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: ZV25N

Calculation Name: 4ECC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ECC

Chain ID: A

ChEMBL ID:

UniProt ID: P08515

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2552434.110263
FMO2-HF: Nuclear repulsion 2467497.393578
FMO2-HF: Total energy -84936.716685
FMO2-MP2: Total energy -85180.657045


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-30.314-31.8122.122-11.115-9.513-0.041
Interaction energy analysis for fragmet #1(A:2:SER)
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 : -0.065
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].
3A4ILE0-0.0210.0003.873-1.1560.034-0.004-0.533-0.6530.002
4A5LEU0-0.022-0.0166.2350.9460.9460.0000.0000.0000.000
5A6GLY00.0230.0219.203-0.170-0.1700.0000.0000.0000.000
6A7TYR00.001-0.02711.9770.2400.2400.0000.0000.0000.000
7A8TRP00.0550.03515.111-0.081-0.0810.0000.0000.0000.000
8A9LYS10.8450.93316.1460.5390.5390.0000.0000.0000.000
9A10ILE0-0.028-0.01717.4290.0440.0440.0000.0000.0000.000
10A11LYS10.8460.94118.0720.0540.0540.0000.0000.0000.000
11A12GLY0-0.007-0.00218.951-0.009-0.0090.0000.0000.0000.000
12A13LEU0-0.046-0.05419.8810.0340.0340.0000.0000.0000.000
13A14VAL00.0240.02014.1230.0460.0460.0000.0000.0000.000
14A15GLN00.0700.06515.863-0.008-0.0080.0000.0000.0000.000
15A16PRO00.023-0.00116.9510.0480.0480.0000.0000.0000.000
16A17THR00.003-0.00712.6290.0760.0760.0000.0000.0000.000
17A18ARG10.8120.88411.6950.4230.4230.0000.0000.0000.000
18A19LEU0-0.050-0.01313.2780.0950.0950.0000.0000.0000.000
19A20LEU00.003-0.00114.4080.0560.0560.0000.0000.0000.000
20A21LEU00.0190.0028.3760.0930.0930.0000.0000.0000.000
21A22GLU-1-0.758-0.84310.6440.6720.6720.0000.0000.0000.000
22A23TYR0-0.046-0.02512.7310.0480.0480.0000.0000.0000.000
23A24LEU0-0.029-0.02812.117-0.013-0.0130.0000.0000.0000.000
24A25GLU-1-0.940-0.96211.4800.8080.8080.0000.0000.0000.000
25A26GLU-1-0.860-0.9086.8443.1453.1450.0000.0000.0000.000
26A27LYS10.7600.8822.167-1.9690.2183.285-2.485-2.9880.029
27A28TYR0-0.033-0.0483.1011.4612.6630.142-0.544-0.8000.003
28A29GLU-1-0.824-0.8791.646-32.141-38.23718.700-7.546-5.059-0.075
29A30GLU-1-0.841-0.9174.4480.0990.120-0.001-0.007-0.0130.000
30A31HIS0-0.050-0.0227.9460.1200.1200.0000.0000.0000.000
31A32LEU0-0.016-0.02310.6860.2100.2100.0000.0000.0000.000
32A33TYR00.0310.02813.6900.0230.0230.0000.0000.0000.000
33A34GLU-1-0.781-0.90917.065-0.413-0.4130.0000.0000.0000.000
34A35ARG10.8140.89620.0430.2390.2390.0000.0000.0000.000
35A36ASP-1-0.925-0.96523.691-0.359-0.3590.0000.0000.0000.000
