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: 85QZY

Calculation Name: 1DEE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DEE

Chain ID: B

ChEMBL ID:

UniProt ID: P02976

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2295204.321267
FMO2-HF: Nuclear repulsion 2210180.078074
FMO2-HF: Total energy -85024.243193
FMO2-MP2: Total energy -85271.793694


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(B:501:GLN)


Summations of interaction energy for fragment #1(B:501:GLN)
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.
0.1021.9440.001-0.7-1.1410.001
Interaction energy analysis for fragmet #1(B:501:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.013
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].
3B503GLN0-0.012-0.0033.872-0.7010.7210.002-0.590-0.8340.001
4B504LEU0-0.019-0.0085.9660.2390.2390.0000.0000.0000.000
5B505VAL00.0190.0059.7110.0100.0100.0000.0000.0000.000
6B506GLU-1-0.786-0.88112.095-0.437-0.4370.0000.0000.0000.000
7B507SER0-0.016-0.01815.6710.0450.0450.0000.0000.0000.000
8B508GLY00.0340.00918.699-0.010-0.0100.0000.0000.0000.000
9B509GLY00.0080.00821.539-0.001-0.0010.0000.0000.0000.000
10B510GLY0-0.005-0.00623.1870.0170.0170.0000.0000.0000.000
11B511VAL0-0.014-0.01126.495-0.011-0.0110.0000.0000.0000.000
12B512VAL0-0.026-0.00630.0550.0100.0100.0000.0000.0000.000
13B513GLN00.0190.01632.712-0.001-0.0010.0000.0000.0000.000
14B514PRO00.028-0.01035.415-0.001-0.0010.0000.0000.0000.000
15B515GLY0-0.029-0.00236.7850.0060.0060.0000.0000.0000.000
16B516LYS10.8750.93833.9880.0630.0630.0000.0000.0000.000
17B517SER00.001-0.01831.801-0.005-0.0050.0000.0000.0000.000
18B518LEU0-0.043-0.01526.0220.0060.0060.0000.0000.0000.000
19B519ARG10.8700.93723.5940.0920.0920.0000.0000.0000.000
20B520LEU00.0150.03120.7520.0060.0060.0000.0000.0000.000
21B521SER00.010-0.01619.2300.0140.0140.0000.0000.0000.000
22B522CYS0-0.092-0.03814.2280.0030.0030.0000.0000.0000.000
23B523ALA00.0320.04612.678-0.002-0.0020.0000.0000.0000.000
24B524ALA00.008-0.00410.129-0.096-0.0960.0000.0000.0000.000
25B525SER0-0.011-0.0096.4740.2100.2100.0000.0000.0000.000
26B526GLY00.0650.0223.949-0.863-0.7160.001-0.093-0.0550.000
27B527PHE0-0.031-0.0194.5750.6530.813-0.001-0.012-0.1460.000
28B528THR00.0380.0167.6940.0300.0300.0000.0000.0000.000
29B529PHE00.0480.03211.496-0.029-0.0290.0000.0000.0000.000
30B530SER00.0190.00312.916-0.019-0.0190.0000.0000.0000.000
31B531GLY0-0.0170.00114.6450.0240.0240.0000.0000.0000.000
32B532TYR0-0.037-0.01811.185-0.056-0.0560.0000.0000.0000.000
33B533GLY00.0270.01815.5800.0270.0270.0000.0000.0000.000
34B534MET0-0.046-0.01212.783-0.078-0.0780.0000.0000.0000.000
35B535HIS00.0450.00916.6400.0620.0620.0000.0000.0000.000
36B536TRP00.008-0.00317.426-0.039-0.0390.0000.0000.0000.000
