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: N2N6Q

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 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 580
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12283927.540206
FMO2-HF: Nuclear repulsion 12050493.689433
FMO2-HF: Total energy -233433.850773
FMO2-MP2: Total energy -234119.475556


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.
-13.415-8.32232.494-17.065-20.522-0.174
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 : 0.854 / q_NPA : 0.926
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].
3A9ILE00.0190.0123.8500.6562.982-0.012-1.125-1.1880.005
4A10VAL0-0.022-0.0036.2911.8681.8680.0000.0000.0000.000
5A11VAL0-0.029-0.0029.8090.3280.3280.0000.0000.0000.000
6A12GLU-1-0.708-0.85213.053-16.789-16.7890.0000.0000.0000.000
7A13SER0-0.039-0.05416.4880.7130.7130.0000.0000.0000.000
8A14PRO00.0550.00316.180-1.074-1.0740.0000.0000.0000.000
9A15ALA00.0070.02317.073-0.622-0.6220.0000.0000.0000.000
10A16LYS10.8090.88114.81317.08417.0840.0000.0000.0000.000
11A17ALA0-0.0010.00412.502-1.290-1.2900.0000.0000.0000.000
12A18LYS10.8240.89312.86413.54013.5400.0000.0000.0000.000
13A19THR00.003-0.00115.020-0.734-0.7340.0000.0000.0000.000
14A20ILE00.0210.0019.207-0.794-0.7940.0000.0000.0000.000
15A21LYS10.8110.8897.58032.26532.2650.0000.0000.0000.000
16A22SER0-0.016-0.02611.210-0.791-0.7910.0000.0000.0000.000
17A23ILE0-0.055-0.00310.5270.1580.1580.0000.0000.0000.000
18A24LEU0-0.016-0.0046.232-0.117-0.1170.0000.0000.0000.000
19A25GLY00.0430.0456.904-4.563-4.5630.0000.0000.0000.000
20A26ASN0-0.006-0.0207.317-0.748-0.7480.0000.0000.0000.000
21A27GLU-1-0.812-0.8751.759-112.736-119.59519.386-7.188-5.339-0.079
22A28TYR00.032-0.0011.925-43.357-38.70511.857-6.473-10.035-0.085
23A29GLU-1-0.821-0.8903.650-18.188-17.6800.002-0.087-0.4240.000
24A30VAL0-0.023-0.0195.765-1.581-1.5810.0000.0000.0000.000
25A31PHE00.007-0.0018.6022.5552.5550.0000.0000.0000.000
26A32ALA00.0360.00811.235-0.038-0.0380.0000.0000.0000.000
27A33SER0-0.010-0.02214.5040.3320.3320.0000.0000.0000.000
28A34MET0-0.020-0.00116.4821.0571.0570.0000.0000.0000.000
29A35GLY00.0220.02419.2690.8730.8730.0000.0000.0000.000
30A36HIS0-0.025-0.01719.211-0.732-0.7320.0000.0000.0000.000
31A37ILE00.0410.00716.2750.1690.1690.0000.0000.0000.000
32A38ILE0-0.014-0.00319.5910.3500.3500.0000.0000.0000.000
33A39ASP-1-0.789-0.85822.666-10.337-10.3370.0000.0000.0000.000
34A40LEU00.0390.02925.9150.0850.0850.0000.0000.0000.000
35A41PRO0-0.020-0.00629.2670.0270.0270.0000.0000.0000.000
36A42LYS10.8780.92429.1189.8729.8720.0000.0000.0000.000
