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

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FMODB ID: 2NK2R

Calculation Name: 3DCF-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3DCF

Chain ID: A

ChEMBL ID:
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UniProt ID: Q47L40

Base Structure: X-ray

Registration Date: 2023-09-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1994035.826877
FMO2-HF: Nuclear repulsion 1918981.254971
FMO2-HF: Total energy -75054.571906
FMO2-MP2: Total energy -75277.994497


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:29:ASN)


Summations of interaction energy for fragment #1(A:29:ASN)
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.
-21.337-14.8953.246-4.166-5.5220.016
Interaction energy analysis for fragmet #1(A:29:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.010
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].
3A31ARG10.8970.9543.8781.0862.279-0.009-0.491-0.6930.002
4A32ARG10.9600.9922.033-21.530-18.3623.025-3.018-3.1750.016
5A33THR00.0650.0172.6312.0193.7600.233-0.633-1.340-0.002
6A34GLN00.0230.0194.642-0.388-0.304-0.001-0.011-0.0730.000
7A35ILE0-0.049-0.0306.7270.0280.0280.0000.0000.0000.000
8A36ILE00.0060.0005.072-0.1140.013-0.001-0.001-0.1250.000
9A37LYS10.8520.9408.593-0.705-0.7050.0000.0000.0000.000
10A38VAL0-0.001-0.00410.648-0.160-0.1600.0000.0000.0000.000
11A39ALA0-0.012-0.00711.702-0.136-0.1360.0000.0000.0000.000
12A40THR0-0.003-0.01312.103-0.117-0.1170.0000.0000.0000.000
13A41GLU-1-0.847-0.91914.5690.2470.2470.0000.0000.0000.000
14A42LEU0-0.016-0.00516.217-0.078-0.0780.0000.0000.0000.000
15A43PHE0-0.018-0.04015.006-0.036-0.0360.0000.0000.0000.000
16A44ARG10.9000.94718.868-0.418-0.4180.0000.0000.0000.000
17A45GLU-1-0.953-0.95520.7920.2710.2710.0000.0000.0000.000
18A46LYS10.8310.91921.901-0.517-0.5170.0000.0000.0000.000
19A47GLY00.0970.06022.269-0.031-0.0310.0000.0000.0000.000
20A48TYR0-0.050-0.05417.3560.0440.0440.0000.0000.0000.000
21A49TYR00.017-0.00521.4850.0450.0450.0000.0000.0000.000
22A50ALA00.0270.03424.360-0.013-0.0130.0000.0000.0000.000
23A51THR0-0.0190.00718.275-0.036-0.0360.0000.0000.0000.000
24A52SER0-0.017-0.01620.1870.0610.0610.0000.0000.0000.000
25A53LEU00.008-0.02514.3470.0140.0140.0000.0000.0000.000
26A54ASP-1-0.860-0.94616.6850.6790.6790.0000.0000.0000.000
27A55ASP-1-0.772-0.84119.1710.4890.4890.0000.0000.0000.000
28A56ILE00.0180.00312.622-0.036-0.0360.0000.0000.0000.000
29A57ALA0-0.027-0.01814.525-0.020-0.0200.0000.0000.0000.000
30A58ASP-1-0.843-0.88615.5510.2670.2670.0000.0000.0000.000
31A59ARG10.8200.88215.967-0.503-0.5030.0000.0000.0000.000
32A60ILE0-0.063-0.02410.581-0.078-0.0780.0000.0000.0000.000
33A61GLY00.0190.02614.187-0.119-0.1190.0000.0000.0000.000
34A62PHE0-0.049-0.0469.112-0.068-0.0680.0000.0000.0000.000
35A63THR00.0640.03014.7520.0430.0430.0000.0000.0000.000
36A64LYS10.9460.96715.348-0.690-0.6900.0000.0000.0000.000
37A65PRO0-0.011-0.02715.9060.1100.1100.0000.0000.0000.000
38A66ALA0-0.0040.01612.2030.0930.0930.0000.0000.0000.000
