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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: 63MLZ

Calculation Name: 7CZ4-A-Xray89

Preferred Name:

Target Type:

Ligand Name: adenosine-5-diphosphoribose

ligand 3-letter code: APR

PDB ID: 7CZ4

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-03-24

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 191
LigandCharge APR=-2
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1857297.573136
FMO2-HF: Nuclear repulsion 1789059.064205
FMO2-HF: Total energy -68238.508931
FMO2-MP2: Total energy -68435.839648


3D Structure
Snapshot
 
Ligand structure

APR

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.
-430.358-398.051135.324-60.117-107.510-0.251


Interactive mode: IFIE and PIEDA for fragment #191(A:201:APR )


Summations of interaction energy for fragment #191(A:201:APR )
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.
-430.358-398.051135.324-60.117-107.510.251
Interaction energy analysis for fragmet #191(A:201:APR )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -2 / q_Mulliken : -1.748 / q_NPA : -1.883
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].
1A4ASN 00.028-0.00515.4781.1721.1720.0000.0000.0000.000
2A5SER 0-0.020-0.00515.798-1.070-1.0700.0000.0000.0000.000
3A6PHE 00.0110.01310.1850.1060.1060.0000.0000.0000.000
4A7SER 00.0330.00512.721-0.929-0.9290.0000.0000.0000.000
5A8GLY 00.008-0.00512.1971.3331.3330.0000.0000.0000.000
6A9TYR 0-0.046-0.0337.7091.2431.2430.0000.0000.0000.000
7A10LEU 00.0210.02411.973-2.202-2.2020.0000.0000.0000.000
8A11LYS 10.8650.95013.195-23.527-23.5270.0000.0000.0000.000
9A12LEU 0-0.0250.00311.869-0.892-0.8920.0000.0000.0000.000
10A13THR 00.006-0.03016.378-1.189-1.1890.0000.0000.0000.000
11A14ASP -1-0.827-0.92618.35723.98423.9840.0000.0000.0000.000
12A15ASN 0-0.057-0.02616.541-1.182-1.1820.0000.0000.0000.000
13A16VAL 00.0270.02512.0421.6821.6820.0000.0000.0000.000
14A17TYR 0-0.006-0.01012.125-2.138-2.1380.0000.0000.0000.000
15A18ILE 00.0020.0067.8433.0783.0780.0000.0000.0000.000
16A19LYS 10.8240.8977.316-38.571-38.5710.0000.0000.0000.000
17A20ASN 0-0.057-0.0145.8650.7580.7580.0000.0000.0000.000
18A21ALA 0-0.005-0.0134.511-3.795-3.607-0.001-0.023-0.1640.000
19A22ASP -1-0.757-0.8801.77943.81342.53011.129-4.840-5.006-0.045
20A23ILE 00.019-0.0042.015-15.954-17.10111.917-4.272-6.4970.031
21A24VAL 00.001-0.0013.093-5.809-4.7740.062-0.262-0.8350.003
22A25GLU -1-0.879-0.9265.10032.51132.5110.0000.0000.0000.000
23A26GLU -1-0.797-0.8626.26633.09933.0990.0000.0000.0000.000
24A27ALA 00.0180.0127.592-2.838-2.8380.0000.0000.0000.000
25A28LYS 10.8730.9228.581-38.088-38.0880.0000.0000.0000.000
26A29LYS 10.8250.91410.560-34.720-34.7200.0000.0000.0000.000
27A30VAL 0-0.057-0.03511.263-2.107-2.1070.0000.0000.0000.000
28A31LYS 10.8770.95113.320-27.851-27.8510.0000.0000.0000.000
29A32PRO 0-0.0180.00711.127-1.340-1.3400.0000.0000.0000.000
30A33THR 00.0080.00314.400-0.521-0.5210.0000.0000.0000.000
31A34VAL 00.0210.00413.781-0.195-0.1950.0000.0000.0000.000
32A35VAL 0-0.0070.0038.6440.4800.4800.0000.0000.0000.000
33A36VAL 0-0.014-0.0147.784-0.604-0.6040.0000.0000.0000.000
34A37ASN 0-0.011-0.0274.20910.87811.052-0.001-0.010-0.1620.000
