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: 5JJMZ

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2274191.495218
FMO2-HF: Nuclear repulsion 2195085.787803
FMO2-HF: Total energy -79105.707415
FMO2-MP2: Total energy -79336.687342


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.
-4.727-0.3920.109-1.978-2.4640.007
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 : 0.018 / q_NPA : 0.010
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].
3A5GLN0-0.035-0.0203.219-3.8640.4660.110-1.977-2.4620.007
4A6GLN00.0220.0085.704-0.893-0.888-0.001-0.001-0.0020.000
5A7SER0-0.013-0.0239.541-0.052-0.0520.0000.0000.0000.000
6A8MET00.0580.01911.234-0.028-0.0280.0000.0000.0000.000
7A9VAL00.0340.02214.588-0.011-0.0110.0000.0000.0000.000
8A10ASP-1-0.771-0.86312.689-0.012-0.0120.0000.0000.0000.000
9A11THR0-0.002-0.00214.2610.0370.0370.0000.0000.0000.000
10A12PHE0-0.023-0.01816.440-0.014-0.0140.0000.0000.0000.000
11A13ARG10.7760.88515.609-0.009-0.0090.0000.0000.0000.000
12A14ALA00.0020.00717.816-0.021-0.0210.0000.0000.0000.000
13A15SER00.0280.03019.828-0.021-0.0210.0000.0000.0000.000
14A16LEU0-0.007-0.00622.202-0.013-0.0130.0000.0000.0000.000
15A17PHE0-0.040-0.04122.570-0.025-0.0250.0000.0000.0000.000
16A18ASP-1-0.907-0.95620.6970.1750.1750.0000.0000.0000.000
17A19ASN0-0.122-0.05824.1110.0110.0110.0000.0000.0000.000
18A20GLN0-0.025-0.02227.379-0.017-0.0170.0000.0000.0000.000
19A21ASP-1-0.835-0.89929.7020.0390.0390.0000.0000.0000.000
20A22ILE0-0.0120.00428.249-0.007-0.0070.0000.0000.0000.000
21A23THR0-0.124-0.07832.298-0.011-0.0110.0000.0000.0000.000
22A24VAL0-0.062-0.03831.7860.0000.0000.0000.0000.0000.000
23A25ALA00.0530.03734.784-0.005-0.0050.0000.0000.0000.000
24A26ASP-1-0.805-0.91736.1860.0070.0070.0000.0000.0000.000
25A27GLN00.001-0.00737.586-0.002-0.0020.0000.0000.0000.000
26A28GLN00.0330.00533.239-0.003-0.0030.0000.0000.0000.000
27A29ILE0-0.0020.00232.0750.0000.0000.0000.0000.0000.000
28A30GLN0-0.082-0.05233.487-0.004-0.0040.0000.0000.0000.000
29A31ALA0-0.039-0.00734.220-0.001-0.0010.0000.0000.0000.000
30A32LEU0-0.0090.01827.9250.0070.0070.0000.0000.0000.000
31A33PRO0-0.0080.01026.799-0.011-0.0110.0000.0000.0000.000
32A34TYR00.0500.01223.860-0.015-0.0150.0000.0000.0000.000
33A35SER00.018-0.00427.2970.0060.0060.0000.0000.0000.000
34A36THR0-0.0010.00027.117-0.005-0.0050.0000.0000.0000.000
35A37MET0-0.044-0.01827.915-0.003-0.0030.0000.0000.0000.000
36A38TYR00.0060.00029.9160.0040.0040.0000.0000.0000.000
37A39LEU00.0190.00827.957-0.007-0.0070.0000.0000.0000.000
38A40ARG10.7880.86431.7250.0630.0630.0000.0000.0000.000
39A41LEU00.0430.01729.154-0.009-0.0090.0000.0000.0000.000
40A42ASN0-0.015-0.01733.7610.0040.0040.0000.0000.0000.000
41A43GLU-1-0.889-0.94936.942-0.071-0.0710.0000.0000.0000.000
42A44GLY00.0000.01435.9270.0060.0060.0000.0000.0000.000
43A45GLN00.006-0.00733.6980.0020.0020.0000.0000.0000.000
44A46ARG10.9160.97033.8640.0130.0130.0000.0000.0000.000
45A47ILE00.003-0.00127.3850.0090.0090.0000.0000.0000.000
46A48PHE0-0.001-0.01427.936-0.004-0.0040.0000.0000.0000.000
