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: 9Y6L2

Calculation Name: 1FLK-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FLK

Chain ID: A

ChEMBL ID:

UniProt ID: Q13114

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2113231.307149
FMO2-HF: Nuclear repulsion 2030803.424782
FMO2-HF: Total energy -82427.882367
FMO2-MP2: Total energy -82664.66014


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:299:ACE )


Summations of interaction energy for fragment #1(A:299:ACE )
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.
0.8682.048-0.004-0.513-0.663-0.001
Interaction energy analysis for fragmet #1(A:299:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.011
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].
3A301GLU -1-0.806-0.8973.7970.4781.658-0.004-0.513-0.663-0.001
4A302SER 0-0.025-0.0155.7050.1040.1040.0000.0000.0000.000
5A303VAL 0-0.086-0.0836.7520.1560.1560.0000.0000.0000.000
6A304ASP -1-0.764-0.8997.620-0.948-0.9480.0000.0000.0000.000
7A305LYS 10.8860.9388.4620.4820.4820.0000.0000.0000.000
8A306SER 0-0.095-0.00510.6400.1100.1100.0000.0000.0000.000
9A307ALA 0-0.030-0.0219.4150.1260.1260.0000.0000.0000.000
10A308GLY 00.1220.0589.785-0.155-0.1550.0000.0000.0000.000
11A309GLN 0-0.0300.01812.0900.1190.1190.0000.0000.0000.000
12A310VAL 00.028-0.01714.7230.0670.0670.0000.0000.0000.000
13A311ALA 00.0140.00614.9200.0450.0450.0000.0000.0000.000
14A312ARG 10.9150.97116.8240.2020.2020.0000.0000.0000.000
15A313ASN 00.0400.00319.3210.0390.0390.0000.0000.0000.000
16A314THR 00.014-0.01419.2200.0190.0190.0000.0000.0000.000
17A315GLY 00.0250.02121.6830.0150.0150.0000.0000.0000.000
18A316LEU 0-0.078-0.00323.2270.0160.0160.0000.0000.0000.000
19A317LEU 00.0010.01423.6610.0120.0120.0000.0000.0000.000
20A318GLU -1-0.835-0.91623.420-0.104-0.1040.0000.0000.0000.000
21A319SER 0-0.009-0.02827.0440.0100.0100.0000.0000.0000.000
22A320GLN 0-0.065-0.03929.4940.0130.0130.0000.0000.0000.000
23A321LEU 00.0150.00228.7210.0060.0060.0000.0000.0000.000
24A322SER 00.0150.00231.4110.0060.0060.0000.0000.0000.000
25A323ARG 10.8690.94533.0700.0680.0680.0000.0000.0000.000
26A324HIS 0-0.009-0.02434.7270.0070.0070.0000.0000.0000.000
27A325ASP -1-0.882-0.93034.951-0.045-0.0450.0000.0000.0000.000
28A326GLN 00.0560.02536.8610.0010.0010.0000.0000.0000.000
29A327MET 0-0.0290.05539.5550.0040.0040.0000.0000.0000.000
30A328LEU 00.0560.03138.8910.0030.0030.0000.0000.0000.000
31A329SER 0-0.006-0.00941.4990.0020.0020.0000.0000.0000.000
32A330VAL 0-0.012-0.03243.3710.0020.0020.0000.0000.0000.000
33A331HIS 0-0.136-0.11444.7150.0020.0020.0000.0000.0000.000
