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: VRM31

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 OptHSide
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 -1781479.269544
FMO2-HF: Nuclear repulsion 1711929.496891
FMO2-HF: Total energy -69549.772652
FMO2-MP2: Total energy -69749.42645


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.
-36.985-33.7820.835-1.115-2.923-0.002
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 : 0.953 / q_NPA : 0.967
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].
3A64TYR0-0.035-0.0613.749-3.214-1.644-0.005-0.642-0.9230.001
4A65ILE0-0.0010.0075.3552.9242.9240.0000.0000.0000.000
5A66PRO0-0.007-0.0087.819-0.683-0.6830.0000.0000.0000.000
6A67SER0-0.032-0.00710.4470.6530.6530.0000.0000.0000.000
7A68VAL00.0500.00212.223-0.013-0.0130.0000.0000.0000.000
8A69ASN0-0.037-0.03115.282-0.038-0.0380.0000.0000.0000.000
9A70ASP-1-0.764-0.82810.732-26.609-26.6090.0000.0000.0000.000
10A71PHE00.0270.01813.8931.0841.0840.0000.0000.0000.000
11A72VAL0-0.031-0.01611.853-2.050-2.0500.0000.0000.0000.000
12A73ILE0-0.005-0.00113.9751.2541.2540.0000.0000.0000.000
13A74GLY00.0050.00014.823-1.194-1.1940.0000.0000.0000.000
14A75VAL0-0.0270.00117.0850.5000.5000.0000.0000.0000.000
15A76ILE0-0.0010.00419.896-0.231-0.2310.0000.0000.0000.000
16A77ILE0-0.003-0.01419.5160.2150.2150.0000.0000.0000.000
17A78GLY00.008-0.00123.1180.3630.3630.0000.0000.0000.000
18A79THR0-0.019-0.00425.854-0.229-0.2290.0000.0000.0000.000
19A80PHE00.0180.01725.5120.2190.2190.0000.0000.0000.000
20A81SER00.0100.01229.9020.0740.0740.0000.0000.0000.000
21A82ASP-1-0.927-0.96929.584-9.535-9.5350.0000.0000.0000.000
22A83SER00.0230.00525.761-0.238-0.2380.0000.0000.0000.000
23A84TYR0-0.052-0.02924.3510.3240.3240.0000.0000.0000.000
24A85LYS10.8240.92120.80912.56112.5610.0000.0000.0000.000
25A86VAL00.0230.01118.0450.1220.1220.0000.0000.0000.000
26A87SER0-0.0120.01115.794-0.783-0.7830.0000.0000.0000.000
27A88LEU00.0720.02712.134-0.145-0.1450.0000.0000.0000.000
28A89GLN0-0.025-0.0368.7330.1060.1060.0000.0000.0000.000
29A90ASN00.0480.04412.1081.3781.3780.0000.0000.0000.000
30A91PHE0-0.019-0.02211.398-1.617-1.6170.0000.0000.0000.000
31A92SER0-0.028-0.0019.904-1.449-1.4490.0000.0000.0000.000
32A93SER00.0290.01312.1480.7780.7780.0000.0000.0000.000
33A94SER0-0.092-0.04414.115-0.671-0.6710.0000.0000.0000.000
34A95VAL0-0.002-0.00514.972-0.229-0.2290.0000.0000.0000.000
35A96SER00.0040.00917.8110.6060.6060.0000.0000.0000.000
36A97LEU00.0450.02921.366-0.252-0.2520.0000.0000.0000.000
37A98SER00.0660.03823.2450.5870.5870.0000.0000.0000.000
38A99TYR0-0.047-0.06026.695-0.074-0.0740.0000.0000.0000.000
39A100MET0-0.047-0.03629.5690.3980.3980.0000.0000.0000.000
40A101ALA00.0240.03625.2280.0780.0780.0000.0000.0000.000
