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

tag_button

FMODB ID: K9KL3

Calculation Name: 1CBY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CBY

Chain ID: A

ChEMBL ID:

UniProt ID: Q04470

Base Structure: X-ray

Registration Date: 2023-06-22

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 227
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2791582.126314
FMO2-HF: Nuclear repulsion 2703220.219938
FMO2-HF: Total energy -88361.906375
FMO2-MP2: Total energy -88624.002565


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:19:CYM)


Summations of interaction energy for fragment #1(A:19:CYM)
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.
7.0168.564-0.008-0.769-0.7710.004
Interaction energy analysis for fragmet #1(A:19:CYM)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.899 / q_NPA : -0.949
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].
3A21ALA00.0310.0173.864-2.234-0.686-0.008-0.769-0.7710.004
4A22PRO0-0.0040.0026.052-1.844-1.8440.0000.0000.0000.000
5A23ILE00.006-0.0068.994-1.332-1.3320.0000.0000.0000.000
6A24ILE0-0.0060.00412.151-1.348-1.3480.0000.0000.0000.000
7A25ARG10.9640.97514.677-16.595-16.5950.0000.0000.0000.000
8A26LYS10.9150.96118.470-11.531-11.5310.0000.0000.0000.000
9A27PRO00.0170.01820.879-0.135-0.1350.0000.0000.0000.000
10A28PHE00.0420.00922.509-0.548-0.5480.0000.0000.0000.000
11A29LYS10.9320.95924.825-10.881-10.8810.0000.0000.0000.000
12A30HIS00.0490.03026.806-0.162-0.1620.0000.0000.0000.000
13A31ILE0-0.006-0.01528.5160.2340.2340.0000.0000.0000.000
14A32VAL00.0490.03131.447-0.160-0.1600.0000.0000.0000.000
15A33LEU0-0.031-0.01133.912-0.029-0.0290.0000.0000.0000.000
16A34THR00.0440.02936.672-0.112-0.1120.0000.0000.0000.000
17A35VAL0-0.026-0.01639.5010.0620.0620.0000.0000.0000.000
18A36PRO0-0.040-0.01542.301-0.080-0.0800.0000.0000.0000.000
19A37SER00.0250.00446.1430.0170.0170.0000.0000.0000.000
20A38SER0-0.011-0.02547.738-0.108-0.1080.0000.0000.0000.000
21A39ASP-1-0.830-0.90750.5445.6495.6490.0000.0000.0000.000
22A40LEU0-0.038-0.01750.5110.1240.1240.0000.0000.0000.000
23A41ASP-1-0.811-0.89844.9866.9226.9220.0000.0000.0000.000
24A42ASN0-0.032-0.01048.456-0.059-0.0590.0000.0000.0000.000
25A43PHE0-0.008-0.02444.599-0.043-0.0430.0000.0000.0000.000
26A44ASN00.0020.01038.6490.1830.1830.0000.0000.0000.000
27A45THR0-0.006-0.00340.3740.0310.0310.0000.0000.0000.000
28A46VAL0-0.032-0.00934.9610.2360.2360.0000.0000.0000.000
29A47PHE00.001-0.01436.430-0.077-0.0770.0000.0000.0000.000
30A48TYR0-0.035-0.01328.1400.4060.4060.0000.0000.0000.000
31A49VAL00.0270.02134.284-0.092-0.0920.0000.0000.0000.000
32A50GLN00.0090.01033.1070.0630.0630.0000.0000.0000.000
33A51PRO00.021-0.01233.462-0.209-0.2090.0000.0000.0000.000
34A52GLN00.0300.02336.344-0.035-0.0350.0000.0000.0000.000
35A53TYR00.0370.01338.226-0.298-0.2980.0000.0000.0000.000
36A54ILE00.0170.01935.731-0.079-0.0790.0000.0000.0000.000
