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: G5491

Calculation Name: 2ICU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ICU

Chain ID: A

ChEMBL ID:

UniProt ID: P76318

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2710302.931656
FMO2-HF: Nuclear repulsion 2624207.927309
FMO2-HF: Total energy -86095.004347
FMO2-MP2: Total energy -86349.294663


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:10:GLY)


Summations of interaction energy for fragment #1(A:10:GLY)
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.
-7.844-3.3210.812-2.332-3.003-0.001
Interaction energy analysis for fragmet #1(A:10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.023
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].
3A12PHE00.0210.0123.870-0.2981.628-0.013-1.113-0.8010.003
4A13ALA00.0080.0257.085-0.083-0.0830.0000.0000.0000.000
5A14GLN0-0.044-0.03610.9050.0790.0790.0000.0000.0000.000
6A15SER0-0.064-0.05413.3800.0440.0440.0000.0000.0000.000
7A16GLN00.007-0.00316.6210.0660.0660.0000.0000.0000.000
8A17THR00.008-0.01919.281-0.012-0.0120.0000.0000.0000.000
9A18ARG10.8690.90720.5950.2040.2040.0000.0000.0000.000
10A19GLU-1-0.818-0.90721.642-0.101-0.1010.0000.0000.0000.000
11A20ASP-1-0.831-0.88821.153-0.194-0.1940.0000.0000.0000.000
12A21TYR0-0.088-0.08215.852-0.016-0.0160.0000.0000.0000.000
13A22LEU00.0150.00219.9070.0220.0220.0000.0000.0000.000
14A23ALA00.0170.01722.7330.0190.0190.0000.0000.0000.000
15A24LEU0-0.056-0.03221.1350.0120.0120.0000.0000.0000.000
16A25LEU0-0.073-0.02519.0880.0170.0170.0000.0000.0000.000
17A26ALA00.0440.01623.7520.0160.0160.0000.0000.0000.000
18A27GLU-1-0.916-0.93926.673-0.037-0.0370.0000.0000.0000.000
19A28ASP-1-0.896-0.96129.368-0.067-0.0670.0000.0000.0000.000
20A29ILE0-0.043-0.03330.513-0.001-0.0010.0000.0000.0000.000
21A30GLU-1-0.797-0.85728.554-0.003-0.0030.0000.0000.0000.000
22A31ARG10.7780.88325.6030.0780.0780.0000.0000.0000.000
23A32ASP-1-0.902-0.94026.648-0.049-0.0490.0000.0000.0000.000
24A33ILE0-0.033-0.03022.165-0.008-0.0080.0000.0000.0000.000
25A34PRO0-0.038-0.02025.554-0.005-0.0050.0000.0000.0000.000
26A35TYR0-0.022-0.00326.355-0.016-0.0160.0000.0000.0000.000
27A36ASP-1-0.820-0.91424.557-0.201-0.2010.0000.0000.0000.000
28A37PRO0-0.054-0.02125.275-0.009-0.0090.0000.0000.0000.000
29A38GLU-1-0.921-0.95623.439-0.247-0.2470.0000.0000.0000.000
30A39PRO0-0.066-0.03721.494-0.010-0.0100.0000.0000.0000.000
31A40ILE0-0.0150.00315.831-0.015-0.0150.0000.0000.0000.000
32A41GLY00.001-0.00117.453-0.044-0.0440.0000.0000.0000.000
33A42ARG10.8370.90110.9840.8020.8020.0000.0000.0000.000
34A43TYR00.0500.01912.632-0.097-0.0970.0000.0000.0000.000
