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: 6Y36Z

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005503.522936
FMO2-HF: Nuclear repulsion 1930448.410069
FMO2-HF: Total energy -75055.112867
FMO2-MP2: Total energy -75278.567728


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.
-33.577-30.25811.68-6.787-8.2120.045
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 : 0.061 / q_NPA : 0.027
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].
3A31ARG10.8520.8983.8721.0112.086-0.007-0.464-0.6040.002
4A32ARG10.9240.9711.858-34.445-34.80411.052-5.284-5.4080.051
5A33THR00.0450.0052.4732.5814.8000.637-1.002-1.855-0.008
6A34GLN00.0260.0194.327-0.226-0.1320.000-0.019-0.0750.000
7A35ILE0-0.037-0.0166.8140.0500.0500.0000.0000.0000.000
8A36ILE00.0190.0134.582-0.1010.064-0.001-0.006-0.1580.000
9A37LYS10.8310.9218.265-0.709-0.7090.0000.0000.0000.000
10A38VAL00.0250.00710.298-0.142-0.1420.0000.0000.0000.000
11A39ALA0-0.019-0.00911.555-0.131-0.1310.0000.0000.0000.000
12A40THR0-0.002-0.00811.810-0.146-0.1460.0000.0000.0000.000
13A41GLU-1-0.840-0.92014.0420.2070.2070.0000.0000.0000.000
14A42LEU0-0.0010.01015.993-0.097-0.0970.0000.0000.0000.000
15A43PHE0-0.030-0.04214.263-0.048-0.0480.0000.0000.0000.000
16A44ARG10.8840.93218.441-0.428-0.4280.0000.0000.0000.000
17A45GLU-1-0.923-0.93220.3970.2790.2790.0000.0000.0000.000
18A46LYS10.8210.89621.618-0.595-0.5950.0000.0000.0000.000
19A47GLY00.0830.05422.142-0.026-0.0260.0000.0000.0000.000
20A48TYR0-0.046-0.05316.5710.0540.0540.0000.0000.0000.000
21A49TYR00.006-0.00920.8770.0460.0460.0000.0000.0000.000
22A50ALA00.0230.02823.7530.0030.0030.0000.0000.0000.000
23A51THR0-0.0090.00117.938-0.033-0.0330.0000.0000.0000.000
24A52SER0-0.010-0.01219.6090.0490.0490.0000.0000.0000.000
25A53LEU00.020-0.01213.8570.0200.0200.0000.0000.0000.000
26A54ASP-1-0.835-0.91916.3760.7790.7790.0000.0000.0000.000
27A55ASP-1-0.778-0.84818.6630.5630.5630.0000.0000.0000.000
28A56ILE00.0090.00612.313-0.037-0.0370.0000.0000.0000.000
29A57ALA0-0.025-0.01314.0450.0070.0070.0000.0000.0000.000
30A58ASP-1-0.831-0.89515.4610.3090.3090.0000.0000.0000.000
31A59ARG10.8290.88715.780-0.563-0.5630.0000.0000.0000.000
32A60ILE0-0.051-0.01410.360-0.069-0.0690.0000.0000.0000.000
33A61GLY00.0070.02514.079-0.118-0.1180.0000.0000.0000.000
34A62PHE0-0.017-0.0229.019-0.092-0.0920.0000.0000.0000.000
35A63THR00.0500.02214.9010.0300.0300.0000.0000.0000.000
36A64LYS10.9010.93815.279-0.761-0.7610.0000.0000.0000.000
37A65PRO00.015-0.00415.6960.1380.1380.0000.0000.0000.000
38A66ALA00.0030.01912.1060.1160.1160.0000.0000.0000.000
39A67ILE00.0220.01110.8440.2490.2490.0000.0000.0000.000
40A68TYR00.0110.00111.3450.3550.3550.0000.0000.0000.000
41A69TYR0-0.0280.0096.7790.0930.0930.0000.0000.0000.000
42A70TYR0-0.024-0.0193.9440.3810.506-0.001-0.012-0.1120.000
43A71PHE0-0.024-0.0246.1130.8280.8280.0000.0000.0000.000
44A72LYS10.8750.93011.327-2.472-2.4720.0000.0000.0000.000