36A37GLU-1-0.893-0.93418.326-0.681-0.6810.0000.0000.0000.000
37A38GLY0-0.069-0.03521.508-0.024-0.0240.0000.0000.0000.000
38A39ASP-1-0.997-0.98821.716-0.349-0.3490.0000.0000.0000.000
39A62GLY00.0300.01115.064-0.017-0.0170.0000.0000.0000.000
40A63LEU0-0.034-0.03613.1050.0460.0460.0000.0000.0000.000
41A64GLU-1-0.895-0.94016.566-0.066-0.0660.0000.0000.0000.000
42A65PHE0-0.034-0.02019.3280.0080.0080.0000.0000.0000.000
43A66PRO0-0.0180.00819.176-0.012-0.0120.0000.0000.0000.000
44A67ASN00.0150.00118.8770.0210.0210.0000.0000.0000.000
45A68LEU0-0.0050.04215.808-0.071-0.0710.0000.0000.0000.000
46A69PRO0-0.047-0.03614.7710.0620.0620.0000.0000.0000.000
47A70TYR00.004-0.01910.9190.0350.0350.0000.0000.0000.000
48A71TYR0-0.068-0.0497.244-0.227-0.2270.0000.0000.0000.000
49A72ILE0-0.0060.0056.7830.2980.2980.0000.0000.0000.000
50A73ASP-1-0.721-0.8325.3630.8210.8210.0000.0000.0000.000
51A74GLY00.0110.0265.1730.0990.0990.0000.0000.0000.000
52A75ASP-1-0.896-0.9496.925-0.250-0.2500.0000.0000.0000.000
53A76VAL0-0.0370.0019.432-0.118-0.1180.0000.0000.0000.000
54A77LYS10.8450.9089.6080.2080.2080.0000.0000.0000.000
55A78LEU00.0040.00512.5040.0490.0490.0000.0000.0000.000
56A79THR00.001-0.02014.431-0.098-0.0980.0000.0000.0000.000
57A80GLN00.0340.01017.2020.0670.0670.0000.0000.0000.000
58A81SER00.0480.01917.7600.0290.0290.0000.0000.0000.000
59A82MET00.0230.00917.8820.0350.0350.0000.0000.0000.000
60A83ALA00.0190.01118.3580.0480.0480.0000.0000.0000.000
61A84ILE00.0020.01512.6380.0710.0710.0000.0000.0000.000
62A85ILE0-0.028-0.00614.1380.1150.1150.0000.0000.0000.000
63A86ARG10.8920.92216.003-0.133-0.1330.0000.0000.0000.000
64A87TYR00.003-0.0139.7690.0410.0410.0000.0000.0000.000
65A88ILE0-0.0010.0039.6150.1240.1240.0000.0000.0000.000
66A89ALA00.0360.01112.7780.1090.1090.0000.0000.0000.000
67A90ASP-1-0.923-0.96516.1020.5210.5210.0000.0000.0000.000
68A91LYS10.9060.9649.899-1.385-1.3850.0000.0000.0000.000
69A92HIS10.7470.8549.973-1.313-1.3130.0000.0000.0000.000
70A93ASN0-0.054-0.02514.982-0.092-0.0920.0000.0000.0000.000
71A94MET0-0.0040.00317.210-0.029-0.0290.0000.0000.0000.000
72A95LEU0-0.045-0.01119.178-0.055-0.0550.0000.0000.0000.000
73A96GLY00.0400.02221.667-0.043-0.0430.0000.0000.0000.000
74A97GLY00.0170.00924.5320.0150.0150.0000.0000.0000.000
75A98CYS0-0.048-0.01726.542-0.009-0.0090.0000.0000.0000.000
76A99PRO00.038-0.00128.9190.0010.0010.0000.0000.0000.000
77A100LYS10.9160.94030.216-0.151-0.1510.0000.0000.0000.000
78A101GLU-1-0.843-0.92327.5130.2570.2570.0000.0000.0000.000
79A102ARG10.9110.95224.339-0.275-0.2750.0000.0000.0000.000
