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: GY571

Calculation Name: 2GAI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GAI

Chain ID: A

ChEMBL ID:

UniProt ID: P46799

Base Structure: X-ray

Registration Date: 2023-09-27

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 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 580
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12255137.640428
FMO2-HF: Nuclear repulsion 12021709.336384
FMO2-HF: Total energy -233428.304044
FMO2-MP2: Total energy -234114.072959


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:7:LYS)


Summations of interaction energy for fragment #1(A:7:LYS)
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.
-2.95912.59710.198-10.246-15.506-0.081
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.949 / q_NPA : 0.988
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].
3A9ILE00.0200.0113.8130.0552.615-0.018-1.281-1.2610.007
4A10VAL0-0.041-0.0125.9251.7921.7920.0000.0000.0000.000
5A11VAL0-0.023-0.0099.4500.3240.3240.0000.0000.0000.000
6A12GLU-1-0.714-0.85812.565-16.281-16.2810.0000.0000.0000.000
7A13SER0-0.010-0.01416.2430.2590.2590.0000.0000.0000.000
8A14PRO00.040-0.00216.176-0.847-0.8470.0000.0000.0000.000
9A15ALA00.0060.01417.158-0.557-0.5570.0000.0000.0000.000
10A16LYS10.8520.90814.33616.91916.9190.0000.0000.0000.000
11A17ALA0-0.035-0.01812.649-1.124-1.1240.0000.0000.0000.000
12A18LYS10.9500.97612.84413.36713.3670.0000.0000.0000.000
13A19THR00.0270.00714.854-0.602-0.6020.0000.0000.0000.000
14A20ILE00.010-0.0099.117-0.701-0.7010.0000.0000.0000.000
15A21LYS10.8520.9197.86928.92128.9210.0000.0000.0000.000
16A22SER0-0.009-0.01211.196-0.514-0.5140.0000.0000.0000.000
17A23ILE0-0.077-0.00310.8120.1780.1780.0000.0000.0000.000
18A24LEU0-0.019-0.0216.117-0.048-0.0480.0000.0000.0000.000
19A25GLY00.0420.0447.826-2.728-2.7280.0000.0000.0000.000
20A26ASN0-0.037-0.0397.960-3.163-3.1630.0000.0000.0000.000
21A27GLU-1-0.854-0.9132.276-103.289-99.5913.781-3.735-3.744-0.049
22A28TYR00.0140.0052.457-23.646-19.1895.068-2.948-6.576-0.026
23A29GLU-1-0.938-0.9593.741-21.151-20.6950.000-0.094-0.3610.000
24A30VAL0-0.037-0.0235.793-0.686-0.6860.0000.0000.0000.000
25A31PHE00.014-0.0028.6802.4592.4590.0000.0000.0000.000
26A32ALA00.0240.00910.9570.0450.0450.0000.0000.0000.000
27A33SER0-0.006-0.00914.1690.2890.2890.0000.0000.0000.000
28A34MET0-0.043-0.03115.9711.1431.1430.0000.0000.0000.000
29A35GLY00.0120.01418.6660.7620.7620.0000.0000.0000.000
30A36HIS00.0000.00318.967-0.535-0.5350.0000.0000.0000.000
31A37ILE00.0530.01616.5200.1980.1980.0000.0000.0000.000
32A38ILE0-0.022-0.00419.2980.3980.3980.0000.0000.0000.000
