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: GYQK1

Calculation Name: 2GDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GDQ

Chain ID: A

ChEMBL ID:

UniProt ID: O06741

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 373
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6513356.786173
FMO2-HF: Nuclear repulsion 6364467.421935
FMO2-HF: Total energy -148889.364238
FMO2-MP2: Total energy -149322.147031


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:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-11.078-3.6493.642-5.071-5.998-0.003
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.011
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].
3A5LYS10.8520.9373.527-6.040-2.110-0.037-2.136-1.756-0.001
4A6ILE00.0120.0045.599-0.896-0.8960.0000.0000.0000.000
5A7VAL0-0.014-0.0036.9840.1110.1110.0000.0000.0000.000
6A8ARG10.8450.8959.6790.3130.3130.0000.0000.0000.000
7A9ILE00.0100.00812.747-0.018-0.0180.0000.0000.0000.000
8A10GLU-1-0.826-0.87115.467-0.221-0.2210.0000.0000.0000.000
9A11THR0-0.010-0.01618.4770.0080.0080.0000.0000.0000.000
10A12PHE00.008-0.00919.232-0.005-0.0050.0000.0000.0000.000
11A13PRO00.0000.01324.2230.0020.0020.0000.0000.0000.000
12A14LEU0-0.0090.00726.022-0.005-0.0050.0000.0000.0000.000
13A15PHE0-0.006-0.02429.5080.0070.0070.0000.0000.0000.000
14A16HIS0-0.003-0.00233.237-0.006-0.0060.0000.0000.0000.000
15A17ARG10.9640.98535.8980.0260.0260.0000.0000.0000.000
16A18LEU0-0.055-0.01838.735-0.002-0.0020.0000.0000.0000.000
17A19GLU-1-0.906-0.95041.218-0.034-0.0340.0000.0000.0000.000
18A20LYS10.7740.87643.9820.0320.0320.0000.0000.0000.000
19A21PRO0-0.027-0.01544.0230.0000.0000.0000.0000.0000.000
20A22TYR0-0.010-0.00738.4840.0010.0010.0000.0000.0000.000
21A23GLY0-0.022-0.01943.2690.0000.0000.0000.0000.0000.000
22A24ASP-1-0.762-0.87641.634-0.007-0.0070.0000.0000.0000.000
23A25ALA00.0450.01745.0960.0000.0000.0000.0000.0000.000
24A26ASN0-0.056-0.02242.8210.0030.0030.0000.0000.0000.000
25A27GLY00.0100.01945.4120.0010.0010.0000.0000.0000.000
26A28PHE0-0.090-0.05344.889-0.001-0.0010.0000.0000.0000.000
27A29LYS10.8620.92138.6890.0110.0110.0000.0000.0000.000
28A30ARG10.8290.88541.4750.0100.0100.0000.0000.0000.000
29A31TYR0-0.037-0.04336.212-0.002-0.0020.0000.0000.0000.000
30A32ARG10.7750.86533.7530.0310.0310.0000.0000.0000.000
31A33THR0-0.006-0.00731.409-0.002-0.0020.0000.0000.0000.000
32A34CYS0-0.0050.01426.391-0.001-0.0010.0000.0000.0000.000
33A35TYR0-0.001-0.02222.7860.0010.0010.0000.0000.0000.000
34A36LEU00.0430.02521.0490.0050.0050.0000.0000.0000.000
35A37ILE0-0.059-0.03417.2000.0070.0070.0000.0000.0000.000
36A38ARG10.8580.92413.6310.3230.3230.0000.0000.0000.000
