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

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FMODB ID: Q1LYY

Calculation Name: 3C38-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C38

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KLK7

Base Structure: X-ray

Registration Date: 2023-03-14

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2519039.465259
FMO2-HF: Nuclear repulsion 2434553.194614
FMO2-HF: Total energy -84486.270644
FMO2-MP2: Total energy -84736.425975


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:52:THR)


Summations of interaction energy for fragment #1(A:52:THR)
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.
-24.684-22.5116.163-9.071-9.264-0.037
Interaction energy analysis for fragmet #1(A:52:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / 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].
3A54VAL00.0360.0143.372-2.914-0.1130.036-1.359-1.4780.005
4A55GLN00.0270.0301.765-21.511-23.20416.081-7.367-7.021-0.042
5A56THR00.0350.0112.859-0.5650.3910.047-0.339-0.6630.000
6A57SER00.0070.0035.2370.5340.644-0.001-0.006-0.1020.000
7A58SER00.021-0.0037.4280.1000.1000.0000.0000.0000.000
8A59LEU0-0.051-0.0057.7400.0880.0880.0000.0000.0000.000
9A60ILE00.0380.0149.1750.1940.1940.0000.0000.0000.000
10A61GLN0-0.012-0.01111.3040.1030.1030.0000.0000.0000.000
11A62SER0-0.044-0.03112.2730.0320.0320.0000.0000.0000.000
12A63LEU0-0.022-0.00912.0340.0560.0560.0000.0000.0000.000
13A64PHE00.0230.00815.3640.0560.0560.0000.0000.0000.000
14A65ASP-1-0.832-0.91817.147-0.167-0.1670.0000.0000.0000.000
15A66PHE0-0.061-0.02018.0330.0290.0290.0000.0000.0000.000
16A67ARG10.8980.96119.7650.1880.1880.0000.0000.0000.000
17A68LEU00.0340.01421.2600.0240.0240.0000.0000.0000.000
18A69ALA0-0.042-0.01922.5970.0220.0220.0000.0000.0000.000
19A70ALA00.0150.01123.9280.0160.0160.0000.0000.0000.000
20A71LEU00.0100.01125.6160.0150.0150.0000.0000.0000.000
21A72ARG10.9410.98424.3000.1330.1330.0000.0000.0000.000
22A73ILE0-0.040-0.01826.5610.0110.0110.0000.0000.0000.000
23A74HIS00.000-0.01329.6630.0140.0140.0000.0000.0000.000
24A75GLN0-0.0160.00631.6420.0040.0040.0000.0000.0000.000
25A76ASP-1-0.774-0.85732.079-0.071-0.0710.0000.0000.0000.000
26A77SER0-0.058-0.01134.2170.0080.0080.0000.0000.0000.000
27A78THR00.019-0.01335.6240.0060.0060.0000.0000.0000.000
28A79ALA0-0.041-0.03037.3510.0040.0040.0000.0000.0000.000
29A80LYS10.8780.93236.6260.0690.0690.0000.0000.0000.000
30A81ASN00.0400.04340.8330.0050.0050.0000.0000.0000.000
31A82ALA00.0670.01142.5830.0020.0020.0000.0000.0000.000
32A83SER0-0.040-0.02144.8350.0030.0030.0000.0000.0000.000
33A84LEU00.0060.02441.0730.0020.0020.0000.0000.0000.000
34A85ILE00.0090.00644.0540.0020.0020.0000.0000.0000.000
35A86ASN0-0.015-0.01847.1100.0030.0030.0000.0000.0000.000
