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: J3J49

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 OptAll
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 -1527349.450403
FMO2-HF: Nuclear repulsion 1452385.972621
FMO2-HF: Total energy -74963.477782
FMO2-MP2: Total energy -75181.046709


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.
-3.2921.7832.9-3.111-4.864-0.006
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 : 0.015
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].
3A0GLY00.0010.0062.539-1.7541.6750.083-1.865-1.6480.004
4A1SER0-0.033-0.0224.4560.5070.675-0.001-0.017-0.1500.000
5A2VAL0-0.039-0.0137.0050.1330.1330.0000.0000.0000.000
6A3ALA00.0160.0119.045-0.002-0.0020.0000.0000.0000.000
7A4SER00.0490.02111.7240.0250.0250.0000.0000.0000.000
8A5ALA00.0300.0116.856-0.042-0.0420.0000.0000.0000.000
9A6TYR00.0100.0018.238-0.072-0.0720.0000.0000.0000.000
10A7ALA00.0180.00510.8180.0100.0100.0000.0000.0000.000
11A8ALA0-0.004-0.0057.8960.0270.0270.0000.0000.0000.000
12A9LEU0-0.0010.0136.471-0.085-0.0850.0000.0000.0000.000
13A10PRO00.0210.0108.372-0.017-0.0170.0000.0000.0000.000
14A11SER00.028-0.01310.916-0.017-0.0170.0000.0000.0000.000
15A12TRP00.0040.0002.474-2.369-0.8912.818-1.229-3.066-0.010
16A13ILE00.0040.0017.1630.0440.0440.0000.0000.0000.000
17A14ALA0-0.0040.0068.2940.0950.0950.0000.0000.0000.000
18A15TYR0-0.022-0.0197.1260.1140.1140.0000.0000.0000.000
19A16GLU-1-0.795-0.8644.990-0.103-0.1030.0000.0000.0000.000
20A17LYS10.8270.8987.2030.3040.3040.0000.0000.0000.000
21A18ALA00.0410.01710.5640.0640.0640.0000.0000.0000.000
22A19ARG10.7970.8445.768-0.065-0.0650.0000.0000.0000.000
23A20ALA0-0.008-0.0069.5520.0680.0680.0000.0000.0000.000
24A21ASP-1-0.782-0.87311.181-0.116-0.1160.0000.0000.0000.000
25A22LEU0-0.038-0.02013.8730.0230.0230.0000.0000.0000.000
26A23GLU-1-0.828-0.89211.8660.1810.1810.0000.0000.0000.000
27A24GLU-1-0.924-0.94314.397-0.004-0.0040.0000.0000.0000.000
28A25ALA00.0670.02016.6330.0110.0110.0000.0000.0000.000
29A26LYS10.8060.88414.857-0.119-0.1190.0000.0000.0000.000
30A27LYS10.8070.89313.818-0.119-0.1190.0000.0000.0000.000
31A28ASN0-0.078-0.04219.9560.0090.0090.0000.0000.0000.000
32A29ASP-1-0.944-0.96422.5070.0300.0300.0000.0000.0000.000
33A30VAL00.0020.02022.072-0.007-0.0070.0000.0000.0000.000
34A31SER00.0350.01324.4370.0020.0020.0000.0000.0000.000
35A32PRO00.0680.00925.502-0.005-0.0050.0000.0000.0000.000
36A33GLN0-0.023-0.01025.538-0.004-0.0040.0000.0000.0000.000
37A34LEU00.0550.04322.515-0.006-0.0060.0000.0000.0000.000
38A35LEU00.0680.03919.986-0.009-0.0090.0000.0000.0000.000
39A36LYS10.9770.99520.5940.0110.0110.0000.0000.0000.000
40A37GLN0-0.068-0.04021.762-0.011-0.0110.0000.0000.0000.000
41A38LEU00.0490.02517.290-0.013-0.0130.0000.0000.0000.000
42A39THR0-0.006-0.01116.890-0.008-0.0080.0000.0000.0000.000
43A40LYS10.9190.96517.5030.0580.0580.0000.0000.0000.000
44A41ALA00.0110.00417.200-0.011-0.0110.0000.0000.0000.000
45A42CYS0-0.0070.02111.614-0.017-0.0170.0000.0000.0000.000