47A49VAL0-0.0010.00224.721-0.003-0.0030.0000.0000.0000.000
48A50VAL00.0040.00722.0930.0080.0080.0000.0000.0000.000
49A51LEU0-0.031-0.01223.234-0.020-0.0200.0000.0000.0000.000
50A52GLY0-0.0120.00119.6450.0220.0220.0000.0000.0000.000
51A53TYR0-0.013-0.01715.6200.0040.0040.0000.0000.0000.000
52A54ILE00.002-0.00620.602-0.006-0.0060.0000.0000.0000.000
53A55GLU-1-0.844-0.90117.738-0.414-0.4140.0000.0000.0000.000
54A56GLN00.018-0.00720.685-0.003-0.0030.0000.0000.0000.000
55A57GLU-1-0.802-0.87525.266-0.153-0.1530.0000.0000.0000.000
56A58GLN00.0050.02123.286-0.001-0.0010.0000.0000.0000.000
57A59SER00.000-0.00624.154-0.001-0.0010.0000.0000.0000.000
58A60LYS10.7870.89519.9050.3220.3220.0000.0000.0000.000
59A61TRP00.012-0.01022.0100.0320.0320.0000.0000.0000.000
60A62LEU00.0190.00617.376-0.023-0.0230.0000.0000.0000.000
61A63SER00.0580.02621.3620.0290.0290.0000.0000.0000.000
62A64GLN00.0700.03020.855-0.012-0.0120.0000.0000.0000.000
63A65ASP-1-0.930-0.96820.261-0.129-0.1290.0000.0000.0000.000
64A66ASN0-0.045-0.01614.342-0.051-0.0510.0000.0000.0000.000
65A67ALA00.0030.01717.907-0.069-0.0690.0000.0000.0000.000
66A68MET0-0.035-0.01718.1620.0250.0250.0000.0000.0000.000
67A69LEU00.0110.00421.301-0.011-0.0110.0000.0000.0000.000
68A70VAL0-0.010-0.00822.1240.0020.0020.0000.0000.0000.000
69A71THR00.0150.00324.8700.0030.0030.0000.0000.0000.000
70A72HIS0-0.007-0.01227.7630.0010.0010.0000.0000.0000.000
71A73ASN0-0.013-0.01230.5010.0080.0080.0000.0000.0000.000
72A74GLY00.0570.02832.4660.0050.0050.0000.0000.0000.000
73A75ARG10.7510.84632.7250.1270.1270.0000.0000.0000.000
74A76LEU0-0.001-0.01628.704-0.009-0.0090.0000.0000.0000.000
75A77LEU0-0.026-0.02727.9570.0000.0000.0000.0000.0000.000
76A78LYS10.8740.92821.5010.3650.3650.0000.0000.0000.000
77A79THR0-0.004-0.00624.1030.0230.0230.0000.0000.0000.000
78A80VAL0-0.023-0.01718.251-0.033-0.0330.0000.0000.0000.000
79A81LYS10.9100.94815.3930.4280.4280.0000.0000.0000.000
80A82LEU00.0360.04121.4090.0220.0220.0000.0000.0000.000
81A83ASN0-0.002-0.00125.053-0.019-0.0190.0000.0000.0000.000
82A84ASN0-0.002-0.00327.066-0.022-0.0220.0000.0000.0000.000
83A85ASN0-0.008-0.01424.5750.0060.0060.0000.0000.0000.000
84A86LEU00.0480.04427.386-0.002-0.0020.0000.0000.0000.000
85A87LEU0-0.036-0.02824.562-0.023-0.0230.0000.0000.0000.000
86A88GLU-1-0.941-0.97125.959-0.325-0.3250.0000.0000.0000.000
87A89VAL00.0320.01728.5790.0200.0200.0000.0000.0000.000
88A90THR00.0200.00131.351-0.002-0.0020.0000.0000.0000.000
89A91ASN00.003-0.03333.4030.0070.0070.0000.0000.0000.000
90A92SER00.0440.02431.1700.0100.0100.0000.0000.0000.000
91A93GLY0-0.036-0.01333.6130.0040.0040.0000.0000.0000.000
92A94GLN0-0.039-0.02334.5210.0060.0060.0000.0000.0000.000
93A95ASP-1-0.742-0.84535.883-0.120-0.1200.0000.0000.0000.000
94A96PRO00.0260.00637.8820.0010.0010.0000.0000.0000.000
95A97LEU0-0.0060.00336.7970.0060.0060.0000.0000.0000.000
96A98ARG10.7820.87331.3960.1610.1610.0000.0000.0000.000
97A99ASN0-0.043-0.02636.7490.0060.0060.0000.0000.0000.000
98A100ALA00.0510.02239.4210.0040.0040.0000.0000.0000.000