37B537VAL0-0.026-0.01218.6800.0220.0220.0000.0000.0000.000
38B538ARG10.7950.87120.0380.1840.1840.0000.0000.0000.000
39B539GLN00.0130.01321.037-0.029-0.0290.0000.0000.0000.000
40B540ALA00.0370.03023.6520.0090.0090.0000.0000.0000.000
41B541PRO00.023-0.00726.644-0.013-0.0130.0000.0000.0000.000
42B542GLY00.0300.03226.7770.0100.0100.0000.0000.0000.000
43B543LYS10.8480.92126.8710.2010.2010.0000.0000.0000.000
44B544GLY00.0630.03124.983-0.019-0.0190.0000.0000.0000.000
45B545LEU0-0.006-0.00519.1820.0100.0100.0000.0000.0000.000
46B546GLU-1-0.792-0.85523.343-0.183-0.1830.0000.0000.0000.000
47B547TRP0-0.005-0.00721.359-0.001-0.0010.0000.0000.0000.000
48B548VAL0-0.014-0.00522.9650.0250.0250.0000.0000.0000.000
49B549ALA00.026-0.00523.0190.0270.0270.0000.0000.0000.000
50B550LEU0-0.0370.00821.127-0.031-0.0310.0000.0000.0000.000
51B551ILE0-0.009-0.01320.1730.0330.0330.0000.0000.0000.000
52B552SER00.000-0.01420.391-0.033-0.0330.0000.0000.0000.000
53B553TYR0-0.012-0.02018.379-0.003-0.0030.0000.0000.0000.000
54B554ASP-1-0.743-0.82619.492-0.102-0.1020.0000.0000.0000.000
55B555GLU-1-0.882-0.94122.067-0.080-0.0800.0000.0000.0000.000
56B556SER0-0.021-0.01524.039-0.001-0.0010.0000.0000.0000.000
57B557ASN0-0.0090.00325.7500.0020.0020.0000.0000.0000.000
58B558LYS10.8580.91125.1610.1170.1170.0000.0000.0000.000
59B559TYR0-0.031-0.01225.8140.0100.0100.0000.0000.0000.000
60B560TYR00.0270.00826.175-0.014-0.0140.0000.0000.0000.000
61B561ALA00.0720.05227.7110.0060.0060.0000.0000.0000.000
62B562ASP-1-0.845-0.92529.314-0.129-0.1290.0000.0000.0000.000
63B563SER0-0.040-0.02429.8350.0110.0110.0000.0000.0000.000
64B564VAL0-0.007-0.01227.7090.0080.0080.0000.0000.0000.000
65B565LYS10.8810.93331.1360.1240.1240.0000.0000.0000.000
66B566GLY0-0.0080.00632.5870.0060.0060.0000.0000.0000.000
67B567ARG10.7300.83431.8950.1320.1320.0000.0000.0000.000
68B568PHE00.010-0.00926.9230.0040.0040.0000.0000.0000.000
69B569THR0-0.047-0.03328.1990.0090.0090.0000.0000.0000.000
70B570ILE0-0.0020.01820.7830.0020.0020.0000.0000.0000.000
71B571SER0-0.032-0.02423.2030.0180.0180.0000.0000.0000.000
72B572ARG10.7900.88616.3130.1830.1830.0000.0000.0000.000
73B573ASP-1-0.714-0.80619.214-0.004-0.0040.0000.0000.0000.000
74B574ASN0-0.003-0.02917.482-0.031-0.0310.0000.0000.0000.000
75B575SER0-0.083-0.05317.3890.0210.0210.0000.0000.0000.000
76B576LYS10.8510.90916.5060.0230.0230.0000.0000.0000.000
77B577ASN0-0.0110.00812.139-0.029-0.0290.0000.0000.0000.000
78B578THR00.0160.00613.437-0.060-0.0600.0000.0000.0000.000
79B579LEU0-0.0070.00216.0830.0240.0240.0000.0000.0000.000
80B580TYR00.007-0.01717.9680.0110.0110.0000.0000.0000.000
81B581LEU00.0160.00421.225-0.010-0.0100.0000.0000.0000.000
82B582GLN00.0250.03323.7470.0080.0080.0000.0000.0000.000
