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: R5338

Calculation Name: 3CVR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CVR

Chain ID: A

ChEMBL ID:

UniProt ID: Q83RJ4

Base Structure: X-ray

Registration Date: 2023-06-21

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 485
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8702534.667312
FMO2-HF: Nuclear repulsion 8508362.674767
FMO2-HF: Total energy -194171.992545
FMO2-MP2: Total energy -194741.023659


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:25:THR)


Summations of interaction energy for fragment #1(A:25:THR)
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.
-33.783-30.83415.573-8.955-9.567-0.1
Interaction energy analysis for fragmet #1(A:25:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : -0.036
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].
3A27ALA0-0.0040.0002.367-2.0980.2951.036-1.266-2.163-0.001
4A28ASP-1-0.852-0.9241.919-37.409-37.21514.537-7.637-7.094-0.099
5A29TYR00.0300.0194.2901.8802.2420.000-0.052-0.3100.000
6A30PHE00.002-0.0046.2570.7700.7700.0000.0000.0000.000
7A31SER00.0190.0116.8430.7010.7010.0000.0000.0000.000
8A32ALA0-0.0160.0088.4360.4370.4370.0000.0000.0000.000
9A33TRP00.034-0.0059.9080.1830.1830.0000.0000.0000.000
10A34ASP-1-0.779-0.88011.348-0.899-0.8990.0000.0000.0000.000
11A35LYS10.7990.88210.6521.9381.9380.0000.0000.0000.000
12A36TRP00.0480.02314.6140.0860.0860.0000.0000.0000.000
13A37GLU-1-0.755-0.85316.204-0.395-0.3950.0000.0000.0000.000
14A38LYS10.7240.84817.5820.6060.6060.0000.0000.0000.000
15A39GLN0-0.038-0.01920.0290.0260.0260.0000.0000.0000.000
16A40ALA00.0050.02222.1390.0190.0190.0000.0000.0000.000
17A41LEU00.0090.00323.6990.0190.0190.0000.0000.0000.000
18A42PRO0-0.032-0.04127.2840.0010.0010.0000.0000.0000.000
19A43GLY0-0.0050.01229.5590.0100.0100.0000.0000.0000.000
20A44GLU-1-0.739-0.81523.662-0.323-0.3230.0000.0000.0000.000
21A45ASN00.0220.01523.738-0.047-0.0470.0000.0000.0000.000
22A46ARG10.8470.89219.4090.4360.4360.0000.0000.0000.000
23A47ASN0-0.100-0.05418.8560.0030.0030.0000.0000.0000.000
24A48GLU-1-0.829-0.91418.780-0.229-0.2290.0000.0000.0000.000
25A49ALA00.0190.01319.1640.0060.0060.0000.0000.0000.000
26A50VAL0-0.044-0.02913.491-0.042-0.0420.0000.0000.0000.000
27A51SER0-0.033-0.02414.734-0.056-0.0560.0000.0000.0000.000
28A52LEU00.0490.03015.6880.0070.0070.0000.0000.0000.000
29A53LEU0-0.0040.00012.9270.0410.0410.0000.0000.0000.000
30A54LYS10.7750.86910.2940.9460.9460.0000.0000.0000.000
31A55GLU-1-0.939-0.96611.6240.0220.0220.0000.0000.0000.000
32A56CYS0-0.0190.01013.9660.1010.1010.0000.0000.0000.000
33A57LEU0-0.0160.0026.3000.0120.0120.0000.0000.0000.000
34A58ILE0-0.076-0.0399.3840.2140.2140.0000.0000.0000.000