35A38ALA 0-0.0020.0122.671-8.397-5.8871.124-1.463-2.1710.017
36A39ALA 00.0220.0102.201-4.516-1.5213.600-2.619-3.976-0.029
37A40ASN 00.008-0.0302.055-18.554-17.7139.159-3.636-6.3640.025
38A41VAL 00.0420.0123.616-4.112-3.8790.020-0.009-0.2440.000
39A42TYR 0-0.018-0.0126.995-4.023-4.0230.0000.0000.0000.000
40A43LEU 0-0.0050.0175.343-1.736-1.7360.0000.0000.0000.000
41A44LYS 10.9751.0064.859-53.509-53.345-0.001-0.011-0.1510.000
42A45HIS 00.031-0.0112.63813.34714.8900.389-0.696-1.2350.000
43A46GLY 00.001-0.0013.575-4.920-4.3380.005-0.151-0.4360.001
44A47GLY 0-0.023-0.0202.713-0.6261.8460.481-1.377-1.577-0.013
45A48GLY 00.0890.0631.664-16.180-21.69819.319-8.389-5.412-0.028
46A49VAL 00.0120.0041.848-42.192-41.58414.287-4.332-10.5620.071
47A50ALA 00.0280.0312.044-25.212-22.8374.851-3.289-3.9360.021
48A51GLY 0-0.004-0.0032.884-9.532-8.7500.020-0.343-0.4600.001
49A52ALA 0-0.065-0.0363.543-7.808-7.3520.014-0.083-0.3870.000
50A53LEU 00.0300.0035.338-7.020-6.861-0.001-0.004-0.1550.000
51A54ASN 00.0380.0147.034-6.468-6.4680.0000.0000.0000.000
52A55LYS 10.9420.9728.206-50.110-50.1100.0000.0000.0000.000
53A56ALA 0-0.0100.0138.312-3.050-3.0500.0000.0000.0000.000
54A57THR 0-0.0230.00110.245-2.137-2.1370.0000.0000.0000.000
55A58ASN 0-0.049-0.03413.255-1.326-1.3260.0000.0000.0000.000
56A59ASN 0-0.013-0.00311.1140.4020.4020.0000.0000.0000.000
57A60ALA 00.0370.02712.579-0.385-0.3850.0000.0000.0000.000
58A61MET 00.0090.0138.2211.1701.1700.0000.0000.0000.000
59A62GLN 0-0.024-0.0226.9493.1503.1500.0000.0000.0000.000
60A63VAL 00.0130.0189.651-0.496-0.4960.0000.0000.0000.000
61A64GLU -1-0.772-0.87912.90932.00032.0000.0000.0000.0000.000
62A65SER 0-0.049-0.0388.6150.9900.9900.0000.0000.0000.000
63A66ASP -1-0.863-0.92810.52435.97935.9790.0000.0000.0000.000
64A67ASP -1-0.962-0.97212.19224.94624.9460.0000.0000.0000.000
65A68TYR 00.0620.01812.353-0.891-0.8910.0000.0000.0000.000
66A69ILE 0-0.035-0.0209.934-0.577-0.5770.0000.0000.0000.000
67A70ALA 0-0.037-0.00313.302-0.876-0.8760.0000.0000.0000.000
68A71THR 0-0.040-0.00816.528-1.526-1.5260.0000.0000.0000.000
69A72ASN 0-0.111-0.06415.779-1.675-1.6750.0000.0000.0000.000
70A73GLY 0-0.0090.00915.434-0.073-0.0730.0000.0000.0000.000
71A74PRO 0-0.061-0.04011.4701.1531.1530.0000.0000.0000.000
72A75LEU 0-0.010-0.0088.710-1.515-1.5150.0000.0000.0000.000
73A76LYS 10.9480.96210.983-30.162-30.1620.0000.0000.0000.000
74A77VAL 00.0240.0068.2772.1252.1250.0000.0000.0000.000
75A78GLY 0-0.004-0.0029.308-3.299-3.2990.0000.0000.0000.000
76A79GLY 0-0.026-0.00510.713-2.548-2.5480.0000.0000.0000.000
77A80SER 0-0.068-0.05310.3153.4033.4030.0000.0000.0000.000
78A81CYS 0-0.0180.00711.619-1.737-1.7370.0000.0000.0000.000
79A82VAL 0-0.017-0.00312.0572.4182.4180.0000.0000.0000.000
80A83LEU 0-0.0010.00410.526-1.475-1.4750.0000.0000.0000.000
81A84SER 00.0370.01614.069-0.030-0.0300.0000.0000.0000.000
82A85GLY 0-0.027-0.01313.4472.2522.2520.0000.0000.0000.000
83A86HIS 0-0.047-0.03913.002-0.177-0.1770.0000.0000.0000.000
84A87ASN 0-0.044-0.04112.668-0.662-0.6620.0000.0000.0000.000
85A88LEU 0-0.048-0.0178.630-0.230-0.2300.0000.0000.0000.000
86A89ALA 00.0140.00212.2330.5340.5340.0000.0000.0000.000
87A90LYS 10.9080.98014.500-25.721-25.7210.0000.0000.0000.000