37A43SER00.007-0.00133.4120.0730.0730.0000.0000.0000.000
38A44LYS10.8860.92935.3318.3208.3200.0000.0000.0000.000
39A45PHE00.0440.00835.573-0.220-0.2200.0000.0000.0000.000
40A46GLY00.0070.01033.294-0.119-0.1190.0000.0000.0000.000
41A47VAL00.0010.00832.378-0.299-0.2990.0000.0000.0000.000
42A48ASP-1-0.834-0.90134.411-7.574-7.5740.0000.0000.0000.000
43A49LEU0-0.006-0.02136.382-0.119-0.1190.0000.0000.0000.000
44A50GLU-1-0.866-0.91439.066-6.783-6.7830.0000.0000.0000.000
45A51LYS10.7980.89334.7567.9667.9660.0000.0000.0000.000
46A52ASP-1-0.753-0.85335.076-8.267-8.2670.0000.0000.0000.000
47A53PHE00.0200.01234.654-0.249-0.2490.0000.0000.0000.000
48A54GLU-1-0.843-0.90529.289-9.900-9.9000.0000.0000.0000.000
49A55PRO0-0.048-0.01527.8200.1650.1650.0000.0000.0000.000
50A56GLU-1-0.832-0.89829.045-8.628-8.6280.0000.0000.0000.000
51A57PHE0-0.008-0.03024.967-0.132-0.1320.0000.0000.0000.000
52A58ALA0-0.0010.00226.1880.0550.0550.0000.0000.0000.000
53A59VAL00.0140.00421.812-0.193-0.1930.0000.0000.0000.000
54A60ILE0-0.052-0.01423.4420.4870.4870.0000.0000.0000.000
55A61LYS10.8920.93724.7809.7509.7500.0000.0000.0000.000
56A62GLY00.0310.01825.3580.1490.1490.0000.0000.0000.000
57A63LYS10.7800.88720.55212.91612.9160.0000.0000.0000.000
58A64GLU-1-0.736-0.87220.102-11.669-11.6690.0000.0000.0000.000
59A65LYS10.9830.98419.63011.58411.5840.0000.0000.0000.000
60A66VAL0-0.0160.01016.118-0.698-0.6980.0000.0000.0000.000
61A67VAL00.0100.00215.312-0.991-0.9910.0000.0000.0000.000
62A68GLU-1-0.782-0.88215.383-14.671-14.6710.0000.0000.0000.000
63A69LYS10.8380.9289.93923.16923.1690.0000.0000.0000.000
64A70LEU0-0.004-0.01010.777-1.399-1.3990.0000.0000.0000.000
65A71LYS10.8570.89710.62213.01013.0100.0000.0000.0000.000
66A72ASP-1-0.841-0.90711.886-19.847-19.8470.0000.0000.0000.000
67A73LEU0-0.022-0.0146.759-0.288-0.2880.0000.0000.0000.000
68A74ALA00.0080.0066.837-1.811-1.8110.0000.0000.0000.000
69A75LYS10.8200.9318.63817.92417.9240.0000.0000.0000.000
70A76LYS10.8270.8987.23221.61621.6160.0000.0000.0000.000
71A77GLY00.0200.0073.483-2.637-2.4350.008-0.060-0.1500.000
72A78GLU-1-0.795-0.8502.555-28.884-27.6840.741-0.605-1.336-0.002
73A79LEU0-0.0150.0003.033-7.464-5.2460.371-1.363-1.226-0.013
74A80LEU00.0290.0163.1012.7343.5800.141-0.164-0.8240.000
75A81ILE0-0.018-0.0115.6980.7330.7330.0000.0000.0000.000
76A82ALA00.0200.0099.3200.3830.3830.0000.0000.0000.000
77A83SER00.005-0.01711.2740.5140.5140.0000.0000.0000.000
78A84ASP-1-0.761-0.83114.724-15.417-15.4170.0000.0000.0000.000
79A85MET00.0030.04717.747-0.081-0.0810.0000.0000.0000.000
80A86ASP-1-0.787-0.88818.949-11.870-11.8700.0000.0000.0000.000
