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: 89VKY

Calculation Name: 2I3F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I3F

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2581651.535374
FMO2-HF: Nuclear repulsion 2499322.149986
FMO2-HF: Total energy -82329.385389
FMO2-MP2: Total energy -82572.560467


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:11:ASP)


Summations of interaction energy for fragment #1(A:11:ASP)
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.
-173.505-179.04230.062-13.376-11.150.143
Interaction energy analysis for fragmet #1(A:11:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.795 / q_NPA : -0.877
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].
3A13GLY00.011-0.0013.301-7.469-5.7150.027-0.734-1.0470.003
4A14ILE00.0070.0043.125-8.705-6.8520.147-0.804-1.1960.005
5A15ILE0-0.027-0.0015.132-5.080-4.930-0.001-0.007-0.1430.000
6A16VAL00.002-0.0018.067-3.523-3.5230.0000.0000.0000.000
7A17ILE00.0000.0076.622-2.400-2.4000.0000.0000.0000.000
8A18LEU0-0.007-0.0167.090-2.261-2.2610.0000.0000.0000.000
9A19TRP00.005-0.00910.605-2.981-2.9810.0000.0000.0000.000
10A20LYS10.8210.92412.947-18.949-18.9490.0000.0000.0000.000
11A21GLN0-0.047-0.02911.938-0.136-0.1360.0000.0000.0000.000
12A22VAL0-0.059-0.01215.018-1.070-1.0700.0000.0000.0000.000
13A23THR0-0.048-0.02817.531-0.641-0.6410.0000.0000.0000.000
14A24VAL00.0350.02420.640-0.324-0.3240.0000.0000.0000.000
15A25LYS10.9390.96323.666-12.989-12.9890.0000.0000.0000.000
16A26GLU-1-0.862-0.93926.6349.9659.9650.0000.0000.0000.000
17A27ASP-1-0.880-0.93629.6969.9239.9230.0000.0000.0000.000
18A28GLY00.0030.01328.116-0.129-0.1290.0000.0000.0000.000
19A29LYS10.8090.89927.004-10.179-10.1790.0000.0000.0000.000
20A30VAL0-0.018-0.02120.8420.3830.3830.0000.0000.0000.000
21A31PRO00.0170.02019.726-0.187-0.1870.0000.0000.0000.000
22A32LEU00.028-0.00120.0160.9340.9340.0000.0000.0000.000
23A33GLU-1-0.813-0.92517.76817.34917.3490.0000.0000.0000.000
24A34PRO0-0.026-0.01115.3031.3441.3440.0000.0000.0000.000
25A35PHE00.0340.01914.7571.5531.5530.0000.0000.0000.000
26A36LEU00.0220.00915.5101.0591.0590.0000.0000.0000.000
27A37THR0-0.038-0.02510.4961.4201.4200.0000.0000.0000.000
28A38ALA00.0060.00210.8572.7832.7830.0000.0000.0000.000
29A39ALA00.010-0.00211.5311.5091.5090.0000.0000.0000.000
30A40LYS10.8740.9337.836-36.367-36.3670.0000.0000.0000.000
31A41GLU-1-0.774-0.8765.29854.57754.644-0.001-0.001-0.0650.000
32A42VAL00.0050.0128.9491.9581.9580.0000.0000.0000.000
33A43LEU0-0.040-0.03111.069-1.226-1.2260.0000.0000.0000.000
34A44ARG10.7950.8591.677-124.297-133.81729.890-11.756-8.6140.135
