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: 3QK1L

Calculation Name: 1FLK-A-Xray372

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: 2023-03-13

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2110346.161184
FMO2-HF: Nuclear repulsion 2028069.314999
FMO2-HF: Total energy -82276.846185
FMO2-MP2: Total energy -82513.20944


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:300:LEU)


Summations of interaction energy for fragment #1(A:300:LEU)
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.
-6.1-11.52521.413-1.366-14.621-0.036
Interaction energy analysis for fragmet #1(A:300:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.004
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].
3A302SER0-0.027-0.0153.806-2.944-1.772-0.008-0.467-0.6970.002
4A303VAL0-0.087-0.0832.071-0.481-0.1713.963-1.156-3.1180.007
5A304ASP-1-0.771-0.9021.938-10.637-12.14516.327-7.109-7.709-0.028
6A305LYS10.8870.9382.5029.6491.709-0.0098.725-0.776-0.007
7A306SER0-0.092-0.0044.8530.3410.3410.0000.0000.0000.000
8A307ALA0-0.030-0.0212.411-0.3410.3560.426-0.328-0.7950.002
9A308GLY00.1190.0562.690-3.488-1.6930.715-1.029-1.481-0.012
10A309GLN0-0.0290.0184.4100.2590.308-0.001-0.002-0.0450.000
11A310VAL00.028-0.0177.1450.3290.3290.0000.0000.0000.000
12A311ALA00.0150.0058.1260.1910.1910.0000.0000.0000.000
13A312ARG10.9150.9729.8540.7740.7740.0000.0000.0000.000
14A313ASN00.0390.00411.7670.1640.1640.0000.0000.0000.000
15A314THR00.015-0.01512.5110.0850.0850.0000.0000.0000.000
16A315GLY00.0240.02114.5290.0410.0410.0000.0000.0000.000
17A316LEU0-0.077-0.00316.0100.0590.0590.0000.0000.0000.000
18A317LEU0-0.0010.01316.3250.0430.0430.0000.0000.0000.000
19A318GLU-1-0.832-0.91617.177-0.488-0.4880.0000.0000.0000.000
20A319SER0-0.010-0.02820.1190.0330.0330.0000.0000.0000.000
21A320GLN0-0.064-0.03922.4420.0490.0490.0000.0000.0000.000
22A321LEU00.0150.00221.9860.0230.0230.0000.0000.0000.000
23A322SER00.0150.00224.6590.0170.0170.0000.0000.0000.000
24A323ARG10.8680.94526.4610.2230.2230.0000.0000.0000.000
25A324HIS0-0.008-0.02327.5370.0220.0220.0000.0000.0000.000
26A325ASP-1-0.881-0.93028.715-0.200-0.2000.0000.0000.0000.000
27A326GLN00.0560.02630.3920.0040.0040.0000.0000.0000.000
28A327MET0-0.0290.05532.8490.0150.0150.0000.0000.0000.000
29A328LEU00.0560.03032.1760.0110.0110.0000.0000.0000.000
30A329SER0-0.007-0.00935.1260.0060.0060.0000.0000.0000.000
31A330VAL0-0.011-0.03236.9250.0090.0090.0000.0000.0000.000
32A331HIS0-0.136-0.11537.8010.0110.0110.0000.0000.0000.000
33A332ASP-1-0.896-0.94539.084-0.114-0.1140.0000.0000.0000.000
34A333ILE0-0.042-0.01940.4810.0050.0050.0000.0000.0000.000
35A334ARG10.8990.95741.9870.1060.1060.0000.0000.0000.000
36A335LEU0-0.033-0.02042.7130.0050.0050.0000.0000.0000.000
37A336ALA00.0590.04245.4920.0050.0050.0000.0000.0000.000
38A337ASP-1-0.929-0.96547.124-0.087-0.0870.0000.0000.0000.000
39A338MET0-0.075-0.04847.4500.0050.0050.0000.0000.0000.000
40A339ASP-1-0.835-0.89749.884-0.076-0.0760.0000.0000.0000.000
41A340LEU00.0240.01152.5890.0040.0040.0000.0000.0000.000
42A341ARG10.9290.96451.8560.0740.0740.0000.0000.0000.000
43A342PHE00.0200.01053.0990.0030.0030.0000.0000.0000.000
44A343GLN00.0030.01956.1530.0010.0010.0000.0000.0000.000