45A73SER0-0.0050.00314.593-0.262-0.2620.0000.0000.0000.000
46A74LYS10.8440.90314.240-0.654-0.6540.0000.0000.0000.000
47A75GLU-1-0.741-0.85814.6871.3501.3500.0000.0000.0000.000
48A76ASP-1-0.816-0.88311.2702.2472.2470.0000.0000.0000.000
49A77VAL0-0.036-0.01210.0150.5300.5300.0000.0000.0000.000
50A78LEU00.0290.01910.7120.2590.2590.0000.0000.0000.000
51A79PHE00.0170.00010.680-0.026-0.0260.0000.0000.0000.000
52A80ALA0-0.024-0.0146.7110.1390.1390.0000.0000.0000.000
53A81ILE0-0.013-0.0048.3610.1690.1690.0000.0000.0000.000
54A82VAL00.0160.01110.383-0.268-0.2680.0000.0000.0000.000
55A83ASN0-0.027-0.0277.642-0.500-0.5000.0000.0000.0000.000
56A84SER0-0.0020.0047.430-0.099-0.0990.0000.0000.0000.000
57A85ILE00.0110.0128.972-0.485-0.4850.0000.0000.0000.000
58A86VAL0-0.025-0.01212.662-0.247-0.2470.0000.0000.0000.000
59A87ASP-1-0.789-0.8918.5090.3310.3310.0000.0000.0000.000
60A88GLU-1-0.928-0.96010.459-0.196-0.1960.0000.0000.0000.000
61A89ALA0-0.058-0.03712.556-0.136-0.1360.0000.0000.0000.000
62A90LEU0-0.026-0.00113.049-0.065-0.0650.0000.0000.0000.000
63A91GLU-1-0.926-0.96810.467-1.113-1.1130.0000.0000.0000.000
64A92ARG10.8210.90914.881-0.036-0.0360.0000.0000.0000.000
65A93PHE0-0.010-0.00317.993-0.002-0.0020.0000.0000.0000.000
66A94HIS0-0.015-0.03016.082-0.033-0.0330.0000.0000.0000.000
67A95ALA0-0.032-0.01218.279-0.007-0.0070.0000.0000.0000.000
68A96ILE0-0.037-0.01720.1070.0030.0030.0000.0000.0000.000
69A97ALA00.0040.00522.7080.0080.0080.0000.0000.0000.000
70A98ALA0-0.041-0.01722.0180.0120.0120.0000.0000.0000.000
71A99GLY00.0090.02024.075-0.028-0.0280.0000.0000.0000.000
72A100PRO0-0.066-0.05725.6140.0190.0190.0000.0000.0000.000
73A101GLY00.0350.02629.3110.0050.0050.0000.0000.0000.000
74A102SER0-0.073-0.07432.051-0.006-0.0060.0000.0000.0000.000
75A103PRO00.019-0.00231.791-0.003-0.0030.0000.0000.0000.000
76A104GLY00.0210.01131.9410.0080.0080.0000.0000.0000.000
77A105GLU-1-0.920-0.94832.575-0.096-0.0960.0000.0000.0000.000
78A106ARG10.7750.87127.5600.1370.1370.0000.0000.0000.000
79A107ILE0-0.003-0.00228.1530.0100.0100.0000.0000.0000.000
80A108HIS00.0280.00729.3420.0190.0190.0000.0000.0000.000
81A109ALA0-0.005-0.00527.2930.0120.0120.0000.0000.0000.000
82A110LEU0-0.0090.00123.2330.0080.0080.0000.0000.0000.000
83A111LEU00.0070.00725.3530.0290.0290.0000.0000.0000.000
84A112VAL0-0.0120.00927.2940.0240.0240.0000.0000.0000.000
85A113GLU-1-0.770-0.85720.6390.0120.0120.0000.0000.0000.000
86A114HIS00.0310.02021.8190.0140.0140.0000.0000.0000.000
87A115THR0-0.014-0.03123.8050.0430.0430.0000.0000.0000.000
88A116ARG10.8240.89623.7550.0540.0540.0000.0000.0000.000
89A117THR0-0.025-0.01319.0970.0230.0230.0000.0000.0000.000
90A118ILE0-0.012-0.00221.6060.0570.0570.0000.0000.0000.000
91A119LEU0-0.011-0.00723.6730.0310.0310.0000.0000.0000.000
92A120ARG10.7730.87021.391-0.087-0.0870.0000.0000.0000.000
93A121ASN0-0.047-0.02617.7470.1050.1050.0000.0000.0000.000