35A59ASN0-0.092-0.05110.5770.1760.1760.0000.0000.0000.000
36A60GLN0-0.113-0.0599.4940.1780.1780.0000.0000.0000.000
37A61PHE00.0020.01012.7630.0190.0190.0000.0000.0000.000
38A62SER00.0490.00215.7300.0160.0160.0000.0000.0000.000
39A63GLU-1-0.846-0.89318.2200.0940.0940.0000.0000.0000.000
40A64LEU0-0.012-0.01415.770-0.016-0.0160.0000.0000.0000.000
41A65GLN0-0.044-0.02719.2230.0020.0020.0000.0000.0000.000
42A66LEU0-0.026-0.02318.101-0.032-0.0320.0000.0000.0000.000
43A67ASN00.009-0.00822.447-0.019-0.0190.0000.0000.0000.000
44A68ARG10.8780.94526.2710.0820.0820.0000.0000.0000.000
45A69LEU0-0.0270.00322.482-0.002-0.0020.0000.0000.0000.000
46A70ASN0-0.071-0.04826.184-0.010-0.0100.0000.0000.0000.000
47A71LEU0-0.035-0.00921.218-0.014-0.0140.0000.0000.0000.000
48A72SER0-0.008-0.02924.8170.0120.0120.0000.0000.0000.000
49A73SER0-0.033-0.01620.952-0.015-0.0150.0000.0000.0000.000
50A74LEU00.0740.02118.0010.0150.0150.0000.0000.0000.000
51A75PRO0-0.042-0.00513.387-0.022-0.0220.0000.0000.0000.000
52A76ASP-1-0.890-0.95713.110-0.711-0.7110.0000.0000.0000.000
53A77ASN0-0.059-0.0339.0110.0230.0230.0000.0000.0000.000
54A78LEU00.0700.04311.627-0.139-0.1390.0000.0000.0000.000
55A79PRO0-0.011-0.02010.5490.0320.0320.0000.0000.0000.000
56A80PRO0-0.0030.0098.4150.0160.0160.0000.0000.0000.000
57A81GLN0-0.020-0.02711.3550.0790.0790.0000.0000.0000.000
58A82ILE0-0.066-0.01913.571-0.023-0.0230.0000.0000.0000.000
59A83THR0-0.012-0.03216.6470.0020.0020.0000.0000.0000.000
60A84VAL0-0.002-0.00120.186-0.018-0.0180.0000.0000.0000.000
61A85LEU0-0.028-0.01418.787-0.011-0.0110.0000.0000.0000.000
62A86GLU-1-0.835-0.87721.668-0.039-0.0390.0000.0000.0000.000
63A87ILE0-0.011-0.02521.381-0.028-0.0280.0000.0000.0000.000
64A88THR0-0.005-0.00324.392-0.013-0.0130.0000.0000.0000.000
65A89GLN0-0.042-0.03028.165-0.009-0.0090.0000.0000.0000.000
66A90ASN0-0.103-0.05925.262-0.020-0.0200.0000.0000.0000.000
67A91ALA0-0.060-0.03627.4250.0130.0130.0000.0000.0000.000
68A92LEU00.0140.02322.906-0.012-0.0120.0000.0000.0000.000
69A93ILE00.0150.00026.3570.0180.0180.0000.0000.0000.000
70A94SER0-0.023-0.01024.0860.0090.0090.0000.0000.0000.000
71A95LEU00.0330.01121.143-0.011-0.0110.0000.0000.0000.000
72A96PRO0-0.035-0.00616.026-0.001-0.0010.0000.0000.0000.000
73A97GLU-1-0.945-0.98213.838-0.162-0.1620.0000.0000.0000.000
74A98LEU00.0070.00716.065-0.019-0.0190.0000.0000.0000.000
75A99PRO0-0.022-0.01014.1540.0280.0280.0000.0000.0000.000
76A100ALA00.0450.01415.4400.0030.0030.0000.0000.0000.000
77A101SER0-0.092-0.05617.2820.0490.0490.0000.0000.0000.000
78A102LEU0-0.0160.01918.8210.0060.0060.0000.0000.0000.000
79A103GLU-1-0.785-0.85120.3480.1260.1260.0000.0000.0000.000
80A104TYR00.0010.00623.510-0.009-0.0090.0000.0000.0000.000
