FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5JQQZ

Calculation Name: 1Y6K-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y6K

Chain ID: L

ChEMBL ID:

UniProt ID: Q13651

Base Structure: X-ray

Registration Date: 2023-09-23

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 143
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1217383.4888
FMO2-HF: Nuclear repulsion 1155977.156383
FMO2-HF: Total energy -61406.332417
FMO2-MP2: Total energy -61579.209545


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(L:12:CYS)


Summations of interaction energy for fragment #1(L:12:CYS)
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.
-42.368-30.05514.745-8.5-18.56-0.057
Interaction energy analysis for fragmet #1(L:12:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : 0.009
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].
3L14HIS00.005-0.0262.990-3.783-1.1333.679-2.662-3.6670.003
4L15PHE00.015-0.0092.799-2.153-4.3208.9760.231-7.041-0.012
5L16PRO00.0010.0084.511-2.240-2.0340.027-0.042-0.1910.001
6L17GLY00.0670.0377.795-0.597-0.5970.0000.0000.0000.000
7L18ASN0-0.040-0.0216.5050.1800.1800.0000.0000.0000.000
8L19LEU00.0430.0265.042-0.194-0.1940.0000.0000.0000.000
9L20PRO00.0370.0188.629-0.227-0.2270.0000.0000.0000.000
10L21ASN0-0.052-0.01912.187-0.018-0.0180.0000.0000.0000.000
11L22MET00.0230.0208.897-0.058-0.0580.0000.0000.0000.000
12L23LEU0-0.012-0.00711.007-0.153-0.1530.0000.0000.0000.000
13L24ARG10.8590.92013.5110.1660.1660.0000.0000.0000.000
14L25ASP-1-0.821-0.91214.380-0.213-0.2130.0000.0000.0000.000
15L26LEU00.0170.01114.0800.0050.0050.0000.0000.0000.000
16L27ARG10.9390.97216.3340.6670.6670.0000.0000.0000.000
17L28ASP-1-0.813-0.89419.429-0.192-0.1920.0000.0000.0000.000
18L29ALA0-0.0090.01919.5920.0440.0440.0000.0000.0000.000
19L30PHE00.0440.01620.8020.0290.0290.0000.0000.0000.000
20L31SER0-0.072-0.05522.5460.0450.0450.0000.0000.0000.000
21L32ARG10.8690.92423.9740.2700.2700.0000.0000.0000.000
22L33VAL00.0390.01324.8040.0150.0150.0000.0000.0000.000
23L34LYS10.9070.97426.1680.3280.3280.0000.0000.0000.000
24L35THR00.014-0.00927.720-0.005-0.0050.0000.0000.0000.000
25L36PHE00.0400.03230.7960.0130.0130.0000.0000.0000.000
26L37PHE00.0420.00327.6640.0020.0020.0000.0000.0000.000
27L38GLN0-0.052-0.03528.5590.0090.0090.0000.0000.0000.000
28L39MET0-0.0180.00331.7820.0190.0190.0000.0000.0000.000
29L40LYS10.7880.88733.5740.2950.2950.0000.0000.0000.000
30L41ASP-1-0.911-0.95431.743-0.349-0.3490.0000.0000.0000.000
31L42GLN0-0.072-0.04334.2150.0210.0210.0000.0000.0000.000
32L43LEU0-0.0230.00234.8210.0160.0160.0000.0000.0000.000
33L44ASP-1-0.902-0.94534.157-0.269-0.2690.0000.0000.0000.000
34L45ASN0-0.092-0.04932.7770.0050.0050.0000.0000.0000.000
35L46LEU00.0410.02626.174-0.014-0.0140.0000.0000.0000.000
36L47LEU00.0210.01926.6260.0010.0010.0000.0000.0000.000
37L48LEU00.006-0.01021.593-0.005-0.0050.0000.0000.0000.000
38L49LYS10.8930.93825.2270.4310.4310.0000.0000.0000.000
39L50GLU-1-0.886-0.94524.215-0.502-0.5020.0000.0000.0000.000