83B583MET0-0.019-0.00125.656-0.012-0.0120.0000.0000.0000.000
84B584ASN00.0500.01829.1210.0140.0140.0000.0000.0000.000
85B585SER00.0150.01032.933-0.003-0.0030.0000.0000.0000.000
86B586LEU0-0.0130.01429.407-0.005-0.0050.0000.0000.0000.000
87B587ARG10.8740.90833.2520.1270.1270.0000.0000.0000.000
88B588ALA00.0540.02733.173-0.006-0.0060.0000.0000.0000.000
89B589GLU-1-0.814-0.90032.778-0.125-0.1250.0000.0000.0000.000
90B590ASP-1-0.770-0.83029.348-0.150-0.1500.0000.0000.0000.000
91B591THR0-0.0070.00628.082-0.006-0.0060.0000.0000.0000.000
92B592ALA0-0.011-0.01124.756-0.005-0.0050.0000.0000.0000.000
93B593VAL00.0200.02319.1850.0160.0160.0000.0000.0000.000
94B594TYR0-0.028-0.03820.608-0.014-0.0140.0000.0000.0000.000
95B595TYR00.0250.00015.4960.0070.0070.0000.0000.0000.000
96B597ALA00.002-0.00712.802-0.089-0.0890.0000.0000.0000.000
97B598LYS10.8360.9099.2570.9170.9170.0000.0000.0000.000
98B599VAL00.0160.01412.883-0.070-0.0700.0000.0000.0000.000
99B600LYS10.8660.9299.7091.1541.1540.0000.0000.0000.000
100B601PHE00.026-0.00613.5820.0060.0060.0000.0000.0000.000
101B602TYR0-0.004-0.01016.305-0.007-0.0070.0000.0000.0000.000
102B603ASP-1-0.796-0.88119.409-0.220-0.2200.0000.0000.0000.000
103B604PRO0-0.026-0.01621.143-0.027-0.0270.0000.0000.0000.000
104B605THR0-0.071-0.04822.774-0.013-0.0130.0000.0000.0000.000
105B606ALA0-0.0370.00117.449-0.031-0.0310.0000.0000.0000.000
106B607PRO0-0.0050.00615.919-0.012-0.0120.0000.0000.0000.000
107B608ASN00.026-0.01614.506-0.051-0.0510.0000.0000.0000.000
108B609ASP-1-0.795-0.88010.275-1.101-1.1010.0000.0000.0000.000
109B610TYR0-0.0150.0004.610-0.0560.057-0.001-0.005-0.1060.000
110B611TRP0-0.005-0.0279.0820.2680.2680.0000.0000.0000.000
111B612GLY00.0400.0259.636-0.160-0.1600.0000.0000.0000.000
112B613GLN0-0.050-0.02710.769-0.061-0.0610.0000.0000.0000.000
113B614GLY0-0.0100.00012.9520.0320.0320.0000.0000.0000.000
114B615THR0-0.044-0.03116.4250.0450.0450.0000.0000.0000.000
115B616LEU0-0.0210.00219.484-0.005-0.0050.0000.0000.0000.000
116B617VAL00.0050.01322.9010.0170.0170.0000.0000.0000.000
117B618THR0-0.048-0.03425.847-0.004-0.0040.0000.0000.0000.000
118B619VAL00.0000.00729.3500.0100.0100.0000.0000.0000.000
119B620SER0-0.016-0.03832.4710.0000.0000.0000.0000.0000.000
120B621SER00.0300.00235.7020.0020.0020.0000.0000.0000.000
121B622GLY0-0.0020.01438.6280.0050.0050.0000.0000.0000.000
122B623SER00.019-0.00137.138-0.003-0.0030.0000.0000.0000.000
123B624ALA0-0.011-0.00233.144-0.003-0.0030.0000.0000.0000.000
124B625SER00.0250.00234.8140.0050.0050.0000.0000.0000.000
125B626ALA00.0080.00735.018-0.006-0.0060.0000.0000.0000.000
126B627PRO0-0.033-0.00134.3840.0000.0000.0000.0000.0000.000
127B628THR00.0150.00437.2140.0060.0060.0000.0000.0000.000
