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: 856RY

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2253634.567708
FMO2-HF: Nuclear repulsion 2169498.419471
FMO2-HF: Total energy -84136.148237
FMO2-MP2: Total energy -84381.182034


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.
-10.152-2.2858.203-5.643-10.427-0.044
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 : -0.024 / q_NPA : -0.021
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-1-0.859-0.9302.914-5.673-3.1280.237-1.375-1.407-0.008
4D30ASN0-0.045-0.0285.3480.3650.3650.0000.0000.0000.000
5D31PRO00.0290.0186.456-0.193-0.1930.0000.0000.0000.000
6D32PRO00.0450.0087.3650.0060.0060.0000.0000.0000.000
7D33ASN00.008-0.0018.4340.0070.0070.0000.0000.0000.000
8D34GLU-1-0.832-0.9037.964-0.247-0.2470.0000.0000.0000.000
9D35ILE00.0090.0272.756-0.5150.0600.172-0.123-0.6230.000
10D36TYR0-0.037-0.0366.4400.0570.0570.0000.0000.0000.000
11D37ALA00.0060.0058.8040.0640.0640.0000.0000.0000.000
12D38THR0-0.016-0.0296.1140.1040.1040.0000.0000.0000.000
13D39ALA0-0.022-0.0146.9020.0720.0720.0000.0000.0000.000
14D40GLN0-0.006-0.0208.5000.1060.1060.0000.0000.0000.000
15D41GLN0-0.133-0.05211.1370.0530.0530.0000.0000.0000.000
16D42LYS10.9400.9717.487-0.276-0.2760.0000.0000.0000.000
17D43LEU0-0.047-0.02511.4150.0230.0230.0000.0000.0000.000
18D44GLN0-0.031-0.01213.3280.0300.0300.0000.0000.0000.000
19D45ASP-1-0.904-0.94913.5720.0980.0980.0000.0000.0000.000
20D46GLY00.0010.00215.7270.0170.0170.0000.0000.0000.000
21D47ASN0-0.029-0.01211.9200.0110.0110.0000.0000.0000.000
22D48TRP00.0410.01310.946-0.004-0.0040.0000.0000.0000.000
23D49ARG10.8980.9288.884-0.022-0.0220.0000.0000.0000.000
24D50GLN00.0100.0066.661-0.039-0.0390.0000.0000.0000.000
25D51ALA00.0370.0226.032-0.099-0.0990.0000.0000.0000.000
26D52ILE0-0.023-0.0076.955-0.179-0.1790.0000.0000.0000.000
27D53THR00.0050.0142.690-0.726-0.0500.448-0.272-0.8510.000
28D54GLN0-0.023-0.0192.235-6.026-3.3874.690-2.676-4.653-0.033
29D55LEU00.0170.0083.554-0.208-0.186-0.0010.136-0.1570.000
30D56GLU-1-0.822-0.8934.810-0.710-0.7100.0000.0000.0000.000
31D57ALA00.0010.0072.379-0.356-0.2272.309-0.772-1.667-0.002
32D58LEU0-0.036-0.0184.2950.1230.281-0.001-0.036-0.1220.000
33D59ASP-1-0.821-0.8976.659-0.418-0.4180.0000.0000.0000.000
34D60ASN0-0.060-0.0427.5040.2370.2370.0000.0000.0000.000
35D61ARG10.7890.8842.4603.2014.3240.349-0.525-0.947-0.001
36D62TYR0-0.034-0.0247.4280.1840.1840.0000.0000.0000.000
37D63PRO00.0250.01311.4140.0620.0620.0000.0000.0000.000
38D64PHE0-0.032-0.01013.4600.0480.0480.0000.0000.0000.000
39D65GLY00.0180.02114.5110.0320.0320.0000.0000.0000.000
40D66PRO0-0.005-0.01015.5930.0110.0110.0000.0000.0000.000
41D67TYR00.0040.00712.6790.0200.0200.0000.0000.0000.000
42D68SER0-0.006-0.00513.234-0.012-0.0120.0000.0000.0000.000
43D69GLN00.030-0.00413.896-0.042-0.0420.0000.0000.0000.000
44D70GLN0-0.020-0.01714.9720.0280.0280.0000.0000.0000.000
45D71VAL00.0180.0149.0620.0100.0100.0000.0000.0000.000
46D72GLN0-0.043-0.03511.9840.0410.0410.0000.0000.0000.000
47D73LEU0-0.041-0.01514.0060.0290.0290.0000.0000.0000.000
48D74ASP-1-0.793-0.87812.152-0.282-0.2820.0000.0000.0000.000