33A39ASP-1-0.853-0.92522.489-10.364-10.3640.0000.0000.0000.000
34A40LEU0-0.0070.01025.6840.0620.0620.0000.0000.0000.000
35A41PRO00.0060.01429.0410.0280.0280.0000.0000.0000.000
36A42LYS10.9750.98329.7859.4909.4900.0000.0000.0000.000
37A43SER0-0.053-0.03933.3670.2080.2080.0000.0000.0000.000
38A44LYS11.0041.03135.0368.2218.2210.0000.0000.0000.000
39A45PHE00.0510.00635.589-0.188-0.1880.0000.0000.0000.000
40A46GLY00.004-0.02033.337-0.147-0.1470.0000.0000.0000.000
41A47VAL00.0380.03432.621-0.287-0.2870.0000.0000.0000.000
42A48ASP-1-0.830-0.92034.574-7.564-7.5640.0000.0000.0000.000
43A49LEU0-0.083-0.06436.594-0.105-0.1050.0000.0000.0000.000
44A50GLU-1-0.859-0.91139.203-6.751-6.7510.0000.0000.0000.000
45A51LYS10.8630.93933.8698.3818.3810.0000.0000.0000.000
46A52ASP-1-0.802-0.89635.053-8.282-8.2820.0000.0000.0000.000
47A53PHE0-0.029-0.03234.255-0.280-0.2800.0000.0000.0000.000
48A54GLU-1-0.911-0.95230.091-9.865-9.8650.0000.0000.0000.000
49A55PRO0-0.054-0.00727.8710.1310.1310.0000.0000.0000.000
50A56GLU-1-0.922-0.95729.481-8.637-8.6370.0000.0000.0000.000
51A57PHE0-0.043-0.04824.816-0.060-0.0600.0000.0000.0000.000
52A58ALA00.000-0.00525.9060.0720.0720.0000.0000.0000.000
53A59VAL00.0050.00321.528-0.173-0.1730.0000.0000.0000.000
54A60ILE0-0.059-0.02023.6140.5000.5000.0000.0000.0000.000
55A61LYS10.9760.97224.8549.0869.0860.0000.0000.0000.000
56A62GLY00.0200.01925.7050.0980.0980.0000.0000.0000.000
57A63LYS10.8320.92520.27112.89712.8970.0000.0000.0000.000
58A64GLU-1-0.800-0.91420.258-11.635-11.6350.0000.0000.0000.000
59A65LYS10.9970.99619.70311.60511.6050.0000.0000.0000.000
60A66VAL0-0.0210.00215.758-0.663-0.6630.0000.0000.0000.000
61A67VAL00.0110.00015.292-0.991-0.9910.0000.0000.0000.000
62A68GLU-1-0.913-0.96115.504-14.591-14.5910.0000.0000.0000.000
63A69LYS10.9360.98710.95120.48720.4870.0000.0000.0000.000
64A70LEU00.003-0.01010.875-1.335-1.3350.0000.0000.0000.000
65A71LYS10.9500.97010.67713.10113.1010.0000.0000.0000.000
66A72ASP-1-0.876-0.92011.838-20.169-20.1690.0000.0000.0000.000
67A73LEU0-0.021-0.0176.998-0.528-0.5280.0000.0000.0000.000
68A74ALA0-0.018-0.0086.760-2.130-2.1300.0000.0000.0000.000
69A75LYS10.9120.9648.37616.85716.8570.0000.0000.0000.000
70A76LYS10.8320.9147.06121.81121.8110.0000.0000.0000.000
71A77GLY00.0140.0083.651-2.262-2.1000.004-0.041-0.1240.000
72A78GLU-1-0.943-0.9582.384-37.684-36.2080.747-0.774-1.450-0.002
73A79LEU0-0.022-0.0092.825-6.026-4.1400.518-1.216-1.188-0.011
74A80LEU00.001-0.0032.9212.4093.2700.098-0.157-0.8020.000
75A81ILE0-0.021-0.0105.5200.9110.9110.0000.0000.0000.000
76A82ALA00.0100.0079.0950.4250.4250.0000.0000.0000.000
77A83SER00.001-0.00710.7650.5130.5130.0000.0000.0000.000