36A87ALA00.0390.02847.5180.0020.0020.0000.0000.0000.000
37A88LEU00.0230.02145.1010.0020.0020.0000.0000.0000.000
38A89VAL0-0.021-0.02348.7700.0020.0020.0000.0000.0000.000
39A90SER0-0.063-0.03451.7700.0020.0020.0000.0000.0000.000
40A91ARG10.7950.89949.4000.0330.0330.0000.0000.0000.000
41A92ASP-1-0.803-0.86852.464-0.034-0.0340.0000.0000.0000.000
42A93SER00.0240.00249.168-0.001-0.0010.0000.0000.0000.000
43A94SER00.009-0.01248.213-0.001-0.0010.0000.0000.0000.000
44A95ARG10.7840.88949.2310.0350.0350.0000.0000.0000.000
45A96LEU0-0.050-0.03344.822-0.002-0.0020.0000.0000.0000.000
46A97ASP-1-0.814-0.88244.293-0.047-0.0470.0000.0000.0000.000
47A98GLU-1-0.935-0.96143.978-0.048-0.0480.0000.0000.0000.000
48A99PHE0-0.003-0.00341.071-0.003-0.0030.0000.0000.0000.000
49A100PHE00.008-0.02938.547-0.003-0.0030.0000.0000.0000.000
50A101SER00.0400.03139.430-0.004-0.0040.0000.0000.0000.000
51A102SER0-0.009-0.03240.296-0.002-0.0020.0000.0000.0000.000
52A103VAL0-0.122-0.05036.168-0.003-0.0030.0000.0000.0000.000
53A104ASP-1-0.760-0.84335.260-0.088-0.0880.0000.0000.0000.000
54A105GLU-1-0.947-0.95235.817-0.069-0.0690.0000.0000.0000.000
55A106LEU0-0.038-0.01935.766-0.002-0.0020.0000.0000.0000.000
56A107GLU-1-0.793-0.86829.437-0.142-0.1420.0000.0000.0000.000
57A108LEU00.0040.01731.724-0.005-0.0050.0000.0000.0000.000
58A109SER0-0.069-0.04627.6290.0000.0000.0000.0000.0000.000
59A110ASN0-0.096-0.07625.780-0.021-0.0210.0000.0000.0000.000
60A111ALA00.0670.04328.4350.0020.0020.0000.0000.0000.000
61A112PRO0-0.064-0.04129.596-0.008-0.0080.0000.0000.0000.000
62A113ASP-1-0.785-0.86428.411-0.108-0.1080.0000.0000.0000.000
63A114LEU0-0.024-0.01431.5540.0070.0070.0000.0000.0000.000
64A115ARG10.7690.83534.1950.0750.0750.0000.0000.0000.000
65A116PHE00.0430.02736.6520.0030.0030.0000.0000.0000.000
66A117ILE0-0.013-0.00939.572-0.002-0.0020.0000.0000.0000.000
67A118SER00.0190.02442.2540.0020.0020.0000.0000.0000.000
68A119SER0-0.013-0.02044.0910.0000.0000.0000.0000.0000.000
69A120HIS00.0090.00246.0040.0020.0020.0000.0000.0000.000
70A121ASP-1-0.815-0.88445.374-0.024-0.0240.0000.0000.0000.000
71A122ASN0-0.0080.01646.3910.0000.0000.0000.0000.0000.000
72A123ILE00.011-0.00242.768-0.001-0.0010.0000.0000.0000.000
73A124LEU0-0.087-0.04445.9380.0010.0010.0000.0000.0000.000
74A125TRP00.002-0.02640.0880.0000.0000.0000.0000.0000.000
75A126ASP-1-0.804-0.91440.773-0.048-0.0480.0000.0000.0000.000
76A127ASP-1-0.799-0.89337.186-0.065-0.0650.0000.0000.0000.000
77A128GLY00.0020.01440.8530.0000.0000.0000.0000.0000.000
78A129ASN0-0.032-0.03235.9700.0020.0020.0000.0000.0000.000
79A130ALA0-0.001-0.00937.107-0.001-0.0010.0000.0000.0000.000
80A131SER0-0.012-0.01038.1280.0020.0020.0000.0000.0000.000
81A132PHE0-0.036-0.00133.6690.0020.0020.0000.0000.0000.000
