Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: P9YZ2

Calculation Name: 3CKF-A-Xray13

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q45040

Base Structure: X-ray

Registration Date: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 224
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2234560.179333
FMO2-HF: Nuclear repulsion 2153546.74853
FMO2-HF: Total energy -81013.430804
FMO2-MP2: Total energy -81253.382174


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:27:ACE)


Summations of interaction energy for fragment #1(A:27:ACE)
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.
-0.1850.734-0.012-0.434-0.4740
Interaction energy analysis for fragmet #1(A:27:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.006
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].
3A29SER00.0300.0143.8470.6001.441-0.011-0.422-0.4090.000
4A30VAL0-0.0210.0067.2540.1170.1170.0000.0000.0000.000
5A31SER0-0.006-0.00110.010-0.015-0.0150.0000.0000.0000.000
6A32VAL0-0.031-0.01313.4730.0430.0430.0000.0000.0000.000
7A33ASP-1-0.905-0.95216.230-0.130-0.1300.0000.0000.0000.000
8A34LEU0-0.033-0.02219.6400.0120.0120.0000.0000.0000.000
9A35PRO00.0410.01822.2940.0000.0000.0000.0000.0000.000
10A36GLY0-0.004-0.01525.946-0.006-0.0060.0000.0000.0000.000
11A37SER0-0.089-0.03524.867-0.002-0.0020.0000.0000.0000.000
12A38MET0-0.0080.01422.724-0.008-0.0080.0000.0000.0000.000
13A39LYS10.9500.96617.5440.1820.1820.0000.0000.0000.000
14A40VAL0-0.0220.00715.144-0.004-0.0040.0000.0000.0000.000
15A41LEU0-0.018-0.00711.1750.0000.0000.0000.0000.0000.000
16A42VAL00.0310.01610.770-0.006-0.0060.0000.0000.0000.000
17A43SER00.0270.0196.307-0.079-0.0790.0000.0000.0000.000
18A44LYS10.9310.9524.315-0.592-0.514-0.001-0.012-0.0650.000
19A45SER0-0.029-0.0195.0850.4500.4500.0000.0000.0000.000
20A46SER00.0230.0256.627-0.214-0.2140.0000.0000.0000.000
21A47ASN00.0440.0188.3820.1320.1320.0000.0000.0000.000
22A48ALA00.002-0.01510.1230.0470.0470.0000.0000.0000.000
23A49ASP-1-0.943-0.95912.924-0.003-0.0030.0000.0000.0000.000
24A50GLY0-0.042-0.02013.350-0.004-0.0040.0000.0000.0000.000
25A51LYS10.8850.94613.4910.0460.0460.0000.0000.0000.000
26A52TYR0-0.011-0.0039.1780.0420.0420.0000.0000.0000.000
27A53ASP-1-0.877-0.9359.571-0.443-0.4430.0000.0000.0000.000
28A54LEU0-0.047-0.04011.222-0.028-0.0280.0000.0000.0000.000
29A55ILE00.0310.00912.7900.0130.0130.0000.0000.0000.000
30A56ALA00.0280.00814.9940.0010.0010.0000.0000.0000.000
31A57THR0-0.0070.01617.9850.0040.0040.0000.0000.0000.000
32A58VAL0-0.012-0.01220.8040.0110.0110.0000.0000.0000.000
33A59ASP-1-0.954-0.97724.208-0.097-0.0970.0000.0000.0000.000
34A60ALA0-0.057-0.03724.7680.0030.0030.0000.0000.0000.000
35A61LEU0-0.0240.00124.107-0.004-0.0040.0000.0000.0000.000
36A62GLU-1-0.947-0.97116.945-0.355-0.3550.0000.0000.0000.000