81A105LEU00.014-0.00522.841-0.007-0.0070.0000.0000.0000.000
82A106ASP-1-0.809-0.85025.194-0.063-0.0630.0000.0000.0000.000
83A107ALA00.026-0.02125.741-0.018-0.0180.0000.0000.0000.000
84A108CYS0-0.0060.01027.424-0.010-0.0100.0000.0000.0000.000
85A109ASP-1-0.812-0.89930.384-0.093-0.0930.0000.0000.0000.000
86A110ASN0-0.070-0.03927.312-0.031-0.0310.0000.0000.0000.000
87A111ARG10.8970.94429.5840.1710.1710.0000.0000.0000.000
88A112LEU0-0.0030.01325.717-0.007-0.0070.0000.0000.0000.000
89A113SER00.0150.00729.5270.0110.0110.0000.0000.0000.000
90A114THR0-0.070-0.03727.7080.0030.0030.0000.0000.0000.000
91A115LEU00.0320.00825.779-0.007-0.0070.0000.0000.0000.000
92A116PRO0-0.032-0.00121.2280.0000.0000.0000.0000.0000.000
93A117GLU-1-0.939-0.97921.549-0.010-0.0100.0000.0000.0000.000
94A118LEU00.0220.01222.239-0.003-0.0030.0000.0000.0000.000
95A119PRO00.0060.01220.1230.0120.0120.0000.0000.0000.000
96A120ALA00.011-0.02122.3270.0040.0040.0000.0000.0000.000
97A121SER0-0.045-0.03521.7760.0060.0060.0000.0000.0000.000
98A122LEU0-0.059-0.01723.7800.0000.0000.0000.0000.0000.000
99A123LYS10.8060.90025.689-0.095-0.0950.0000.0000.0000.000
100A124HIS0-0.001-0.00327.789-0.004-0.0040.0000.0000.0000.000
101A125LEU00.0190.01026.621-0.003-0.0030.0000.0000.0000.000
102A126ASP-1-0.825-0.90929.020-0.038-0.0380.0000.0000.0000.000
103A127VAL0-0.020-0.01829.309-0.012-0.0120.0000.0000.0000.000
104A128ASP-1-0.757-0.86331.153-0.063-0.0630.0000.0000.0000.000
105A129ASN0-0.075-0.06033.477-0.010-0.0100.0000.0000.0000.000
106A130ASN0-0.055-0.02230.507-0.023-0.0230.0000.0000.0000.000
107A131GLN0-0.073-0.04532.9180.0030.0030.0000.0000.0000.000
108A132LEU00.0090.01529.930-0.003-0.0030.0000.0000.0000.000
109A133THR0-0.015-0.01733.9770.0070.0070.0000.0000.0000.000
110A134MET0-0.039-0.02331.9950.0050.0050.0000.0000.0000.000
111A135LEU00.0320.00931.829-0.006-0.0060.0000.0000.0000.000
112A136PRO0-0.013-0.00127.5100.0010.0010.0000.0000.0000.000
113A137GLU-1-0.903-0.97029.032-0.043-0.0430.0000.0000.0000.000
114A138LEU0-0.0010.00529.0110.0000.0000.0000.0000.0000.000
115A139PRO0-0.019-0.00126.3780.0070.0070.0000.0000.0000.000
116A140ALA0-0.011-0.03329.0770.0010.0010.0000.0000.0000.000
117A141LEU0-0.033-0.00926.8120.0040.0040.0000.0000.0000.000
118A142LEU0-0.0080.00928.7190.0010.0010.0000.0000.0000.000
119A143GLU-1-0.816-0.89931.2690.0620.0620.0000.0000.0000.000
120A144TYR0-0.089-0.06932.354-0.002-0.0020.0000.0000.0000.000
121A145ILE00.011-0.00332.216-0.002-0.0020.0000.0000.0000.000
122A146ASN0-0.027-0.00133.254-0.004-0.0040.0000.0000.0000.000
123A147ALA00.0470.00833.352-0.006-0.0060.0000.0000.0000.000
124A148ASP-1-0.761-0.85335.301-0.036-0.0360.0000.0000.0000.000