46A43ASN0-0.020-0.02913.398-0.021-0.0210.0000.0000.0000.000
47A44ILE0-0.0060.00915.636-0.011-0.0110.0000.0000.0000.000
48A45ALA00.0490.03712.422-0.016-0.0160.0000.0000.0000.000
49A46LYS10.8320.90111.0040.0310.0310.0000.0000.0000.000
50A47SER0-0.066-0.04312.055-0.026-0.0260.0000.0000.0000.000
51A48GLU-1-0.773-0.85114.451-0.223-0.2230.0000.0000.0000.000
52A49PHE00.0180.0036.476-0.058-0.0580.0000.0000.0000.000
53A50GLU-1-0.833-0.90011.424-0.170-0.1700.0000.0000.0000.000
54A51ARG10.7390.82913.0970.2590.2590.0000.0000.0000.000
55A52GLU-1-0.785-0.86213.120-0.342-0.3420.0000.0000.0000.000
56A53ALA00.0030.00710.9400.0030.0030.0000.0000.0000.000
57A54SER0-0.103-0.06612.8340.0520.0520.0000.0000.0000.000
58A55VAL0-0.011-0.01116.4200.0300.0300.0000.0000.0000.000
59A56GLN0-0.013-0.01713.3520.0230.0230.0000.0000.0000.000
60A57LYS10.9800.99012.7620.2820.2820.0000.0000.0000.000
61A58LYS10.8770.95617.7310.1890.1890.0000.0000.0000.000
62A59LEU00.0110.00918.7460.0190.0190.0000.0000.0000.000
63A60ASP-1-0.833-0.91716.451-0.279-0.2790.0000.0000.0000.000
64A61LYS10.9570.98520.0880.1030.1030.0000.0000.0000.000
65A62MET0-0.020-0.00822.5000.0160.0160.0000.0000.0000.000
66A63ALA00.0120.00423.0180.0120.0120.0000.0000.0000.000
67A64GLU-1-0.932-0.96122.451-0.092-0.0920.0000.0000.0000.000
68A65GLN00.002-0.01924.8510.0080.0080.0000.0000.0000.000
69A66ALA00.0060.02027.9720.0090.0090.0000.0000.0000.000
70A67ALA00.0200.01527.3150.0080.0080.0000.0000.0000.000
71A68ALA0-0.013-0.00928.7270.0070.0070.0000.0000.0000.000
72A69SER0-0.091-0.05030.4190.0070.0070.0000.0000.0000.000
73A70MET00.017-0.00432.6920.0030.0030.0000.0000.0000.000
74A71TYR00.0050.00432.2400.0030.0030.0000.0000.0000.000
75A72LYS10.8720.92734.2660.0410.0410.0000.0000.0000.000
76A73GLU-1-0.793-0.87837.499-0.039-0.0390.0000.0000.0000.000
77A74ALA0-0.057-0.02139.1330.0010.0010.0000.0000.0000.000
78A75ARG10.9030.93737.1560.0430.0430.0000.0000.0000.000
79A76ALA00.0360.02340.649-0.001-0.0010.0000.0000.0000.000
80A77VAL0-0.059-0.02743.5350.0020.0020.0000.0000.0000.000
81A78ASP-1-0.814-0.90245.682-0.033-0.0330.0000.0000.0000.000
82A79ARG10.8500.91343.4790.0370.0370.0000.0000.0000.000
83A80LYS10.9550.95746.6980.0320.0320.0000.0000.0000.000
84A81SER00.1540.10650.1890.0000.0000.0000.0000.0000.000
85A82LYS10.9630.97652.8200.0270.0270.0000.0000.0000.000
86A83ILE0-0.011-0.00746.8980.0000.0000.0000.0000.0000.000
87A84VAL00.0410.02750.650-0.001-0.0010.0000.0000.0000.000
88A85SER0-0.005-0.02052.2540.0000.0000.0000.0000.0000.000
89A86ALA0-0.056-0.02251.9940.0000.0000.0000.0000.0000.000
90A87MET00.001-0.00348.368-0.001-0.0010.0000.0000.0000.000
91A88HIS00.0550.02752.2090.0000.0000.0000.0000.0000.000
92A89SER0-0.032-0.01055.6150.0010.0010.0000.0000.0000.000
93A90LEU0-0.003-0.00250.8430.0000.0000.0000.0000.0000.000
94A91LEU00.0150.01853.0870.0000.0000.0000.0000.0000.000
95A92PHE00.0410.00055.0590.0000.0000.0000.0000.0000.000
96A93GLY00.0040.01458.3800.0010.0010.0000.0000.0000.000