45A344VAL0-0.108-0.07357.6130.0030.0030.0000.0000.0000.000
46A345LEU0-0.028-0.01559.3570.0020.0020.0000.0000.0000.000
47A346GLU-1-0.938-0.98058.765-0.057-0.0570.0000.0000.0000.000
48A347THR0-0.110-0.05262.3600.0020.0020.0000.0000.0000.000
49A348ALA00.0190.03564.2550.0010.0010.0000.0000.0000.000
50A349SER0-0.038-0.04665.8980.0000.0000.0000.0000.0000.000
51A350TYR00.003-0.01864.7560.0000.0000.0000.0000.0000.000
52A351ASN00.0600.02771.3730.0000.0000.0000.0000.0000.000
53A352GLY00.0520.02073.7030.0010.0010.0000.0000.0000.000
54A353VAL0-0.086-0.03274.9510.0000.0000.0000.0000.0000.000
55A354LEU00.0490.05268.155-0.001-0.0010.0000.0000.0000.000
56A355ILE0-0.007-0.01570.6090.0010.0010.0000.0000.0000.000
57A356TRP00.0750.03963.5010.0000.0000.0000.0000.0000.000
58A357LYS10.8730.92964.6580.0510.0510.0000.0000.0000.000
59A358ILE0-0.026-0.00364.073-0.002-0.0020.0000.0000.0000.000
60A359ARG10.9990.98861.0480.0570.0570.0000.0000.0000.000
61A360ASP-1-0.837-0.91258.959-0.062-0.0620.0000.0000.0000.000
62A361TYR0-0.055-0.06162.556-0.001-0.0010.0000.0000.0000.000
63A362LYS11.0531.01964.1350.0490.0490.0000.0000.0000.000
64A363ARG10.9030.96556.3470.0650.0650.0000.0000.0000.000
65A364ARG10.8910.95558.1160.0590.0590.0000.0000.0000.000
66A365LYS10.8180.90361.9400.0450.0450.0000.0000.0000.000
67A366GLN0-0.005-0.03361.7130.0020.0020.0000.0000.0000.000
68A367GLU-1-0.872-0.94157.417-0.066-0.0660.0000.0000.0000.000
69A368ALA0-0.0110.01860.583-0.001-0.0010.0000.0000.0000.000
70A369VAL0-0.042-0.03363.5070.0000.0000.0000.0000.0000.000
71A370MET0-0.093-0.03758.4240.0000.0000.0000.0000.0000.000
72A371GLY00.0180.00559.451-0.002-0.0020.0000.0000.0000.000
73A372LYS10.9510.98154.6760.0670.0670.0000.0000.0000.000
74A373THR0-0.035-0.03556.777-0.002-0.0020.0000.0000.0000.000
75A374LEU0-0.0070.01459.3480.0020.0020.0000.0000.0000.000
76A375SER0-0.035-0.02861.9770.0020.0020.0000.0000.0000.000
77A376LEU0-0.034-0.01260.891-0.002-0.0020.0000.0000.0000.000
78A377TYR00.0570.01061.3600.0020.0020.0000.0000.0000.000
79A378SER0-0.011-0.00162.638-0.001-0.0010.0000.0000.0000.000
80A379GLN0-0.020-0.00362.415-0.002-0.0020.0000.0000.0000.000
81A380PRO0-0.021-0.04161.8030.0020.0020.0000.0000.0000.000
82A381PHE0-0.0240.01564.8380.0000.0000.0000.0000.0000.000
83A382TYR00.0190.00264.048-0.001-0.0010.0000.0000.0000.000
84A383THR00.0340.00670.6240.0000.0000.0000.0000.0000.000
85A384GLY00.1050.05672.6270.0010.0010.0000.0000.0000.000
86A385TYR0-0.026-0.02568.719-0.001-0.0010.0000.0000.0000.000
87A386PHE0-0.0240.00067.056-0.001-0.0010.0000.0000.0000.000
88A387GLY0-0.0020.01270.5510.0010.0010.0000.0000.0000.000
89A388TYR0-0.006-0.02170.521-0.001-0.0010.0000.0000.0000.000
90A389LYS10.9741.00461.7340.0550.0550.0000.0000.0000.000
91A390MET0-0.109-0.04068.3030.0010.0010.0000.0000.0000.000
92A391CYS00.042-0.01065.694-0.002-0.0020.0000.0000.0000.000
93A392ALA00.0010.02267.4360.0010.0010.0000.0000.0000.000
94A393ARG10.9030.96162.8940.0510.0510.0000.0000.0000.000
95A394VAL00.0170.00965.9680.0020.0020.0000.0000.0000.000
96A395TYR00.0400.02365.570-0.002-0.0020.0000.0000.0000.000
97A396LEU00.0040.00464.4110.0020.0020.0000.0000.0000.000
98A397ASN00.0350.02266.8960.0020.0020.0000.0000.0000.000
