FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8N99Y

Calculation Name: 1VKN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VKN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X2A2

Base Structure: X-ray

Registration Date: 2023-09-27

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 340
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5479851.183365
FMO2-HF: Nuclear repulsion 5346410.756955
FMO2-HF: Total energy -133440.42641
FMO2-MP2: Total energy -133830.111499


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-27.386-19.3534.072-4.582-7.522-0.037
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.007
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].
3A2ILE00.0390.0182.919-4.501-0.7041.574-1.966-3.405-0.001
4A3ARG10.7740.8682.43010.31811.5570.761-0.424-1.5760.000
5A4ALA00.0520.0224.9710.0070.068-0.001-0.003-0.0580.000
6A5GLY00.0390.0128.4060.5480.5480.0000.0000.0000.000
7A6ILE0-0.046-0.02611.522-0.019-0.0190.0000.0000.0000.000
8A7ILE00.0140.00715.0990.1500.1500.0000.0000.0000.000
9A8GLY00.0080.00518.0340.0180.0180.0000.0000.0000.000
10A9ALA00.014-0.00418.3860.0030.0030.0000.0000.0000.000
11A10THR00.0370.01820.1550.0240.0240.0000.0000.0000.000
12A11GLY0-0.034-0.00323.4150.0500.0500.0000.0000.0000.000
13A12TYR00.0380.00423.683-0.030-0.0300.0000.0000.0000.000
14A13THR00.0410.02121.7140.0040.0040.0000.0000.0000.000
15A14GLY00.0470.03719.397-0.073-0.0730.0000.0000.0000.000
16A15LEU00.0110.00419.183-0.041-0.0410.0000.0000.0000.000
17A16GLU-1-0.809-0.88020.566-0.509-0.5090.0000.0000.0000.000
18A17LEU0-0.0050.00015.324-0.019-0.0190.0000.0000.0000.000
19A18VAL00.0050.00215.942-0.074-0.0740.0000.0000.0000.000
20A19ARG10.8060.89916.6230.5160.5160.0000.0000.0000.000
21A20LEU0-0.030-0.02016.5110.0410.0410.0000.0000.0000.000
22A21LEU00.014-0.00310.665-0.060-0.0600.0000.0000.0000.000
23A22LYS10.7740.88212.7540.3010.3010.0000.0000.0000.000
24A23ASN0-0.070-0.03313.8740.0690.0690.0000.0000.0000.000
25A24HIS0-0.015-0.0089.6860.1010.1010.0000.0000.0000.000
26A25PRO00.0440.0289.1320.0350.0350.0000.0000.0000.000
27A26GLU-1-0.859-0.9305.608-2.210-2.2100.0000.0000.0000.000
28A27ALA0-0.015-0.0046.483-1.339-1.3390.0000.0000.0000.000
29A28LYS10.9460.9784.219-2.628-2.421-0.001-0.020-0.1850.000
30A29ILE00.0180.0137.862-0.719-0.7190.0000.0000.0000.000
31A30THR0-0.044-0.0415.8980.3080.3080.0000.0000.0000.000
32A31TYR00.012-0.0039.2470.2180.2180.0000.0000.0000.000
33A32LEU00.0350.03012.460-0.098-0.0980.0000.0000.0000.000
34A33SER00.0230.02216.0120.0900.0900.0000.0000.0000.000
35A34SER00.009-0.01419.086-0.006-0.0060.0000.0000.0000.000
36A35ARG10.9981.00522.7890.3600.3600.0000.0000.0000.000