34A332ASP -1-0.896-0.94545.487-0.028-0.0280.0000.0000.0000.000
35A333ILE 0-0.043-0.02046.5150.0020.0020.0000.0000.0000.000
36A334ARG 10.8990.95748.7750.0300.0300.0000.0000.0000.000
37A335LEU 0-0.035-0.02049.3850.0010.0010.0000.0000.0000.000
38A336ALA 00.0620.04351.9070.0010.0010.0000.0000.0000.000
39A337ASP -1-0.929-0.96553.524-0.021-0.0210.0000.0000.0000.000
40A338MET 0-0.076-0.04954.3840.0010.0010.0000.0000.0000.000
41A339ASP -1-0.837-0.89856.268-0.020-0.0200.0000.0000.0000.000
42A340LEU 00.0230.01158.9570.0010.0010.0000.0000.0000.000
43A341ARG 10.9320.96758.7010.0210.0210.0000.0000.0000.000
44A342PHE 00.0190.00959.9820.0000.0000.0000.0000.0000.000
45A343GLN 00.0020.01862.3060.0000.0000.0000.0000.0000.000
46A344VAL 0-0.109-0.07363.9860.0010.0010.0000.0000.0000.000
47A345LEU 0-0.026-0.01466.1950.0010.0010.0000.0000.0000.000
48A346GLU -1-0.939-0.98065.377-0.016-0.0160.0000.0000.0000.000
49A347THR 0-0.113-0.05368.7330.0010.0010.0000.0000.0000.000
50A348ALA 00.0100.03270.7840.0010.0010.0000.0000.0000.000
51A349SER 0-0.034-0.04772.4100.0000.0000.0000.0000.0000.000
52A350TYR 00.004-0.01771.5120.0000.0000.0000.0000.0000.000
53A351ASN 00.0740.03578.0450.0000.0000.0000.0000.0000.000
54A352GLY 00.0530.01980.2270.0000.0000.0000.0000.0000.000
55A353VAL 0-0.089-0.03381.2550.0000.0000.0000.0000.0000.000
56A354LEU 00.0490.05274.3380.0000.0000.0000.0000.0000.000
57A355ILE 0-0.008-0.01676.6160.0010.0010.0000.0000.0000.000
58A356TRP 00.0760.04069.1290.0000.0000.0000.0000.0000.000
59A357LYS 10.8760.93070.2950.0110.0110.0000.0000.0000.000
60A358ILE 0-0.029-0.00469.4340.0000.0000.0000.0000.0000.000
61A359ARG 10.9980.98866.6720.0130.0130.0000.0000.0000.000
62A360ASP -1-0.837-0.91364.047-0.011-0.0110.0000.0000.0000.000
63A361TYR 0-0.052-0.05867.6210.0000.0000.0000.0000.0000.000
64A362LYS 11.0521.01868.6080.0070.0070.0000.0000.0000.000
65A363ARG 10.9030.96561.3060.0110.0110.0000.0000.0000.000
66A364ARG 10.8890.95463.4960.0110.0110.0000.0000.0000.000
67A365LYS 10.8190.90266.7680.0060.0060.0000.0000.0000.000
68A366GLN 0-0.010-0.03566.0330.0000.0000.0000.0000.0000.000
69A367GLU -1-0.871-0.94162.083-0.010-0.0100.0000.0000.0000.000
70A368ALA 0-0.0080.02065.0790.0000.0000.0000.0000.0000.000
71A369VAL 0-0.043-0.03468.0410.0000.0000.0000.0000.0000.000
72A370MET 0-0.093-0.03762.4460.0000.0000.0000.0000.0000.000
73A371GLY 00.0180.00663.6520.0000.0000.0000.0000.0000.000
74A372LYS 10.9490.98058.9460.0080.0080.0000.0000.0000.000
75A373THR 0-0.036-0.03661.419-0.001-0.0010.0000.0000.0000.000
76A374LEU 0-0.0080.01364.0900.0000.0000.0000.0000.0000.000
77A375SER 0-0.035-0.02866.9250.0000.0000.0000.0000.0000.000
