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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: 823GY

Calculation Name: 3UB0-A-Xray372

Preferred Name: Replicase polyprotein 1ab

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3UB0

Chain ID: A

ChEMBL ID: CHEMBL4295624

UniProt ID: Q98VG9

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1521456.128975
FMO2-HF: Nuclear repulsion 1446494.675121
FMO2-HF: Total energy -74961.453854
FMO2-MP2: Total energy -75179.034803


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:-2:PRO)


Summations of interaction energy for fragment #1(A:-2:PRO)
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.
-2.7541.6681.72-2.279-3.863-0.008
Interaction energy analysis for fragmet #1(A:-2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.005
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].
3A0GLY00.0180.0072.598-1.4691.3720.100-1.425-1.516-0.001
4A1SER00.0010.0024.1400.3910.6390.000-0.040-0.2080.000
5A2VAL0-0.064-0.0236.4870.1350.1350.0000.0000.0000.000
6A3ALA00.0390.0298.5130.0260.0260.0000.0000.0000.000
7A4SER00.0570.02411.595-0.013-0.0130.0000.0000.0000.000
8A5ALA00.0350.0096.984-0.032-0.0320.0000.0000.0000.000
9A6TYR0-0.003-0.0058.449-0.042-0.0420.0000.0000.0000.000
10A7ALA00.0140.00111.1220.0190.0190.0000.0000.0000.000
11A8ALA00.003-0.0078.0600.0300.0300.0000.0000.0000.000
12A9LEU0-0.0020.0116.937-0.053-0.0530.0000.0000.0000.000
13A10PRO00.0180.0078.684-0.003-0.0030.0000.0000.0000.000
14A11SER00.0640.03610.939-0.016-0.0160.0000.0000.0000.000
15A12TRP0-0.004-0.0122.388-1.656-0.4221.621-0.812-2.043-0.007
16A13ILE0-0.0050.0057.3270.0460.0460.0000.0000.0000.000
17A14ALA0-0.0020.0108.7570.0700.0700.0000.0000.0000.000
18A15TYR0-0.015-0.0137.2930.1020.1020.0000.0000.0000.000
19A16GLU-1-0.896-0.9565.044-0.330-0.231-0.001-0.002-0.0960.000
20A17LYS10.9640.9717.5100.3940.3940.0000.0000.0000.000
21A18ALA00.0410.03010.9750.0460.0460.0000.0000.0000.000
22A19ARG10.8820.9126.178-0.079-0.0790.0000.0000.0000.000
23A20ALA0-0.028-0.0069.9960.0530.0530.0000.0000.0000.000
24A21ASP-1-0.867-0.92411.528-0.107-0.1070.0000.0000.0000.000
25A22LEU0-0.057-0.02914.2580.0230.0230.0000.0000.0000.000
26A23GLU-1-0.924-0.97312.3430.1390.1390.0000.0000.0000.000
27A24GLU-1-0.962-0.98114.794-0.044-0.0440.0000.0000.0000.000
28A25ALA0-0.015-0.01517.0660.0070.0070.0000.0000.0000.000
29A26LYS10.9100.95615.890-0.085-0.0850.0000.0000.0000.000
30A27LYS10.8970.95414.237-0.048-0.0480.0000.0000.0000.000
31A28ASN0-0.010-0.00519.9430.0090.0090.0000.0000.0000.000
32A29ASP-1-0.982-0.97422.6730.0220.0220.0000.0000.0000.000
33A30VAL0-0.0060.01322.612-0.005-0.0050.0000.0000.0000.000
34A31SER00.0370.01124.9650.0030.0030.0000.0000.0000.000
35A32PRO00.0710.01425.704-0.002-0.0020.0000.0000.0000.000
36A33GLN0-0.067-0.03326.021-0.003-0.0030.0000.0000.0000.000
37A34LEU00.0630.03222.822-0.003-0.0030.0000.0000.0000.000
38A35LEU00.1010.04721.035-0.006-0.0060.0000.0000.0000.000
39A36LYS10.9380.98821.0940.0070.0070.0000.0000.0000.000
40A37GLN0-0.056-0.02622.337-0.008-0.0080.0000.0000.0000.000