35A44ASN0-0.042-0.0228.822-0.608-0.6080.0000.0000.0000.000
36A45VAL00.0170.0357.643-0.036-0.0360.0000.0000.0000.000
37A46ALA0-0.005-0.0225.635-1.095-1.0950.0000.0000.0000.000
38A47PRO00.0240.0133.4580.3440.7440.016-0.110-0.3060.000
39A48GLY0-0.046-0.0056.317-0.059-0.0590.0000.0000.0000.000
40A49THR0-0.043-0.0239.4370.1420.1420.0000.0000.0000.000
41A50LYS10.8280.91010.8640.1840.1840.0000.0000.0000.000
42A51VAL0-0.064-0.0388.845-0.141-0.1410.0000.0000.0000.000
43A52LEU00.0140.02212.3310.0870.0870.0000.0000.0000.000
44A53LEU0-0.010-0.01211.990-0.028-0.0280.0000.0000.0000.000
45A54LEU00.0150.01114.7560.0080.0080.0000.0000.0000.000
46A55SER0-0.008-0.01417.1320.0400.0400.0000.0000.0000.000
47A56GLU-1-0.780-0.88919.7400.0370.0370.0000.0000.0000.000
48A57ARG10.7450.84521.9180.0300.0300.0000.0000.0000.000
49A58ASP-1-0.920-0.95926.2550.0080.0080.0000.0000.0000.000
50A59GLU-1-0.966-0.97029.4940.0160.0160.0000.0000.0000.000
51A60HIS0-0.058-0.02028.087-0.007-0.0070.0000.0000.0000.000
52A61LEU0-0.006-0.02122.3050.0070.0070.0000.0000.0000.000
53A62HIS00.0640.03522.668-0.018-0.0180.0000.0000.0000.000
54A63LEU0-0.014-0.01817.288-0.003-0.0030.0000.0000.0000.000
55A64ASP-1-0.764-0.84018.169-0.048-0.0480.0000.0000.0000.000
56A65PRO0-0.024-0.01616.355-0.031-0.0310.0000.0000.0000.000
57A66VAL00.0190.01213.9200.0230.0230.0000.0000.0000.000
58A67PHE00.0060.00712.568-0.080-0.0800.0000.0000.0000.000
59A68TRP0-0.014-0.0082.877-1.484-0.7130.349-0.464-0.656-0.005
60A69GLY0-0.004-0.0148.116-0.062-0.0620.0000.0000.0000.000
61A70TYR0-0.072-0.0429.648-0.067-0.0670.0000.0000.0000.000
62A71ALA00.008-0.00212.6500.1150.1150.0000.0000.0000.000
63A72PRO00.0290.02315.054-0.052-0.0520.0000.0000.0000.000
64A73GLY00.0330.00117.980-0.021-0.0210.0000.0000.0000.000
65A74TRP0-0.017-0.00720.6120.0100.0100.0000.0000.0000.000
66A75TRP00.0080.00316.577-0.006-0.0060.0000.0000.0000.000
67A76ASP-1-0.791-0.87714.7320.2610.2610.0000.0000.0000.000
68A77LYS10.7130.85314.384-0.232-0.2320.0000.0000.0000.000
69A78PRO0-0.016-0.0079.380-0.001-0.0010.0000.0000.0000.000
70A79PRO00.017-0.00810.4840.1030.1030.0000.0000.0000.000
71A80LEU0-0.027-0.0049.1060.2150.2150.0000.0000.0000.000
72A81ILE00.0670.0212.730-0.734-0.0720.427-0.377-0.7120.001
73A82ASN00.0020.0043.035-2.439-1.9780.034-0.194-0.3000.000
74A83ALA00.0270.0206.813-0.246-0.2460.0000.0000.0000.000
75A84ARG10.7810.90110.428-1.158-1.1580.0000.0000.0000.000
76A85VAL00.0880.04012.250-0.138-0.1380.0000.0000.0000.000
77A86GLU-1-0.790-0.87413.8860.8730.8730.0000.0000.0000.000
78A87THR0-0.051-0.03116.134-0.043-0.0430.0000.0000.0000.000
79A88ALA00.0140.01414.218-0.056-0.0560.0000.0000.0000.000
