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: YVG12

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:


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 190
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1948688.4263
FMO2-HF: Nuclear repulsion 1875470.950818
FMO2-HF: Total energy -73217.475482
FMO2-MP2: Total energy -73429.448166


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.
-24.867-20.89212.281-6.984-9.2720.014
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 : 0.055 / q_NPA : 0.033
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].
3A5GLN00.0220.0082.639-4.873-1.8041.739-1.855-2.9520.015
4A6SER00.005-0.0111.963-17.874-17.60310.522-4.893-5.900-0.002
5A7LYS10.8410.9093.769-1.431-0.7960.020-0.236-0.4200.001
6A8ALA00.0090.0125.939-0.525-0.5250.0000.0000.0000.000
7A9ASP-1-0.816-0.9076.7281.7501.7500.0000.0000.0000.000
8A10ASP-1-0.825-0.9057.453-1.294-1.2940.0000.0000.0000.000
9A11ILE0-0.068-0.0319.441-0.124-0.1240.0000.0000.0000.000
10A12LEU0-0.0080.00511.028-0.109-0.1090.0000.0000.0000.000
11A13GLN00.0190.01811.319-0.083-0.0830.0000.0000.0000.000
12A14CYS0-0.052-0.00313.452-0.057-0.0570.0000.0000.0000.000
13A15ALA00.0310.00415.259-0.022-0.0220.0000.0000.0000.000
14A16ARG10.7560.82915.585-0.254-0.2540.0000.0000.0000.000
15A17THR00.0460.02217.577-0.025-0.0250.0000.0000.0000.000
16A18LEU0-0.055-0.02818.276-0.014-0.0140.0000.0000.0000.000
17A19ILE0-0.0130.00621.273-0.010-0.0100.0000.0000.0000.000
18A20ILE00.0480.03122.278-0.006-0.0060.0000.0000.0000.000
19A21ARG10.8570.93023.488-0.033-0.0330.0000.0000.0000.000
20A22GLY00.010-0.00826.741-0.007-0.0070.0000.0000.0000.000
21A23GLY00.0540.04827.1640.0010.0010.0000.0000.0000.000
22A24TYR0-0.005-0.02723.282-0.004-0.0040.0000.0000.0000.000
23A25ASN0-0.077-0.05225.3270.0080.0080.0000.0000.0000.000
24A26SER0-0.059-0.01026.134-0.011-0.0110.0000.0000.0000.000
25A27PHE00.0200.01119.609-0.008-0.0080.0000.0000.0000.000
26A28SER0-0.021-0.03021.8590.0190.0190.0000.0000.0000.000
27A29TYR00.038-0.01817.348-0.014-0.0140.0000.0000.0000.000
28A30ALA0-0.0020.00917.192-0.018-0.0180.0000.0000.0000.000
29A31ASP-1-0.798-0.87718.4080.0070.0070.0000.0000.0000.000
30A32ILE00.025-0.00313.564-0.028-0.0280.0000.0000.0000.000
31A33SER0-0.048-0.04913.756-0.030-0.0300.0000.0000.0000.000
32A34GLN0-0.076-0.02814.321-0.048-0.0480.0000.0000.0000.000
33A35VAL0-0.0030.00214.488-0.026-0.0260.0000.0000.0000.000
34A36VAL00.0010.0049.173-0.066-0.0660.0000.0000.0000.000
35A37GLY00.0160.0109.662-0.198-0.1980.0000.0000.0000.000
36A38ILE0-0.045-0.0107.724-0.012-0.0120.0000.0000.0000.000
37A39ARG11.0171.00910.4610.0970.0970.0000.0000.0000.000
38A40ASN00.0950.03013.2390.0590.0590.0000.0000.0000.000
39A41ALA00.016-0.00415.2050.0400.0400.0000.0000.0000.000
40A42SER0-0.016-0.0159.8720.0160.0160.0000.0000.0000.000
41A43ILE00.0010.01611.1470.1050.1050.0000.0000.0000.000
42A44HIS0-0.018-0.01413.1690.1350.1350.0000.0000.0000.000
