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: 22VLR

Calculation Name: 3QC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QC1

Chain ID: A

ChEMBL ID:

UniProt ID: Q61249

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2063555.910067
FMO2-HF: Nuclear repulsion 1986554.376429
FMO2-HF: Total energy -77001.533638
FMO2-MP2: Total energy -77226.579453


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:10:LEU)


Summations of interaction energy for fragment #1(A:10:LEU)
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.
-1.1610.6680.004-0.742-1.0910.003
Interaction energy analysis for fragmet #1(A:10:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.008
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].
3A12ARG10.9450.9703.5022.4144.2430.004-0.742-1.0910.003
4A13LEU00.1000.0415.8830.2040.2040.0000.0000.0000.000
5A14PRO0-0.023-0.0098.5630.0840.0840.0000.0000.0000.000
6A15GLU-1-0.836-0.9145.283-4.487-4.4870.0000.0000.0000.000
7A16LEU0-0.0070.0148.0300.2120.2120.0000.0000.0000.000
8A17PHE00.0380.02610.7850.1870.1870.0000.0000.0000.000
9A18GLU-1-0.775-0.87313.128-0.468-0.4680.0000.0000.0000.000
10A19THR0-0.051-0.02910.8860.1110.1110.0000.0000.0000.000
11A20SER00.007-0.01413.5460.1160.1160.0000.0000.0000.000
12A21LYS10.8060.91616.0020.4280.4280.0000.0000.0000.000
13A22LYS10.8170.89116.4740.5570.5570.0000.0000.0000.000
14A23LEU0-0.019-0.01915.3360.0450.0450.0000.0000.0000.000
15A24LEU0-0.0040.01118.7240.0390.0390.0000.0000.0000.000
16A25GLU-1-0.772-0.88621.478-0.307-0.3070.0000.0000.0000.000
17A26ASP-1-0.847-0.89820.741-0.226-0.2260.0000.0000.0000.000
18A27VAL00.016-0.00422.1730.0280.0280.0000.0000.0000.000
19A28GLU-1-0.983-1.00124.465-0.189-0.1890.0000.0000.0000.000
20A29VAL0-0.048-0.01425.9240.0170.0170.0000.0000.0000.000
21A30ALA0-0.027-0.00126.0800.0120.0120.0000.0000.0000.000
22A31THR0-0.009-0.00428.1100.0060.0060.0000.0000.0000.000
23A32GLU-1-0.863-0.90927.401-0.125-0.1250.0000.0000.0000.000
24A33PRO00.0300.00131.316-0.006-0.0060.0000.0000.0000.000
25A34THR00.0800.04129.4940.0020.0020.0000.0000.0000.000
26A35GLY00.0120.01228.602-0.008-0.0080.0000.0000.0000.000
27A36SER0-0.056-0.03728.7160.0090.0090.0000.0000.0000.000
28A37ARG10.8190.87222.8360.1010.1010.0000.0000.0000.000
29A38THR00.017-0.01323.502-0.005-0.0050.0000.0000.0000.000
30A39ILE00.0060.02022.762-0.022-0.0220.0000.0000.0000.000
31A40GLN00.008-0.01623.421-0.018-0.0180.0000.0000.0000.000
32A41ASP-1-0.819-0.85519.719-0.147-0.1470.0000.0000.0000.000
33A42LYS10.7810.87318.7760.2020.2020.0000.0000.0000.000
34A43VAL00.0210.00919.106-0.037-0.0370.0000.0000.0000.000
35A44SER0-0.020-0.02220.063-0.016-0.0160.0000.0000.0000.000
36A45LYS10.9670.98310.8560.5360.5360.0000.0000.0000.000
37A46GLY00.0210.00915.319-0.074-0.0740.0000.0000.0000.000
38A47LEU0-0.013-0.01117.187-0.035-0.0350.0000.0000.0000.000
39A48GLU-1-0.927-0.95412.501-0.410-0.4100.0000.0000.0000.000
40A49LEU0-0.036-0.03810.570-0.069-0.0690.0000.0000.0000.000
