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: YY352

Calculation Name: 2JA9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JA9

Chain ID: A

ChEMBL ID:

UniProt ID: Q08285

Base Structure: X-ray

Registration Date: 2023-06-20

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 175
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1781753.766162
FMO2-HF: Nuclear repulsion 1712204.608089
FMO2-HF: Total energy -69549.158073
FMO2-MP2: Total energy -69748.807788


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:62:LYS)


Summations of interaction energy for fragment #1(A:62:LYS)
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.
-38.537-35.0071.882-1.544-3.87-0.004
Interaction energy analysis for fragmet #1(A:62:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.959 / q_NPA : 0.974
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].
3A64TYR0-0.050-0.0753.752-3.043-1.405-0.004-0.675-0.9590.002
4A65ILE0-0.0030.0065.3063.0273.0270.0000.0000.0000.000
5A66PRO00.002-0.0037.815-0.711-0.7110.0000.0000.0000.000
6A67SER0-0.0220.01110.4090.8440.8440.0000.0000.0000.000
7A68VAL00.0580.00612.245-0.054-0.0540.0000.0000.0000.000
8A69ASN0-0.043-0.03615.1380.0610.0610.0000.0000.0000.000
9A70ASP-1-0.842-0.87710.319-26.327-26.3270.0000.0000.0000.000
10A71PHE00.0280.01913.5831.1121.1120.0000.0000.0000.000
11A72VAL0-0.044-0.01711.755-2.130-2.1300.0000.0000.0000.000
12A73ILE00.0080.00413.8021.2951.2950.0000.0000.0000.000
13A74GLY00.0070.00414.628-1.288-1.2880.0000.0000.0000.000
14A75VAL0-0.0220.00616.8730.4930.4930.0000.0000.0000.000
15A76ILE00.0030.00819.679-0.234-0.2340.0000.0000.0000.000
16A77ILE0-0.012-0.02119.6610.2140.2140.0000.0000.0000.000
17A78GLY00.001-0.00722.8750.3680.3680.0000.0000.0000.000
18A79THR0-0.0160.00025.603-0.232-0.2320.0000.0000.0000.000
19A80PHE00.0060.01125.4240.2220.2220.0000.0000.0000.000
20A81SER00.0110.00629.8280.0730.0730.0000.0000.0000.000
21A82ASP-1-0.958-0.98529.774-9.532-9.5320.0000.0000.0000.000
22A83SER00.0390.01925.484-0.261-0.2610.0000.0000.0000.000
23A84TYR0-0.018-0.00623.9510.3200.3200.0000.0000.0000.000
24A85LYS10.9340.98420.41312.78412.7840.0000.0000.0000.000
25A86VAL00.0210.00917.5100.1100.1100.0000.0000.0000.000
26A87SER0-0.0230.00015.785-0.894-0.8940.0000.0000.0000.000
27A88LEU00.0650.02611.928-0.167-0.1670.0000.0000.0000.000
28A89GLN0-0.029-0.0348.429-0.738-0.7380.0000.0000.0000.000
29A90ASN00.0530.04211.8781.5421.5420.0000.0000.0000.000
30A91PHE0-0.027-0.02311.306-1.630-1.6300.0000.0000.0000.000
31A92SER0-0.0230.00110.035-1.429-1.4290.0000.0000.0000.000
32A93SER00.0270.01212.1790.8890.8890.0000.0000.0000.000
33A94SER0-0.078-0.02414.136-0.597-0.5970.0000.0000.0000.000
34A95VAL0-0.010-0.00314.740-0.229-0.2290.0000.0000.0000.000
35A96SER00.0300.02617.6670.5460.5460.0000.0000.0000.000