43A45HIS0-0.066-0.03211.0060.0180.0180.0000.0000.0000.000
44A46HIS0-0.0100.0206.4980.4700.4700.0000.0000.0000.000
45A47PHE00.0130.00010.9320.0530.0530.0000.0000.0000.000
46A48PRO00.0050.01114.842-0.098-0.0980.0000.0000.0000.000
47A49SER00.0160.00217.924-0.053-0.0530.0000.0000.0000.000
48A50LYS10.8830.93619.055-0.115-0.1150.0000.0000.0000.000
49A51SER00.0290.01220.639-0.005-0.0050.0000.0000.0000.000
50A52ASP-1-0.816-0.88216.3770.6550.6550.0000.0000.0000.000
51A53LEU00.0090.00815.0650.0220.0220.0000.0000.0000.000
52A54VAL00.0270.00217.0660.0170.0170.0000.0000.0000.000
53A55CYS0-0.062-0.01619.797-0.026-0.0260.0000.0000.0000.000
54A56LYS10.8430.90714.143-0.775-0.7750.0000.0000.0000.000
55A57LEU0-0.0090.01216.4360.0050.0050.0000.0000.0000.000
56A58VAL00.002-0.01117.294-0.031-0.0310.0000.0000.0000.000
57A59SER0-0.008-0.02118.155-0.019-0.0190.0000.0000.0000.000
58A60GLN0-0.0010.01511.965-0.111-0.1110.0000.0000.0000.000
59A61TYR00.005-0.08517.057-0.050-0.0500.0000.0000.0000.000
60A62ARG10.7980.86019.931-0.260-0.2600.0000.0000.0000.000
61A63GLN0-0.035-0.00817.054-0.002-0.0020.0000.0000.0000.000
62A64GLU-1-0.774-0.84716.2030.2010.2010.0000.0000.0000.000
63A65ALA00.0100.00920.178-0.034-0.0340.0000.0000.0000.000
64A66GLU-1-0.810-0.87723.8660.1640.1640.0000.0000.0000.000
65A67ALA00.0050.00721.503-0.014-0.0140.0000.0000.0000.000
66A68GLY00.0160.01223.522-0.021-0.0210.0000.0000.0000.000
67A69ILE0-0.012-0.01524.827-0.015-0.0150.0000.0000.0000.000
68A70ALA00.0100.01426.340-0.009-0.0090.0000.0000.0000.000
69A71GLU-1-0.792-0.86424.857-0.009-0.0090.0000.0000.0000.000
70A72LEU0-0.038-0.02827.172-0.012-0.0120.0000.0000.0000.000
71A73GLU-1-0.832-0.88830.1590.0520.0520.0000.0000.0000.000
72A74LYS10.7680.87426.677-0.004-0.0040.0000.0000.0000.000
73A75ASN0-0.068-0.04727.822-0.008-0.0080.0000.0000.0000.000
74A76ILE0-0.034-0.00132.072-0.006-0.0060.0000.0000.0000.000
75A77SER00.0050.00635.3140.0050.0050.0000.0000.0000.000
76A78ASP-1-0.785-0.88038.4060.0130.0130.0000.0000.0000.000
77A79PRO00.010-0.00838.672-0.001-0.0010.0000.0000.0000.000
78A80LEU00.0250.01639.1580.0020.0020.0000.0000.0000.000
79A81GLU-1-0.794-0.88438.262-0.001-0.0010.0000.0000.0000.000
80A82GLN0-0.0030.00534.9460.0030.0030.0000.0000.0000.000
81A83LEU0-0.009-0.00234.6480.0020.0020.0000.0000.0000.000
82A84ARG10.7660.83236.289-0.001-0.0010.0000.0000.0000.000
83A85ALA00.0010.00432.563-0.004-0.0040.0000.0000.0000.000
84A86TYR00.0160.01029.873-0.002-0.0020.0000.0000.0000.000
85A87ILE0-0.029-0.01532.1970.0020.0020.0000.0000.0000.000
86A88GLY00.0230.01233.367-0.002-0.0020.0000.0000.0000.000
87A89TYR0-0.009-0.00424.479-0.007-0.0070.0000.0000.0000.000
88A90TRP00.0330.00626.655-0.002-0.0020.0000.0000.0000.000
89A91GLU-1-0.782-0.86330.609-0.012-0.0120.0000.0000.0000.000
90A92GLY00.0220.02129.144-0.006-0.0060.0000.0000.0000.000
91A93CYS0-0.024-0.01426.164-0.004-0.0040.0000.0000.0000.000
92A94ILE0-0.071-0.04227.451-0.001-0.0010.0000.0000.0000.000
93A95ALA0-0.030-0.01030.418-0.004-0.0040.0000.0000.0000.000