128B629LEU0-0.013-0.00237.265-0.004-0.0040.0000.0000.0000.000
129B630PHE0-0.003-0.00141.0880.0050.0050.0000.0000.0000.000
130B631PRO00.0280.02142.945-0.004-0.0040.0000.0000.0000.000
131B632LEU0-0.047-0.02142.088-0.001-0.0010.0000.0000.0000.000
132B633VAL00.0420.01145.588-0.001-0.0010.0000.0000.0000.000
133B634SER00.0010.01348.2820.0000.0000.0000.0000.0000.000
134B635CYS0-0.027-0.03049.8290.0020.0020.0000.0000.0000.000
135B636GLU-1-0.892-0.94053.469-0.041-0.0410.0000.0000.0000.000
136B637ASN00.0090.02350.971-0.001-0.0010.0000.0000.0000.000
137B638SER0-0.023-0.01648.763-0.002-0.0020.0000.0000.0000.000
138B639ASN00.014-0.00850.984-0.001-0.0010.0000.0000.0000.000
139B640PRO0-0.038-0.00352.6410.0010.0010.0000.0000.0000.000
140B641SER00.014-0.00547.391-0.004-0.0040.0000.0000.0000.000
141B642SER00.0140.00647.5160.0030.0030.0000.0000.0000.000
142B643THR0-0.083-0.03343.1380.0000.0000.0000.0000.0000.000
143B644VAL00.0480.04146.303-0.003-0.0030.0000.0000.0000.000
144B645ALA0-0.001-0.00544.248-0.002-0.0020.0000.0000.0000.000
145B646VAL00.0170.02443.0290.0020.0020.0000.0000.0000.000
146B647GLY00.019-0.01740.987-0.005-0.0050.0000.0000.0000.000
147B648CYS0-0.084-0.00238.3360.0020.0020.0000.0000.0000.000
148B649LEU00.0110.01738.961-0.006-0.0060.0000.0000.0000.000
149B650ALA00.0340.02236.1540.0050.0050.0000.0000.0000.000
150B651GLN0-0.009-0.03138.033-0.005-0.0050.0000.0000.0000.000
151B652ASP-1-0.784-0.88739.331-0.060-0.0600.0000.0000.0000.000
152B653PHE0-0.0280.01431.9550.0040.0040.0000.0000.0000.000
153B654LEU0-0.0090.00532.862-0.007-0.0070.0000.0000.0000.000
154B655PRO00.0440.01428.2480.0090.0090.0000.0000.0000.000
155B656ASP-1-0.812-0.89328.521-0.137-0.1370.0000.0000.0000.000
156B657SER0-0.042-0.03526.303-0.012-0.0120.0000.0000.0000.000
157B658ILE00.0190.02227.5640.0130.0130.0000.0000.0000.000
158B659THR0-0.044-0.02426.734-0.012-0.0120.0000.0000.0000.000
159B660PHE00.0250.00329.1710.0100.0100.0000.0000.0000.000
160B661SER0-0.029-0.00431.005-0.001-0.0010.0000.0000.0000.000
161B662TRP00.0410.00333.3100.0040.0040.0000.0000.0000.000
162B663LYS10.8020.89433.8930.0340.0340.0000.0000.0000.000
163B664TYR00.0560.02638.919-0.002-0.0020.0000.0000.0000.000
164B665LYS10.8630.92542.4000.0260.0260.0000.0000.0000.000
165B666ASN0-0.0170.01742.6720.0010.0010.0000.0000.0000.000
166B667ASN0-0.021-0.01138.7610.0000.0000.0000.0000.0000.000
167B668SER0-0.002-0.01638.1520.0010.0010.0000.0000.0000.000
168B669ASP-1-0.814-0.90933.889-0.043-0.0430.0000.0000.0000.000
169B670ILE00.0000.01336.4190.0000.0000.0000.0000.0000.000
170B671SER00.016-0.00734.071-0.003-0.0030.0000.0000.0000.000
171B672SER0-0.048-0.02234.416-0.007-0.0070.0000.0000.0000.000
172B673THR00.0130.00633.6740.0000.0000.0000.0000.0000.000