39A67ILE00.0390.01910.8120.1830.1830.0000.0000.0000.000
40A68TYR00.0230.02411.4200.3330.3330.0000.0000.0000.000
41A69TYR0-0.0350.0056.7320.1060.1060.0000.0000.0000.000
42A70TYR0-0.019-0.0063.9490.3130.442-0.001-0.012-0.1160.000
43A71PHE0-0.021-0.0326.7090.6390.6390.0000.0000.0000.000
44A72LYS10.9150.93911.649-2.006-2.0060.0000.0000.0000.000
45A73SER00.003-0.00714.899-0.226-0.2260.0000.0000.0000.000
46A74LYS10.8720.91114.777-0.566-0.5660.0000.0000.0000.000
47A75GLU-1-0.760-0.86215.5991.1141.1140.0000.0000.0000.000
48A76ASP-1-0.835-0.88512.1621.8581.8580.0000.0000.0000.000
49A77VAL0-0.056-0.02210.8710.4580.4580.0000.0000.0000.000
50A78LEU00.0380.02011.3950.2500.2500.0000.0000.0000.000
51A79PHE00.005-0.00310.9000.0110.0110.0000.0000.0000.000
52A80ALA0-0.026-0.0157.3090.1040.1040.0000.0000.0000.000
53A81ILE00.0000.0038.6560.2720.2720.0000.0000.0000.000
54A82VAL00.0320.01810.849-0.201-0.2010.0000.0000.0000.000
55A83ASN0-0.022-0.0278.330-0.506-0.5060.0000.0000.0000.000
56A84SER00.0140.0177.7830.0060.0060.0000.0000.0000.000
57A85ILE00.0040.0099.148-0.412-0.4120.0000.0000.0000.000
58A86VAL0-0.033-0.02212.857-0.220-0.2200.0000.0000.0000.000
59A87ASP-1-0.835-0.9107.952-0.033-0.0330.0000.0000.0000.000
60A88GLU-1-0.932-0.96710.800-0.083-0.0830.0000.0000.0000.000
61A89ALA0-0.070-0.04012.546-0.146-0.1460.0000.0000.0000.000
62A90LEU0-0.0060.00613.465-0.075-0.0750.0000.0000.0000.000
63A91GLU-1-0.918-0.96210.618-0.878-0.8780.0000.0000.0000.000
64A92ARG10.8260.90414.947-0.150-0.1500.0000.0000.0000.000
65A93PHE0-0.020-0.00118.006-0.004-0.0040.0000.0000.0000.000
66A94HIS00.008-0.01216.125-0.033-0.0330.0000.0000.0000.000
67A95ALA0-0.0170.00618.684-0.012-0.0120.0000.0000.0000.000
68A96ILE0-0.031-0.01020.373-0.002-0.0020.0000.0000.0000.000
69A97ALA00.0130.00522.8210.0040.0040.0000.0000.0000.000
70A98ALA0-0.044-0.01521.9380.0070.0070.0000.0000.0000.000
71A99GLY00.0070.01923.947-0.028-0.0280.0000.0000.0000.000
72A100PRO0-0.056-0.04625.7670.0150.0150.0000.0000.0000.000
73A101GLY00.0290.02629.4420.0070.0070.0000.0000.0000.000
74A102SER0-0.052-0.06932.067-0.007-0.0070.0000.0000.0000.000
75A103PRO00.029-0.00931.491-0.001-0.0010.0000.0000.0000.000
76A104GLY00.0380.01431.8700.0090.0090.0000.0000.0000.000
77A105GLU-1-0.921-0.93932.958-0.068-0.0680.0000.0000.0000.000
78A106ARG10.8390.92127.3720.1130.1130.0000.0000.0000.000
79A107ILE0-0.0020.00328.3500.0110.0110.0000.0000.0000.000
80A108HIS00.0220.00829.5580.0190.0190.0000.0000.0000.000
81A109ALA0-0.015-0.01427.5550.0120.0120.0000.0000.0000.000
82A110LEU0-0.008-0.00623.4760.0100.0100.0000.0000.0000.000
83A111LEU00.0220.01725.4840.0280.0280.0000.0000.0000.000
84A112VAL0-0.0100.01127.8670.0240.0240.0000.0000.0000.000
85A113GLU-1-0.801-0.87720.8170.0630.0630.0000.0000.0000.000
86A114HIS00.0240.01122.1030.0160.0160.0000.0000.0000.000
87A115THR00.003-0.02224.0330.0400.0400.0000.0000.0000.000
88A116ARG10.8580.91923.9450.0110.0110.0000.0000.0000.000
89A117THR0-0.020-0.01319.2090.0220.0220.0000.0000.0000.000