80A103ALA0-0.0190.00427.001-0.005-0.0050.0000.0000.0000.000
81A104GLU-1-0.799-0.86929.7830.1360.1360.0000.0000.0000.000
82A105ILE00.0240.02223.330-0.011-0.0110.0000.0000.0000.000
83A106SER0-0.020-0.03925.642-0.002-0.0020.0000.0000.0000.000
84A107MET0-0.055-0.01327.121-0.016-0.0160.0000.0000.0000.000
85A108LEU0-0.009-0.00627.793-0.013-0.0130.0000.0000.0000.000
86A109GLU-1-0.749-0.85122.9690.1680.1680.0000.0000.0000.000
87A110GLY0-0.0050.00026.495-0.016-0.0160.0000.0000.0000.000
88A111ALA00.0220.00929.221-0.013-0.0130.0000.0000.0000.000
89A112VAL0-0.023-0.00925.941-0.011-0.0110.0000.0000.0000.000
90A113LEU0-0.032-0.02824.321-0.016-0.0160.0000.0000.0000.000
91A114ASP-1-0.891-0.93228.1970.0150.0150.0000.0000.0000.000
92A115ILE0-0.006-0.00230.415-0.011-0.0110.0000.0000.0000.000
93A116ARG10.8360.90823.4460.0390.0390.0000.0000.0000.000
94A117TYR0-0.020-0.03724.899-0.012-0.0120.0000.0000.0000.000
95A118GLY0-0.0110.01129.510-0.010-0.0100.0000.0000.0000.000
96A119VAL00.0300.01829.710-0.007-0.0070.0000.0000.0000.000
97A120SER0-0.034-0.03027.437-0.015-0.0150.0000.0000.0000.000
98A121ARG10.9020.95629.7060.0070.0070.0000.0000.0000.000
99A122ILE00.0120.00632.710-0.003-0.0030.0000.0000.0000.000
100A123ALA0-0.0140.01230.581-0.003-0.0030.0000.0000.0000.000
101A124TYR00.0340.00826.535-0.012-0.0120.0000.0000.0000.000
102A125SER0-0.0290.00833.286-0.003-0.0030.0000.0000.0000.000
103A126LYS10.9510.96836.9990.0590.0590.0000.0000.0000.000
104A127ASP-1-0.879-0.95139.961-0.054-0.0540.0000.0000.0000.000
105A128PHE00.0050.00935.0550.0050.0050.0000.0000.0000.000
106A129GLU-1-0.764-0.88938.566-0.043-0.0430.0000.0000.0000.000
107A130THR00.0190.01141.0040.0040.0040.0000.0000.0000.000
108A131LEU00.001-0.00638.8870.0040.0040.0000.0000.0000.000
109A132LYS10.8140.89937.7960.0460.0460.0000.0000.0000.000
110A133VAL0-0.023-0.00539.2570.0060.0060.0000.0000.0000.000
111A134ASP-1-0.882-0.94541.799-0.014-0.0140.0000.0000.0000.000
112A135PHE0-0.044-0.03533.2640.0050.0050.0000.0000.0000.000
113A136LEU00.012-0.00736.8430.0060.0060.0000.0000.0000.000
114A137SER0-0.019-0.00639.5890.0050.0050.0000.0000.0000.000
115A138LYS10.8000.87840.025-0.010-0.0100.0000.0000.0000.000
116A139LEU00.0180.02734.2220.0060.0060.0000.0000.0000.000
117A140PRO00.0240.01137.7590.0080.0080.0000.0000.0000.000
118A141GLU-1-0.822-0.89439.7860.0270.0270.0000.0000.0000.000
119A142MET0-0.053-0.02034.4560.0040.0040.0000.0000.0000.000
120A143LEU0-0.007-0.00433.5990.0090.0090.0000.0000.0000.000
121A144LYS10.8840.92636.149-0.049-0.0490.0000.0000.0000.000
122A145MET00.0160.01136.2630.0040.0040.0000.0000.0000.000
