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: VQ671

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 OptH
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 -2703431.688194
FMO2-HF: Nuclear repulsion 2617337.330276
FMO2-HF: Total energy -86094.357918
FMO2-MP2: Total energy -86348.725945


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.
-2.6361.2181.307-2.138-3.02-0.006
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 : -0.008 / q_NPA : -0.003
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].
3A12PHE00.0180.0183.792-0.1151.485-0.023-0.832-0.7440.000
4A13ALA00.0110.0306.953-0.040-0.0400.0000.0000.0000.000
5A14GLN0-0.050-0.03910.7370.0060.0060.0000.0000.0000.000
6A15SER0-0.046-0.04613.3830.0090.0090.0000.0000.0000.000
7A16GLN00.0230.00716.4050.0300.0300.0000.0000.0000.000
8A17THR00.0190.00219.358-0.023-0.0230.0000.0000.0000.000
9A18ARG10.9950.97820.6480.1650.1650.0000.0000.0000.000
10A19GLU-1-0.888-0.95721.674-0.079-0.0790.0000.0000.0000.000
11A20ASP-1-0.822-0.89721.190-0.090-0.0900.0000.0000.0000.000
12A21TYR0-0.096-0.08315.885-0.011-0.0110.0000.0000.0000.000
13A22LEU00.003-0.00620.0600.0030.0030.0000.0000.0000.000
14A23ALA00.0080.02022.7970.0090.0090.0000.0000.0000.000
15A24LEU0-0.054-0.03521.5820.0070.0070.0000.0000.0000.000
16A25LEU0-0.066-0.01819.3000.0040.0040.0000.0000.0000.000
17A26ALA00.0340.02323.9710.0040.0040.0000.0000.0000.000
18A27GLU-1-0.927-0.95826.818-0.044-0.0440.0000.0000.0000.000
19A28ASP-1-0.915-0.97329.482-0.070-0.0700.0000.0000.0000.000
20A29ILE0-0.043-0.03430.654-0.003-0.0030.0000.0000.0000.000
21A30GLU-1-0.782-0.86328.656-0.058-0.0580.0000.0000.0000.000
22A31ARG10.8450.92426.1350.0740.0740.0000.0000.0000.000
23A32ASP-1-0.902-0.93826.736-0.089-0.0890.0000.0000.0000.000
24A33ILE0-0.053-0.03722.354-0.013-0.0130.0000.0000.0000.000
25A34PRO0-0.040-0.02125.8490.0050.0050.0000.0000.0000.000
26A35TYR00.0010.00526.420-0.009-0.0090.0000.0000.0000.000
27A36ASP-1-0.908-0.96724.747-0.130-0.1300.0000.0000.0000.000
28A37PRO0-0.076-0.02725.452-0.004-0.0040.0000.0000.0000.000
29A38GLU-1-0.954-0.96823.376-0.109-0.1090.0000.0000.0000.000
30A39PRO0-0.065-0.03121.216-0.013-0.0130.0000.0000.0000.000
31A40ILE0-0.046-0.01615.754-0.011-0.0110.0000.0000.0000.000
32A41GLY0-0.0020.00417.909-0.019-0.0190.0000.0000.0000.000
33A42ARG10.8330.91010.9990.5810.5810.0000.0000.0000.000
34A43TYR00.0760.03113.033-0.028-0.0280.0000.0000.0000.000
35A44ASN0-0.038-0.0238.516-0.130-0.1300.0000.0000.0000.000
36A45VAL00.0070.0177.527-0.002-0.0020.0000.0000.0000.000
37A46ALA00.003-0.0135.642-0.796-0.7960.0000.0000.0000.000
38A47PRO00.000-0.0043.2340.1070.6410.042-0.176-0.4000.000