37A63LEU0-0.057-0.03119.7170.0200.0200.0000.0000.0000.000
38A64SER00.0420.00416.007-0.033-0.0330.0000.0000.0000.000
39A65GLY00.0260.01215.9730.0380.0380.0000.0000.0000.000
40A66THR0-0.039-0.00913.920-0.025-0.0250.0000.0000.0000.000
41A67SER0-0.033-0.02014.7840.0270.0270.0000.0000.0000.000
42A68ASP-1-0.915-0.95715.065-0.017-0.0170.0000.0000.0000.000
43A69LYS10.9020.96716.6280.0370.0370.0000.0000.0000.000
44A70ASN00.008-0.00612.162-0.043-0.0430.0000.0000.0000.000
45A71ASN0-0.007-0.00713.270-0.019-0.0190.0000.0000.0000.000
46A72GLY00.0500.02515.366-0.011-0.0110.0000.0000.0000.000
47A73SER0-0.023-0.01216.241-0.009-0.0090.0000.0000.0000.000
48A74GLY00.0380.02417.903-0.005-0.0050.0000.0000.0000.000
49A75VAL0-0.020-0.01419.9530.0010.0010.0000.0000.0000.000
50A76LEU0-0.027-0.00317.071-0.012-0.0120.0000.0000.0000.000
51A77GLU-1-0.945-0.98720.425-0.088-0.0880.0000.0000.0000.000
52A78GLY00.0690.02721.492-0.023-0.0230.0000.0000.0000.000
53A79VAL0-0.057-0.02323.9070.0150.0150.0000.0000.0000.000
54A80LYS10.9700.99326.9910.0820.0820.0000.0000.0000.000
55A81ALA00.0440.01229.3130.0020.0020.0000.0000.0000.000
56A82ASP-1-0.892-0.92831.214-0.078-0.0780.0000.0000.0000.000
57A83ALA0-0.002-0.01231.6990.0060.0060.0000.0000.0000.000
58A84SER0-0.070-0.04032.1670.0030.0030.0000.0000.0000.000
59A85LYS10.9350.97728.9630.0720.0720.0000.0000.0000.000
60A86VAL0-0.003-0.00825.8760.0080.0080.0000.0000.0000.000
61A87LYS10.9781.00024.8540.0730.0730.0000.0000.0000.000
62A88LEU0-0.0020.00420.9600.0090.0090.0000.0000.0000.000
63A89THR0-0.008-0.00722.949-0.005-0.0050.0000.0000.0000.000
64A90ILE0-0.028-0.00319.4720.0060.0060.0000.0000.0000.000
65A91SER00.0360.00822.6130.0010.0010.0000.0000.0000.000
66A92ASP-1-0.836-0.94122.275-0.030-0.0300.0000.0000.0000.000
67A93ASP-1-0.883-0.94422.031-0.024-0.0240.0000.0000.0000.000
68A94LEU0-0.062-0.03419.128-0.001-0.0010.0000.0000.0000.000
69A95GLY0-0.0070.01523.289-0.004-0.0040.0000.0000.0000.000
70A96GLN0-0.042-0.04626.300-0.001-0.0010.0000.0000.0000.000
71A97THR0-0.0040.00823.872-0.004-0.0040.0000.0000.0000.000
72A98THR0-0.010-0.00726.4830.0080.0080.0000.0000.0000.000
73A99LEU00.0080.01525.792-0.007-0.0070.0000.0000.0000.000
74A100GLU-1-0.913-0.96728.323-0.056-0.0560.0000.0000.0000.000
75A101VAL0-0.0020.00629.433-0.007-0.0070.0000.0000.0000.000
76A102PHE00.0120.00030.0140.0070.0070.0000.0000.0000.000
77A103LYS10.9860.97533.6090.0440.0440.0000.0000.0000.000
78A104SER00.0440.02333.5360.0000.0000.0000.0000.0000.000
79A105ASP-1-0.848-0.91433.420-0.055-0.0550.0000.0000.0000.000
80A106GLY0-0.089-0.04632.5170.0000.0000.0000.0000.0000.000
81A107SER0-0.029-0.00933.2780.0020.0020.0000.0000.0000.000
82A108THR0-0.030-0.01636.4070.0040.0040.0000.0000.0000.000
83A109LEU0-0.0110.00333.510-0.003-0.0030.0000.0000.0000.000
84A110VAL0-0.038-0.02335.5840.0040.0040.0000.0000.0000.000
