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: V5R41

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945376.430505
FMO2-HF: Nuclear repulsion 1874942.022751
FMO2-HF: Total energy -70434.407753
FMO2-MP2: Total energy -70639.542701


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.
10.07617.6256.814-6.531-7.8320.046
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 : -0.892 / q_NPA : -0.938
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].
3A3LEU0-0.011-0.0083.2630.1782.5890.076-1.242-1.2440.004
4A4LEU0-0.017-0.0175.005-1.594-1.5940.0000.0000.0000.000
5A5ASP-1-0.803-0.9197.43819.77119.7710.0000.0000.0000.000
6A6ILE0-0.058-0.04611.2010.5610.5610.0000.0000.0000.000
7A7ASN0-0.090-0.04913.419-1.011-1.0110.0000.0000.0000.000
8A8GLY0-0.0060.0139.835-0.288-0.2880.0000.0000.0000.000
9A9ASN0-0.040-0.01210.1421.4241.4240.0000.0000.0000.000
10A10VAL00.0100.0016.9060.6510.6510.0000.0000.0000.000
11A11VAL0-0.0020.0068.373-2.628-2.6280.0000.0000.0000.000
12A12GLU-1-0.931-0.98710.10919.52819.5280.0000.0000.0000.000
13A13ALA00.0250.00212.869-0.797-0.7970.0000.0000.0000.000
14A14SER0-0.067-0.03014.808-0.715-0.7150.0000.0000.0000.000
15A15ARG10.8540.92115.965-17.125-17.1250.0000.0000.0000.000
16A16ASP-1-0.828-0.86417.61713.45713.4570.0000.0000.0000.000
17A17TYR00.0450.02413.6280.2390.2390.0000.0000.0000.000
18A18TYR0-0.010-0.00217.975-0.767-0.7670.0000.0000.0000.000
19A19LEU00.0060.01013.8280.7850.7850.0000.0000.0000.000
20A20VAL00.002-0.01217.241-0.956-0.9560.0000.0000.0000.000
21A21SER0-0.004-0.01617.6310.8860.8860.0000.0000.0000.000
22A22VAL0-0.0040.01116.116-0.464-0.4640.0000.0000.0000.000
23A23ILE0-0.0120.00215.951-0.500-0.5000.0000.0000.0000.000
24A24GLY00.0270.02219.2020.0720.0720.0000.0000.0000.000
25A25GLY0-0.0020.00221.605-0.216-0.2160.0000.0000.0000.000
26A26ALA0-0.003-0.01322.919-0.429-0.4290.0000.0000.0000.000
27A27GLY00.0300.00525.235-0.405-0.4050.0000.0000.0000.000
28A28GLY0-0.050-0.01624.818-0.295-0.2950.0000.0000.0000.000
29A29GLY00.0290.02223.9610.2340.2340.0000.0000.0000.000
30A30GLY0-0.012-0.00121.3840.6020.6020.0000.0000.0000.000
31A31LEU0-0.021-0.00718.471-0.435-0.4350.0000.0000.0000.000
32A32THR0-0.018-0.03522.757-0.197-0.1970.0000.0000.0000.000
33A33LEU00.0020.02025.7260.1460.1460.0000.0000.0000.000
34A34TYR0-0.020-0.01928.108-0.389-0.3890.0000.0000.0000.000
35A35ARG11.0131.01630.952-8.014-8.0140.0000.0000.0000.000
36A36GLY00.1270.06932.8890.1970.1970.0000.0000.0000.000
37A37ARG10.6440.80030.457-9.887-9.8870.0000.0000.0000.000
38A38ASN0-0.002-0.00335.469-0.317-0.3170.0000.0000.0000.000
39A39GLU-1-0.891-0.95537.9277.3017.3010.0000.0000.0000.000
40A40LEU0-0.088-0.03737.724-0.016-0.0160.0000.0000.0000.000
41A41CYS0-0.056-0.00633.065-0.104-0.1040.0000.0000.0000.000
