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: 43R4N

Calculation Name: 3UB0-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1527863.229771
FMO2-HF: Nuclear repulsion 1452730.943295
FMO2-HF: Total energy -75132.286476
FMO2-MP2: Total energy -75350.411873


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:-3:ACE )


Summations of interaction energy for fragment #1(A:-3:ACE )
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.
2.6013.9640.118-0.526-0.9550
Interaction energy analysis for fragmet #1(A:-3:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / 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].
3A-1LEU 0-0.019-0.0093.8170.5491.3390.006-0.322-0.4740.000
4A0GLY 00.002-0.0033.0270.8651.3030.108-0.214-0.3320.000
5A1SER 0-0.003-0.0014.0020.3020.4370.0040.010-0.1490.000
6A2VAL 0-0.065-0.0246.7670.2590.2590.0000.0000.0000.000
7A3ALA 00.0370.0299.3470.0750.0750.0000.0000.0000.000
8A4SER 00.0570.02412.1010.0470.0470.0000.0000.0000.000
9A5ALA 00.0340.0088.011-0.041-0.0410.0000.0000.0000.000
10A6TYR 0-0.002-0.0059.824-0.010-0.0100.0000.0000.0000.000
11A7ALA 00.0130.00112.9920.0050.0050.0000.0000.0000.000
12A8ALA 00.000-0.00710.8410.0030.0030.0000.0000.0000.000
13A9LEU 00.0020.01210.256-0.041-0.0410.0000.0000.0000.000
14A10PRO 00.0160.00612.470-0.005-0.0050.0000.0000.0000.000
15A11SER 00.0640.03615.164-0.021-0.0210.0000.0000.0000.000
16A12TRP 0-0.002-0.0127.8830.0090.0090.0000.0000.0000.000
17A13ILE 0-0.0060.00512.4040.0010.0010.0000.0000.0000.000
18A14ALA 00.0010.01113.7100.0250.0250.0000.0000.0000.000
19A15TYR 0-0.019-0.01512.2100.0530.0530.0000.0000.0000.000
20A16GLU -1-0.894-0.95510.306-0.496-0.4960.0000.0000.0000.000
21A17LYS 10.9630.97013.1510.1880.1880.0000.0000.0000.000
22A18ALA 00.0480.03216.3980.0260.0260.0000.0000.0000.000
23A19ARG 10.8760.90910.4240.4850.4850.0000.0000.0000.000
24A20ALA 0-0.028-0.00614.6930.0250.0250.0000.0000.0000.000
25A21ASP -1-0.865-0.92316.244-0.106-0.1060.0000.0000.0000.000
26A22LEU 0-0.056-0.02919.1010.0170.0170.0000.0000.0000.000
27A23GLU -1-0.927-0.97416.011-0.094-0.0940.0000.0000.0000.000
28A24GLU -1-0.960-0.98018.810-0.045-0.0450.0000.0000.0000.000
29A25ALA 0-0.012-0.01421.0500.0120.0120.0000.0000.0000.000
30A26LYS 10.9070.95619.5290.1390.1390.0000.0000.0000.000
31A27LYS 10.8950.95417.6820.0660.0660.0000.0000.0000.000
32A28ASN 0-0.009-0.00523.4610.0130.0130.0000.0000.0000.000
33A29ASP -1-0.982-0.97426.366-0.040-0.0400.0000.0000.0000.000
34A30VAL 0-0.0070.01227.0810.0020.0020.0000.0000.0000.000
35A31SER 00.0370.01029.206-0.003-0.0030.0000.0000.0000.000
36A32PRO 00.0720.01530.329-0.006-0.0060.0000.0000.0000.000
37A33GLN 0-0.068-0.03330.788-0.007-0.0070.0000.0000.0000.000
38A34LEU 00.0630.03227.788-0.005-0.0050.0000.0000.0000.000
39A35LEU 00.1020.04825.275-0.010-0.0100.0000.0000.0000.000
40A36LYS 10.9400.98926.0270.0630.0630.0000.0000.0000.000
41A37GLN 0-0.058-0.02627.539-0.010-0.0100.0000.0000.0000.000
42A38LEU 00.0590.02322.971-0.010-0.0100.0000.0000.0000.000
43A39THR 0-0.013-0.01622.544-0.019-0.0190.0000.0000.0000.000