99A101LEU0-0.0040.00941.2560.0030.0030.0000.0000.0000.000
100A102ALA0-0.036-0.00843.6680.0030.0030.0000.0000.0000.000
101A103ILE0-0.0400.00641.541-0.001-0.0010.0000.0000.0000.000
102A104LYS10.8780.94145.6570.0750.0750.0000.0000.0000.000
103A105ASP-1-0.770-0.86648.844-0.064-0.0640.0000.0000.0000.000
104A106GLY00.0380.03050.1860.0010.0010.0000.0000.0000.000
105A107SER0-0.081-0.05745.631-0.003-0.0030.0000.0000.0000.000
106A108ARG10.9440.96945.6770.0870.0870.0000.0000.0000.000
107A109TRP0-0.0190.00035.0510.0000.0000.0000.0000.0000.000
108A110THR00.011-0.00741.7260.0030.0030.0000.0000.0000.000
109A111ARG10.7740.89536.3390.1280.1280.0000.0000.0000.000
110A112ASP-1-0.769-0.85135.486-0.164-0.1640.0000.0000.0000.000
111A113ILE0-0.038-0.00833.160-0.008-0.0080.0000.0000.0000.000
112A114LEU00.0190.01028.3980.0060.0060.0000.0000.0000.000
113A115TRP0-0.021-0.02329.691-0.011-0.0110.0000.0000.0000.000
114A116SER0-0.007-0.00327.723-0.007-0.0070.0000.0000.0000.000
115A117GLU-1-0.872-0.95329.814-0.143-0.1430.0000.0000.0000.000
116A118ASP-1-0.841-0.91330.907-0.155-0.1550.0000.0000.0000.000
117A119ASN0-0.064-0.04025.3000.0110.0110.0000.0000.0000.000
118A120HIS00.0080.03428.812-0.013-0.0130.0000.0000.0000.000
119A121PHE00.0080.00225.843-0.002-0.0020.0000.0000.0000.000
120A122ARG10.8580.93231.5540.1920.1920.0000.0000.0000.000
121A123SER00.0420.01233.343-0.015-0.0150.0000.0000.0000.000
122A124ALA0-0.030-0.00635.5720.0090.0090.0000.0000.0000.000
123A125THR00.004-0.00637.834-0.004-0.0040.0000.0000.0000.000
124A126LEU0-0.038-0.03537.7080.0080.0080.0000.0000.0000.000
125A127SER0-0.014-0.01141.140-0.004-0.0040.0000.0000.0000.000
126A128SER0-0.043-0.02542.0160.0010.0010.0000.0000.0000.000
127A129THR0-0.026-0.03044.5130.0000.0000.0000.0000.0000.000
128A130PHE0-0.009-0.00540.2500.0010.0010.0000.0000.0000.000
129A131SER0-0.045-0.03846.3600.0030.0030.0000.0000.0000.000
130A132PHE0-0.018-0.01248.3980.0000.0000.0000.0000.0000.000
131A133ALA00.0140.00749.1990.0020.0020.0000.0000.0000.000
132A134GLY00.0090.01050.4390.0030.0030.0000.0000.0000.000
133A135LEU0-0.040-0.00849.308-0.002-0.0020.0000.0000.0000.000
134A136GLU-1-0.846-0.91746.954-0.041-0.0410.0000.0000.0000.000
135A137THR0-0.087-0.06447.3040.0010.0010.0000.0000.0000.000
136A138LEU00.0510.05441.7610.0020.0020.0000.0000.0000.000
137A139ASN0-0.061-0.05343.9280.0030.0030.0000.0000.0000.000
138A140ILE0-0.015-0.01237.683-0.002-0.0020.0000.0000.0000.000
139A141ALA0-0.010-0.00136.9150.0010.0010.0000.0000.0000.000
140A142GLY00.0730.05038.9870.0020.0020.0000.0000.0000.000
141A143ARG10.8920.95640.2310.0080.0080.0000.0000.0000.000
142A144ASN00.0250.01643.177-0.003-0.0030.0000.0000.0000.000
143A145VAL0-0.017-0.00941.5810.0010.0010.0000.0000.0000.000
144A146LEU00.0250.03144.753-0.002-0.0020.0000.0000.0000.000
145A147CYS0-0.046-0.01743.599-0.003-0.0030.0000.0000.0000.000
146A148ASN00.0540.01945.5010.0040.0040.0000.0000.0000.000
147A149VAL0-0.003-0.00244.957-0.004-0.0040.0000.0000.0000.000
148A150TRP00.0070.00043.4600.0000.0000.0000.0000.0000.000