80A89ALA00.0540.04016.257-0.045-0.0450.0000.0000.0000.000
81A90THR0-0.026-0.02319.669-0.032-0.0320.0000.0000.0000.000
82A91SER00.0210.02017.181-0.062-0.0620.0000.0000.0000.000
83A92ARG10.9120.93719.948-0.306-0.3060.0000.0000.0000.000
84A93MET00.0070.02116.498-0.012-0.0120.0000.0000.0000.000
85A94PHE00.0490.01012.500-0.006-0.0060.0000.0000.0000.000
86A95LYS10.8890.96617.242-0.318-0.3180.0000.0000.0000.000
87A96PRO00.018-0.00420.294-0.020-0.0200.0000.0000.0000.000
88A97LEU00.0430.02915.342-0.017-0.0170.0000.0000.0000.000
89A98TRP0-0.007-0.00414.9750.0080.0080.0000.0000.0000.000
90A99GLN0-0.085-0.05918.949-0.030-0.0300.0000.0000.0000.000
91A100HIS00.0290.01621.768-0.021-0.0210.0000.0000.0000.000
92A101GLY00.0440.04318.906-0.025-0.0250.0000.0000.0000.000
93A102ARG10.7760.88216.729-0.152-0.1520.0000.0000.0000.000
94A103ALA00.0190.02014.666-0.037-0.0370.0000.0000.0000.000
95A104ILE00.0120.00914.1270.0570.0570.0000.0000.0000.000
96A105CYS0-0.048-0.01910.055-0.111-0.1110.0000.0000.0000.000
97A106PHE00.0230.02311.8240.0080.0080.0000.0000.0000.000
98A107ALA00.004-0.00110.488-0.102-0.1020.0000.0000.0000.000
99A108ASP-1-0.734-0.80912.440-0.421-0.4210.0000.0000.0000.000
100A109GLY00.020-0.00511.2020.0980.0980.0000.0000.0000.000
101A110TRP0-0.015-0.0195.007-0.082-0.0820.0000.0000.0000.000
102A111PHE0-0.030-0.0155.6300.2530.2530.0000.0000.0000.000
103A112GLU-1-0.859-0.9144.326-0.702-0.561-0.001-0.029-0.1120.000
104A113TRP0-0.077-0.0533.6960.2230.3850.000-0.045-0.1160.000
105A114LYS10.9320.9918.3710.2540.2540.0000.0000.0000.000
106A115LYS10.8090.89311.422-0.174-0.1740.0000.0000.0000.000
107A116GLU-1-0.784-0.89013.102-0.031-0.0310.0000.0000.0000.000
108A117GLY00.0510.03415.990-0.020-0.0200.0000.0000.0000.000
109A118ASP-1-0.820-0.88516.6970.0450.0450.0000.0000.0000.000
110A119LYS10.7470.86215.7770.0470.0470.0000.0000.0000.000
111A120LYS10.9360.9477.0490.1130.1130.0000.0000.0000.000
112A121GLN00.0120.00011.826-0.006-0.0060.0000.0000.0000.000
113A122PRO0-0.0150.0119.4920.0520.0520.0000.0000.0000.000
114A123PHE00.0330.0059.9690.1520.1520.0000.0000.0000.000
115A124PHE00.0200.0169.622-0.221-0.2210.0000.0000.0000.000
116A125ILE0-0.022-0.0178.6220.1530.1530.0000.0000.0000.000
117A126TYR00.0250.01011.109-0.033-0.0330.0000.0000.0000.000
118A127ARG10.8280.87913.9730.1020.1020.0000.0000.0000.000
119A128ALA0-0.017-0.00817.115-0.024-0.0240.0000.0000.0000.000
120A129ASP-1-0.820-0.88520.280-0.080-0.0800.0000.0000.0000.000
121A130GLY0-0.019-0.01319.7590.0020.0020.0000.0000.0000.000
122A131GLN0-0.043-0.00619.880-0.019-0.0190.0000.0000.0000.000
123A132PRO00.0370.01116.180-0.016-0.0160.0000.0000.0000.000
124A133ILE0-0.074-0.0259.6230.0620.0620.0000.0000.0000.000