36A97LEU00.0350.02521.126-0.257-0.2570.0000.0000.0000.000
37A98SER00.0880.04623.0070.5790.5790.0000.0000.0000.000
38A99TYR0-0.062-0.06526.459-0.130-0.1300.0000.0000.0000.000
39A100MET0-0.058-0.03829.3070.3900.3900.0000.0000.0000.000
40A101ALA00.0270.04025.0230.0880.0880.0000.0000.0000.000
41A102PHE00.026-0.00325.890-0.444-0.4440.0000.0000.0000.000
42A103PRO00.0460.02128.5510.2600.2600.0000.0000.0000.000
43A104ASN0-0.045-0.01731.3550.1240.1240.0000.0000.0000.000
44A105ALA00.0180.05131.6010.3050.3050.0000.0000.0000.000
45A106SER00.009-0.01533.5940.1890.1890.0000.0000.0000.000
46A107LYS10.9680.96235.2148.4048.4040.0000.0000.0000.000
47A108LYS10.9300.97737.3887.0567.0560.0000.0000.0000.000
48A109ASN0-0.075-0.03735.4400.0380.0380.0000.0000.0000.000
49A110ARG10.9921.00331.0989.0489.0480.0000.0000.0000.000
50A111PRO00.0180.02229.3600.1200.1200.0000.0000.0000.000
51A112THR0-0.019-0.02331.5120.1480.1480.0000.0000.0000.000
52A113LEU0-0.0160.00925.1830.0210.0210.0000.0000.0000.000
53A114GLN0-0.017-0.02228.1930.4380.4380.0000.0000.0000.000
54A115VAL0-0.016-0.02125.356-0.413-0.4130.0000.0000.0000.000
55A116GLY0-0.019-0.01124.0430.2630.2630.0000.0000.0000.000
56A117ASP-1-0.810-0.88224.268-11.331-11.3310.0000.0000.0000.000
57A118LEU0-0.032-0.02519.780-0.629-0.6290.0000.0000.0000.000
58A119VAL0-0.003-0.00219.7750.5970.5970.0000.0000.0000.000
59A120TYR0-0.015-0.02816.229-0.960-0.9600.0000.0000.0000.000
60A121ALA00.0300.00018.0540.9100.9100.0000.0000.0000.000
61A122ARG10.8690.95017.40012.35212.3520.0000.0000.0000.000
62A123VAL0-0.019-0.00213.2850.7180.7180.0000.0000.0000.000
63A124CYS0-0.065-0.00316.696-0.183-0.1830.0000.0000.0000.000
64A125THR00.002-0.01819.0600.0010.0010.0000.0000.0000.000
65A126ALA00.007-0.01614.143-0.446-0.4460.0000.0000.0000.000
66A127GLU-1-0.932-0.94915.589-14.239-14.2390.0000.0000.0000.000
67A128LYS10.8320.88913.64015.96515.9650.0000.0000.0000.000
68A129DGL-1-0.849-0.91713.233-16.131-16.1310.0000.0000.0000.000
69A130LEU0-0.029-0.00316.9270.8100.8100.0000.0000.0000.000
70A131GLU-1-0.946-0.96716.873-14.252-14.2520.0000.0000.0000.000
71A132ALA00.0010.00715.0880.1910.1910.0000.0000.0000.000
72A133GLU-1-0.858-0.92217.164-12.086-12.0860.0000.0000.0000.000
73A134ILE0-0.026-0.03316.668-0.726-0.7260.0000.0000.0000.000
74A135GLU-1-0.879-0.96519.480-11.478-11.4780.0000.0000.0000.000
75A136CYS0-0.048-0.03621.519-0.652-0.6520.0000.0000.0000.000
76A137PHE0-0.001-0.00623.9720.5080.5080.0000.0000.0000.000
77A138ASP-1-0.839-0.90624.597-12.293-12.2930.0000.0000.0000.000
78A139SER00.010-0.01624.5030.3430.3430.0000.0000.0000.000
79A140THR0-0.037-0.00326.8000.3930.3930.0000.0000.0000.000
80A141THR0-0.056-0.04628.8260.4230.4230.0000.0000.0000.000
81A142GLY00.0250.02429.6660.3740.3740.0000.0000.0000.000
82A143ARG10.9160.94830.0449.6819.6810.0000.0000.0000.000
