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: N1JMQ

Calculation Name: 2I1S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I1S

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PRU3

Base Structure: X-ray

Registration Date: 2023-06-19

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1970933.115627
FMO2-HF: Nuclear repulsion 1898065.424079
FMO2-HF: Total energy -72867.691548
FMO2-MP2: Total energy -73081.722968


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:4:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-8.212-4.9340.84-1.719-2.40.012
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.016
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].
3A6GLU-1-0.869-0.9223.742-2.128-0.445-0.009-0.773-0.9010.001
4A7LYS10.8800.9236.0440.6920.6920.0000.0000.0000.000
5A8VAL00.0190.0079.0920.2600.2600.0000.0000.0000.000
6A9TYR00.005-0.00711.552-0.171-0.1710.0000.0000.0000.000
7A10HIS00.0220.01014.5730.0370.0370.0000.0000.0000.000
8A11LEU00.0420.01916.187-0.070-0.0700.0000.0000.0000.000
9A12LYS10.8680.93419.418-0.164-0.1640.0000.0000.0000.000
10A13LEU00.0410.02419.865-0.009-0.0090.0000.0000.0000.000
11A14SER0-0.062-0.04423.971-0.009-0.0090.0000.0000.0000.000
12A15ILE00.1040.06827.733-0.002-0.0020.0000.0000.0000.000
13A16LYS10.7750.86929.993-0.135-0.1350.0000.0000.0000.000
14A17GLY00.008-0.00232.6070.0010.0010.0000.0000.0000.000
15A18ILE00.0690.07234.300-0.004-0.0040.0000.0000.0000.000
16A19THR0-0.141-0.06535.6470.0020.0020.0000.0000.0000.000
17A20PRO00.1010.02336.833-0.003-0.0030.0000.0000.0000.000
18A21GLN0-0.0130.01330.7860.0110.0110.0000.0000.0000.000
19A22ILE00.1110.08629.3660.0020.0020.0000.0000.0000.000
20A23TRP0-0.075-0.05625.5260.0080.0080.0000.0000.0000.000
21A24ARG10.8760.94122.884-0.258-0.2580.0000.0000.0000.000
22A25ARG10.7660.86121.411-0.232-0.2320.0000.0000.0000.000
23A26ILE00.0840.05016.3620.0150.0150.0000.0000.0000.000
24A27GLN0-0.074-0.04313.930-0.018-0.0180.0000.0000.0000.000
25A28VAL00.0580.01911.7540.1060.1060.0000.0000.0000.000
26A29PRO00.0400.0196.358-0.237-0.2370.0000.0000.0000.000
27A30GLU-1-0.808-0.9027.612-0.716-0.7160.0000.0000.0000.000
28A31ASN0-0.052-0.0273.412-0.728-0.3090.011-0.148-0.2830.001
29A32TYR00.0470.0167.522-0.053-0.0530.0000.0000.0000.000
30A33THR0-0.049-0.0349.956-0.302-0.3020.0000.0000.0000.000
31A34PHE00.0550.00312.4540.0630.0630.0000.0000.0000.000
32A35LEU0-0.0140.01614.9630.0120.0120.0000.0000.0000.000
33A36ASP-1-0.808-0.89511.0561.0451.0450.0000.0000.0000.000
34A37LEU0-0.0060.00213.6510.0210.0210.0000.0000.0000.000
35A38HIS0-0.058-0.01615.875-0.029-0.0290.0000.0000.0000.000
36A39LYS10.9210.94913.589-0.815-0.8150.0000.0000.0000.000
37A40ALA0-0.0240.00015.1920.0010.0010.0000.0000.0000.000
38A41ILE0-0.027-0.03117.231-0.036-0.0360.0000.0000.0000.000