99A398GLY00.0430.02868.7100.0000.0000.0000.0000.0000.000
100A399ASP-1-0.936-1.00968.427-0.048-0.0480.0000.0000.0000.000
101A400GLY00.0220.01670.7400.0010.0010.0000.0000.0000.000
102A401MET00.0520.00973.3440.0000.0000.0000.0000.0000.000
103A402GLY00.015-0.00975.4880.0010.0010.0000.0000.0000.000
104A403LYS10.8960.96167.5720.0460.0460.0000.0000.0000.000
105A404GLY0-0.054-0.01371.1040.0010.0010.0000.0000.0000.000
106A405THR0-0.008-0.00272.0300.0010.0010.0000.0000.0000.000
107A406HIS00.0020.01374.0900.0010.0010.0000.0000.0000.000
108A407LEU0-0.0020.01770.371-0.002-0.0020.0000.0000.0000.000
109A408SER0-0.016-0.00470.2640.0010.0010.0000.0000.0000.000
110A409LEU00.0140.00870.640-0.001-0.0010.0000.0000.0000.000
111A410PHE0-0.0180.01569.7360.0010.0010.0000.0000.0000.000
112A411PHE00.0310.00970.883-0.001-0.0010.0000.0000.0000.000
113A412VAL0-0.004-0.01266.3440.0000.0000.0000.0000.0000.000
114A413ILE00.0470.03269.0070.0000.0000.0000.0000.0000.000
115A414MET0-0.054-0.02562.238-0.001-0.0010.0000.0000.0000.000
116A415ARG10.9780.98658.9600.0580.0580.0000.0000.0000.000
117A416GLY0-0.044-0.02364.190-0.002-0.0020.0000.0000.0000.000
118A417GLU-1-0.955-0.98160.949-0.055-0.0550.0000.0000.0000.000
119A418TYR00.021-0.00164.4740.0000.0000.0000.0000.0000.000
120A419ASP-1-0.833-0.90467.451-0.045-0.0450.0000.0000.0000.000
121A420ALA0-0.069-0.06168.891-0.001-0.0010.0000.0000.0000.000
122A421LEU00.0160.01470.8950.0010.0010.0000.0000.0000.000
123A422LEU0-0.0410.00471.9430.0010.0010.0000.0000.0000.000
124A423PRO00.0010.00075.2480.0000.0000.0000.0000.0000.000
125A424TRP00.0300.04371.706-0.001-0.0010.0000.0000.0000.000
126A425PRO0-0.042-0.04377.3760.0010.0010.0000.0000.0000.000
127A426PHE00.0380.01874.4700.0010.0010.0000.0000.0000.000
128A427LYS10.8990.94277.4100.0320.0320.0000.0000.0000.000
129A428GLN00.0400.04978.4100.0010.0010.0000.0000.0000.000
130A429LYS10.9540.96579.6640.0300.0300.0000.0000.0000.000
131A430VAL00.0530.03476.478-0.001-0.0010.0000.0000.0000.000
132A431THR00.004-0.00378.5690.0010.0010.0000.0000.0000.000
133A432LEU0-0.0320.03575.126-0.001-0.0010.0000.0000.0000.000
134A433MET00.020-0.02076.2800.0010.0010.0000.0000.0000.000
135A434LEU00.0030.01073.573-0.001-0.0010.0000.0000.0000.000
136A435MET0-0.029-0.01174.6660.0010.0010.0000.0000.0000.000
137A436ASP-1-0.733-0.84075.925-0.035-0.0350.0000.0000.0000.000
138A437GLN0-0.030-0.00172.1190.0000.0000.0000.0000.0000.000
139A438GLY00.034-0.02177.1890.0000.0000.0000.0000.0000.000
140A439SER0-0.018-0.03480.3340.0000.0000.0000.0000.0000.000
141A440SER0-0.0100.01382.8740.0010.0010.0000.0000.0000.000
142A441ARG10.8240.96580.7470.0340.0340.0000.0000.0000.000
143A442ARG10.9980.99883.2810.0310.0310.0000.0000.0000.000
144A443HIS00.0950.01179.430-0.001-0.0010.0000.0000.0000.000
145A444LEU0-0.051-0.01178.5300.0010.0010.0000.0000.0000.000
146A445GLY00.0120.00379.382-0.001-0.0010.0000.0000.0000.000
147A446ASP-1-0.890-0.94180.903-0.032-0.0320.0000.0000.0000.000
148A447ALA0-0.048-0.02980.807-0.001-0.0010.0000.0000.0000.000
149A448PHE00.015-0.00176.4920.0000.0000.0000.0000.0000.000
150A449LYS10.9470.96481.5920.0300.0300.0000.0000.0000.000
151A450PRO0-0.0030.00678.6280.0000.0000.0000.0000.0000.000
152A451ASP-1-0.823-0.90480.038-0.032-0.0320.0000.0000.0000.000
