FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 4JVYN

Calculation Name: 2G7S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2G7S

Chain ID: A

ChEMBL ID:

UniProt ID: A9CKG4

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1941116.313249
FMO2-HF: Nuclear repulsion 1867900.472441
FMO2-HF: Total energy -73215.840808
FMO2-MP2: Total energy -73428.255148


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-18.431-10.8885.269-5.314-7.4980.024
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.072 / q_NPA : 0.037
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].
3A5GLN00.0350.0202.982-3.7460.0320.311-1.869-2.2190.010
4A6SER00.0100.0132.134-13.057-9.7954.926-3.352-4.8360.013
5A7LYS10.9710.9923.623-3.311-2.8080.032-0.093-0.4430.001
6A8ALA00.0110.0076.019-0.541-0.5410.0000.0000.0000.000
7A9ASP-1-0.858-0.9366.8112.4412.4410.0000.0000.0000.000
8A10ASP-1-0.904-0.9517.5490.7370.7370.0000.0000.0000.000
9A11ILE0-0.083-0.0479.773-0.327-0.3270.0000.0000.0000.000
10A12LEU0-0.013-0.00511.364-0.190-0.1900.0000.0000.0000.000
11A13GLN00.0390.03312.313-0.071-0.0710.0000.0000.0000.000
12A14CYS0-0.071-0.01913.872-0.143-0.1430.0000.0000.0000.000
13A15ALA00.0480.00515.724-0.077-0.0770.0000.0000.0000.000
14A16ARG10.8230.91516.571-0.526-0.5260.0000.0000.0000.000
15A17THR00.0340.01818.109-0.058-0.0580.0000.0000.0000.000
16A18LEU0-0.057-0.07019.117-0.047-0.0470.0000.0000.0000.000
17A19ILE00.0060.00521.529-0.032-0.0320.0000.0000.0000.000
18A20ILE00.0200.01922.250-0.027-0.0270.0000.0000.0000.000
19A21ARG10.8860.97923.723-0.236-0.2360.0000.0000.0000.000
20A22GLY00.009-0.00126.641-0.016-0.0160.0000.0000.0000.000
21A23GLY00.0380.04726.992-0.009-0.0090.0000.0000.0000.000
22A24TYR00.009-0.02223.9610.0200.0200.0000.0000.0000.000
23A25ASN0-0.056-0.05225.5980.0150.0150.0000.0000.0000.000
24A26SER0-0.0460.00326.453-0.007-0.0070.0000.0000.0000.000
25A27PHE00.0050.01019.7100.0080.0080.0000.0000.0000.000
26A28SER00.0020.00322.274-0.001-0.0010.0000.0000.0000.000
27A29TYR00.016-0.02717.7600.0180.0180.0000.0000.0000.000
28A30ALA00.0180.00917.7400.0130.0130.0000.0000.0000.000
29A31ASP-1-0.801-0.89219.0760.2100.2100.0000.0000.0000.000
30A32ILE00.013-0.01513.9030.0080.0080.0000.0000.0000.000
31A33SER0-0.081-0.05014.3110.0190.0190.0000.0000.0000.000
32A34GLN0-0.049-0.00815.021-0.003-0.0030.0000.0000.0000.000
33A35VAL0-0.027-0.01014.752-0.011-0.0110.0000.0000.0000.000
34A36VAL00.003-0.0029.7560.0000.0000.0000.0000.0000.000
35A37GLY0-0.0050.00510.467-0.011-0.0110.0000.0000.0000.000
36A38ILE0-0.067-0.0148.076-0.056-0.0560.0000.0000.0000.000
37A39ARG11.0331.00211.035-0.132-0.1320.0000.0000.0000.000
38A40ASN00.0810.01013.5870.0210.0210.0000.0000.0000.000
39A41ALA00.004-0.00615.3270.0220.0220.0000.0000.0000.000
40A42SER0-0.002-0.00110.009-0.006-0.0060.0000.0000.0000.000
41A43ILE00.0020.00411.6040.0620.0620.0000.0000.0000.000
42A44HIS00.000-0.00313.3110.0560.0560.0000.0000.0000.000
