Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4JJ7N

Calculation Name: 2IN5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IN5

Chain ID: A

ChEMBL ID:

UniProt ID: P75884

Base Structure: X-ray

Registration Date: 2023-09-21

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2273321.583238
FMO2-HF: Nuclear repulsion 2194216.429687
FMO2-HF: Total energy -79105.153551
FMO2-MP2: Total energy -79336.130114


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:3:HIS)


Summations of interaction energy for fragment #1(A:3:HIS)
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.
-3.987-0.197-0.009-1.781-20.008
Interaction energy analysis for fragmet #1(A:3:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.008
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].
3A5GLN0-0.031-0.0133.707-3.5060.285-0.008-1.780-2.0020.008
4A6GLN00.0260.0015.951-0.741-0.742-0.001-0.0010.0020.000
5A7SER0-0.028-0.0169.754-0.039-0.0390.0000.0000.0000.000
6A8MET00.0720.01511.782-0.033-0.0330.0000.0000.0000.000
7A9VAL00.0260.01715.034-0.016-0.0160.0000.0000.0000.000
8A10ASP-1-0.804-0.88412.8400.0420.0420.0000.0000.0000.000
9A11THR00.0040.00114.3620.0270.0270.0000.0000.0000.000
10A12PHE0-0.030-0.02516.475-0.014-0.0140.0000.0000.0000.000
11A13ARG10.8130.91916.129-0.028-0.0280.0000.0000.0000.000
12A14ALA00.0030.00017.494-0.021-0.0210.0000.0000.0000.000
13A15SER00.0680.03519.600-0.018-0.0180.0000.0000.0000.000
14A16LEU0-0.042-0.00821.843-0.015-0.0150.0000.0000.0000.000
15A17PHE0-0.057-0.04922.279-0.018-0.0180.0000.0000.0000.000
16A18ASP-1-0.920-0.94120.3660.1840.1840.0000.0000.0000.000
17A19ASN0-0.134-0.07023.9840.0060.0060.0000.0000.0000.000
18A20GLN0-0.026-0.02227.082-0.018-0.0180.0000.0000.0000.000
19A21ASP-1-0.829-0.90829.3890.0510.0510.0000.0000.0000.000
20A22ILE0-0.022-0.00927.993-0.007-0.0070.0000.0000.0000.000
21A23THR0-0.101-0.06332.077-0.011-0.0110.0000.0000.0000.000
22A24VAL0-0.076-0.01632.6570.0000.0000.0000.0000.0000.000
23A25ALA00.0560.02535.110-0.003-0.0030.0000.0000.0000.000
24A26ASP-1-0.843-0.94336.6200.0140.0140.0000.0000.0000.000
25A27GLN0-0.023-0.01138.733-0.003-0.0030.0000.0000.0000.000
26A28GLN00.042-0.00433.568-0.002-0.0020.0000.0000.0000.000
27A29ILE00.0120.01932.7230.0020.0020.0000.0000.0000.000
28A30GLN0-0.061-0.03233.883-0.003-0.0030.0000.0000.0000.000
29A31ALA0-0.0210.00334.4380.0000.0000.0000.0000.0000.000
30A32LEU0-0.0120.01528.3490.0080.0080.0000.0000.0000.000
31A33PRO00.0190.01127.589-0.011-0.0110.0000.0000.0000.000
32A34TYR00.0170.00624.738-0.014-0.0140.0000.0000.0000.000
33A35SER00.018-0.01028.2530.0050.0050.0000.0000.0000.000
34A36THR00.0060.00727.688-0.001-0.0010.0000.0000.0000.000
35A37MET0-0.038-0.01728.284-0.005-0.0050.0000.0000.0000.000
36A38TYR0-0.012-0.00230.6290.0050.0050.0000.0000.0000.000
37A39LEU00.0310.00428.283-0.006-0.0060.0000.0000.0000.000
38A40ARG10.8200.88531.9900.0500.0500.0000.0000.0000.000
39A41LEU00.0230.01429.176-0.007-0.0070.0000.0000.0000.000
40A42ASN00.0150.00533.3680.0040.0040.0000.0000.0000.000
41A43GLU-1-0.908-0.95636.479-0.057-0.0570.0000.0000.0000.000
42A44GLY0-0.015-0.00335.0360.0060.0060.0000.0000.0000.000
