FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6NK1Z

Calculation Name: 1TKI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TKI

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WZ42

Base Structure: X-ray

Registration Date: 2023-09-19

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 321
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5274511.735738
FMO2-HF: Nuclear repulsion 5144452.697311
FMO2-HF: Total energy -130059.038427
FMO2-MP2: Total energy -130438.944473


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:18:LYS)


Summations of interaction energy for fragment #1(A:18:LYS)
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.
-81.532-86.91742.574-19.09-18.1-0.179
Interaction energy analysis for fragmet #1(A:18:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.878
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].
3A20LEU0-0.0010.0102.2530.8314.5150.886-1.188-3.383-0.005
4A21TYR00.023-0.0082.0283.2164.0228.186-3.687-5.305-0.011
5A22GLU-1-0.798-0.8461.722-147.038-158.33133.386-13.680-8.413-0.161
6A23LYS10.7710.8664.89539.78239.851-0.001-0.004-0.0640.000
7A24TYR0-0.051-0.0367.0646.0846.0840.0000.0000.0000.000
8A25MET00.0010.0117.478-2.857-2.8570.0000.0000.0000.000
9A26ILE0-0.005-0.0135.9541.3111.3110.0000.0000.0000.000
10A27ALA0-0.017-0.0058.9050.9210.9210.0000.0000.0000.000
11A28GLU-1-0.749-0.84411.743-16.318-16.3180.0000.0000.0000.000
12A29ASP-1-0.917-0.95012.138-16.131-16.1310.0000.0000.0000.000
13A30LEU0-0.055-0.05013.3920.9660.9660.0000.0000.0000.000
14A31GLY00.0730.02014.4500.9190.9190.0000.0000.0000.000
15A32ARG10.8900.94512.06414.55714.5570.0000.0000.0000.000
16A33GLY00.1090.04414.0710.8070.8070.0000.0000.0000.000
17A34GLU-1-0.941-0.93514.466-13.073-13.0730.0000.0000.0000.000
18A35PHE00.0230.00913.132-0.415-0.4150.0000.0000.0000.000
19A36GLY00.0270.01610.708-1.080-1.0800.0000.0000.0000.000
20A37ILE0-0.063-0.0217.9921.3241.3240.0000.0000.0000.000
21A38VAL0-0.004-0.0029.510-1.413-1.4130.0000.0000.0000.000
22A39HIS00.0020.0068.4820.4620.4620.0000.0000.0000.000
23A40ARG10.8070.88911.38715.70115.7010.0000.0000.0000.000
24A41CYS0-0.026-0.0039.913-0.874-0.8740.0000.0000.0000.000
25A42VAL0-0.004-0.00811.5341.6471.6470.0000.0000.0000.000
26A43GLU-1-0.762-0.82811.914-22.764-22.7640.0000.0000.0000.000
27A44THR00.017-0.01110.1732.0762.0760.0000.0000.0000.000
28A45SER0-0.014-0.00712.9011.3961.3960.0000.0000.0000.000
29A46SER0-0.058-0.07014.7381.4121.4120.0000.0000.0000.000
30A47LYS10.9480.97116.14117.32517.3250.0000.0000.0000.000
31A48LYS10.9340.99417.13817.20617.2060.0000.0000.0000.000
32A49THR00.002-0.00915.922-1.152-1.1520.0000.0000.0000.000