39A42GLN00.0330.00720.650-0.030-0.0300.0000.0000.0000.000
40A43ALA00.0280.03718.970-0.022-0.0220.0000.0000.0000.000
41A44VAL0-0.062-0.05719.776-0.025-0.0250.0000.0000.0000.000
42A45MET0-0.115-0.05622.334-0.032-0.0320.0000.0000.0000.000
43A46ASP-1-0.903-0.93124.5060.2510.2510.0000.0000.0000.000
44A47TRP0-0.098-0.04725.198-0.014-0.0140.0000.0000.0000.000
45A48GLU-1-0.815-0.90025.3800.2630.2630.0000.0000.0000.000
46A49ASP-1-0.928-0.95522.5970.3260.3260.0000.0000.0000.000
47A50TYR0-0.053-0.04125.697-0.011-0.0110.0000.0000.0000.000
48A51HIS10.7630.90728.429-0.187-0.1870.0000.0000.0000.000
49A52LEU0-0.026-0.00527.5880.0140.0140.0000.0000.0000.000
50A53HIS10.8670.90421.382-0.280-0.2800.0000.0000.0000.000
51A54GLU-1-0.893-0.92524.4520.1220.1220.0000.0000.0000.000
52A55PHE0-0.016-0.01319.3090.0080.0080.0000.0000.0000.000
53A56GLU-1-0.853-0.91024.0130.0880.0880.0000.0000.0000.000
54A57MET0-0.062-0.02420.4180.0200.0200.0000.0000.0000.000
55A58VAL00.0240.02524.664-0.010-0.0100.0000.0000.0000.000
56A59ASN00.006-0.00622.381-0.009-0.0090.0000.0000.0000.000
57A60PRO0-0.0080.01120.465-0.011-0.0110.0000.0000.0000.000
58A61LYS10.8110.89217.4120.0810.0810.0000.0000.0000.000
59A62THR0-0.009-0.01523.899-0.004-0.0040.0000.0000.0000.000
60A63GLY0-0.0150.00026.5550.0000.0000.0000.0000.0000.000
61A64MET0-0.029-0.01028.0420.0050.0050.0000.0000.0000.000
62A65LEU0-0.016-0.00527.1580.0020.0020.0000.0000.0000.000
63A66ASP-1-0.778-0.86323.3890.0400.0400.0000.0000.0000.000
64A67LYS10.8030.87625.501-0.094-0.0940.0000.0000.0000.000
65A68ILE0-0.041-0.02219.309-0.005-0.0050.0000.0000.0000.000
66A69GLY00.0920.03722.4340.0160.0160.0000.0000.0000.000
67A70ALA00.0070.00621.9240.0000.0000.0000.0000.0000.000
68A71GLU-1-0.827-0.89419.5020.1500.1500.0000.0000.0000.000
69A72GLY00.0590.05623.1790.0030.0030.0000.0000.0000.000
70A73ASP-1-1.018-1.00825.9670.0620.0620.0000.0000.0000.000
71A81PRO00.0230.00528.211-0.004-0.0040.0000.0000.0000.000
72A82LEU0-0.041-0.01324.7490.0040.0040.0000.0000.0000.000
73A83VAL0-0.010-0.00220.093-0.008-0.0080.0000.0000.0000.000
74A84SER0-0.028-0.04218.9830.0320.0320.0000.0000.0000.000
75A85GLU-1-0.772-0.87918.0040.3030.3030.0000.0000.0000.000
76A86LYS10.8760.92515.178-0.194-0.1940.0000.0000.0000.000
77A87LYS10.8360.90713.775-0.072-0.0720.0000.0000.0000.000
78A88ALA00.0000.01314.194-0.032-0.0320.0000.0000.0000.000
79A89LYS10.9310.9748.459-0.181-0.1810.0000.0000.0000.000
80A90LEU00.0390.01012.748-0.070-0.0700.0000.0000.0000.000
81A91SER00.0130.00911.441-0.031-0.0310.0000.0000.0000.000
82A92ASP-1-0.926-0.93613.427-0.192-0.1920.0000.0000.0000.000
83A93TYR0-0.077-0.08915.946-0.014-0.0140.0000.0000.0000.000
84A94PHE0-0.0130.00016.783-0.008-0.0080.0000.0000.0000.000
85A95THR0-0.023-0.03317.432-0.020-0.0200.0000.0000.0000.000
86A96LEU0-0.034-0.04219.6270.0310.0310.0000.0000.0000.000