82A133TYR0-0.037-0.04030.8490.0000.0000.0000.0000.0000.000
83A134GLY00.0880.05035.8490.0010.0010.0000.0000.0000.000
84A135ILE0-0.108-0.04534.4960.0040.0040.0000.0000.0000.000
85A136ALA00.0140.01238.8110.0010.0010.0000.0000.0000.000
86A137GLN00.020-0.01041.7600.0000.0000.0000.0000.0000.000
87A138GLN00.0280.00343.500-0.002-0.0020.0000.0000.0000.000
88A139GLU-1-0.822-0.89739.364-0.025-0.0250.0000.0000.0000.000
89A140LEU00.0320.02037.743-0.001-0.0010.0000.0000.0000.000
90A141ASN0-0.018-0.01840.1140.0010.0010.0000.0000.0000.000
91A142LYS10.8100.88240.2900.0250.0250.0000.0000.0000.000
92A143LEU0-0.005-0.00634.8770.0010.0010.0000.0000.0000.000
93A144ILE0-0.0330.00337.518-0.001-0.0010.0000.0000.0000.000
94A145ARG10.8160.86039.4320.0210.0210.0000.0000.0000.000
95A146ARG10.8570.93134.8160.0340.0340.0000.0000.0000.000
96A147VAL00.0110.02733.1190.0010.0010.0000.0000.0000.000
97A148ALA0-0.0010.00035.157-0.001-0.0010.0000.0000.0000.000
98A149ILE0-0.035-0.01731.5540.0020.0020.0000.0000.0000.000
99A150SER00.0360.00734.308-0.002-0.0020.0000.0000.0000.000
100A151GLY0-0.0020.01332.2080.0030.0030.0000.0000.0000.000
101A152ASN0-0.015-0.00427.064-0.003-0.0030.0000.0000.0000.000
102A153TRP0-0.033-0.03725.7330.0050.0050.0000.0000.0000.000
103A154HIS0-0.018-0.00327.5570.0090.0090.0000.0000.0000.000
104A155LEU0-0.0040.00424.143-0.008-0.0080.0000.0000.0000.000
105A156VAL0-0.038-0.01627.9010.0100.0100.0000.0000.0000.000
106A157GLN00.0300.00628.702-0.002-0.0020.0000.0000.0000.000
107A158THR0-0.023-0.01032.0920.0070.0070.0000.0000.0000.000
108A159PRO0-0.018-0.00934.956-0.002-0.0020.0000.0000.0000.000
109A160SER00.002-0.00436.145-0.002-0.0020.0000.0000.0000.000
110A161GLU-1-0.932-0.96138.102-0.039-0.0390.0000.0000.0000.000
111A162GLY00.003-0.00936.9410.0010.0010.0000.0000.0000.000
112A163LYS10.7920.88528.5630.0710.0710.0000.0000.0000.000
113A164SER0-0.006-0.00231.097-0.001-0.0010.0000.0000.0000.000
114A165VAL00.0220.01831.048-0.004-0.0040.0000.0000.0000.000
115A166HIS00.0630.04026.8810.0030.0030.0000.0000.0000.000
116A167ILE0-0.001-0.01228.254-0.008-0.0080.0000.0000.0000.000
117A168LEU00.0240.03122.9320.0070.0070.0000.0000.0000.000
118A169MET0-0.034-0.01727.5250.0000.0000.0000.0000.0000.000
119A170ARG10.7980.86028.8480.0840.0840.0000.0000.0000.000
120A171ARG10.8530.95731.7530.0400.0400.0000.0000.0000.000
121A172SER0-0.015-0.03734.6790.0010.0010.0000.0000.0000.000
122A173SER0-0.013-0.02136.7440.0020.0020.0000.0000.0000.000
123A174LEU00.0100.02740.297-0.002-0.0020.0000.0000.0000.000
124A175ILE0-0.049-0.02142.2940.0030.0030.0000.0000.0000.000
125A176GLU-1-0.905-0.95245.091-0.034-0.0340.0000.0000.0000.000
126A177ALA0-0.001-0.01247.908-0.001-0.0010.0000.0000.0000.000
127A178GLY0-0.0050.00548.5060.0020.0020.0000.0000.0000.000