85A111SER0-0.066-0.05434.1600.0010.0010.0000.0000.0000.000
86A112LYS10.9770.99032.3590.0450.0450.0000.0000.0000.000
87A113LYS10.9590.99129.4050.0900.0900.0000.0000.0000.000
88A114VAL00.0180.00730.567-0.004-0.0040.0000.0000.0000.000
89A115THR0-0.042-0.02228.2730.0030.0030.0000.0000.0000.000
90A116ARG10.8380.88229.3120.0400.0400.0000.0000.0000.000
91A117ALA00.1050.05428.511-0.004-0.0040.0000.0000.0000.000
92A118ASP-1-0.769-0.83029.333-0.040-0.0400.0000.0000.0000.000
93A119GLY0-0.054-0.03429.842-0.002-0.0020.0000.0000.0000.000
94A120THR0-0.117-0.06030.787-0.003-0.0030.0000.0000.0000.000
95A121ARG10.8480.90331.9870.0620.0620.0000.0000.0000.000
96A122LEU00.0020.01534.1110.0030.0030.0000.0000.0000.000
97A123GLU-1-0.861-0.92134.767-0.065-0.0650.0000.0000.0000.000
98A124TYR00.000-0.02236.1050.0030.0030.0000.0000.0000.000
99A125THR00.018-0.00837.248-0.003-0.0030.0000.0000.0000.000
100A126GLY0-0.011-0.00939.6350.0030.0030.0000.0000.0000.000
101A127ILE0-0.018-0.00137.3620.0030.0030.0000.0000.0000.000
102A128LYS10.8950.95441.4550.0370.0370.0000.0000.0000.000
103A129SER00.0330.00743.1270.0000.0000.0000.0000.0000.000
104A130ASP-1-0.848-0.89244.476-0.028-0.0280.0000.0000.0000.000
105A131GLY0-0.014-0.00741.9750.0010.0010.0000.0000.0000.000
106A132SER0-0.056-0.04542.857-0.001-0.0010.0000.0000.0000.000
107A133GLY00.029-0.00342.820-0.002-0.0020.0000.0000.0000.000
108A134LYS10.8790.94843.0080.0370.0370.0000.0000.0000.000
109A135ALA00.0300.01441.023-0.002-0.0020.0000.0000.0000.000
110A136LYS10.9340.98139.8350.0450.0450.0000.0000.0000.000
111A137GLU-1-0.738-0.83038.546-0.036-0.0360.0000.0000.0000.000
112A138VAL0-0.038-0.02736.1280.0010.0010.0000.0000.0000.000
113A139LEU00.0130.00436.703-0.002-0.0020.0000.0000.0000.000
114A140LYS10.9560.96332.1740.0480.0480.0000.0000.0000.000
115A141GLY00.0600.04038.3110.0020.0020.0000.0000.0000.000
116A142TYR0-0.056-0.02841.1400.0010.0010.0000.0000.0000.000
117A143VAL0-0.005-0.00240.373-0.002-0.0020.0000.0000.0000.000
118A144LEU0-0.037-0.00442.4520.0020.0020.0000.0000.0000.000
119A145GLU-1-0.829-0.92543.223-0.041-0.0410.0000.0000.0000.000
120A146GLY00.007-0.00945.1310.0020.0020.0000.0000.0000.000
121A147THR0-0.076-0.02645.652-0.001-0.0010.0000.0000.0000.000
122A148LEU00.0120.02040.3070.0000.0000.0000.0000.0000.000
123A149THR0-0.016-0.01344.1110.0010.0010.0000.0000.0000.000
124A150ALA00.0310.00543.344-0.001-0.0010.0000.0000.0000.000
125A151GLU-1-0.985-0.97143.379-0.019-0.0190.0000.0000.0000.000
126A152LYS10.9420.97143.6260.0200.0200.0000.0000.0000.000
127A153THR0-0.0090.02041.427-0.002-0.0020.0000.0000.0000.000
128A154THR00.0090.00143.7770.0010.0010.0000.0000.0000.000
129A155LEU0-0.054-0.01741.898-0.001-0.0010.0000.0000.0000.000
130A156VAL00.007-0.00546.3730.0020.0020.0000.0000.0000.000
131A157VAL0-0.0060.00648.884-0.001-0.0010.0000.0000.0000.000