42A42PRO00.0490.03830.025-0.205-0.2050.0000.0000.0000.000
43A43LEU0-0.039-0.02729.945-0.071-0.0710.0000.0000.0000.000
44A44ASP-1-0.738-0.84828.20210.18710.1870.0000.0000.0000.000
45A45VAL00.0190.01222.264-0.104-0.1040.0000.0000.0000.000
46A46ILE0-0.066-0.02425.649-0.077-0.0770.0000.0000.0000.000
47A47GLN00.0510.04022.522-0.161-0.1610.0000.0000.0000.000
48A48LEU0-0.039-0.02524.611-0.555-0.5550.0000.0000.0000.000
49A49SER00.011-0.01126.0930.3270.3270.0000.0000.0000.000
50A50PRO00.0190.03228.5040.0370.0370.0000.0000.0000.000
51A51ASP-1-0.826-0.92023.73412.49512.4950.0000.0000.0000.000
52A52LEU0-0.042-0.02825.5350.2400.2400.0000.0000.0000.000
53A53HIS0-0.0200.00127.5400.0940.0940.0000.0000.0000.000
54A54LYS10.9840.98822.180-12.175-12.1750.0000.0000.0000.000
55A55GLY0-0.0020.01222.9560.4740.4740.0000.0000.0000.000
56A56THR0-0.040-0.00124.553-0.294-0.2940.0000.0000.0000.000
57A57ARG10.9260.96721.811-11.377-11.3770.0000.0000.0000.000
58A58LEU00.000-0.00116.842-0.491-0.4910.0000.0000.0000.000
59A59ARG10.9570.98817.632-13.429-13.4290.0000.0000.0000.000
60A60PHE00.0170.00513.014-0.067-0.0670.0000.0000.0000.000
61A61ALA00.0510.02814.9480.0130.0130.0000.0000.0000.000
62A62ALA00.0280.01410.817-0.090-0.0900.0000.0000.0000.000
63A63TYR00.017-0.01110.640-1.836-1.8360.0000.0000.0000.000
64A64ASN0-0.049-0.02510.487-0.858-0.8580.0000.0000.0000.000
65A65ASN0-0.064-0.02614.254-0.117-0.1170.0000.0000.0000.000
66A66THR00.0110.00310.007-0.658-0.6580.0000.0000.0000.000
67A67SER00.001-0.01112.681-0.582-0.5820.0000.0000.0000.000
68A68ILE00.0080.0206.971-0.759-0.7590.0000.0000.0000.000
69A69ILE0-0.0100.0038.8380.3060.3060.0000.0000.0000.000
70A70HIS0-0.007-0.0023.8005.7406.1940.008-0.145-0.3170.000
71A71GLU-1-0.784-0.8832.82847.85750.2870.330-1.106-1.654-0.005
72A72ALA0-0.001-0.0034.0771.7941.990-0.001-0.049-0.1470.000
73A73VAL0-0.053-0.0185.400-1.621-1.6210.0000.0000.0000.000
74A74ASP-1-0.795-0.8927.96918.53618.5360.0000.0000.0000.000
75A75LEU0-0.017-0.01710.107-0.031-0.0310.0000.0000.0000.000
76A76ASN00.0200.01813.273-0.982-0.9820.0000.0000.0000.000
77A77VAL00.0680.02915.5780.6500.6500.0000.0000.0000.000
78A78LYS10.9690.99517.927-12.744-12.7440.0000.0000.0000.000
79A79PHE00.0370.02021.0670.2730.2730.0000.0000.0000.000
80A80SER0-0.112-0.11222.509-0.247-0.2470.0000.0000.0000.000
81A81THR0-0.068-0.04624.877-0.349-0.3490.0000.0000.0000.000
82A82GLU-1-0.915-0.93628.3819.2859.2850.0000.0000.0000.000
83A83THR00.001-0.01330.247-0.087-0.0870.0000.0000.0000.000
84A84SER00.0180.00132.987-0.019-0.0190.0000.0000.0000.000
85A86ASN0-0.052-0.01134.4150.0600.0600.0000.0000.0000.000
86A87GLU-1-0.849-0.93330.2699.3359.3350.0000.0000.0000.000
87A88PRO0-0.006-0.00226.2090.1380.1380.0000.0000.0000.000
88A89THR0-0.011-0.01525.4350.0870.0870.0000.0000.0000.000