90A118ILE0-0.0140.00521.5130.0580.0580.0000.0000.0000.000
91A119LEU0-0.019-0.01723.7800.0290.0290.0000.0000.0000.000
92A120ARG10.8740.95321.403-0.127-0.1270.0000.0000.0000.000
93A121ASN0-0.072-0.03017.8590.0980.0980.0000.0000.0000.000
94A122LEU00.0780.05220.7820.0350.0350.0000.0000.0000.000
95A123ASP-1-0.877-0.93921.2480.4820.4820.0000.0000.0000.000
96A124ALA0-0.021-0.02017.6450.0450.0450.0000.0000.0000.000
97A125ASN00.000-0.01619.4850.0200.0200.0000.0000.0000.000
98A126THR00.0060.00322.172-0.021-0.0210.0000.0000.0000.000
99A127LEU0-0.036-0.01117.9470.0070.0070.0000.0000.0000.000
100A128PHE0-0.051-0.02017.0030.0490.0490.0000.0000.0000.000
101A129TYR0-0.037-0.02720.8430.0010.0010.0000.0000.0000.000
102A130ASN0-0.0120.01724.576-0.046-0.0460.0000.0000.0000.000
103A131GLU-1-0.856-0.94825.0100.4640.4640.0000.0000.0000.000
104A132ARG10.7290.86818.828-0.737-0.7370.0000.0000.0000.000
105A133GLY00.0210.02423.505-0.004-0.0040.0000.0000.0000.000
106A134LEU0-0.071-0.06123.044-0.024-0.0240.0000.0000.0000.000
107A135LEU00.0050.02820.4230.0180.0180.0000.0000.0000.000
108A136SER0-0.025-0.02017.826-0.020-0.0200.0000.0000.0000.000
109A137PRO00.0700.01719.2290.0360.0360.0000.0000.0000.000
110A138GLU-1-0.810-0.89816.1320.6050.6050.0000.0000.0000.000
111A139ARG10.8230.90413.225-1.763-1.7630.0000.0000.0000.000
112A140GLU-1-0.742-0.86115.8980.7470.7470.0000.0000.0000.000
113A141ARG10.8240.88718.164-0.537-0.5370.0000.0000.0000.000
114A142GLU-1-0.809-0.87911.9260.5850.5850.0000.0000.0000.000
115A143MET0-0.0130.00113.317-0.056-0.0560.0000.0000.0000.000
116A144ARG10.8190.89017.026-0.611-0.6110.0000.0000.0000.000
117A145LYS10.7800.87512.513-0.492-0.4920.0000.0000.0000.000
118A146ARG10.8250.89610.581-0.469-0.4690.0000.0000.0000.000
119A147GLU-1-0.762-0.87416.8320.3460.3460.0000.0000.0000.000
120A148ARG10.9280.96420.321-0.314-0.3140.0000.0000.0000.000
121A149GLU-1-0.825-0.90215.3360.0620.0620.0000.0000.0000.000
122A150TYR00.0180.00717.438-0.023-0.0230.0000.0000.0000.000
123A151THR0-0.032-0.02321.405-0.028-0.0280.0000.0000.0000.000
124A152GLU-1-0.880-0.93623.0590.0320.0320.0000.0000.0000.000
125A153ILE0-0.066-0.02219.546-0.023-0.0230.0000.0000.0000.000
126A154MET00.0180.01824.174-0.010-0.0100.0000.0000.0000.000
127A155GLN00.001-0.01127.0220.0070.0070.0000.0000.0000.000
128A156ARG10.8500.91222.9620.0190.0190.0000.0000.0000.000
129A157LEU00.0410.04027.332-0.005-0.0050.0000.0000.0000.000
130A158TYR0-0.012-0.03630.079-0.001-0.0010.0000.0000.0000.000
131A159ALA0-0.010-0.01332.7060.0000.0000.0000.0000.0000.000
132A160GLU-1-0.915-0.95930.374-0.075-0.0750.0000.0000.0000.000
133A161GLY00.0560.01934.534-0.003-0.0030.0000.0000.0000.000
134A162VAL0-0.0340.00536.3310.0000.0000.0000.0000.0000.000
135A163ALA0-0.043-0.01838.144-0.001-0.0010.0000.0000.0000.000
136A164THR0-0.068-0.04238.126-0.002-0.0020.0000.0000.0000.000
137A165GLY0-0.032-0.00840.905-0.002-0.0020.0000.0000.0000.000
138A166GLU-1-0.828-0.86736.503-0.040-0.0400.0000.0000.0000.000
139A167LEU0-0.057-0.02634.5930.0050.0050.0000.0000.0000.000