37A39ILE0-0.012-0.01010.7340.0210.0210.0000.0000.0000.000
38A40ILE00.0050.0009.535-0.065-0.0650.0000.0000.0000.000
39A41THR0-0.038-0.0365.210-0.195-0.057-0.001-0.024-0.1120.000
40A42GLU-1-0.840-0.9272.942-0.1800.8960.061-0.404-0.733-0.003
41A43SER0-0.057-0.0272.050-0.9680.0153.539-2.250-2.2720.001
42A44GLY00.0010.0094.0280.1110.3640.003-0.067-0.1890.000
43A45ILE0-0.0170.0113.281-0.3020.2640.051-0.106-0.5110.000
44A46ASP-1-0.772-0.8786.838-0.430-0.4300.0000.0000.0000.000
45A47GLY0-0.0220.00110.005-0.008-0.0080.0000.0000.0000.000
46A48TRP00.0340.00112.1870.0540.0540.0000.0000.0000.000
47A49GLY0-0.011-0.00415.9110.0150.0150.0000.0000.0000.000
48A50GLU-1-0.740-0.85018.373-0.066-0.0660.0000.0000.0000.000
49A51CYS0-0.065-0.02222.1750.0150.0150.0000.0000.0000.000
50A52VAL00.0730.02224.918-0.008-0.0080.0000.0000.0000.000
51A53ASP-1-0.837-0.91328.6550.0230.0230.0000.0000.0000.000
52A54TRP00.0380.01530.993-0.004-0.0040.0000.0000.0000.000
53A55LEU00.016-0.00529.3450.0040.0040.0000.0000.0000.000
54A56PRO0-0.0040.01030.8120.0020.0020.0000.0000.0000.000
55A57ALA0-0.0030.00131.6410.0030.0030.0000.0000.0000.000
56A58LEU0-0.019-0.00726.0660.0080.0080.0000.0000.0000.000
57A59HIS00.0810.05125.2020.0060.0060.0000.0000.0000.000
58A60VAL0-0.0140.00526.1800.0030.0030.0000.0000.0000.000
59A61GLY00.0060.00926.6060.0080.0080.0000.0000.0000.000
60A62PHE00.0640.01519.9030.0160.0160.0000.0000.0000.000
61A63THR0-0.023-0.02021.9520.0130.0130.0000.0000.0000.000
62A64LYS10.9120.95622.908-0.022-0.0220.0000.0000.0000.000
63A65ARG10.9280.97623.469-0.073-0.0730.0000.0000.0000.000
64A66ILE0-0.023-0.00719.3030.0200.0200.0000.0000.0000.000
65A67ILE00.0170.00516.7310.0280.0280.0000.0000.0000.000
66A68PRO00.0030.00016.8180.0250.0250.0000.0000.0000.000
67A69PHE0-0.0080.00617.3410.0350.0350.0000.0000.0000.000
68A70LEU00.0340.00214.0120.0660.0660.0000.0000.0000.000
69A71LEU00.0010.02112.3260.0720.0720.0000.0000.0000.000
70A72GLY0-0.007-0.0129.9790.0120.0120.0000.0000.0000.000
71A73LYS10.8140.91810.112-0.207-0.2070.0000.0000.0000.000
72A74GLN00.0360.0084.956-0.377-0.3770.0000.0000.0000.000
73A75ALA00.0610.0196.784-0.209-0.2090.0000.0000.0000.000
74A76GLY00.0250.0166.964-0.197-0.1970.0000.0000.0000.000
75A77SER0-0.036-0.0068.000-0.080-0.0800.0000.0000.0000.000
76A78ARG10.8580.89211.447-0.206-0.2060.0000.0000.0000.000
77A79LEU00.0510.02113.195-0.029-0.0290.0000.0000.0000.000
78A80SER00.0170.00315.211-0.032-0.0320.0000.0000.0000.000
79A81LEU0-0.021-0.00512.043-0.045-0.0450.0000.0000.0000.000
80A82VAL00.0230.02116.211-0.036-0.0360.0000.0000.0000.000
81A83ARG11.0431.02718.603-0.192-0.1920.0000.0000.0000.000
82A84THR0-0.096-0.05619.185-0.017-0.0170.0000.0000.0000.000
83A85ILE00.0200.00617.775-0.019-0.0190.0000.0000.0000.000