89A90VAL0-0.030-0.02320.8340.3770.3770.0000.0000.0000.000
90A91TRP00.000-0.01317.727-0.230-0.2300.0000.0000.0000.000
91A92ARG10.9310.96621.443-10.315-10.3150.0000.0000.0000.000
92A93VAL0-0.0070.01421.067-0.368-0.3680.0000.0000.0000.000
93A94ASP-1-0.819-0.89223.7639.6779.6770.0000.0000.0000.000
94A95ASN0-0.072-0.05527.4190.4490.4490.0000.0000.0000.000
95A96TYR0-0.0030.00429.7970.0060.0060.0000.0000.0000.000
96A97ASP-1-0.736-0.86030.8718.5248.5240.0000.0000.0000.000
97A98PRO00.026-0.00933.4390.0770.0770.0000.0000.0000.000
98A99SER0-0.095-0.03635.926-0.140-0.1400.0000.0000.0000.000
99A100ARG10.8230.89933.518-8.582-8.5820.0000.0000.0000.000
100A101GLY0-0.0140.01632.9590.1560.1560.0000.0000.0000.000
101A102LYS10.9180.95528.177-10.131-10.1310.0000.0000.0000.000
102A103TRP00.0560.03025.497-0.302-0.3020.0000.0000.0000.000
103A104PHE0-0.014-0.01425.5160.3350.3350.0000.0000.0000.000
104A105ILE00.0030.00921.2100.0690.0690.0000.0000.0000.000
105A106THR0-0.001-0.00624.287-0.302-0.3020.0000.0000.0000.000
106A107THR0-0.049-0.04124.7670.4330.4330.0000.0000.0000.000
107A108GLY00.0790.03126.610-0.206-0.2060.0000.0000.0000.000
108A109GLY0-0.084-0.02424.194-0.173-0.1730.0000.0000.0000.000
109A110VAL0-0.011-0.02123.970-0.214-0.2140.0000.0000.0000.000
110A111GLU-1-0.929-0.97220.02314.04014.0400.0000.0000.0000.000
111A112GLY0-0.0030.00019.436-0.415-0.4150.0000.0000.0000.000
112A113ASN0-0.021-0.02620.4820.0060.0060.0000.0000.0000.000
113A114PRO00.0140.03617.274-0.196-0.1960.0000.0000.0000.000
114A115GLY00.0470.01619.317-0.170-0.1700.0000.0000.0000.000
115A116ALA0-0.001-0.01821.2750.0520.0520.0000.0000.0000.000
116A117GLN0-0.022-0.01524.079-0.077-0.0770.0000.0000.0000.000
117A118THR00.0230.00121.541-0.085-0.0850.0000.0000.0000.000
118A119LEU0-0.0020.01719.5950.4670.4670.0000.0000.0000.000
119A120LYS10.9140.94720.050-10.761-10.7610.0000.0000.0000.000
120A121ASN00.018-0.00120.531-0.211-0.2110.0000.0000.0000.000
121A122TRP0-0.075-0.00315.0040.6060.6060.0000.0000.0000.000
122A123PHE0-0.026-0.01514.650-0.600-0.6000.0000.0000.0000.000
123A124LYS10.8890.9549.640-22.074-22.0740.0000.0000.0000.000
124A125LEU0-0.013-0.0049.009-1.492-1.4920.0000.0000.0000.000
125A126GLU-1-0.830-0.9317.05629.43829.4380.0000.0000.0000.000
126A127ARG10.7650.8751.957-84.507-83.7846.073-3.483-3.3130.052
127A128VAL00.0020.0018.230-1.291-1.2910.0000.0000.0000.000
128A129GLY0-0.006-0.00311.170-1.654-1.6540.0000.0000.0000.000
129A130THR00.004-0.0118.5650.6560.6560.0000.0000.0000.000
130A131ASP-1-0.940-0.9477.39431.06831.0680.0000.0000.0000.000
131A132GLN0-0.008-0.0202.8276.5447.8790.328-0.506-1.157-0.005
132A133GLY00.0180.0096.834-3.420-3.4200.0000.0000.0000.000
133A134THR0-0.047-0.0289.149-3.450-3.4500.0000.0000.0000.000
134A135TYR00.0020.0115.1490.1150.1150.0000.0000.0000.000