37A55ASN00.0530.01240.095-0.142-0.1420.0000.0000.0000.000
38A56GLN0-0.009-0.00743.4140.0070.0070.0000.0000.0000.000
39A57ALA00.003-0.01140.937-0.116-0.1160.0000.0000.0000.000
40A58LEU00.0110.01042.936-0.041-0.0410.0000.0000.0000.000
41A59HIS0-0.036-0.01644.688-0.247-0.2470.0000.0000.0000.000
42A60LEU0-0.017-0.01545.204-0.129-0.1290.0000.0000.0000.000
43A61ALA00.003-0.00844.252-0.079-0.0790.0000.0000.0000.000
44A62ASN0-0.009-0.01846.3870.0220.0220.0000.0000.0000.000
45A63ALA0-0.015-0.00249.406-0.127-0.1270.0000.0000.0000.000
46A64PHE0-0.023-0.02648.234-0.129-0.1290.0000.0000.0000.000
47A65GLN00.0320.02047.126-0.116-0.1160.0000.0000.0000.000
48A66GLY00.0090.02051.369-0.090-0.0900.0000.0000.0000.000
49A67ALA0-0.014-0.01852.422-0.140-0.1400.0000.0000.0000.000
50A68ILE0-0.030-0.00250.280-0.044-0.0440.0000.0000.0000.000
51A69ASP-1-0.841-0.91254.2355.2055.2050.0000.0000.0000.000
52A70PRO0-0.003-0.01556.8380.0570.0570.0000.0000.0000.000
53A71LEU0-0.052-0.02258.377-0.030-0.0300.0000.0000.0000.000
54A72ASN0-0.073-0.04958.633-0.076-0.0760.0000.0000.0000.000
55A73LEU0-0.0050.00653.3260.0500.0500.0000.0000.0000.000
56A74ASN00.0150.01153.2870.2270.2270.0000.0000.0000.000
57A75PHE00.0320.02149.722-0.082-0.0820.0000.0000.0000.000
58A76ASN00.0210.01253.434-0.036-0.0360.0000.0000.0000.000
59A77PHE00.0130.00052.2610.0370.0370.0000.0000.0000.000
60A78GLU-1-0.841-0.93155.5395.4055.4050.0000.0000.0000.000
61A79LYS10.8650.92557.650-5.440-5.4400.0000.0000.0000.000
62A80ALA00.0470.02452.6060.0210.0210.0000.0000.0000.000
63A81LEU00.0300.00654.3490.0600.0600.0000.0000.0000.000
64A82GLN0-0.040-0.00356.2340.0330.0330.0000.0000.0000.000
65A83ILE0-0.0220.00853.452-0.041-0.0410.0000.0000.0000.000
66A84ALA00.0080.00152.6670.0200.0200.0000.0000.0000.000
67A85ASN0-0.096-0.06453.8980.0420.0420.0000.0000.0000.000
68A86GLY00.0090.01356.488-0.100-0.1000.0000.0000.0000.000
69A87ILE0-0.0230.00450.5940.0000.0000.0000.0000.0000.000
70A88PRO00.0230.03153.397-0.004-0.0040.0000.0000.0000.000
71A89ASN0-0.022-0.02751.6680.0440.0440.0000.0000.0000.000
72A90SER0-0.022-0.02650.3300.1630.1630.0000.0000.0000.000
73A91ALA00.0290.01850.426-0.133-0.1330.0000.0000.0000.000
74A92ILE00.0080.00249.9630.1380.1380.0000.0000.0000.000
75A93VAL0-0.029-0.00345.641-0.068-0.0680.0000.0000.0000.000
76A94LYS10.8930.94347.535-6.473-6.4730.0000.0000.0000.000
77A95THR00.0190.01449.0510.0520.0520.0000.0000.0000.000
78A96LEU0-0.009-0.01047.5290.0090.0090.0000.0000.0000.000
79A97ASN00.0670.02950.9570.0540.0540.0000.0000.0000.000
80A98GLN0-0.029-0.00851.338-0.139-0.1390.0000.0000.0000.000
81A99SER00.019-0.00951.5420.0900.0900.0000.0000.0000.000
82A100VAL0-0.061-0.02346.821-0.015-0.0150.0000.0000.0000.000
83A101ILE0-0.024-0.00644.3970.1090.1090.0000.0000.0000.000
84A102GLN0-0.042-0.04148.479-0.105-0.1050.0000.0000.0000.000
85A103GLN0-0.037-0.01747.570-0.076-0.0760.0000.0000.0000.000