78A376LEU 0-0.032-0.01266.1330.0000.0000.0000.0000.0000.000
79A377TYR 00.0560.00966.8290.0010.0010.0000.0000.0000.000
80A378SER 0-0.0100.00068.3690.0000.0000.0000.0000.0000.000
81A379GLN 0-0.028-0.00768.5510.0000.0000.0000.0000.0000.000
82A380PRO 0-0.022-0.04067.9990.0000.0000.0000.0000.0000.000
83A381PHE 0-0.0220.01671.1050.0000.0000.0000.0000.0000.000
84A382TYR 00.0210.00270.6230.0000.0000.0000.0000.0000.000
85A383THR 00.0260.00277.1280.0000.0000.0000.0000.0000.000
86A384GLY 00.1250.06879.2700.0000.0000.0000.0000.0000.000
87A385TYR 0-0.023-0.02375.6600.0000.0000.0000.0000.0000.000
88A386PHE 0-0.0240.00074.0740.0000.0000.0000.0000.0000.000
89A387GLY 00.0040.01477.3810.0000.0000.0000.0000.0000.000
90A388TYR 0-0.012-0.02577.1130.0000.0000.0000.0000.0000.000
91A389LYS 10.9681.00368.1030.0140.0140.0000.0000.0000.000
92A390MET 0-0.102-0.03774.6170.0010.0010.0000.0000.0000.000
93A391CYS 00.036-0.01271.6060.0000.0000.0000.0000.0000.000
94A392ALA 00.0040.02373.3250.0000.0000.0000.0000.0000.000
95A393ARG 10.8990.96068.0440.0090.0090.0000.0000.0000.000
96A394VAL 00.0170.00871.3330.0000.0000.0000.0000.0000.000
97A395TYR 00.0430.02370.4340.0000.0000.0000.0000.0000.000
98A396LEU 00.0020.00369.3250.0000.0000.0000.0000.0000.000
99A397ASN 00.0350.02171.2470.0000.0000.0000.0000.0000.000
100A398GLY 00.0440.02973.2910.0000.0000.0000.0000.0000.000
101A399ASP -1-0.937-1.01073.021-0.007-0.0070.0000.0000.0000.000
102A400GLY 00.0210.01675.3400.0000.0000.0000.0000.0000.000
103A401MET 00.0500.00877.8820.0000.0000.0000.0000.0000.000
104A402GLY 00.016-0.01180.0800.0000.0000.0000.0000.0000.000
105A403LYS 10.9000.96471.9170.0060.0060.0000.0000.0000.000
106A404GLY 0-0.057-0.01475.4450.0000.0000.0000.0000.0000.000
107A405THR 0-0.010-0.00376.3650.0000.0000.0000.0000.0000.000
108A406HIS 00.0020.01278.6240.0000.0000.0000.0000.0000.000
109A407LEU 0-0.0070.01675.4290.0000.0000.0000.0000.0000.000
110A408SER 0-0.014-0.00375.2640.0000.0000.0000.0000.0000.000
111A409LEU 00.0230.01275.8640.0000.0000.0000.0000.0000.000
112A410PHE 0-0.0260.01274.9810.0000.0000.0000.0000.0000.000
113A411PHE 00.0340.01076.4910.0000.0000.0000.0000.0000.000
114A412VAL 0-0.006-0.01372.0720.0000.0000.0000.0000.0000.000
115A413ILE 00.0500.03374.9560.0000.0000.0000.0000.0000.000
116A414MET 0-0.059-0.02668.3840.0000.0000.0000.0000.0000.000
117A415ARG 10.9810.98665.0780.0140.0140.0000.0000.0000.000
118A416GLY 0-0.042-0.02370.5180.0000.0000.0000.0000.0000.000
119A417GLU -1-0.958-0.98167.646-0.016-0.0160.0000.0000.0000.000
120A418TYR 00.0230.00171.0950.0000.0000.0000.0000.0000.000
