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: G64J1

Calculation Name: 5D0O-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0O

Chain ID: D

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-26

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2249234.723435
FMO2-HF: Nuclear repulsion 2165099.333479
FMO2-HF: Total energy -84135.389956
FMO2-MP2: Total energy -84380.562942


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(D:27:VAL)


Summations of interaction energy for fragment #1(D:27:VAL)
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.
-10.736-2.8728.641-5.882-10.625-0.045
Interaction energy analysis for fragmet #1(D:27:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.036
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].
3D29ASP-1-0.871-0.9302.688-6.711-4.0030.579-1.483-1.804-0.012
4D30ASN0-0.056-0.0344.9640.4020.4020.0000.0000.0000.000
5D31PRO00.0350.0206.303-0.178-0.1780.0000.0000.0000.000
6D32PRO00.0840.0147.3980.0290.0290.0000.0000.0000.000
7D33ASN0-0.013-0.0118.4370.0350.0350.0000.0000.0000.000
8D34GLU-1-0.829-0.9018.172-0.286-0.2860.0000.0000.0000.000
9D35ILE00.0060.0192.973-0.3720.0860.080-0.090-0.4480.000
10D36TYR0-0.029-0.0226.8050.0830.0830.0000.0000.0000.000
11D37ALA00.0390.0169.2340.0620.0620.0000.0000.0000.000
12D38THR0-0.020-0.0266.1780.0950.0950.0000.0000.0000.000
13D39ALA0-0.037-0.0256.9900.0850.0850.0000.0000.0000.000
14D40GLN0-0.037-0.0228.7260.0620.0620.0000.0000.0000.000
15D41GLN0-0.112-0.04911.2420.0380.0380.0000.0000.0000.000
16D42LYS10.9420.9748.243-0.464-0.4640.0000.0000.0000.000
17D43LEU0-0.021-0.00811.6720.0220.0220.0000.0000.0000.000
18D44GLN0-0.017-0.01613.8000.0230.0230.0000.0000.0000.000
19D45ASP-1-0.904-0.93514.1390.1560.1560.0000.0000.0000.000
20D46GLY0-0.026-0.00515.6750.0110.0110.0000.0000.0000.000
21D47ASN0-0.054-0.03312.4550.0220.0220.0000.0000.0000.000
22D48TRP00.0840.02911.6110.0030.0030.0000.0000.0000.000
23D49ARG10.8770.9268.784-0.165-0.1650.0000.0000.0000.000
24D50GLN0-0.020-0.0097.1130.1260.1260.0000.0000.0000.000
25D51ALA00.0440.0256.368-0.021-0.0210.0000.0000.0000.000
26D52ILE0-0.014-0.0066.979-0.153-0.1530.0000.0000.0000.000
27D53THR00.0340.0262.944-0.649-0.0450.217-0.179-0.6430.000
28D54GLN00.0030.0042.412-5.920-2.8813.510-2.355-4.194-0.030
29D55LEU00.0210.0053.822-0.462-0.3050.0010.011-0.1690.000
30D56GLU-1-0.825-0.9034.971-0.548-0.5480.0000.0000.0000.000
31D57ALA0-0.034-0.0022.222-0.055-0.6453.614-1.119-1.905-0.001
32D58LEU0-0.012-0.0154.129-0.0050.2360.001-0.090-0.1520.000
33D59ASP-1-0.874-0.9326.388-0.366-0.3660.0000.0000.0000.000