35A45VAL0-0.012-0.0068.839-1.136-1.1360.0000.0000.0000.000
36A46VAL0-0.024-0.01311.646-1.824-1.8240.0000.0000.0000.000
37A47ASP-1-0.811-0.90110.41724.72024.7200.0000.0000.0000.000
38A48ALA0-0.0190.00210.243-1.090-1.0900.0000.0000.0000.000
39A49PHE0-0.006-0.00312.051-1.668-1.6680.0000.0000.0000.000
40A50GLY00.0010.01015.378-1.044-1.0440.0000.0000.0000.000
41A51SER00.0170.00116.785-0.189-0.1890.0000.0000.0000.000
42A52GLY00.0130.01119.727-0.592-0.5920.0000.0000.0000.000
43A53PHE00.019-0.00116.867-0.581-0.5810.0000.0000.0000.000
44A54ARG10.9681.00019.540-12.702-12.7020.0000.0000.0000.000
45A55ILE0-0.013-0.01020.8500.2240.2240.0000.0000.0000.000
46A56VAL00.0780.03818.582-0.049-0.0490.0000.0000.0000.000
47A57LYS10.8330.90513.026-23.019-23.0190.0000.0000.0000.000
48A58ASN0-0.027-0.02517.8680.8830.8830.0000.0000.0000.000
49A59ASP-1-0.864-0.92420.47213.42413.4240.0000.0000.0000.000
50A60ILE0-0.016-0.01215.573-0.129-0.1290.0000.0000.0000.000
51A61ALA00.0110.00516.4360.0730.0730.0000.0000.0000.000
52A62GLY0-0.032-0.02017.653-0.234-0.2340.0000.0000.0000.000
53A63ASN00.0150.00321.020-1.028-1.0280.0000.0000.0000.000
54A64ILE00.0790.04314.769-0.392-0.3920.0000.0000.0000.000
55A65LYS10.9410.98218.907-15.053-15.0530.0000.0000.0000.000
56A66LYS10.8420.90520.377-13.288-13.2880.0000.0000.0000.000
57A67LEU00.0470.04021.219-0.518-0.5180.0000.0000.0000.000
58A68TYR0-0.012-0.00716.230-0.036-0.0360.0000.0000.0000.000
59A69ARG10.8900.94921.940-11.803-11.8030.0000.0000.0000.000
60A70ALA0-0.023-0.02325.117-0.431-0.4310.0000.0000.0000.000
61A71ASN00.0490.03023.699-0.863-0.8630.0000.0000.0000.000
62A72GLN0-0.056-0.02025.199-0.310-0.3100.0000.0000.0000.000
63A73THR0-0.045-0.02926.895-0.098-0.0980.0000.0000.0000.000
64A74VAL0-0.0050.00029.164-0.231-0.2310.0000.0000.0000.000
65A75HIS0-0.042-0.01426.7690.0990.0990.0000.0000.0000.000
66A76ALA0-0.0040.01726.877-0.068-0.0680.0000.0000.0000.000
67A77GLU-1-0.889-0.94725.00012.35912.3590.0000.0000.0000.000
68A78THR0-0.052-0.03823.9560.5740.5740.0000.0000.0000.000
69A79LEU0-0.004-0.01321.343-0.228-0.2280.0000.0000.0000.000
70A80GLN00.0620.03225.223-0.095-0.0950.0000.0000.0000.000
71A81GLU-1-0.831-0.90428.49310.54210.5420.0000.0000.0000.000
72A82LEU00.0190.01125.662-0.280-0.2800.0000.0000.0000.000
73A83ILE0-0.042-0.01927.394-0.291-0.2910.0000.0000.0000.000
74A84ILE0-0.032-0.02630.567-0.378-0.3780.0000.0000.0000.000
75A85ALA0-0.027-0.00632.212-0.339-0.3390.0000.0000.0000.000
76A86GLU-1-0.782-0.86830.86710.35110.3510.0000.0000.0000.000
77A87ASN0-0.043-0.00534.194-0.147-0.1470.0000.0000.0000.000