84A86GLN0-0.039-0.02921.706-0.007-0.0070.0000.0000.0000.000
85A87LYS10.8390.93723.875-0.176-0.1760.0000.0000.0000.000
86A88TRP0-0.057-0.02120.912-0.011-0.0110.0000.0000.0000.000
87A89HIS00.0550.00425.264-0.007-0.0070.0000.0000.0000.000
88A90GLN00.0670.03424.6880.0040.0040.0000.0000.0000.000
89A91ARG10.8590.93324.669-0.017-0.0170.0000.0000.0000.000
90A92ALA00.008-0.00122.555-0.006-0.0060.0000.0000.0000.000
91A93ALA0-0.003-0.00320.442-0.001-0.0010.0000.0000.0000.000
92A94SER00.036-0.00119.7360.0030.0030.0000.0000.0000.000
93A95ALA00.0250.03319.755-0.007-0.0070.0000.0000.0000.000
94A96VAL00.012-0.00815.381-0.012-0.0120.0000.0000.0000.000
95A97SER0-0.038-0.03015.201-0.001-0.0010.0000.0000.0000.000
96A98MET0-0.0070.02815.195-0.009-0.0090.0000.0000.0000.000
97A99ALA00.0290.03113.568-0.025-0.0250.0000.0000.0000.000
98A100LEU0-0.024-0.03510.527-0.039-0.0390.0000.0000.0000.000
99A101THR0-0.049-0.02810.3680.0150.0150.0000.0000.0000.000
100A102GLU-1-0.795-0.89311.480-0.320-0.3200.0000.0000.0000.000
101A103ILE0-0.016-0.0095.993-0.065-0.0650.0000.0000.0000.000
102A104ALA0-0.018-0.0086.863-0.153-0.1530.0000.0000.0000.000
103A105ALA00.0090.0027.555-0.098-0.0980.0000.0000.0000.000
104A106LYS10.8460.9147.7180.4290.4290.0000.0000.0000.000
105A107ALA0-0.072-0.0313.198-0.508-0.1660.027-0.074-0.2950.000
106A108ALA0-0.046-0.0194.560-0.402-0.261-0.001-0.010-0.1300.000
107A109ASP-1-0.828-0.8877.044-0.499-0.4990.0000.0000.0000.000
108A110CYS0-0.028-0.0159.0680.1100.1100.0000.0000.0000.000
109A111SER0-0.005-0.02711.991-0.021-0.0210.0000.0000.0000.000
110A112VAL00.0310.00214.1890.0160.0160.0000.0000.0000.000
111A113CYS0-0.048-0.01715.3370.0250.0250.0000.0000.0000.000
112A114GLU-1-0.837-0.88715.148-0.176-0.1760.0000.0000.0000.000
113A115LEU0-0.010-0.00110.5500.0260.0260.0000.0000.0000.000
114A116TRP0-0.097-0.07014.0160.0300.0300.0000.0000.0000.000
115A117GLY0-0.0080.00317.1440.0180.0180.0000.0000.0000.000
116A118GLY0-0.0230.00118.755-0.002-0.0020.0000.0000.0000.000
117A119ARG10.8440.90320.2730.1180.1180.0000.0000.0000.000
118A120TYR0-0.026-0.01923.1650.0020.0020.0000.0000.0000.000
119A121ARG10.8090.90426.4520.0310.0310.0000.0000.0000.000
120A122GLU-1-0.734-0.85625.348-0.095-0.0950.0000.0000.0000.000
121A123GLU-1-0.883-0.93327.503-0.065-0.0650.0000.0000.0000.000
122A124ILE0-0.050-0.02628.0740.0060.0060.0000.0000.0000.000
123A125PRO00.0610.03331.100-0.003-0.0030.0000.0000.0000.000
124A126VAL0-0.031-0.01932.1770.0010.0010.0000.0000.0000.000
125A127TYR00.0310.02435.1370.0010.0010.0000.0000.0000.000
126A128ALA0-0.0070.00537.183-0.001-0.0010.0000.0000.0000.000
127A129SER0-0.046-0.04537.4610.0040.0040.0000.0000.0000.000
