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

tag_button

FMODB ID: R1358

Calculation Name: 3GGY-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GGY

Chain ID: A

ChEMBL ID:

UniProt ID: P53843

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2031892.23205
FMO2-HF: Nuclear repulsion 1955938.986399
FMO2-HF: Total energy -75953.245651
FMO2-MP2: Total energy -76175.161022


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:5:ACE )


Summations of interaction energy for fragment #1(A:5:ACE )
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.
0.5051.4572.592-1.771-1.772-0.002
Interaction energy analysis for fragmet #1(A:5:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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].
3A7PRO 00.0480.0263.4310.7341.7700.026-0.479-0.5820.000
4A8PHE 00.0430.0135.3210.0670.0670.0000.0000.0000.000
5A9THR 00.1010.0437.4730.0780.0780.0000.0000.0000.000
6A10ILE 0-0.031-0.0102.3800.3860.0012.561-1.219-0.958-0.002
7A11LYS 10.8880.9503.7391.2561.4480.005-0.063-0.1340.000
8A12LEU 00.0810.0494.9250.0620.0930.000-0.003-0.0280.000
9A13LYS 10.9710.9936.946-1.185-1.1850.0000.0000.0000.000
10A14THR 0-0.050-0.0364.4450.0950.1730.000-0.007-0.0700.000
11A15CYS 0-0.0040.0077.099-0.131-0.1310.0000.0000.0000.000
12A16LEU 00.0400.0249.605-0.021-0.0210.0000.0000.0000.000
13A17LYS 10.9230.9649.733-0.550-0.5500.0000.0000.0000.000
14A18MET 0-0.0150.01211.082-0.027-0.0270.0000.0000.0000.000
15A19CYS 00.0120.00112.816-0.051-0.0510.0000.0000.0000.000
16A20ILE 00.0400.02815.192-0.016-0.0160.0000.0000.0000.000
17A21GLN 0-0.024-0.01415.466-0.023-0.0230.0000.0000.0000.000
18A22ARG 10.8370.92216.219-0.099-0.0990.0000.0000.0000.000
19A23LEU 00.0440.02018.715-0.015-0.0150.0000.0000.0000.000
20A24ARG 10.8600.93920.060-0.175-0.1750.0000.0000.0000.000
21A25TYR 0-0.025-0.00421.463-0.013-0.0130.0000.0000.0000.000
22A26ALA 0-0.031-0.01722.833-0.010-0.0100.0000.0000.0000.000
23A27GLN 00.003-0.01623.786-0.011-0.0110.0000.0000.0000.000
24A28GLU -1-0.897-0.93426.1250.0810.0810.0000.0000.0000.000
25A29LYS 10.9180.95327.231-0.048-0.0480.0000.0000.0000.000
26A30GLN 00.000-0.02927.021-0.007-0.0070.0000.0000.0000.000
27A31GLN 00.0660.04630.259-0.001-0.0010.0000.0000.0000.000
28A32ALA 0-0.031-0.01032.067-0.004-0.0040.0000.0000.0000.000
29A33ILE 0-0.032-0.02931.565-0.004-0.0040.0000.0000.0000.000
30A34ALA 00.1030.06634.628-0.004-0.0040.0000.0000.0000.000
31A35LYS 10.9560.97636.554-0.039-0.0390.0000.0000.0000.000
32A36GLN 0-0.063-0.04337.937-0.004-0.0040.0000.0000.0000.000
33A37SER 00.0200.00038.035-0.003-0.0030.0000.0000.0000.000
34A38ARG 10.9430.98439.734-0.029-0.0290.0000.0000.0000.000
35A39ARG 10.9160.97242.094-0.028-0.0280.0000.0000.0000.000
36A40GLN 0-0.020-0.00741.379-0.002-0.0020.0000.0000.0000.000
37A41VAL 00.0410.03644.377-0.002-0.0020.0000.0000.0000.000
38A42ALA 00.0580.03046.730-0.001-0.0010.0000.0000.0000.000
39A43GLN 0-0.008-0.00248.3610.0000.0000.0000.0000.0000.000
40A44LEU 0-0.081-0.03647.005-0.001-0.0010.0000.0000.0000.000
