Manual

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: N15ZQ

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1522566.994501
FMO2-HF: Nuclear repulsion 1447604.349955
FMO2-HF: Total energy -74962.644547
FMO2-MP2: Total energy -75180.268682


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.
-2.7792.0331.557-2.43-3.94-0.006
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 : 0.048 / q_NPA : 0.011
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].
3A0GLY00.0170.0062.577-1.4491.5670.104-1.541-1.5790.001
4A1SER00.0040.0054.1280.4400.6880.000-0.040-0.2080.000
5A2VAL0-0.065-0.0266.4590.1850.1850.0000.0000.0000.000
6A3ALA00.0350.0288.4910.0340.0340.0000.0000.0000.000
7A4SER00.0560.02111.599-0.004-0.0040.0000.0000.0000.000
8A5ALA00.0340.0097.053-0.037-0.0370.0000.0000.0000.000
9A6TYR00.001-0.0038.512-0.047-0.0470.0000.0000.0000.000
10A7ALA00.0110.00111.1830.0180.0180.0000.0000.0000.000
11A8ALA00.005-0.0068.0880.0280.0280.0000.0000.0000.000
12A9LEU0-0.0020.0116.921-0.067-0.0670.0000.0000.0000.000
13A10PRO00.0160.0078.659-0.004-0.0040.0000.0000.0000.000
14A11SER00.023-0.01411.137-0.011-0.0110.0000.0000.0000.000
15A12TRP0-0.017-0.0092.554-2.069-0.5211.453-0.849-2.153-0.007
16A13ILE00.0100.0107.3610.0440.0440.0000.0000.0000.000
17A14ALA0-0.0070.0088.6490.0780.0780.0000.0000.0000.000
18A15TYR0-0.008-0.0097.5830.1060.1060.0000.0000.0000.000
19A16GLU-1-0.803-0.8755.326-0.172-0.1720.0000.0000.0000.000
20A17LYS10.9430.9667.5120.3350.3350.0000.0000.0000.000
21A18ALA00.0390.02210.9960.0530.0530.0000.0000.0000.000
22A19ARG10.7950.8455.778-0.019-0.0190.0000.0000.0000.000
23A20ALA0-0.027-0.0129.9620.0590.0590.0000.0000.0000.000
24A21ASP-1-0.875-0.93611.490-0.115-0.1150.0000.0000.0000.000
25A22LEU0-0.031-0.01514.1720.0230.0230.0000.0000.0000.000
26A23GLU-1-0.823-0.89212.3290.1520.1520.0000.0000.0000.000
27A24GLU-1-0.923-0.95414.714-0.023-0.0230.0000.0000.0000.000
28A25ALA00.0270.00317.0530.0070.0070.0000.0000.0000.000
29A26LYS10.8280.90515.147-0.104-0.1040.0000.0000.0000.000
30A27LYS10.8260.90313.899-0.088-0.0880.0000.0000.0000.000
31A28ASN0-0.059-0.03420.0240.0100.0100.0000.0000.0000.000
32A29ASP-1-0.973-0.97122.7090.0270.0270.0000.0000.0000.000
33A30VAL00.0070.01922.503-0.006-0.0060.0000.0000.0000.000
34A31SER00.0240.00524.9000.0030.0030.0000.0000.0000.000
35A32PRO00.0810.01725.632-0.003-0.0030.0000.0000.0000.000
36A33GLN0-0.051-0.02025.941-0.003-0.0030.0000.0000.0000.000
37A34LEU00.0540.02922.763-0.004-0.0040.0000.0000.0000.000
38A35LEU00.0970.04820.364-0.008-0.0080.0000.0000.0000.000
39A36LYS10.9600.99121.0180.0090.0090.0000.0000.0000.000
40A37GLN0-0.083-0.04322.269-0.010-0.0100.0000.0000.0000.000
41A38LEU00.0500.01917.624-0.010-0.0100.0000.0000.0000.000
42A39THR0-0.008-0.00617.163-0.005-0.0050.0000.0000.0000.000
43A40LYS10.9130.95917.6930.0510.0510.0000.0000.0000.000
44A41ALA00.0220.01117.432-0.009-0.0090.0000.0000.0000.000
45A42CYS0-0.0010.02312.153-0.018-0.0180.0000.0000.0000.000