81A87ARG10.8420.88520.8769.9289.9280.0000.0000.0000.000
82A88GLU-1-0.823-0.87822.257-11.849-11.8490.0000.0000.0000.000
83A89GLY00.0310.01518.610-0.245-0.2450.0000.0000.0000.000
84A90GLU-1-0.759-0.85116.902-16.672-16.6720.0000.0000.0000.000
85A91ALA0-0.0010.00118.028-0.208-0.2080.0000.0000.0000.000
86A92ILE0-0.005-0.00415.854-0.056-0.0560.0000.0000.0000.000
87A93ALA00.0150.00813.813-0.457-0.4570.0000.0000.0000.000
88A94TRP00.0610.02414.762-0.188-0.1880.0000.0000.0000.000
89A95HIS0-0.059-0.03417.409-0.142-0.1420.0000.0000.0000.000
90A96ILE00.0250.01111.5350.1520.1520.0000.0000.0000.000
91A97ALA00.0440.03613.085-0.282-0.2820.0000.0000.0000.000
92A98ARG10.9110.96613.99912.31112.3110.0000.0000.0000.000
93A99VAL0-0.056-0.02115.8610.2180.2180.0000.0000.0000.000
94A100THR0-0.045-0.04211.630-0.139-0.1390.0000.0000.0000.000
95A101ASN0-0.042-0.01013.4810.0990.0990.0000.0000.0000.000
96A102THR00.002-0.0139.853-0.414-0.4140.0000.0000.0000.000
97A103LEU0-0.036-0.02412.646-0.547-0.5470.0000.0000.0000.000
98A104GLY00.0600.04114.7220.6090.6090.0000.0000.0000.000
99A105ARG10.7920.8647.11924.59924.5990.0000.0000.0000.000
100A106LYS10.9360.97010.03719.19819.1980.0000.0000.0000.000
101A107ASN00.0130.0017.211-1.041-1.0410.0000.0000.0000.000
102A108ARG10.7720.8488.28616.56916.5690.0000.0000.0000.000
103A109ILE00.011-0.0016.6940.2830.2830.0000.0000.0000.000
104A110VAL0-0.029-0.01910.6381.6871.6870.0000.0000.0000.000
105A111PHE00.0070.00712.202-0.592-0.5920.0000.0000.0000.000
106A112SER00.032-0.01616.2570.6290.6290.0000.0000.0000.000
107A113GLU-1-0.721-0.83618.229-14.348-14.3480.0000.0000.0000.000
108A114ILE0-0.0260.00414.463-1.033-1.0330.0000.0000.0000.000
109A115THR00.030-0.00716.728-0.264-0.2640.0000.0000.0000.000
110A116PRO00.039-0.00513.587-1.167-1.1670.0000.0000.0000.000
111A117ARG10.8880.95213.15414.39314.3930.0000.0000.0000.000
112A118VAL00.0020.01014.392-0.525-0.5250.0000.0000.0000.000
113A119ILE00.0100.01010.234-1.091-1.0910.0000.0000.0000.000
114A120ARG10.9150.9408.71024.26224.2620.0000.0000.0000.000
115A121GLU-1-0.795-0.8659.013-27.449-27.4490.0000.0000.0000.000
116A122ALA0-0.001-0.00410.340-0.348-0.3480.0000.0000.0000.000
117A123VAL0-0.042-0.0265.0480.6740.6740.0000.0000.0000.000
118A124LYS10.8280.9025.75126.73826.7380.0000.0000.0000.000
119A125ASN0-0.099-0.0407.7602.5922.5920.0000.0000.0000.000
120A126PRO0-0.0170.0096.8631.9891.9890.0000.0000.0000.000
121A127ARG10.9130.9449.90018.92818.9280.0000.0000.0000.000
122A128GLU-1-0.889-0.94112.168-15.987-15.9870.0000.0000.0000.000
123A129ILE0-0.030-0.02613.3210.2700.2700.0000.0000.0000.000
124A130ASP-1-0.813-0.90215.969-12.185-12.1850.0000.0000.0000.000