125A149ASN0-0.103-0.05237.099-0.005-0.0050.0000.0000.0000.000
126A150ASN0-0.0020.00234.192-0.015-0.0150.0000.0000.0000.000
127A151GLN0-0.028-0.01837.412-0.002-0.0020.0000.0000.0000.000
128A152LEU00.0120.02735.1860.0000.0000.0000.0000.0000.000
129A153THR0-0.014-0.01539.1760.0040.0040.0000.0000.0000.000
130A154MET0-0.047-0.02239.8440.0030.0030.0000.0000.0000.000
131A155LEU00.0260.00837.275-0.004-0.0040.0000.0000.0000.000
132A156PRO0-0.026-0.00833.7360.0030.0030.0000.0000.0000.000
133A157GLU-1-0.952-0.97636.3230.0040.0040.0000.0000.0000.000
134A158LEU00.0180.00935.7320.0000.0000.0000.0000.0000.000
135A159PRO00.0050.02432.8750.0030.0030.0000.0000.0000.000
136A160THR0-0.011-0.03635.4140.0000.0000.0000.0000.0000.000
137A161SER0-0.067-0.04034.6020.0060.0060.0000.0000.0000.000
138A162LEU00.0010.03134.8440.0020.0020.0000.0000.0000.000
139A163GLU-1-0.916-0.93836.7920.0370.0370.0000.0000.0000.000
140A164VAL0-0.051-0.03437.376-0.004-0.0040.0000.0000.0000.000
141A165LEU00.0110.01037.056-0.001-0.0010.0000.0000.0000.000
142A166SER0-0.071-0.05437.9390.0020.0020.0000.0000.0000.000
143A167VAL00.0490.01037.944-0.004-0.0040.0000.0000.0000.000
144A168ARG10.8350.91740.0310.0270.0270.0000.0000.0000.000
145A169ASN0-0.085-0.06341.449-0.003-0.0030.0000.0000.0000.000
146A170ASN0-0.0110.00738.738-0.009-0.0090.0000.0000.0000.000
147A171GLN0-0.050-0.04042.432-0.002-0.0020.0000.0000.0000.000
148A172LEU00.0330.03640.7430.0000.0000.0000.0000.0000.000
149A173THR00.000-0.01544.6760.0020.0020.0000.0000.0000.000
150A174PHE0-0.065-0.04143.6600.0030.0030.0000.0000.0000.000
151A175LEU00.0240.01043.295-0.002-0.0020.0000.0000.0000.000
152A176PRO0-0.0190.00140.0600.0010.0010.0000.0000.0000.000
153A177GLU-1-0.957-0.98443.1180.0060.0060.0000.0000.0000.000
154A178LEU00.0010.00042.292-0.001-0.0010.0000.0000.0000.000
155A179PRO00.0230.02039.1110.0010.0010.0000.0000.0000.000
156A180GLU-1-0.929-0.99342.1200.0230.0230.0000.0000.0000.000
157A181SER0-0.063-0.03639.5260.0020.0020.0000.0000.0000.000
158A182LEU0-0.059-0.01040.1400.0000.0000.0000.0000.0000.000
159A183GLU-1-0.775-0.87842.1650.0240.0240.0000.0000.0000.000
160A184ALA0-0.081-0.04341.949-0.003-0.0030.0000.0000.0000.000
161A185LEU00.0490.03241.995-0.001-0.0010.0000.0000.0000.000
162A186ASP-1-0.794-0.87042.722-0.021-0.0210.0000.0000.0000.000
163A187VAL00.0880.03442.766-0.002-0.0020.0000.0000.0000.000
164A188SER0-0.034-0.03745.078-0.001-0.0010.0000.0000.0000.000
165A189THR0-0.071-0.06145.909-0.002-0.0020.0000.0000.0000.000
166A190ASN0-0.023-0.00143.473-0.006-0.0060.0000.0000.0000.000
167A191LEU0-0.069-0.05347.3040.0000.0000.0000.0000.0000.000
168A192LEU00.0370.03446.6080.0010.0010.0000.0000.0000.000
169A193GLU-1-0.749-0.87350.324-0.029-0.0290.0000.0000.0000.000