41A38LEU00.0570.02217.807-0.008-0.0080.0000.0000.0000.000
42A39THR0-0.010-0.01517.220-0.004-0.0040.0000.0000.0000.000
43A40LYS10.9150.96217.7660.0410.0410.0000.0000.0000.000
44A41ALA00.0230.01217.380-0.007-0.0070.0000.0000.0000.000
45A42CYS0-0.0050.02312.213-0.014-0.0140.0000.0000.0000.000
46A43ASN0-0.008-0.01714.038-0.008-0.0080.0000.0000.0000.000
47A44ILE0-0.009-0.00316.249-0.006-0.0060.0000.0000.0000.000
48A45ALA00.0520.03112.572-0.010-0.0100.0000.0000.0000.000
49A46LYS10.9350.97711.359-0.068-0.0680.0000.0000.0000.000
50A47SER0-0.047-0.02612.529-0.015-0.0150.0000.0000.0000.000
51A48GLU-1-0.815-0.91315.175-0.183-0.1830.0000.0000.0000.000
52A49PHE00.0020.0067.048-0.040-0.0400.0000.0000.0000.000
53A50GLU-1-0.949-0.98411.938-0.082-0.0820.0000.0000.0000.000
54A51ARG10.8650.93613.5710.1860.1860.0000.0000.0000.000
55A52GLU-1-0.888-0.96413.877-0.313-0.3130.0000.0000.0000.000
56A53ALA00.0040.01511.759-0.003-0.0030.0000.0000.0000.000
57A54SER0-0.111-0.05613.5910.0360.0360.0000.0000.0000.000
58A55VAL0-0.0030.00016.8610.0210.0210.0000.0000.0000.000
59A56GLN00.015-0.00114.0250.0220.0220.0000.0000.0000.000
60A57LYS10.9760.99013.6050.1320.1320.0000.0000.0000.000
61A58LYS10.8890.94717.6660.1200.1200.0000.0000.0000.000
62A59LEU00.005-0.00419.6390.0150.0150.0000.0000.0000.000
63A60ASP-1-0.853-0.91416.732-0.217-0.2170.0000.0000.0000.000
64A61LYS10.9490.97820.3950.0630.0630.0000.0000.0000.000
65A62MET0-0.005-0.00422.7050.0100.0100.0000.0000.0000.000
66A63ALA00.0210.01123.1960.0090.0090.0000.0000.0000.000
67A64GLU-1-0.943-0.96421.588-0.064-0.0640.0000.0000.0000.000
68A65GLN0-0.037-0.03624.7930.0060.0060.0000.0000.0000.000
69A66ALA00.0000.00628.0200.0060.0060.0000.0000.0000.000
70A67ALA00.0180.00727.2620.0050.0050.0000.0000.0000.000
71A68ALA0-0.011-0.00728.7970.0050.0050.0000.0000.0000.000
72A69SER0-0.093-0.04030.4550.0050.0050.0000.0000.0000.000
73A70MET00.0160.00632.7830.0010.0010.0000.0000.0000.000
74A71TYR00.0030.00731.5780.0020.0020.0000.0000.0000.000
75A72LYS10.9280.96334.2050.0290.0290.0000.0000.0000.000
76A73GLU-1-0.967-0.97537.559-0.039-0.0390.0000.0000.0000.000
77A74ALA0-0.033-0.01238.5610.0000.0000.0000.0000.0000.000
78A75ARG10.9100.93137.3500.0350.0350.0000.0000.0000.000
79A76ALA00.0370.02840.796-0.002-0.0020.0000.0000.0000.000
80A77VAL0-0.066-0.03243.4490.0020.0020.0000.0000.0000.000
81A78ASP-1-0.819-0.89545.526-0.028-0.0280.0000.0000.0000.000
82A79ARG10.9550.97644.0270.0270.0270.0000.0000.0000.000
83A80LYS10.8810.93346.7750.0240.0240.0000.0000.0000.000
84A81SER00.2080.11650.0480.0000.0000.0000.0000.0000.000
85A82LYS10.9560.95652.5110.0200.0200.0000.0000.0000.000
86A83ILE00.010-0.00246.4230.0000.0000.0000.0000.0000.000
87A84VAL00.0800.05650.215-0.001-0.0010.0000.0000.0000.000
88A85SER0-0.017-0.02351.9670.0000.0000.0000.0000.0000.000
89A86ALA0-0.058-0.02551.8190.0000.0000.0000.0000.0000.000
90A87MET00.0060.00248.294-0.001-0.0010.0000.0000.0000.000
91A88HIS00.0430.02452.367-0.001-0.0010.0000.0000.0000.000
92A89SER0-0.031-0.01455.8020.0000.0000.0000.0000.0000.000
93A90LEU00.005-0.00551.0410.0000.0000.0000.0000.0000.000