125A131MET00.026-0.00819.4990.2570.2570.0000.0000.0000.000
126A132LYS10.8780.98521.79210.39110.3910.0000.0000.0000.000
127A133LYS10.8310.91520.07313.48913.4890.0000.0000.0000.000
128A134VAL0-0.027-0.01719.8150.2400.2400.0000.0000.0000.000
129A135ARG10.8840.92522.79710.57710.5770.0000.0000.0000.000
130A136ALA00.0290.02926.3060.3880.3880.0000.0000.0000.000
131A137GLN00.0090.00524.0670.5070.5070.0000.0000.0000.000
132A138LEU0-0.063-0.03824.3980.2730.2730.0000.0000.0000.000
133A139ALA00.0570.02927.5790.2810.2810.0000.0000.0000.000
134A140ARG10.8460.91029.5279.4269.4260.0000.0000.0000.000
135A141ARG10.8030.87526.81210.34610.3460.0000.0000.0000.000
136A142ILE00.0200.01430.6550.2010.2010.0000.0000.0000.000
137A143LEU00.0310.02533.1610.2490.2490.0000.0000.0000.000
138A144ASP-1-0.845-0.91433.774-8.262-8.2620.0000.0000.0000.000
139A145ARG10.7460.88033.2578.6868.6860.0000.0000.0000.000
140A146ILE00.0440.02035.8200.1870.1870.0000.0000.0000.000
141A147VAL00.0360.03338.8170.1960.1960.0000.0000.0000.000
142A148GLY0-0.0130.00338.7220.1600.1600.0000.0000.0000.000
143A149TYR0-0.047-0.04436.3630.1150.1150.0000.0000.0000.000
144A150SER0-0.0210.00140.7650.1590.1590.0000.0000.0000.000
145A151LEU00.0460.02143.5730.1370.1370.0000.0000.0000.000
146A152SER0-0.069-0.04641.8400.1060.1060.0000.0000.0000.000
147A153PRO0-0.011-0.00443.7330.1000.1000.0000.0000.0000.000
148A154VAL00.0600.03946.7700.1180.1180.0000.0000.0000.000
149A155LEU00.0300.01645.9370.1250.1250.0000.0000.0000.000
150A156TRP0-0.021-0.00147.2610.0830.0830.0000.0000.0000.000
151A157ARG10.9200.96349.2775.6305.6300.0000.0000.0000.000
152A158ASN0-0.047-0.03252.2750.2470.2470.0000.0000.0000.000
153A159PHE00.0270.01751.4890.1030.1030.0000.0000.0000.000
154A160LYS10.8480.95150.3915.6275.6270.0000.0000.0000.000
155A161SER00.003-0.00847.185-0.073-0.0730.0000.0000.0000.000
156A162ASN0-0.007-0.00740.7590.0600.0600.0000.0000.0000.000
157A163LEU00.0500.03442.399-0.012-0.0120.0000.0000.0000.000
158A164SER00.0240.01137.326-0.092-0.0920.0000.0000.0000.000
159A165ALA0-0.004-0.01935.7120.0610.0610.0000.0000.0000.000
160A166GLY00.0450.03436.8470.0380.0380.0000.0000.0000.000
161A167ARG10.8460.91034.7808.3958.3950.0000.0000.0000.000
162A168VAL00.0790.03735.9150.1160.1160.0000.0000.0000.000
163A169GLN0-0.0120.00039.2150.0330.0330.0000.0000.0000.000
164A170SER00.007-0.01341.0170.1550.1550.0000.0000.0000.000
165A171ALA00.0740.04442.1950.1390.1390.0000.0000.0000.000
166A172THR0-0.011-0.04540.9940.0510.0510.0000.0000.0000.000
167A173LEU0-0.065-0.03243.5770.0800.0800.0000.0000.0000.000
168A174LYS10.9010.94546.3586.1126.1120.0000.0000.0000.000