123A146PHE00.010-0.00430.3520.0110.0110.0000.0000.0000.000
124A147GLU-1-0.740-0.87634.3590.0770.0770.0000.0000.0000.000
125A148ASP-1-0.865-0.91336.7440.0710.0710.0000.0000.0000.000
126A149ARG10.7590.85130.985-0.139-0.1390.0000.0000.0000.000
127A150LEU00.000-0.00830.7160.0090.0090.0000.0000.0000.000
128A151CYS0-0.122-0.05334.867-0.001-0.0010.0000.0000.0000.000
129A152HIS0-0.028-0.01137.3170.0010.0010.0000.0000.0000.000
130A153LYS10.9060.96332.250-0.146-0.1460.0000.0000.0000.000
131A154THR0-0.0020.01929.411-0.012-0.0120.0000.0000.0000.000
132A155TYR00.0180.00126.005-0.013-0.0130.0000.0000.0000.000
133A156LEU00.0210.00226.944-0.009-0.0090.0000.0000.0000.000
134A157ASN0-0.011-0.00626.859-0.030-0.0300.0000.0000.0000.000
135A158GLY0-0.046-0.01328.7760.0070.0070.0000.0000.0000.000
136A159ASP-1-0.877-0.94729.2410.1970.1970.0000.0000.0000.000
137A160HIS0-0.014-0.01023.8030.0220.0220.0000.0000.0000.000
138A161VAL0-0.0210.00320.836-0.020-0.0200.0000.0000.0000.000
139A162THR0-0.043-0.02921.3560.0260.0260.0000.0000.0000.000
140A163HIS00.045-0.00918.6810.0150.0150.0000.0000.0000.000
141A164PRO00.022-0.00420.390-0.026-0.0260.0000.0000.0000.000
142A165ASP-1-0.744-0.86223.0990.1910.1910.0000.0000.0000.000
143A166PHE00.0550.01718.542-0.018-0.0180.0000.0000.0000.000
144A167MET0-0.048-0.00221.441-0.023-0.0230.0000.0000.0000.000
145A168LEU00.0150.00822.988-0.024-0.0240.0000.0000.0000.000
146A169TYR0-0.073-0.06822.234-0.017-0.0170.0000.0000.0000.000
147A170ASP-1-0.820-0.91421.690-0.035-0.0350.0000.0000.0000.000
148A171ALA0-0.009-0.00423.746-0.021-0.0210.0000.0000.0000.000
149A172LEU0-0.022-0.01227.112-0.011-0.0110.0000.0000.0000.000
150A173ASP-1-0.827-0.92124.996-0.020-0.0200.0000.0000.0000.000
151A174VAL0-0.018-0.01225.518-0.014-0.0140.0000.0000.0000.000
152A175VAL0-0.003-0.01828.173-0.008-0.0080.0000.0000.0000.000
153A176LEU0-0.011-0.00430.142-0.001-0.0010.0000.0000.0000.000
154A177TYR0-0.035-0.01726.654-0.010-0.0100.0000.0000.0000.000
155A178MET0-0.099-0.03432.000-0.004-0.0040.0000.0000.0000.000
156A179ASP-1-0.836-0.93334.430-0.005-0.0050.0000.0000.0000.000
157A180PRO0-0.022-0.00335.3610.0070.0070.0000.0000.0000.000
158A181MET00.0130.01736.4240.0050.0050.0000.0000.0000.000
159A182CYS0-0.058-0.00335.2280.0080.0080.0000.0000.0000.000
160A183LEU0-0.015-0.03132.2200.0070.0070.0000.0000.0000.000
161A184ASP-1-0.894-0.93736.9620.0240.0240.0000.0000.0000.000
162A185ALA0-0.081-0.03540.2330.0030.0030.0000.0000.0000.000
163A186PHE0-0.070-0.03837.1610.0040.0040.0000.0000.0000.000
164A187PRO00.0690.02936.8880.0030.0030.0000.0000.0000.000