78A88SER00.0560.01835.207-0.284-0.2840.0000.0000.0000.000
79A89PRO00.0210.01834.5380.3430.3430.0000.0000.0000.000
80A90ASP-1-0.929-0.96633.9738.9858.9850.0000.0000.0000.000
81A91GLY0-0.039-0.00632.8960.0770.0770.0000.0000.0000.000
82A92LEU0-0.030-0.03129.1100.3310.3310.0000.0000.0000.000
83A93ALA0-0.005-0.02826.6270.5300.5300.0000.0000.0000.000
84A94THR00.001-0.01026.9570.4250.4250.0000.0000.0000.000
85A95VAL00.0180.01228.7250.3180.3180.0000.0000.0000.000
86A96ALA0-0.062-0.02924.0820.3570.3570.0000.0000.0000.000
87A97LEU00.023-0.00122.7120.6790.6790.0000.0000.0000.000
88A98LEU00.0300.03524.8110.3780.3780.0000.0000.0000.000
89A99TRP0-0.009-0.02025.1200.2550.2550.0000.0000.0000.000
90A100LEU0-0.046-0.01317.8970.5100.5100.0000.0000.0000.000
91A101LYS10.8490.92021.188-11.170-11.1700.0000.0000.0000.000
92A102ARG10.8320.88923.159-10.557-10.5570.0000.0000.0000.000
93A103ALA0-0.030-0.01720.2820.1580.1580.0000.0000.0000.000
94A104PHE00.020-0.00615.7480.7960.7960.0000.0000.0000.000
95A105GLN00.0370.02119.9190.1580.1580.0000.0000.0000.000
96A106PHE0-0.051-0.01820.229-0.062-0.0620.0000.0000.0000.000
97A107ILE0-0.019-0.02315.6560.1210.1210.0000.0000.0000.000
98A108ALA00.0560.03018.7020.3970.3970.0000.0000.0000.000
99A109SER0-0.021-0.03119.785-0.311-0.3110.0000.0000.0000.000
100A110PHE0-0.031-0.03316.696-0.271-0.2710.0000.0000.0000.000
101A111LEU00.015-0.00414.5260.0080.0080.0000.0000.0000.000
102A112ARG10.9090.94318.217-12.695-12.6950.0000.0000.0000.000
103A113ARG10.8300.89720.729-12.549-12.5490.0000.0000.0000.000
104A114LEU0-0.032-0.00616.469-0.304-0.3040.0000.0000.0000.000
105A115VAL0-0.032-0.01516.127-0.076-0.0760.0000.0000.0000.000
106A116VAL0-0.0040.01119.333-0.267-0.2670.0000.0000.0000.000
107A117THR0-0.081-0.04222.855-0.805-0.8050.0000.0000.0000.000
108A118ASP-1-0.855-0.92223.50012.51012.5100.0000.0000.0000.000
109A119LYS10.8070.89825.511-11.304-11.3040.0000.0000.0000.000
110A120SER00.0490.01924.0920.7160.7160.0000.0000.0000.000
111A121LEU00.0530.03117.604-0.071-0.0710.0000.0000.0000.000
112A122GLU-1-0.800-0.90221.98611.65511.6550.0000.0000.0000.000
113A123GLN0-0.006-0.01024.566-0.190-0.1900.0000.0000.0000.000
114A124CYS0-0.057-0.01622.308-0.192-0.1920.0000.0000.0000.000
115A125VAL00.0210.00121.544-0.007-0.0070.0000.0000.0000.000
116A126THR0-0.013-0.00823.521-0.320-0.3200.0000.0000.0000.000
117A127GLU-1-0.805-0.88227.11210.89910.8990.0000.0000.0000.000
118A128ALA00.0040.02123.539-0.212-0.2120.0000.0000.0000.000
119A129TYR00.014-0.01125.523-0.316-0.3160.0000.0000.0000.000
120A130ASN0-0.013-0.01426.828-0.459-0.4590.0000.0000.0000.000
121A131CYS0-0.091-0.01227.971-0.188-0.1880.0000.0000.0000.000