44A40LYS 10.9160.96322.9640.0880.0880.0000.0000.0000.000
45A41ALA 00.0230.01223.058-0.010-0.0100.0000.0000.0000.000
46A42CYS 0-0.0080.02217.584-0.026-0.0260.0000.0000.0000.000
47A43ASN 0-0.004-0.01619.385-0.038-0.0380.0000.0000.0000.000
48A44ILE 0-0.011-0.00421.292-0.010-0.0100.0000.0000.0000.000
49A45ALA 00.0500.03018.062-0.008-0.0080.0000.0000.0000.000
50A46LYS 10.9280.97515.8550.3260.3260.0000.0000.0000.000
51A47SER 0-0.039-0.02417.342-0.017-0.0170.0000.0000.0000.000
52A48GLU -1-0.813-0.91219.935-0.199-0.1990.0000.0000.0000.000
53A49PHE 00.0000.00410.331-0.033-0.0330.0000.0000.0000.000
54A50GLU -1-0.947-0.98315.935-0.369-0.3690.0000.0000.0000.000
55A51ARG 10.8640.93517.1520.2020.2020.0000.0000.0000.000
56A52GLU -1-0.886-0.96417.698-0.236-0.2360.0000.0000.0000.000
57A53ALA 00.0020.01514.7230.0070.0070.0000.0000.0000.000
58A54SER 0-0.110-0.05616.2770.0300.0300.0000.0000.0000.000
59A55VAL 0-0.0040.00019.3540.0240.0240.0000.0000.0000.000
60A56GLN 00.016-0.00115.9380.0380.0380.0000.0000.0000.000
61A57LYS 10.9760.99014.6840.3500.3500.0000.0000.0000.000
62A58LYS 10.8880.94619.0660.2000.2000.0000.0000.0000.000
63A59LEU 00.005-0.00421.8430.0170.0170.0000.0000.0000.000
64A60ASP -1-0.852-0.91417.612-0.182-0.1820.0000.0000.0000.000
65A61LYS 10.9480.97821.2070.1330.1330.0000.0000.0000.000
66A62MET 0-0.007-0.00523.3070.0140.0140.0000.0000.0000.000
67A63ALA 00.0240.01223.8910.0110.0110.0000.0000.0000.000
68A64GLU -1-0.944-0.96421.697-0.091-0.0910.0000.0000.0000.000
69A65GLN 0-0.037-0.03625.0880.0070.0070.0000.0000.0000.000
70A66ALA 0-0.0010.00628.3570.0070.0070.0000.0000.0000.000
71A67ALA 00.0220.01027.4370.0070.0070.0000.0000.0000.000
72A68ALA 0-0.010-0.00628.7600.0070.0070.0000.0000.0000.000
73A69SER 0-0.098-0.04330.4680.0050.0050.0000.0000.0000.000
74A70MET 00.0170.00733.0190.0020.0020.0000.0000.0000.000
75A71TYR 00.0220.01931.2050.0040.0040.0000.0000.0000.000
76A72LYS 10.9590.98634.1450.0290.0290.0000.0000.0000.000
77A73GLU -1-0.933-0.96637.575-0.024-0.0240.0000.0000.0000.000
78A74ALA 00.0070.00038.4670.0010.0010.0000.0000.0000.000
79A75ARG 10.7920.89240.1580.0180.0180.0000.0000.0000.000
80A76ALA 00.0170.00644.582-0.001-0.0010.0000.0000.0000.000
81A77VAL 0-0.002-0.02040.681-0.001-0.0010.0000.0000.0000.000
82A78ASP -1-0.808-0.89243.902-0.014-0.0140.0000.0000.0000.000
83A79ARG 10.8890.98544.3160.0180.0180.0000.0000.0000.000
84A80LYS 10.8760.92247.0790.0190.0190.0000.0000.0000.000
85A81SER 00.1530.07550.3310.0000.0000.0000.0000.0000.000
86A82LYS 10.9840.97152.9360.0160.0160.0000.0000.0000.000
87A83ILE 00.0300.00946.8870.0000.0000.0000.0000.0000.000
88A84VAL 00.0810.05350.6180.0000.0000.0000.0000.0000.000
89A85SER 0-0.014-0.02152.5200.0000.0000.0000.0000.0000.000
90A86ALA 0-0.052-0.02252.5310.0000.0000.0000.0000.0000.000
91A87MET 00.0150.00548.913-0.001-0.0010.0000.0000.0000.000
92A88HIS 00.0400.02253.3360.0000.0000.0000.0000.0000.000
93A89SER 0-0.032-0.01556.6890.0000.0000.0000.0000.0000.000
94A90LEU 00.008-0.00452.4140.0000.0000.0000.0000.0000.000
95A91LEU 00.0080.01254.9850.0000.0000.0000.0000.0000.000
96A92PHE 00.0370.00156.6450.0000.0000.0000.0000.0000.000