128A130PHE00.000-0.01839.300-0.003-0.0030.0000.0000.0000.000
129A131GLN00.0210.00539.2100.0040.0040.0000.0000.0000.000
130A132SER00.0430.00742.9510.0000.0000.0000.0000.0000.000
131A133TYR0-0.0350.01146.5690.0000.0000.0000.0000.0000.000
132A134SER00.038-0.01047.190-0.001-0.0010.0000.0000.0000.000
133A135ASP-1-0.801-0.88949.400-0.010-0.0100.0000.0000.0000.000
134A136SER0-0.052-0.04351.670-0.001-0.0010.0000.0000.0000.000
135A137PRO00.0720.02954.6710.0000.0000.0000.0000.0000.000
136A138GLN0-0.030-0.01056.3910.0010.0010.0000.0000.0000.000
137A139TRP0-0.019-0.01350.933-0.002-0.0020.0000.0000.0000.000
138A140ILE00.0620.03552.240-0.001-0.0010.0000.0000.0000.000
139A141SER00.0040.00353.430-0.001-0.0010.0000.0000.0000.000
140A142ARG10.9220.97150.5680.0170.0170.0000.0000.0000.000
141A143SER0-0.007-0.00348.768-0.002-0.0020.0000.0000.0000.000
142A144VAL00.0560.01849.118-0.001-0.0010.0000.0000.0000.000
143A145SER0-0.026-0.01750.653-0.001-0.0010.0000.0000.0000.000
144A146ASN0-0.005-0.01743.620-0.003-0.0030.0000.0000.0000.000
145A147VAL00.0480.01245.904-0.002-0.0020.0000.0000.0000.000
146A148GLU-1-0.831-0.90246.561-0.025-0.0250.0000.0000.0000.000
147A149ALA0-0.074-0.03245.761-0.002-0.0020.0000.0000.0000.000
148A150GLN00.0350.01741.095-0.005-0.0050.0000.0000.0000.000
149A151LEU00.0340.02043.211-0.002-0.0020.0000.0000.0000.000
150A152LYS10.8350.91545.5020.0270.0270.0000.0000.0000.000
151A153LYS10.8410.92639.2160.0430.0430.0000.0000.0000.000
152A154GLY0-0.016-0.01941.049-0.003-0.0030.0000.0000.0000.000
153A155PHE0-0.044-0.02136.778-0.001-0.0010.0000.0000.0000.000
154A156GLU-1-0.886-0.93741.464-0.029-0.0290.0000.0000.0000.000
155A157GLN0-0.014-0.01940.1190.0040.0040.0000.0000.0000.000
156A158ILE0-0.023-0.01041.432-0.002-0.0020.0000.0000.0000.000
157A159LYS10.8020.89337.7260.0140.0140.0000.0000.0000.000
158A160VAL0-0.023-0.01142.675-0.002-0.0020.0000.0000.0000.000
159A161LYS10.7660.87240.4440.0110.0110.0000.0000.0000.000
160A162ILE0-0.046-0.02946.284-0.001-0.0010.0000.0000.0000.000
161A163GLY00.021-0.00248.2570.0010.0010.0000.0000.0000.000
162A164GLY00.0540.03550.3160.0010.0010.0000.0000.0000.000
163A165THR0-0.050-0.02250.8830.0000.0000.0000.0000.0000.000
164A166SER0-0.051-0.01354.6040.0010.0010.0000.0000.0000.000
165A167PHE00.1150.03356.000-0.001-0.0010.0000.0000.0000.000
166A168LYS10.9260.96357.3240.0030.0030.0000.0000.0000.000
167A169GLU-1-0.917-0.94056.562-0.008-0.0080.0000.0000.0000.000
168A170ASP-1-0.697-0.82852.576-0.006-0.0060.0000.0000.0000.000
169A171VAL00.0130.00754.512-0.001-0.0010.0000.0000.0000.000
170A172ARG10.9070.95756.7810.0060.0060.0000.0000.0000.000
171A173HIS00.0460.04349.084-0.002-0.0020.0000.0000.0000.000
172A174ILE00.0450.02050.090-0.001-0.0010.0000.0000.0000.000