94A96ASP-1-0.894-0.94525.193-0.080-0.0800.0000.0000.0000.000
95A97ALA0-0.048-0.02426.186-0.009-0.0090.0000.0000.0000.000
96A98THR0-0.064-0.02421.0090.0000.0000.0000.0000.0000.000
97A99HIS0-0.058-0.06018.5930.0180.0180.0000.0000.0000.000
98A100PRO00.0230.03624.3750.0110.0110.0000.0000.0000.000
99A101PHE0-0.050-0.05627.1530.0020.0020.0000.0000.0000.000
100A102CYM-1-0.869-0.79226.4500.1120.1120.0000.0000.0000.000
101A103VAL00.0370.01021.943-0.001-0.0010.0000.0000.0000.000
102A104CYS0-0.032-0.01125.3040.0090.0090.0000.0000.0000.000
103A105ALA00.049-0.00827.372-0.002-0.0020.0000.0000.0000.000
104A106LEU0-0.0280.00427.466-0.005-0.0050.0000.0000.0000.000
105A107LEU00.0010.00824.2070.0000.0000.0000.0000.0000.000
106A108ALA0-0.007-0.01528.8680.0010.0010.0000.0000.0000.000
107A109SER0-0.072-0.03732.063-0.005-0.0050.0000.0000.0000.000
108A110GLU-1-0.721-0.85328.6440.1100.1100.0000.0000.0000.000
109A111ILE0-0.033-0.01331.5460.0060.0060.0000.0000.0000.000
110A112PRO0-0.042-0.03132.8750.0060.0060.0000.0000.0000.000
111A113VAL0-0.0130.00131.825-0.002-0.0020.0000.0000.0000.000
112A114LEU0-0.0450.00127.0020.0090.0090.0000.0000.0000.000
113A115PRO00.009-0.00525.2700.0010.0010.0000.0000.0000.000
114A116GLU-1-0.875-0.94027.8730.1670.1670.0000.0000.0000.000
115A117THR0-0.009-0.02123.919-0.010-0.0100.0000.0000.0000.000
116A118VAL00.0310.01123.1430.0110.0110.0000.0000.0000.000
117A119VAL00.0000.00425.429-0.008-0.0080.0000.0000.0000.000
118A120LEU0-0.034-0.02127.498-0.011-0.0110.0000.0000.0000.000
119A121GLU-1-0.774-0.86222.1830.2940.2940.0000.0000.0000.000
120A122VAL00.0070.00325.847-0.011-0.0110.0000.0000.0000.000
121A123ARG10.9480.96127.764-0.143-0.1430.0000.0000.0000.000
122A124ALA0-0.057-0.02426.808-0.012-0.0120.0000.0000.0000.000
123A125HIS00.0590.00426.1590.0050.0050.0000.0000.0000.000
124A126PHE0-0.010-0.01628.019-0.014-0.0140.0000.0000.0000.000
125A127ARG10.9100.96930.205-0.159-0.1590.0000.0000.0000.000
126A128SER00.028-0.00228.158-0.014-0.0140.0000.0000.0000.000
127A129LEU00.0130.01230.365-0.009-0.0090.0000.0000.0000.000
128A130SER0-0.010-0.03131.825-0.011-0.0110.0000.0000.0000.000
129A131ASP-1-0.849-0.91233.3980.0950.0950.0000.0000.0000.000
130A132TRP0-0.027-0.01431.903-0.007-0.0070.0000.0000.0000.000
131A133LEU00.011-0.00234.049-0.008-0.0080.0000.0000.0000.000
132A134THR0-0.031-0.03136.518-0.007-0.0070.0000.0000.0000.000
133A135ALA00.0350.02336.344-0.005-0.0050.0000.0000.0000.000
134A136VAL0-0.049-0.01135.421-0.005-0.0050.0000.0000.0000.000
135A137LEU00.003-0.00638.399-0.005-0.0050.0000.0000.0000.000
136A138GLU-1-0.948-0.98841.6470.0510.0510.0000.0000.0000.000
137A139ARG10.7940.86235.031-0.051-0.0510.0000.0000.0000.000
138A140GLY00.0320.00842.376-0.004-0.0040.0000.0000.0000.000
139A141ILE0-0.030-0.01243.908-0.003-0.0030.0000.0000.0000.000
140A142ALA0-0.041-0.01844.956-0.002-0.0020.0000.0000.0000.000
141A143GLN0-0.066-0.03341.212-0.004-0.0040.0000.0000.0000.000