165A188LYS10.8710.91935.613-0.085-0.0850.0000.0000.0000.000
166A189LEU00.0220.01331.9770.0110.0110.0000.0000.0000.000
167A190VAL00.0110.01931.9070.0050.0050.0000.0000.0000.000
168A191CYS0-0.081-0.04232.1480.0080.0080.0000.0000.0000.000
169A192PHE0-0.011-0.00326.2240.0110.0110.0000.0000.0000.000
170A193LYS10.8720.93926.547-0.027-0.0270.0000.0000.0000.000
171A194LYS10.9390.97127.116-0.054-0.0540.0000.0000.0000.000
172A195ARG10.8940.95127.347-0.137-0.1370.0000.0000.0000.000
173A196ILE0-0.019-0.01222.2390.0210.0210.0000.0000.0000.000
174A197GLU-1-0.817-0.89022.9650.0870.0870.0000.0000.0000.000
175A198ALA0-0.024-0.00123.8680.0010.0010.0000.0000.0000.000
176A199ILE0-0.048-0.00619.8960.0190.0190.0000.0000.0000.000
177A200PRO00.0280.01620.541-0.008-0.0080.0000.0000.0000.000
178A201GLN00.012-0.01015.602-0.096-0.0960.0000.0000.0000.000
179A202ILE0-0.013-0.00316.762-0.013-0.0130.0000.0000.0000.000
180A203ASP-1-0.795-0.87118.7850.0810.0810.0000.0000.0000.000
181A204LYS10.8760.93014.073-0.552-0.5520.0000.0000.0000.000
182A205TYR00.0180.01213.217-0.032-0.0320.0000.0000.0000.000
183A206LEU0-0.0050.00216.329-0.067-0.0670.0000.0000.0000.000
184A207LYS10.7780.88119.495-0.125-0.1250.0000.0000.0000.000
185A208SER0-0.096-0.04515.182-0.038-0.0380.0000.0000.0000.000
186A209SER00.005-0.01914.971-0.001-0.0010.0000.0000.0000.000
187A210LYS10.8600.9159.274-0.295-0.2950.0000.0000.0000.000
188A211TYR0-0.0170.01513.695-0.024-0.0240.0000.0000.0000.000
189A212ILE00.0160.01815.417-0.030-0.0300.0000.0000.0000.000
190A213ALA00.012-0.00618.2170.0340.0340.0000.0000.0000.000
191A214TRP0-0.036-0.00521.7770.0340.0340.0000.0000.0000.000
192A215PRO00.0210.02222.033-0.025-0.0250.0000.0000.0000.000
193A216LEU0-0.035-0.02422.702-0.004-0.0040.0000.0000.0000.000
194A217GLN0-0.0130.00223.8470.0130.0130.0000.0000.0000.000
195A218GLY00.0680.03024.320-0.018-0.0180.0000.0000.0000.000
196A219TRP00.0690.01920.5230.0370.0370.0000.0000.0000.000
197A220GLN0-0.010-0.00826.8870.0070.0070.0000.0000.0000.000
198A221ALA0-0.057-0.01729.0230.0120.0120.0000.0000.0000.000
199A222THR0-0.019-0.00630.812-0.005-0.0050.0000.0000.0000.000
200A223PHE0-0.002-0.00230.3910.0030.0030.0000.0000.0000.000
201A224GLY00.0320.00128.801-0.004-0.0040.0000.0000.0000.000
202A225GLY00.0160.03027.282-0.014-0.0140.0000.0000.0000.000
203A226GLY00.017-0.00228.8520.0080.0080.0000.0000.0000.000
204A227ASP-1-0.833-0.93326.411-0.226-0.2260.0000.0000.0000.000
205A228HIS0-0.069-0.03926.540-0.007-0.0070.0000.0000.0000.000
206A229PRO00.0100.02827.7730.0040.0040.0000.0000.0000.000