78A84ASP-1-0.775-0.86614.314-15.419-15.4190.0000.0000.0000.000
79A85MET0-0.0110.01017.3100.0130.0130.0000.0000.0000.000
80A86ASP-1-0.796-0.88418.483-12.123-12.1230.0000.0000.0000.000
81A87ARG10.8570.88320.5059.8999.8990.0000.0000.0000.000
82A88GLU-1-0.919-0.96021.714-11.974-11.9740.0000.0000.0000.000
83A89GLY00.0490.02218.391-0.246-0.2460.0000.0000.0000.000
84A90GLU-1-0.800-0.88616.895-16.676-16.6760.0000.0000.0000.000
85A91ALA0-0.007-0.01017.791-0.272-0.2720.0000.0000.0000.000
86A92ILE0-0.0060.00615.478-0.113-0.1130.0000.0000.0000.000
87A93ALA00.0090.00213.620-0.467-0.4670.0000.0000.0000.000
88A94TRP00.0460.01514.559-0.239-0.2390.0000.0000.0000.000
89A95HIS0-0.035-0.02417.100-0.184-0.1840.0000.0000.0000.000
90A96ILE00.0160.00811.5550.1400.1400.0000.0000.0000.000
91A97ALA00.0420.03513.040-0.374-0.3740.0000.0000.0000.000
92A98ARG10.9160.96613.98312.45212.4520.0000.0000.0000.000
93A99VAL0-0.063-0.02115.3890.2760.2760.0000.0000.0000.000
94A100THR0-0.044-0.03711.226-0.015-0.0150.0000.0000.0000.000
95A101ASN0-0.040-0.00313.328-0.341-0.3410.0000.0000.0000.000
96A102THR0-0.001-0.0169.904-0.621-0.6210.0000.0000.0000.000
97A103LEU0-0.022-0.02712.719-0.607-0.6070.0000.0000.0000.000
98A104GLY00.0420.02914.9260.4010.4010.0000.0000.0000.000
99A105ARG10.9340.9797.81124.18324.1830.0000.0000.0000.000
100A106LYS10.9450.9729.55321.02821.0280.0000.0000.0000.000
101A107ASN00.0600.0367.476-1.565-1.5650.0000.0000.0000.000
102A108ARG10.8200.9148.48617.54717.5470.0000.0000.0000.000
103A109ILE0-0.014-0.0046.9110.3860.3860.0000.0000.0000.000
104A110VAL0-0.019-0.01410.4031.4221.4220.0000.0000.0000.000
105A111PHE00.0140.00211.723-0.494-0.4940.0000.0000.0000.000
106A112SER00.0410.00915.8770.5230.5230.0000.0000.0000.000
107A113GLU-1-0.836-0.92417.823-13.950-13.9500.0000.0000.0000.000
108A114ILE0-0.0120.01314.309-1.055-1.0550.0000.0000.0000.000
109A115THR00.019-0.00316.488-0.047-0.0470.0000.0000.0000.000
110A116PRO00.0790.02113.991-1.028-1.0280.0000.0000.0000.000
111A117ARG10.9640.99113.50714.18714.1870.0000.0000.0000.000
112A118VAL00.0180.01814.083-0.918-0.9180.0000.0000.0000.000
113A119ILE00.0110.00410.256-0.957-0.9570.0000.0000.0000.000
114A120ARG10.9150.9509.29321.83021.8300.0000.0000.0000.000
115A121GLU-1-0.912-0.9518.994-25.240-25.2400.0000.0000.0000.000
116A122ALA0-0.010-0.01110.116-0.862-0.8620.0000.0000.0000.000
117A123VAL0-0.049-0.0335.0590.0550.0550.0000.0000.0000.000
118A124LYS10.9310.9735.40927.74627.7460.0000.0000.0000.000
119A125ASN0-0.062-0.0087.1560.8600.8600.0000.0000.0000.000
120A126PRO0-0.0140.0066.5252.6202.6200.0000.0000.0000.000
121A127ARG10.9340.9519.58218.33818.3380.0000.0000.0000.000