33A50TYR0-0.080-0.04713.7001.1061.1060.0000.0000.0000.000
34A51MET0-0.018-0.00813.9050.2120.2120.0000.0000.0000.000
35A52ALA00.0150.0158.447-0.253-0.2530.0000.0000.0000.000
36A53LYS10.8790.93910.09417.77817.7780.0000.0000.0000.000
37A54PHE0-0.020-0.0032.691-0.4300.1700.086-0.181-0.5040.000
38A55VAL0-0.004-0.0217.1432.4522.4520.0000.0000.0000.000
39A56LYS10.8810.9355.77322.62522.6250.0000.0000.0000.000
40A57VAL00.0130.0079.4191.7121.7120.0000.0000.0000.000
41A58LYS10.8570.91110.55518.49818.4980.0000.0000.0000.000
42A59GLY00.0320.01412.8001.1191.1190.0000.0000.0000.000
43A60THR00.009-0.01215.871-0.514-0.5140.0000.0000.0000.000
44A61ASP-1-0.836-0.92216.166-14.047-14.0470.0000.0000.0000.000
45A62GLN0-0.033-0.02010.0720.4780.4780.0000.0000.0000.000
46A63VAL0-0.022-0.00514.727-0.182-0.1820.0000.0000.0000.000
47A64LEU0-0.021-0.01418.0250.3390.3390.0000.0000.0000.000
48A65VAL00.0510.02612.7100.2730.2730.0000.0000.0000.000
49A66LYS10.8840.93513.06222.47722.4770.0000.0000.0000.000
50A67LYS10.9210.97616.74713.07513.0750.0000.0000.0000.000
51A68GLU-1-0.773-0.88616.843-15.512-15.5120.0000.0000.0000.000
52A69ILE0-0.004-0.01313.0370.2810.2810.0000.0000.0000.000
53A70SER0-0.043-0.03017.5790.1510.1510.0000.0000.0000.000
54A71ILE0-0.0120.00020.7730.4230.4230.0000.0000.0000.000
55A72LEU00.000-0.00117.6700.2900.2900.0000.0000.0000.000
56A73ASN0-0.0210.01019.065-0.177-0.1770.0000.0000.0000.000
57A74ILE0-0.017-0.00420.9510.2030.2030.0000.0000.0000.000
58A75ALA0-0.0170.00124.5470.5060.5060.0000.0000.0000.000
59A76ARG10.8000.88518.87315.64415.6440.0000.0000.0000.000
60A77HIS00.0900.03525.7360.2180.2180.0000.0000.0000.000
61A78ARG10.9050.96226.7049.1899.1890.0000.0000.0000.000
62A79ASN0-0.080-0.06927.8550.0100.0100.0000.0000.0000.000
63A80ILE0-0.0110.01323.4190.1410.1410.0000.0000.0000.000
64A81LEU0-0.062-0.01918.032-0.148-0.1480.0000.0000.0000.000
65A82HIS00.015-0.00419.4830.1830.1830.0000.0000.0000.000
66A83LEU00.0050.00714.207-0.547-0.5470.0000.0000.0000.000
67A84HIS0-0.064-0.03713.8951.6841.6840.0000.0000.0000.000
68A85GLU-1-0.749-0.84410.515-29.793-29.7930.0000.0000.0000.000
69A86SER0-0.017-0.00611.4411.0171.0170.0000.0000.0000.000
70A87PHE0-0.024-0.0076.621-1.206-1.2060.0000.0000.0000.000
71A88GLU-1-0.877-0.9538.396-21.463-21.4630.0000.0000.0000.000
72A89SER00.0440.0055.508-1.163-1.1630.0000.0000.0000.000
73A90MET00.0160.0058.3242.8492.8490.0000.0000.0000.000
74A91GLU-1-0.879-0.9467.580-19.429-19.4290.0000.0000.0000.000
75A92GLU-1-0.842-0.9003.331-34.184-33.5260.032-0.330-0.361-0.002
76A93LEU0-0.036-0.0036.988-1.612-1.6120.0000.0000.0000.000
77A94VAL0-0.0120.0044.3270.8610.952-0.001-0.020-0.0700.000