37A36THR0-0.058-0.03725.8260.0230.0230.0000.0000.0000.000
38A37TYR00.0280.00325.1730.0320.0320.0000.0000.0000.000
39A38ALA00.0270.03423.1750.0060.0060.0000.0000.0000.000
40A39GLY00.0080.00022.8340.0310.0310.0000.0000.0000.000
41A40LYS10.9010.95924.3700.2040.2040.0000.0000.0000.000
42A41LYS10.8520.92821.5300.0390.0390.0000.0000.0000.000
43A42LEU00.0420.01819.490-0.004-0.0040.0000.0000.0000.000
44A43GLU-1-0.867-0.92122.136-0.082-0.0820.0000.0000.0000.000
45A44GLU-1-0.882-0.95824.148-0.104-0.1040.0000.0000.0000.000
46A45ILE0-0.089-0.03225.5190.0050.0050.0000.0000.0000.000
47A46PHE00.011-0.00724.957-0.001-0.0010.0000.0000.0000.000
48A47PRO00.0610.04525.245-0.017-0.0170.0000.0000.0000.000
49A48SER0-0.025-0.01525.8920.0090.0090.0000.0000.0000.000
50A49THR0-0.041-0.03621.097-0.004-0.0040.0000.0000.0000.000
51A50LEU0-0.0030.00221.066-0.017-0.0170.0000.0000.0000.000
52A51GLU-1-0.796-0.85516.360-0.309-0.3090.0000.0000.0000.000
53A52ASN00.0050.00518.037-0.026-0.0260.0000.0000.0000.000
54A53SER00.009-0.02215.2860.0250.0250.0000.0000.0000.000
55A54ILE0-0.039-0.02117.472-0.024-0.0240.0000.0000.0000.000
56A55LEU0-0.055-0.02218.023-0.081-0.0810.0000.0000.0000.000
57A56SER0-0.032-0.02517.0750.0580.0580.0000.0000.0000.000
58A57GLU-1-0.915-0.97019.350-0.348-0.3480.0000.0000.0000.000
59A58PHE0-0.042-0.04117.106-0.011-0.0110.0000.0000.0000.000
60A59ASP-1-0.763-0.86118.241-0.449-0.4490.0000.0000.0000.000
61A60PRO00.0620.02616.928-0.097-0.0970.0000.0000.0000.000
62A61GLU-1-0.889-0.93615.705-0.584-0.5840.0000.0000.0000.000
63A62LYS10.7900.87214.1320.3330.3330.0000.0000.0000.000
64A63VAL00.0040.00212.193-0.133-0.1330.0000.0000.0000.000
65A64SER0-0.014-0.02110.763-0.382-0.3820.0000.0000.0000.000
66A65LYS10.9220.98210.2750.1420.1420.0000.0000.0000.000
67A66ASN0-0.033-0.0197.9310.0830.0830.0000.0000.0000.000
68A67CYS0-0.0410.0026.980-0.128-0.1280.0000.0000.0000.000
69A68ASP-1-0.733-0.8382.220-26.872-24.1431.739-2.169-2.298-0.036
70A69VAL0-0.010-0.0075.8340.9450.9450.0000.0000.0000.000
71A70LEU0-0.026-0.0068.7780.1280.1280.0000.0000.0000.000
72A71PHE00.0170.01011.2650.1330.1330.0000.0000.0000.000
73A72THR0-0.028-0.02314.9250.0670.0670.0000.0000.0000.000
74A73ALA0-0.005-0.00618.2820.0340.0340.0000.0000.0000.000
75A74LEU0-0.008-0.00521.3900.0570.0570.0000.0000.0000.000
76A75PRO0-0.038-0.02324.0400.0060.0060.0000.0000.0000.000
77A76ALA00.002-0.00726.658-0.025-0.0250.0000.0000.0000.000
78A77GLY00.012-0.01227.0540.0350.0350.0000.0000.0000.000
79A78ALA00.012-0.00325.009-0.007-0.0070.0000.0000.0000.000
80A79SER0-0.002-0.00819.778-0.029-0.0290.0000.0000.0000.000
81A80TYR0-0.028-0.03821.354-0.051-0.0510.0000.0000.0000.000