88A91HIS 00.001-0.01516.221-0.581-0.5810.0000.0000.0000.000
89A92CYS 00.001-0.0059.6682.4812.4810.0000.0000.0000.000
90A93LEU 0-0.0490.00712.004-1.207-1.2070.0000.0000.0000.000
91A94HIS 00.0770.0257.1738.3798.3790.0000.0000.0000.000
92A95VAL 0-0.003-0.0107.685-4.169-4.1690.0000.0000.0000.000
93A96VAL 0-0.0140.0175.2468.4958.4950.0000.0000.0000.000
94A97GLY 00.0330.0214.924-6.739-6.7390.0000.0000.0000.000
95A98PRO 0-0.032-0.0095.7043.1333.1330.0000.0000.0000.000
96A99ASN 00.0240.0104.5756.8107.014-0.001-0.013-0.1900.000
97A100VAL 00.0290.0096.973-7.459-7.4590.0000.0000.0000.000
98A101ASN 0-0.030-0.0046.721-11.894-11.8940.0000.0000.0000.000
99A102LYS 10.8030.9127.393-57.041-57.0410.0000.0000.0000.000
100A103GLY 00.0010.00010.642-2.718-2.7180.0000.0000.0000.000
101A104GLU -1-0.801-0.8678.33354.82354.8230.0000.0000.0000.000
102A105ASP -1-0.834-0.93012.03537.41137.4110.0000.0000.0000.000
103A106ILE 00.0450.01010.0372.7772.7770.0000.0000.0000.000
104A107GLN 0-0.024-0.00711.9572.1392.1390.0000.0000.0000.000
105A108LEU 00.004-0.00711.201-0.206-0.2060.0000.0000.0000.000
106A109LEU 0-0.009-0.0076.8521.5801.5800.0000.0000.0000.000
107A110LYS 10.8710.9239.870-32.531-32.5310.0000.0000.0000.000
108A111SER 00.0260.00713.125-0.878-0.8780.0000.0000.0000.000
109A112ALA 0-0.011-0.0088.493-0.645-0.6450.0000.0000.0000.000
110A113TYR 00.0440.0006.6080.5130.5130.0000.0000.0000.000
111A114GLU -1-0.853-0.89711.65930.24030.2400.0000.0000.0000.000
112A115ASN 0-0.043-0.00311.948-4.347-4.3470.0000.0000.0000.000
113A116PHE 00.045-0.0018.454-0.968-0.9680.0000.0000.0000.000
114A117ASN 0-0.015-0.00414.642-1.789-1.7890.0000.0000.0000.000
115A118GLN 0-0.049-0.01617.637-2.396-2.3960.0000.0000.0000.000
116A119HIS 00.0260.01916.460-1.540-1.5400.0000.0000.0000.000
117A120GLU -1-0.849-0.93218.55526.82926.8290.0000.0000.0000.000
118A121VAL 0-0.036-0.02314.669-0.124-0.1240.0000.0000.0000.000
119A122LEU 0-0.0530.00712.3270.6130.6130.0000.0000.0000.000
120A123LEU 0-0.0060.0156.367-0.769-0.7690.0000.0000.0000.000
121A124ALA 00.0110.0037.7111.3401.3400.0000.0000.0000.000
122A125PRO 00.0220.0302.959-4.087-2.1240.219-0.593-1.5900.005
123A126LEU 00.0090.0012.404-9.663-6.9930.663-0.918-2.4150.006
124A127LEU 00.0120.0012.4208.14411.0622.301-1.923-3.297-0.024
125A128SER 00.032-0.0042.278-21.788-18.6913.078-2.877-3.2970.037
126A129ALA 0-0.0320.0052.334-9.875-8.0641.688-0.147-3.3510.003
127A130GLY 00.0210.0051.906-29.507-32.26016.474-6.789-6.9330.043
128A131ILE 0-0.029-0.0131.908-41.401-44.29612.4130.307-9.8240.062
129A132PHE 0-0.073-0.0392.093-49.229-42.66810.596-5.236-11.9210.033
130A133GLY 00.0430.0243.927-18.505-18.0150.010-0.157-0.3430.001
131A134ALA 0-0.030-0.0175.271-11.389-11.3890.0000.0000.0000.000
132A135ASP -1-0.799-0.9146.63950.78150.7810.0000.0000.0000.000
133A136PRO 0-0.009-0.0074.113-1.211-0.9260.000-0.048-0.2380.000
134A137ILE 0-0.004-0.0035.952-0.830-0.8300.0000.0000.0000.000
135A138HIS 00.0450.0359.205-3.108-3.1080.0000.0000.0000.000
136A139SER 0-0.007-0.0225.829-4.201-4.2010.0000.0000.0000.000
137A140LEU 00.010-0.0017.878-1.438-1.4380.0000.0000.0000.000
138A141ARG 10.8960.9339.069-35.588-35.5880.0000.0000.0000.000
139A142VAL 0-0.015-0.00511.261-2.357-2.3570.0000.0000.0000.000