39A48GLY0-0.022-0.0056.0910.1940.1940.0000.0000.0000.000
40A49THR0-0.049-0.0169.2770.2110.2110.0000.0000.0000.000
41A50LYS10.9070.94910.9490.2590.2590.0000.0000.0000.000
42A51VAL0-0.031-0.0238.919-0.036-0.0360.0000.0000.0000.000
43A52LEU0-0.0120.01112.4140.0430.0430.0000.0000.0000.000
44A53LEU0-0.004-0.01212.261-0.030-0.0300.0000.0000.0000.000
45A54LEU00.0020.01115.1010.0240.0240.0000.0000.0000.000
46A55SER0-0.009-0.02417.5030.0020.0020.0000.0000.0000.000
47A56GLU-1-0.811-0.91120.073-0.070-0.0700.0000.0000.0000.000
48A57ARG10.8090.89922.0700.1310.1310.0000.0000.0000.000
49A58ASP-1-0.927-0.95526.343-0.080-0.0800.0000.0000.0000.000
50A59GLU-1-0.972-0.97829.482-0.050-0.0500.0000.0000.0000.000
51A60HIS0-0.042-0.01528.0950.0040.0040.0000.0000.0000.000
52A61LEU0-0.042-0.03722.559-0.007-0.0070.0000.0000.0000.000
53A62HIS00.0500.02722.847-0.005-0.0050.0000.0000.0000.000
54A63LEU0-0.009-0.01817.298-0.013-0.0130.0000.0000.0000.000
55A64ASP-1-0.785-0.87018.612-0.161-0.1610.0000.0000.0000.000
56A65PRO0-0.054-0.02116.314-0.037-0.0370.0000.0000.0000.000
57A66VAL00.0200.00813.7420.0150.0150.0000.0000.0000.000
58A67PHE0-0.0050.01112.225-0.100-0.1000.0000.0000.0000.000
59A68TRP0-0.024-0.0122.869-1.051-0.4900.369-0.334-0.596-0.004
60A69GLY00.017-0.0038.501-0.165-0.1650.0000.0000.0000.000
61A70TYR0-0.019-0.0039.7510.0740.0740.0000.0000.0000.000
62A71ALA0-0.004-0.00212.6870.0040.0040.0000.0000.0000.000
63A72PRO00.0290.02315.0430.0190.0190.0000.0000.0000.000
64A73GLY00.0390.00818.081-0.007-0.0070.0000.0000.0000.000
65A74TRP0-0.001-0.00220.8900.0110.0110.0000.0000.0000.000
66A75TRP00.000-0.00317.0150.0100.0100.0000.0000.0000.000
67A76ASP-1-0.795-0.87815.046-0.169-0.1690.0000.0000.0000.000
68A77LYS10.7070.85714.4550.0970.0970.0000.0000.0000.000
69A78PRO0-0.004-0.0129.6700.0390.0390.0000.0000.0000.000
70A79PRO00.0200.00110.1630.0190.0190.0000.0000.0000.000
71A80LEU0-0.0110.0069.112-0.059-0.0590.0000.0000.0000.000
72A81ILE00.0470.0122.381-0.668-0.0610.917-0.676-0.847-0.002
73A82ASN00.0100.0063.809-0.323-0.1850.000-0.024-0.1130.000
74A83ALA00.0110.0127.276-0.033-0.0330.0000.0000.0000.000
75A84ARG10.9030.95910.462-0.165-0.1650.0000.0000.0000.000
76A85VAL00.1050.04712.540-0.027-0.0270.0000.0000.0000.000
77A86GLU-1-0.829-0.88514.6430.1280.1280.0000.0000.0000.000
78A87THR0-0.035-0.02816.252-0.007-0.0070.0000.0000.0000.000
79A88ALA00.0310.01914.726-0.013-0.0130.0000.0000.0000.000
80A89ALA00.0530.03016.768-0.012-0.0120.0000.0000.0000.000
81A90THR0-0.047-0.03020.098-0.003-0.0030.0000.0000.0000.000
82A91SER0-0.0280.01817.267-0.001-0.0010.0000.0000.0000.000
83A92ARG10.9190.93420.0580.0120.0120.0000.0000.0000.000