140A168LEU0-0.011-0.00639.2110.0000.0000.0000.0000.0000.000
141A169ASP-1-0.877-0.93439.7200.0180.0180.0000.0000.0000.000
142A170VAL0-0.049-0.02137.9940.0050.0050.0000.0000.0000.000
143A171ASP-1-0.795-0.90535.7540.0600.0600.0000.0000.0000.000
144A172PRO00.0360.00732.9610.0070.0070.0000.0000.0000.000
145A173THR0-0.035-0.00830.9560.0060.0060.0000.0000.0000.000
146A174VAL0-0.023-0.01132.3290.0130.0130.0000.0000.0000.000
147A175ALA00.0070.03334.3120.0090.0090.0000.0000.0000.000
148A176THR00.004-0.01627.9360.0030.0030.0000.0000.0000.000
149A177ALA00.0160.00129.6220.0120.0120.0000.0000.0000.000
150A178THR0-0.043-0.02630.6720.0160.0160.0000.0000.0000.000
151A179LEU0-0.030-0.01531.3060.0060.0060.0000.0000.0000.000
152A180LEU00.0230.00425.2470.0050.0050.0000.0000.0000.000
153A181GLY00.0170.01428.5170.0190.0190.0000.0000.0000.000
154A182ALA0-0.044-0.02830.4150.0120.0120.0000.0000.0000.000
155A183ALA00.0010.01128.0230.0030.0030.0000.0000.0000.000
156A184ILE00.0050.00725.0910.0110.0110.0000.0000.0000.000
157A185TRP00.0220.00027.7860.0240.0240.0000.0000.0000.000
158A186THR0-0.007-0.01928.8810.0090.0090.0000.0000.0000.000
159A187TYR0-0.028-0.01926.453-0.009-0.0090.0000.0000.0000.000
160A188ARG10.8770.95228.398-0.233-0.2330.0000.0000.0000.000
161A189TRP0-0.061-0.02631.528-0.009-0.0090.0000.0000.0000.000
162A190TYR0-0.029-0.01429.482-0.011-0.0110.0000.0000.0000.000
163A191ASP-1-0.869-0.92831.5120.1970.1970.0000.0000.0000.000
164A192PRO0-0.045-0.04329.084-0.014-0.0140.0000.0000.0000.000
165A193GLU-1-0.971-0.96631.6060.1720.1720.0000.0000.0000.000
166A194GLY0-0.0110.00834.667-0.011-0.0110.0000.0000.0000.000
167A195ARG10.8870.92536.802-0.101-0.1010.0000.0000.0000.000
168A196LEU0-0.045-0.00836.835-0.006-0.0060.0000.0000.0000.000
169A197SER00.032-0.02033.1200.0110.0110.0000.0000.0000.000
170A198ALA00.038-0.00628.7590.0010.0010.0000.0000.0000.000
171A199ASP-1-0.901-0.96529.5580.0610.0610.0000.0000.0000.000
172A200GLU-1-0.847-0.88432.0070.0620.0620.0000.0000.0000.000
173A201VAL0-0.009-0.00332.235-0.004-0.0040.0000.0000.0000.000
174A202VAL00.0180.00828.8100.0010.0010.0000.0000.0000.000
175A203GLU-1-0.787-0.83431.9180.0270.0270.0000.0000.0000.000
176A204GLN00.007-0.00234.861-0.002-0.0020.0000.0000.0000.000
177A205ILE0-0.0080.00832.346-0.003-0.0030.0000.0000.0000.000
178A206THR0-0.016-0.03431.054-0.007-0.0070.0000.0000.0000.000
179A207ARG10.7950.86634.248-0.040-0.0400.0000.0000.0000.000
180A208LEU0-0.036-0.01437.868-0.004-0.0040.0000.0000.0000.000
181A209LEU0-0.034-0.03233.182-0.002-0.0020.0000.0000.0000.000
182A210LEU0-0.0220.01636.426-0.002-0.0020.0000.0000.0000.000
183A211ASN0-0.079-0.04637.992-0.009-0.0090.0000.0000.0000.000
184A212GLY00.0250.03440.838-0.001-0.0010.0000.0000.0000.000
185A213TYR00.006-0.01842.431-0.001-0.0010.0000.0000.0000.000
186A214ARG10.9000.96244.572-0.034-0.0340.0000.0000.0000.000
187A215ARG10.9910.98547.405-0.024-0.0240.0000.0000.0000.000
188A216PRO00.0220.01347.5970.0010.0010.0000.0000.0000.000
189A217ALA00.0070.01450.194-0.001-0.0010.0000.0000.0000.000