122A132THR00.042-0.01125.2320.1620.1620.0000.0000.0000.000
123A133LEU00.0350.00423.533-0.311-0.3110.0000.0000.0000.000
124A134ARG10.8400.93027.959-9.985-9.9850.0000.0000.0000.000
125A135PRO0-0.002-0.00330.759-0.218-0.2180.0000.0000.0000.000
126A136CYS0-0.0240.01229.931-0.116-0.1160.0000.0000.0000.000
127A137HIS00.0070.02726.300-0.101-0.1010.0000.0000.0000.000
128A138SER00.0980.05032.030-0.212-0.2120.0000.0000.0000.000
129A139ALA00.0600.00834.0860.2040.2040.0000.0000.0000.000
130A140VAL0-0.031-0.01534.5320.1050.1050.0000.0000.0000.000
131A141ILE00.0530.02129.1720.1800.1800.0000.0000.0000.000
132A142GLN00.0200.01930.1520.2680.2680.0000.0000.0000.000
133A143LYS10.9240.96530.920-8.618-8.6180.0000.0000.0000.000
134A144VAL0-0.0140.00027.4910.1460.1460.0000.0000.0000.000
135A145PHE00.0160.00923.2660.4000.4000.0000.0000.0000.000
136A146TRP00.005-0.01026.7440.4100.4100.0000.0000.0000.000
137A147GLY0-0.0010.00628.5500.0330.0330.0000.0000.0000.000
138A148GLY00.0060.00024.6190.1950.1950.0000.0000.0000.000
139A149VAL00.000-0.01123.7160.5470.5470.0000.0000.0000.000
140A150LYS10.8390.91224.945-10.983-10.9830.0000.0000.0000.000
141A151LEU0-0.062-0.01922.704-0.059-0.0590.0000.0000.0000.000
142A152ALA0-0.030-0.00420.9490.8080.8080.0000.0000.0000.000
143A153PRO0-0.040-0.00316.736-0.366-0.3660.0000.0000.0000.000
144A154SER00.003-0.03319.575-0.095-0.0950.0000.0000.0000.000
145A155ARG10.9040.95017.693-13.711-13.7110.0000.0000.0000.000
146A156GLU-1-0.819-0.89816.17916.45416.4540.0000.0000.0000.000
147A157ARG10.9030.94814.839-15.227-15.2270.0000.0000.0000.000
148A158PHE0-0.002-0.00213.5771.5811.5810.0000.0000.0000.000
149A159TYR00.0800.01311.8991.7451.7450.0000.0000.0000.000
150A160ARG10.9450.96410.182-16.637-16.6370.0000.0000.0000.000
151A161LYS10.8040.9209.531-20.665-20.6650.0000.0000.0000.000
152A162LEU0-0.0580.0047.1063.3263.3260.0000.0000.0000.000
153A163HIS00.0460.0014.3116.0006.1590.000-0.074-0.0850.000
154A164PRO00.0140.0106.393-4.118-4.1180.0000.0000.0000.000
155A165ASP-1-0.827-0.9028.97818.50618.5060.0000.0000.0000.000
156A166LEU0-0.005-0.02310.5641.1781.1780.0000.0000.0000.000
157A167ASN0-0.015-0.01113.166-0.840-0.8400.0000.0000.0000.000
158A168ILE00.0020.0116.924-0.088-0.0880.0000.0000.0000.000
159A169ALA0-0.0180.0039.1910.9090.9090.0000.0000.0000.000
160A170LYS10.8330.89810.135-16.038-16.0380.0000.0000.0000.000
161A171ALA00.0640.03711.716-0.355-0.3550.0000.0000.0000.000
162A172LYS10.7820.8636.877-26.366-26.3660.0000.0000.0000.000
163A173ILE0-0.017-0.00210.0980.2080.2080.0000.0000.0000.000
164A174GLU-1-0.833-0.90712.45316.23816.2380.0000.0000.0000.000
