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

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FMODB ID: 173MZ

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2247986.965832
FMO2-HF: Nuclear repulsion 2163853.14682
FMO2-HF: Total energy -84133.819012
FMO2-MP2: Total energy -84379.065406


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.
-10.743-4.10611.418-6.538-11.518-0.048
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 : -0.032 / q_NPA : -0.037
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-1-0.922-0.9642.479-7.115-4.5961.291-1.631-2.180-0.018
4D30ASN0-0.035-0.0114.7760.3710.484-0.001-0.006-0.1060.000
5D31PRO00.0310.0176.185-0.201-0.2010.0000.0000.0000.000
6D32PRO00.0820.0167.3730.0060.0060.0000.0000.0000.000
7D33ASN0-0.010-0.0168.4320.0490.0490.0000.0000.0000.000
8D34GLU-1-0.830-0.9187.881-0.486-0.4860.0000.0000.0000.000
9D35ILE0-0.0070.0173.304-0.2400.1360.029-0.063-0.3420.000
10D36TYR00.0050.0086.7750.1170.1170.0000.0000.0000.000
11D37ALA00.0420.0159.2620.0850.0850.0000.0000.0000.000
12D38THR0-0.024-0.0276.2260.1180.1180.0000.0000.0000.000
13D39ALA0-0.040-0.0297.1690.1160.1160.0000.0000.0000.000
14D40GLN0-0.027-0.0238.8010.0870.0870.0000.0000.0000.000
15D41GLN0-0.114-0.05111.3190.0540.0540.0000.0000.0000.000
16D42LYS10.9550.9858.115-0.523-0.5230.0000.0000.0000.000
17D43LEU0-0.014-0.01211.8030.0370.0370.0000.0000.0000.000
18D44GLN00.0060.00213.9230.0230.0230.0000.0000.0000.000
19D45ASP-1-0.894-0.93114.3110.1570.1570.0000.0000.0000.000
20D46GLY0-0.029-0.00615.7920.0150.0150.0000.0000.0000.000
21D47ASN0-0.040-0.02812.4100.0470.0470.0000.0000.0000.000
22D48TRP00.0670.02911.7200.0070.0070.0000.0000.0000.000
23D49ARG10.9130.9578.676-0.320-0.3200.0000.0000.0000.000
24D50GLN0-0.044-0.0247.2530.2440.2440.0000.0000.0000.000
25D51ALA00.0330.0186.462-0.033-0.0330.0000.0000.0000.000
26D52ILE0-0.001-0.0037.063-0.176-0.1760.0000.0000.0000.000
27D53THR00.0160.0203.004-0.604-0.0860.115-0.133-0.5010.000
28D54GLN00.0160.0092.446-6.055-2.9802.766-2.189-3.652-0.027
29D55LEU00.0170.0043.948-0.583-0.4140.000-0.009-0.1610.000
30D56GLU-1-0.859-0.9485.320-0.443-0.4430.0000.0000.0000.000
31D57ALA0-0.063-0.0152.1060.085-0.7804.055-1.248-1.9420.002
32D58LEU0-0.012-0.0174.1010.0380.2770.002-0.087-0.1530.000
33D59ASP-1-0.921-0.9626.342-0.358-0.3580.0000.0000.0000.000
34D60ASN0-0.036-0.0166.8640.1920.1920.0000.0000.0000.000
35D61ARG10.8120.9122.2503.6194.1123.161-1.172-2.481-0.005
36D62TYR0-0.065-0.0367.7060.1730.1730.0000.0000.0000.000
37D63PRO00.0490.03510.8610.0350.0350.0000.0000.0000.000
38D64PHE0-0.057-0.02513.4060.0490.0490.0000.0000.0000.000
39D65GLY00.0190.01114.6540.0160.0160.0000.0000.0000.000
40D66PRO0-0.004-0.00315.6820.0230.0230.0000.0000.0000.000
41D67TYR00.0070.00213.2400.0190.0190.0000.0000.0000.000
42D68SER00.0160.00313.348-0.025-0.0250.0000.0000.0000.000
43D69GLN00.0610.02214.008-0.033-0.0330.0000.0000.0000.000
44D70GLN0-0.022-0.01515.6140.0150.0150.0000.0000.0000.000
45D71VAL00.0320.0329.5980.0120.0120.0000.0000.0000.000
46D72GLN00.0200.00812.6820.0540.0540.0000.0000.0000.000
47D73LEU0-0.035-0.01514.2130.0320.0320.0000.0000.0000.000
48D74ASP-1-0.853-0.92212.592-0.214-0.2140.0000.0000.0000.000