140A143CYS 0-0.0290.0069.219-2.346-2.3460.0000.0000.0000.000
141A144VAL 00.0020.00311.383-2.170-2.1700.0000.0000.0000.000
142A145ASP -1-0.784-0.84114.09330.04430.0440.0000.0000.0000.000
143A146THR 0-0.073-0.03914.152-2.211-2.2110.0000.0000.0000.000
144A147VAL 0-0.053-0.01512.420-1.208-1.2080.0000.0000.0000.000
145A148ARG 10.9330.98015.652-29.155-29.1550.0000.0000.0000.000
146A149THR 00.0230.04117.431-0.762-0.7620.0000.0000.0000.000
147A150ASN 0-0.039-0.01316.3340.6180.6180.0000.0000.0000.000
148A151VAL 00.0220.00810.5100.9140.9140.0000.0000.0000.000
149A152TYR 0-0.037-0.0219.707-1.146-1.1460.0000.0000.0000.000
150A153LEU 00.011-0.0086.8452.4612.4610.0000.0000.0000.000
151A154ALA 0-0.008-0.0032.781-4.750-4.0320.155-0.234-0.6390.000
152A155VAL 0-0.008-0.0072.6707.30210.3561.593-1.583-3.064-0.008
153A156PHE 00.0170.0052.289-16.846-13.6688.150-3.312-8.0150.030
154A157ASP -1-0.817-0.9233.83740.94341.5920.1060.070-0.8250.003
155A158LYS 10.8940.9375.805-34.232-34.2320.0000.0000.0000.000
156A159ASN 00.0090.0048.876-2.581-2.5810.0000.0000.0000.000
157A160LEU 0-0.029-0.0172.361-3.291-2.1031.506-0.855-1.8380.005
158A161TYR 00.018-0.0016.495-0.829-0.8290.0000.0000.0000.000
159A162ASP -1-0.811-0.8947.72032.69632.6960.0000.0000.0000.000
160A163LYS 10.9531.0018.127-46.829-46.8290.0000.0000.0000.000
161A164LEU 0-0.029-0.0074.900-1.030-1.0300.0000.0000.0000.000
162A165VAL 0-0.007-0.0059.442-1.552-1.5520.0000.0000.0000.000
163A166SER 0-0.042-0.02512.461-2.112-2.1120.0000.0000.0000.000
164A167SER 00.0420.00212.235-1.044-1.0440.0000.0000.0000.000
165A168PHE 0-0.049-0.02412.754-1.174-1.1740.0000.0000.0000.000
166A169LEU 0-0.022-0.02514.529-1.400-1.4000.0000.0000.0000.000
167A170GLU -1-0.967-0.98116.87926.85026.8500.0000.0000.0000.000
168A171MET 0-0.081-0.04314.201-0.684-0.6840.0000.0000.0000.000
169A172LYS 10.8560.95718.757-26.818-26.8180.0000.0000.0000.000
170A173SER -1-0.932-0.94620.04022.25022.2500.0000.0000.0000.000
171A302HOH 0-0.026-0.02717.762-0.758-0.7580.0000.0000.0000.000
172A304HOH 0-0.028-0.01216.9120.1350.1350.0000.0000.0000.000
173A305HOH 0-0.014-0.02115.0260.2490.2490.0000.0000.0000.000
174A307HOH 0-0.045-0.04117.1540.1150.1150.0000.0000.0000.000
175A308HOH 0-0.012-0.00917.878-0.669-0.6690.0000.0000.0000.000
176A309HOH 0-0.016-0.01722.548-0.150-0.1500.0000.0000.0000.000
177A310HOH 0-0.032-0.02615.713-0.006-0.0060.0000.0000.0000.000
178A311HOH 0-0.003-0.00714.465-0.855-0.8550.0000.0000.0000.000
179A313HOH 0-0.027-0.03018.6760.3570.3570.0000.0000.0000.000
180A314HOH 0-0.0140.00018.716-0.558-0.5580.0000.0000.0000.000
181A315HOH 0-0.023-0.02020.7800.0460.0460.0000.0000.0000.000
182A316HOH 00.0310.01914.5751.0421.0420.0000.0000.0000.000
183A318HOH 0-0.050-0.0418.626-0.434-0.4340.0000.0000.0000.000
184A319HOH 0-0.035-0.02819.443-0.178-0.1780.0000.0000.0000.000
185A320HOH 00.0370.0176.8980.0570.0570.0000.0000.0000.000
186A321HOH 0-0.002-0.01518.0870.0170.0170.0000.0000.0000.000
187A322HOH 00.0220.01413.4060.2500.2500.0000.0000.0000.000
188A327HOH 00.000-0.00614.9680.2510.2510.0000.0000.0000.000
189A328HOH 0-0.045-0.0395.872-0.013-0.0130.0000.0000.0000.000
190A329HOH 0-0.031-0.02420.064-0.475-0.4750.0000.0000.0000.000