASP-1-0.755-0.84429.8429.7339.7330.0000.0000.0000.000
157A160TYR0-0.028-0.02130.870-0.417-0.4170.0000.0000.0000.000
158A161ARG10.9160.95131.468-8.390-8.3900.0000.0000.0000.000
159A162ARG10.8490.91426.372-11.098-11.0980.0000.0000.0000.000
160A163ARG10.8320.90626.435-9.190-9.1900.0000.0000.0000.000
161A164LEU00.0120.01619.9930.1110.1110.0000.0000.0000.000
162A165ALA0-0.016-0.01523.207-0.470-0.4700.0000.0000.0000.000
163A166LEU0-0.0160.00620.1580.4750.4750.0000.0000.0000.000
164A167THR0-0.050-0.02220.461-0.826-0.8260.0000.0000.0000.000
165A168ALA00.004-0.00821.9760.1810.1810.0000.0000.0000.000
166A169GLY00.0760.04620.234-0.242-0.2420.0000.0000.0000.000
167A170ASN0-0.079-0.03620.9820.1280.1280.0000.0000.0000.000
168A171GLU-1-0.951-0.96823.03610.79210.7920.0000.0000.0000.000
169A172ARG10.8710.92520.811-13.374-13.3740.0000.0000.0000.000
170A173VAL00.0770.04715.103-0.527-0.5270.0000.0000.0000.000
171A174PHE0-0.034-0.01918.195-0.291-0.2910.0000.0000.0000.000
172A175GLY00.0440.02714.7980.8260.8260.0000.0000.0000.000
173A176VAL0-0.029-0.02613.573-1.342-1.3420.0000.0000.0000.000
174A177VAL00.0500.03012.7501.6041.6040.0000.0000.0000.000
175A178ILE00.0230.0029.394-1.561-1.5610.0000.0000.0000.000
176A179VAL00.0220.01213.3910.4090.4090.0000.0000.0000.000
177A180PRO00.001-0.00115.236-0.692-0.6920.0000.0000.0000.000
178A181ALA0-0.023-0.01717.564-0.626-0.6260.0000.0000.0000.000
179A182ASN00.0130.02220.478-0.579-0.5790.0000.0000.0000.000