46A43ASN00.004-0.01313.983-0.014-0.0140.0000.0000.0000.000
47A44ILE0-0.014-0.00316.195-0.008-0.0080.0000.0000.0000.000
48A45ALA00.0530.03512.605-0.012-0.0120.0000.0000.0000.000
49A46LYS10.8420.91211.4220.0040.0040.0000.0000.0000.000
50A47SER0-0.071-0.04012.480-0.018-0.0180.0000.0000.0000.000
51A48GLU-1-0.783-0.86515.049-0.207-0.2070.0000.0000.0000.000
52A49PHE00.0140.0006.882-0.044-0.0440.0000.0000.0000.000
53A50GLU-1-0.847-0.91511.826-0.129-0.1290.0000.0000.0000.000
54A51ARG10.7730.85413.5450.2290.2290.0000.0000.0000.000
55A52GLU-1-0.808-0.89013.577-0.332-0.3320.0000.0000.0000.000
56A53ALA00.0110.01311.698-0.002-0.0020.0000.0000.0000.000
57A54SER0-0.076-0.03813.5140.0380.0380.0000.0000.0000.000
58A55VAL0-0.004-0.00416.8660.0230.0230.0000.0000.0000.000
59A56GLN0-0.017-0.01213.8240.0180.0180.0000.0000.0000.000
60A57LYS10.9740.98913.2440.2070.2070.0000.0000.0000.000
61A58LYS10.8810.94817.6660.1540.1540.0000.0000.0000.000
62A59LEU00.000-0.00219.3810.0180.0180.0000.0000.0000.000
63A60ASP-1-0.839-0.91516.679-0.259-0.2590.0000.0000.0000.000
64A61LYS10.9530.97920.3850.0870.0870.0000.0000.0000.000
65A62MET00.0010.00022.6820.0130.0130.0000.0000.0000.000
66A63ALA00.0170.00923.1650.0110.0110.0000.0000.0000.000
67A64GLU-1-0.939-0.96322.279-0.083-0.0830.0000.0000.0000.000
68A65GLN0-0.033-0.03224.7790.0070.0070.0000.0000.0000.000
69A66ALA00.0030.00728.0010.0080.0080.0000.0000.0000.000
70A67ALA00.0150.00827.2230.0070.0070.0000.0000.0000.000
71A68ALA0-0.012-0.00828.7370.0060.0060.0000.0000.0000.000
72A69SER0-0.085-0.03730.4390.0060.0060.0000.0000.0000.000
73A70MET00.0190.00232.7790.0020.0020.0000.0000.0000.000
74A71TYR00.0040.00931.7380.0030.0030.0000.0000.0000.000
75A72LYS10.8970.95334.1990.0370.0370.0000.0000.0000.000
76A73GLU-1-0.956-0.97037.565-0.044-0.0440.0000.0000.0000.000
77A74ALA0-0.021-0.01338.5610.0000.0000.0000.0000.0000.000
78A75ARG10.9120.93737.0350.0420.0420.0000.0000.0000.000
79A76ALA00.0360.02540.493-0.002-0.0020.0000.0000.0000.000
80A77VAL0-0.068-0.03443.4900.0020.0020.0000.0000.0000.000
81A78ASP-1-0.829-0.89945.398-0.032-0.0320.0000.0000.0000.000
82A79ARG10.9840.99043.9570.0320.0320.0000.0000.0000.000
83A80LYS10.8740.91846.7830.0290.0290.0000.0000.0000.000
84A81SER00.1990.12150.0530.0000.0000.0000.0000.0000.000
85A82LYS10.9690.96952.3950.0240.0240.0000.0000.0000.000
86A83ILE00.0120.00246.3550.0000.0000.0000.0000.0000.000
87A84VAL00.0720.05650.346-0.001-0.0010.0000.0000.0000.000
88A85SER0-0.025-0.03751.9800.0010.0010.0000.0000.0000.000
89A86ALA0-0.062-0.02651.8360.0010.0010.0000.0000.0000.000
90A87MET00.0110.00248.301-0.001-0.0010.0000.0000.0000.000
91A88HIS00.0420.02352.3880.0000.0000.0000.0000.0000.000
92A89SER0-0.036-0.01555.8290.0010.0010.0000.0000.0000.000
93A90LEU0-0.003-0.00651.1280.0000.0000.0000.0000.0000.000
94A91LEU00.0100.01253.4680.0000.0000.0000.0000.0000.000
95A92PHE00.0440.00455.3400.0000.0000.0000.0000.0000.000
96A93GLY00.0080.01958.5500.0010.0010.0000.0000.0000.000