142A144GLY0-0.018-0.00646.655-0.003-0.0030.0000.0000.0000.000
143A145ARG10.8620.92544.174-0.009-0.0090.0000.0000.0000.000
144A146LEU0-0.023-0.00142.519-0.001-0.0010.0000.0000.0000.000
145A147VAL0-0.011-0.00347.1620.0010.0010.0000.0000.0000.000
146A148LEU00.0090.00545.2270.0010.0010.0000.0000.0000.000
147A149THR0-0.020-0.01949.478-0.002-0.0020.0000.0000.0000.000
148A150GLY00.0270.02649.6860.0010.0010.0000.0000.0000.000
149A151THR00.009-0.00446.549-0.001-0.0010.0000.0000.0000.000
150A152ALA00.0800.04543.339-0.001-0.0010.0000.0000.0000.000
151A153ARG10.8700.91736.930-0.079-0.0790.0000.0000.0000.000
152A154ALA0-0.009-0.00441.9650.0020.0020.0000.0000.0000.000
153A155ASN0-0.041-0.04443.718-0.003-0.0030.0000.0000.0000.000
154A156ALA00.0490.03238.459-0.002-0.0020.0000.0000.0000.000
155A157GLU-1-0.865-0.89938.6720.0760.0760.0000.0000.0000.000
156A158ILE0-0.014-0.00740.001-0.001-0.0010.0000.0000.0000.000
157A159PHE00.0390.02536.355-0.002-0.0020.0000.0000.0000.000
158A160MET00.0080.01634.3540.0010.0010.0000.0000.0000.000
159A161ALA0-0.049-0.02636.3980.0010.0010.0000.0000.0000.000
160A162THR0-0.026-0.02638.704-0.003-0.0030.0000.0000.0000.000
161A163VAL00.0350.01533.604-0.004-0.0040.0000.0000.0000.000
162A164HIS10.8550.89430.862-0.076-0.0760.0000.0000.0000.000
163A165GLY00.0260.01935.257-0.001-0.0010.0000.0000.0000.000
164A166ALA00.0050.01637.150-0.004-0.0040.0000.0000.0000.000
165A167MET0-0.0070.03030.4160.0000.0000.0000.0000.0000.000
166A168LEU0-0.016-0.00934.594-0.003-0.0030.0000.0000.0000.000
167A169SER0-0.026-0.02836.333-0.004-0.0040.0000.0000.0000.000
168A170ALA00.0010.00335.450-0.003-0.0030.0000.0000.0000.000
169A171ARG10.8000.91028.235-0.034-0.0340.0000.0000.0000.000
170A172ALA0-0.029-0.00535.294-0.002-0.0020.0000.0000.0000.000
171A173HIS0-0.024-0.01538.625-0.002-0.0020.0000.0000.0000.000
172A174GLY00.0150.02738.274-0.003-0.0030.0000.0000.0000.000
173A175ASP-1-0.832-0.93038.550-0.016-0.0160.0000.0000.0000.000
174A176ALA00.0020.00735.6120.0040.0040.0000.0000.0000.000
175A177ALA00.0010.00136.9010.0020.0020.0000.0000.0000.000
176A178THR0-0.042-0.03539.2810.0030.0030.0000.0000.0000.000
177A179PHE00.0240.01034.1870.0040.0040.0000.0000.0000.000
178A180GLY00.0800.04637.8610.0040.0040.0000.0000.0000.000
179A181ALA0-0.060-0.03939.2990.0020.0020.0000.0000.0000.000
180A182ILE0-0.032-0.00840.6810.0020.0020.0000.0000.0000.000
181A183THR0-0.024-0.02637.1920.0020.0020.0000.0000.0000.000
182A184ARG10.8110.86837.2020.0090.0090.0000.0000.0000.000
183A185PRO00.0150.00542.0520.0010.0010.0000.0000.0000.000
184A186MET0-0.0670.00342.7990.0010.0010.0000.0000.0000.000
185A187LEU00.0310.01439.1560.0010.0010.0000.0000.0000.000
186A188GLU-1-0.817-0.89543.7250.0020.0020.0000.0000.0000.000
187A189ARG10.8730.93846.222-0.022-0.0220.0000.0000.0000.000
188A190ILE0-0.046-0.01543.0530.0010.0010.0000.0000.0000.000
189A191THR00.0150.00446.2770.0010.0010.0000.0000.0000.000
190A192ALA0-0.063-0.01747.837-0.002-0.0020.0000.0000.0000.000