86A104THR00.013-0.00547.9130.0170.0170.0000.0000.0000.000
87A105VAL0-0.041-0.01143.6310.0280.0280.0000.0000.0000.000
88A106GLU-1-0.829-0.87637.3238.2538.2530.0000.0000.0000.000
89A107ILE0-0.008-0.01138.3280.0100.0100.0000.0000.0000.000
90A108SER0-0.047-0.05535.5360.0130.0130.0000.0000.0000.000
91A109VAL00.0490.02736.9940.0420.0420.0000.0000.0000.000
92A110MET0-0.0400.00239.150-0.144-0.1440.0000.0000.0000.000
93A111VAL0-0.010-0.01135.034-0.022-0.0220.0000.0000.0000.000
94A112GLU-1-0.946-0.97134.8598.7568.7560.0000.0000.0000.000
95A113GLN0-0.001-0.00937.3060.0380.0380.0000.0000.0000.000
96A114LEU00.0060.00540.564-0.083-0.0830.0000.0000.0000.000
97A115LYS10.8560.92330.950-9.639-9.6390.0000.0000.0000.000
98A116LYS10.8350.91138.056-7.611-7.6110.0000.0000.0000.000
99A117ILE00.008-0.00639.601-0.114-0.1140.0000.0000.0000.000
100A118ILE0-0.004-0.00439.458-0.107-0.1070.0000.0000.0000.000
101A119GLN00.0000.00436.139-0.161-0.1610.0000.0000.0000.000
102A120GLU-1-0.870-0.93039.8197.2837.2830.0000.0000.0000.000
103A121VAL0-0.069-0.03243.352-0.167-0.1670.0000.0000.0000.000
104A122LEU0-0.0030.03238.147-0.091-0.0910.0000.0000.0000.000
105A123GLY00.0170.02442.345-0.083-0.0830.0000.0000.0000.000
106A124LEU0-0.040-0.03639.5940.0620.0620.0000.0000.0000.000
107A125VAL00.002-0.00436.5990.1300.1300.0000.0000.0000.000
108A126ILE0-0.0110.00532.7180.1520.1520.0000.0000.0000.000
109A127ASN0-0.065-0.03930.2900.2100.2100.0000.0000.0000.000
110A128SER00.028-0.00328.1150.4720.4720.0000.0000.0000.000
111A129THR00.017-0.00424.197-0.128-0.1280.0000.0000.0000.000
112A130SER0-0.004-0.00625.242-0.001-0.0010.0000.0000.0000.000
113A131PHE00.0540.05127.305-0.152-0.1520.0000.0000.0000.000
114A132TRP00.039-0.00330.329-0.236-0.2360.0000.0000.0000.000
115A133ASN0-0.027-0.02325.508-0.354-0.3540.0000.0000.0000.000
116A134SER0-0.010-0.00929.550-0.068-0.0680.0000.0000.0000.000
117A135VAL0-0.0080.01831.656-0.206-0.2060.0000.0000.0000.000
118A136GLU-1-0.825-0.89430.8939.7519.7510.0000.0000.0000.000
119A137ALA0-0.029-0.01930.866-0.146-0.1460.0000.0000.0000.000
120A138THR00.0250.00132.925-0.155-0.1550.0000.0000.0000.000
121A139ILE0-0.0090.00236.386-0.211-0.2110.0000.0000.0000.000
122A140LYS10.8750.92630.456-9.954-9.9540.0000.0000.0000.000
123A141GLY00.0360.03636.365-0.118-0.1180.0000.0000.0000.000
124A142THR00.0100.01637.806-0.214-0.2140.0000.0000.0000.000
125A143PHE0-0.014-0.00939.979-0.236-0.2360.0000.0000.0000.000
126A144THR0-0.056-0.03136.8020.0680.0680.0000.0000.0000.000
127A145ASN0-0.005-0.00634.057-0.007-0.0070.0000.0000.0000.000
128A146LEU00.0310.02138.455-0.028-0.0280.0000.0000.0000.000
129A147ASP-1-0.820-0.90539.7897.7557.7550.0000.0000.0000.000
130A148THR0-0.135-0.08036.552-0.016-0.0160.0000.0000.0000.000
131A149GLN0-0.008-0.00639.6040.0310.0310.0000.0000.0000.000
132A150ILE0-0.037-0.01442.348-0.184-0.1840.0000.0000.0000.000