121A419ASP -1-0.832-0.90273.791-0.011-0.0110.0000.0000.0000.000
122A420ALA 0-0.074-0.06475.4300.0000.0000.0000.0000.0000.000
123A421LEU 00.0160.01477.7640.0000.0000.0000.0000.0000.000
124A422LEU 0-0.0350.00778.5150.0000.0000.0000.0000.0000.000
125A423PRO 00.0020.00181.8130.0000.0000.0000.0000.0000.000
126A424TRP 00.0290.04178.0030.0000.0000.0000.0000.0000.000
127A425PRO 0-0.045-0.04683.4460.0000.0000.0000.0000.0000.000
128A426PHE 00.0350.01980.7080.0000.0000.0000.0000.0000.000
129A427LYS 10.8960.94183.5420.0080.0080.0000.0000.0000.000
130A428GLN 00.0530.05384.6130.0000.0000.0000.0000.0000.000
131A429LYS 10.9460.96185.7240.0070.0070.0000.0000.0000.000
132A430VAL 00.0560.03682.3300.0000.0000.0000.0000.0000.000
133A431THR 00.007-0.00284.5040.0000.0000.0000.0000.0000.000
134A432LEU 0-0.0330.03480.6550.0000.0000.0000.0000.0000.000
135A433MET 00.019-0.02081.9940.0000.0000.0000.0000.0000.000
136A434LEU 00.0030.00978.8600.0000.0000.0000.0000.0000.000
137A435MET 0-0.029-0.01180.3190.0000.0000.0000.0000.0000.000
138A436ASP -1-0.735-0.84281.391-0.006-0.0060.0000.0000.0000.000
139A437GLN 0-0.029-0.00177.6680.0000.0000.0000.0000.0000.000
140A438GLY 00.036-0.02282.6590.0000.0000.0000.0000.0000.000
141A439SER 0-0.021-0.03485.6830.0000.0000.0000.0000.0000.000
142A440SER 0-0.0070.01488.2850.0000.0000.0000.0000.0000.000
143A441ARG 10.8230.96485.7310.0060.0060.0000.0000.0000.000
144A442ARG 10.9980.99888.4180.0050.0050.0000.0000.0000.000
145A443HIS 00.0940.01185.0230.0000.0000.0000.0000.0000.000
146A444LEU 0-0.054-0.01283.7190.0000.0000.0000.0000.0000.000
147A445GLY 00.0210.00784.8610.0000.0000.0000.0000.0000.000
148A446ASP -1-0.897-0.94586.351-0.006-0.0060.0000.0000.0000.000
149A447ALA 0-0.047-0.02886.4050.0000.0000.0000.0000.0000.000
150A448PHE 00.015-0.00182.1770.0000.0000.0000.0000.0000.000
151A449LYS 10.9450.96487.4060.0070.0070.0000.0000.0000.000
152A450PRO 0-0.0060.00584.4890.0000.0000.0000.0000.0000.000
153A451ASP -1-0.821-0.90585.692-0.006-0.0060.0000.0000.0000.000
154A452PRO 0-0.054-0.02685.7600.0000.0000.0000.0000.0000.000
155A453ASN 00.001-0.01085.9560.0000.0000.0000.0000.0000.000
156A454SER 00.0530.03882.2250.0000.0000.0000.0000.0000.000
157A455SER 0-0.021-0.04878.1640.0000.0000.0000.0000.0000.000
158A456SER 0-0.108-0.07878.0640.0000.0000.0000.0000.0000.000
159A457PHE 00.0590.02178.8160.0000.0000.0000.0000.0000.000
160A458LYS 10.8930.96278.9130.0080.0080.0000.0000.0000.000
161A459LYS 10.9850.99974.3870.0110.0110.0000.0000.0000.000
162A460PRO 0-0.0330.00972.9390.0000.0000.0000.0000.0000.000
163A461THR 0-0.0150.01570.7730.0000.0000.0000.0000.0000.000