82A81ASP-1-0.821-0.91523.058-0.504-0.5040.0000.0000.0000.000
83A82LEU0-0.0140.00418.025-0.006-0.0060.0000.0000.0000.000
84A83VAL00.011-0.00417.403-0.047-0.0470.0000.0000.0000.000
85A84ARG10.8540.93318.4650.4910.4910.0000.0000.0000.000
86A85GLU-1-0.917-0.95119.731-0.590-0.5900.0000.0000.0000.000
87A86LEU0-0.044-0.00414.3980.0040.0040.0000.0000.0000.000
88A87LYS10.8880.92314.4140.8070.8070.0000.0000.0000.000
89A88GLY00.0100.00711.182-0.079-0.0790.0000.0000.0000.000
90A89VAL0-0.0170.0109.285-0.465-0.4650.0000.0000.0000.000
91A90LYS10.8440.9439.1633.2763.2760.0000.0000.0000.000
92A91ILE00.005-0.00511.384-0.110-0.1100.0000.0000.0000.000
93A92ILE00.0050.01412.5170.0940.0940.0000.0000.0000.000
94A93ASP-1-0.778-0.89415.713-0.820-0.8200.0000.0000.0000.000
95A94LEU0-0.027-0.02417.7200.0500.0500.0000.0000.0000.000
96A95GLY0-0.044-0.00121.1750.0830.0830.0000.0000.0000.000
97A96ALA00.021-0.02123.968-0.026-0.0260.0000.0000.0000.000
98A97ASP-1-0.772-0.85823.553-0.588-0.5880.0000.0000.0000.000
99A98PHE00.0790.03220.7470.0120.0120.0000.0000.0000.000
100A99ARG10.7500.88023.7680.6170.6170.0000.0000.0000.000
101A100PHE00.0020.00125.6290.0090.0090.0000.0000.0000.000
102A101ASP-1-0.758-0.84127.925-0.569-0.5690.0000.0000.0000.000
103A102ASP-1-0.822-0.90429.336-0.367-0.3670.0000.0000.0000.000
104A103PRO00.011-0.00229.8470.0020.0020.0000.0000.0000.000
105A104GLY00.0170.00431.5060.0100.0100.0000.0000.0000.000
106A105VAL00.0150.01233.7180.0150.0150.0000.0000.0000.000
107A106TYR0-0.035-0.03727.9580.0200.0200.0000.0000.0000.000
108A107ARG10.8550.91932.3970.3270.3270.0000.0000.0000.000
109A108GLU-1-0.900-0.94334.674-0.277-0.2770.0000.0000.0000.000
110A109TRP0-0.008-0.01634.7700.0090.0090.0000.0000.0000.000
111A110TYR0-0.109-0.08430.483-0.002-0.0020.0000.0000.0000.000
112A111GLY0-0.0160.01833.922-0.001-0.0010.0000.0000.0000.000
113A112LYS10.8140.92227.7590.4830.4830.0000.0000.0000.000
114A113GLU-1-0.872-0.92532.754-0.339-0.3390.0000.0000.0000.000
115A114LEU0-0.016-0.00127.220-0.008-0.0080.0000.0000.0000.000
116A115SER00.0260.00729.060-0.002-0.0020.0000.0000.0000.000
117A116GLY00.0380.01727.861-0.031-0.0310.0000.0000.0000.000
118A117TYR0-0.025-0.03125.489-0.055-0.0550.0000.0000.0000.000
119A118GLU-1-0.854-0.92325.975-0.493-0.4930.0000.0000.0000.000
120A119ASN0-0.080-0.05324.552-0.010-0.0100.0000.0000.0000.000
121A120ILE0-0.043-0.00620.430-0.068-0.0680.0000.0000.0000.000
122A121LYS10.9070.95317.8211.0351.0350.0000.0000.0000.000
123A122ARG10.7790.88019.3350.5440.5440.0000.0000.0000.000
124A123VAL00.0070.00619.1970.0540.0540.0000.0000.0000.000
125A124TYR0-0.018-0.02621.358-0.051-0.0510.0000.0000.0000.000