132A158LYS10.8750.92051.3830.0210.0210.0000.0000.0000.000
133A159GLU-1-0.896-0.96255.083-0.020-0.0200.0000.0000.0000.000
134A160GLY00.0500.04057.5500.0010.0010.0000.0000.0000.000
135A161THR0-0.073-0.06360.7440.0000.0000.0000.0000.0000.000
136A162VAL00.0300.03556.6210.0000.0000.0000.0000.0000.000
137A163THR0-0.061-0.02754.224-0.001-0.0010.0000.0000.0000.000
138A164LEU00.0200.01949.8940.0010.0010.0000.0000.0000.000
139A165SER0-0.007-0.01750.114-0.002-0.0020.0000.0000.0000.000
140A166LYS10.8710.92540.8460.0300.0300.0000.0000.0000.000
141A167ASN0-0.031-0.02045.970-0.003-0.0030.0000.0000.0000.000
142A168ILE00.0060.00039.3560.0000.0000.0000.0000.0000.000
143A169SER00.0640.03741.032-0.002-0.0020.0000.0000.0000.000
144A170LYS11.0160.99337.1400.0260.0260.0000.0000.0000.000
145A171SER0-0.049-0.02936.453-0.003-0.0030.0000.0000.0000.000
146A172GLY00.0060.00236.4230.0000.0000.0000.0000.0000.000
147A173GLU-1-0.973-0.97637.830-0.015-0.0150.0000.0000.0000.000
148A174VAL00.0080.00240.578-0.001-0.0010.0000.0000.0000.000
149A175SER0-0.013-0.00343.0900.0020.0020.0000.0000.0000.000
150A176VAL0-0.011-0.01046.841-0.001-0.0010.0000.0000.0000.000
151A177GLU-1-0.857-0.92349.345-0.015-0.0150.0000.0000.0000.000
152A178LEU0-0.010-0.01452.911-0.001-0.0010.0000.0000.0000.000
153A179ASN0-0.046-0.01555.6420.0020.0020.0000.0000.0000.000
154A180ASP-1-0.646-0.80758.735-0.014-0.0140.0000.0000.0000.000
155A181THR0-0.032-0.02861.5790.0000.0000.0000.0000.0000.000
156A182ASP-1-0.870-0.89864.431-0.012-0.0120.0000.0000.0000.000
157A183SER0-0.051-0.03866.6170.0000.0000.0000.0000.0000.000
158A184SER00.0380.02569.2510.0010.0010.0000.0000.0000.000
159A185ALA00.0180.01069.1490.0000.0000.0000.0000.0000.000
160A186ALA0-0.038-0.01769.2790.0000.0000.0000.0000.0000.000
161A187THR0-0.051-0.08066.8690.0000.0000.0000.0000.0000.000
162A188LYS10.8790.96464.0560.0110.0110.0000.0000.0000.000
163A189LYS10.8160.90859.9630.0140.0140.0000.0000.0000.000
164A190THR0-0.058-0.02960.5850.0000.0000.0000.0000.0000.000
165A191ALA00.024-0.00755.8590.0000.0000.0000.0000.0000.000
166A192ALA0-0.0180.00956.2590.0000.0000.0000.0000.0000.000
167A193TRP00.0370.02546.1390.0000.0000.0000.0000.0000.000
168A194ASN0-0.0050.00850.5550.0010.0010.0000.0000.0000.000
169A195SER00.038-0.00147.1470.0000.0000.0000.0000.0000.000
170A196GLY00.0210.01946.3020.0000.0000.0000.0000.0000.000
171A197THR0-0.009-0.01946.3020.0000.0000.0000.0000.0000.000
172A198SER00.0020.01844.123-0.001-0.0010.0000.0000.0000.000
173A199THR0-0.047-0.02546.417-0.001-0.0010.0000.0000.0000.000
174A200LEU0-0.027-0.01049.5580.0000.0000.0000.0000.0000.000
175A201THR0-0.015-0.02152.1310.0000.0000.0000.0000.0000.000
176A202ILE0-0.008-0.00754.9910.0000.0000.0000.0000.0000.000
177A203THR0-0.033-0.01957.9270.0010.0010.0000.0000.0000.000