84A93MET00.0070.01716.361-0.007-0.0070.0000.0000.0000.000
85A94PHE00.0530.00312.818-0.001-0.0010.0000.0000.0000.000
86A95LYS10.9611.00317.7770.0260.0260.0000.0000.0000.000
87A96PRO00.002-0.01120.7940.0010.0010.0000.0000.0000.000
88A97LEU00.0340.02215.8070.0000.0000.0000.0000.0000.000
89A98TRP0-0.040-0.00715.422-0.005-0.0050.0000.0000.0000.000
90A99GLN0-0.065-0.05019.1420.0010.0010.0000.0000.0000.000
91A100HIS00.0200.01021.8730.0010.0010.0000.0000.0000.000
92A101GLY00.0300.02418.770-0.003-0.0030.0000.0000.0000.000
93A102ARG10.7830.89317.1230.0470.0470.0000.0000.0000.000
94A103ALA00.0240.02315.061-0.002-0.0020.0000.0000.0000.000
95A104ILE00.0080.00014.5110.0140.0140.0000.0000.0000.000
96A105CYS0-0.032-0.0039.179-0.033-0.0330.0000.0000.0000.000
97A106PHE00.0450.02412.1110.0080.0080.0000.0000.0000.000
98A107ALA0-0.002-0.00510.586-0.076-0.0760.0000.0000.0000.000
99A108ASP-1-0.743-0.81812.537-0.140-0.1400.0000.0000.0000.000
100A109GLY00.019-0.00311.1310.0670.0670.0000.0000.0000.000
101A110TRP0-0.029-0.0245.426-0.230-0.2300.0000.0000.0000.000
102A111PHE0-0.028-0.0155.6980.1770.1770.0000.0000.0000.000
103A112GLU-1-0.839-0.9014.7623.0933.269-0.001-0.009-0.1660.000
104A113TRP0-0.080-0.0514.073-0.897-0.6590.003-0.087-0.1540.000
105A114LYS10.9941.0218.918-0.307-0.3070.0000.0000.0000.000
106A115LYS10.7630.86411.988-0.358-0.3580.0000.0000.0000.000
107A116GLU-1-0.800-0.89613.7560.2230.2230.0000.0000.0000.000
108A117GLY00.0770.04416.693-0.012-0.0120.0000.0000.0000.000
109A118ASP-1-0.844-0.90417.2090.2410.2410.0000.0000.0000.000
110A119LYS10.7590.86616.413-0.231-0.2310.0000.0000.0000.000
111A120LYS10.9140.9408.260-1.084-1.0840.0000.0000.0000.000
112A121GLN00.016-0.00812.634-0.075-0.0750.0000.0000.0000.000
113A122PRO00.0030.0249.9280.0820.0820.0000.0000.0000.000
114A123PHE00.016-0.0019.920-0.166-0.1660.0000.0000.0000.000
115A124PHE00.0410.0269.4900.1030.1030.0000.0000.0000.000
116A125ILE0-0.026-0.0208.8660.0040.0040.0000.0000.0000.000
117A126TYR00.0260.01311.375-0.058-0.0580.0000.0000.0000.000
118A127ARG10.8390.91014.1220.0430.0430.0000.0000.0000.000
119A128ALA00.0080.00417.234-0.006-0.0060.0000.0000.0000.000
120A129ASP-1-0.845-0.91720.358-0.011-0.0110.0000.0000.0000.000
121A130GLY0-0.017-0.00919.774-0.005-0.0050.0000.0000.0000.000
122A131GLN0-0.0040.01020.098-0.019-0.0190.0000.0000.0000.000
123A132PRO00.0410.02416.4640.0030.0030.0000.0000.0000.000
124A133ILE0-0.083-0.03810.0680.0320.0320.0000.0000.0000.000
125A134PHE00.0640.02313.998-0.044-0.0440.0000.0000.0000.000
126A135MET0-0.042-0.0168.2100.0600.0600.0000.0000.0000.000
127A136ALA00.0510.03411.957-0.028-0.0280.0000.0000.0000.000