34D60ASN0-0.066-0.0457.0150.1990.1990.0000.0000.0000.000
35D61ARG10.7760.8852.4203.2564.5030.639-0.577-1.310-0.002
36D62TYR0-0.058-0.0367.4840.1740.1740.0000.0000.0000.000
37D63PRO00.0250.02010.9920.0450.0450.0000.0000.0000.000
38D64PHE0-0.047-0.01713.4760.0450.0450.0000.0000.0000.000
39D65GLY00.0210.01314.7140.0180.0180.0000.0000.0000.000
40D66PRO00.001-0.00415.7820.0190.0190.0000.0000.0000.000
41D67TYR0-0.008-0.00513.3300.0200.0200.0000.0000.0000.000
42D68SER00.0140.00813.347-0.019-0.0190.0000.0000.0000.000
43D69GLN00.0530.01913.981-0.032-0.0320.0000.0000.0000.000
44D70GLN0-0.032-0.02515.6150.0180.0180.0000.0000.0000.000
45D71VAL00.0340.0319.4740.0120.0120.0000.0000.0000.000
46D72GLN0-0.034-0.02112.5990.0550.0550.0000.0000.0000.000
47D73LEU0-0.030-0.01114.2430.0240.0240.0000.0000.0000.000
48D74ASP-1-0.810-0.89612.441-0.198-0.1980.0000.0000.0000.000
49D75LEU0-0.019-0.0128.2770.0320.0320.0000.0000.0000.000
50D76ILE0-0.017-0.00212.1310.0400.0400.0000.0000.0000.000
51D77TYR0-0.029-0.01715.6440.0360.0360.0000.0000.0000.000
52D78ALA00.000-0.00811.7410.0310.0310.0000.0000.0000.000
53D79TYR0-0.060-0.06810.0060.0430.0430.0000.0000.0000.000
54D80TYR0-0.023-0.01514.4870.0300.0300.0000.0000.0000.000
55D81LYS10.8930.96116.7550.0170.0170.0000.0000.0000.000
56D82ASN0-0.067-0.04713.0220.0480.0480.0000.0000.0000.000
57D83ALA00.0030.01115.8100.0160.0160.0000.0000.0000.000
58D84ASP-1-0.777-0.85113.4370.0240.0240.0000.0000.0000.000
59D85LEU00.031-0.00216.628-0.027-0.0270.0000.0000.0000.000
60D86PRO0-0.004-0.01119.052-0.016-0.0160.0000.0000.0000.000
61D87LEU00.0080.00812.823-0.011-0.0110.0000.0000.0000.000
62D88ALA00.0470.03115.818-0.029-0.0290.0000.0000.0000.000
63D89GLN0-0.009-0.01417.340-0.018-0.0180.0000.0000.0000.000
64D90ALA0-0.0050.00517.602-0.007-0.0070.0000.0000.0000.000
65D91ALA0-0.029-0.00815.112-0.022-0.0220.0000.0000.0000.000
66D92ILE00.0450.00717.020-0.008-0.0080.0000.0000.0000.000
67D93ASP-1-0.808-0.90020.209-0.106-0.1060.0000.0000.0000.000
68D94ARG10.8860.95113.5650.3100.3100.0000.0000.0000.000
69D95PHE00.0470.02117.9240.0010.0010.0000.0000.0000.000
70D96ILE0-0.012-0.01220.3680.0060.0060.0000.0000.0000.000
71D97ARG10.9000.94921.1240.1610.1610.0000.0000.0000.000
72D98LEU0-0.024-0.00419.4950.0040.0040.0000.0000.0000.000
73D99ASN0-0.059-0.04022.068-0.005-0.0050.0000.0000.0000.000
74D100PRO00.0610.03724.4260.0030.0030.0000.0000.0000.000
75D101THR0-0.025-0.01927.6270.0050.0050.0000.0000.0000.000
76D102HIS00.0110.01921.3860.0110.0110.0000.0000.0000.000
77D103PRO00.019-0.00425.0010.0060.0060.0000.0000.0000.000
78D104ASN00.0050.01122.3390.0130.0130.0000.0000.0000.000