125A134PHE00.0610.01913.669-0.045-0.0450.0000.0000.0000.000
126A135MET0-0.041-0.0178.2260.1110.1110.0000.0000.0000.000
127A136ALA00.0620.03711.760-0.035-0.0350.0000.0000.0000.000
128A137ALA0-0.010-0.00510.8700.1450.1450.0000.0000.0000.000
129A138ILE0-0.008-0.01011.928-0.043-0.0430.0000.0000.0000.000
130A139GLY00.025-0.01012.6950.0730.0730.0000.0000.0000.000
131A140SER0-0.055-0.03115.021-0.017-0.0170.0000.0000.0000.000
132A141THR00.0140.03018.274-0.023-0.0230.0000.0000.0000.000
133A142PRO0-0.035-0.02120.8660.0090.0090.0000.0000.0000.000
134A143PHE00.0440.00615.7280.0040.0040.0000.0000.0000.000
135A144GLU-1-0.821-0.92119.739-0.001-0.0010.0000.0000.0000.000
136A145ARG10.6820.82720.499-0.106-0.1060.0000.0000.0000.000
137A146GLY00.0120.01319.375-0.005-0.0050.0000.0000.0000.000
138A147ASP-1-0.764-0.87817.6220.0520.0520.0000.0000.0000.000
139A148GLU-1-0.866-0.92816.671-0.161-0.1610.0000.0000.0000.000
140A149ALA0-0.071-0.02915.597-0.001-0.0010.0000.0000.0000.000
141A150GLU-1-0.855-0.88315.0270.2740.2740.0000.0000.0000.000
142A151GLY00.0260.02113.214-0.035-0.0350.0000.0000.0000.000
143A152PHE00.001-0.0188.3590.0490.0490.0000.0000.0000.000
144A153LEU0-0.066-0.0288.1410.0540.0540.0000.0000.0000.000
145A154ILE00.0160.0175.491-0.179-0.1790.0000.0000.0000.000
146A155VAL0-0.005-0.0047.7410.4440.4440.0000.0000.0000.000
147A156THR0-0.0070.0006.4430.0710.0710.0000.0000.0000.000
148A157ALA00.024-0.0019.527-0.127-0.1270.0000.0000.0000.000
149A158ALA00.017-0.00810.9140.1410.1410.0000.0000.0000.000
150A159ALA0-0.037-0.00311.668-0.065-0.0650.0000.0000.0000.000
151A160ASP-1-0.768-0.87313.0680.2000.2000.0000.0000.0000.000
152A161GLN0-0.024-0.04416.192-0.055-0.0550.0000.0000.0000.000
153A162GLY00.0510.02017.6710.0200.0200.0000.0000.0000.000
154A163LEU0-0.0020.00911.722-0.023-0.0230.0000.0000.0000.000
155A164VAL0-0.012-0.00513.1020.0400.0400.0000.0000.0000.000
156A165ASP-1-0.958-0.96015.3090.1100.1100.0000.0000.0000.000
157A166ILE0-0.082-0.04910.174-0.066-0.0660.0000.0000.0000.000
158A167HIS0-0.016-0.0176.492-0.071-0.0710.0000.0000.0000.000
159A168ASP-1-0.797-0.91310.6471.2021.2020.0000.0000.0000.000
160A169ARG10.7180.8457.168-1.398-1.3980.0000.0000.0000.000
161A170ARG10.8160.8927.684-0.570-0.5700.0000.0000.0000.000
162A171PRO00.0400.0196.1240.2800.2800.0000.0000.0000.000
163A172LEU0-0.0190.0018.411-0.131-0.1310.0000.0000.0000.000
164A173VAL0-0.027-0.01511.304-0.040-0.0400.0000.0000.0000.000
165A174LEU00.0150.02313.5700.0180.0180.0000.0000.0000.000
166A175SER00.0330.01717.203-0.034-0.0340.0000.0000.0000.000
167A176PRO00.0410.00220.3790.0110.0110.0000.0000.0000.000
168A177GLU-1-0.916-0.94821.7250.0570.0570.0000.0000.0000.000