43A45GLN00.016-0.00733.4100.0020.0020.0000.0000.0000.000
44A46ARG10.9050.96133.1770.0050.0050.0000.0000.0000.000
45A47ILE00.0070.00627.1090.0070.0070.0000.0000.0000.000
46A48PHE00.010-0.00228.295-0.006-0.0060.0000.0000.0000.000
47A49VAL0-0.013-0.00525.082-0.002-0.0020.0000.0000.0000.000
48A50VAL00.0280.01322.6620.0080.0080.0000.0000.0000.000
49A51LEU0-0.038-0.01023.917-0.020-0.0200.0000.0000.0000.000
50A52GLY0-0.0090.00620.1630.0190.0190.0000.0000.0000.000
51A53TYR0-0.002-0.01315.7590.0070.0070.0000.0000.0000.000
52A54ILE0-0.001-0.00821.165-0.014-0.0140.0000.0000.0000.000
53A55GLU-1-0.852-0.90317.698-0.349-0.3490.0000.0000.0000.000
54A56GLN00.012-0.00620.807-0.009-0.0090.0000.0000.0000.000
55A57GLU-1-0.824-0.89325.344-0.131-0.1310.0000.0000.0000.000
56A58GLN00.0090.01623.761-0.007-0.0070.0000.0000.0000.000
57A59SER0-0.020-0.01424.2650.0020.0020.0000.0000.0000.000
58A60LYS10.8230.90519.9700.2850.2850.0000.0000.0000.000
59A61TRP0-0.007-0.02422.2460.0290.0290.0000.0000.0000.000
60A62LEU00.0170.00717.760-0.022-0.0220.0000.0000.0000.000
61A63SER00.0460.02421.7220.0270.0270.0000.0000.0000.000
62A64GLN00.0820.03021.494-0.007-0.0070.0000.0000.0000.000
63A65ASP-1-0.964-0.98220.087-0.099-0.0990.0000.0000.0000.000
64A66ASN0-0.062-0.03214.800-0.029-0.0290.0000.0000.0000.000
65A67ALA00.0050.02718.517-0.053-0.0530.0000.0000.0000.000
66A68MET0-0.027-0.02518.3400.0210.0210.0000.0000.0000.000
67A69LEU00.005-0.00321.550-0.012-0.0120.0000.0000.0000.000
68A70VAL0-0.025-0.01022.6470.0050.0050.0000.0000.0000.000
69A71THR00.008-0.00425.3560.0050.0050.0000.0000.0000.000
70A72HIS0-0.012-0.01628.2180.0030.0030.0000.0000.0000.000
71A73ASN00.0110.00430.9070.0070.0070.0000.0000.0000.000
72A74GLY00.0460.01632.8350.0030.0030.0000.0000.0000.000
73A75ARG10.7700.86633.1810.1110.1110.0000.0000.0000.000
74A76LEU0-0.016-0.01828.913-0.008-0.0080.0000.0000.0000.000
75A77LEU0-0.015-0.02228.106-0.002-0.0020.0000.0000.0000.000
76A78LYS10.9340.97321.5740.3570.3570.0000.0000.0000.000
77A79THR00.0180.02324.5670.0170.0170.0000.0000.0000.000
78A80VAL0-0.037-0.02418.627-0.033-0.0330.0000.0000.0000.000
79A81LYS10.9540.97615.1290.4700.4700.0000.0000.0000.000
80A82LEU00.0560.04521.3420.0280.0280.0000.0000.0000.000
81A83ASN0-0.011-0.00724.826-0.016-0.0160.0000.0000.0000.000
82A84ASN00.0440.03526.886-0.021-0.0210.0000.0000.0000.000
83A85ASN0-0.035-0.02924.5580.0030.0030.0000.0000.0000.000
84A86LEU00.0380.03727.320-0.001-0.0010.0000.0000.0000.000
85A87LEU0-0.060-0.07224.712-0.019-0.0190.0000.0000.0000.000
86A88GLU-1-0.944-0.97826.262-0.291-0.2910.0000.0000.0000.000
87A89VAL00.0240.01828.7600.0180.0180.0000.0000.0000.000
88A90THR00.0180.02031.058-0.004-0.0040.0000.0000.0000.000
89A91ASN00.014-0.02733.3360.0080.0080.0000.0000.0000.000
90A92SER00.0620.03230.7830.0110.0110.0000.0000.0000.000
91A93GLY0-0.023-0.01233.9780.0070.0070.0000.0000.0000.000
92A94GLN0-0.037-0.02235.0230.0040.0040.0000.0000.0000.000
93A95ASP-1-0.740-0.83736.220-0.105-0.1050.0000.0000.0000.000
94A96PRO00.0550.01938.2250.0020.0020.0000.0000.0000.000
95A97LEU0-0.024-0.00237.1890.0050.0050.0000.0000.0000.000