94A122LEU00.0570.05220.6930.0550.0550.0000.0000.0000.000
95A123ASP-1-0.862-0.91721.0370.5050.5050.0000.0000.0000.000
96A124ALA0-0.010-0.00917.2490.0500.0500.0000.0000.0000.000
97A125ASN0-0.018-0.03119.1610.0220.0220.0000.0000.0000.000
98A126THR00.005-0.01221.668-0.021-0.0210.0000.0000.0000.000
99A127LEU0-0.039-0.01817.7150.0090.0090.0000.0000.0000.000
100A128PHE0-0.055-0.02216.7750.0500.0500.0000.0000.0000.000
101A129TYR0-0.023-0.03420.435-0.001-0.0010.0000.0000.0000.000
102A130ASN0-0.0140.02124.141-0.057-0.0570.0000.0000.0000.000
103A131GLU-1-0.846-0.93024.3960.5240.5240.0000.0000.0000.000
104A132ARG10.7100.82618.305-0.830-0.8300.0000.0000.0000.000
105A133GLY00.0120.02323.328-0.002-0.0020.0000.0000.0000.000
106A134LEU0-0.078-0.05722.618-0.021-0.0210.0000.0000.0000.000
107A135LEU00.0290.01619.8270.0190.0190.0000.0000.0000.000
108A136SER0-0.019-0.01117.6220.0170.0170.0000.0000.0000.000
109A137PRO00.0530.01418.8760.0350.0350.0000.0000.0000.000
110A138GLU-1-0.817-0.89515.6840.6590.6590.0000.0000.0000.000
111A139ARG10.8300.91312.962-1.995-1.9950.0000.0000.0000.000
112A140GLU-1-0.745-0.84315.6240.8520.8520.0000.0000.0000.000
113A141ARG10.8260.89317.788-0.587-0.5870.0000.0000.0000.000
114A142GLU-1-0.788-0.87011.5210.5730.5730.0000.0000.0000.000
115A143MET0-0.015-0.00412.734-0.088-0.0880.0000.0000.0000.000
116A144ARG10.8250.88116.452-0.673-0.6730.0000.0000.0000.000
117A145LYS10.7640.87012.068-0.470-0.4700.0000.0000.0000.000
118A146ARG10.8040.88510.227-0.474-0.4740.0000.0000.0000.000
119A147GLU-1-0.732-0.84616.4880.3650.3650.0000.0000.0000.000
120A148ARG10.9140.98119.733-0.320-0.3200.0000.0000.0000.000
121A149GLU-1-0.784-0.87714.8660.0040.0040.0000.0000.0000.000
122A150TYR00.0140.00316.922-0.023-0.0230.0000.0000.0000.000
123A151THR0-0.045-0.03721.144-0.027-0.0270.0000.0000.0000.000
124A152GLU-1-0.834-0.91823.0840.0190.0190.0000.0000.0000.000
125A153ILE0-0.058-0.01719.625-0.024-0.0240.0000.0000.0000.000
126A154MET00.0200.01924.155-0.010-0.0100.0000.0000.0000.000
127A155GLN0-0.012-0.01526.953-0.002-0.0020.0000.0000.0000.000
128A156ARG10.8220.89222.9170.0290.0290.0000.0000.0000.000
129A157LEU00.0310.03227.287-0.005-0.0050.0000.0000.0000.000
130A158TYR0-0.011-0.04029.770-0.002-0.0020.0000.0000.0000.000
131A159ALA0-0.005-0.00732.4050.0000.0000.0000.0000.0000.000
132A160GLU-1-0.823-0.88729.965-0.108-0.1080.0000.0000.0000.000
133A161GLY00.0590.03134.403-0.003-0.0030.0000.0000.0000.000
134A162VAL0-0.041-0.01036.2580.0010.0010.0000.0000.0000.000
135A163ALA0-0.042-0.01937.7150.0000.0000.0000.0000.0000.000
136A164THR0-0.071-0.05137.779-0.003-0.0030.0000.0000.0000.000
137A165GLY0-0.034-0.00940.513-0.002-0.0020.0000.0000.0000.000
138A166GLU-1-0.816-0.86336.464-0.058-0.0580.0000.0000.0000.000
139A167LEU0-0.048-0.02034.3560.0050.0050.0000.0000.0000.000
140A168LEU0-0.015-0.00738.9010.0000.0000.0000.0000.0000.000
141A169ASP-1-0.874-0.93539.4590.0130.0130.0000.0000.0000.000