173A175ASN0-0.037-0.03053.473-0.001-0.0010.0000.0000.0000.000
174A176ALA00.0040.01255.437-0.001-0.0010.0000.0000.0000.000
175A177LEU00.0120.00049.202-0.001-0.0010.0000.0000.0000.000
176A178GLN0-0.0010.00052.584-0.002-0.0020.0000.0000.0000.000
177A179HIS0-0.095-0.04554.2550.0000.0000.0000.0000.0000.000
178A180THR0-0.024-0.00852.7190.0000.0000.0000.0000.0000.000
179A181ALA0-0.036-0.00949.840-0.001-0.0010.0000.0000.0000.000
180A182GLY00.0230.02051.785-0.001-0.0010.0000.0000.0000.000
181A183SER0-0.001-0.02451.792-0.001-0.0010.0000.0000.0000.000
182A184SER0-0.013-0.00149.3690.0010.0010.0000.0000.0000.000
183A185ILE0-0.050-0.00146.092-0.001-0.0010.0000.0000.0000.000
184A186THR00.0050.01244.0510.0020.0020.0000.0000.0000.000
185A187MET0-0.028-0.02545.226-0.001-0.0010.0000.0000.0000.000
186A188ILE0-0.0150.00940.5550.0020.0020.0000.0000.0000.000
187A189LEU00.0140.00344.681-0.001-0.0010.0000.0000.0000.000
188A190ASP-1-0.760-0.86741.411-0.003-0.0030.0000.0000.0000.000
189A191ALA00.0100.00344.509-0.001-0.0010.0000.0000.0000.000
190A192ASN0-0.031-0.01541.175-0.001-0.0010.0000.0000.0000.000
191A193GLN0-0.058-0.05040.6370.0020.0020.0000.0000.0000.000
192A194SER0-0.060-0.03245.6260.0010.0010.0000.0000.0000.000
193A195TYR0-0.033-0.00648.9250.0000.0000.0000.0000.0000.000
194A196ASP-1-0.783-0.89250.4000.0090.0090.0000.0000.0000.000
195A197ALA00.043-0.01352.736-0.001-0.0010.0000.0000.0000.000
196A198ALA0-0.0030.00153.631-0.001-0.0010.0000.0000.0000.000
197A199ALA0-0.049-0.03054.436-0.001-0.0010.0000.0000.0000.000
198A200ALA00.0320.01251.256-0.001-0.0010.0000.0000.0000.000
199A201PHE0-0.006-0.00653.093-0.001-0.0010.0000.0000.0000.000
200A202LYS10.8840.95555.629-0.002-0.0020.0000.0000.0000.000
201A203TRP00.010-0.01253.081-0.001-0.0010.0000.0000.0000.000
202A204GLU-1-0.755-0.83354.799-0.001-0.0010.0000.0000.0000.000
203A205ARG10.9000.94556.3970.0020.0020.0000.0000.0000.000
204A206TYR00.0160.00356.3540.0000.0000.0000.0000.0000.000
205A207PHE0-0.012-0.01650.657-0.001-0.0010.0000.0000.0000.000
206A208SER0-0.037-0.00654.9760.0000.0000.0000.0000.0000.000
207A209GLU-1-0.983-0.97858.021-0.006-0.0060.0000.0000.0000.000
208A210TRP0-0.056-0.03553.341-0.001-0.0010.0000.0000.0000.000
209A211THR00.0220.00653.3080.0000.0000.0000.0000.0000.000
210A212ASN0-0.014-0.00949.6400.0010.0010.0000.0000.0000.000
211A213ILE0-0.0020.00948.015-0.001-0.0010.0000.0000.0000.000
212A214GLY0-0.0030.00244.2040.0000.0000.0000.0000.0000.000
213A215TRP0-0.081-0.07738.0470.0010.0010.0000.0000.0000.000
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215A217GLU-1-0.768-0.86839.098-0.005-0.0050.0000.0000.0000.000
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