133A151ASP-1-0.969-0.99545.6306.4066.4060.0000.0000.0000.000
134A152GLU-1-0.884-0.93442.3247.2207.2200.0000.0000.0000.000
135A153ALA0-0.015-0.00345.874-0.095-0.0950.0000.0000.0000.000
136A154TRP0-0.075-0.02140.487-0.117-0.1170.0000.0000.0000.000
137A155ILE0-0.031-0.01745.0310.0200.0200.0000.0000.0000.000
138A156PHE00.0080.01747.538-0.084-0.0840.0000.0000.0000.000
139A157TRP00.0810.00146.195-0.090-0.0900.0000.0000.0000.000
140A158HIS00.0050.01252.190-0.190-0.1900.0000.0000.0000.000
141A159SER0-0.021-0.03655.0020.0190.0190.0000.0000.0000.000
142A160LEU0-0.0140.02152.6750.0120.0120.0000.0000.0000.000
143A161SER0-0.048-0.03355.964-0.173-0.1730.0000.0000.0000.000
144A162ALA0-0.025-0.02055.8350.1000.1000.0000.0000.0000.000
145A163HIS00.0110.00255.7590.1250.1250.0000.0000.0000.000
146A164ASN0-0.026-0.00854.4330.0000.0000.0000.0000.0000.000
147A165THR00.018-0.00649.466-0.021-0.0210.0000.0000.0000.000
148A166SER0-0.0060.00551.7270.0580.0580.0000.0000.0000.000
149A167TYR0-0.020-0.03744.455-0.045-0.0450.0000.0000.0000.000
150A168TYR0-0.028-0.00250.404-0.034-0.0340.0000.0000.0000.000
151A169TYR00.016-0.01040.6870.0600.0600.0000.0000.0000.000
152A170ASN0-0.0270.00146.180-0.046-0.0460.0000.0000.0000.000
153A171ILE00.0170.00140.4510.1410.1410.0000.0000.0000.000
154A172LEU0-0.0160.00041.944-0.155-0.1550.0000.0000.0000.000
155A173PHE00.0290.02636.8390.1910.1910.0000.0000.0000.000
156A174SER00.0110.00438.861-0.191-0.1910.0000.0000.0000.000
157A175ILE0-0.014-0.00834.4710.2750.2750.0000.0000.0000.000
158A176GLN00.0420.00336.619-0.145-0.1450.0000.0000.0000.000
159A177ASN0-0.050-0.06032.0930.0030.0030.0000.0000.0000.000
160A178GLU-1-0.892-0.94630.5229.7279.7270.0000.0000.0000.000
161A179ASP-1-0.802-0.86333.1329.2209.2200.0000.0000.0000.000
162A180THR0-0.026-0.01835.892-0.124-0.1240.0000.0000.0000.000
163A181GLY00.0090.01038.082-0.236-0.2360.0000.0000.0000.000
164A182ALA0-0.028-0.01339.668-0.020-0.0200.0000.0000.0000.000
165A183VAL0-0.021-0.01042.387-0.179-0.1790.0000.0000.0000.000
166A184MET0-0.0140.01740.3790.2170.2170.0000.0000.0000.000
167A185ALA0-0.001-0.00941.091-0.206-0.2060.0000.0000.0000.000
168A186VAL0-0.015-0.01441.4910.1750.1750.0000.0000.0000.000
169A187LEU0-0.028-0.00741.719-0.129-0.1290.0000.0000.0000.000
170A188PRO00.0070.01443.5580.1210.1210.0000.0000.0000.000
171A189LEU0-0.034-0.02242.083-0.078-0.0780.0000.0000.0000.000
172A190ALA00.0300.01845.9060.0200.0200.0000.0000.0000.000
173A191PHE0-0.009-0.01642.613-0.051-0.0510.0000.0000.0000.000
174A192GLU-1-0.795-0.89148.1065.7345.7340.0000.0000.0000.000
175A193VAL00.0060.00946.573-0.019-0.0190.0000.0000.0000.000
176A194SER0-0.025-0.03049.909-0.121-0.1210.0000.0000.0000.000
177A195VAL00.0310.01547.7650.0940.0940.0000.0000.0000.000
178A196ASP-1-0.845-0.92350.6026.1276.1270.0000.0000.0000.000
179A197VAL0-0.0110.00048.470-0.046-0.0460.0000.0000.0000.000
