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: 16JGZ

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 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 373
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6509570.620382
FMO2-HF: Nuclear repulsion 6360683.122618
FMO2-HF: Total energy -148887.497764
FMO2-MP2: Total energy -149320.388892


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.
-11.374-4.733.585-4.925-5.303-0.005
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 : 0.057 / q_NPA : 0.015
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].
3A5LYS10.9571.0063.541-5.383-1.545-0.036-2.086-1.715-0.002
4A6ILE00.0180.0045.619-0.846-0.8460.0000.0000.0000.000
5A7VAL0-0.014-0.0026.9600.1000.1000.0000.0000.0000.000
6A8ARG10.8920.9289.6900.3070.3070.0000.0000.0000.000
7A9ILE00.0030.00112.759-0.011-0.0110.0000.0000.0000.000
8A10GLU-1-0.868-0.90815.481-0.185-0.1850.0000.0000.0000.000
9A11THR0-0.021-0.01918.4890.0100.0100.0000.0000.0000.000
10A12PHE00.015-0.00619.444-0.006-0.0060.0000.0000.0000.000
11A13PRO0-0.0050.01124.4970.0030.0030.0000.0000.0000.000
12A14LEU0-0.0070.00226.463-0.005-0.0050.0000.0000.0000.000
13A15PHE0-0.015-0.02630.0730.0060.0060.0000.0000.0000.000
14A16HIS0-0.003-0.00733.859-0.005-0.0050.0000.0000.0000.000
15A17ARG10.9590.98236.5300.0190.0190.0000.0000.0000.000
16A18LEU0-0.060-0.01739.350-0.002-0.0020.0000.0000.0000.000
17A19GLU-1-0.940-0.97141.831-0.029-0.0290.0000.0000.0000.000
18A20LYS10.8560.92244.5680.0220.0220.0000.0000.0000.000
19A21PRO0-0.017-0.01044.6180.0000.0000.0000.0000.0000.000
20A22TYR0-0.014-0.01539.1930.0000.0000.0000.0000.0000.000
21A23GLY0-0.031-0.02443.8140.0010.0010.0000.0000.0000.000
22A24ASP-1-0.820-0.90342.2930.0000.0000.0000.0000.0000.000
23A25ALA00.0350.01145.6200.0000.0000.0000.0000.0000.000
24A26ASN0-0.035-0.00942.6920.0020.0020.0000.0000.0000.000
25A27GLY00.0030.01645.9770.0010.0010.0000.0000.0000.000
26A28PHE0-0.081-0.04945.465-0.001-0.0010.0000.0000.0000.000
27A29LYS10.9010.94739.1740.0040.0040.0000.0000.0000.000
28A30ARG10.9320.95042.1220.0050.0050.0000.0000.0000.000
29A31TYR00.0290.01237.040-0.002-0.0020.0000.0000.0000.000
30A32ARG10.7810.88934.4010.0200.0200.0000.0000.0000.000
31A33THR0-0.029-0.01632.257-0.002-0.0020.0000.0000.0000.000
32A34CYS00.0100.02527.2140.0010.0010.0000.0000.0000.000
33A35TYR0-0.012-0.04423.039-0.001-0.0010.0000.0000.0000.000
34A36LEU00.0310.01821.7580.0060.0060.0000.0000.0000.000
35A37ILE0-0.048-0.02417.7650.0050.0050.0000.0000.0000.000
36A38ARG10.8780.94013.4990.2850.2850.0000.0000.0000.000
37A39ILE0-0.013-0.01110.8960.0140.0140.0000.0000.0000.000
38A40ILE00.003-0.0019.553-0.052-0.0520.0000.0000.0000.000