49D75LEU0-0.018-0.0128.2790.0430.0430.0000.0000.0000.000
50D76ILE0-0.0100.00612.1550.0510.0510.0000.0000.0000.000
51D77TYR0-0.039-0.01815.6820.0430.0430.0000.0000.0000.000
52D78ALA00.000-0.01111.8530.0350.0350.0000.0000.0000.000
53D79TYR0-0.026-0.02510.4090.0350.0350.0000.0000.0000.000
54D80TYR0-0.022-0.01514.5910.0320.0320.0000.0000.0000.000
55D81LYS10.8830.95316.7990.0020.0020.0000.0000.0000.000
56D82ASN0-0.046-0.03113.3980.0560.0560.0000.0000.0000.000
57D83ALA0-0.0030.00915.9670.0200.0200.0000.0000.0000.000
58D84ASP-1-0.822-0.88813.7100.1080.1080.0000.0000.0000.000
59D85LEU00.031-0.00616.737-0.028-0.0280.0000.0000.0000.000
60D86PRO0-0.027-0.02319.046-0.019-0.0190.0000.0000.0000.000
61D87LEU00.0160.01113.156-0.013-0.0130.0000.0000.0000.000
62D88ALA00.0550.03615.866-0.031-0.0310.0000.0000.0000.000
63D89GLN00.004-0.00517.404-0.021-0.0210.0000.0000.0000.000
64D90ALA0-0.0010.00917.624-0.010-0.0100.0000.0000.0000.000
65D91ALA0-0.028-0.00115.191-0.023-0.0230.0000.0000.0000.000
66D92ILE00.020-0.00417.021-0.012-0.0120.0000.0000.0000.000
67D93ASP-1-0.883-0.94720.211-0.097-0.0970.0000.0000.0000.000
68D94ARG10.9160.94914.3980.2520.2520.0000.0000.0000.000
69D95PHE00.0440.02317.9760.0000.0000.0000.0000.0000.000
70D96ILE0-0.019-0.01320.3160.0040.0040.0000.0000.0000.000
71D97ARG10.8890.94420.9630.1520.1520.0000.0000.0000.000
72D98LEU0-0.026-0.00819.6210.0040.0040.0000.0000.0000.000
73D99ASN0-0.093-0.04921.405-0.015-0.0150.0000.0000.0000.000
74D100PRO00.0730.03424.4710.0040.0040.0000.0000.0000.000
75D101THR0-0.037-0.01927.5720.0050.0050.0000.0000.0000.000
76D102HIS00.0120.01621.7680.0100.0100.0000.0000.0000.000
77D103PRO00.029-0.00325.0490.0070.0070.0000.0000.0000.000
78D104ASN00.0050.01622.5610.0170.0170.0000.0000.0000.000
79D105ILE00.0400.01824.170-0.005-0.0050.0000.0000.0000.000
80D106ASP-1-0.772-0.85126.101-0.079-0.0790.0000.0000.0000.000
81D107TYR00.022-0.01319.7690.0040.0040.0000.0000.0000.000
82D108VAL00.0030.00320.9030.0070.0070.0000.0000.0000.000
83D109MET0-0.051-0.02523.1270.0040.0040.0000.0000.0000.000
84D110TYR0-0.044-0.04025.5280.0090.0090.0000.0000.0000.000
85D111MET0-0.014-0.00219.7390.0120.0120.0000.0000.0000.000
86D112ARG10.9330.98623.4920.0760.0760.0000.0000.0000.000
87D113GLY00.0340.01324.6970.0070.0070.0000.0000.0000.000
88D114LEU0-0.048-0.03624.3200.0080.0080.0000.0000.0000.000
89D115THR00.0120.00121.0840.0120.0120.0000.0000.0000.000
90D116ASN0-0.041-0.01023.8160.0100.0100.0000.0000.0000.000
91D117MET0-0.037-0.02727.1040.0050.0050.0000.0000.0000.000
92D118ALA0-0.046-0.02124.4160.0060.0060.0000.0000.0000.000
93D119LEU0-0.035-0.01624.0700.0070.0070.0000.0000.0000.000
94D120ASP-1-0.884-0.92027.2830.0070.0070.0000.0000.0000.000
95D121ASP-1-0.876-0.90829.7040.0390.0390.0000.0000.0000.000
96D122SER0-0.044-0.03731.2660.0010.0010.0000.0000.0000.000
97D133SER00.022-0.02436.9550.0000.0000.0000.0000.0000.000
98D134ASP-1-0.895-0.95238.7340.0140.0140.0000.0000.0000.000
99D135ARG10.8410.92932.555-0.029-0.0290.0000.0000.0000.000
100D136ASP-1-0.799-0.92334.164-0.004-0.0040.0000.0000.0000.000
101D137PRO0-0.021-0.00134.6130.0000.0000.0000.0000.0000.000
102D138GLN0-0.088-0.04531.603-0.008-0.0080.0000.0000.0000.000