79D105ILE00.0330.01624.115-0.006-0.0060.0000.0000.0000.000
80D106ASP-1-0.785-0.86426.130-0.076-0.0760.0000.0000.0000.000
81D107TYR00.0300.00919.6670.0020.0020.0000.0000.0000.000
82D108VAL00.0160.00820.7900.0050.0050.0000.0000.0000.000
83D109MET0-0.031-0.01323.1240.0020.0020.0000.0000.0000.000
84D110TYR0-0.048-0.04525.3890.0060.0060.0000.0000.0000.000
85D111MET00.0100.00919.4190.0120.0120.0000.0000.0000.000
86D112ARG10.8050.93123.4290.0910.0910.0000.0000.0000.000
87D113GLY00.0330.01124.6510.0060.0060.0000.0000.0000.000
88D114LEU0-0.037-0.02424.2380.0070.0070.0000.0000.0000.000
89D115THR0-0.021-0.03021.6520.0070.0070.0000.0000.0000.000
90D116ASN0-0.0180.00023.7280.0080.0080.0000.0000.0000.000
91D117MET0-0.018-0.00927.0150.0050.0050.0000.0000.0000.000
92D118ALA0-0.067-0.03224.2940.0060.0060.0000.0000.0000.000
93D119LEU0-0.028-0.00823.8110.0060.0060.0000.0000.0000.000
94D120ASP-1-0.845-0.89427.162-0.007-0.0070.0000.0000.0000.000
95D121ASP-1-0.862-0.89329.3850.0190.0190.0000.0000.0000.000
96D122SER0-0.009-0.01831.1260.0020.0020.0000.0000.0000.000
97D133SER00.017-0.01936.8140.0000.0000.0000.0000.0000.000
98D134ASP-1-0.897-0.95338.6020.0040.0040.0000.0000.0000.000
99D135ARG10.8080.89632.005-0.011-0.0110.0000.0000.0000.000
100D136ASP-1-0.778-0.89833.618-0.019-0.0190.0000.0000.0000.000
101D137PRO0-0.0080.00534.501-0.001-0.0010.0000.0000.0000.000
102D138GLN0-0.084-0.05731.872-0.007-0.0070.0000.0000.0000.000
103D139HIS00.0500.02828.949-0.007-0.0070.0000.0000.0000.000
104D140ALA00.0590.03331.238-0.004-0.0040.0000.0000.0000.000
105D141ARG10.8870.93933.4980.0170.0170.0000.0000.0000.000
106D142ALA00.0090.01029.989-0.003-0.0030.0000.0000.0000.000
107D143ALA00.0380.01730.111-0.005-0.0050.0000.0000.0000.000
108D144PHE00.0160.00331.042-0.003-0.0030.0000.0000.0000.000
109D145SER0-0.0080.00432.699-0.003-0.0030.0000.0000.0000.000
110D146ASP-1-0.834-0.92628.228-0.066-0.0660.0000.0000.0000.000
111D147PHE00.0550.01528.941-0.003-0.0030.0000.0000.0000.000
112D148SER0-0.043-0.02932.5120.0010.0010.0000.0000.0000.000
113D149LYS10.7850.88430.7080.0610.0610.0000.0000.0000.000
114D150LEU0-0.0280.00029.684-0.001-0.0010.0000.0000.0000.000
115D151VAL0-0.006-0.01032.443-0.001-0.0010.0000.0000.0000.000
116D152ARG10.9070.95535.8070.0470.0470.0000.0000.0000.000
117D153GLY0-0.0100.00534.5780.0000.0000.0000.0000.0000.000
118D154TYR00.006-0.01130.254-0.001-0.0010.0000.0000.0000.000
119D155PRO00.0350.02234.5930.0010.0010.0000.0000.0000.000
120D156ASN0-0.037-0.02636.6480.0040.0040.0000.0000.0000.000
121D157SER0-0.026-0.03630.3660.0000.0000.0000.0000.0000.000