164A462GLY 00.006-0.00468.4920.0000.0000.0000.0000.0000.000
165A463GLU -1-0.935-0.97963.359-0.014-0.0140.0000.0000.0000.000
166A464MET 0-0.003-0.00565.9650.0000.0000.0000.0000.0000.000
167A465ASN 00.0050.01170.4700.0000.0000.0000.0000.0000.000
168A466ILE 00.0580.02772.9290.0000.0000.0000.0000.0000.000
169A467ALA 0-0.0280.01373.6460.0000.0000.0000.0000.0000.000
170A468SER 0-0.011-0.01575.6140.0000.0000.0000.0000.0000.000
171A469GLY 00.020-0.02479.1340.0000.0000.0000.0000.0000.000
172A470CYS 00.003-0.00580.0650.0000.0000.0000.0000.0000.000
173A471PRO 0-0.006-0.00879.2330.0000.0000.0000.0000.0000.000
174A472VAL 0-0.0140.01179.8430.0000.0000.0000.0000.0000.000
175A473PHE 0-0.0400.01280.9580.0000.0000.0000.0000.0000.000
176A474VAL 00.0320.00381.5900.0000.0000.0000.0000.0000.000
177A475ALA 00.0920.04081.1850.0000.0000.0000.0000.0000.000
178A476GLN 00.0510.01575.6060.0000.0000.0000.0000.0000.000
179A477THR 0-0.0010.00179.7990.0000.0000.0000.0000.0000.000
180A478VAL 0-0.014-0.00282.1620.0000.0000.0000.0000.0000.000
181A479LEU 0-0.041-0.03177.3540.0000.0000.0000.0000.0000.000
182A480GLU -1-0.800-0.92675.664-0.006-0.0060.0000.0000.0000.000
183A481ASN 0-0.064-0.00379.5290.0000.0000.0000.0000.0000.000
184A482GLY 0-0.050-0.04482.1450.0000.0000.0000.0000.0000.000
185A483THR 0-0.079-0.09781.6930.0000.0000.0000.0000.0000.000
186A484TYR 0-0.031-0.00780.4880.0000.0000.0000.0000.0000.000
187A485ILE 0-0.0230.05375.2870.0000.0000.0000.0000.0000.000
188A486LYS 10.9140.96676.5800.0080.0080.0000.0000.0000.000
189A487ASP -1-0.896-0.95472.846-0.009-0.0090.0000.0000.0000.000
190A488ASP -1-0.830-0.91768.475-0.009-0.0090.0000.0000.0000.000
191A489THR 0-0.104-0.04070.535-0.001-0.0010.0000.0000.0000.000
192A490ILE 00.0570.03572.7990.0000.0000.0000.0000.0000.000
193A491PHE 00.015-0.01574.330-0.001-0.0010.0000.0000.0000.000
194A492ILE 00.0060.01675.3780.0000.0000.0000.0000.0000.000
195A493LYS 10.8920.94877.5400.0080.0080.0000.0000.0000.000
196A494VAL 00.019-0.00677.6800.0000.0000.0000.0000.0000.000
197A495ILE 0-0.073-0.05180.9560.0000.0000.0000.0000.0000.000
198A496VAL 00.0010.00780.6230.0000.0000.0000.0000.0000.000
199A497ASP -1-0.906-0.96083.885-0.008-0.0080.0000.0000.0000.000
200A498THR 00.014-0.00883.3350.0000.0000.0000.0000.0000.000
201A499SER 00.0470.03786.6310.0000.0000.0000.0000.0000.000
202A500ASP -1-0.983-0.96289.877-0.008-0.0080.0000.0000.0000.000
203A501LEU 0-0.121-0.09086.3970.0000.0000.0000.0000.0000.000
204A502PRO 0-0.049-0.02388.3140.0000.0000.0000.0000.0000.000
205A503ASP -1-0.947-0.96584.439-0.011-0.0110.0000.0000.0000.000
206A504PRO -1-0.982-0.97585.608-0.010-0.0100.0000.0000.0000.000