142A170VAL0-0.034-0.01737.7500.0070.0070.0000.0000.0000.000
143A171ASP-1-0.791-0.89935.1430.0590.0590.0000.0000.0000.000
144A172PRO00.0440.02132.5280.0080.0080.0000.0000.0000.000
145A173THR0-0.0210.00430.2770.0040.0040.0000.0000.0000.000
146A174VAL0-0.020-0.00631.9070.0140.0140.0000.0000.0000.000
147A175ALA00.0060.02533.8250.0090.0090.0000.0000.0000.000
148A176THR0-0.006-0.02327.3790.0020.0020.0000.0000.0000.000
149A177ALA0-0.001-0.00629.5590.0120.0120.0000.0000.0000.000
150A178THR0-0.058-0.03330.5880.0150.0150.0000.0000.0000.000
151A179LEU0-0.027-0.01330.8960.0070.0070.0000.0000.0000.000
152A180LEU00.0370.00424.6920.0030.0030.0000.0000.0000.000
153A181GLY00.0170.01827.9710.0220.0220.0000.0000.0000.000
154A182ALA0-0.028-0.01929.9070.0150.0150.0000.0000.0000.000
155A183ALA00.0170.01527.5300.0050.0050.0000.0000.0000.000
156A184ILE00.0030.01024.5550.0140.0140.0000.0000.0000.000
157A185TRP00.013-0.00927.1750.0290.0290.0000.0000.0000.000
158A186THR0-0.010-0.01828.3540.0120.0120.0000.0000.0000.000
159A187TYR0-0.030-0.03025.887-0.009-0.0090.0000.0000.0000.000
160A188ARG10.8660.94727.832-0.249-0.2490.0000.0000.0000.000
161A189TRP0-0.072-0.03131.087-0.014-0.0140.0000.0000.0000.000
162A190TYR0-0.044-0.02829.305-0.013-0.0130.0000.0000.0000.000
163A191ASP-1-0.852-0.93231.5660.1980.1980.0000.0000.0000.000
164A192PRO0-0.045-0.03528.571-0.017-0.0170.0000.0000.0000.000
165A193GLU-1-0.966-0.96331.1550.1790.1790.0000.0000.0000.000
166A194GLY00.0140.02434.277-0.012-0.0120.0000.0000.0000.000
167A195ARG10.8810.92536.383-0.100-0.1000.0000.0000.0000.000
168A196LEU0-0.046-0.02336.227-0.010-0.0100.0000.0000.0000.000
169A197SER00.007-0.01632.2520.0120.0120.0000.0000.0000.000
170A198ALA00.0700.02128.243-0.001-0.0010.0000.0000.0000.000
171A199ASP-1-0.792-0.88928.1770.0470.0470.0000.0000.0000.000
172A200GLU-1-0.844-0.87930.9550.0500.0500.0000.0000.0000.000
173A201VAL0-0.0060.00332.030-0.004-0.0040.0000.0000.0000.000
174A202VAL00.0030.00428.3000.0000.0000.0000.0000.0000.000
175A203GLU-1-0.788-0.83631.4230.0140.0140.0000.0000.0000.000
176A204GLN0-0.011-0.00534.4720.0010.0010.0000.0000.0000.000
177A205ILE00.0000.00531.895-0.001-0.0010.0000.0000.0000.000
178A206THR0-0.017-0.02430.716-0.008-0.0080.0000.0000.0000.000
179A207ARG10.7990.86133.853-0.030-0.0300.0000.0000.0000.000
180A208LEU0-0.020-0.01037.513-0.004-0.0040.0000.0000.0000.000
181A209LEU0-0.037-0.02832.5460.0000.0000.0000.0000.0000.000
182A210LEU0-0.0240.00836.112-0.003-0.0030.0000.0000.0000.000
183A211ASN0-0.090-0.05337.632-0.010-0.0100.0000.0000.0000.000
184A212GLY00.0130.02640.4150.0000.0000.0000.0000.0000.000
185A213TYR00.008-0.01242.065-0.002-0.0020.0000.0000.0000.000
186A214ARG10.8960.95444.235-0.029-0.0290.0000.0000.0000.000
187A215ARG10.9870.98347.376-0.018-0.0180.0000.0000.0000.000
188A216PRO00.0300.02647.3730.0020.0020.0000.0000.0000.000
189A217ALA00.0050.00550.054-0.001-0.0010.0000.0000.0000.000