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: 8519Y

Calculation Name: 4M85-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M85

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2173814.642942
FMO2-HF: Nuclear repulsion 2098080.130861
FMO2-HF: Total energy -75734.51208
FMO2-MP2: Total energy -75954.425005


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.
-37.997-48.78937.079-14.977-11.31-0.077
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 : -0.029 / q_NPA : -0.047
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].
3A0ALA0-0.0080.0013.8540.1112.078-0.011-1.018-0.9380.005
4A1MET0-0.041-0.0186.5860.0450.0450.0000.0000.0000.000
5A2ILE0-0.0100.0078.9800.1340.1340.0000.0000.0000.000
6A3ARG10.6700.7839.437-0.616-0.6160.0000.0000.0000.000
7A4GLN00.0470.01313.5290.0010.0010.0000.0000.0000.000
8A5ALA0-0.0200.00714.4850.0660.0660.0000.0000.0000.000
9A6ARG10.8500.9008.581-0.936-0.9360.0000.0000.0000.000
10A7PRO00.0530.02116.102-0.011-0.0110.0000.0000.0000.000
11A8GLU-1-0.878-0.94214.2040.4290.4290.0000.0000.0000.000
12A9ASP-1-0.749-0.83812.6200.5390.5390.0000.0000.0000.000
13A10ARG10.9100.94915.032-0.296-0.2960.0000.0000.0000.000
14A11PHE00.0100.01916.349-0.026-0.0260.0000.0000.0000.000
15A12ASP-1-0.930-0.95413.2880.1910.1910.0000.0000.0000.000
16A13ILE0-0.013-0.01816.368-0.055-0.0550.0000.0000.0000.000
17A14ALA00.0780.03818.313-0.034-0.0340.0000.0000.0000.000
18A15LYS10.8630.92816.829-0.162-0.1620.0000.0000.0000.000
19A16LEU0-0.069-0.04415.792-0.032-0.0320.0000.0000.0000.000
20A17VAL00.0150.00520.278-0.018-0.0180.0000.0000.0000.000
21A18TYR00.0390.02823.503-0.012-0.0120.0000.0000.0000.000
22A19MET0-0.090-0.04921.041-0.015-0.0150.0000.0000.0000.000
23A20VAL00.0310.02623.963-0.006-0.0060.0000.0000.0000.000
24A21TRP00.0590.01026.5400.0040.0040.0000.0000.0000.000
25A22ASP-1-0.811-0.89428.402-0.029-0.0290.0000.0000.0000.000
26A23ASP-1-0.927-0.96527.041-0.088-0.0880.0000.0000.0000.000
27A24MET0-0.092-0.05330.331-0.001-0.0010.0000.0000.0000.000
28A25GLU-1-0.963-0.98732.588-0.040-0.0400.0000.0000.0000.000
29A26LEU00.0120.02631.7960.0040.0040.0000.0000.0000.000
30A27GLU-1-0.835-0.91835.013-0.010-0.0100.0000.0000.0000.000
31A28LEU0-0.024-0.00332.5150.0010.0010.0000.0000.0000.000
32A29VAL0-0.067-0.03530.1960.0060.0060.0000.0000.0000.000
33A30LYS10.7850.89332.9080.0360.0360.0000.0000.0000.000
34A31HIS0-0.071-0.03335.4700.0000.0000.0000.0000.0000.000
35A32LEU0-0.0300.00134.4030.0040.0040.0000.0000.0000.000
36A33PRO0-0.019-0.01333.078-0.003-0.0030.0000.0000.0000.000
37A34LYS10.8710.91428.3320.0200.0200.0000.0000.0000.000
38A35ASP-1-0.949-0.96627.3230.0730.0730.0000.0000.0000.000
39A36MET00.0550.03527.9250.0100.0100.0000.0000.0000.000
40A37VAL00.0040.00428.8280.0040.0040.0000.0000.0000.000
41A38LEU0-0.033-0.01722.8800.0010.0010.0000.0000.0000.000
42A39ASP-1-0.813-0.88525.3120.1080.1080.0000.0000.0000.000
43A40ALA00.0140.00126.9790.0090.0090.0000.0000.0000.000
44A41ILE00.0060.01123.8880.0040.0040.0000.0000.0000.000
45A42GLU-1-0.901-0.96621.3840.1720.1720.0000.0000.0000.000
46A43LYS10.8240.89523.571-0.085-0.0850.0000.0000.0000.000
47A44SER00.0020.00126.3670.0030.0030.0000.0000.0000.000
48A45CYS0-0.097-0.04021.437-0.007-0.0070.0000.0000.0000.000
49A46VAL0-0.119-0.06721.4310.0180.0180.0000.0000.0000.000