41A50LEU00.0140.01312.706-0.099-0.0990.0000.0000.0000.000
42A51GLU-1-0.929-0.95115.490-0.229-0.2290.0000.0000.0000.000
43A52LYS10.9190.9608.2730.4860.4860.0000.0000.0000.000
44A53ALA0-0.013-0.01711.981-0.037-0.0370.0000.0000.0000.000
45A54ALA00.0520.02312.9350.0230.0230.0000.0000.0000.000
46A55GLY00.0070.02014.1910.0440.0440.0000.0000.0000.000
47A56MET0-0.081-0.0436.540-0.014-0.0140.0000.0000.0000.000
48A57LEU00.003-0.00412.2540.0270.0270.0000.0000.0000.000
49A58SER0-0.031-0.02415.5120.0470.0470.0000.0000.0000.000
50A59GLN0-0.101-0.03812.5260.0510.0510.0000.0000.0000.000
51A60LEU0-0.056-0.03511.2710.0170.0170.0000.0000.0000.000
52A61ASP-1-0.832-0.89415.410-0.168-0.1680.0000.0000.0000.000
53A62LEU0-0.026-0.01915.2640.0140.0140.0000.0000.0000.000
54A63PHE0-0.039-0.04019.1940.0000.0000.0000.0000.0000.000
55A64SER0-0.023-0.00622.7280.0190.0190.0000.0000.0000.000
56A65ARG10.7920.88424.5310.1330.1330.0000.0000.0000.000
57A66ASN00.0080.02027.731-0.004-0.0040.0000.0000.0000.000
58A67GLU-1-0.965-1.00829.548-0.098-0.0980.0000.0000.0000.000
59A68ASP-1-0.811-0.89427.928-0.141-0.1410.0000.0000.0000.000
60A69LEU0-0.0250.00827.1870.0030.0030.0000.0000.0000.000
61A70GLU-1-0.919-0.98527.309-0.161-0.1610.0000.0000.0000.000
62A71GLU-1-0.930-0.96127.392-0.131-0.1310.0000.0000.0000.000
63A72ILE0-0.0310.01121.666-0.009-0.0090.0000.0000.0000.000
64A73ALA00.0390.02019.8960.0050.0050.0000.0000.0000.000
65A74SER00.001-0.04521.437-0.019-0.0190.0000.0000.0000.000
66A75THR0-0.038-0.02617.164-0.011-0.0110.0000.0000.0000.000
67A76ASP-1-0.878-0.95016.668-0.455-0.4550.0000.0000.0000.000
68A77LEU00.005-0.00418.773-0.006-0.0060.0000.0000.0000.000
69A78LYS10.8300.91014.6230.6510.6510.0000.0000.0000.000
70A79TYR0-0.002-0.01113.642-0.061-0.0610.0000.0000.0000.000
71A80LEU00.0320.03718.5740.0060.0060.0000.0000.0000.000
72A81MET0-0.050-0.01421.3470.0230.0230.0000.0000.0000.000
73A82VAL0-0.031-0.00116.9590.0020.0020.0000.0000.0000.000
74A83PRO00.0680.03519.9860.0030.0030.0000.0000.0000.000
75A84ALA00.0310.01922.9290.0150.0150.0000.0000.0000.000
76A85LEU0-0.028-0.01119.4670.0090.0090.0000.0000.0000.000
77A86GLN00.0260.00519.1950.0090.0090.0000.0000.0000.000
78A87GLY00.0210.02922.3330.0180.0180.0000.0000.0000.000
79A88ALA00.0330.01525.3250.0140.0140.0000.0000.0000.000
80A89LEU0-0.039-0.01919.6350.0120.0120.0000.0000.0000.000
81A90THR0-0.035-0.03523.9990.0160.0160.0000.0000.0000.000
82A91MET0-0.055-0.01725.9130.0190.0190.0000.0000.0000.000
83A92LYS10.8550.93625.9730.1800.1800.0000.0000.0000.000
84A93GLN00.0020.01324.878-0.007-0.0070.0000.0000.0000.000
85A94VAL0-0.060-0.03327.5530.0110.0110.0000.0000.0000.000
86A95ASN00.0580.03929.6890.0120.0120.0000.0000.0000.000
87A96PRO00.0600.02031.8770.0000.0000.0000.0000.0000.000
88A97SER0-0.049-0.02433.8010.0020.0020.0000.0000.0000.000
89A98LYS10.8560.91430.7130.0710.0710.0000.0000.0000.000
90A99ARG10.8690.92332.2950.1040.1040.0000.0000.0000.000
91A100LEU00.0480.02133.500-0.005-0.0050.0000.0000.0000.000