165A175GLU-1-0.746-0.86811.00423.34423.3440.0000.0000.0000.000
166A176PHE0-0.018-0.01611.059-0.216-0.2160.0000.0000.0000.000
167A177LEU0-0.030-0.00612.997-1.038-1.0380.0000.0000.0000.000
168A178ILE00.0290.03416.300-0.953-0.9530.0000.0000.0000.000
169A179GLU-1-0.810-0.91114.27017.01317.0130.0000.0000.0000.000
170A180LEU0-0.056-0.01315.977-0.389-0.3890.0000.0000.0000.000
171A181HIS10.8030.91217.427-14.197-14.1970.0000.0000.0000.000
172A182ASP-1-0.788-0.88520.93712.89112.8910.0000.0000.0000.000
173A183PRO00.0220.00818.558-0.630-0.6300.0000.0000.0000.000
174A184LEU0-0.0180.00220.344-0.473-0.4730.0000.0000.0000.000
175A185CYS0-0.038-0.02922.113-0.686-0.6860.0000.0000.0000.000
176A186CYS0-0.059-0.00224.723-0.550-0.5500.0000.0000.0000.000
177A187ILE00.022-0.00121.787-0.467-0.4670.0000.0000.0000.000
178A188VAL0-0.026-0.01525.540-0.427-0.4270.0000.0000.0000.000
179A189GLN0-0.0140.00127.873-0.472-0.4720.0000.0000.0000.000
180A190PHE00.017-0.00228.780-0.387-0.3870.0000.0000.0000.000
181A191PHE00.016-0.01127.383-0.247-0.2470.0000.0000.0000.000
182A192PHE0-0.016-0.00531.258-0.219-0.2190.0000.0000.0000.000
183A193GLN0-0.023-0.00333.340-0.175-0.1750.0000.0000.0000.000
184A194ARG10.8320.90932.940-9.428-9.4280.0000.0000.0000.000
185A195GLU-1-0.956-0.96435.7017.8827.8820.0000.0000.0000.000
186A196LEU0-0.024-0.01631.832-0.014-0.0140.0000.0000.0000.000
187A197GLU-1-0.765-0.83230.02811.04611.0460.0000.0000.0000.000
188A198ASP-1-0.801-0.89233.3119.0679.0670.0000.0000.0000.000
189A199GLN0-0.080-0.05833.3110.1330.1330.0000.0000.0000.000
190A200CYS0-0.061-0.01228.5090.2300.2300.0000.0000.0000.000
191A201TRP00.0020.00630.9300.1700.1700.0000.0000.0000.000
192A202GLY00.0280.01627.9180.2220.2220.0000.0000.0000.000
193A203ASP-1-0.797-0.85125.61612.13012.1300.0000.0000.0000.000
194A204GLU-1-0.779-0.87227.55510.36010.3600.0000.0000.0000.000
195A205VAL00.0120.01126.8510.0440.0440.0000.0000.0000.000
196A206TYR0-0.059-0.05719.1390.0140.0140.0000.0000.0000.000
197A207GLN0-0.042-0.03925.0930.5510.5510.0000.0000.0000.000
198A208ARG10.7910.88527.048-10.524-10.5240.0000.0000.0000.000
199A209LYS10.9920.97927.387-10.085-10.0850.0000.0000.0000.000
200A210ASP-1-0.869-0.94326.10612.33912.3390.0000.0000.0000.000
201A211SER00.0330.02121.298-0.040-0.0400.0000.0000.0000.000
202A212SER00.0460.01421.5770.8930.8930.0000.0000.0000.000
203A213GLU-1-0.902-0.94723.01110.39010.3900.0000.0000.0000.000
204A214TRP0-0.033-0.04917.998-0.245-0.2450.0000.0000.0000.000
205A215LEU0-0.0170.00319.199-0.035-0.0350.0000.0000.0000.000
206A216LYS10.8650.96923.290-11.776-11.7760.0000.0000.0000.000