41A45LEU 00.0730.05250.646-0.001-0.0010.0000.0000.0000.000
42A46LEU 0-0.020-0.00352.676-0.001-0.0010.0000.0000.0000.000
43A47THR 0-0.144-0.08453.124-0.001-0.0010.0000.0000.0000.000
44A48ASN 00.0530.02755.7230.0000.0000.0000.0000.0000.000
45A49LYS 10.8770.95151.832-0.011-0.0110.0000.0000.0000.000
46A50GLU -1-0.702-0.88352.2160.0110.0110.0000.0000.0000.000
47A51GLN 0-0.0100.00551.5630.0000.0000.0000.0000.0000.000
48A52LYS 10.9310.95348.805-0.008-0.0080.0000.0000.0000.000
49A53ALA 00.0100.00547.6070.0010.0010.0000.0000.0000.000
50A54HIS 00.000-0.00147.2990.0010.0010.0000.0000.0000.000
51A55TYR 00.0350.01545.6190.0000.0000.0000.0000.0000.000
52A56ARG 10.8210.89541.553-0.015-0.0150.0000.0000.0000.000
53A57VAL 00.0120.00242.4100.0020.0020.0000.0000.0000.000
54A58GLU -1-0.849-0.93142.4660.0090.0090.0000.0000.0000.000
55A59THR 0-0.063-0.02838.1130.0000.0000.0000.0000.0000.000
56A60LEU 0-0.027-0.00838.0970.0010.0010.0000.0000.0000.000
57A61ILE 00.0020.00838.0660.0020.0020.0000.0000.0000.000
58A62HIS 0-0.0070.00132.7660.0000.0000.0000.0000.0000.000
59A63ASP -1-0.912-0.97133.9530.0230.0230.0000.0000.0000.000
60A64ASP -1-0.816-0.90433.2820.0340.0340.0000.0000.0000.000
61A65ILE 0-0.0180.00933.4810.0030.0030.0000.0000.0000.000
62A66HIS 10.7990.87627.142-0.024-0.0240.0000.0000.0000.000
63A67ILE 00.012-0.00129.1410.0040.0040.0000.0000.0000.000
64A68GLU -1-0.846-0.91929.0220.0370.0370.0000.0000.0000.000
65A69LEU 0-0.061-0.03026.5490.0040.0040.0000.0000.0000.000
66A70LEU 0-0.044-0.03124.0770.0060.0060.0000.0000.0000.000
67A71GLU -1-0.879-0.93424.4050.0650.0650.0000.0000.0000.000
68A72ILE 0-0.054-0.02725.4430.0060.0060.0000.0000.0000.000
69A73LEU 0-0.008-0.01621.8070.0050.0050.0000.0000.0000.000
70A74GLU -1-0.811-0.89120.6620.1260.1260.0000.0000.0000.000
71A75LEU 00.0330.01920.6310.0150.0150.0000.0000.0000.000
72A76TYR 0-0.074-0.06721.1760.0060.0060.0000.0000.0000.000
73A77CYS 0-0.048-0.02416.7170.0070.0070.0000.0000.0000.000
74A78GLU -1-0.891-0.95316.7920.1760.1760.0000.0000.0000.000
75A79LEU 0-0.0340.00218.4380.0170.0170.0000.0000.0000.000
76A80LEU 00.008-0.01215.8510.0090.0090.0000.0000.0000.000
77A81LEU 0-0.067-0.03712.1760.0470.0470.0000.0000.0000.000
78A82ALA 0-0.036-0.02514.5700.0400.0400.0000.0000.0000.000
79A83ARG 10.9590.99217.030-0.097-0.0970.0000.0000.0000.000
80A84VAL 0-0.0120.00410.424-0.007-0.0070.0000.0000.0000.000
81A85GLN 0-0.042-0.03813.633-0.047-0.0470.0000.0000.0000.000
82A86VAL 00.0610.03914.628-0.027-0.0270.0000.0000.0000.000
83A87ILE 00.0360.01614.509-0.023-0.0230.0000.0000.0000.000
84A88ASN 0-0.069-0.04112.493-0.063-0.0630.0000.0000.0000.000
85A89ASP -1-0.918-0.93514.379-0.005-0.0050.0000.0000.0000.000
86A90ILE 0-0.063-0.00717.322-0.004-0.0040.0000.0000.0000.000
87A91SER 0-0.020-0.02017.795-0.016-0.0160.0000.0000.0000.000
88A92THR 00.001-0.00619.901-0.006-0.0060.0000.0000.0000.000
89A93GLU -1-0.773-0.89223.072-0.027-0.0270.0000.0000.0000.000
90A94GLU -1-0.840-0.92824.693-0.009-0.0090.0000.0000.0000.000