78A95MET0-0.0270.0007.5110.2910.2910.0000.0000.0000.000
79A96ILE00.0080.0088.8650.6810.6810.0000.0000.0000.000
80A97PHE00.0660.01912.2400.7800.7800.0000.0000.0000.000
81A98GLU-1-0.767-0.85815.736-13.664-13.6640.0000.0000.0000.000
82A99PHE0-0.019-0.02216.7250.1560.1560.0000.0000.0000.000
83A100ILE0-0.0420.00319.0840.6480.6480.0000.0000.0000.000
84A101SER00.009-0.02021.4320.0510.0510.0000.0000.0000.000
85A102GLY0-0.052-0.01723.7980.3450.3450.0000.0000.0000.000
86A103LEU0-0.027-0.01825.485-0.229-0.2290.0000.0000.0000.000
87A104ASP-1-0.683-0.80027.299-9.512-9.5120.0000.0000.0000.000
88A105ILE00.026-0.00128.8610.1570.1570.0000.0000.0000.000
89A106PHE00.0750.02132.0150.2440.2440.0000.0000.0000.000
90A107GLU-1-0.824-0.87726.996-10.059-10.0590.0000.0000.0000.000
91A108ARG10.8200.91531.6278.8068.8060.0000.0000.0000.000
92A109ILE00.0000.01433.2920.1690.1690.0000.0000.0000.000
93A110ASN0-0.040-0.00733.6810.4030.4030.0000.0000.0000.000
94A111THR0-0.089-0.04133.6110.0830.0830.0000.0000.0000.000
95A112SER00.036-0.00236.4840.1170.1170.0000.0000.0000.000
96A113ALA0-0.024-0.00537.0610.1190.1190.0000.0000.0000.000
97A114PHE0-0.036-0.01936.5980.0030.0030.0000.0000.0000.000
98A115GLU-1-0.880-0.93438.708-6.553-6.5530.0000.0000.0000.000
99A116LEU0-0.028-0.00738.756-0.087-0.0870.0000.0000.0000.000
100A117ASN00.0320.01541.3280.1770.1770.0000.0000.0000.000
101A118GLU-1-0.682-0.82942.349-6.552-6.5520.0000.0000.0000.000
102A119ARG10.8950.96242.2036.9066.9060.0000.0000.0000.000
103A120GLU-1-0.938-0.98437.835-8.005-8.0050.0000.0000.0000.000
104A121ILE0-0.013-0.00338.333-0.246-0.2460.0000.0000.0000.000
105A122VAL00.0550.03738.894-0.190-0.1900.0000.0000.0000.000
106A123SER0-0.007-0.00137.669-0.187-0.1870.0000.0000.0000.000
107A124TYR00.000-0.00831.086-0.223-0.2230.0000.0000.0000.000
108A125VAL00.031-0.00634.907-0.244-0.2440.0000.0000.0000.000
109A126HIS0-0.019-0.00136.8900.0710.0710.0000.0000.0000.000
110A127GLN00.0350.00332.808-0.407-0.4070.0000.0000.0000.000
111A128VAL0-0.013-0.00331.612-0.255-0.2550.0000.0000.0000.000
112A129CYS0-0.020-0.00833.327-0.073-0.0730.0000.0000.0000.000
113A130GLU-1-0.875-0.93134.446-8.700-8.7000.0000.0000.0000.000
114A131ALA0-0.031-0.01329.781-0.126-0.1260.0000.0000.0000.000
115A132LEU00.013-0.00231.668-0.170-0.1700.0000.0000.0000.000
116A133GLN00.0620.04833.3970.2190.2190.0000.0000.0000.000
117A134PHE0-0.017-0.00228.1980.0880.0880.0000.0000.0000.000
118A135LEU00.0240.01827.235-0.103-0.1030.0000.0000.0000.000
119A136HIS0-0.024-0.03631.2650.1340.1340.0000.0000.0000.000
120A137SER0-0.083-0.02834.3050.1160.1160.0000.0000.0000.000
121A138HIS0-0.041-0.02330.828-0.101-0.1010.0000.0000.0000.000