43A45HIS0-0.070-0.02610.990-0.005-0.0050.0000.0000.0000.000
44A46HIS0-0.047-0.0146.5380.1520.1520.0000.0000.0000.000
45A47PHE00.0130.01211.6770.0340.0340.0000.0000.0000.000
46A48PRO00.0150.01915.367-0.043-0.0430.0000.0000.0000.000
47A49SER00.011-0.00218.260-0.041-0.0410.0000.0000.0000.000
48A50LYS10.9250.97619.487-0.202-0.2020.0000.0000.0000.000
49A51SER00.0570.01920.9530.0130.0130.0000.0000.0000.000
50A52ASP-1-0.879-0.94017.1910.4270.4270.0000.0000.0000.000
51A53LEU0-0.0110.00815.6260.0240.0240.0000.0000.0000.000
52A54VAL00.023-0.00517.5580.0330.0330.0000.0000.0000.000
53A55CYS0-0.038-0.00720.242-0.011-0.0110.0000.0000.0000.000
54A56LYS10.9140.95814.995-0.501-0.5010.0000.0000.0000.000
55A57LEU0-0.0030.02116.7030.0260.0260.0000.0000.0000.000
56A58VAL0-0.007-0.02217.616-0.014-0.0140.0000.0000.0000.000
57A59SER0-0.0010.01118.647-0.007-0.0070.0000.0000.0000.000
58A60GLN00.0340.01812.431-0.074-0.0740.0000.0000.0000.000
59A61TYR0-0.006-0.08917.587-0.026-0.0260.0000.0000.0000.000
60A62ARG10.9380.96920.246-0.244-0.2440.0000.0000.0000.000
61A63GLN0-0.0030.01317.3020.0240.0240.0000.0000.0000.000
62A64GLU-1-0.824-0.91216.5380.4370.4370.0000.0000.0000.000
63A65ALA0-0.038-0.01220.703-0.031-0.0310.0000.0000.0000.000
64A66GLU-1-0.942-0.99424.1860.1510.1510.0000.0000.0000.000
65A67ALA0-0.0140.00422.007-0.021-0.0210.0000.0000.0000.000
66A68GLY00.0190.00624.007-0.020-0.0200.0000.0000.0000.000
67A69ILE00.003-0.01425.581-0.017-0.0170.0000.0000.0000.000
68A70ALA00.0290.02026.934-0.014-0.0140.0000.0000.0000.000
69A71GLU-1-0.943-0.96925.3510.0740.0740.0000.0000.0000.000
70A72LEU0-0.039-0.02228.352-0.013-0.0130.0000.0000.0000.000
71A73GLU-1-0.936-0.97731.4100.0700.0700.0000.0000.0000.000
72A74LYS10.8620.94427.126-0.067-0.0670.0000.0000.0000.000
73A75ASN0-0.044-0.02228.917-0.014-0.0140.0000.0000.0000.000
74A76ILE0-0.052-0.01033.090-0.006-0.0060.0000.0000.0000.000
75A77SER00.0120.00636.2710.0020.0020.0000.0000.0000.000
76A78ASP-1-0.874-0.93639.4180.0440.0440.0000.0000.0000.000
77A79PRO00.0270.00739.6210.0040.0040.0000.0000.0000.000
78A80LEU00.0370.01539.8740.0050.0050.0000.0000.0000.000
79A81GLU-1-0.823-0.90439.3510.0540.0540.0000.0000.0000.000
80A82GLN00.0220.02335.7340.0070.0070.0000.0000.0000.000
81A83LEU0-0.007-0.00135.5930.0070.0070.0000.0000.0000.000
82A84ARG10.8030.87937.005-0.047-0.0470.0000.0000.0000.000
83A85ALA0-0.010-0.00733.5500.0030.0030.0000.0000.0000.000
84A86TYR00.0180.00530.7430.0110.0110.0000.0000.0000.000
85A87ILE0-0.023-0.02332.7410.0080.0080.0000.0000.0000.000
86A88GLY00.0130.00834.2510.0030.0030.0000.0000.0000.000
87A89TYR0-0.0130.00325.3120.0090.0090.0000.0000.0000.000
88A90TRP00.0480.00326.9080.0100.0100.0000.0000.0000.000
89A91GLU-1-0.783-0.86431.1060.0840.0840.0000.0000.0000.000
90A92GLY00.0140.00930.085-0.001-0.0010.0000.0000.0000.000
91A93CYS0-0.0100.01126.7270.0100.0100.0000.0000.0000.000
92A94ILE0-0.087-0.07128.0560.0070.0070.0000.0000.0000.000
93A95ALA0-0.067-0.01130.778-0.001-0.0010.0000.0000.0000.000