91A95GLN 00.0770.03322.542-0.001-0.0010.0000.0000.0000.000
92A96LEU 0-0.052-0.01720.7840.0100.0100.0000.0000.0000.000
93A97VAL 00.024-0.00323.8730.0080.0080.0000.0000.0000.000
94A98LYS 10.8690.94627.4310.0130.0130.0000.0000.0000.000
95A99GLU -1-0.969-0.98325.5440.0050.0050.0000.0000.0000.000
96A100HIS 10.7650.87421.984-0.025-0.0250.0000.0000.0000.000
97A101MET 00.0280.03024.9540.0040.0040.0000.0000.0000.000
98A102ASP -1-0.941-0.95927.7220.0440.0440.0000.0000.0000.000
99A103ASP -1-0.820-0.90323.3200.0560.0560.0000.0000.0000.000
100A104GLY 00.0500.00523.8920.0100.0100.0000.0000.0000.000
101A105ILE 0-0.059-0.03019.1990.0030.0030.0000.0000.0000.000
102A106ASN 00.0120.01721.732-0.008-0.0080.0000.0000.0000.000
103A107GLU -1-0.799-0.88123.7320.0330.0330.0000.0000.0000.000
104A108ALA 00.0000.00120.797-0.002-0.0020.0000.0000.0000.000
105A109ILE 0-0.033-0.02716.6070.0000.0000.0000.0000.0000.000
106A110ARG 10.8120.87620.0390.0020.0020.0000.0000.0000.000
107A111SER 00.011-0.00323.114-0.006-0.0060.0000.0000.0000.000
108A112LEU 0-0.047-0.02317.6220.0000.0000.0000.0000.0000.000
109A113ILE 0-0.044-0.02218.502-0.008-0.0080.0000.0000.0000.000
110A114TYR 00.0170.00020.906-0.005-0.0050.0000.0000.0000.000
111A115ALA 00.0240.00422.648-0.002-0.0020.0000.0000.0000.000
112A116ILE 0-0.065-0.01718.713-0.002-0.0020.0000.0000.0000.000
113A117LEU 0-0.041-0.01722.157-0.001-0.0010.0000.0000.0000.000
114A118PHE 00.0250.00725.4700.0010.0010.0000.0000.0000.000
115A119VAL 0-0.032-0.00822.8270.0060.0060.0000.0000.0000.000
116A120ASP -1-0.881-0.92422.4820.0030.0030.0000.0000.0000.000
117A121GLU -1-0.818-0.89722.5880.0280.0280.0000.0000.0000.000
118A122VAL 0-0.097-0.05517.7410.0130.0130.0000.0000.0000.000
119A123LYS 11.0200.99417.340-0.002-0.0020.0000.0000.0000.000
120A124GLU -1-0.839-0.92512.8380.0430.0430.0000.0000.0000.000
121A125LEU 00.0490.02314.188-0.008-0.0080.0000.0000.0000.000
122A126SER 0-0.019-0.01616.506-0.019-0.0190.0000.0000.0000.000
123A127GLN 00.0340.0009.882-0.026-0.0260.0000.0000.0000.000
124A128LEU 00.001-0.00512.655-0.028-0.0280.0000.0000.0000.000
125A129LYS 11.0021.01714.2590.0940.0940.0000.0000.0000.000
126A130ASP -1-0.930-0.96313.370-0.191-0.1910.0000.0000.0000.000
127A131LEU 0-0.100-0.0588.608-0.043-0.0430.0000.0000.0000.000
128A132MET 00.010-0.00812.679-0.004-0.0040.0000.0000.0000.000
129A133ALA 00.0030.01815.9530.0040.0040.0000.0000.0000.000
130A134TRP 0-0.073-0.02512.158-0.031-0.0310.0000.0000.0000.000
131A135LYS 10.7710.88013.4400.0960.0960.0000.0000.0000.000
132A136ILE 0-0.0330.00115.6840.0140.0140.0000.0000.0000.000
133A137ASN 00.0300.01319.371-0.004-0.0040.0000.0000.0000.000
134A138VAL 00.0400.00021.1570.0050.0050.0000.0000.0000.000
135A139GLU -1-0.897-0.95422.499-0.077-0.0770.0000.0000.0000.000
136A140PHE 00.0210.01619.6100.0080.0080.0000.0000.0000.000
137A141VAL 0-0.051-0.02519.2960.0070.0070.0000.0000.0000.000
138A142ASN 0-0.009-0.01522.6500.0050.0050.0000.0000.0000.000
139A143GLY 00.0710.05025.9340.0050.0050.0000.0000.0000.000