122D158GLN00.0350.01028.0600.0000.0000.0000.0000.0000.000
123D159TYR0-0.006-0.01426.0410.0030.0030.0000.0000.0000.000
124D160THR0-0.0150.01130.8040.0030.0030.0000.0000.0000.000
125D161THR00.0700.02334.1110.0020.0020.0000.0000.0000.000
126D162ASP-1-0.775-0.82130.762-0.023-0.0230.0000.0000.0000.000
127D163ALA00.0630.03531.7840.0030.0030.0000.0000.0000.000
128D164THR0-0.037-0.02433.2640.0030.0030.0000.0000.0000.000
129D165LYS10.9670.99035.7980.0140.0140.0000.0000.0000.000
130D166ARG10.8620.89029.2170.0240.0240.0000.0000.0000.000
131D167LEU0-0.0170.00234.6160.0010.0010.0000.0000.0000.000
132D168VAL0-0.036-0.02236.8230.0010.0010.0000.0000.0000.000
133D169PHE0-0.032-0.01334.4550.0020.0020.0000.0000.0000.000
134D170LEU00.014-0.00432.6420.0010.0010.0000.0000.0000.000
135D171LYS10.8550.91137.0810.0190.0190.0000.0000.0000.000
136D172ASP-1-0.748-0.87740.589-0.005-0.0050.0000.0000.0000.000
137D173ARG10.7550.88634.6670.0100.0100.0000.0000.0000.000
138D174LEU0-0.039-0.02737.0070.0010.0010.0000.0000.0000.000
139D175ALA00.0100.01240.4530.0000.0000.0000.0000.0000.000
140D176LYS10.9200.93740.8720.0040.0040.0000.0000.0000.000
141D177TYR0-0.064-0.01340.3410.0000.0000.0000.0000.0000.000
142D178GLU-1-0.831-0.91042.452-0.011-0.0110.0000.0000.0000.000
143D179TYR0-0.065-0.05645.7140.0000.0000.0000.0000.0000.000
144D180SER00.0200.00744.2170.0010.0010.0000.0000.0000.000
145D181VAL0-0.0080.00244.9130.0010.0010.0000.0000.0000.000
146D182ALA0-0.020-0.01547.5680.0000.0000.0000.0000.0000.000
147D183GLU-1-0.824-0.88349.0050.0040.0040.0000.0000.0000.000
148D184TYR00.0530.03348.6770.0000.0000.0000.0000.0000.000
149D185TYR0-0.043-0.04849.4760.0000.0000.0000.0000.0000.000
150D186THR0-0.034-0.04753.1480.0000.0000.0000.0000.0000.000
151D187GLU-1-0.966-0.97452.2940.0070.0070.0000.0000.0000.000
152D188ARG10.7830.90553.730-0.003-0.0030.0000.0000.0000.000
153D189GLY00.0380.01455.7190.0010.0010.0000.0000.0000.000
154D190ALA0-0.079-0.03255.555-0.001-0.0010.0000.0000.0000.000
155D191TRP00.1010.04856.9360.0000.0000.0000.0000.0000.000
156D192VAL00.0300.00657.688-0.001-0.0010.0000.0000.0000.000
157D193ALA00.0120.00353.247-0.001-0.0010.0000.0000.0000.000
158D194VAL00.0260.03253.288-0.001-0.0010.0000.0000.0000.000
159D195VAL00.000-0.00254.031-0.001-0.0010.0000.0000.0000.000
160D196ASN0-0.029-0.02153.603-0.001-0.0010.0000.0000.0000.000
161D197ARG10.9470.97945.3360.0080.0080.0000.0000.0000.000
162D198VAL0-0.003-0.00450.721-0.001-0.0010.0000.0000.0000.000
163D199GLU-1-0.938-0.96352.748-0.013-0.0130.0000.0000.0000.000
164D200GLY00.023-0.00550.166-0.001-0.0010.0000.0000.0000.000
165D201MET0-0.060-0.01947.465-0.001-0.0010.0000.0000.0000.000