103D139HIS00.0730.03828.215-0.008-0.0080.0000.0000.0000.000
104D140ALA00.0510.03331.328-0.004-0.0040.0000.0000.0000.000
105D141ARG10.9900.99133.5900.0070.0070.0000.0000.0000.000
106D142ALA0-0.0100.00030.038-0.003-0.0030.0000.0000.0000.000
107D143ALA00.0600.03430.164-0.005-0.0050.0000.0000.0000.000
108D144PHE00.0150.00031.111-0.004-0.0040.0000.0000.0000.000
109D145SER0-0.042-0.01632.887-0.005-0.0050.0000.0000.0000.000
110D146ASP-1-0.842-0.93828.595-0.052-0.0520.0000.0000.0000.000
111D147PHE00.0430.01528.983-0.004-0.0040.0000.0000.0000.000
112D148SER0-0.031-0.02132.5550.0000.0000.0000.0000.0000.000
113D149LYS10.8520.91830.9290.0530.0530.0000.0000.0000.000
114D150LEU0-0.0260.00629.598-0.002-0.0020.0000.0000.0000.000
115D151VAL0-0.005-0.00932.456-0.001-0.0010.0000.0000.0000.000
116D152ARG10.8950.95235.8260.0430.0430.0000.0000.0000.000
117D153GLY0-0.0170.00134.5620.0000.0000.0000.0000.0000.000
118D154TYR0-0.002-0.01330.638-0.003-0.0030.0000.0000.0000.000
119D155PRO00.0360.02134.5970.0010.0010.0000.0000.0000.000
120D156ASN0-0.035-0.02136.7480.0050.0050.0000.0000.0000.000
121D157SER0-0.029-0.03930.432-0.001-0.0010.0000.0000.0000.000
122D158GLN00.0270.00328.5940.0010.0010.0000.0000.0000.000
123D159TYR00.0110.00625.7800.0060.0060.0000.0000.0000.000
124D160THR0-0.0100.01030.8420.0040.0040.0000.0000.0000.000
125D161THR00.0840.02734.1460.0020.0020.0000.0000.0000.000
126D162ASP-1-0.792-0.83831.168-0.014-0.0140.0000.0000.0000.000
127D163ALA00.0510.02531.8730.0030.0030.0000.0000.0000.000
128D164THR0-0.050-0.04333.3250.0030.0030.0000.0000.0000.000
129D165LYS10.9710.98835.8930.0080.0080.0000.0000.0000.000
130D166ARG10.8860.93529.0740.0160.0160.0000.0000.0000.000
131D167LEU0-0.0150.00234.7030.0020.0020.0000.0000.0000.000
132D168VAL0-0.037-0.01936.8980.0020.0020.0000.0000.0000.000
133D169PHE0-0.041-0.01634.3690.0020.0020.0000.0000.0000.000
134D170LEU00.027-0.00332.7140.0020.0020.0000.0000.0000.000
135D171LYS10.8580.92237.1760.0140.0140.0000.0000.0000.000
136D172ASP-1-0.789-0.91040.6760.0030.0030.0000.0000.0000.000
137D173ARG10.7940.91934.991-0.003-0.0030.0000.0000.0000.000
138D174LEU0-0.056-0.03437.1600.0010.0010.0000.0000.0000.000
139D175ALA00.0240.02240.5510.0000.0000.0000.0000.0000.000
140D176LYS10.9580.97140.300-0.008-0.0080.0000.0000.0000.000
141D177TYR0-0.045-0.00540.2940.0010.0010.0000.0000.0000.000
142D178GLU-1-0.878-0.92542.567-0.002-0.0020.0000.0000.0000.000
143D179TYR0-0.002-0.01545.8210.0010.0010.0000.0000.0000.000
144D180SER00.024-0.00344.4490.0010.0010.0000.0000.0000.000
145D181VAL0-0.0070.00545.1630.0000.0000.0000.0000.0000.000
146D182ALA0-0.026-0.02347.6880.0000.0000.0000.0000.0000.000
147D183GLU-1-0.899-0.91249.1210.0130.0130.0000.0000.0000.000
148D184TYR00.0590.03948.8360.0000.0000.0000.0000.0000.000
149D185TYR0-0.057-0.05849.5160.0000.0000.0000.0000.0000.000
150D186THR0-0.039-0.07253.271-0.001-0.0010.0000.0000.0000.000
151D187GLU-1-0.968-0.97452.1580.0140.0140.0000.0000.0000.000
152D188ARG10.7840.90653.908-0.010-0.0100.0000.0000.0000.000
153D189GLY00.0350.01655.8520.0000.0000.0000.0000.0000.000
154D190ALA0-0.078-0.03455.676-0.001-0.0010.0000.0000.0000.000
155D191TRP00.1210.05857.0530.0000.0000.0000.0000.0000.000