92A101ASP-1-0.855-0.90529.138-0.112-0.1120.0000.0000.0000.000
93A102HIS0-0.019-0.02728.615-0.005-0.0050.0000.0000.0000.000
94A103LEU00.0360.02129.828-0.009-0.0090.0000.0000.0000.000
95A104GLN0-0.0130.00632.1950.0030.0030.0000.0000.0000.000
96A105ARG10.8240.86826.1630.1120.1120.0000.0000.0000.000
97A106ALA00.0180.01627.659-0.012-0.0120.0000.0000.0000.000
98A107ARG10.7910.84928.9540.0920.0920.0000.0000.0000.000
99A108GLU-1-0.832-0.89428.186-0.119-0.1190.0000.0000.0000.000
100A109HIS00.0200.01422.403-0.008-0.0080.0000.0000.0000.000
101A110PHE00.0330.00326.537-0.010-0.0100.0000.0000.0000.000
102A111VAL0-0.015-0.00929.0590.0020.0020.0000.0000.0000.000
103A112HIS00.0130.02922.6420.0150.0150.0000.0000.0000.000
104A113PHE0-0.005-0.00925.118-0.005-0.0050.0000.0000.0000.000
105A114LEU0-0.034-0.02326.8680.0020.0020.0000.0000.0000.000
106A115THR0-0.081-0.04629.1400.0040.0040.0000.0000.0000.000
107A116GLN00.010-0.00724.213-0.008-0.0080.0000.0000.0000.000
108A117CYS0-0.0330.01326.1840.0050.0050.0000.0000.0000.000
109A118HIS00.0210.00626.5470.0050.0050.0000.0000.0000.000
110A120TYR00.0040.01030.9370.0080.0080.0000.0000.0000.000
111A121HIS10.9340.96933.4200.1290.1290.0000.0000.0000.000
112A145ALA00.009-0.00870.5900.0000.0000.0000.0000.0000.000
113A146TYR00.0630.02267.443-0.001-0.0010.0000.0000.0000.000
114A147PRO00.0260.02765.773-0.001-0.0010.0000.0000.0000.000
115A148ASN00.0410.00564.036-0.001-0.0010.0000.0000.0000.000
116A149LEU00.0450.02163.007-0.002-0.0020.0000.0000.0000.000
117A150VAL00.0600.03360.942-0.002-0.0020.0000.0000.0000.000
118A151ALA00.0220.03059.391-0.002-0.0020.0000.0000.0000.000
119A152MET0-0.044-0.03358.248-0.002-0.0020.0000.0000.0000.000
120A153ALA00.0090.01057.923-0.002-0.0020.0000.0000.0000.000
121A154SER00.012-0.00855.599-0.002-0.0020.0000.0000.0000.000
122A155GLN00.0130.00753.877-0.003-0.0030.0000.0000.0000.000
123A156ARG10.8520.92753.1240.0500.0500.0000.0000.0000.000
124A157GLN0-0.012-0.01351.8930.0000.0000.0000.0000.0000.000
125A158ALA00.0700.03849.591-0.003-0.0030.0000.0000.0000.000
126A159LYS10.9120.95847.9230.0620.0620.0000.0000.0000.000
127A160ILE00.0160.00546.812-0.004-0.0040.0000.0000.0000.000
128A161GLU-1-0.810-0.90246.123-0.075-0.0750.0000.0000.0000.000
129A162ARG10.9810.99942.6270.0800.0800.0000.0000.0000.000
130A163TYR0-0.010-0.00242.032-0.005-0.0050.0000.0000.0000.000
131A164LYS10.8830.94241.4510.0730.0730.0000.0000.0000.000
132A165GLN00.0030.00040.131-0.006-0.0060.0000.0000.0000.000
133A166LYS10.9190.96235.1780.1250.1250.0000.0000.0000.000
134A167LYS10.8430.90036.5790.0910.0910.0000.0000.0000.000
135A168GLU-1-0.783-0.89836.845-0.106-0.1060.0000.0000.0000.000
136A169VAL0-0.0100.00332.745-0.006-0.0060.0000.0000.0000.000
137A170GLU-1-0.796-0.87132.352-0.166-0.1660.0000.0000.0000.000
138A171HIS0-0.0150.00431.974-0.013-0.0130.0000.0000.0000.000
139A172ARG10.8390.89732.1970.1330.1330.0000.0000.0000.000
140A173LEU00.0220.00427.835-0.007-0.0070.0000.0000.0000.000