39A41THR0-0.045-0.0405.218-0.208-0.075-0.001-0.022-0.1100.000
40A42GLU-1-0.944-0.9932.900-2.214-0.9830.059-0.474-0.816-0.004
41A43SER0-0.058-0.0212.019-0.716-0.0363.551-2.194-2.0380.001
42A44GLY00.0030.0094.0440.1200.3550.003-0.064-0.1740.000
43A45ILE0-0.0310.0063.664-0.0700.2670.007-0.049-0.2940.000
44A46ASP-1-0.788-0.8946.913-0.357-0.3570.0000.0000.0000.000
45A47GLY0-0.016-0.00410.3780.0020.0020.0000.0000.0000.000
46A48TRP00.0290.00312.7850.0420.0420.0000.0000.0000.000
47A49GLY0-0.004-0.00616.5160.0160.0160.0000.0000.0000.000
48A50GLU-1-0.756-0.86918.981-0.045-0.0450.0000.0000.0000.000
49A51CYS0-0.058-0.02322.7840.0140.0140.0000.0000.0000.000
50A52VAL00.0640.01825.542-0.007-0.0070.0000.0000.0000.000
51A53ASP-1-0.870-0.95329.2910.0330.0330.0000.0000.0000.000
52A54TRP00.0260.02131.572-0.003-0.0030.0000.0000.0000.000
53A55LEU0-0.005-0.01529.7340.0040.0040.0000.0000.0000.000
54A56PRO00.0080.01630.9020.0020.0020.0000.0000.0000.000
55A57ALA00.0040.00531.6580.0030.0030.0000.0000.0000.000
56A58LEU0-0.0050.00026.4950.0070.0070.0000.0000.0000.000
57A59HIS00.0740.05825.0890.0080.0080.0000.0000.0000.000
58A60VAL0-0.027-0.01026.1960.0030.0030.0000.0000.0000.000
59A61GLY00.0110.01026.6240.0070.0070.0000.0000.0000.000
60A62PHE00.0630.01420.2470.0150.0150.0000.0000.0000.000
61A63THR0-0.025-0.00921.9690.0120.0120.0000.0000.0000.000
62A64LYS10.9190.95922.923-0.028-0.0280.0000.0000.0000.000
63A65ARG10.9300.97723.495-0.081-0.0810.0000.0000.0000.000
64A66ILE0-0.023-0.00519.3180.0190.0190.0000.0000.0000.000
65A67ILE00.0170.00416.7510.0280.0280.0000.0000.0000.000
66A68PRO00.002-0.00116.8350.0240.0240.0000.0000.0000.000
67A69PHE0-0.0070.00817.3440.0360.0360.0000.0000.0000.000
68A70LEU00.018-0.00214.0520.0640.0640.0000.0000.0000.000
69A71LEU00.0080.02312.3420.0700.0700.0000.0000.0000.000
70A72GLY00.004-0.0029.9990.0120.0120.0000.0000.0000.000
71A73LYS10.8210.91310.130-0.202-0.2020.0000.0000.0000.000
72A74GLN00.0200.0014.889-0.324-0.3240.0000.0000.0000.000
73A75ALA00.0700.0226.756-0.194-0.1940.0000.0000.0000.000
74A76GLY00.0190.0176.715-0.188-0.1880.0000.0000.0000.000
75A77SER0-0.050-0.0097.995-0.146-0.1460.0000.0000.0000.000
76A78ARG10.8850.92611.270-0.243-0.2430.0000.0000.0000.000
77A79LEU00.0510.02213.155-0.030-0.0300.0000.0000.0000.000
78A80SER0-0.025-0.01314.989-0.047-0.0470.0000.0000.0000.000
79A81LEU00.0140.00111.797-0.047-0.0470.0000.0000.0000.000
80A82VAL00.0500.03516.053-0.035-0.0350.0000.0000.0000.000
81A83ARG10.9971.00018.336-0.207-0.2070.0000.0000.0000.000
82A84THR0-0.090-0.04719.089-0.020-0.0200.0000.0000.0000.000
83A85ILE00.008-0.00417.544-0.020-0.0200.0000.0000.0000.000
84A86GLN0-0.003-0.01221.469-0.021-0.0210.0000.0000.0000.000