135A136GLU-1-0.864-0.92310.62118.75218.7520.0000.0000.0000.000
136A137ILE0-0.052-0.03111.6231.1061.1060.0000.0000.0000.000
137A138VAL00.0760.04412.213-1.253-1.2530.0000.0000.0000.000
138A139HIS0-0.084-0.05014.588-0.379-0.3790.0000.0000.0000.000
139A140CYS00.019-0.01014.2740.1040.1040.0000.0000.0000.000
140A141PRO00.0030.03014.4371.0461.0460.0000.0000.0000.000
141A142SER0-0.023-0.02812.9160.3730.3730.0000.0000.0000.000
142A143VAL0-0.012-0.00614.941-0.106-0.1060.0000.0000.0000.000
143A144CYS0-0.069-0.02316.916-1.428-1.4280.0000.0000.0000.000
144A145LYS10.9380.95814.475-18.094-18.0940.0000.0000.0000.000
145A146SER0-0.0110.01019.859-0.010-0.0100.0000.0000.0000.000
146A148VAL00.0410.02622.8570.3360.3360.0000.0000.0000.000
147A149PHE0-0.044-0.03717.968-0.210-0.2100.0000.0000.0000.000
148A150LEU0-0.015-0.00321.904-0.087-0.0870.0000.0000.0000.000
149A152ASN0-0.026-0.01318.636-0.463-0.4630.0000.0000.0000.000
150A153ASP-1-0.759-0.86715.57218.55318.5530.0000.0000.0000.000
151A154VAL0-0.053-0.03317.046-1.241-1.2410.0000.0000.0000.000
152A155GLY00.013-0.00318.4510.5100.5100.0000.0000.0000.000
153A156VAL0-0.027-0.00521.173-0.341-0.3410.0000.0000.0000.000
154A157SER0-0.008-0.00424.028-0.312-0.3120.0000.0000.0000.000
155A158TYR0-0.008-0.02924.515-0.382-0.3820.0000.0000.0000.000
156A159ASP-1-0.859-0.92429.7699.5029.5020.0000.0000.0000.000
157A160TYR0-0.025-0.02530.960-0.428-0.4280.0000.0000.0000.000
158A161ARG10.9040.93431.117-8.277-8.2770.0000.0000.0000.000
159A162ARG10.8770.93826.404-10.879-10.8790.0000.0000.0000.000
160A163ARG10.8210.91826.306-9.155-9.1550.0000.0000.0000.000
161A164LEU00.0320.01720.1630.0480.0480.0000.0000.0000.000
162A165ALA0-0.011-0.01723.203-0.458-0.4580.0000.0000.0000.000
163A166LEU0-0.0120.01620.2620.3750.3750.0000.0000.0000.000
164A167THR0-0.029-0.02020.563-0.848-0.8480.0000.0000.0000.000
165A168ALA0-0.024-0.02321.8010.3990.3990.0000.0000.0000.000
166A169GLY00.0420.03020.9110.2420.2420.0000.0000.0000.000
167A170ASN0-0.028-0.01621.7010.3350.3350.0000.0000.0000.000
168A171GLU-1-0.964-0.97323.73310.58210.5820.0000.0000.0000.000
169A172ARG10.8880.93320.802-13.312-13.3120.0000.0000.0000.000
170A173VAL00.0730.04715.562-0.515-0.5150.0000.0000.0000.000
171A174PHE0-0.030-0.02118.317-0.325-0.3250.0000.0000.0000.000
172A175GLY00.0470.01814.8260.8660.8660.0000.0000.0000.000
173A176VAL0-0.039-0.03013.550-1.167-1.1670.0000.0000.0000.000
174A177VAL00.0550.03313.1101.4261.4260.0000.0000.0000.000
175A178ILE00.0210.0039.917-1.416-1.4160.0000.0000.0000.000
176A179VAL00.0190.01113.7840.2490.2490.0000.0000.0000.000
177A180PRO0-0.003-0.00415.523-0.573-0.5730.0000.0000.0000.000
178A181ALA0-0.0030.00317.830-0.559-0.5590.0000.0000.0000.000
179A182ASN00.0310.03520.692-0.664-0.6640.0000.0000.0000.000