96A98ARG10.7850.89131.5260.1390.1390.0000.0000.0000.000
97A99ASN0-0.046-0.03137.1370.0060.0060.0000.0000.0000.000
98A100ALA00.0480.01739.7710.0030.0030.0000.0000.0000.000
99A101LEU00.0030.01841.5370.0020.0020.0000.0000.0000.000
100A102ALA0-0.084-0.02643.8700.0030.0030.0000.0000.0000.000
101A103ILE0-0.0310.00841.843-0.002-0.0020.0000.0000.0000.000
102A104LYS10.9240.96845.9480.0660.0660.0000.0000.0000.000
103A105ASP-1-0.812-0.90648.973-0.057-0.0570.0000.0000.0000.000
104A106GLY00.0410.03250.1030.0010.0010.0000.0000.0000.000
105A107SER0-0.101-0.05845.508-0.003-0.0030.0000.0000.0000.000
106A108ARG10.9590.98545.8720.0810.0810.0000.0000.0000.000
107A109TRP0-0.031-0.01335.3390.0000.0000.0000.0000.0000.000
108A110THR00.013-0.00641.6670.0040.0040.0000.0000.0000.000
109A111ARG10.7880.90936.2770.1150.1150.0000.0000.0000.000
110A112ASP-1-0.801-0.88435.672-0.150-0.1500.0000.0000.0000.000
111A113ILE0-0.043-0.02033.254-0.007-0.0070.0000.0000.0000.000
112A114LEU00.0190.01028.5080.0040.0040.0000.0000.0000.000
113A115TRP0-0.015-0.01829.847-0.011-0.0110.0000.0000.0000.000
114A116SER0-0.030-0.01228.061-0.005-0.0050.0000.0000.0000.000
115A117GLU-1-0.877-0.95530.092-0.133-0.1330.0000.0000.0000.000
116A118ASP-1-0.865-0.93030.385-0.142-0.1420.0000.0000.0000.000
117A119ASN0-0.091-0.05524.9140.0090.0090.0000.0000.0000.000
118A120HIS00.0250.02928.572-0.008-0.0080.0000.0000.0000.000
119A121PHE0-0.009-0.00526.1070.0040.0040.0000.0000.0000.000
120A122ARG10.8930.96031.8750.1760.1760.0000.0000.0000.000
121A123SER00.0580.01333.549-0.014-0.0140.0000.0000.0000.000
122A124ALA0-0.068-0.02135.7420.0090.0090.0000.0000.0000.000
123A125THR00.022-0.00438.068-0.004-0.0040.0000.0000.0000.000
124A126LEU0-0.045-0.02737.7930.0080.0080.0000.0000.0000.000
125A127SER0-0.002-0.00441.246-0.004-0.0040.0000.0000.0000.000
126A128SER0-0.040-0.02842.2590.0020.0020.0000.0000.0000.000
127A129THR00.001-0.02644.8050.0000.0000.0000.0000.0000.000
128A130PHE0-0.048-0.02740.7720.0010.0010.0000.0000.0000.000
129A131SER00.0120.01246.8620.0020.0020.0000.0000.0000.000
130A132PHE0-0.020-0.01949.1390.0010.0010.0000.0000.0000.000
131A133ALA00.009-0.00549.4590.0010.0010.0000.0000.0000.000
132A134GLY00.0000.01251.1580.0030.0030.0000.0000.0000.000
133A135LEU0-0.035-0.01050.009-0.002-0.0020.0000.0000.0000.000
134A136GLU-1-0.842-0.92247.536-0.034-0.0340.0000.0000.0000.000
135A137THR0-0.053-0.02147.9530.0000.0000.0000.0000.0000.000
136A138LEU00.0130.02342.4100.0010.0010.0000.0000.0000.000
137A139ASN0-0.022-0.03744.8050.0030.0030.0000.0000.0000.000
138A140ILE0-0.023-0.02038.248-0.001-0.0010.0000.0000.0000.000
139A141ALA0-0.038-0.01737.7050.0010.0010.0000.0000.0000.000
140A142GLY00.1020.06139.7810.0030.0030.0000.0000.0000.000
141A143ARG10.8890.95740.8940.0010.0010.0000.0000.0000.000
142A144ASN00.0070.00944.116-0.003-0.0030.0000.0000.0000.000
143A145VAL0-0.022-0.01041.9990.0010.0010.0000.0000.0000.000
144A146LEU00.0090.02145.166-0.001-0.0010.0000.0000.0000.000
145A147CYS0-0.029-0.04343.952-0.002-0.0020.0000.0000.0000.000
146A148ASN00.0140.00245.6860.0040.0040.0000.0000.0000.000
147A149VAL00.013-0.00745.498-0.003-0.0030.0000.0000.0000.000