94A96ASP-1-0.901-0.95625.8080.1390.1390.0000.0000.0000.000
95A97ALA0-0.077-0.04027.0060.0070.0070.0000.0000.0000.000
96A98THR0-0.0140.01421.0820.0080.0080.0000.0000.0000.000
97A99HIS0-0.070-0.06218.8330.0060.0060.0000.0000.0000.000
98A100PRO00.0270.02824.481-0.004-0.0040.0000.0000.0000.000
99A101PHE0-0.004-0.02327.102-0.016-0.0160.0000.0000.0000.000
100A102CYM-1-0.871-0.79926.4910.2080.2080.0000.0000.0000.000
101A103VAL00.0460.01321.921-0.006-0.0060.0000.0000.0000.000
102A104CYS0-0.013-0.01325.209-0.004-0.0040.0000.0000.0000.000
103A105ALA00.021-0.02927.476-0.012-0.0120.0000.0000.0000.000
104A106LEU0-0.020-0.00227.726-0.010-0.0100.0000.0000.0000.000
105A107LEU00.0140.00524.401-0.006-0.0060.0000.0000.0000.000
106A108ALA0-0.010-0.00829.037-0.008-0.0080.0000.0000.0000.000
107A109SER0-0.098-0.04332.128-0.010-0.0100.0000.0000.0000.000
108A110GLU-1-0.760-0.88629.1090.1720.1720.0000.0000.0000.000
109A111ILE0-0.036-0.02231.9860.0000.0000.0000.0000.0000.000
110A112PRO0-0.037-0.01733.3280.0020.0020.0000.0000.0000.000
111A113VAL0-0.0050.00031.746-0.004-0.0040.0000.0000.0000.000
112A114LEU0-0.076-0.01627.8060.0090.0090.0000.0000.0000.000
113A115PRO00.004-0.00425.933-0.008-0.0080.0000.0000.0000.000
114A116GLU-1-0.859-0.93528.8270.1300.1300.0000.0000.0000.000
115A117THR0-0.005-0.01624.788-0.002-0.0020.0000.0000.0000.000
116A118VAL00.0320.00723.8580.0100.0100.0000.0000.0000.000
117A119VAL00.0100.00526.1080.0000.0000.0000.0000.0000.000
118A120LEU0-0.039-0.01327.773-0.006-0.0060.0000.0000.0000.000
119A121GLU-1-0.894-0.95523.1830.2570.2570.0000.0000.0000.000
120A122VAL00.0230.00826.233-0.004-0.0040.0000.0000.0000.000
121A123ARG10.9430.96028.201-0.130-0.1300.0000.0000.0000.000
122A124ALA0-0.052-0.02227.708-0.011-0.0110.0000.0000.0000.000
123A125HIS00.0450.02026.926-0.001-0.0010.0000.0000.0000.000
124A126PHE0-0.017-0.00628.698-0.010-0.0100.0000.0000.0000.000
125A127ARG10.9450.96431.059-0.133-0.1330.0000.0000.0000.000
126A128SER00.0160.02728.946-0.009-0.0090.0000.0000.0000.000
127A129LEU00.0560.03330.765-0.006-0.0060.0000.0000.0000.000
128A130SER0-0.012-0.02332.214-0.010-0.0100.0000.0000.0000.000
129A131ASP-1-0.858-0.92733.9510.0890.0890.0000.0000.0000.000
130A132TRP0-0.035-0.01432.306-0.005-0.0050.0000.0000.0000.000
131A133LEU00.007-0.00534.479-0.007-0.0070.0000.0000.0000.000
132A134THR0-0.034-0.03037.000-0.008-0.0080.0000.0000.0000.000
133A135ALA00.0550.03436.991-0.005-0.0050.0000.0000.0000.000
134A136VAL0-0.034-0.00336.150-0.006-0.0060.0000.0000.0000.000
135A137LEU0-0.021-0.02839.082-0.006-0.0060.0000.0000.0000.000
136A138GLU-1-0.933-0.97141.7690.0540.0540.0000.0000.0000.000
137A139ARG10.8870.93636.239-0.069-0.0690.0000.0000.0000.000
138A140GLY00.0240.00043.124-0.003-0.0030.0000.0000.0000.000
139A141ILE0-0.038-0.01644.750-0.003-0.0030.0000.0000.0000.000
140A142ALA0-0.047-0.02045.898-0.003-0.0030.0000.0000.0000.000
141A143GLN0-0.036-0.02242.313-0.003-0.0030.0000.0000.0000.000
