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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QYMYY

Calculation Name: 1VK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FNG3

Base Structure: X-ray

Registration Date: 2023-06-22

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2379061.68769
FMO2-HF: Nuclear repulsion 2299147.904763
FMO2-HF: Total energy -79913.782926
FMO2-MP2: Total energy -80152.138592


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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-0.8960.193-0.004-0.462-0.6230.002
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.023
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].
3A3SER00.0050.0043.869-1.286-0.197-0.004-0.462-0.6230.002
4A4PHE00.040-0.0026.2340.3750.3750.0000.0000.0000.000
5A5ASP-1-0.825-0.8947.091-1.291-1.2910.0000.0000.0000.000
6A6GLY00.0280.0279.9940.0310.0310.0000.0000.0000.000
7A7PRO0-0.0030.01313.450-0.065-0.0650.0000.0000.0000.000
8A8LYS10.9310.97614.4160.5570.5570.0000.0000.0000.000
9A9PHE00.0370.01217.3410.0060.0060.0000.0000.0000.000
10A10LYS10.8730.96121.0150.1920.1920.0000.0000.0000.000
11A11MET00.0330.02522.4410.0210.0210.0000.0000.0000.000
12A12THR00.007-0.01525.688-0.009-0.0090.0000.0000.0000.000
13A13ASP-1-0.799-0.85725.933-0.099-0.0990.0000.0000.0000.000
14A14GLY0-0.093-0.05626.326-0.005-0.0050.0000.0000.0000.000
15A15SER0-0.041-0.04721.869-0.026-0.0260.0000.0000.0000.000
16A16TYR0-0.018-0.03418.561-0.003-0.0030.0000.0000.0000.000
17A17VAL00.0500.04318.231-0.004-0.0040.0000.0000.0000.000
18A18GLN0-0.069-0.04010.8590.0000.0000.0000.0000.0000.000
19A19THR0-0.028-0.02814.9030.0820.0820.0000.0000.0000.000
20A20LYS10.8020.8908.0850.4060.4060.0000.0000.0000.000
21A21THR00.0510.02913.4920.0850.0850.0000.0000.0000.000
22A22ILE0-0.058-0.03111.499-0.003-0.0030.0000.0000.0000.000
23A23ASP-1-0.814-0.85914.8960.0800.0800.0000.0000.0000.000
24A24VAL0-0.040-0.02115.9120.0640.0640.0000.0000.0000.000
25A25GLY00.0510.01816.793-0.053-0.0530.0000.0000.0000.000
26A26SER0-0.012-0.01318.4110.0450.0450.0000.0000.0000.000
27A27SER0-0.020-0.01715.9940.0140.0140.0000.0000.0000.000
28A28THR0-0.0140.01312.4270.0800.0800.0000.0000.0000.000
29A29ASP-1-0.764-0.8619.7431.6321.6320.0000.0000.0000.000
30A30ILE00.0340.00410.2860.1580.1580.0000.0000.0000.000
31A31SER0-0.030-0.02111.2490.0170.0170.0000.0000.0000.000
32A32PRO0-0.002-0.0026.288-0.060-0.0600.0000.0000.0000.000
33A33TYR00.0150.0046.808-0.325-0.3250.0000.0000.0000.000
34A34LEU00.0310.01610.420-0.151-0.1510.0000.0000.0000.000
35A35SER0-0.054-0.04310.114-0.195-0.1950.0000.0000.0000.000
36A36LEU00.0400.0336.369-0.155-0.1550.0000.0000.0000.000
37A37ILE00.0110.02310.731-0.148-0.1480.0000.0000.0000.000
38A38ARG10.8960.94513.626-0.820-0.8200.0000.0000.0000.000
39A39GLU-1-0.976-0.98910.3150.5670.5670.0000.0000.0000.000
40A40ASP-1-0.747-0.83513.705-0.035-0.0350.0000.0000.0000.000
41A41SER00.027-0.00715.230-0.041-0.0410.0000.0000.0000.000
42A42ILE0-0.112-0.06017.857-0.026-0.0260.0000.0000.0000.000
43A43LEU0-0.068-0.02114.499-0.024-0.0240.0000.0000.0000.000
44A44ASN0-0.039-0.04015.753-0.036-0.0360.0000.0000.0000.000
45A45GLY00.0030.01319.624-0.021-0.0210.0000.0000.0000.000