180A198GLU-1-0.753-0.83151.8466.1356.1350.0000.0000.0000.000
181A199LYS10.9290.97948.750-6.215-6.2150.0000.0000.0000.000
182A200GLN0-0.022-0.02448.1250.1230.1230.0000.0000.0000.000
183A201LYS10.8030.88746.528-6.096-6.0960.0000.0000.0000.000
184A202VAL00.0240.01444.9800.1500.1500.0000.0000.0000.000
185A203LEU0-0.030-0.01743.9040.1310.1310.0000.0000.0000.000
186A204PHE0-0.042-0.01640.9910.1270.1270.0000.0000.0000.000
187A205PHE00.0100.02340.5110.0970.0970.0000.0000.0000.000
188A206THR0-0.020-0.04235.8290.2710.2710.0000.0000.0000.000
189A207ILE0-0.015-0.03632.963-0.086-0.0860.0000.0000.0000.000
190A208LYS10.9700.98032.030-9.380-9.3800.0000.0000.0000.000
191A209ASP-1-0.829-0.86737.5677.6107.6100.0000.0000.0000.000
192A210SER00.000-0.01841.1030.0370.0370.0000.0000.0000.000
193A211ALA0-0.0040.01344.040-0.087-0.0870.0000.0000.0000.000
194A212ARG10.8320.92047.444-5.896-5.8960.0000.0000.0000.000
195A213TYR00.0480.02043.799-0.076-0.0760.0000.0000.0000.000
196A214GLU-1-0.823-0.88449.0055.8215.8210.0000.0000.0000.000
197A215VAL00.008-0.00246.1330.0420.0420.0000.0000.0000.000
198A216LYS10.8610.93749.404-5.757-5.7570.0000.0000.0000.000
199A217MET0-0.0170.00344.2810.0890.0890.0000.0000.0000.000
200A218LYS10.7380.86449.147-6.016-6.0160.0000.0000.0000.000
201A219ALA00.0340.01446.4390.1170.1170.0000.0000.0000.000
202A220LEU0-0.011-0.01547.920-0.145-0.1450.0000.0000.0000.000
203A221THR00.003-0.01344.0530.1160.1160.0000.0000.0000.000
204A222LEU0-0.0210.00346.511-0.134-0.1340.0000.0000.0000.000
205A223VAL00.001-0.00844.2760.1970.1970.0000.0000.0000.000
206A224GLN00.0350.00745.905-0.061-0.0610.0000.0000.0000.000
207A225ALA0-0.0020.01145.7130.1710.1710.0000.0000.0000.000
208A226LEU0-0.0280.00239.944-0.019-0.0190.0000.0000.0000.000
209A227HIS0-0.020-0.00744.542-0.116-0.1160.0000.0000.0000.000
210A228SER0-0.039-0.01942.4090.1110.1110.0000.0000.0000.000
211A229SER0-0.012-0.01243.042-0.173-0.1730.0000.0000.0000.000
212A230ASN0-0.020-0.00940.1110.2650.2650.0000.0000.0000.000
213A231ALA0-0.0010.00742.798-0.080-0.0800.0000.0000.0000.000
214A232PRO00.0220.00143.5500.2000.2000.0000.0000.0000.000
215A233ILE00.0240.00338.719-0.058-0.0580.0000.0000.0000.000
216A234VAL0-0.003-0.00642.8160.0080.0080.0000.0000.0000.000
217A235ASP-1-0.848-0.93445.6886.2716.2710.0000.0000.0000.000
218A236ILE0-0.069-0.02642.325-0.066-0.0660.0000.0000.0000.000
219A237PHE00.009-0.00440.3590.0150.0150.0000.0000.0000.000
220A238ASN0-0.0260.01246.349-0.066-0.0660.0000.0000.0000.000
221A239VAL0-0.060-0.00448.807-0.158-0.1580.0000.0000.0000.000
222A240ASN00.0150.00750.2150.0790.0790.0000.0000.0000.000
223A241ASN0-0.016-0.03051.3380.1460.1460.0000.0000.0000.000
224A242TYR0-0.050-0.02453.706-0.134-0.1340.0000.0000.0000.000
225A243ASN0-0.060-0.04156.170-0.001-0.0010.0000.0000.0000.000
226A244LEU00.0210.02751.6130.0110.0110.0000.0000.0000.000
227A245TYR0-0.080-0.03354.5310.0280.0280.0000.0000.0000.000