126A125GLY00.0430.00020.436-0.007-0.0070.0000.0000.0000.000
127A126LEU00.0100.00521.122-0.008-0.0080.0000.0000.0000.000
128A127PRO00.0090.00819.4000.0390.0390.0000.0000.0000.000
129A128GLU-1-0.768-0.87521.506-0.688-0.6880.0000.0000.0000.000
130A129LEU0-0.046-0.01324.7370.0490.0490.0000.0000.0000.000
131A130HIS10.7930.86322.9500.6540.6540.0000.0000.0000.000
132A131ARG10.7790.82419.0260.6870.6870.0000.0000.0000.000
133A132GLU-1-0.842-0.91118.778-0.878-0.8780.0000.0000.0000.000
134A133GLU-1-0.861-0.92019.721-0.709-0.7090.0000.0000.0000.000
135A134ILE0-0.048-0.02615.928-0.070-0.0700.0000.0000.0000.000
136A135LYS10.8590.92814.7090.8020.8020.0000.0000.0000.000
137A136ASN0-0.069-0.02614.102-0.172-0.1720.0000.0000.0000.000
138A137ALA0-0.0090.01616.2160.0550.0550.0000.0000.0000.000
139A138GLN00.002-0.01112.208-0.331-0.3310.0000.0000.0000.000
140A139VAL00.0150.00514.474-0.160-0.1600.0000.0000.0000.000
141A140VAL00.0200.01916.1980.1070.1070.0000.0000.0000.000
142A141GLY00.0200.00818.240-0.020-0.0200.0000.0000.0000.000
143A142ASN0-0.042-0.03019.500-0.034-0.0340.0000.0000.0000.000
144A143PRO0-0.0060.02021.3030.0490.0490.0000.0000.0000.000
145A144GLY0-0.014-0.00524.743-0.012-0.0120.0000.0000.0000.000
146A145CYS0-0.023-0.00327.5170.0040.0040.0000.0000.0000.000
147A146TYR00.005-0.02828.7060.0130.0130.0000.0000.0000.000
148A147PRO00.0070.01129.2520.0140.0140.0000.0000.0000.000
149A148THR00.0230.02826.063-0.006-0.0060.0000.0000.0000.000
150A149SER00.0130.00728.6930.0080.0080.0000.0000.0000.000
151A150VAL00.0390.01531.6510.0190.0190.0000.0000.0000.000
152A151ILE00.0070.00129.6360.0170.0170.0000.0000.0000.000
153A152LEU00.0170.01227.0060.0110.0110.0000.0000.0000.000
154A153ALA0-0.0190.01031.1820.0170.0170.0000.0000.0000.000
155A154LEU00.0470.03234.6380.0220.0220.0000.0000.0000.000
156A155ALA00.0150.02831.8620.0120.0120.0000.0000.0000.000
157A156PRO0-0.0020.00133.5040.0080.0080.0000.0000.0000.000
158A157ALA00.0400.01335.4760.0130.0130.0000.0000.0000.000
159A158LEU0-0.031-0.01336.2940.0120.0120.0000.0000.0000.000
160A159LYS10.9030.95532.5840.3400.3400.0000.0000.0000.000
161A160HIS0-0.012-0.00836.133-0.008-0.0080.0000.0000.0000.000
162A161ASN0-0.032-0.00639.3780.0140.0140.0000.0000.0000.000
163A162LEU00.0510.03640.3950.0100.0100.0000.0000.0000.000
164A163VAL0-0.045-0.01641.6640.0070.0070.0000.0000.0000.000
165A164ASP-1-0.883-0.93744.360-0.202-0.2020.0000.0000.0000.000
166A165PRO0-0.050-0.04141.180-0.003-0.0030.0000.0000.0000.000
167A166GLU-1-0.920-0.94143.003-0.206-0.2060.0000.0000.0000.000
168A167THR0-0.023-0.02344.960-0.004-0.0040.0000.0000.0000.000