170A194SER0-0.041-0.01553.1080.0010.0010.0000.0000.0000.000
171A195LEU00.0190.00052.483-0.001-0.0010.0000.0000.0000.000
172A196PRO0-0.002-0.00448.1830.0010.0010.0000.0000.0000.000
173A197ALA0-0.0200.00150.0370.0010.0010.0000.0000.0000.000
174A198VAL0-0.008-0.00849.2180.0000.0000.0000.0000.0000.000
175A199PRO00.0050.01846.1680.0000.0000.0000.0000.0000.000
176A208THR0-0.079-0.05545.7720.0030.0030.0000.0000.0000.000
177A209GLU-1-1.023-1.01747.4930.0130.0130.0000.0000.0000.000
178A210ILE00.0110.00646.5580.0000.0000.0000.0000.0000.000
179A211PHE0-0.034-0.02046.971-0.003-0.0030.0000.0000.0000.000
180A212PHE00.0340.01946.857-0.002-0.0020.0000.0000.0000.000
181A213ARG10.8720.91745.6330.0110.0110.0000.0000.0000.000
182A214CYS00.0410.02147.662-0.001-0.0010.0000.0000.0000.000
183A215ARG10.7740.86650.1570.0220.0220.0000.0000.0000.000
184A216GLU-1-0.809-0.86349.713-0.033-0.0330.0000.0000.0000.000
185A217ASN0-0.069-0.02048.384-0.004-0.0040.0000.0000.0000.000
186A218ARG10.8410.91051.0490.0320.0320.0000.0000.0000.000
187A219ILE00.0340.01652.1370.0010.0010.0000.0000.0000.000
188A220THR00.002-0.02755.9340.0000.0000.0000.0000.0000.000
189A221HIS0-0.060-0.02358.3690.0020.0020.0000.0000.0000.000
190A222ILE00.0030.00257.3440.0000.0000.0000.0000.0000.000
191A223PRO00.0430.01157.0990.0000.0000.0000.0000.0000.000
192A224GLU-1-0.749-0.87860.298-0.005-0.0050.0000.0000.0000.000
193A225ASN0-0.024-0.01558.1650.0000.0000.0000.0000.0000.000
194A226ILE00.0320.03556.2030.0010.0010.0000.0000.0000.000
195A227LEU00.012-0.00359.3100.0010.0010.0000.0000.0000.000
196A228SER0-0.114-0.07161.0260.0010.0010.0000.0000.0000.000
197A229LEU0-0.010-0.00254.9930.0010.0010.0000.0000.0000.000
198A230ASP-1-0.808-0.88254.7190.0130.0130.0000.0000.0000.000
199A231PRO0-0.027-0.03656.386-0.001-0.0010.0000.0000.0000.000
200A232THR0-0.088-0.04552.0380.0000.0000.0000.0000.0000.000
201A233CYS00.0110.03151.922-0.001-0.0010.0000.0000.0000.000
202A234THR0-0.044-0.02650.920-0.002-0.0020.0000.0000.0000.000
203A235ILE00.0240.00751.592-0.001-0.0010.0000.0000.0000.000
204A236ILE0-0.064-0.02350.2940.0000.0000.0000.0000.0000.000
205A237LEU00.0530.00352.879-0.001-0.0010.0000.0000.0000.000
206A238GLU-1-0.945-0.95354.511-0.016-0.0160.0000.0000.0000.000
207A239ASP-1-0.885-0.93154.727-0.024-0.0240.0000.0000.0000.000
208A240ASN0-0.017-0.01653.564-0.003-0.0030.0000.0000.0000.000
209A241PRO0-0.042-0.00556.8970.0010.0010.0000.0000.0000.000
210A242LEU00.0130.01758.6030.0010.0010.0000.0000.0000.000
211A243SER00.019-0.00461.6990.0000.0000.0000.0000.0000.000
212A244SER0-0.038-0.05565.4310.0010.0010.0000.0000.0000.000
213A245ARG10.8740.92067.9720.0110.0110.0000.0000.0000.000
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