97A93GLY 00.0110.02059.8870.0000.0000.0000.0000.0000.000
98A94MET 0-0.061-0.04354.1820.0000.0000.0000.0000.0000.000
99A95LEU 0-0.005-0.00158.4070.0000.0000.0000.0000.0000.000
100A96LYS 10.9810.99461.1270.0120.0120.0000.0000.0000.000
101A97LYS 10.9230.95959.4530.0180.0180.0000.0000.0000.000
102A98LEU 0-0.044-0.02158.8280.0000.0000.0000.0000.0000.000
103A99ASP -1-0.929-0.95362.752-0.012-0.0120.0000.0000.0000.000
104A100MET 00.0140.02561.2670.0000.0000.0000.0000.0000.000
105A101SER 00.0340.00766.1170.0000.0000.0000.0000.0000.000
106A102SER 00.0180.01364.2250.0000.0000.0000.0000.0000.000
107A103VAL 00.0410.02061.6850.0000.0000.0000.0000.0000.000
108A104ASN 00.027-0.00264.3120.0000.0000.0000.0000.0000.000
109A105THR 0-0.056-0.02367.5910.0010.0010.0000.0000.0000.000
110A106ILE 0-0.016-0.00161.6130.0000.0000.0000.0000.0000.000
111A107ILE 0-0.014-0.00961.8080.0000.0000.0000.0000.0000.000
112A108GLU -1-0.826-0.91365.802-0.008-0.0080.0000.0000.0000.000
113A109GLN 0-0.034-0.03467.8050.0000.0000.0000.0000.0000.000
114A110ALA 00.0310.02664.7480.0000.0000.0000.0000.0000.000
115A111ARG 10.8330.93066.6960.0080.0080.0000.0000.0000.000
116A112ASN 0-0.101-0.04868.9070.0000.0000.0000.0000.0000.000
117A113GLY 00.0370.01568.7620.0000.0000.0000.0000.0000.000
118A114VAL 0-0.046-0.01968.6790.0000.0000.0000.0000.0000.000
119A115LEU 0-0.018-0.01062.966-0.001-0.0010.0000.0000.0000.000
120A116PRO 0-0.019-0.01760.5150.0000.0000.0000.0000.0000.000
121A117LEU 00.0160.01762.0340.0000.0000.0000.0000.0000.000
122A118SER 0-0.025-0.02458.4060.0000.0000.0000.0000.0000.000
123A119ILE 00.012-0.00256.4130.0000.0000.0000.0000.0000.000
124A120ILE 00.0050.01354.0860.0000.0000.0000.0000.0000.000
125A121PRO 00.0050.00451.4100.0000.0000.0000.0000.0000.000
126A122ALA 00.0300.00850.9370.0010.0010.0000.0000.0000.000
127A123ALA 00.0570.02752.7260.0000.0000.0000.0000.0000.000
128A124SER 0-0.104-0.04654.3470.0000.0000.0000.0000.0000.000
129A125ALA 00.0380.01955.516-0.001-0.0010.0000.0000.0000.000
130A126THR 0-0.030-0.01156.1540.0000.0000.0000.0000.0000.000
131A127ARG 10.9080.94057.9020.0030.0030.0000.0000.0000.000
132A128LEU 0-0.029-0.00659.4020.0000.0000.0000.0000.0000.000
133A129ILE 00.0190.01261.9160.0000.0000.0000.0000.0000.000
134A130VAL 00.002-0.01563.8490.0000.0000.0000.0000.0000.000
135A131VAL 00.0070.02266.0480.0000.0000.0000.0000.0000.000
136A132THR 0-0.018-0.02168.5150.0000.0000.0000.0000.0000.000
137A133PRO 00.012-0.01171.4110.0000.0000.0000.0000.0000.000
138A134ASN 00.0350.02773.9800.0000.0000.0000.0000.0000.000
139A135LEU 00.0840.03877.1480.0000.0000.0000.0000.0000.000
140A136GLU -1-0.928-0.94679.696-0.005-0.0050.0000.0000.0000.000
141A137VAL 0-0.070-0.05974.2650.0000.0000.0000.0000.0000.000
142A138LEU 00.0060.00774.7000.0000.0000.0000.0000.0000.000
143A139SER 0-0.012-0.01575.7490.0000.0000.0000.0000.0000.000
144A140LYS 10.9090.97475.2860.0060.0060.0000.0000.0000.000
145A141VAL 0-0.003-0.00170.6190.0000.0000.0000.0000.0000.000
146A142ARG 10.9130.97672.4460.0040.0040.0000.0000.0000.000
147A143GLN 0-0.057-0.03174.1750.0000.0000.0000.0000.0000.000