87A97GLU-1-0.897-0.92722.077-0.020-0.0200.0000.0000.0000.000
88A98ASN0-0.043-0.02621.8850.0000.0000.0000.0000.0000.000
89A99LYS10.9000.94621.951-0.086-0.0860.0000.0000.0000.000
90A100GLU-1-0.844-0.90622.5580.1520.1520.0000.0000.0000.000
91A101ALA00.0350.02322.045-0.012-0.0120.0000.0000.0000.000
92A102LEU0-0.049-0.02224.1150.0050.0050.0000.0000.0000.000
93A103TYR00.002-0.02522.216-0.005-0.0050.0000.0000.0000.000
94A104THR00.0350.01925.393-0.008-0.0080.0000.0000.0000.000
95A105TYR0-0.049-0.07026.2330.0140.0140.0000.0000.0000.000
96A106ASP-1-0.735-0.88128.1590.1400.1400.0000.0000.0000.000
97A107PHE0-0.092-0.05328.745-0.007-0.0070.0000.0000.0000.000
98A108GLY0-0.032-0.00133.641-0.010-0.0100.0000.0000.0000.000
99A109ASP-1-0.773-0.89534.5080.1280.1280.0000.0000.0000.000
100A110ASN0-0.114-0.05733.2630.0020.0020.0000.0000.0000.000
101A111TRP00.0700.05830.044-0.002-0.0020.0000.0000.0000.000
102A112GLN0-0.001-0.01229.2220.0020.0020.0000.0000.0000.000
103A113VAL00.0200.01024.336-0.003-0.0030.0000.0000.0000.000
104A114LYS10.8670.94226.156-0.125-0.1250.0000.0000.0000.000
105A115VAL00.0410.02420.0170.0210.0210.0000.0000.0000.000
106A116ARG10.8220.89322.999-0.154-0.1540.0000.0000.0000.000
107A117LEU00.0120.00717.4100.0280.0280.0000.0000.0000.000
108A118GLU-1-0.908-0.94320.6550.1610.1610.0000.0000.0000.000
109A119LYS10.8540.92118.806-0.255-0.2550.0000.0000.0000.000
110A120ILE00.0530.04613.6090.0550.0550.0000.0000.0000.000
111A121LEU0-0.051-0.03214.072-0.067-0.0670.0000.0000.0000.000
112A122PRO0-0.012-0.00110.5310.0590.0590.0000.0000.0000.000
113A123ARG10.8900.9592.800-7.467-6.2910.838-0.798-1.2160.010
114A124LYS10.9300.9649.896-0.499-0.4990.0000.0000.0000.000
115A125GLU-1-0.893-0.96810.3520.5240.5240.0000.0000.0000.000
116A126GLY0-0.0010.00510.677-0.065-0.0650.0000.0000.0000.000
117A127VAL0-0.095-0.03611.776-0.030-0.0300.0000.0000.0000.000
118A128GLU-1-0.926-0.9549.7681.3201.3200.0000.0000.0000.000
119A129TYR0-0.074-0.0268.626-0.215-0.2150.0000.0000.0000.000
120A130PRO00.0210.0009.5870.2800.2800.0000.0000.0000.000
121A131ILE0-0.0100.00812.442-0.068-0.0680.0000.0000.0000.000
122A132CYS00.0220.01415.516-0.038-0.0380.0000.0000.0000.000
123A133THR0-0.052-0.03218.497-0.018-0.0180.0000.0000.0000.000
124A134ALA00.000-0.00820.949-0.034-0.0340.0000.0000.0000.000
125A135GLY00.0290.00824.0660.0240.0240.0000.0000.0000.000
126A136LYS10.8630.94026.708-0.163-0.1630.0000.0000.0000.000
127A137ARG10.8750.90530.388-0.130-0.1300.0000.0000.0000.000
128A138ALA00.0950.06730.6020.0200.0200.0000.0000.0000.000
129A139ALA0-0.056-0.03628.228-0.005-0.0050.0000.0000.0000.000
130A140VAL0-0.0240.00530.345-0.006-0.0060.0000.0000.0000.000
131A141PRO00.0810.04231.4300.0130.0130.0000.0000.0000.000
132A142GLU-1-0.727-0.83028.9470.2130.2130.0000.0000.0000.000