169A175LEU00.0160.01544.3130.1200.1200.0000.0000.0000.000
170A176VAL0-0.037-0.02346.7470.1020.1020.0000.0000.0000.000
171A177CYS0-0.030-0.01949.4990.1280.1280.0000.0000.0000.000
172A178ASP-1-0.748-0.87751.698-5.786-5.7860.0000.0000.0000.000
173A179ARG10.7580.88050.6966.1356.1350.0000.0000.0000.000
174A180GLU-1-0.780-0.85953.584-5.553-5.5530.0000.0000.0000.000
175A181ARG10.7620.85653.7705.7545.7540.0000.0000.0000.000
176A182GLU-1-0.821-0.87254.566-5.662-5.6620.0000.0000.0000.000
177A183ILE0-0.053-0.03955.4030.0870.0870.0000.0000.0000.000
178A184LEU0-0.071-0.02959.2960.0790.0790.0000.0000.0000.000
179A185ARG10.9100.95458.7495.2945.2940.0000.0000.0000.000
180A186PHE0-0.030-0.00161.7800.0360.0360.0000.0000.0000.000
181A187VAL00.0310.01063.8050.0470.0470.0000.0000.0000.000
182A188PRO0-0.076-0.03565.937-0.008-0.0080.0000.0000.0000.000
183A189LYS10.8410.92067.7704.5484.5480.0000.0000.0000.000
184A190LYS10.8530.90069.6664.3244.3240.0000.0000.0000.000
185A191TYR0-0.060-0.05666.452-0.016-0.0160.0000.0000.0000.000
186A192HIS00.0590.03972.363-0.016-0.0160.0000.0000.0000.000
187A193ARG10.7950.90065.1534.8784.8780.0000.0000.0000.000
188A194ILE00.0170.00070.6780.0480.0480.0000.0000.0000.000
189A195THR0-0.037-0.00968.555-0.041-0.0410.0000.0000.0000.000
190A196VAL00.0150.01271.6590.0720.0720.0000.0000.0000.000
191A197ASN0-0.021-0.00869.998-0.148-0.1480.0000.0000.0000.000
192A198PHE00.0460.01770.6390.0810.0810.0000.0000.0000.000
193A199ASP-1-0.872-0.93971.303-4.622-4.6220.0000.0000.0000.000
194A200GLY0-0.0090.00968.207-0.056-0.0560.0000.0000.0000.000
195A201LEU0-0.058-0.01465.962-0.112-0.1120.0000.0000.0000.000
196A202THR0-0.014-0.03266.4880.0450.0450.0000.0000.0000.000
197A203ALA0-0.041-0.01567.529-0.058-0.0580.0000.0000.0000.000
198A204GLU-1-0.824-0.89866.244-4.793-4.7930.0000.0000.0000.000
199A205ILE00.0050.00069.4740.0190.0190.0000.0000.0000.000
200A206ASP-1-0.849-0.90171.015-4.584-4.5840.0000.0000.0000.000
201A207VAL0-0.022-0.00970.6230.0790.0790.0000.0000.0000.000
202A208LYS10.9570.96770.4214.2204.2200.0000.0000.0000.000
203A209GLU-1-0.813-0.89169.363-4.551-4.5510.0000.0000.0000.000
204A210LYS10.8940.95464.8694.9154.9150.0000.0000.0000.000
205A211LYS10.9050.96070.4884.0834.0830.0000.0000.0000.000
206A212PHE00.0090.01574.080-0.037-0.0370.0000.0000.0000.000
207A213PHE0-0.024-0.03774.5250.0520.0520.0000.0000.0000.000
208A214ASP-1-0.768-0.85078.886-3.909-3.9090.0000.0000.0000.000
209A215ALA00.0490.00182.566-0.015-0.0150.0000.0000.0000.000
210A216GLU-1-0.814-0.87084.366-3.642-3.6420.0000.0000.0000.000
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