156D192VAL00.0310.00757.654-0.001-0.0010.0000.0000.0000.000
157D193ALA0-0.0010.00353.336-0.001-0.0010.0000.0000.0000.000
158D194VAL00.0340.03653.389-0.001-0.0010.0000.0000.0000.000
159D195VAL00.0310.01254.133-0.001-0.0010.0000.0000.0000.000
160D196ASN0-0.026-0.02953.679-0.002-0.0020.0000.0000.0000.000
161D197ARG10.9240.97645.9930.0000.0000.0000.0000.0000.000
162D198VAL00.007-0.00450.814-0.001-0.0010.0000.0000.0000.000
163D199GLU-1-0.960-0.97252.839-0.007-0.0070.0000.0000.0000.000
164D200GLY0-0.023-0.02350.246-0.001-0.0010.0000.0000.0000.000
165D201MET0-0.030-0.00247.727-0.001-0.0010.0000.0000.0000.000
166D202LEU0-0.005-0.00849.501-0.001-0.0010.0000.0000.0000.000
167D203ARG10.8820.95949.6100.0100.0100.0000.0000.0000.000
168D204ASP-1-0.926-0.96145.597-0.014-0.0140.0000.0000.0000.000
169D205TYR0-0.057-0.04442.190-0.002-0.0020.0000.0000.0000.000
170D206PRO00.0590.09647.1210.0020.0020.0000.0000.0000.000
171D207ASP-1-0.892-0.92947.260-0.010-0.0100.0000.0000.0000.000
172D208THR0-0.046-0.02744.6500.0010.0010.0000.0000.0000.000
173D209GLN00.0420.06546.838-0.001-0.0010.0000.0000.0000.000
174D210ALA00.0280.01045.8440.0010.0010.0000.0000.0000.000
175D211THR0-0.091-0.11447.9600.0000.0000.0000.0000.0000.000
176D212ARG10.8600.93850.4450.0020.0020.0000.0000.0000.000
177D213ASP-1-0.860-0.92350.1360.0060.0060.0000.0000.0000.000
178D214ALA00.005-0.00551.1140.0010.0010.0000.0000.0000.000
179D215LEU0-0.010-0.00253.1140.0000.0000.0000.0000.0000.000
180D216PRO00.0550.01955.8750.0000.0000.0000.0000.0000.000
181D217LEU00.0200.03153.3990.0000.0000.0000.0000.0000.000
182D218MET0-0.0190.02056.7250.0000.0000.0000.0000.0000.000
183D219GLU-1-0.891-0.96358.3470.0020.0020.0000.0000.0000.000
184D220ASN00.0240.00460.1290.0000.0000.0000.0000.0000.000
185D221ALA00.0470.01858.7040.0000.0000.0000.0000.0000.000
186D222TYR0-0.013-0.03460.2380.0000.0000.0000.0000.0000.000
187D223ARG10.8860.93663.735-0.002-0.0020.0000.0000.0000.000
188D224GLN0-0.055-0.01062.5730.0000.0000.0000.0000.0000.000
189D225MET0-0.075-0.02361.5740.0000.0000.0000.0000.0000.000
190D226GLN00.0100.01366.255-0.001-0.0010.0000.0000.0000.000
191D227MET0-0.0080.01264.0160.0000.0000.0000.0000.0000.000
192D228ASN00.0410.00067.2660.0000.0000.0000.0000.0000.000
193D229ALA00.0060.01168.9690.0000.0000.0000.0000.0000.000
194D230GLN0-0.021-0.01263.028-0.001-0.0010.0000.0000.0000.000
195D231ALA00.0300.00264.2650.0000.0000.0000.0000.0000.000
196D232GLU-1-0.918-0.95365.0630.0000.0000.0000.0000.0000.000
197D233LYS10.8740.93564.5510.0030.0030.0000.0000.0000.000
198D234VAL00.0090.01359.7960.0000.0000.0000.0000.0000.000
199D235ALA00.0780.04361.9920.0000.0000.0000.0000.0000.000
200D236LYS10.9150.96064.1630.0020.0020.0000.0000.0000.000
201D237ILE0-0.055-0.02658.7210.0000.0000.0000.0000.0000.000
202D238ILE0-0.021-0.00359.1410.0000.0000.0000.0000.0000.000
203D239ALA00.0030.00060.7590.0000.0000.0000.0000.0000.000
204D240ALA0-0.070-0.02163.0790.0000.0000.0000.0000.0000.000
205D241ASN0-0.049-0.03756.498-0.001-0.0010.0000.0000.0000.000
206D242SER00.0250.02056.2980.0000.0000.0000.0000.0000.000
207D243SER00.0760.03155.5810.0000.0000.0000.0000.0000.000
208D244ASN0-0.083-0.08151.157-0.001-0.0010.0000.0000.0000.000