46A46ASN00.0000.00221.4900.0060.0060.0000.0000.0000.000
47A47ARG10.8400.91122.043-0.222-0.2220.0000.0000.0000.000
48A48ALA00.0720.06223.0640.0080.0080.0000.0000.0000.000
49A49VAL0-0.032-0.01619.5760.0100.0100.0000.0000.0000.000
50A50ILE00.0000.01822.1140.0020.0020.0000.0000.0000.000
51A51PHE0-0.035-0.03122.5320.0170.0170.0000.0000.0000.000
52A52ASP-1-0.777-0.86624.4180.0440.0440.0000.0000.0000.000
53A53VAL0-0.028-0.01724.9310.0230.0230.0000.0000.0000.000
54A54TYR0-0.038-0.02924.076-0.016-0.0160.0000.0000.0000.000
55A55TRP0-0.017-0.03527.9950.0190.0190.0000.0000.0000.000
56A56ASP-1-0.901-0.94230.3120.0690.0690.0000.0000.0000.000
57A57VAL00.0150.01431.9860.0060.0060.0000.0000.0000.000
58A58GLY00.0550.03135.701-0.003-0.0030.0000.0000.0000.000
59A59PHE0-0.034-0.03537.345-0.003-0.0030.0000.0000.0000.000
60A60PRO0-0.097-0.06839.8950.0030.0030.0000.0000.0000.000
61A61GLU-1-0.732-0.82240.4710.0620.0620.0000.0000.0000.000
62A62THR00.0260.00939.407-0.003-0.0030.0000.0000.0000.000
63A63GLU-1-0.818-0.89341.7670.0860.0860.0000.0000.0000.000
64A64THR0-0.048-0.05542.824-0.004-0.0040.0000.0000.0000.000
65A65LYS10.7670.88545.186-0.064-0.0640.0000.0000.0000.000
66A66THR00.0430.02941.362-0.005-0.0050.0000.0000.0000.000
67A67LYS10.8860.92342.136-0.053-0.0530.0000.0000.0000.000
68A68THR00.0510.04738.793-0.003-0.0030.0000.0000.0000.000
69A69SER0-0.050-0.03037.6980.0050.0050.0000.0000.0000.000
70A70GLY00.003-0.00536.6420.0060.0060.0000.0000.0000.000
71A71TRP0-0.040-0.00234.269-0.002-0.0020.0000.0000.0000.000
72A72SER0-0.0110.01129.9790.0090.0090.0000.0000.0000.000
73A73LEU00.001-0.00725.212-0.006-0.0060.0000.0000.0000.000
74A74SER0-0.020-0.00226.3530.0130.0130.0000.0000.0000.000
75A75SER0-0.018-0.03122.5940.0040.0040.0000.0000.0000.000
76A76VAL0-0.0090.00720.449-0.001-0.0010.0000.0000.0000.000
77A77LYS10.8920.96120.514-0.035-0.0350.0000.0000.0000.000
78A78LEU0-0.042-0.02417.6990.0180.0180.0000.0000.0000.000
79A79SER00.0360.00318.333-0.015-0.0150.0000.0000.0000.000
80A80THR0-0.064-0.05216.8280.0170.0170.0000.0000.0000.000
81A81ARG10.8540.90419.5180.0030.0030.0000.0000.0000.000
82A82ASN0-0.022-0.03615.755-0.049-0.0490.0000.0000.0000.000
83A83LEU0-0.0240.01112.296-0.063-0.0630.0000.0000.0000.000
84A84CYS0-0.028-0.00815.7710.0410.0410.0000.0000.0000.000
85A85LEU0-0.035-0.01512.878-0.027-0.0270.0000.0000.0000.000
86A86PHE00.0380.01215.9880.0200.0200.0000.0000.0000.000
87A87LEU0-0.022-0.01314.9850.0330.0330.0000.0000.0000.000
88A88ARG10.8620.88118.331-0.070-0.0700.0000.0000.0000.000
89A89LEU0-0.0130.00019.8750.0360.0360.0000.0000.0000.000
90A90PRO00.0150.01720.660-0.027-0.0270.0000.0000.0000.000
91A91LYS10.8820.91623.514-0.113-0.1130.0000.0000.0000.000
92A92PRO0-0.040-0.00125.817-0.002-0.0020.0000.0000.0000.000
93A93PHE00.0520.01423.6670.0200.0200.0000.0000.0000.000
94A94HIS00.0370.01021.4790.0010.0010.0000.0000.0000.000
95A95ASP-1-0.781-0.90221.2270.3600.3600.0000.0000.0000.000
96A96ASN0-0.059-0.03216.114-0.028-0.0280.0000.0000.0000.000
97A97LEU00.0380.01517.4830.0540.0540.0000.0000.0000.000
98A98LYS10.8160.89919.896-0.367-0.3670.0000.0000.0000.000
99A99ASP-1-0.838-0.90616.1320.7270.7270.0000.0000.0000.000
100A100LEU00.0140.02018.161-0.002-0.0020.0000.0000.0000.000