97A94MET0-0.054-0.04152.4750.0000.0000.0000.0000.0000.000
98A95LEU00.0040.00256.8770.0000.0000.0000.0000.0000.000
99A96LYS10.9760.99459.5010.0220.0220.0000.0000.0000.000
100A97LYS10.9270.96057.7660.0290.0290.0000.0000.0000.000
101A98LEU0-0.057-0.02756.7060.0000.0000.0000.0000.0000.000
102A99ASP-1-0.897-0.93560.719-0.023-0.0230.0000.0000.0000.000
103A100MET00.0040.01858.7580.0000.0000.0000.0000.0000.000
104A101SER00.0500.01664.0980.0000.0000.0000.0000.0000.000
105A102SER00.0200.02362.3710.0000.0000.0000.0000.0000.000
106A103VAL00.0240.01160.0150.0000.0000.0000.0000.0000.000
107A104ASN0-0.002-0.01862.6730.0000.0000.0000.0000.0000.000
108A105THR0-0.048-0.02866.0270.0010.0010.0000.0000.0000.000
109A106ILE0-0.0080.00060.4030.0000.0000.0000.0000.0000.000
110A107ILE0-0.017-0.00960.6880.0000.0000.0000.0000.0000.000
111A108GLU-1-0.796-0.87764.625-0.019-0.0190.0000.0000.0000.000
112A109GLN0-0.024-0.01966.6630.0000.0000.0000.0000.0000.000
113A110ALA00.0280.02263.9250.0000.0000.0000.0000.0000.000
114A111ARG10.8260.90965.8900.0190.0190.0000.0000.0000.000
115A112ASN0-0.127-0.07868.1280.0010.0010.0000.0000.0000.000
116A113GLY00.0260.01368.2710.0010.0010.0000.0000.0000.000
117A114VAL0-0.030-0.01267.7310.0000.0000.0000.0000.0000.000
118A115LEU0-0.024-0.01362.809-0.001-0.0010.0000.0000.0000.000
119A116PRO0-0.016-0.01759.9000.0000.0000.0000.0000.0000.000
120A117LEU00.0140.01961.6240.0000.0000.0000.0000.0000.000
121A118SER0-0.026-0.02857.988-0.001-0.0010.0000.0000.0000.000
122A119ILE00.0060.00255.2970.0010.0010.0000.0000.0000.000
123A120ILE00.0280.02053.423-0.002-0.0020.0000.0000.0000.000
124A121PRO0-0.014-0.00950.7510.0000.0000.0000.0000.0000.000
125A122ALA00.0340.01250.1480.0010.0010.0000.0000.0000.000
126A123ALA00.0600.02951.9060.0010.0010.0000.0000.0000.000
127A124SER0-0.100-0.04253.4020.0010.0010.0000.0000.0000.000
128A125ALA00.0310.01254.4430.0000.0000.0000.0000.0000.000
129A126THR0-0.034-0.00854.8500.0000.0000.0000.0000.0000.000
130A127ARG10.8670.90756.9550.0280.0280.0000.0000.0000.000
131A128LEU0-0.026-0.00658.781-0.001-0.0010.0000.0000.0000.000
132A129ILE00.0180.01561.2400.0010.0010.0000.0000.0000.000
133A130VAL00.020-0.00663.3820.0000.0000.0000.0000.0000.000
134A131VAL0-0.0060.01965.5060.0010.0010.0000.0000.0000.000
135A132THR0-0.010-0.01768.0910.0000.0000.0000.0000.0000.000
136A133PRO00.014-0.01170.8480.0010.0010.0000.0000.0000.000
137A134ASN00.0260.02573.5940.0000.0000.0000.0000.0000.000
138A135LEU00.0770.03276.531-0.001-0.0010.0000.0000.0000.000
139A136GLU-1-0.855-0.90778.699-0.017-0.0170.0000.0000.0000.000
140A137VAL0-0.048-0.04373.3760.0000.0000.0000.0000.0000.000
141A138LEU00.0000.00573.914-0.001-0.0010.0000.0000.0000.000
142A139SER0-0.025-0.03274.8330.0000.0000.0000.0000.0000.000
143A140LYS10.8380.93274.0200.0170.0170.0000.0000.0000.000
144A141VAL0-0.0040.00469.6650.0000.0000.0000.0000.0000.000
145A142ARG10.8860.95371.2960.0170.0170.0000.0000.0000.000
146A143GLN0-0.038-0.02973.0130.0000.0000.0000.0000.0000.000