49D75LEU0-0.026-0.0148.2860.0300.0300.0000.0000.0000.000
50D76ILE0-0.023-0.00312.1490.0420.0420.0000.0000.0000.000
51D77TYR0-0.014-0.00915.7290.0400.0400.0000.0000.0000.000
52D78ALA00.0300.00611.6380.0330.0330.0000.0000.0000.000
53D79TYR0-0.054-0.0799.5640.0470.0470.0000.0000.0000.000
54D80TYR0-0.023-0.00614.0830.0370.0370.0000.0000.0000.000
55D81LYS10.8930.95716.5140.0760.0760.0000.0000.0000.000
56D82ASN0-0.050-0.03513.1540.0430.0430.0000.0000.0000.000
57D83ALA00.0140.01615.6470.0170.0170.0000.0000.0000.000
58D84ASP-1-0.773-0.83412.951-0.095-0.0950.0000.0000.0000.000
59D85LEU0-0.004-0.01916.270-0.032-0.0320.0000.0000.0000.000
60D86PRO00.012-0.01018.475-0.012-0.0120.0000.0000.0000.000
61D87LEU00.0080.01212.311-0.009-0.0090.0000.0000.0000.000
62D88ALA00.0330.02015.849-0.028-0.0280.0000.0000.0000.000
63D89GLN0-0.010-0.00917.218-0.012-0.0120.0000.0000.0000.000
64D90ALA00.0080.00716.970-0.004-0.0040.0000.0000.0000.000
65D91ALA0-0.027-0.00614.773-0.021-0.0210.0000.0000.0000.000
66D92ILE00.0330.00816.675-0.002-0.0020.0000.0000.0000.000
67D93ASP-1-0.782-0.87420.109-0.138-0.1380.0000.0000.0000.000
68D94ARG10.8050.91512.9690.4210.4210.0000.0000.0000.000
69D95PHE00.0440.02018.0650.0070.0070.0000.0000.0000.000
70D96ILE0-0.002-0.01420.3360.0100.0100.0000.0000.0000.000
71D97ARG10.8860.92821.4710.1960.1960.0000.0000.0000.000
72D98LEU0-0.0020.01619.2410.0050.0050.0000.0000.0000.000
73D99ASN0-0.047-0.02522.030-0.002-0.0020.0000.0000.0000.000
74D100PRO00.0530.03624.1120.0020.0020.0000.0000.0000.000
75D101THR0-0.029-0.02527.1140.0060.0060.0000.0000.0000.000
76D102HIS00.0380.03621.2500.0120.0120.0000.0000.0000.000
77D103PRO0-0.005-0.01824.9390.0070.0070.0000.0000.0000.000
78D104ASN00.0260.02122.2800.0130.0130.0000.0000.0000.000
79D105ILE00.0080.00224.395-0.005-0.0050.0000.0000.0000.000
80D106ASP-1-0.795-0.86626.190-0.103-0.1030.0000.0000.0000.000
81D107TYR00.0380.00919.572-0.001-0.0010.0000.0000.0000.000
82D108VAL00.0060.01020.9490.0010.0010.0000.0000.0000.000
83D109MET0-0.031-0.02223.2100.0030.0030.0000.0000.0000.000
84D110TYR0-0.062-0.04525.1290.0060.0060.0000.0000.0000.000
85D111MET00.0190.01519.1840.0120.0120.0000.0000.0000.000
86D112ARG10.7760.90023.1000.1250.1250.0000.0000.0000.000
87D113GLY00.0510.02324.4780.0060.0060.0000.0000.0000.000
88D114LEU0-0.020-0.01624.2370.0080.0080.0000.0000.0000.000
89D115THR0-0.019-0.03021.1990.0050.0050.0000.0000.0000.000
90D116ASN0-0.044-0.02823.5110.0100.0100.0000.0000.0000.000
91D117MET0-0.021-0.01226.7380.0060.0060.0000.0000.0000.000
92D118ALA0-0.046-0.01823.9380.0070.0070.0000.0000.0000.000
93D119LEU0-0.025-0.00723.4610.0050.0050.0000.0000.0000.000
94D120ASP-1-0.797-0.86926.780-0.030-0.0300.0000.0000.0000.000
95D121ASP-1-0.875-0.90429.351-0.005-0.0050.0000.0000.0000.000
96D122SER00.0100.00330.9270.0040.0040.0000.0000.0000.000
97D133SER00.026-0.01536.3830.0010.0010.0000.0000.0000.000
98D134ASP-1-0.857-0.91338.058-0.012-0.0120.0000.0000.0000.000
99D135ARG10.8260.89731.7120.0110.0110.0000.0000.0000.000
100D136ASP-1-0.748-0.86133.173-0.040-0.0400.0000.0000.0000.000
101D137PRO00.0150.02434.563-0.002-0.0020.0000.0000.0000.000
102D138GLN0-0.079-0.05731.683-0.007-0.0070.0000.0000.0000.000