101A101TYR0-0.030-0.03219.646-0.018-0.0180.0000.0000.0000.000
102A102ARG10.8080.88017.865-0.591-0.5910.0000.0000.0000.000
103A103PHE0-0.029-0.01416.5110.0000.0000.0000.0000.0000.000
104A104PHE00.0690.02420.155-0.023-0.0230.0000.0000.0000.000
105A105ALA00.0170.02623.361-0.030-0.0300.0000.0000.0000.000
106A106SER0-0.0310.00121.415-0.027-0.0270.0000.0000.0000.000
107A107LYS10.9820.98223.935-0.209-0.2090.0000.0000.0000.000
108A108PHE0-0.070-0.03019.567-0.011-0.0110.0000.0000.0000.000
109A109VAL00.0400.02420.438-0.007-0.0070.0000.0000.0000.000
110A110THR00.0400.03023.7360.0090.0090.0000.0000.0000.000
111A111PHE0-0.048-0.01221.5430.0000.0000.0000.0000.0000.000
112A112VAL00.0210.00325.909-0.009-0.0090.0000.0000.0000.000
113A113GLY00.0600.03027.0720.0010.0010.0000.0000.0000.000
114A114VAL0-0.014-0.02229.414-0.006-0.0060.0000.0000.0000.000
115A115GLN0-0.082-0.05132.3640.0050.0050.0000.0000.0000.000
116A116ILE00.0540.03030.1820.0030.0030.0000.0000.0000.000
117A117GLU-1-0.888-0.93833.4670.0780.0780.0000.0000.0000.000
118A118GLU-1-0.894-0.94736.4760.0740.0740.0000.0000.0000.000
119A119ASP-1-0.794-0.89031.1710.0960.0960.0000.0000.0000.000
120A120LEU0-0.047-0.04030.7650.0150.0150.0000.0000.0000.000
121A121ASP-1-0.778-0.86633.0480.1100.1100.0000.0000.0000.000
122A122LEU00.0530.04033.7920.0050.0050.0000.0000.0000.000
123A123LEU0-0.052-0.02627.6600.0110.0110.0000.0000.0000.000
124A124ARG10.7630.86431.163-0.109-0.1090.0000.0000.0000.000
125A125GLU-1-0.990-1.00433.1620.1030.1030.0000.0000.0000.000
126A126ASN0-0.056-0.04433.0490.0000.0000.0000.0000.0000.000
127A127HIS0-0.0210.00527.875-0.007-0.0070.0000.0000.0000.000
128A128GLY00.0350.04529.3440.0180.0180.0000.0000.0000.000
129A129LEU0-0.086-0.03824.3860.0200.0200.0000.0000.0000.000
130A130VAL0-0.010-0.01628.250-0.016-0.0160.0000.0000.0000.000
131A131ILE00.0310.02226.4890.0200.0200.0000.0000.0000.000
132A132ARG10.7690.85726.511-0.255-0.2550.0000.0000.0000.000
133A133ASN0-0.046-0.01927.230-0.023-0.0230.0000.0000.0000.000
134A134ALA00.0210.01828.1870.0080.0080.0000.0000.0000.000
135A135ILE00.0220.01329.982-0.006-0.0060.0000.0000.0000.000
136A136ASN0-0.020-0.01131.371-0.001-0.0010.0000.0000.0000.000
137A137VAL00.0480.00131.448-0.004-0.0040.0000.0000.0000.000
138A138GLY00.0360.02133.755-0.006-0.0060.0000.0000.0000.000
139A139LYS10.8430.91836.823-0.066-0.0660.0000.0000.0000.000
140A140LEU00.0480.03433.997-0.002-0.0020.0000.0000.0000.000
141A141ALA00.0360.01236.387-0.004-0.0040.0000.0000.0000.000
142A142ALA0-0.041-0.01238.115-0.004-0.0040.0000.0000.0000.000
143A143GLU-1-0.980-1.00141.0600.0510.0510.0000.0000.0000.000
144A144ALA0-0.042-0.01438.848-0.002-0.0020.0000.0000.0000.000
145A145ARG10.7370.81837.017-0.015-0.0150.0000.0000.0000.000
146A146GLY00.0120.02542.509-0.003-0.0030.0000.0000.0000.000
147A147THR0-0.107-0.05043.436-0.004-0.0040.0000.0000.0000.000
148A148LEU00.0470.00443.8510.0010.0010.0000.0000.0000.000
149A149VAL00.015-0.00643.8140.0020.0020.0000.0000.0000.000
150A150LEU00.0050.00339.5010.0000.0000.0000.0000.0000.000
151A151GLU-1-0.824-0.89539.3240.0500.0500.0000.0000.0000.000
152A152PHE0-0.074-0.02440.0630.0030.0030.0000.0000.0000.000
153A153LEU0-0.053-0.00138.540-0.004-0.0040.0000.0000.0000.000