169A168ILE0-0.0200.00540.0000.0020.0020.0000.0000.0000.000
170A169LEU00.0050.00343.160-0.004-0.0040.0000.0000.0000.000
171A170VAL0-0.006-0.01237.854-0.004-0.0040.0000.0000.0000.000
172A171ASP-1-0.824-0.91241.276-0.219-0.2190.0000.0000.0000.000
173A172ALA00.0180.01337.142-0.002-0.0020.0000.0000.0000.000
174A173LYS10.8090.90138.2880.2420.2420.0000.0000.0000.000
175A174SER00.022-0.01134.237-0.022-0.0220.0000.0000.0000.000
176A175GLY00.0170.02234.9830.0160.0160.0000.0000.0000.000
177A176VAL00.0460.00634.732-0.019-0.0190.0000.0000.0000.000
178A177SER0-0.028-0.03229.843-0.019-0.0190.0000.0000.0000.000
179A178GLY00.0000.00230.527-0.029-0.0290.0000.0000.0000.000
180A179ALA0-0.043-0.01231.801-0.010-0.0100.0000.0000.0000.000
181A180GLY0-0.008-0.00229.801-0.005-0.0050.0000.0000.0000.000
182A181ARG10.7610.83527.1890.3990.3990.0000.0000.0000.000
183A182LYS10.9180.97430.9480.3240.3240.0000.0000.0000.000
184A183GLU-1-0.747-0.85032.776-0.316-0.3160.0000.0000.0000.000
185A184LYS10.9370.97536.4220.2400.2400.0000.0000.0000.000
186A185VAL00.0880.02039.985-0.005-0.0050.0000.0000.0000.000
187A186ASP-1-0.866-0.91741.796-0.201-0.2010.0000.0000.0000.000
188A187TYR0-0.037-0.03937.095-0.004-0.0040.0000.0000.0000.000
189A188LEU00.0170.03339.011-0.005-0.0050.0000.0000.0000.000
190A189PHE00.0250.00240.371-0.001-0.0010.0000.0000.0000.000
191A190SER0-0.011-0.03041.9170.0000.0000.0000.0000.0000.000
192A191GLU-1-0.948-0.94844.011-0.154-0.1540.0000.0000.0000.000
193A192VAL0-0.070-0.03240.149-0.001-0.0010.0000.0000.0000.000
194A193ASN0-0.023-0.01843.342-0.006-0.0060.0000.0000.0000.000
195A194GLU-1-0.926-0.96044.280-0.145-0.1450.0000.0000.0000.000
196A195SER0-0.0060.01245.3990.0050.0050.0000.0000.0000.000
197A196LEU0-0.020-0.01543.629-0.011-0.0110.0000.0000.0000.000
198A197ARG10.8980.94541.2350.2190.2190.0000.0000.0000.000
199A198PRO00.0200.00543.358-0.013-0.0130.0000.0000.0000.000
200A199TYR0-0.0040.00036.485-0.003-0.0030.0000.0000.0000.000
201A200ASN0-0.042-0.03439.920-0.006-0.0060.0000.0000.0000.000
202A201VAL00.0470.02241.497-0.010-0.0100.0000.0000.0000.000
203A202ALA00.0170.02143.1220.0040.0040.0000.0000.0000.000
204A203LYS10.8580.95640.3440.2690.2690.0000.0000.0000.000
205A204HIS00.0460.01133.832-0.004-0.0040.0000.0000.0000.000
206A205ARG10.9600.98132.2330.3850.3850.0000.0000.0000.000
207A206HIS00.008-0.01730.354-0.008-0.0080.0000.0000.0000.000
208A207VAL00.0490.04033.751-0.011-0.0110.0000.0000.0000.000
209A208PRO00.0420.02434.447-0.004-0.0040.0000.0000.0000.000
210A209GLU-1-0.752-0.84928.261-0.556-0.5560.0000.0000.0000.000
211A210MET0-0.013-0.00732.028-0.005-0.0050.0000.0000.0000.000
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