128A179THR0-0.065-0.04849.8920.0010.0010.0000.0000.0000.000
129A180GLY00.0640.06551.2970.0020.0020.0000.0000.0000.000
130A181GLN0-0.030-0.04346.761-0.002-0.0020.0000.0000.0000.000
131A182VAL0-0.029-0.02044.273-0.001-0.0010.0000.0000.0000.000
132A183VAL00.0380.03646.6380.0020.0020.0000.0000.0000.000
133A184GLY00.008-0.00845.3640.0010.0010.0000.0000.0000.000
134A185TYR0-0.048-0.02339.9500.0000.0000.0000.0000.0000.000
135A186LEU00.0380.02836.9010.0010.0010.0000.0000.0000.000
136A187TYR0-0.028-0.02435.965-0.002-0.0020.0000.0000.0000.000
137A188VAL00.0220.00231.1090.0000.0000.0000.0000.0000.000
138A189GLY00.000-0.01130.3170.0020.0020.0000.0000.0000.000
139A190ILE00.0110.01924.700-0.004-0.0040.0000.0000.0000.000
140A191VAL0-0.048-0.00927.7610.0060.0060.0000.0000.0000.000
141A192LEU00.012-0.01022.683-0.011-0.0110.0000.0000.0000.000
142A193ASN0-0.044-0.02324.832-0.009-0.0090.0000.0000.0000.000
143A194ASP-1-0.785-0.89326.447-0.079-0.0790.0000.0000.0000.000
144A195ASN00.0100.02024.617-0.012-0.0120.0000.0000.0000.000
145A196PHE00.014-0.00822.264-0.019-0.0190.0000.0000.0000.000
146A197ALA00.0020.00722.133-0.019-0.0190.0000.0000.0000.000
147A198LEU00.0070.00920.621-0.020-0.0200.0000.0000.0000.000
148A199LEU0-0.006-0.00316.888-0.030-0.0300.0000.0000.0000.000
149A200GLU-1-0.760-0.84517.307-0.317-0.3170.0000.0000.0000.000
150A201ASN0-0.0500.00317.703-0.028-0.0280.0000.0000.0000.000
151A202ILE00.0180.01213.347-0.038-0.0380.0000.0000.0000.000
152A203ARG10.7740.84013.3140.2430.2430.0000.0000.0000.000
153A204SER0-0.052-0.04913.171-0.055-0.0550.0000.0000.0000.000
154A205GLY00.0170.01513.868-0.028-0.0280.0000.0000.0000.000
155A206SER0-0.049-0.0658.944-0.037-0.0370.0000.0000.0000.000
156A207ASN0-0.098-0.0528.936-0.094-0.0940.0000.0000.0000.000
157A208SER00.0030.0398.8690.0120.0120.0000.0000.0000.000
158A209GLU-1-0.785-0.84710.657-0.053-0.0530.0000.0000.0000.000
159A210ASN0-0.037-0.05012.8990.0480.0480.0000.0000.0000.000
160A211LEU0-0.0040.01511.356-0.074-0.0740.0000.0000.0000.000
161A212VAL0-0.018-0.01514.9360.0450.0450.0000.0000.0000.000
162A213LEU0-0.0080.02717.102-0.010-0.0100.0000.0000.0000.000
163A214ALA00.0250.00419.1330.0150.0150.0000.0000.0000.000
164A215VAL0-0.019-0.01321.165-0.001-0.0010.0000.0000.0000.000
165A216ASP-1-0.866-0.90822.6550.0070.0070.0000.0000.0000.000
166A217THR0-0.023-0.03322.003-0.008-0.0080.0000.0000.0000.000
167A218THR0-0.043-0.01523.905-0.004-0.0040.0000.0000.0000.000
168A219PRO0-0.014-0.01322.768-0.008-0.0080.0000.0000.0000.000
169A220LEU0-0.064-0.02323.0550.0090.0090.0000.0000.0000.000
170A221VAL00.0210.01121.3480.0040.0040.0000.0000.0000.000
171A222SER00.0310.00219.960-0.016-0.0160.0000.0000.0000.000
172A223THR00.0660.02917.417-0.006-0.0060.0000.0000.0000.000