40L51SER00.0270.00823.590-0.022-0.0220.0000.0000.0000.000
41L52LEU00.0490.03419.797-0.029-0.0290.0000.0000.0000.000
42L53LEU0-0.026-0.00718.046-0.116-0.1160.0000.0000.0000.000
43L54GLU-1-0.780-0.88919.186-0.654-0.6540.0000.0000.0000.000
44L55ASP-1-0.894-0.94720.005-0.759-0.7590.0000.0000.0000.000
45L56PHE0-0.116-0.07315.483-0.144-0.1440.0000.0000.0000.000
46L57LYS10.7630.86715.2750.4850.4850.0000.0000.0000.000
47L58GLY00.0450.04517.4830.0500.0500.0000.0000.0000.000
48L59TYR0-0.034-0.02916.856-0.131-0.1310.0000.0000.0000.000
49L60LEU00.0290.00917.327-0.013-0.0130.0000.0000.0000.000
50L61GLY00.0290.03115.015-0.088-0.0880.0000.0000.0000.000
51L62CYS0-0.082-0.0288.224-0.041-0.0410.0000.0000.0000.000
52L63GLN0-0.022-0.01412.315-0.335-0.3350.0000.0000.0000.000
53L64ALA00.0740.04114.987-0.024-0.0240.0000.0000.0000.000
54L65LEU0-0.013-0.00310.481-0.006-0.0060.0000.0000.0000.000
55L66SER0-0.026-0.04111.476-0.231-0.2310.0000.0000.0000.000
56L67GLU-1-0.871-0.91813.142-0.954-0.9540.0000.0000.0000.000
57L68MET00.0010.00916.5920.1190.1190.0000.0000.0000.000
58L69ILE0-0.043-0.03111.2830.0230.0230.0000.0000.0000.000
59L70GLN0-0.034-0.00414.924-0.165-0.1650.0000.0000.0000.000
60L71PHE00.0700.03717.1300.0970.0970.0000.0000.0000.000
61L72TYR0-0.017-0.02118.2870.0990.0990.0000.0000.0000.000
62L73LEU0-0.058-0.04314.4600.0600.0600.0000.0000.0000.000
63L74GLU-1-0.921-0.95518.337-0.959-0.9590.0000.0000.0000.000
64L75GLU-1-0.902-0.94321.274-0.619-0.6190.0000.0000.0000.000
65L76VAL0-0.022-0.01023.1010.0510.0510.0000.0000.0000.000
66L77MET0-0.052-0.01619.6730.0100.0100.0000.0000.0000.000
67L78PRO00.0320.02222.2050.0650.0650.0000.0000.0000.000
68L79GLN0-0.014-0.00625.1660.0320.0320.0000.0000.0000.000
69L80ALA00.0220.01026.7740.0400.0400.0000.0000.0000.000
70L81GLU-1-0.879-0.94823.060-0.535-0.5350.0000.0000.0000.000
71L82ASN0-0.059-0.04527.8890.0330.0330.0000.0000.0000.000
72L83GLN0-0.0230.01130.7150.0080.0080.0000.0000.0000.000
73L84ASP-1-0.771-0.86731.948-0.274-0.2740.0000.0000.0000.000
74L85PRO00.005-0.01531.893-0.012-0.0120.0000.0000.0000.000
75L86ASP-1-0.913-0.94732.102-0.232-0.2320.0000.0000.0000.000
76L87ILE0-0.032-0.01628.5380.0040.0040.0000.0000.0000.000
77L88LYS10.9150.97727.5570.3160.3160.0000.0000.0000.000
78L89ALA00.0270.00726.160-0.037-0.0370.0000.0000.0000.000
79L90HIS00.0130.02324.772-0.044-0.0440.0000.0000.0000.000
80L91VAL00.0170.00523.572-0.040-0.0400.0000.0000.0000.000
81L92ASN0-0.036-0.01421.980-0.067-0.0670.0000.0000.0000.000
82L93SER0-0.014-0.02520.272-0.056-0.0560.0000.0000.0000.000
83L94LEU0-0.042-0.01518.680-0.051-0.0510.0000.0000.0000.000
84L95GLY00.0660.02417.607-0.134-0.1340.0000.0000.0000.000
85L96GLU-1-0.850-0.91715.902-0.985-0.9850.0000.0000.0000.000
86L97ASN0-0.063-0.02814.325-0.139-0.1390.0000.0000.0000.000
87L98LEU00.0350.01812.964-0.250-0.2500.0000.0000.0000.000
88L99LYS10.8800.93311.7780.4340.4340.0000.0000.0000.000
89L100THR0-0.037-0.03510.049-0.569-0.5690.0000.0000.0000.000
90L101LEU0-0.027-0.0168.672-0.526-0.5260.0000.0000.0000.000
91L102ARG10.8490.9047.1551.0841.0840.0000.0000.0000.000