153A452PRO0-0.057-0.02880.105-0.001-0.0010.0000.0000.0000.000
154A453ASN00.003-0.01080.252-0.001-0.0010.0000.0000.0000.000
155A454SER00.0540.03976.763-0.001-0.0010.0000.0000.0000.000
156A455SER0-0.022-0.04872.7480.0000.0000.0000.0000.0000.000
157A456SER0-0.105-0.07872.467-0.001-0.0010.0000.0000.0000.000
158A457PHE00.0520.01873.062-0.001-0.0010.0000.0000.0000.000
159A458LYS10.8970.96473.0740.0380.0380.0000.0000.0000.000
160A459LYS10.9830.99868.0980.0440.0440.0000.0000.0000.000
161A460PRO0-0.0290.01066.9000.0000.0000.0000.0000.0000.000
162A461THR0-0.0130.01665.042-0.001-0.0010.0000.0000.0000.000
163A462GLY00.007-0.00462.662-0.001-0.0010.0000.0000.0000.000
164A463GLU-1-0.935-0.97957.456-0.063-0.0630.0000.0000.0000.000
165A464MET0-0.004-0.00560.2370.0020.0020.0000.0000.0000.000
166A465ASN00.0030.00964.6400.0010.0010.0000.0000.0000.000
167A466ILE00.0650.03067.317-0.001-0.0010.0000.0000.0000.000
168A467ALA0-0.0300.01268.2220.0010.0010.0000.0000.0000.000
169A468SER0-0.012-0.01670.1620.0010.0010.0000.0000.0000.000
170A469GLY00.016-0.02473.8050.0010.0010.0000.0000.0000.000
171A470CYS00.004-0.00474.7930.0010.0010.0000.0000.0000.000
172A471PRO00.000-0.00674.310-0.001-0.0010.0000.0000.0000.000
173A472VAL0-0.0130.01175.008-0.001-0.0010.0000.0000.0000.000
174A473PHE0-0.0430.01075.8460.0010.0010.0000.0000.0000.000
175A474VAL00.0350.00576.6190.0010.0010.0000.0000.0000.000
176A475ALA00.0940.04276.353-0.001-0.0010.0000.0000.0000.000
177A476GLN00.0510.01371.1260.0000.0000.0000.0000.0000.000
178A477THR0-0.004-0.00175.1820.0000.0000.0000.0000.0000.000
179A478VAL0-0.013-0.00277.6660.0010.0010.0000.0000.0000.000
180A479LEU0-0.037-0.03072.4390.0000.0000.0000.0000.0000.000
181A480GLU-1-0.802-0.92671.101-0.043-0.0430.0000.0000.0000.000
182A481ASN0-0.063-0.00374.857-0.001-0.0010.0000.0000.0000.000
183A482GLY0-0.051-0.04477.3810.0010.0010.0000.0000.0000.000
184A483THR0-0.076-0.09576.769-0.001-0.0010.0000.0000.0000.000
185A484TYR0-0.029-0.00775.2660.0000.0000.0000.0000.0000.000
186A485ILE0-0.0240.05270.285-0.001-0.0010.0000.0000.0000.000
187A486LYS10.9140.96671.3710.0390.0390.0000.0000.0000.000
188A487ASP-1-0.895-0.95367.631-0.044-0.0440.0000.0000.0000.000
189A488ASP-1-0.830-0.91763.596-0.053-0.0530.0000.0000.0000.000
190A489THR0-0.105-0.04165.243-0.002-0.0020.0000.0000.0000.000
191A490ILE00.0550.03567.5320.0010.0010.0000.0000.0000.000
192A491PHE00.014-0.01668.654-0.002-0.0020.0000.0000.0000.000
193A492ILE00.0090.01869.8710.0010.0010.0000.0000.0000.000
194A493LYS10.8940.94871.7150.0360.0360.0000.0000.0000.000
195A494VAL00.015-0.00771.7640.0000.0000.0000.0000.0000.000
196A495ILE0-0.072-0.05174.9960.0000.0000.0000.0000.0000.000
197A496VAL00.0080.01174.4560.0010.0010.0000.0000.0000.000
198A497ASP-1-0.905-0.95977.705-0.032-0.0320.0000.0000.0000.000
199A498THR00.007-0.01076.836-0.001-0.0010.0000.0000.0000.000
200A499SER00.0420.03280.1440.0000.0000.0000.0000.0000.000
201A500ASP-1-0.976-0.95983.320-0.029-0.0290.0000.0000.0000.000
202A501LEU0-0.110-0.08279.7520.0000.0000.0000.0000.0000.000
203A502PRO0-0.030-0.01281.625-0.001-0.0010.0000.0000.0000.000
204A503ASP-1-0.907-0.94177.686-0.036-0.0360.0000.0000.0000.000
205A504PRO0-0.059-0.02278.5960.0010.0010.0000.0000.0000.000