94A91LEU00.0060.01153.5970.0000.0000.0000.0000.0000.000
95A92PHE00.0380.00155.3240.0000.0000.0000.0000.0000.000
96A93GLY00.0090.02058.5410.0010.0010.0000.0000.0000.000
97A94MET0-0.062-0.04452.2950.0000.0000.0000.0000.0000.000
98A95LEU0-0.0030.00056.8900.0000.0000.0000.0000.0000.000
99A96LYS10.9810.99359.4920.0200.0200.0000.0000.0000.000
100A97LYS10.9240.95957.3040.0260.0260.0000.0000.0000.000
101A98LEU0-0.048-0.02356.9210.0000.0000.0000.0000.0000.000
102A99ASP-1-0.927-0.95360.724-0.021-0.0210.0000.0000.0000.000
103A100MET00.0160.02758.8920.0000.0000.0000.0000.0000.000
104A101SER00.0340.00864.0920.0000.0000.0000.0000.0000.000
105A102SER00.0170.01262.3150.0000.0000.0000.0000.0000.000
106A103VAL00.0400.02059.9250.0000.0000.0000.0000.0000.000
107A104ASN00.030-0.00262.6530.0000.0000.0000.0000.0000.000
108A105THR0-0.058-0.02366.0080.0010.0010.0000.0000.0000.000
109A106ILE0-0.015-0.00160.3260.0000.0000.0000.0000.0000.000
110A107ILE0-0.014-0.00960.5500.0000.0000.0000.0000.0000.000
111A108GLU-1-0.824-0.91364.593-0.017-0.0170.0000.0000.0000.000
112A109GLN0-0.034-0.03366.5880.0000.0000.0000.0000.0000.000
113A110ALA00.0260.02363.8630.0000.0000.0000.0000.0000.000
114A111ARG10.8370.93165.8420.0170.0170.0000.0000.0000.000
115A112ASN0-0.102-0.04868.0850.0010.0010.0000.0000.0000.000
116A113GLY00.0370.01568.2140.0000.0000.0000.0000.0000.000
117A114VAL0-0.039-0.01767.7560.0000.0000.0000.0000.0000.000
118A115LEU0-0.023-0.01262.447-0.001-0.0010.0000.0000.0000.000
119A116PRO0-0.017-0.01659.7130.0000.0000.0000.0000.0000.000
120A117LEU00.0190.01761.5540.0000.0000.0000.0000.0000.000
121A118SER0-0.028-0.02558.104-0.001-0.0010.0000.0000.0000.000
122A119ILE00.011-0.00255.5280.0010.0010.0000.0000.0000.000
123A120ILE00.0060.01353.595-0.001-0.0010.0000.0000.0000.000
124A121PRO00.0060.00550.6270.0000.0000.0000.0000.0000.000
125A122ALA00.0300.00950.1940.0000.0000.0000.0000.0000.000
126A123ALA00.0580.02751.8600.0010.0010.0000.0000.0000.000
127A124SER0-0.105-0.04653.3530.0010.0010.0000.0000.0000.000
128A125ALA00.0320.01454.3680.0000.0000.0000.0000.0000.000
129A126THR0-0.028-0.00954.9620.0000.0000.0000.0000.0000.000
130A127ARG10.9060.94056.8850.0270.0270.0000.0000.0000.000
131A128LEU0-0.027-0.00658.717-0.001-0.0010.0000.0000.0000.000
132A129ILE00.0130.01061.1680.0010.0010.0000.0000.0000.000
133A130VAL00.011-0.01263.3150.0000.0000.0000.0000.0000.000
134A131VAL00.0020.02065.6510.0010.0010.0000.0000.0000.000
135A132THR0-0.014-0.02068.0200.0000.0000.0000.0000.0000.000
136A133PRO00.012-0.01170.8460.0000.0000.0000.0000.0000.000
137A134ASN00.0350.02773.5260.0000.0000.0000.0000.0000.000
138A135LEU00.0800.03876.468-0.001-0.0010.0000.0000.0000.000
139A136GLU-1-0.926-0.94678.855-0.015-0.0150.0000.0000.0000.000
140A137VAL0-0.071-0.05973.3590.0000.0000.0000.0000.0000.000
141A138LEU00.0070.00773.848-0.001-0.0010.0000.0000.0000.000
142A139SER0-0.015-0.01774.7750.0000.0000.0000.0000.0000.000
143A140LYS10.9100.97574.0400.0170.0170.0000.0000.0000.000
144A141VAL0-0.003-0.00169.5460.0000.0000.0000.0000.0000.000