166D202LEU0-0.013-0.01249.413-0.001-0.0010.0000.0000.0000.000
167D203ARG10.7620.88848.4240.0160.0160.0000.0000.0000.000
168D204ASP-1-0.860-0.91245.613-0.019-0.0190.0000.0000.0000.000
169D205TYR0-0.051-0.03641.971-0.002-0.0020.0000.0000.0000.000
170D206PRO00.0560.05047.0400.0020.0020.0000.0000.0000.000
171D207ASP-1-0.894-0.91347.017-0.015-0.0150.0000.0000.0000.000
172D208THR0-0.062-0.03344.5810.0000.0000.0000.0000.0000.000
173D209GLN0-0.039-0.03846.7370.0000.0000.0000.0000.0000.000
174D210ALA00.0400.01645.7100.0010.0010.0000.0000.0000.000
175D211THR0-0.015-0.03847.8460.0010.0010.0000.0000.0000.000
176D212ARG10.8520.93050.3410.0070.0070.0000.0000.0000.000
177D213ASP-1-0.850-0.91050.1220.0000.0000.0000.0000.0000.000
178D214ALA00.0210.00850.9920.0010.0010.0000.0000.0000.000
179D215LEU0-0.0040.00052.9990.0000.0000.0000.0000.0000.000
180D216PRO00.0430.01355.8160.0000.0000.0000.0000.0000.000
181D217LEU00.0200.02652.8150.0000.0000.0000.0000.0000.000
182D218MET0-0.0180.00756.6890.0000.0000.0000.0000.0000.000
183D219GLU-1-0.817-0.90658.238-0.002-0.0020.0000.0000.0000.000
184D220ASN00.0280.00859.6890.0000.0000.0000.0000.0000.000
185D221ALA00.0360.01658.5970.0000.0000.0000.0000.0000.000
186D222TYR0-0.017-0.04059.8610.0000.0000.0000.0000.0000.000
187D223ARG10.8160.88663.6280.0020.0020.0000.0000.0000.000
188D224GLN0-0.055-0.01262.6420.0000.0000.0000.0000.0000.000
189D225MET0-0.081-0.02461.5360.0000.0000.0000.0000.0000.000
190D226GLN00.0030.00766.145-0.001-0.0010.0000.0000.0000.000
191D227MET00.0000.01664.2670.0000.0000.0000.0000.0000.000
192D228ASN00.0580.00967.1650.0000.0000.0000.0000.0000.000
193D229ALA00.0160.01268.8670.0000.0000.0000.0000.0000.000
194D230GLN00.0150.01562.5080.0000.0000.0000.0000.0000.000
195D231ALA00.0330.00864.1600.0000.0000.0000.0000.0000.000
196D232GLU-1-0.851-0.92164.959-0.003-0.0030.0000.0000.0000.000
197D233LYS10.8380.92064.7100.0070.0070.0000.0000.0000.000
198D234VAL00.0250.01459.6540.0000.0000.0000.0000.0000.000
199D235ALA00.0660.04161.8900.0000.0000.0000.0000.0000.000
200D236LYS10.8270.91064.0560.0050.0050.0000.0000.0000.000
201D237ILE0-0.052-0.02458.5800.0000.0000.0000.0000.0000.000
202D238ILE0-0.024-0.00858.8640.0000.0000.0000.0000.0000.000
203D239ALA00.0050.00260.6530.0000.0000.0000.0000.0000.000
204D240ALA0-0.064-0.01763.0280.0000.0000.0000.0000.0000.000
205D241ASN0-0.019-0.01956.579-0.001-0.0010.0000.0000.0000.000
206D242SER00.0260.02556.0470.0000.0000.0000.0000.0000.000
207D243SER00.0750.03355.5540.0000.0000.0000.0000.0000.000
208D244ASN0-0.040-0.01151.712-0.001-0.0010.0000.0000.0000.000