41A102PHE00.0300.00226.068-0.435-0.4350.0000.0000.0000.000
42A103PRO00.0500.02428.7330.2460.2460.0000.0000.0000.000
43A104ASN0-0.041-0.01731.5330.1340.1340.0000.0000.0000.000
44A105ALA00.0100.05131.8120.2980.2980.0000.0000.0000.000
45A106SER00.003-0.01133.7990.1860.1860.0000.0000.0000.000
46A107LYS10.9590.95835.3778.3798.3790.0000.0000.0000.000
47A108LYS10.9290.97537.6177.0057.0050.0000.0000.0000.000
48A109ASN0-0.063-0.03335.2640.0840.0840.0000.0000.0000.000
49A110ARG10.9300.96631.6179.0079.0070.0000.0000.0000.000
50A111PRO00.0310.02529.5510.1060.1060.0000.0000.0000.000
51A112THR0-0.002-0.00531.6890.1620.1620.0000.0000.0000.000
52A113LEU00.0020.02225.3890.0220.0220.0000.0000.0000.000
53A114GLN0-0.026-0.01828.3890.5160.5160.0000.0000.0000.000
54A115VAL0-0.010-0.02125.572-0.398-0.3980.0000.0000.0000.000
55A116GLY0-0.010-0.00824.2520.2680.2680.0000.0000.0000.000
56A117ASP-1-0.797-0.88124.465-11.148-11.1480.0000.0000.0000.000
57A118LEU0-0.033-0.02120.092-0.591-0.5910.0000.0000.0000.000
58A119VAL0-0.003-0.00619.9680.5730.5730.0000.0000.0000.000
59A120TYR0-0.013-0.02116.412-0.879-0.8790.0000.0000.0000.000
60A121ALA00.028-0.00118.2270.8850.8850.0000.0000.0000.000
61A122ARG10.8210.90617.56612.32612.3260.0000.0000.0000.000
62A123VAL0-0.018-0.00713.4660.7100.7100.0000.0000.0000.000
63A124CYS0-0.058-0.00316.886-0.187-0.1870.0000.0000.0000.000
64A125THR00.001-0.03319.167-0.023-0.0230.0000.0000.0000.000
65A126ALA00.003-0.01914.090-0.431-0.4310.0000.0000.0000.000
66A127GLU-1-0.920-0.94315.521-14.532-14.5320.0000.0000.0000.000
67A128LYS10.8300.89013.61916.13216.1320.0000.0000.0000.000
68A129DGL-1-0.850-0.91813.264-16.243-16.2430.0000.0000.0000.000
69A130LEU0-0.0220.00216.9690.8380.8380.0000.0000.0000.000
70A131GLU-1-0.839-0.89016.859-14.217-14.2170.0000.0000.0000.000
71A132ALA00.0130.01115.0870.2100.2100.0000.0000.0000.000
72A133GLU-1-0.868-0.91317.159-12.043-12.0430.0000.0000.0000.000
73A134ILE0-0.025-0.03116.831-0.697-0.6970.0000.0000.0000.000
74A135GLU-1-0.844-0.93119.696-11.561-11.5610.0000.0000.0000.000
75A136CYS0-0.048-0.03621.705-0.648-0.6480.0000.0000.0000.000
76A137PHE00.001-0.00324.1560.4990.4990.0000.0000.0000.000
77A138ASP-1-0.763-0.84624.753-12.080-12.0800.0000.0000.0000.000
78A139SER00.000-0.00425.0400.2540.2540.0000.0000.0000.000
79A140THR0-0.059-0.01727.0620.3680.3680.0000.0000.0000.000
80A141THR0-0.078-0.08929.3110.4280.4280.0000.0000.0000.000
81A142GLY00.0100.01930.0240.3720.3720.0000.0000.0000.000
82A143ARG10.9050.94830.4029.7189.7180.0000.0000.0000.000
83A144ASP-1-0.819-0.92627.860-10.903-10.9030.0000.0000.0000.000
84A145ALA0-0.034-0.01425.747-0.466-0.4660.0000.0000.0000.000
85A146GLY00.0140.01524.481-0.497-0.4970.0000.0000.0000.000