85A87LYS10.8830.96324.037-0.173-0.1730.0000.0000.0000.000
86A88TRP0-0.048-0.02120.921-0.011-0.0110.0000.0000.0000.000
87A89HIS00.0290.00125.085-0.007-0.0070.0000.0000.0000.000
88A90GLN00.1060.05224.6390.0110.0110.0000.0000.0000.000
89A91ARG10.9210.98624.867-0.026-0.0260.0000.0000.0000.000
90A92ALA00.0140.00022.706-0.004-0.0040.0000.0000.0000.000
91A93ALA0-0.011-0.00220.4920.0010.0010.0000.0000.0000.000
92A94SER00.0400.01319.9900.0060.0060.0000.0000.0000.000
93A95ALA00.0350.02920.298-0.004-0.0040.0000.0000.0000.000
94A96VAL00.007-0.01015.498-0.008-0.0080.0000.0000.0000.000
95A97SER0-0.028-0.01815.6820.0050.0050.0000.0000.0000.000
96A98MET0-0.0080.02615.659-0.003-0.0030.0000.0000.0000.000
97A99ALA00.0380.03514.122-0.017-0.0170.0000.0000.0000.000
98A100LEU0-0.031-0.03910.612-0.024-0.0240.0000.0000.0000.000
99A101THR0-0.050-0.02510.7940.0270.0270.0000.0000.0000.000
100A102GLU-1-0.813-0.89911.762-0.223-0.2230.0000.0000.0000.000
101A103ILE0-0.013-0.0096.490-0.050-0.0500.0000.0000.0000.000
102A104ALA0-0.031-0.0157.155-0.091-0.0910.0000.0000.0000.000
103A105ALA00.0070.0028.124-0.071-0.0710.0000.0000.0000.000
104A106LYS10.8830.9438.1690.3640.3640.0000.0000.0000.000
105A107ALA0-0.066-0.0293.773-0.321-0.1310.002-0.036-0.1560.000
106A108ALA0-0.055-0.0235.340-0.244-0.2440.0000.0000.0000.000
107A109ASP-1-0.848-0.8967.878-0.466-0.4660.0000.0000.0000.000
108A110CYS0-0.022-0.0079.7430.0800.0800.0000.0000.0000.000
109A111SER0-0.0030.00212.697-0.007-0.0070.0000.0000.0000.000
110A112VAL00.028-0.00214.5370.0160.0160.0000.0000.0000.000
111A113CYS0-0.048-0.01815.8490.0240.0240.0000.0000.0000.000
112A114GLU-1-0.849-0.92415.971-0.143-0.1430.0000.0000.0000.000
113A115LEU0-0.013-0.00211.4580.0220.0220.0000.0000.0000.000
114A116TRP0-0.096-0.06814.9410.0250.0250.0000.0000.0000.000
115A117GLY0-0.0060.00518.0470.0140.0140.0000.0000.0000.000
116A118GLY0-0.0210.00119.683-0.004-0.0040.0000.0000.0000.000
117A119ARG10.8430.89821.1390.0880.0880.0000.0000.0000.000
118A120TYR0-0.040-0.02924.0990.0000.0000.0000.0000.0000.000
119A121ARG10.8440.92127.3160.0160.0160.0000.0000.0000.000
120A122GLU-1-0.840-0.93526.545-0.060-0.0600.0000.0000.0000.000
121A123GLU-1-0.882-0.94328.255-0.050-0.0500.0000.0000.0000.000
122A124ILE0-0.056-0.02128.4070.0050.0050.0000.0000.0000.000
123A125PRO00.0540.03331.572-0.003-0.0030.0000.0000.0000.000
124A126VAL0-0.024-0.01332.4360.0020.0020.0000.0000.0000.000
125A127TYR00.0280.02135.3860.0000.0000.0000.0000.0000.000
126A128ALA0-0.0010.00837.517-0.001-0.0010.0000.0000.0000.000
127A129SER0-0.060-0.05537.8730.0030.0030.0000.0000.0000.000
128A130PHE00.019-0.01839.702-0.002-0.0020.0000.0000.0000.000