103D139HIS00.0040.01029.313-0.009-0.0090.0000.0000.0000.000
104D140ALA00.0540.02531.051-0.005-0.0050.0000.0000.0000.000
105D141ARG10.8340.89333.4250.0330.0330.0000.0000.0000.000
106D142ALA00.0010.01029.755-0.002-0.0020.0000.0000.0000.000
107D143ALA00.0360.00929.782-0.004-0.0040.0000.0000.0000.000
108D144PHE0-0.0070.00230.734-0.002-0.0020.0000.0000.0000.000
109D145SER00.0250.01532.882-0.002-0.0020.0000.0000.0000.000
110D146ASP-1-0.822-0.89928.321-0.096-0.0960.0000.0000.0000.000
111D147PHE00.0360.00128.719-0.003-0.0030.0000.0000.0000.000
112D148SER0-0.030-0.02632.2780.0020.0020.0000.0000.0000.000
113D149LYS10.7410.85130.7230.0850.0850.0000.0000.0000.000
114D150LEU0-0.0260.00129.4470.0000.0000.0000.0000.0000.000
115D151VAL00.015-0.00332.3050.0000.0000.0000.0000.0000.000
116D152ARG10.9230.96735.7640.0650.0650.0000.0000.0000.000
117D153GLY0-0.0090.01034.4220.0010.0010.0000.0000.0000.000
118D154TYR00.016-0.00730.300-0.002-0.0020.0000.0000.0000.000
119D155PRO00.0380.02834.3650.0010.0010.0000.0000.0000.000
120D156ASN0-0.019-0.01636.3530.0030.0030.0000.0000.0000.000
121D157SER0-0.021-0.02930.1210.0000.0000.0000.0000.0000.000
122D158GLN00.0300.01127.5270.0000.0000.0000.0000.0000.000
123D159TYR0-0.006-0.01125.7080.0020.0020.0000.0000.0000.000
124D160THR0-0.046-0.01730.6720.0030.0030.0000.0000.0000.000
125D161THR00.0490.01834.0720.0020.0020.0000.0000.0000.000
126D162ASP-1-0.771-0.83030.228-0.049-0.0490.0000.0000.0000.000
127D163ALA00.0480.02531.7450.0020.0020.0000.0000.0000.000
128D164THR0-0.049-0.03133.1720.0030.0030.0000.0000.0000.000
129D165LYS10.9420.96935.5040.0320.0320.0000.0000.0000.000
130D166ARG10.8600.90129.4570.0520.0520.0000.0000.0000.000
131D167LEU0-0.0110.00234.4770.0020.0020.0000.0000.0000.000
132D168VAL00.000-0.00136.7330.0020.0020.0000.0000.0000.000
133D169PHE0-0.017-0.00634.2670.0020.0020.0000.0000.0000.000
134D170LEU00.004-0.00232.4050.0020.0020.0000.0000.0000.000
135D171LYS10.8560.91136.8210.0330.0330.0000.0000.0000.000
136D172ASP-1-0.741-0.87440.365-0.019-0.0190.0000.0000.0000.000
137D173ARG10.6740.80934.2820.0310.0310.0000.0000.0000.000
138D174LEU0-0.034-0.02136.9330.0010.0010.0000.0000.0000.000
139D175ALA00.0140.01540.3170.0010.0010.0000.0000.0000.000
140D176LYS10.8950.91340.3490.0200.0200.0000.0000.0000.000
141D177TYR0-0.0430.00540.0700.0010.0010.0000.0000.0000.000
142D178GLU-1-0.812-0.90042.202-0.025-0.0250.0000.0000.0000.000
143D179TYR0-0.074-0.05945.2740.0010.0010.0000.0000.0000.000
144D180SER00.017-0.00243.3630.0010.0010.0000.0000.0000.000
145D181VAL0-0.0060.00144.3710.0010.0010.0000.0000.0000.000
146D182ALA0-0.011-0.01147.0960.0010.0010.0000.0000.0000.000
147D183GLU-1-0.843-0.89248.836-0.007-0.0070.0000.0000.0000.000
148D184TYR00.0560.03348.5330.0010.0010.0000.0000.0000.000
149D185TYR0-0.045-0.04349.3190.0000.0000.0000.0000.0000.000
150D186THR0-0.046-0.04352.8980.0000.0000.0000.0000.0000.000
151D187GLU-1-0.939-0.96751.489-0.003-0.0030.0000.0000.0000.000
152D188ARG10.8160.91653.4990.0060.0060.0000.0000.0000.000
153D189GLY00.0510.02755.5250.0010.0010.0000.0000.0000.000
154D190ALA0-0.049-0.01155.0210.0000.0000.0000.0000.0000.000
155D191TRP00.0470.00356.364-0.001-0.0010.0000.0000.0000.000