178A204VAL00.0240.00761.654-0.001-0.0010.0000.0000.0000.000
179A205ASN0-0.0030.00564.5960.0010.0010.0000.0000.0000.000
180A206SER0-0.041-0.02166.8290.0000.0000.0000.0000.0000.000
181A207LYS10.8940.95265.2650.0080.0080.0000.0000.0000.000
182A208LYS10.9600.99658.5770.0060.0060.0000.0000.0000.000
183A209THR00.001-0.01260.0790.0000.0000.0000.0000.0000.000
184A210LYS10.8940.94055.2780.0140.0140.0000.0000.0000.000
185A211ASP-1-0.778-0.84552.044-0.010-0.0100.0000.0000.0000.000
186A212LEU0-0.039-0.02949.939-0.001-0.0010.0000.0000.0000.000
187A213VAL00.0190.01245.2200.0000.0000.0000.0000.0000.000
188A214PHE0-0.030-0.02344.002-0.002-0.0020.0000.0000.0000.000
189A215THR00.045-0.00540.6170.0000.0000.0000.0000.0000.000
190A216SER00.0280.00737.307-0.002-0.0020.0000.0000.0000.000
191A217SER0-0.023-0.00835.961-0.001-0.0010.0000.0000.0000.000
192A218ASN0-0.091-0.06235.831-0.001-0.0010.0000.0000.0000.000
193A219THR00.0120.03538.909-0.001-0.0010.0000.0000.0000.000
194A220ILE00.005-0.00141.2770.0010.0010.0000.0000.0000.000
195A221THR00.0150.01744.7330.0000.0000.0000.0000.0000.000
196A222VAL00.006-0.00347.1580.0000.0000.0000.0000.0000.000
197A223GLN0-0.009-0.00350.9270.0000.0000.0000.0000.0000.000
198A224GLN00.0170.01053.3280.0000.0000.0000.0000.0000.000
199A225TYR0-0.066-0.05356.0250.0010.0010.0000.0000.0000.000
200A226ASP-1-0.715-0.86659.686-0.006-0.0060.0000.0000.0000.000
201A227SER00.020-0.00362.8270.0000.0000.0000.0000.0000.000
202A228ASN0-0.109-0.05365.7690.0000.0000.0000.0000.0000.000
203A229GLY00.0150.02662.8160.0000.0000.0000.0000.0000.000
204A230THR0-0.075-0.04762.7560.0000.0000.0000.0000.0000.000
205A231SER0-0.060-0.02560.1510.0010.0010.0000.0000.0000.000
206A232LEU0-0.0160.01553.7190.0000.0000.0000.0000.0000.000
207A233GLU-1-0.900-0.95857.520-0.008-0.0080.0000.0000.0000.000
208A234GLY0-0.016-0.00755.917-0.001-0.0010.0000.0000.0000.000
209A235SER0-0.037-0.03150.3900.0000.0000.0000.0000.0000.000
210A236ALA0-0.006-0.00148.252-0.001-0.0010.0000.0000.0000.000
211A237VAL00.0060.00948.3190.0000.0000.0000.0000.0000.000
212A238GLU-1-0.962-0.98541.398-0.025-0.0250.0000.0000.0000.000
213A239ILE0-0.047-0.02145.7460.0000.0000.0000.0000.0000.000
214A240THR0-0.006-0.00943.727-0.002-0.0020.0000.0000.0000.000
215A241LYS10.8390.91244.2310.0210.0210.0000.0000.0000.000
216A242LEU00.0440.01246.5070.0010.0010.0000.0000.0000.000
217A243ASP-1-0.812-0.92048.444-0.022-0.0220.0000.0000.0000.000
218A244GLU-1-0.819-0.91048.328-0.021-0.0210.0000.0000.0000.000
219A245ILE00.0060.01346.5500.0010.0010.0000.0000.0000.000
220A246LYS10.8900.94250.9750.0240.0240.0000.0000.0000.000
221A247ASN00.0390.00554.0960.0010.0010.0000.0000.0000.000
222A248ALA0-0.047-0.01453.3120.0010.0010.0000.0000.0000.000
223A249LEU0-0.041-0.02153.1360.0010.0010.0000.0000.0000.000
224A250LYS00.0480.06056.8080.0040.0040.0000.0000.0000.000