129A131GLN00.0250.00539.5610.0030.0030.0000.0000.0000.000
130A132SER00.0480.00943.445-0.001-0.0010.0000.0000.0000.000
131A133TYR0-0.0240.01147.0470.0000.0000.0000.0000.0000.000
132A134SER00.028-0.01347.726-0.001-0.0010.0000.0000.0000.000
133A135ASP-1-0.917-0.94949.945-0.005-0.0050.0000.0000.0000.000
134A136SER0-0.014-0.03052.248-0.001-0.0010.0000.0000.0000.000
135A137PRO00.0520.02455.2300.0000.0000.0000.0000.0000.000
136A138GLN0-0.023-0.00856.9010.0010.0010.0000.0000.0000.000
137A139TRP0-0.014-0.00551.554-0.001-0.0010.0000.0000.0000.000
138A140ILE00.0540.03252.723-0.001-0.0010.0000.0000.0000.000
139A141SER0-0.048-0.03253.876-0.001-0.0010.0000.0000.0000.000
140A142ARG10.9400.97151.1570.0120.0120.0000.0000.0000.000
141A143SER0-0.020-0.03249.222-0.002-0.0020.0000.0000.0000.000
142A144VAL00.0600.02349.539-0.001-0.0010.0000.0000.0000.000
143A145SER0-0.001-0.00351.043-0.001-0.0010.0000.0000.0000.000
144A146ASN0-0.019-0.01744.262-0.003-0.0030.0000.0000.0000.000
145A147VAL00.0250.00446.299-0.002-0.0020.0000.0000.0000.000
146A148GLU-1-0.894-0.94946.909-0.018-0.0180.0000.0000.0000.000
147A149ALA0-0.068-0.03546.060-0.002-0.0020.0000.0000.0000.000
148A150GLN0-0.003-0.01740.948-0.003-0.0030.0000.0000.0000.000
149A151LEU00.0510.03143.514-0.002-0.0020.0000.0000.0000.000
150A152LYS10.9170.97045.7620.0220.0220.0000.0000.0000.000
151A153LYS10.8770.95139.2730.0350.0350.0000.0000.0000.000
152A154GLY0-0.018-0.01841.286-0.002-0.0020.0000.0000.0000.000
153A155PHE0-0.042-0.02037.086-0.001-0.0010.0000.0000.0000.000
154A156GLU-1-0.882-0.93841.716-0.021-0.0210.0000.0000.0000.000
155A157GLN00.000-0.00739.9810.0040.0040.0000.0000.0000.000
156A158ILE0-0.023-0.01341.724-0.002-0.0020.0000.0000.0000.000
157A159LYS10.7970.89838.1710.0040.0040.0000.0000.0000.000
158A160VAL0-0.027-0.01043.042-0.002-0.0020.0000.0000.0000.000
159A161LYS10.8120.90840.5650.0040.0040.0000.0000.0000.000
160A162ILE0-0.039-0.01946.734-0.001-0.0010.0000.0000.0000.000
161A163GLY00.0270.00748.7250.0010.0010.0000.0000.0000.000
162A164GLY00.0580.02950.8330.0010.0010.0000.0000.0000.000
163A165THR0-0.057-0.01851.3980.0000.0000.0000.0000.0000.000
164A166SER0-0.068-0.02155.1150.0000.0000.0000.0000.0000.000
165A167PHE00.1160.03256.354-0.001-0.0010.0000.0000.0000.000
166A168LYS10.9090.95757.7700.0000.0000.0000.0000.0000.000
167A169GLU-1-0.937-0.95756.918-0.003-0.0030.0000.0000.0000.000
168A170ASP-1-0.694-0.83153.190-0.002-0.0020.0000.0000.0000.000
169A171VAL00.0120.00854.932-0.001-0.0010.0000.0000.0000.000
170A172ARG10.9130.95757.1870.0020.0020.0000.0000.0000.000
171A173HIS00.0480.07349.565-0.002-0.0020.0000.0000.0000.000
172A174ILE00.0480.01950.735-0.001-0.0010.0000.0000.0000.000