156D192VAL00.0510.01357.367-0.001-0.0010.0000.0000.0000.000
157D193ALA0-0.0020.00952.680-0.001-0.0010.0000.0000.0000.000
158D194VAL0-0.0020.01552.982-0.001-0.0010.0000.0000.0000.000
159D195VAL0-0.015-0.01453.905-0.001-0.0010.0000.0000.0000.000
160D196ASN0-0.039-0.02353.325-0.002-0.0020.0000.0000.0000.000
161D197ARG10.9360.97244.9950.0200.0200.0000.0000.0000.000
162D198VAL00.0030.00150.392-0.001-0.0010.0000.0000.0000.000
163D199GLU-1-0.873-0.92752.695-0.024-0.0240.0000.0000.0000.000
164D200GLY00.0420.01449.731-0.001-0.0010.0000.0000.0000.000
165D201MET0-0.070-0.02946.977-0.001-0.0010.0000.0000.0000.000
166D202LEU0-0.005-0.01349.412-0.001-0.0010.0000.0000.0000.000
167D203ARG10.7040.84348.3130.0260.0260.0000.0000.0000.000
168D204ASP-1-0.842-0.89545.604-0.032-0.0320.0000.0000.0000.000
169D205TYR0-0.041-0.02641.730-0.003-0.0030.0000.0000.0000.000
170D206PRO00.0230.03246.8780.0010.0010.0000.0000.0000.000
171D207ASP-1-0.870-0.90646.380-0.028-0.0280.0000.0000.0000.000
172D208THR0-0.088-0.04344.3860.0010.0010.0000.0000.0000.000
173D209GLN0-0.0140.01046.2820.0010.0010.0000.0000.0000.000
174D210ALA00.0500.01745.8050.0010.0010.0000.0000.0000.000
175D211THR0-0.011-0.03047.8020.0010.0010.0000.0000.0000.000
176D212ARG10.8540.93950.1960.0180.0180.0000.0000.0000.000
177D213ASP-1-0.837-0.91049.788-0.011-0.0110.0000.0000.0000.000
178D214ALA00.0270.00950.7640.0010.0010.0000.0000.0000.000
179D215LEU0-0.0110.00252.7390.0000.0000.0000.0000.0000.000
180D216PRO00.0430.00855.6870.0000.0000.0000.0000.0000.000
181D217LEU00.0070.02552.4160.0010.0010.0000.0000.0000.000
182D218MET0-0.0210.00256.2510.0000.0000.0000.0000.0000.000
183D219GLU-1-0.809-0.90657.856-0.009-0.0090.0000.0000.0000.000
184D220ASN00.0340.01559.4800.0010.0010.0000.0000.0000.000
185D221ALA00.0240.01958.4330.0000.0000.0000.0000.0000.000
186D222TYR00.020-0.02159.5000.0000.0000.0000.0000.0000.000
187D223ARG10.7750.86363.2310.0090.0090.0000.0000.0000.000
188D224GLN0-0.032-0.00762.6510.0010.0010.0000.0000.0000.000
189D225MET0-0.085-0.03360.8950.0000.0000.0000.0000.0000.000
190D226GLN00.0110.01165.6080.0000.0000.0000.0000.0000.000
191D227MET00.0150.03264.0120.0000.0000.0000.0000.0000.000
192D228ASN00.027-0.00967.0080.0000.0000.0000.0000.0000.000
193D229ALA00.0100.00668.5540.0000.0000.0000.0000.0000.000
194D230GLN0-0.0090.00861.9580.0000.0000.0000.0000.0000.000
195D231ALA00.0380.00963.7840.0000.0000.0000.0000.0000.000
196D232GLU-1-0.826-0.90664.558-0.009-0.0090.0000.0000.0000.000
197D233LYS10.8340.91964.2580.0140.0140.0000.0000.0000.000
198D234VAL00.0170.00859.3320.0000.0000.0000.0000.0000.000
199D235ALA00.0520.03661.6770.0000.0000.0000.0000.0000.000
200D236LYS10.8250.90363.9910.0100.0100.0000.0000.0000.000
201D237ILE0-0.024-0.00958.3290.0000.0000.0000.0000.0000.000
202D238ILE0-0.017-0.00558.6250.0000.0000.0000.0000.0000.000
203D239ALA0-0.019-0.01160.4250.0000.0000.0000.0000.0000.000
204D240ALA0-0.0380.00162.2750.0000.0000.0000.0000.0000.000
205D241ASN0-0.046-0.04156.062-0.001-0.0010.0000.0000.0000.000
206D242SER00.0230.02855.5950.0010.0010.0000.0000.0000.000
207D243SER00.0460.01554.876-0.001-0.0010.0000.0000.0000.000
208D244ASN0-0.032-0.03550.536-0.001-0.0010.0000.0000.0000.000