122A139ASN0-0.050-0.03431.991-0.103-0.1030.0000.0000.0000.000
123A140ILE0-0.039-0.01827.302-0.159-0.1590.0000.0000.0000.000
124A141GLY00.0110.02230.4200.2570.2570.0000.0000.0000.000
125A142HIS0-0.038-0.04325.448-0.057-0.0570.0000.0000.0000.000
126A143PHE00.000-0.02727.553-0.206-0.2060.0000.0000.0000.000
127A144ASP-1-0.789-0.85925.632-10.685-10.6850.0000.0000.0000.000
128A145ILE00.0100.01927.910-0.194-0.1940.0000.0000.0000.000
129A146ARG10.8310.89526.06910.23710.2370.0000.0000.0000.000
130A147PRO00.0350.01529.360-0.266-0.2660.0000.0000.0000.000
131A148GLU-1-0.804-0.88826.060-9.824-9.8240.0000.0000.0000.000
132A149ASN0-0.024-0.01824.778-0.607-0.6070.0000.0000.0000.000
133A150ILE0-0.0100.00425.588-0.304-0.3040.0000.0000.0000.000
134A151ILE0-0.022-0.01423.2330.2190.2190.0000.0000.0000.000
135A152TYR00.0200.01326.517-0.075-0.0750.0000.0000.0000.000
136A153GLN00.0400.01125.7570.0640.0640.0000.0000.0000.000
137A154THR00.032-0.00525.534-0.227-0.2270.0000.0000.0000.000
138A155ARG10.9820.97926.14610.32810.3280.0000.0000.0000.000
139A156ARG10.9690.98630.1169.7639.7630.0000.0000.0000.000
140A157SER0-0.0260.00930.3330.3390.3390.0000.0000.0000.000
141A158SER00.0840.05132.411-0.076-0.0760.0000.0000.0000.000
142A159THR0-0.0150.00029.1480.0910.0910.0000.0000.0000.000
143A160ILE0-0.0290.00429.114-0.214-0.2140.0000.0000.0000.000
144A161LYS10.8380.90223.93912.19712.1970.0000.0000.0000.000
145A162ILE00.0230.01725.1900.0280.0280.0000.0000.0000.000
146A163ILE0-0.028-0.04120.672-0.445-0.4450.0000.0000.0000.000
147A164GLU-1-0.805-0.88020.458-13.511-13.5110.0000.0000.0000.000
148A165PHE00.003-0.02420.9360.4910.4910.0000.0000.0000.000
149A166GLY00.0050.00720.429-0.172-0.1720.0000.0000.0000.000
150A167GLN0-0.041-0.02621.2900.1020.1020.0000.0000.0000.000
151A168ALA00.0030.01624.1830.4190.4190.0000.0000.0000.000
152A169ARG10.9030.94824.80010.32110.3210.0000.0000.0000.000
153A170GLN0-0.031-0.01427.1790.1410.1410.0000.0000.0000.000
154A171LEU0-0.041-0.01629.951-0.009-0.0090.0000.0000.0000.000
155A172LYS10.9300.97531.8529.6619.6610.0000.0000.0000.000
156A173PRO00.031-0.00833.9630.0450.0450.0000.0000.0000.000
157A174GLY0-0.0070.00737.004-0.061-0.0610.0000.0000.0000.000
158A175ASP-1-0.905-0.93431.091-9.760-9.7600.0000.0000.0000.000
159A176ASN0-0.066-0.04333.2140.3460.3460.0000.0000.0000.000
160A177PHE0-0.040-0.02228.961-0.357-0.3570.0000.0000.0000.000
161A178ARG10.9500.97828.3509.7919.7910.0000.0000.0000.000
162A179LEU00.0030.02328.411-0.334-0.3340.0000.0000.0000.000
163A180LEU0-0.020-0.02624.4180.2630.2630.0000.0000.0000.000
164A181PHE00.0290.01028.341-0.129-0.1290.0000.0000.0000.000
165A182THR00.022-0.00628.1790.1390.1390.0000.0000.0000.000