141A174SER0-0.075-0.04627.847-0.012-0.0120.0000.0000.0000.000
142A175ALA0-0.018-0.01128.372-0.007-0.0070.0000.0000.0000.000
143A176LEU0-0.011-0.00227.008-0.002-0.0020.0000.0000.0000.000
144A177LYS10.7980.89621.3460.3160.3160.0000.0000.0000.000
145A178SER00.0090.00122.620-0.030-0.0300.0000.0000.0000.000
146A179ALA00.0480.04022.194-0.019-0.0190.0000.0000.0000.000
147A180VAL00.000-0.00721.470-0.012-0.0120.0000.0000.0000.000
148A181GLU-1-0.776-0.87218.370-0.416-0.4160.0000.0000.0000.000
149A182SER0-0.062-0.03217.339-0.056-0.0560.0000.0000.0000.000
150A183GLY0-0.034-0.01318.6660.0010.0010.0000.0000.0000.000
151A184GLN0-0.045-0.02719.5340.0230.0230.0000.0000.0000.000
152A185ALA0-0.047-0.01322.9480.0240.0240.0000.0000.0000.000
153A186ASP-1-0.781-0.87524.359-0.173-0.1730.0000.0000.0000.000
154A187ASP-1-0.787-0.88124.202-0.224-0.2240.0000.0000.0000.000
155A188GLU-1-0.820-0.87626.029-0.137-0.1370.0000.0000.0000.000
156A189ARG10.7710.83727.5690.1470.1470.0000.0000.0000.000
157A190VAL0-0.038-0.01521.888-0.011-0.0110.0000.0000.0000.000
158A191ARG10.8390.90524.9740.1740.1740.0000.0000.0000.000
159A192GLU-1-0.822-0.88426.624-0.150-0.1500.0000.0000.0000.000
160A193TYR0-0.053-0.03322.3310.0130.0130.0000.0000.0000.000
161A194HIS00.0400.01420.7290.0020.0020.0000.0000.0000.000
162A195LEU00.0420.02525.1680.0040.0040.0000.0000.0000.000
163A196LEU0-0.061-0.02828.2500.0120.0120.0000.0000.0000.000
164A197HIS00.007-0.01624.883-0.003-0.0030.0000.0000.0000.000
165A198LEU0-0.0040.01024.3790.0070.0070.0000.0000.0000.000
166A199ARG10.8880.93527.9630.1440.1440.0000.0000.0000.000
167A200ARG10.8300.89628.5090.1930.1930.0000.0000.0000.000
168A201TRP00.0700.01724.7560.0090.0090.0000.0000.0000.000
169A202ILE0-0.0080.01629.4970.0050.0050.0000.0000.0000.000
170A203ALA0-0.049-0.01032.3090.0060.0060.0000.0000.0000.000
171A204VAL00.0700.03330.1720.0040.0040.0000.0000.0000.000
172A205SER00.008-0.01529.813-0.001-0.0010.0000.0000.0000.000
173A206LEU0-0.052-0.02231.9130.0070.0070.0000.0000.0000.000
174A207GLU-1-0.942-0.97435.354-0.120-0.1200.0000.0000.0000.000
175A208GLU-1-0.860-0.93031.192-0.137-0.1370.0000.0000.0000.000
176A209LEU0-0.032-0.02032.6970.0060.0060.0000.0000.0000.000
177A210GLU-1-0.977-0.97635.498-0.080-0.0800.0000.0000.0000.000
178A211SER0-0.013-0.02036.7140.0070.0070.0000.0000.0000.000
179A212ILE0-0.017-0.01732.0990.0050.0050.0000.0000.0000.000
180A213ASP-1-0.754-0.84136.496-0.088-0.0880.0000.0000.0000.000
181A214GLN0-0.063-0.02839.2490.0040.0040.0000.0000.0000.000
182A215GLU-1-0.791-0.86137.093-0.090-0.0900.0000.0000.0000.000
183A216ILE0-0.021-0.02535.0530.0050.0050.0000.0000.0000.000
184A217LYS10.9090.95739.2270.0630.0630.0000.0000.0000.000
185A218ILE00.0410.02942.9520.0030.0030.0000.0000.0000.000
186A219LEU0-0.035-0.01537.9750.0030.0030.0000.0000.0000.000
187A220LYS10.8680.92937.7130.0710.0710.0000.0000.0000.000
188A221GLU-1-0.929-0.94543.006-0.049-0.0490.0000.0000.0000.000
189A222LYS10.8470.92344.2870.0520.0520.0000.0000.0000.000