128A137ALA0-0.004-0.00311.289-0.007-0.0070.0000.0000.0000.000
129A138ILE0-0.017-0.01312.3140.0340.0340.0000.0000.0000.000
130A139GLY00.021-0.01713.054-0.039-0.0390.0000.0000.0000.000
131A140SER0-0.0230.01115.3080.0290.0290.0000.0000.0000.000
132A141THR00.0270.04618.335-0.010-0.0100.0000.0000.0000.000
133A142PRO00.002-0.00421.1360.0060.0060.0000.0000.0000.000
134A143PHE00.0500.00015.827-0.013-0.0130.0000.0000.0000.000
135A144GLU-1-0.877-0.94119.601-0.149-0.1490.0000.0000.0000.000
136A145ARG10.7350.86820.1010.1630.1630.0000.0000.0000.000
137A146GLY0-0.029-0.00319.2350.0020.0020.0000.0000.0000.000
138A147ASP-1-0.780-0.88717.935-0.187-0.1870.0000.0000.0000.000
139A148GLU-1-0.906-0.96217.118-0.282-0.2820.0000.0000.0000.000
140A149ALA0-0.058-0.02515.512-0.029-0.0290.0000.0000.0000.000
141A150GLU-1-1.013-1.01014.910-0.169-0.1690.0000.0000.0000.000
142A151GLY00.0410.01913.3940.0160.0160.0000.0000.0000.000
143A152PHE0-0.010-0.0188.5200.0350.0350.0000.0000.0000.000
144A153LEU0-0.064-0.0368.498-0.082-0.0820.0000.0000.0000.000
145A154ILE00.0350.0236.0210.0180.0180.0000.0000.0000.000
146A155VAL00.005-0.0048.1360.1000.1000.0000.0000.0000.000
147A156THR0-0.0120.0006.8370.0330.0330.0000.0000.0000.000
148A157ALA00.015-0.0039.809-0.051-0.0510.0000.0000.0000.000
149A158ALA00.009-0.00811.2610.0600.0600.0000.0000.0000.000
150A159ALA0-0.034-0.00612.034-0.022-0.0220.0000.0000.0000.000
151A160ASP-1-0.778-0.89113.3630.1250.1250.0000.0000.0000.000
152A161GLN0-0.011-0.03516.4780.0100.0100.0000.0000.0000.000
153A162GLY00.0570.02218.1960.0120.0120.0000.0000.0000.000
154A163LEU00.0070.00811.9360.0240.0240.0000.0000.0000.000
155A164VAL0-0.045-0.01313.4220.0610.0610.0000.0000.0000.000
156A165ASP-1-0.920-0.94515.4380.2440.2440.0000.0000.0000.000
157A166ILE0-0.127-0.06010.3420.0300.0300.0000.0000.0000.000
158A167HIS00.002-0.0167.0160.0550.0550.0000.0000.0000.000
159A168ASP-1-0.862-0.92810.6230.3980.3980.0000.0000.0000.000
160A169ARG10.6920.8207.808-0.369-0.3690.0000.0000.0000.000
161A170ARG10.8250.9137.869-0.050-0.0500.0000.0000.0000.000
162A171PRO00.0440.0226.194-0.016-0.0160.0000.0000.0000.000
163A172LEU0-0.010-0.0028.5150.0010.0010.0000.0000.0000.000
164A173VAL0-0.032-0.01711.449-0.040-0.0400.0000.0000.0000.000
165A174LEU00.0200.01713.5860.0210.0210.0000.0000.0000.000
166A175SER00.0060.00417.131-0.012-0.0120.0000.0000.0000.000
167A176PRO00.0570.01620.229-0.006-0.0060.0000.0000.0000.000
168A177GLU-1-0.917-0.94321.858-0.024-0.0240.0000.0000.0000.000
169A178ALA00.0330.01220.744-0.003-0.0030.0000.0000.0000.000
170A179ALA0-0.034-0.02418.698-0.005-0.0050.0000.0000.0000.000
171A180ARG10.8520.89820.0560.0560.0560.0000.0000.0000.000