86A147PHE0-0.076-0.02219.486-0.471-0.4710.0000.0000.0000.000
87A148GLY00.0220.00323.1110.6250.6250.0000.0000.0000.000
88A149ILE0-0.027-0.00623.492-0.680-0.6800.0000.0000.0000.000
89A150LEU0-0.039-0.01219.974-0.120-0.1200.0000.0000.0000.000
90A151GLU-1-0.900-0.95924.348-10.439-10.4390.0000.0000.0000.000
91A152ASP-1-0.865-0.94627.181-10.419-10.4190.0000.0000.0000.000
92A153GLY0-0.012-0.00924.0610.0790.0790.0000.0000.0000.000
93A154MET0-0.096-0.04521.6120.1410.1410.0000.0000.0000.000
94A155ILE00.0360.01116.009-0.434-0.4340.0000.0000.0000.000
95A156ILE0-0.068-0.02513.9850.3080.3080.0000.0000.0000.000
96A157ASP-1-0.798-0.88211.734-23.636-23.6360.0000.0000.0000.000
97A158VAL0-0.035-0.0229.023-0.115-0.1150.0000.0000.0000.000
98A159ASN00.0140.0014.493-8.383-8.281-0.001-0.005-0.0950.000
99A160LEU00.0480.0022.284-1.009-0.0720.827-0.337-1.428-0.002
100A161ASN0-0.038-0.0183.1103.8204.3410.015-0.126-0.410-0.001
101A162PHE00.0370.0224.8786.2236.296-0.001-0.005-0.0670.000
102A163ALA00.0400.0268.0033.2373.2370.0000.0000.0000.000
103A164ARG10.9040.9446.93435.11935.1190.0000.0000.0000.000
104A165GLN0-0.004-0.0058.4015.1265.1260.0000.0000.0000.000
105A166LEU0-0.017-0.00710.5692.3262.3260.0000.0000.0000.000
106A167LEU0-0.0140.00012.5931.4491.4490.0000.0000.0000.000
107A168PHE0-0.001-0.00611.5481.0331.0330.0000.0000.0000.000
108A169ASN0-0.038-0.01413.0412.2982.2980.0000.0000.0000.000
109A170ASN00.0370.01014.8800.2280.2280.0000.0000.0000.000
110A171ASP-1-0.874-0.92617.411-15.073-15.0730.0000.0000.0000.000
111A172PHE0-0.030-0.01011.723-0.061-0.0610.0000.0000.0000.000
112A173PRO00.007-0.00316.0760.6550.6550.0000.0000.0000.000
113A174LEU0-0.0070.00614.8990.8520.8520.0000.0000.0000.000
114A175LEU00.0650.02918.1100.7940.7940.0000.0000.0000.000
115A176LYS10.8850.93219.00616.52716.5270.0000.0000.0000.000
116A177VAL0-0.038-0.01620.9650.6880.6880.0000.0000.0000.000
117A178LEU00.017-0.00119.8100.5220.5220.0000.0000.0000.000
118A179ALA0-0.0030.00823.5720.5340.5340.0000.0000.0000.000
119A180ALA0-0.048-0.01826.1820.4900.4900.0000.0000.0000.000
120A181HIS0-0.076-0.03225.8010.6150.6150.0000.0000.0000.000
121A182THR00.0180.01626.6820.5860.5860.0000.0000.0000.000
122A183LYS10.9861.00227.8129.1709.1700.0000.0000.0000.000
123A184PHE0-0.018-0.01922.081-0.095-0.0950.0000.0000.0000.000
124A185GLU-1-0.860-0.92324.854-11.426-11.4260.0000.0000.0000.000
125A186VAL0-0.032-0.04018.336-0.347-0.3470.0000.0000.0000.000
126A187ALA00.0260.03419.0510.2620.2620.0000.0000.0000.000
127A188ILE0-0.014-0.01213.148-0.689-0.6890.0000.0000.0000.000
128A189GLY00.0550.04713.3040.4510.4510.0000.0000.0000.000
129A190LEU0-0.014-0.0279.424-2.428-2.4280.0000.0000.0000.000
130A191ASN0-0.061-0.0397.829-3.894-3.8940.0000.0000.0000.000