92L103LEU0-0.019-0.0156.045-2.236-2.2360.0000.0000.0000.000
93L104ARG10.8420.9154.029-4.689-4.2360.012-0.157-0.307-0.001
94L105LEU00.0260.0132.814-8.987-5.7870.432-1.389-2.244-0.015
95L106ARG10.9040.9552.427-7.994-3.1261.398-3.339-2.927-0.034
98L110ARG10.9580.9723.903-0.5271.356-0.012-0.896-0.9760.001
99L111PHE0-0.015-0.0042.7250.7341.8110.235-0.227-1.0850.000
100L112LEU00.0300.0095.5560.7140.7140.0000.0000.0000.000
101L113PRO00.006-0.0056.9770.0010.0010.0000.0000.0000.000
102L115GLU-1-0.721-0.8287.925-3.781-3.7810.0000.0000.0000.000
103L116ASN0-0.104-0.0594.362-0.779-0.636-0.002-0.019-0.1220.000
104L117LYS10.8770.9278.1591.0151.0150.0000.0000.0000.000
105L118SER00.0540.02510.3930.3810.3810.0000.0000.0000.000
106L119LYS10.9660.97411.150-1.109-1.1090.0000.0000.0000.000
107L120ALA00.0500.02512.984-0.043-0.0430.0000.0000.0000.000
108L121VAL00.0620.03116.165-0.028-0.0280.0000.0000.0000.000
109L122GLU-1-0.763-0.86614.588-0.289-0.2890.0000.0000.0000.000
110L123GLN0-0.020-0.02216.0690.0710.0710.0000.0000.0000.000
111L124VAL00.0380.02518.698-0.012-0.0120.0000.0000.0000.000
112L125LYS10.9030.95017.2720.2480.2480.0000.0000.0000.000
113L126ASN0-0.012-0.01118.8120.0190.0190.0000.0000.0000.000
114L127ALA0-0.0030.00122.0340.0000.0000.0000.0000.0000.000
115L128PHE00.0220.01524.846-0.007-0.0070.0000.0000.0000.000
116L129ASN0-0.027-0.03623.296-0.006-0.0060.0000.0000.0000.000
117L130LYS10.8760.93721.957-0.177-0.1770.0000.0000.0000.000
118L131LEU00.0030.01827.9620.0050.0050.0000.0000.0000.000
119L132GLN00.0000.00229.917-0.007-0.0070.0000.0000.0000.000
120L133GLU-1-0.752-0.86431.6230.0000.0000.0000.0000.0000.000
121L134LYS10.8070.88434.063-0.027-0.0270.0000.0000.0000.000
122L135GLY00.0010.00730.2340.0060.0060.0000.0000.0000.000
123L136ILE0-0.011-0.00830.915-0.005-0.0050.0000.0000.0000.000
124L137TYR00.0050.00032.514-0.006-0.0060.0000.0000.0000.000
125L138LYS10.8740.93429.643-0.062-0.0620.0000.0000.0000.000
126L139ALA00.0210.00328.9110.0010.0010.0000.0000.0000.000
127L140MET0-0.024-0.01330.379-0.012-0.0120.0000.0000.0000.000
128L141SER0-0.086-0.04833.5190.0010.0010.0000.0000.0000.000
129L142GLU-1-0.827-0.89129.5540.0580.0580.0000.0000.0000.000
130L143PHE0-0.007-0.00929.747-0.005-0.0050.0000.0000.0000.000
131L144ASP-1-0.827-0.92131.197-0.020-0.0200.0000.0000.0000.000
132L145ILE0-0.0110.00428.057-0.002-0.0020.0000.0000.0000.000
133L146PHE0-0.060-0.02523.776-0.005-0.0050.0000.0000.0000.000
134L147ILE00.0340.01127.169-0.016-0.0160.0000.0000.0000.000
135L148ASN00.0320.01229.201-0.014-0.0140.0000.0000.0000.000
136L149TYR0-0.068-0.03323.8490.0140.0140.0000.0000.0000.000
137L150ILE0-0.027-0.00524.907-0.014-0.0140.0000.0000.0000.000
138L151GLU-1-0.893-0.94826.120-0.094-0.0940.0000.0000.0000.000
139L152ALA0-0.0050.01025.813-0.003-0.0030.0000.0000.0000.000
140L153TYR0-0.047-0.02319.001-0.014-0.0140.0000.0000.0000.000
141L154MET0-0.036-0.01823.722-0.023-0.0230.0000.0000.0000.000
142L155THR0-0.058-0.02326.202-0.006-0.0060.0000.0000.0000.000
143L156MET0-0.118-0.06019.8120.0050.0050.0000.0000.0000.000