169A178ALA00.0220.01220.7790.0070.0070.0000.0000.0000.000
170A179ALA0-0.026-0.02318.6070.0210.0210.0000.0000.0000.000
171A180ARG10.8370.89219.842-0.004-0.0040.0000.0000.0000.000
172A181GLU-1-0.823-0.90523.0810.0810.0810.0000.0000.0000.000
173A182TRP0-0.090-0.06615.2180.0420.0420.0000.0000.0000.000
174A183MET0-0.051-0.02619.1260.0110.0110.0000.0000.0000.000
175A184ARG10.8070.90321.254-0.070-0.0700.0000.0000.0000.000
176A185GLN0-0.052-0.04624.5680.0170.0170.0000.0000.0000.000
177A186GLU-1-0.905-0.93126.0090.0670.0670.0000.0000.0000.000
178A187ILE0-0.0480.01424.2700.0050.0050.0000.0000.0000.000
179A188SER0-0.030-0.06025.1590.0200.0200.0000.0000.0000.000
180A189GLY00.043-0.00522.5740.0110.0110.0000.0000.0000.000
181A190LYS10.8870.94022.965-0.154-0.1540.0000.0000.0000.000
182A191GLU-1-0.782-0.85425.2560.1390.1390.0000.0000.0000.000
183A192ALA00.0700.04620.3500.0030.0030.0000.0000.0000.000
184A193SER0-0.079-0.05320.5880.0210.0210.0000.0000.0000.000
185A194GLU-1-0.931-0.93121.7160.1700.1700.0000.0000.0000.000
186A195ILE00.1000.05920.6330.0100.0100.0000.0000.0000.000
187A196ALA0-0.062-0.03517.5080.0040.0040.0000.0000.0000.000
188A197ALA0-0.078-0.03918.0540.0320.0320.0000.0000.0000.000
189A198SER0-0.053-0.05520.651-0.007-0.0070.0000.0000.0000.000
190A199GLY00.0580.02821.079-0.020-0.0200.0000.0000.0000.000
191A200CYS0-0.100-0.04016.222-0.002-0.0020.0000.0000.0000.000
192A201VAL00.0240.01315.973-0.022-0.0220.0000.0000.0000.000
193A202PRO00.0100.01716.0070.0350.0350.0000.0000.0000.000
194A203ALA00.0600.00215.574-0.038-0.0380.0000.0000.0000.000
195A204ASN0-0.0130.00216.697-0.021-0.0210.0000.0000.0000.000
196A205GLN00.0130.01418.668-0.012-0.0120.0000.0000.0000.000
197A206PHE0-0.018-0.00613.139-0.026-0.0260.0000.0000.0000.000
198A207SER0-0.035-0.01816.0560.0200.0200.0000.0000.0000.000
199A208TRP00.0140.00613.628-0.031-0.0310.0000.0000.0000.000
200A209HIS0-0.0100.01414.7290.0930.0930.0000.0000.0000.000
201A210PRO0-0.011-0.00514.401-0.078-0.0780.0000.0000.0000.000
202A211VAL00.0510.03411.9770.0220.0220.0000.0000.0000.000
203A212SER00.0440.01614.8560.0140.0140.0000.0000.0000.000
204A213ARG10.9020.91812.9910.2670.2670.0000.0000.0000.000
205A214ALA0-0.0150.01012.883-0.087-0.0870.0000.0000.0000.000
206A215VAL00.0920.0679.251-0.017-0.0170.0000.0000.0000.000
207A216GLY0-0.0040.0048.795-0.321-0.3210.0000.0000.0000.000
208A217ASN0-0.010-0.0049.024-0.283-0.2830.0000.0000.0000.000
209A218VAL00.0880.0357.9340.0430.0430.0000.0000.0000.000
210A219LYS10.9180.96310.6380.6500.6500.0000.0000.0000.000
211A220ASN0-0.056-0.02013.7020.1630.1630.0000.0000.0000.000
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