83A144ASP-1-0.817-0.92027.651-11.115-11.1150.0000.0000.0000.000
84A145ALA0-0.042-0.01225.258-0.443-0.4430.0000.0000.0000.000
85A146GLY00.0150.01324.146-0.514-0.5140.0000.0000.0000.000
86A147PHE0-0.086-0.02519.308-0.515-0.5150.0000.0000.0000.000
87A148GLY00.0270.00322.9360.6360.6360.0000.0000.0000.000
88A149ILE0-0.015-0.00323.319-0.696-0.6960.0000.0000.0000.000
89A150LEU0-0.041-0.01319.870-0.122-0.1220.0000.0000.0000.000
90A151GLU-1-0.909-0.96024.152-10.552-10.5520.0000.0000.0000.000
91A152ASP-1-0.881-0.95626.807-10.555-10.5550.0000.0000.0000.000
92A153GLY0-0.008-0.00923.6360.0840.0840.0000.0000.0000.000
93A154MET0-0.092-0.04521.0980.1640.1640.0000.0000.0000.000
94A155ILE00.0320.01015.554-0.467-0.4670.0000.0000.0000.000
95A156ILE0-0.060-0.01913.3590.3530.3530.0000.0000.0000.000
96A157ASP-1-0.844-0.90011.128-22.701-22.7010.0000.0000.0000.000
97A158VAL0-0.035-0.0268.519-0.162-0.1620.0000.0000.0000.000
98A159ASN0-0.005-0.0083.985-8.495-8.320-0.001-0.021-0.1540.000
99A160LEU00.045-0.0032.133-1.831-0.9881.858-0.588-2.114-0.004
100A161ASN0-0.041-0.0172.9334.0094.7780.030-0.243-0.557-0.002
101A162PHE00.0370.0194.4946.7226.827-0.001-0.017-0.0860.000
102A163ALA00.0530.0327.7573.5123.5120.0000.0000.0000.000
103A164ARG10.9730.9866.47836.62036.6200.0000.0000.0000.000
104A165GLN0-0.011-0.0058.1885.3375.3370.0000.0000.0000.000
105A166LEU0-0.013-0.00610.3272.3932.3930.0000.0000.0000.000
106A167LEU0-0.023-0.00312.2771.5311.5310.0000.0000.0000.000
107A168PHE00.006-0.00510.9620.9680.9680.0000.0000.0000.000
108A169ASN0-0.038-0.01712.8442.3722.3720.0000.0000.0000.000
109A170ASN00.0410.00914.763-0.131-0.1310.0000.0000.0000.000
110A171ASP-1-0.876-0.93017.296-15.143-15.1430.0000.0000.0000.000
111A172PHE0-0.045-0.01411.635-0.126-0.1260.0000.0000.0000.000
112A173PRO00.0140.00115.8320.6910.6910.0000.0000.0000.000
113A174LEU0-0.0040.00214.7570.8560.8560.0000.0000.0000.000
114A175LEU00.0630.03017.7630.8080.8080.0000.0000.0000.000
115A176LYS10.8860.94118.75916.70416.7040.0000.0000.0000.000
116A177VAL0-0.043-0.02120.7010.6990.6990.0000.0000.0000.000
117A178LEU00.008-0.01219.4650.5130.5130.0000.0000.0000.000
118A179ALA0-0.0080.00823.1990.5530.5530.0000.0000.0000.000
119A180ALA0-0.036-0.01625.7250.5040.5040.0000.0000.0000.000
120A181HIS0-0.063-0.01825.4900.6700.6700.0000.0000.0000.000
121A182THR00.0050.00826.3060.6030.6030.0000.0000.0000.000
122A183LYS10.9870.99927.3419.3639.3630.0000.0000.0000.000
123A184PHE0-0.033-0.02421.759-0.083-0.0830.0000.0000.0000.000
124A185GLU-1-0.913-0.93824.543-11.572-11.5720.0000.0000.0000.000
125A186VAL0-0.032-0.03818.086-0.380-0.3800.0000.0000.0000.000
126A187ALA00.0350.03718.7580.2830.2830.0000.0000.0000.000
127A188ILE0-0.009-0.01112.867-0.733-0.7330.0000.0000.0000.000
128A189GLY00.0480.04613.1400.5280.5280.0000.0000.0000.000
129A190LEU00.000-0.0228.840-2.609-2.6090.0000.0000.0000.000