97A94MET0-0.056-0.04151.8470.0000.0000.0000.0000.0000.000
98A95LEU0-0.006-0.00556.3070.0000.0000.0000.0000.0000.000
99A96LYS11.0000.99858.9580.0230.0230.0000.0000.0000.000
100A97LYS10.9100.95957.7880.0300.0300.0000.0000.0000.000
101A98LEU0-0.049-0.02956.5100.0000.0000.0000.0000.0000.000
102A99ASP-1-0.884-0.92660.599-0.023-0.0230.0000.0000.0000.000
103A100MET0-0.0090.01458.2040.0000.0000.0000.0000.0000.000
104A101SER00.0520.02063.6260.0000.0000.0000.0000.0000.000
105A102SER00.0200.02462.1590.0010.0010.0000.0000.0000.000
106A103VAL00.0240.01159.6720.0000.0000.0000.0000.0000.000
107A104ASN0-0.024-0.03262.3510.0000.0000.0000.0000.0000.000
108A105THR0-0.035-0.02465.5920.0010.0010.0000.0000.0000.000
109A106ILE00.0110.00560.5030.0000.0000.0000.0000.0000.000
110A107ILE0-0.023-0.00760.4730.0000.0000.0000.0000.0000.000
111A108GLU-1-0.792-0.87764.344-0.020-0.0200.0000.0000.0000.000
112A109GLN0-0.023-0.01566.3980.0000.0000.0000.0000.0000.000
113A110ALA00.0160.01363.7230.0000.0000.0000.0000.0000.000
114A111ARG10.8180.90165.7340.0200.0200.0000.0000.0000.000
115A112ASN0-0.105-0.06267.9980.0010.0010.0000.0000.0000.000
116A113GLY00.0200.00968.1900.0000.0000.0000.0000.0000.000
117A114VAL0-0.026-0.01167.7940.0000.0000.0000.0000.0000.000
118A115LEU0-0.010-0.01062.737-0.001-0.0010.0000.0000.0000.000
119A116PRO0-0.012-0.01659.7990.0010.0010.0000.0000.0000.000
120A117LEU00.0210.02461.3670.0000.0000.0000.0000.0000.000
121A118SER0-0.035-0.02658.007-0.001-0.0010.0000.0000.0000.000
122A119ILE00.010-0.00154.8740.0010.0010.0000.0000.0000.000
123A120ILE00.0030.01053.021-0.001-0.0010.0000.0000.0000.000
124A121PRO0-0.011-0.00550.6400.0010.0010.0000.0000.0000.000
125A122ALA00.0210.00150.1630.0000.0000.0000.0000.0000.000
126A123ALA00.0450.01551.7460.0010.0010.0000.0000.0000.000
127A124SER0-0.087-0.03153.4410.0010.0010.0000.0000.0000.000
128A125ALA00.0390.02054.6980.0000.0000.0000.0000.0000.000
129A126THR0-0.048-0.01254.7750.0000.0000.0000.0000.0000.000
130A127ARG10.8760.92256.9190.0270.0270.0000.0000.0000.000
131A128LEU0-0.020-0.01758.490-0.001-0.0010.0000.0000.0000.000
132A129ILE00.0030.00361.1510.0010.0010.0000.0000.0000.000
133A130VAL00.003-0.00363.5140.0000.0000.0000.0000.0000.000
134A131VAL00.0080.02165.3450.0010.0010.0000.0000.0000.000
135A132THR00.003-0.02367.8740.0000.0000.0000.0000.0000.000
136A133PRO00.017-0.00670.9440.0010.0010.0000.0000.0000.000
137A134ASN00.0350.02973.6690.0000.0000.0000.0000.0000.000
138A135LEU00.0570.02376.335-0.001-0.0010.0000.0000.0000.000
139A136GLU-1-0.811-0.87678.425-0.016-0.0160.0000.0000.0000.000
140A137VAL0-0.058-0.03973.3660.0000.0000.0000.0000.0000.000
141A138LEU00.0070.00973.595-0.001-0.0010.0000.0000.0000.000
142A139SER0-0.040-0.04474.4260.0000.0000.0000.0000.0000.000
143A140LYS10.7990.89773.7800.0170.0170.0000.0000.0000.000
144A141VAL00.0000.01069.1540.0000.0000.0000.0000.0000.000
145A142ARG10.8400.93170.8140.0170.0170.0000.0000.0000.000
146A143GLN0-0.029-0.03272.9760.0000.0000.0000.0000.0000.000