154A154GLY00.0730.03236.2320.0050.0050.0000.0000.0000.000
155A155THR0-0.008-0.01029.7390.0000.0000.0000.0000.0000.000
156A156ARG10.8630.89633.1400.0190.0190.0000.0000.0000.000
157A157GLU-1-0.796-0.88034.170-0.008-0.0080.0000.0000.0000.000
158A158LEU00.0230.01233.884-0.001-0.0010.0000.0000.0000.000
159A159ALA00.0480.01632.244-0.001-0.0010.0000.0000.0000.000
160A160HIS0-0.108-0.06334.123-0.006-0.0060.0000.0000.0000.000
161A161ARG10.8350.90337.162-0.002-0.0020.0000.0000.0000.000
162A162VAL00.0050.01634.9790.0010.0010.0000.0000.0000.000
163A163LEU0-0.019-0.02131.227-0.002-0.0020.0000.0000.0000.000
164A164TRP0-0.106-0.03335.618-0.005-0.0050.0000.0000.0000.000
165A165SER00.0370.02633.186-0.003-0.0030.0000.0000.0000.000
166A166ASP-1-0.950-0.97134.171-0.059-0.0590.0000.0000.0000.000
167A167LEU00.009-0.01132.490-0.003-0.0030.0000.0000.0000.000
168A168GLY00.0390.02434.4620.0020.0020.0000.0000.0000.000
169A169GLN0-0.054-0.04428.1400.0070.0070.0000.0000.0000.000
170A170LEU0-0.0030.00029.392-0.001-0.0010.0000.0000.0000.000
171A171ASP-1-0.772-0.85831.711-0.027-0.0270.0000.0000.0000.000
172A172SER0-0.055-0.01533.7520.0050.0050.0000.0000.0000.000
173A173ILE0-0.0110.00128.1980.0020.0020.0000.0000.0000.000
174A174GLH0-0.072-0.08231.7040.0050.0050.0000.0000.0000.000
175A175ALA0-0.029-0.00734.0750.0060.0060.0000.0000.0000.000
176A176LYS10.7580.87432.0970.0730.0730.0000.0000.0000.000
177A177TRP00.0640.03528.324-0.007-0.0070.0000.0000.0000.000
178A178GLU-1-0.834-0.91433.027-0.026-0.0260.0000.0000.0000.000
179A179LYS10.7890.87534.5680.0310.0310.0000.0000.0000.000
180A180ALA0-0.0180.01930.319-0.008-0.0080.0000.0000.0000.000
181A181GLY00.0110.01328.5390.0060.0060.0000.0000.0000.000
182A182PRO00.020-0.01423.9730.0000.0000.0000.0000.0000.000
183A183GLU-1-0.876-0.94520.852-0.201-0.2010.0000.0000.0000.000
184A184GLU-1-0.786-0.89323.684-0.086-0.0860.0000.0000.0000.000
185A185GLN0-0.036-0.00526.5400.0100.0100.0000.0000.0000.000
186A186LEU0-0.016-0.00618.8870.0110.0110.0000.0000.0000.000
187A187GLU-1-0.844-0.90923.092-0.123-0.1230.0000.0000.0000.000
188A188ALA00.001-0.00824.0760.0060.0060.0000.0000.0000.000
189A189ALA00.0060.01423.7490.0100.0100.0000.0000.0000.000
190A190ALA00.008-0.01221.0440.0130.0130.0000.0000.0000.000
191A191ILE0-0.002-0.00522.5630.0080.0080.0000.0000.0000.000
192A192GLU-1-0.820-0.90925.6080.0120.0120.0000.0000.0000.000
193A193GLY00.0000.00423.3290.0120.0120.0000.0000.0000.000
194A194TRP00.0140.00222.7830.0140.0140.0000.0000.0000.000
195A195LEU0-0.019-0.00424.4760.0050.0050.0000.0000.0000.000
196A196ILE00.0100.01027.3530.0040.0040.0000.0000.0000.000
197A197VAL0-0.027-0.01022.4920.0090.0090.0000.0000.0000.000
198A198ASN00.0240.00325.8210.0020.0020.0000.0000.0000.000
199A199VAL0-0.032-0.00928.3980.0020.0020.0000.0000.0000.000
200A200TRP0-0.006-0.01127.2640.0060.0060.0000.0000.0000.000
201A201ASP-1-0.829-0.91626.2390.0300.0300.0000.0000.0000.000
202A202GLN0-0.026-0.00529.3440.0010.0010.0000.0000.0000.000
203A203LEU0-0.017-0.02132.9970.0020.0020.0000.0000.0000.000
204A204SER0-0.058-0.02130.6950.0070.0070.0000.0000.0000.000
205A205ASP-1-1.017-1.00231.2770.0390.0390.0000.0000.0000.000
206A206GLU-1-0.828-0.85634.2370.0170.0170.0000.0000.0000.000