173A175ASN00.017-0.00153.856-0.001-0.0010.0000.0000.0000.000
174A176ALA0-0.0090.00855.754-0.001-0.0010.0000.0000.0000.000
175A177LEU00.001-0.00849.557-0.001-0.0010.0000.0000.0000.000
176A178GLN00.0100.00252.834-0.002-0.0020.0000.0000.0000.000
177A179HIS0-0.108-0.05254.5710.0000.0000.0000.0000.0000.000
178A180THR0-0.034-0.00853.420-0.001-0.0010.0000.0000.0000.000
179A181ALA0-0.037-0.01150.100-0.001-0.0010.0000.0000.0000.000
180A182GLY00.0110.01352.075-0.001-0.0010.0000.0000.0000.000
181A183SER0-0.017-0.03152.041-0.001-0.0010.0000.0000.0000.000
182A184SER0-0.043-0.01549.8690.0000.0000.0000.0000.0000.000
183A185ILE0-0.0010.02446.400-0.001-0.0010.0000.0000.0000.000
184A186THR0-0.0030.00744.4740.0020.0020.0000.0000.0000.000
185A187MET0-0.023-0.01545.502-0.001-0.0010.0000.0000.0000.000
186A188ILE0-0.0170.00440.7740.0010.0010.0000.0000.0000.000
187A189LEU00.007-0.00245.006-0.001-0.0010.0000.0000.0000.000
188A190ASP-1-0.769-0.88641.7070.0040.0040.0000.0000.0000.000
189A191ALA00.0100.00044.922-0.001-0.0010.0000.0000.0000.000
190A192ASN0-0.043-0.02541.482-0.001-0.0010.0000.0000.0000.000
191A193GLN0-0.088-0.06741.1870.0010.0010.0000.0000.0000.000
192A194SER0-0.060-0.02446.0940.0010.0010.0000.0000.0000.000
193A195TYR0-0.021-0.00649.412-0.001-0.0010.0000.0000.0000.000
194A196ASP-1-0.794-0.90350.8500.0120.0120.0000.0000.0000.000
195A197ALA00.029-0.01153.120-0.001-0.0010.0000.0000.0000.000
196A198ALA00.000-0.00354.016-0.001-0.0010.0000.0000.0000.000
197A199ALA0-0.035-0.01354.812-0.001-0.0010.0000.0000.0000.000
198A200ALA00.0320.01151.677-0.001-0.0010.0000.0000.0000.000
199A201PHE0-0.007-0.00553.481-0.001-0.0010.0000.0000.0000.000
200A202LYS10.8860.95455.982-0.005-0.0050.0000.0000.0000.000
201A203TRP00.005-0.01353.683-0.001-0.0010.0000.0000.0000.000
202A204GLU-1-0.734-0.79755.1350.0030.0030.0000.0000.0000.000
203A205ARG10.9190.95556.706-0.002-0.0020.0000.0000.0000.000
204A206TYR0-0.011-0.01156.6420.0000.0000.0000.0000.0000.000
205A207PHE0-0.011-0.01251.121-0.001-0.0010.0000.0000.0000.000
206A208SER0-0.036-0.00655.2550.0000.0000.0000.0000.0000.000
207A209GLU-1-0.985-0.97858.284-0.003-0.0030.0000.0000.0000.000
208A210TRP0-0.042-0.03053.720-0.001-0.0010.0000.0000.0000.000
209A211THR00.0140.00053.6580.0000.0000.0000.0000.0000.000
210A212ASN0-0.0090.00149.9210.0010.0010.0000.0000.0000.000
211A213ILE00.0040.01248.261-0.001-0.0010.0000.0000.0000.000
212A214GLY0-0.005-0.00344.4580.0000.0000.0000.0000.0000.000
213A215TRP0-0.083-0.07438.4940.0010.0010.0000.0000.0000.000
214A216LEU00.0040.00945.286-0.001-0.0010.0000.0000.0000.000
215A217GLU-1-0.754-0.86739.4600.0040.0040.0000.0000.0000.000
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