147A144GLU-1-0.917-0.95974.132-0.019-0.0190.0000.0000.0000.000
148A145ASN0-0.0030.00673.0010.0000.0000.0000.0000.0000.000
149A146ASN00.0010.00269.842-0.001-0.0010.0000.0000.0000.000
150A147VAL00.0230.02266.8910.0010.0010.0000.0000.0000.000
151A148HIS00.0430.02067.632-0.001-0.0010.0000.0000.0000.000
152A149TYR00.052-0.00261.7370.0000.0000.0000.0000.0000.000
153A150ALA00.0140.01160.161-0.001-0.0010.0000.0000.0000.000
154A151GLY0-0.030-0.00861.020-0.001-0.0010.0000.0000.0000.000
155A152ALA0-0.056-0.01261.1920.0000.0000.0000.0000.0000.000
156A153ILE00.0540.02463.3270.0010.0010.0000.0000.0000.000
157A154TRP0-0.067-0.04358.762-0.002-0.0020.0000.0000.0000.000
158A155SER00.0730.04865.5030.0010.0010.0000.0000.0000.000
159A156ILE0-0.055-0.05066.836-0.001-0.0010.0000.0000.0000.000
160A157VAL0-0.055-0.01964.7220.0000.0000.0000.0000.0000.000
161A158GLU-1-0.794-0.89467.239-0.021-0.0210.0000.0000.0000.000
162A159VAL0-0.001-0.00569.4010.0000.0000.0000.0000.0000.000
163A160LYS10.8140.91166.6710.0210.0210.0000.0000.0000.000
164A161ASP-1-0.762-0.86771.888-0.016-0.0160.0000.0000.0000.000
165A162ALA00.0030.01771.387-0.001-0.0010.0000.0000.0000.000
166A163ASN0-0.064-0.04171.5060.0000.0000.0000.0000.0000.000
167A164GLY0-0.034-0.01870.3130.0000.0000.0000.0000.0000.000
168A165ALA0-0.013-0.00471.0200.0000.0000.0000.0000.0000.000
169A166GLN0-0.023-0.03270.2620.0000.0000.0000.0000.0000.000
170A167VAL00.0330.02074.4750.0010.0010.0000.0000.0000.000
171A168HIS00.0220.02275.609-0.001-0.0010.0000.0000.0000.000
172A169LEU00.045-0.00573.9170.0000.0000.0000.0000.0000.000
173A170LYS10.7900.89378.1110.0160.0160.0000.0000.0000.000
174A171GLU-1-0.815-0.90881.258-0.015-0.0150.0000.0000.0000.000
175A172VAL0-0.0210.01677.9130.0000.0000.0000.0000.0000.000
176A173THR0-0.017-0.01181.3490.0000.0000.0000.0000.0000.000
177A174ALA00.0420.00784.4000.0000.0000.0000.0000.0000.000
178A175ALA0-0.025-0.01586.2200.0000.0000.0000.0000.0000.000
179A176ASN0-0.005-0.01484.0680.0000.0000.0000.0000.0000.000
180A177GLU-1-0.850-0.91680.821-0.015-0.0150.0000.0000.0000.000
181A178LEU0-0.010-0.01082.4210.0000.0000.0000.0000.0000.000
182A179ASN0-0.046-0.02883.8400.0000.0000.0000.0000.0000.000
183A180ILE0-0.0010.02278.1680.0000.0000.0000.0000.0000.000
184A181THR0-0.062-0.04076.4340.0000.0000.0000.0000.0000.000
185A182TRP0-0.0030.01775.356-0.001-0.0010.0000.0000.0000.000
186A183PRO0-0.043-0.03470.2990.0000.0000.0000.0000.0000.000
187A184LEU00.0260.01272.4410.0000.0000.0000.0000.0000.000
188A185SER0-0.029-0.01367.289-0.001-0.0010.0000.0000.0000.000
189A186ILE0-0.008-0.01668.3760.0000.0000.0000.0000.0000.000
190A187THR0-0.0200.00163.798-0.001-0.0010.0000.0000.0000.000
191A188CYS0-0.047-0.01264.5140.0000.0000.0000.0000.0000.000
192A189GLU-1-0.768-0.87160.764-0.029-0.0290.0000.0000.0000.000
193A190ARG10.9260.97558.1870.0320.0320.0000.0000.0000.000
194A191THR0-0.003-0.01461.243-0.001-0.0010.0000.0000.0000.000
195A192THR0-0.047-0.01758.0970.0000.0000.0000.0000.0000.000