173B674ARG10.9230.96032.6550.1120.1120.0000.0000.0000.000
174B675GLY00.0210.02632.1370.0090.0090.0000.0000.0000.000
175B676PHE0-0.044-0.01732.345-0.009-0.0090.0000.0000.0000.000
176B677PRO00.007-0.00730.1180.0030.0030.0000.0000.0000.000
177B678SER0-0.020-0.03330.6960.0110.0110.0000.0000.0000.000
178B679VAL0-0.029-0.00932.813-0.007-0.0070.0000.0000.0000.000
179B680LEU00.0190.01234.1910.0060.0060.0000.0000.0000.000
180B681ARG10.9490.98436.2930.0760.0760.0000.0000.0000.000
181B682GLY00.0070.00039.7970.0050.0050.0000.0000.0000.000
182B683GLY00.0180.00837.2420.0040.0040.0000.0000.0000.000
183B684LYS10.7990.91636.1970.0620.0620.0000.0000.0000.000
184B685TYR0-0.005-0.01331.473-0.008-0.0080.0000.0000.0000.000
185B686ALA0-0.023-0.01235.7680.0080.0080.0000.0000.0000.000
186B687ALA00.0270.01933.584-0.008-0.0080.0000.0000.0000.000
187B688THR00.0050.00235.5900.0090.0090.0000.0000.0000.000
188B689SER0-0.037-0.01635.005-0.006-0.0060.0000.0000.0000.000
189B690GLN00.015-0.01636.6280.0000.0000.0000.0000.0000.000
190B691VAL00.0210.01537.607-0.004-0.0040.0000.0000.0000.000
191B692LEU0-0.0150.00339.4560.0010.0010.0000.0000.0000.000
192B693LEU00.0350.03141.507-0.001-0.0010.0000.0000.0000.000
193B694PRO00.006-0.00443.5500.0000.0000.0000.0000.0000.000
194B695SER00.025-0.02446.3280.0020.0020.0000.0000.0000.000
195B696LYS10.9160.97449.5600.0470.0470.0000.0000.0000.000
196B697ASP-1-0.848-0.91451.180-0.033-0.0330.0000.0000.0000.000
197B698VAL0-0.084-0.05947.6160.0020.0020.0000.0000.0000.000
198B699ALA0-0.0260.00149.009-0.001-0.0010.0000.0000.0000.000
199B700GLN00.0560.03649.561-0.002-0.0020.0000.0000.0000.000
200B701GLY00.0070.00950.8700.0010.0010.0000.0000.0000.000
201B702THR0-0.020-0.01451.3270.0000.0000.0000.0000.0000.000
202B703ASN0-0.019-0.00546.5820.0010.0010.0000.0000.0000.000
203B704GLU-1-0.793-0.89949.567-0.026-0.0260.0000.0000.0000.000
204B705HIS0-0.042-0.02545.938-0.001-0.0010.0000.0000.0000.000
205B706VAL00.0020.01642.3390.0010.0010.0000.0000.0000.000
206B707VAL00.016-0.00140.4040.0000.0000.0000.0000.0000.000
207B709LYS10.8420.89135.2360.0330.0330.0000.0000.0000.000
208B710VAL0-0.008-0.01133.029-0.007-0.0070.0000.0000.0000.000
209B711GLN00.0270.00828.4790.0110.0110.0000.0000.0000.000
210B712HIS00.019-0.02129.897-0.003-0.0030.0000.0000.0000.000
211B713PRO00.0030.00826.9360.0090.0090.0000.0000.0000.000
212B714ASN0-0.036-0.00529.5150.0100.0100.0000.0000.0000.000
213B715GLY00.0180.01232.7000.0050.0050.0000.0000.0000.000
214B716ASN00.0530.02330.887-0.009-0.0090.0000.0000.0000.000
215B717LYS10.8300.91834.3160.0450.0450.0000.0000.0000.000
216B718GLU-1-0.795-0.88836.888-0.031-0.0310.0000.0000.0000.000
217B719LYS10.8460.91139.5440.0430.0430.0000.0000.0000.000
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