130A191ASN0-0.078-0.0577.706-4.337-4.3370.0000.0000.0000.000
131A192GLY0-0.031-0.0077.854-1.458-1.4580.0000.0000.0000.000
132A193LYS10.8650.9278.53022.01222.0120.0000.0000.0000.000
133A194ILE0-0.022-0.00312.013-0.017-0.0170.0000.0000.0000.000
134A195TRP00.0320.02314.6430.2180.2180.0000.0000.0000.000
135A196VAL0-0.012-0.01118.327-0.001-0.0010.0000.0000.0000.000
136A197LYS10.9630.98921.05011.56411.5640.0000.0000.0000.000
137A198CYS0-0.084-0.03524.825-0.170-0.1700.0000.0000.0000.000
138A199GLU-1-0.920-0.95227.788-9.114-9.1140.0000.0000.0000.000
139A200GLU-1-0.857-0.91131.333-9.017-9.0170.0000.0000.0000.000
140A201LEU00.018-0.00928.128-0.455-0.4550.0000.0000.0000.000
141A202SER00.0410.00728.289-0.352-0.3520.0000.0000.0000.000
142A203ASN00.0390.00028.121-0.204-0.2040.0000.0000.0000.000
143A204THR00.0470.02524.217-0.614-0.6140.0000.0000.0000.000
144A205LEU00.016-0.00523.613-0.741-0.7410.0000.0000.0000.000
145A206ALA00.0150.02823.526-0.584-0.5840.0000.0000.0000.000
146A207CYS0-0.0140.01921.543-0.638-0.6380.0000.0000.0000.000
147A208TYR00.0100.00518.616-1.103-1.1030.0000.0000.0000.000
148A209ARG10.8950.94018.61811.47411.4740.0000.0000.0000.000
149A210THR0-0.021-0.03119.018-0.562-0.5620.0000.0000.0000.000
150A211ILE0-0.002-0.00214.634-0.950-0.9500.0000.0000.0000.000
151A212MET00.0060.00514.580-1.594-1.5940.0000.0000.0000.000
152A213GLU-1-0.735-0.86314.284-16.546-16.5460.0000.0000.0000.000
153A214CYS0-0.063-0.03714.711-0.324-0.3240.0000.0000.0000.000
154A215CYS0-0.054-0.0199.331-2.376-2.3760.0000.0000.0000.000
155A216GLN0-0.052-0.0209.941-2.832-2.8320.0000.0000.0000.000
156A217LYS10.8710.93111.60016.39116.3910.0000.0000.0000.000
157A218ASN0-0.029-0.0048.016-3.126-3.1260.0000.0000.0000.000
158A219ASP-1-0.802-0.88411.154-21.079-21.0790.0000.0000.0000.000
159A220THR0-0.038-0.03913.4781.2781.2780.0000.0000.0000.000
160A221ALA0-0.007-0.00415.8000.8660.8660.0000.0000.0000.000
161A222ALA00.0180.01017.6470.9400.9400.0000.0000.0000.000
162A223PHE00.006-0.00512.9550.4840.4840.0000.0000.0000.000
163A224LYS10.9820.98918.91012.20712.2070.0000.0000.0000.000
164A225ASP-1-0.887-0.94722.505-12.042-12.0420.0000.0000.0000.000
165A226ILE0-0.088-0.03817.4250.4650.4650.0000.0000.0000.000
166A227ALA00.0250.01121.6530.3310.3310.0000.0000.0000.000
167A228LYS10.9690.98923.21211.21211.2120.0000.0000.0000.000
168A229ARG10.8090.90221.50114.05414.0540.0000.0000.0000.000
169A230GLN0-0.019-0.01221.3940.8920.8920.0000.0000.0000.000
170A231PHE00.0410.00623.7480.1500.1500.0000.0000.0000.000
171A232LYS10.8560.94427.99210.27610.2760.0000.0000.0000.000
172A233GLU-1-0.919-0.96330.091-10.338-10.3380.0000.0000.0000.000
173A234ILE00.0020.00029.1180.1250.1250.0000.0000.0000.000
174A235LEU0-0.041-0.00832.877-0.034-0.0340.0000.0000.0000.000
175A236THR0-0.022-0.01630.9960.1100.1100.0000.0000.0000.000