142A144GLY0-0.019-0.00547.784-0.002-0.0020.0000.0000.0000.000
143A145ARG10.9100.95445.457-0.037-0.0370.0000.0000.0000.000
144A146LEU0-0.0160.01043.3740.0020.0020.0000.0000.0000.000
145A147VAL0-0.021-0.01548.100-0.002-0.0020.0000.0000.0000.000
146A148LEU00.001-0.00145.8440.0020.0020.0000.0000.0000.000
147A149THR0-0.014-0.00450.025-0.003-0.0030.0000.0000.0000.000
148A150GLY00.0130.00750.1560.0020.0020.0000.0000.0000.000
149A151THR00.0260.01147.1390.0000.0000.0000.0000.0000.000
150A152ALA00.0970.05643.4610.0020.0020.0000.0000.0000.000
151A153ARG10.8780.93337.482-0.080-0.0800.0000.0000.0000.000
152A154ALA0-0.016-0.01042.5620.0040.0040.0000.0000.0000.000
153A155ASN0-0.027-0.04444.3190.0020.0020.0000.0000.0000.000
154A156ALA00.0370.03038.9660.0020.0020.0000.0000.0000.000
155A157GLU-1-0.887-0.93139.0500.0960.0960.0000.0000.0000.000
156A158ILE0-0.013-0.00240.5520.0030.0030.0000.0000.0000.000
157A159PHE00.0320.02036.7000.0030.0030.0000.0000.0000.000
158A160MET0-0.0010.00934.8910.0080.0080.0000.0000.0000.000
159A161ALA0-0.030-0.01736.7080.0060.0060.0000.0000.0000.000
160A162THR0-0.028-0.02339.1090.0000.0000.0000.0000.0000.000
161A163VAL00.0300.01833.8930.0010.0010.0000.0000.0000.000
162A164HIS10.8830.92531.817-0.126-0.1260.0000.0000.0000.000
163A165GLY00.0140.01535.5100.0030.0030.0000.0000.0000.000
164A166ALA0-0.002-0.00337.589-0.002-0.0020.0000.0000.0000.000
165A167MET0-0.0200.00830.5810.0010.0010.0000.0000.0000.000
166A168LEU0-0.030-0.00434.7970.0020.0020.0000.0000.0000.000
167A169SER0-0.012-0.01936.430-0.003-0.0030.0000.0000.0000.000
168A170ALA0-0.0030.00435.480-0.002-0.0020.0000.0000.0000.000
169A171ARG10.8270.92828.402-0.158-0.1580.0000.0000.0000.000
170A172ALA0-0.018-0.00435.329-0.001-0.0010.0000.0000.0000.000
171A173HIS0-0.045-0.00438.8020.0010.0010.0000.0000.0000.000
172A174GLY00.0330.01139.001-0.005-0.0050.0000.0000.0000.000
173A175ASP-1-0.853-0.93938.2080.0710.0710.0000.0000.0000.000
174A176ALA0-0.026-0.01636.2150.0020.0020.0000.0000.0000.000
175A177ALA0-0.0190.00637.4160.0000.0000.0000.0000.0000.000
176A178THR00.0460.00739.324-0.003-0.0030.0000.0000.0000.000
177A179PHE00.000-0.00434.640-0.001-0.0010.0000.0000.0000.000
178A180GLY00.0770.03538.205-0.001-0.0010.0000.0000.0000.000
179A181ALA0-0.041-0.01639.999-0.004-0.0040.0000.0000.0000.000
180A182ILE0-0.025-0.00940.980-0.003-0.0030.0000.0000.0000.000
181A183THR0-0.057-0.04637.795-0.003-0.0030.0000.0000.0000.000
182A184ARG10.8130.88237.649-0.074-0.0740.0000.0000.0000.000
183A185PRO00.0270.01642.800-0.003-0.0030.0000.0000.0000.000
184A186MET0-0.067-0.01943.660-0.002-0.0020.0000.0000.0000.000
185A187LEU00.0290.01639.787-0.001-0.0010.0000.0000.0000.000
186A188GLU-1-0.843-0.92144.2780.0470.0470.0000.0000.0000.000
187A189ARG10.8690.94647.055-0.056-0.0560.0000.0000.0000.000
188A190ILE0-0.050-0.01743.731-0.002-0.0020.0000.0000.0000.000
189A191THR00.0150.01346.9630.0000.0000.0000.0000.0000.000
190A192ALA0-0.034-0.00448.584-0.002-0.0020.0000.0000.0000.000