148A150TRP0-0.0060.00044.100-0.001-0.0010.0000.0000.0000.000
149A151GLN00.0520.03544.788-0.005-0.0050.0000.0000.0000.000
150A152GLU-1-0.718-0.79340.621-0.101-0.1010.0000.0000.0000.000
151A153GLU-1-0.780-0.88144.725-0.067-0.0670.0000.0000.0000.000
152A154VAL0-0.021-0.02641.208-0.004-0.0040.0000.0000.0000.000
153A155THR00.0310.01144.5780.0040.0040.0000.0000.0000.000
154A156SER0-0.005-0.00941.951-0.004-0.0040.0000.0000.0000.000
155A157THR00.0240.00343.4800.0050.0050.0000.0000.0000.000
156A158ARG10.8730.97143.4220.1100.1100.0000.0000.0000.000
157A159PRO00.0530.01142.983-0.006-0.0060.0000.0000.0000.000
158A160GLU-1-0.943-0.98545.167-0.084-0.0840.0000.0000.0000.000
159A161LYS10.8070.91341.7920.1050.1050.0000.0000.0000.000
160A162GLN00.0300.01145.935-0.001-0.0010.0000.0000.0000.000
161A163TRP0-0.0150.00439.4540.0010.0010.0000.0000.0000.000
162A164GLN0-0.017-0.01845.2280.0010.0010.0000.0000.0000.000
163A165ASN0-0.050-0.02539.538-0.001-0.0010.0000.0000.0000.000
164A166THR00.006-0.01441.6110.0030.0030.0000.0000.0000.000
165A167PHE0-0.038-0.02336.842-0.003-0.0030.0000.0000.0000.000
166A168TRP00.002-0.02041.0270.0000.0000.0000.0000.0000.000
167A169VAL0-0.017-0.01340.903-0.001-0.0010.0000.0000.0000.000
168A170ASP-1-0.768-0.85241.221-0.027-0.0270.0000.0000.0000.000
169A171SER0-0.067-0.03942.964-0.002-0.0020.0000.0000.0000.000
170A172ALA00.0030.00644.7300.0000.0000.0000.0000.0000.000
171A173THR0-0.053-0.03739.673-0.002-0.0020.0000.0000.0000.000
172A174GLY00.000-0.00540.566-0.004-0.0040.0000.0000.0000.000
173A175GLN0-0.018-0.01134.356-0.002-0.0020.0000.0000.0000.000
174A176VAL0-0.0070.00136.4170.0050.0050.0000.0000.0000.000
175A177ARG10.8660.92536.4670.0270.0270.0000.0000.0000.000
176A178GLN00.0150.00737.6980.0060.0060.0000.0000.0000.000
177A179SER0-0.032-0.00135.872-0.005-0.0050.0000.0000.0000.000
178A180ARG10.9650.97937.7340.0600.0600.0000.0000.0000.000
179A181GLN00.007-0.00734.864-0.007-0.0070.0000.0000.0000.000
180A182MET0-0.0290.02037.1350.0010.0010.0000.0000.0000.000
181A183LEU0-0.0200.00129.579-0.005-0.0050.0000.0000.0000.000
182A184GLY00.0510.01733.167-0.014-0.0140.0000.0000.0000.000
183A185ALA0-0.012-0.00935.3840.0080.0080.0000.0000.0000.000
184A186GLY0-0.011-0.01038.8800.0040.0040.0000.0000.0000.000
185A187VAL0-0.028-0.02036.5210.0070.0070.0000.0000.0000.000
186A188ILE00.0240.00232.921-0.006-0.0060.0000.0000.0000.000
187A189PRO00.0560.03535.544-0.006-0.0060.0000.0000.0000.000
188A190VAL0-0.018-0.01532.191-0.001-0.0010.0000.0000.0000.000
189A191GLU-1-0.805-0.86935.166-0.048-0.0480.0000.0000.0000.000
190A192MET0-0.039-0.02331.423-0.004-0.0040.0000.0000.0000.000
191A193THR00.0110.00434.5380.0000.0000.0000.0000.0000.000
192A194PHE0-0.004-0.00430.6970.0020.0020.0000.0000.0000.000
193A195LEU00.0200.01932.5680.0030.0030.0000.0000.0000.000
194A196LYS10.8540.93631.581-0.012-0.0120.0000.0000.0000.000
195A197PRO0-0.049-0.01534.478-0.007-0.0070.0000.0000.0000.000
196A198ALA00.0270.00935.4460.0050.0050.0000.0000.0000.000
197A199PRO0-0.018-0.00636.4680.0000.0000.0000.0000.0000.000
198A200LEU00.0230.01339.297-0.005-0.0050.0000.0000.0000.000