133A143ASP-1-0.878-0.94432.8300.1520.1520.0000.0000.0000.000
134A144SER0-0.050-0.03935.242-0.010-0.0100.0000.0000.0000.000
135A145GLY00.0650.02637.737-0.006-0.0060.0000.0000.0000.000
136A146GLY0-0.0060.00536.124-0.006-0.0060.0000.0000.0000.000
137A147VAL0-0.082-0.06135.3440.0000.0000.0000.0000.0000.000
138A148TRP0-0.058-0.03537.697-0.002-0.0020.0000.0000.0000.000
139A149GLY00.0900.06440.694-0.003-0.0030.0000.0000.0000.000
140A150TYR00.0520.01535.5920.0000.0000.0000.0000.0000.000
141A151GLU-1-0.865-0.97039.3730.1120.1120.0000.0000.0000.000
142A152GLU-1-0.983-0.98441.4470.0830.0830.0000.0000.0000.000
143A153MET00.0250.02439.581-0.002-0.0020.0000.0000.0000.000
144A154LEU0-0.010-0.01338.446-0.001-0.0010.0000.0000.0000.000
145A155GLU-1-0.897-0.93442.9220.0830.0830.0000.0000.0000.000
146A156VAL00.0290.02746.347-0.003-0.0030.0000.0000.0000.000
147A157LEU0-0.003-0.00342.129-0.002-0.0020.0000.0000.0000.000
148A158LYS10.6580.82245.025-0.089-0.0890.0000.0000.0000.000
149A159ASP-1-0.894-0.95948.2440.0640.0640.0000.0000.0000.000
150A160SER0-0.007-0.01051.2720.0000.0000.0000.0000.0000.000
151A161GLU-1-1.036-1.01052.1420.0600.0600.0000.0000.0000.000
152A162HIS0-0.0150.00851.6130.0000.0000.0000.0000.0000.000
153A163GLU-1-0.960-0.99353.7620.0650.0650.0000.0000.0000.000
154A164GLU-1-0.935-0.96849.1280.0780.0780.0000.0000.0000.000
155A165TYR0-0.0160.00647.6720.0050.0050.0000.0000.0000.000
156A166GLU-1-0.954-0.99248.3350.0780.0780.0000.0000.0000.000
157A167ASP-1-0.931-0.96348.3550.0830.0830.0000.0000.0000.000
158A168THR0-0.047-0.02744.0360.0060.0060.0000.0000.0000.000
159A169VAL0-0.015-0.01243.7400.0060.0060.0000.0000.0000.000
160A170LEU0-0.047-0.00843.5050.0050.0050.0000.0000.0000.000
161A171TRP0-0.070-0.02737.3590.0070.0070.0000.0000.0000.000
162A172LEU0-0.041-0.03238.2980.0070.0070.0000.0000.0000.000
163A173GLY00.0090.01938.7320.0090.0090.0000.0000.0000.000
164A174ASP-1-0.952-0.99140.8660.1050.1050.0000.0000.0000.000
165A175ASP-1-1.018-1.00536.9190.1460.1460.0000.0000.0000.000
166A176PHE0-0.0140.00734.7990.0070.0070.0000.0000.0000.000
167A177ASP-1-0.811-0.91636.7870.1300.1300.0000.0000.0000.000
168A178PRO00.0130.00835.9670.0110.0110.0000.0000.0000.000
169A179GLU-1-0.867-0.91935.4220.1420.1420.0000.0000.0000.000
170A180TYR0-0.103-0.05629.927-0.002-0.0020.0000.0000.0000.000
171A181PHE0-0.018-0.02724.1060.0140.0140.0000.0000.0000.000
172A182ASP-1-0.753-0.84726.7140.2430.2430.0000.0000.0000.000
173A183PRO0-0.062-0.04022.6880.0160.0160.0000.0000.0000.000
174A184LYS10.7370.83322.295-0.221-0.2210.0000.0000.0000.000
175A185ASP-1-0.787-0.86423.5480.2650.2650.0000.0000.0000.000
176A186VAL0-0.058-0.01719.6190.0100.0100.0000.0000.0000.000
177A187SER0-0.0010.00319.2430.0410.0410.0000.0000.0000.000
178A188PHE0-0.022-0.01214.6940.0150.0150.0000.0000.0000.000