140A144VAL 0-0.062-0.02423.5170.0060.0060.0000.0000.0000.000
141A145ILE 0-0.045-0.04122.4440.0040.0040.0000.0000.0000.000
142A146ALA 0-0.067-0.02326.7490.0030.0030.0000.0000.0000.000
143A147ASP -1-0.903-0.94729.878-0.027-0.0270.0000.0000.0000.000
144A148HIS 0-0.022-0.00928.9040.0020.0020.0000.0000.0000.000
145A149ILE 00.0060.00028.7500.0050.0050.0000.0000.0000.000
146A150ASP -1-0.856-0.94128.123-0.001-0.0010.0000.0000.0000.000
147A151VAL 0-0.067-0.01326.6280.0050.0050.0000.0000.0000.000
148A152PRO 0-0.009-0.01027.7810.0000.0000.0000.0000.0000.000
149A153GLU -1-0.836-0.92630.7880.0060.0060.0000.0000.0000.000
150A154LYS 10.9250.95928.818-0.041-0.0410.0000.0000.0000.000
151A155ILE 00.0130.00426.7160.0020.0020.0000.0000.0000.000
152A156ILE 00.0570.03730.002-0.001-0.0010.0000.0000.0000.000
153A157LYS 10.8910.94132.028-0.009-0.0090.0000.0000.0000.000
154A158LYS 10.8620.93630.914-0.029-0.0290.0000.0000.0000.000
155A159CYS 0-0.056-0.00228.5390.0010.0010.0000.0000.0000.000
156A160SER 0-0.036-0.01331.046-0.003-0.0030.0000.0000.0000.000
157A161PRO 0-0.0260.00934.360-0.001-0.0010.0000.0000.0000.000
158A162SER 0-0.042-0.03037.138-0.002-0.0020.0000.0000.0000.000
159A163VAL 00.000-0.01040.7800.0010.0010.0000.0000.0000.000
160A164PRO 0-0.0060.00341.6810.0000.0000.0000.0000.0000.000
161A165LYS 10.9420.98944.157-0.011-0.0110.0000.0000.0000.000
162A166GLU -1-0.719-0.87147.6710.0090.0090.0000.0000.0000.000
163A167GLU -1-0.895-0.95549.7800.0110.0110.0000.0000.0000.000
164A168LEU 0-0.051-0.02242.2940.0010.0010.0000.0000.0000.000
165A169VAL 00.0400.02146.0230.0020.0020.0000.0000.0000.000
166A170ASP -1-0.844-0.93347.4760.0120.0120.0000.0000.0000.000
167A171LEU 0-0.083-0.03646.1350.0010.0010.0000.0000.0000.000
168A172TYR 0-0.007-0.04739.4500.0010.0010.0000.0000.0000.000
169A173LEU 0-0.0160.00246.3260.0010.0010.0000.0000.0000.000
170A174LYS 10.9490.97149.183-0.014-0.0140.0000.0000.0000.000
171A175GLU -1-0.971-0.97844.9360.0250.0250.0000.0000.0000.000
172A176ILE 0-0.072-0.04144.4700.0010.0010.0000.0000.0000.000
173A177ALA 00.006-0.00947.3650.0000.0000.0000.0000.0000.000
174A178LYS 10.9620.98649.581-0.024-0.0240.0000.0000.0000.000
175A179THR 0-0.077-0.03544.7250.0010.0010.0000.0000.0000.000
176A180TYR 0-0.093-0.06243.0910.0020.0020.0000.0000.0000.000
177A181ASP -1-0.908-0.92549.7040.0210.0210.0000.0000.0000.000
178A182VAL 0-0.057-0.02151.497-0.001-0.0010.0000.0000.0000.000
179A183PRO 0-0.022-0.01854.2030.0000.0000.0000.0000.0000.000
180A184TYR 00.0590.02257.5270.0000.0000.0000.0000.0000.000
181A185SER 0-0.003-0.00959.0250.0000.0000.0000.0000.0000.000
182A186LYS 10.8500.92356.241-0.012-0.0120.0000.0000.0000.000
183A187LEU 00.0510.03952.2430.0000.0000.0000.0000.0000.000
184A188GLU -1-0.903-0.94855.6780.0120.0120.0000.0000.0000.000
185A189ASN 0-0.101-0.04058.460-0.001-0.0010.0000.0000.0000.000
186A190SER 0-0.076-0.04953.1520.0000.0000.0000.0000.0000.000
187A191LEU 0-0.052-0.01553.5380.0000.0000.0000.0000.0000.000
188A192NME 00.0110.01755.5920.0000.0000.0000.0000.0000.000