149A151GLN00.0650.05444.161-0.005-0.0050.0000.0000.0000.000
150A152GLU-1-0.708-0.80440.199-0.115-0.1150.0000.0000.0000.000
151A153GLU-1-0.799-0.87744.109-0.076-0.0760.0000.0000.0000.000
152A154VAL0-0.026-0.03041.033-0.004-0.0040.0000.0000.0000.000
153A155THR00.0180.01044.4150.0040.0040.0000.0000.0000.000
154A156SER00.0230.00641.701-0.005-0.0050.0000.0000.0000.000
155A157THR00.016-0.00143.3210.0060.0060.0000.0000.0000.000
156A158ARG10.8970.96843.1490.1180.1180.0000.0000.0000.000
157A159PRO00.0460.02042.590-0.006-0.0060.0000.0000.0000.000
158A160GLU-1-0.950-0.98544.911-0.091-0.0910.0000.0000.0000.000
159A161LYS10.7870.89141.8120.1140.1140.0000.0000.0000.000
160A162GLN00.0220.00645.653-0.001-0.0010.0000.0000.0000.000
161A163TRP0-0.044-0.02139.3720.0010.0010.0000.0000.0000.000
162A164GLN00.000-0.00644.8330.0010.0010.0000.0000.0000.000
163A165ASN0-0.055-0.02539.121-0.002-0.0020.0000.0000.0000.000
164A166THR00.006-0.01640.9950.0040.0040.0000.0000.0000.000
165A167PHE0-0.026-0.02436.432-0.004-0.0040.0000.0000.0000.000
166A168TRP00.001-0.01640.7840.0000.0000.0000.0000.0000.000
167A169VAL0-0.028-0.01640.347-0.001-0.0010.0000.0000.0000.000
168A170ASP-1-0.805-0.89640.573-0.038-0.0380.0000.0000.0000.000
169A171SER0-0.051-0.04742.310-0.002-0.0020.0000.0000.0000.000
170A172ALA0-0.018-0.00544.0750.0000.0000.0000.0000.0000.000
171A173THR0-0.065-0.05039.130-0.002-0.0020.0000.0000.0000.000
172A174GLY00.0080.00739.699-0.005-0.0050.0000.0000.0000.000
173A175GLN00.0060.00133.912-0.002-0.0020.0000.0000.0000.000
174A176VAL0-0.018-0.00435.9150.0060.0060.0000.0000.0000.000
175A177ARG10.8750.95135.9520.0370.0370.0000.0000.0000.000
176A178GLN00.0200.01837.1370.0050.0050.0000.0000.0000.000
177A179SER0-0.034-0.00335.578-0.005-0.0050.0000.0000.0000.000
178A180ARG10.9660.97137.5110.0720.0720.0000.0000.0000.000
179A181GLN0-0.006-0.00234.430-0.007-0.0070.0000.0000.0000.000
180A182MET0-0.0320.01236.5900.0030.0030.0000.0000.0000.000
181A183LEU0-0.0220.00229.209-0.006-0.0060.0000.0000.0000.000
182A184GLY00.0540.01632.682-0.016-0.0160.0000.0000.0000.000
183A185ALA0-0.005-0.00935.2150.0090.0090.0000.0000.0000.000
184A186GLY00.0230.02238.7170.0060.0060.0000.0000.0000.000
185A187VAL0-0.047-0.02536.3640.0080.0080.0000.0000.0000.000
186A188ILE00.0360.01432.662-0.006-0.0060.0000.0000.0000.000
187A189PRO00.0680.03435.256-0.007-0.0070.0000.0000.0000.000
188A190VAL0-0.023-0.01931.622-0.002-0.0020.0000.0000.0000.000
189A191GLU-1-0.817-0.86234.718-0.062-0.0620.0000.0000.0000.000
190A192MET0-0.027-0.01730.767-0.006-0.0060.0000.0000.0000.000
191A193THR00.020-0.00333.872-0.001-0.0010.0000.0000.0000.000
192A194PHE00.008-0.00229.9650.0020.0020.0000.0000.0000.000
193A195LEU00.0010.00732.0810.0030.0030.0000.0000.0000.000
194A196LYS10.8740.93831.2310.0000.0000.0000.0000.0000.000
195A197PRO0-0.034-0.00334.176-0.008-0.0080.0000.0000.0000.000
196A198ALA00.0330.01235.3630.0040.0040.0000.0000.0000.000
197A199PRO0-0.030-0.01135.7990.0020.0020.0000.0000.0000.000
198A200LEU00.0060.00438.604-0.005-0.0050.0000.0000.0000.000