145A142ARG10.9150.97671.2430.0160.0160.0000.0000.0000.000
146A143GLN0-0.059-0.03272.9510.0000.0000.0000.0000.0000.000
147A144GLU-1-0.912-0.95974.076-0.018-0.0180.0000.0000.0000.000
148A145ASN0-0.015-0.01172.8350.0000.0000.0000.0000.0000.000
149A146ASN00.0140.01369.802-0.001-0.0010.0000.0000.0000.000
150A147VAL00.0240.01767.0490.0010.0010.0000.0000.0000.000
151A148HIS00.0370.02467.578-0.001-0.0010.0000.0000.0000.000
152A149TYR00.049-0.00261.5040.0000.0000.0000.0000.0000.000
153A150ALA00.0080.00760.106-0.001-0.0010.0000.0000.0000.000
154A151GLY0-0.031-0.01060.982-0.001-0.0010.0000.0000.0000.000
155A152ALA0-0.053-0.00861.1650.0000.0000.0000.0000.0000.000
156A153ILE00.0520.01963.2850.0010.0010.0000.0000.0000.000
157A154TRP0-0.070-0.04358.869-0.001-0.0010.0000.0000.0000.000
158A155SER00.0600.03465.4430.0010.0010.0000.0000.0000.000
159A156ILE0-0.058-0.04666.762-0.001-0.0010.0000.0000.0000.000
160A157VAL0-0.060-0.01564.8240.0000.0000.0000.0000.0000.000
161A158GLU-1-0.875-0.94267.477-0.020-0.0200.0000.0000.0000.000
162A159VAL00.002-0.00369.4550.0000.0000.0000.0000.0000.000
163A160LYS10.8860.95766.8060.0200.0200.0000.0000.0000.000
164A161ASP-1-0.816-0.90972.064-0.015-0.0150.0000.0000.0000.000
165A162ALA0-0.0150.00571.537-0.001-0.0010.0000.0000.0000.000
166A163ASN0-0.023-0.02671.6210.0000.0000.0000.0000.0000.000
167A164GLY0-0.031-0.01670.5860.0000.0000.0000.0000.0000.000
168A165ALA0-0.016-0.00371.2870.0000.0000.0000.0000.0000.000
169A166GLN0-0.049-0.04570.6770.0000.0000.0000.0000.0000.000
170A167VAL00.0470.02874.7130.0010.0010.0000.0000.0000.000
171A168HIS00.0150.01075.728-0.001-0.0010.0000.0000.0000.000
172A169LEU00.049-0.00774.0640.0000.0000.0000.0000.0000.000
173A170LYS10.8880.95378.0820.0150.0150.0000.0000.0000.000
174A171GLU-1-0.910-0.95681.275-0.014-0.0140.0000.0000.0000.000
175A172VAL00.0020.02677.9650.0000.0000.0000.0000.0000.000
176A173THR0-0.015-0.00881.3260.0000.0000.0000.0000.0000.000
177A174ALA00.0550.00684.3280.0000.0000.0000.0000.0000.000
178A175ALA0-0.035-0.01986.1520.0000.0000.0000.0000.0000.000
179A176ASN00.008-0.00283.8450.0000.0000.0000.0000.0000.000
180A177GLU-1-0.905-0.95381.121-0.014-0.0140.0000.0000.0000.000
181A178LEU0-0.010-0.01282.4400.0000.0000.0000.0000.0000.000
182A179ASN0-0.058-0.03783.9250.0000.0000.0000.0000.0000.000
183A180ILE00.0240.03578.2530.0000.0000.0000.0000.0000.000
184A181THR0-0.055-0.01176.3040.0000.0000.0000.0000.0000.000
185A182TRP00.0130.02575.294-0.001-0.0010.0000.0000.0000.000
186A183PRO0-0.046-0.03870.4640.0000.0000.0000.0000.0000.000
187A184LEU00.0370.01972.5260.0000.0000.0000.0000.0000.000
188A185SER0-0.035-0.01767.351-0.001-0.0010.0000.0000.0000.000
189A186ILE0-0.010-0.01568.3340.0000.0000.0000.0000.0000.000
190A187THR00.0080.01063.794-0.001-0.0010.0000.0000.0000.000
191A188CYS0-0.027-0.00764.4640.0000.0000.0000.0000.0000.000
192A189GLU-1-0.801-0.89460.357-0.028-0.0280.0000.0000.0000.000
193A190ARG10.9290.97357.6500.0300.0300.0000.0000.0000.000
194A191THR0-0.012-0.00961.179-0.001-0.0010.0000.0000.0000.000
195A192THR0-0.041-0.01658.0850.0000.0000.0000.0000.0000.000