131A192GLY0-0.028-0.0158.301-1.366-1.3660.0000.0000.0000.000
132A193LYS10.8080.9048.94822.64622.6460.0000.0000.0000.000
133A194ILE0-0.018-0.00412.201-0.056-0.0560.0000.0000.0000.000
134A195TRP00.0130.01915.0340.2060.2060.0000.0000.0000.000
135A196VAL0-0.010-0.01318.726-0.017-0.0170.0000.0000.0000.000
136A197LYS10.9160.97421.43711.46911.4690.0000.0000.0000.000
137A198CYS0-0.086-0.04225.216-0.180-0.1800.0000.0000.0000.000
138A199GLU-1-0.922-0.95328.167-9.047-9.0470.0000.0000.0000.000
139A200GLU-1-0.858-0.91531.655-8.907-8.9070.0000.0000.0000.000
140A201LEU00.018-0.00628.491-0.449-0.4490.0000.0000.0000.000
141A202SER00.0450.01428.732-0.352-0.3520.0000.0000.0000.000
142A203ASN00.043-0.00128.540-0.230-0.2300.0000.0000.0000.000
143A204THR00.0500.03524.672-0.593-0.5930.0000.0000.0000.000
144A205LEU00.0190.00024.040-0.714-0.7140.0000.0000.0000.000
145A206ALA00.0140.02923.962-0.567-0.5670.0000.0000.0000.000
146A207CYS0-0.0180.00921.930-0.605-0.6050.0000.0000.0000.000
147A208TYR00.0100.00219.366-0.829-0.8290.0000.0000.0000.000
148A209ARG10.8300.89819.05111.04711.0470.0000.0000.0000.000
149A210THR0-0.026-0.03019.501-0.579-0.5790.0000.0000.0000.000
150A211ILE00.0010.00115.057-0.939-0.9390.0000.0000.0000.000
151A212MET00.0030.00515.008-1.491-1.4910.0000.0000.0000.000
152A213GLU-1-0.727-0.82114.782-16.099-16.0990.0000.0000.0000.000
153A214CYS0-0.060-0.03415.106-0.321-0.3210.0000.0000.0000.000
154A215CYS0-0.055-0.0239.659-2.209-2.2090.0000.0000.0000.000
155A216GLN0-0.047-0.02110.361-2.805-2.8050.0000.0000.0000.000
156A217LYS10.8810.92911.99116.08216.0820.0000.0000.0000.000
157A218ASN0-0.040-0.0128.327-2.664-2.6640.0000.0000.0000.000
158A219ASP-1-0.815-0.89211.396-20.366-20.3660.0000.0000.0000.000
159A220THR0-0.034-0.03213.5561.1931.1930.0000.0000.0000.000
160A221ALA0-0.008-0.00315.9260.8850.8850.0000.0000.0000.000
161A222ALA00.0040.00217.8630.9670.9670.0000.0000.0000.000
162A223PHE00.009-0.00113.0870.5780.5780.0000.0000.0000.000
163A224LYS10.9910.99419.17112.13312.1330.0000.0000.0000.000
164A225ASP-1-0.789-0.90022.722-11.404-11.4040.0000.0000.0000.000
165A226ILE0-0.049-0.01417.8050.4590.4590.0000.0000.0000.000
166A227ALA00.0200.01022.0060.3250.3250.0000.0000.0000.000
167A228LYS10.8330.91523.57111.69411.6940.0000.0000.0000.000
168A229ARG10.7800.85821.78113.88513.8850.0000.0000.0000.000
169A230GLN0-0.021-0.01721.9230.7940.7940.0000.0000.0000.000
170A231PHE00.0640.02224.2140.1610.1610.0000.0000.0000.000
171A232LYS10.8590.94328.40510.17910.1790.0000.0000.0000.000
172A233GLU-1-0.874-0.92730.368-10.283-10.2830.0000.0000.0000.000
173A234ILE0-0.007-0.00529.3700.1310.1310.0000.0000.0000.000
174A235LEU0-0.035-0.00533.300-0.037-0.0370.0000.0000.0000.000
175A236THR0-0.025-0.02131.5140.1340.1340.0000.0000.0000.000