122A128GLU-1-0.918-0.95411.996-16.505-16.5050.0000.0000.0000.000
123A129ILE0-0.050-0.03413.3340.4500.4500.0000.0000.0000.000
124A130ASP-1-0.824-0.91115.855-12.477-12.4770.0000.0000.0000.000
125A131MET00.006-0.03219.3750.2500.2500.0000.0000.0000.000
126A132LYS10.9731.00221.77411.22211.2220.0000.0000.0000.000
127A133LYS10.9220.98019.96713.77013.7700.0000.0000.0000.000
128A134VAL0-0.044-0.01919.7630.3140.3140.0000.0000.0000.000
129A135ARG10.8790.91422.60510.83910.8390.0000.0000.0000.000
130A136ALA00.0500.04626.1240.3770.3770.0000.0000.0000.000
131A137GLN0-0.019-0.01123.7210.4230.4230.0000.0000.0000.000
132A138LEU0-0.046-0.03724.2910.2930.2930.0000.0000.0000.000
133A139ALA00.0680.03627.4180.2720.2720.0000.0000.0000.000
134A140ARG10.8650.91929.3939.4179.4170.0000.0000.0000.000
135A141ARG10.8080.89826.40910.33910.3390.0000.0000.0000.000
136A142ILE00.0120.00130.5450.2310.2310.0000.0000.0000.000
137A143LEU00.0290.02533.0900.2500.2500.0000.0000.0000.000
138A144ASP-1-0.923-0.96733.459-8.305-8.3050.0000.0000.0000.000
139A145ARG10.7630.89231.9388.8618.8610.0000.0000.0000.000
140A146ILE00.0460.03035.8330.1780.1780.0000.0000.0000.000
141A147VAL00.0300.03138.8370.2030.2030.0000.0000.0000.000
142A148GLY0-0.015-0.01338.7010.1660.1660.0000.0000.0000.000
143A149TYR0-0.063-0.07436.1430.0630.0630.0000.0000.0000.000
144A150SER0-0.0150.01640.7780.1520.1520.0000.0000.0000.000
145A151LEU00.0420.01643.4610.1420.1420.0000.0000.0000.000
146A152SER0-0.051-0.02341.7660.1120.1120.0000.0000.0000.000
147A153PRO0-0.008-0.00243.6760.0870.0870.0000.0000.0000.000
148A154VAL00.0500.04246.6730.1100.1100.0000.0000.0000.000
149A155LEU0-0.002-0.01245.7600.1260.1260.0000.0000.0000.000
150A156TRP0-0.0260.00347.0210.0450.0450.0000.0000.0000.000
151A157ARG10.9200.95349.0125.5775.5770.0000.0000.0000.000
152A158ASN0-0.045-0.04152.1190.2180.2180.0000.0000.0000.000
153A159PHE00.0330.02551.0900.0970.0970.0000.0000.0000.000
154A160LYS10.8620.95850.2725.5785.5780.0000.0000.0000.000
155A161SER0-0.030-0.02146.958-0.068-0.0680.0000.0000.0000.000
156A162ASN00.0400.01840.5880.0980.0980.0000.0000.0000.000
157A163LEU00.0310.04442.026-0.016-0.0160.0000.0000.0000.000
158A164SER00.0420.02036.886-0.089-0.0890.0000.0000.0000.000
159A165ALA0-0.040-0.04635.5850.0840.0840.0000.0000.0000.000
160A166GLY00.0470.02136.553-0.017-0.0170.0000.0000.0000.000
161A167ARG10.9400.99834.7168.2468.2460.0000.0000.0000.000
162A168VAL00.0760.04035.7590.1180.1180.0000.0000.0000.000
163A169GLN0-0.008-0.00738.8830.1050.1050.0000.0000.0000.000
164A170SER0-0.001-0.01940.4870.1590.1590.0000.0000.0000.000
165A171ALA00.0640.04741.9060.1490.1490.0000.0000.0000.000
166A172THR00.003-0.02440.6920.0730.0730.0000.0000.0000.000