172A181GLU-1-0.837-0.92023.255-0.040-0.0400.0000.0000.0000.000
173A182TRP0-0.087-0.05015.6630.0110.0110.0000.0000.0000.000
174A183MET0-0.053-0.02819.297-0.011-0.0110.0000.0000.0000.000
175A184ARG10.8370.94121.4780.0390.0390.0000.0000.0000.000
176A185GLN00.016-0.01624.9780.0050.0050.0000.0000.0000.000
177A186GLU-1-0.943-0.95126.494-0.040-0.0400.0000.0000.0000.000
178A187ILE0-0.0130.03024.4440.0060.0060.0000.0000.0000.000
179A188SER0-0.028-0.02225.636-0.004-0.0040.0000.0000.0000.000
180A189GLY00.0590.00323.0520.0000.0000.0000.0000.0000.000
181A190LYS10.9030.94423.4390.0100.0100.0000.0000.0000.000
182A191GLU-1-0.801-0.90125.588-0.023-0.0230.0000.0000.0000.000
183A192ALA00.0540.03520.7650.0030.0030.0000.0000.0000.000
184A193SER0-0.088-0.05421.0920.0040.0040.0000.0000.0000.000
185A194GLU-1-0.960-0.97522.1600.0060.0060.0000.0000.0000.000
186A195ILE00.0840.05320.9150.0050.0050.0000.0000.0000.000
187A196ALA0-0.061-0.03517.7670.0030.0030.0000.0000.0000.000
188A197ALA0-0.076-0.03518.7600.0110.0110.0000.0000.0000.000
189A198SER0-0.047-0.02321.0620.0070.0070.0000.0000.0000.000
190A199GLY00.0600.02921.1120.0020.0020.0000.0000.0000.000
191A200CYS0-0.073-0.03115.986-0.002-0.0020.0000.0000.0000.000
192A201VAL0-0.0050.00016.1250.0020.0020.0000.0000.0000.000
193A202PRO00.0190.02416.2100.0200.0200.0000.0000.0000.000
194A203ALA00.047-0.00615.813-0.007-0.0070.0000.0000.0000.000
195A204ASN0-0.0100.00417.0430.0050.0050.0000.0000.0000.000
196A205GLN0-0.028-0.01518.936-0.007-0.0070.0000.0000.0000.000
197A206PHE0-0.023-0.00814.041-0.012-0.0120.0000.0000.0000.000
198A207SER0-0.034-0.00816.6060.0010.0010.0000.0000.0000.000
199A208TRP00.023-0.00213.7280.0130.0130.0000.0000.0000.000
200A209HIS0-0.022-0.00114.675-0.004-0.0040.0000.0000.0000.000
201A210PRO0-0.021-0.00414.3290.0300.0300.0000.0000.0000.000
202A211VAL00.0610.03711.898-0.041-0.0410.0000.0000.0000.000
203A212SER00.0480.02014.9810.0500.0500.0000.0000.0000.000
204A213ARG10.9040.92313.248-0.292-0.2920.0000.0000.0000.000
205A214ALA0-0.016-0.00112.9230.0430.0430.0000.0000.0000.000
206A215VAL00.0970.0708.808-0.024-0.0240.0000.0000.0000.000
207A216GLY0-0.0080.0038.501-0.021-0.0210.0000.0000.0000.000
208A217ASN0-0.018-0.0118.836-0.094-0.0940.0000.0000.0000.000
209A218VAL00.0780.0317.7740.0010.0010.0000.0000.0000.000
210A219LYS10.9250.97010.4740.1480.1480.0000.0000.0000.000
211A220ASN0-0.056-0.02813.383-0.009-0.0090.0000.0000.0000.000
212A221GLN0-0.021-0.04811.218-0.034-0.0340.0000.0000.0000.000
213A222GLY00.0440.04715.178-0.011-0.0110.0000.0000.0000.000
214A223ALA00.0680.01216.164-0.003-0.0030.0000.0000.0000.000
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