148A144GLU -1-0.912-0.96075.378-0.004-0.0040.0000.0000.0000.000
149A145ASN 0-0.019-0.01273.8760.0000.0000.0000.0000.0000.000
150A146ASN 00.0170.01571.1240.0000.0000.0000.0000.0000.000
151A147VAL 00.0230.01668.1730.0000.0000.0000.0000.0000.000
152A148HIS 00.0410.02668.8650.0000.0000.0000.0000.0000.000
153A149TYR 00.047-0.00462.5400.0000.0000.0000.0000.0000.000
154A150ALA 00.0090.00861.4970.0000.0000.0000.0000.0000.000
155A151GLY 0-0.034-0.01162.5470.0000.0000.0000.0000.0000.000
156A152ALA 0-0.052-0.00862.7460.0000.0000.0000.0000.0000.000
157A153ILE 00.0520.01964.8750.0000.0000.0000.0000.0000.000
158A154TRP 0-0.066-0.04260.0170.0000.0000.0000.0000.0000.000
159A155SER 00.0580.03266.6670.0000.0000.0000.0000.0000.000
160A156ILE 0-0.057-0.04567.7080.0000.0000.0000.0000.0000.000
161A157VAL 0-0.063-0.01665.5000.0000.0000.0000.0000.0000.000
162A158GLU -1-0.874-0.94267.641-0.001-0.0010.0000.0000.0000.000
163A159VAL 00.002-0.00369.9300.0000.0000.0000.0000.0000.000
164A160LYS 10.8840.95566.7900.0020.0020.0000.0000.0000.000
165A161ASP -1-0.818-0.91172.197-0.002-0.0020.0000.0000.0000.000
166A162ALA 0-0.0080.00871.5040.0000.0000.0000.0000.0000.000
167A163ASN 0-0.024-0.02671.5200.0000.0000.0000.0000.0000.000
168A164GLY 0-0.032-0.01770.4410.0000.0000.0000.0000.0000.000
169A165ALA 0-0.016-0.00371.1180.0000.0000.0000.0000.0000.000
170A166GLN 0-0.047-0.04370.7340.0000.0000.0000.0000.0000.000
171A167VAL 00.0430.02774.7660.0000.0000.0000.0000.0000.000
172A168HIS 00.0160.01076.0650.0000.0000.0000.0000.0000.000
173A169LEU 00.050-0.00674.8060.0000.0000.0000.0000.0000.000
174A170LYS 10.8870.95478.6910.0010.0010.0000.0000.0000.000
175A171GLU -1-0.908-0.95581.794-0.001-0.0010.0000.0000.0000.000
176A172VAL 00.0040.02878.4160.0000.0000.0000.0000.0000.000
177A173THR 0-0.016-0.00981.8260.0000.0000.0000.0000.0000.000
178A174ALA 00.0540.00584.9280.0000.0000.0000.0000.0000.000
179A175ALA 0-0.036-0.01986.7740.0000.0000.0000.0000.0000.000
180A176ASN 00.007-0.00384.1830.0000.0000.0000.0000.0000.000
181A177GLU -1-0.907-0.95481.649-0.004-0.0040.0000.0000.0000.000
182A178LEU 0-0.007-0.01082.6720.0000.0000.0000.0000.0000.000
183A179ASN 0-0.060-0.03783.9730.0000.0000.0000.0000.0000.000
184A180ILE 00.0250.03578.4030.0000.0000.0000.0000.0000.000
185A181THR 0-0.055-0.01176.2430.0000.0000.0000.0000.0000.000
186A182TRP 00.0130.02575.5860.0000.0000.0000.0000.0000.000
187A183PRO 0-0.048-0.03970.6140.0000.0000.0000.0000.0000.000
188A184LEU 00.0380.01972.6700.0000.0000.0000.0000.0000.000
189A185SER 0-0.035-0.01767.6050.0000.0000.0000.0000.0000.000
190A186ILE 0-0.009-0.01468.8430.0000.0000.0000.0000.0000.000
191A187THR 00.0070.01064.250-0.001-0.0010.0000.0000.0000.000
192A188CYS 0-0.024-0.00565.1570.0000.0000.0000.0000.0000.000
193A189GLU -1-0.803-0.89661.138-0.003-0.0030.0000.0000.0000.000
194A190ARG 10.9290.97259.2270.0090.0090.0000.0000.0000.000
195A191THR 0-0.012-0.01562.4660.0000.0000.0000.0000.0000.000
196A192THR 0-0.089-0.04659.663-0.001-0.0010.0000.0000.0000.000
197A193NME 00.0470.03660.4400.0000.0000.0000.0000.0000.000