167A173LEU0-0.051-0.02143.2840.0880.0880.0000.0000.0000.000
168A174LYS10.9620.98345.9696.1066.1060.0000.0000.0000.000
169A175LEU00.0000.01643.9340.1120.1120.0000.0000.0000.000
170A176VAL0-0.049-0.03046.2340.1110.1110.0000.0000.0000.000
171A177CYS0-0.021-0.01848.9820.1350.1350.0000.0000.0000.000
172A178ASP-1-0.811-0.89051.114-5.808-5.8080.0000.0000.0000.000
173A179ARG10.8320.92449.8376.1446.1440.0000.0000.0000.000
174A180GLU-1-0.797-0.88052.978-5.505-5.5050.0000.0000.0000.000
175A181ARG10.8840.92753.1945.7045.7040.0000.0000.0000.000
176A182GLU-1-0.962-0.98654.367-5.600-5.6000.0000.0000.0000.000
177A183ILE0-0.078-0.04354.8620.0810.0810.0000.0000.0000.000
178A184LEU0-0.061-0.02658.8080.0770.0770.0000.0000.0000.000
179A185ARG10.9500.96957.8645.2715.2710.0000.0000.0000.000
180A186PHE0-0.053-0.01061.3330.0520.0520.0000.0000.0000.000
181A187VAL00.0290.01963.3260.0380.0380.0000.0000.0000.000
182A188PRO0-0.062-0.02465.320-0.011-0.0110.0000.0000.0000.000
183A189LYS10.9951.00367.2044.4644.4640.0000.0000.0000.000
184A190LYS10.9990.99369.1164.1684.1680.0000.0000.0000.000
185A191TYR0-0.097-0.06065.785-0.013-0.0130.0000.0000.0000.000
186A192HIS00.0850.04271.747-0.026-0.0260.0000.0000.0000.000
187A193ARG10.8160.90264.7704.8314.8310.0000.0000.0000.000
188A194ILE00.0200.00370.1950.0340.0340.0000.0000.0000.000
189A195THR0-0.052-0.02467.902-0.054-0.0540.0000.0000.0000.000
190A196VAL00.0130.01871.2330.0610.0610.0000.0000.0000.000
191A197ASN0-0.035-0.01569.952-0.150-0.1500.0000.0000.0000.000
192A198PHE00.0590.02270.6610.0750.0750.0000.0000.0000.000
193A199ASP-1-0.862-0.93271.115-4.564-4.5640.0000.0000.0000.000
194A200GLY0-0.0290.00067.886-0.055-0.0550.0000.0000.0000.000
195A201LEU0-0.064-0.01765.927-0.104-0.1040.0000.0000.0000.000
196A202THR0-0.011-0.03666.4090.0370.0370.0000.0000.0000.000
197A203ALA0-0.046-0.02067.361-0.053-0.0530.0000.0000.0000.000
198A204GLU-1-0.834-0.91265.904-4.743-4.7430.0000.0000.0000.000
199A205ILE0-0.0230.00169.2280.0090.0090.0000.0000.0000.000
200A206ASP-1-0.889-0.95270.553-4.543-4.5430.0000.0000.0000.000
201A207VAL0-0.031-0.01470.3610.0820.0820.0000.0000.0000.000
202A208LYS10.9560.97070.1984.1864.1860.0000.0000.0000.000
203A209GLU-1-0.947-0.96668.931-4.486-4.4860.0000.0000.0000.000
204A210LYS10.8990.94564.2234.9104.9100.0000.0000.0000.000
205A211LYS10.9991.00969.8034.1374.1370.0000.0000.0000.000
206A212PHE0-0.0160.01173.411-0.032-0.0320.0000.0000.0000.000
207A213PHE0-0.017-0.02174.1510.0460.0460.0000.0000.0000.000
208A214ASP-1-0.813-0.90078.607-3.831-3.8310.0000.0000.0000.000
209A215ALA00.023-0.01482.153-0.014-0.0140.0000.0000.0000.000
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