147A144GLU-1-0.911-0.95673.897-0.018-0.0180.0000.0000.0000.000
148A145ASN0-0.0070.00873.1190.0000.0000.0000.0000.0000.000
149A146ASN0-0.010-0.00869.687-0.001-0.0010.0000.0000.0000.000
150A147VAL00.0350.01866.4080.0010.0010.0000.0000.0000.000
151A148HIS00.0250.01167.350-0.001-0.0010.0000.0000.0000.000
152A149TYR00.040-0.00561.9340.0000.0000.0000.0000.0000.000
153A150ALA0-0.0040.00359.754-0.001-0.0010.0000.0000.0000.000
154A151GLY0-0.0120.00260.650-0.001-0.0010.0000.0000.0000.000
155A152ALA0-0.056-0.01961.0970.0000.0000.0000.0000.0000.000
156A153ILE00.0550.02763.2370.0010.0010.0000.0000.0000.000
157A154TRP0-0.053-0.02758.512-0.002-0.0020.0000.0000.0000.000
158A155SER00.0760.05665.2070.0010.0010.0000.0000.0000.000
159A156ILE0-0.051-0.04066.574-0.001-0.0010.0000.0000.0000.000
160A157VAL0-0.057-0.01864.8070.0000.0000.0000.0000.0000.000
161A158GLU-1-0.799-0.88967.034-0.020-0.0200.0000.0000.0000.000
162A159VAL0-0.009-0.01269.1060.0000.0000.0000.0000.0000.000
163A160LYS10.8100.91666.8510.0210.0210.0000.0000.0000.000
164A161ASP-1-0.713-0.83972.053-0.016-0.0160.0000.0000.0000.000
165A162ALA00.0140.02071.5070.0000.0000.0000.0000.0000.000
166A163ASN0-0.105-0.05771.2840.0000.0000.0000.0000.0000.000
167A164GLY0-0.025-0.01370.1620.0000.0000.0000.0000.0000.000
168A165ALA0-0.013-0.00670.8080.0000.0000.0000.0000.0000.000
169A166GLN0-0.008-0.02969.7630.0000.0000.0000.0000.0000.000
170A167VAL00.0050.00074.1490.0010.0010.0000.0000.0000.000
171A168HIS00.0240.02175.478-0.001-0.0010.0000.0000.0000.000
172A169LEU00.0220.00073.5060.0000.0000.0000.0000.0000.000
173A170LYS10.8150.89477.8580.0150.0150.0000.0000.0000.000
174A171GLU-1-0.760-0.86881.298-0.014-0.0140.0000.0000.0000.000
175A172VAL0-0.050-0.00777.6400.0000.0000.0000.0000.0000.000
176A173THR0-0.0040.00081.0120.0000.0000.0000.0000.0000.000
177A174ALA00.0660.01883.9340.0000.0000.0000.0000.0000.000
178A175ALA0-0.035-0.01885.7080.0000.0000.0000.0000.0000.000
179A176ASN0-0.012-0.01983.5690.0000.0000.0000.0000.0000.000
180A177GLU-1-0.844-0.90980.639-0.015-0.0150.0000.0000.0000.000
181A178LEU0-0.001-0.00582.1830.0000.0000.0000.0000.0000.000
182A179ASN0-0.056-0.02784.0150.0000.0000.0000.0000.0000.000
183A180ILE0-0.0020.01677.8100.0000.0000.0000.0000.0000.000
184A181THR0-0.059-0.05076.1370.0000.0000.0000.0000.0000.000
185A182TRP0-0.0220.00275.170-0.001-0.0010.0000.0000.0000.000
186A183PRO0-0.048-0.03470.1870.0000.0000.0000.0000.0000.000
187A184LEU00.0250.01772.1990.0000.0000.0000.0000.0000.000
188A185SER0-0.020-0.00867.411-0.001-0.0010.0000.0000.0000.000
189A186ILE0-0.004-0.01567.9350.0000.0000.0000.0000.0000.000
190A187THR0-0.0140.00463.679-0.001-0.0010.0000.0000.0000.000
191A188CYS0-0.036-0.01164.3730.0010.0010.0000.0000.0000.000
192A189GLU-1-0.777-0.87260.796-0.027-0.0270.0000.0000.0000.000
193A190ARG10.9250.97358.3050.0310.0310.0000.0000.0000.000
194A191THR0-0.025-0.02861.2400.0000.0000.0000.0000.0000.000
195A192THR0-0.028-0.01357.6500.0000.0000.0000.0000.0000.000