166A183ALA00.0020.02330.9430.2030.2030.0000.0000.0000.000
167A184PRO00.0450.01033.269-0.106-0.1060.0000.0000.0000.000
168A185GLU-1-0.722-0.84935.851-7.809-7.8090.0000.0000.0000.000
169A186TYR0-0.046-0.04133.3300.0390.0390.0000.0000.0000.000
170A187TYR0-0.081-0.05729.280-0.167-0.1670.0000.0000.0000.000
171A188ALA00.0660.03135.7300.1610.1610.0000.0000.0000.000
172A189PRO00.0430.03638.892-0.097-0.0970.0000.0000.0000.000
173A190GLU-1-0.733-0.84238.575-7.481-7.4810.0000.0000.0000.000
174A191VAL0-0.044-0.02434.218-0.103-0.1030.0000.0000.0000.000
175A192HIS0-0.019-0.00336.574-0.059-0.0590.0000.0000.0000.000
176A193GLN0-0.005-0.00339.0720.0560.0560.0000.0000.0000.000
177A194HIS0-0.051-0.00536.275-0.101-0.1010.0000.0000.0000.000
178A195ASP-1-0.818-0.91138.908-7.014-7.0140.0000.0000.0000.000
179A196VAL0-0.057-0.03838.367-0.235-0.2350.0000.0000.0000.000
180A197VAL00.0270.01333.9760.1150.1150.0000.0000.0000.000
181A198SER0-0.032-0.03536.6920.0630.0630.0000.0000.0000.000
182A199THR00.0820.03434.601-0.013-0.0130.0000.0000.0000.000
183A200ALA00.0350.02136.282-0.053-0.0530.0000.0000.0000.000
184A201THR0-0.023-0.03134.9840.0960.0960.0000.0000.0000.000
185A202ASP-1-0.766-0.86232.259-9.268-9.2680.0000.0000.0000.000
186A203MET0-0.052-0.01034.904-0.122-0.1220.0000.0000.0000.000
187A204TRP00.0500.04437.5930.1380.1380.0000.0000.0000.000
188A205SER0-0.014-0.01733.2560.0370.0370.0000.0000.0000.000
189A206LEU0-0.045-0.03135.428-0.027-0.0270.0000.0000.0000.000
190A207GLY00.0720.02936.8320.0780.0780.0000.0000.0000.000
191A208THR00.021-0.01137.3500.1730.1730.0000.0000.0000.000
192A209LEU0-0.052-0.01632.9410.0320.0320.0000.0000.0000.000
193A210VAL0-0.007-0.01436.7560.0230.0230.0000.0000.0000.000
194A211TYR00.0350.01439.7090.0780.0780.0000.0000.0000.000
195A212VAL0-0.020-0.00836.4540.1030.1030.0000.0000.0000.000
196A213LEU0-0.059-0.01935.2630.0150.0150.0000.0000.0000.000
197A214LEU0-0.010-0.00239.2420.0620.0620.0000.0000.0000.000
198A215SER00.0090.00542.7950.1190.1190.0000.0000.0000.000
199A216GLY0-0.054-0.03040.2820.0660.0660.0000.0000.0000.000
200A217ILE0-0.080-0.05441.3510.0040.0040.0000.0000.0000.000
201A218ASN0-0.0050.00538.6050.0330.0330.0000.0000.0000.000
202A219PRO00.0300.00940.7150.1050.1050.0000.0000.0000.000
203A220PHE00.0400.01641.1370.0800.0800.0000.0000.0000.000
204A221LEU0-0.057-0.02641.783-0.031-0.0310.0000.0000.0000.000
205A222ALA00.0480.01843.8920.1320.1320.0000.0000.0000.000
206A223GLU-1-0.894-0.94644.410-6.040-6.0400.0000.0000.0000.000
207A224THR0-0.016-0.00743.957-0.114-0.1140.0000.0000.0000.000
208A225ASN00.022-0.00437.5060.0080.0080.0000.0000.0000.000
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