173A224LEU0-0.074-0.01918.2180.0010.0010.0000.0000.0000.000
174A225LYS10.8030.87818.4680.1810.1810.0000.0000.0000.000
175A226GLY0-0.0130.00123.5330.0090.0090.0000.0000.0000.000
176A227ASN0-0.069-0.03823.7310.0050.0050.0000.0000.0000.000
177A228GLU-1-0.716-0.82719.020-0.121-0.1210.0000.0000.0000.000
178A229PRO0-0.042-0.02519.6160.0070.0070.0000.0000.0000.000
179A230TYR0-0.043-0.03315.8660.0030.0030.0000.0000.0000.000
180A231SER00.0320.01920.946-0.011-0.0110.0000.0000.0000.000
181A232LEU00.046-0.00121.067-0.004-0.0040.0000.0000.0000.000
182A233ASP-1-0.889-0.93421.552-0.022-0.0220.0000.0000.0000.000
183A234TYR0-0.003-0.00815.2790.0120.0120.0000.0000.0000.000
184A235VAL0-0.001-0.00116.0380.0030.0030.0000.0000.0000.000
185A236VAL00.0060.02017.533-0.001-0.0010.0000.0000.0000.000
186A237HIS0-0.069-0.03519.9200.0110.0110.0000.0000.0000.000
187A238SER0-0.073-0.02915.5010.0160.0160.0000.0000.0000.000
188A239ALA0-0.003-0.01115.5590.0100.0100.0000.0000.0000.000
189A240LYS10.8510.9168.088-0.251-0.2510.0000.0000.0000.000
190A241ASP-1-0.822-0.9016.279-0.201-0.2010.0000.0000.0000.000
191A242ALA00.0340.0439.0720.1140.1140.0000.0000.0000.000
192A243MET0-0.018-0.0285.9650.0460.0460.0000.0000.0000.000
193A244ARG10.7720.8659.959-0.102-0.1020.0000.0000.0000.000
194A245ASP-1-0.801-0.86313.3390.1000.1000.0000.0000.0000.000
195A246SER0-0.037-0.02913.2500.0080.0080.0000.0000.0000.000
196A247PHE00.0210.00313.343-0.002-0.0020.0000.0000.0000.000
197A248ILE00.0210.0327.1500.0070.0070.0000.0000.0000.000
198A249VAL00.0380.01610.593-0.085-0.0850.0000.0000.0000.000
199A250GLY00.0260.0328.6180.0720.0720.0000.0000.0000.000
200A251GLN0-0.017-0.0359.4790.0550.0550.0000.0000.0000.000
201A252THR00.0120.01110.4130.0380.0380.0000.0000.0000.000
202A253PHE0-0.031-0.00112.538-0.022-0.0220.0000.0000.0000.000
203A254LEU00.0120.01914.9380.0140.0140.0000.0000.0000.000
204A255GLU-1-0.886-0.92715.9380.0370.0370.0000.0000.0000.000
205A256VAL00.009-0.01018.404-0.033-0.0330.0000.0000.0000.000
206A257GLU-1-0.868-0.92821.718-0.077-0.0770.0000.0000.0000.000
207A258SER0-0.044-0.03018.0340.0040.0040.0000.0000.0000.000
208A259VAL0-0.0220.00320.2460.0230.0230.0000.0000.0000.000
209A260PRO0-0.006-0.00518.294-0.016-0.0160.0000.0000.0000.000
210A261THR0-0.040-0.02619.502-0.004-0.0040.0000.0000.0000.000
211A262TYR0-0.014-0.03119.9700.0080.0080.0000.0000.0000.000
212A263LEU0-0.009-0.00419.9790.0000.0000.0000.0000.0000.000
213A264CYS0-0.0040.02716.419-0.012-0.0120.0000.0000.0000.000
214A265VAL00.0370.01013.105-0.004-0.0040.0000.0000.0000.000
215A266TYR00.009-0.01213.407-0.028-0.0280.0000.0000.0000.000
216A267SER0-0.021-0.0238.6940.0250.0250.0000.0000.0000.000
217A268ILE00.002-0.00211.1180.0370.0370.0000.0000.0000.000
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