50A47ASP-1-0.851-0.92624.3820.1420.1420.0000.0000.0000.000
51A48ALA00.0030.00227.986-0.008-0.0080.0000.0000.0000.000
52A49THR0-0.072-0.02028.2040.0010.0010.0000.0000.0000.000
53A50TYR00.006-0.02827.762-0.009-0.0090.0000.0000.0000.000
54A51ARG10.7840.86528.0700.0020.0020.0000.0000.0000.000
55A52THR00.0310.00023.681-0.004-0.0040.0000.0000.0000.000
56A53PHE0-0.0150.01523.2050.0170.0170.0000.0000.0000.000
57A54TYR00.0490.00619.298-0.008-0.0080.0000.0000.0000.000
58A55GLN0-0.001-0.00120.473-0.018-0.0180.0000.0000.0000.000
59A56HIS10.7810.90822.433-0.065-0.0650.0000.0000.0000.000
60A57ILE0-0.0080.00517.944-0.023-0.0230.0000.0000.0000.000
61A58LEU0-0.0090.01616.7930.0240.0240.0000.0000.0000.000
62A59VAL0-0.007-0.01812.173-0.026-0.0260.0000.0000.0000.000
63A60TYR00.003-0.01310.0780.0020.0020.0000.0000.0000.000
64A61GLU-1-0.739-0.8305.9471.2291.2290.0000.0000.0000.000
65A62VAL0-0.024-0.0455.679-0.532-0.5320.0000.0000.0000.000
66A63GLU-1-0.842-0.8861.645-37.399-50.17234.051-13.561-7.717-0.094
67A64ASN0-0.051-0.0232.289-1.590-1.6593.040-0.390-2.5810.012
68A65LYS10.9891.0044.839-1.141-1.058-0.001-0.008-0.0740.000
69A66VAL00.0580.0358.150-0.091-0.0910.0000.0000.0000.000
70A67ALA0-0.0070.0019.944-0.108-0.1080.0000.0000.0000.000
71A68GLY0-0.011-0.03211.687-0.053-0.0530.0000.0000.0000.000
72A69CYS0-0.0060.01014.2990.0490.0490.0000.0000.0000.000
73A70ILE0-0.047-0.01017.073-0.039-0.0390.0000.0000.0000.000
74A71ILE00.0310.02220.2700.0250.0250.0000.0000.0000.000
75A72SER0-0.023-0.01923.071-0.017-0.0170.0000.0000.0000.000
76A73TYR0-0.053-0.05725.8670.0130.0130.0000.0000.0000.000
77A74SER0-0.009-0.02028.809-0.006-0.0060.0000.0000.0000.000
78A75GLY00.0550.01832.2740.0030.0030.0000.0000.0000.000
79A76GLU-1-0.804-0.86035.0530.0140.0140.0000.0000.0000.000
80A77ASN0-0.065-0.04934.4760.0070.0070.0000.0000.0000.000
81A78GLU-1-0.742-0.84133.724-0.004-0.0040.0000.0000.0000.000
82A79LEU00.0500.00734.6570.0040.0040.0000.0000.0000.000
83A80LYS10.8520.93534.642-0.035-0.0350.0000.0000.0000.000
84A81TYR0-0.044-0.02830.9370.0100.0100.0000.0000.0000.000
85A82GLU-1-0.698-0.80432.5170.0230.0230.0000.0000.0000.000
86A83LYS10.8580.89534.214-0.026-0.0260.0000.0000.0000.000
87A84ALA0-0.018-0.00932.3500.0020.0020.0000.0000.0000.000
88A85TRP00.0600.01928.9400.0080.0080.0000.0000.0000.000
89A86GLU-1-0.851-0.91233.4680.0350.0350.0000.0000.0000.000
90A87LEU0-0.074-0.03633.9370.0000.0000.0000.0000.0000.000
91A88LEU00.0000.03429.5690.0060.0060.0000.0000.0000.000
92A89ASP-1-0.880-0.93332.0420.0830.0830.0000.0000.0000.000
93A90LEU0-0.046-0.01030.8460.0050.0050.0000.0000.0000.000
94A91PRO00.0290.01033.659-0.003-0.0030.0000.0000.0000.000
95A92GLU-1-0.850-0.95736.6520.0370.0370.0000.0000.0000.000
96A93GLU-1-0.955-0.97837.5400.0270.0270.0000.0000.0000.000
97A94ILE00.0310.00532.521-0.004-0.0040.0000.0000.0000.000
98A95LYS10.8440.93036.427-0.056-0.0560.0000.0000.0000.000
99A96GLN0-0.062-0.02838.413-0.005-0.0050.0000.0000.0000.000
100A97TYR0-0.018-0.01237.765-0.005-0.0050.0000.0000.0000.000
101A98GLY0-0.0280.00539.412-0.003-0.0030.0000.0000.0000.000
102A99THR0-0.100-0.07735.4330.0030.0030.0000.0000.0000.000
103A100PRO00.0130.00031.647-0.004-0.0040.0000.0000.0000.000
104A101LEU0-0.002-0.00230.232-0.006-0.0060.0000.0000.0000.000
105A102PRO0-0.0110.00234.6300.0000.0000.0000.0000.0000.000
106A103VAL0-0.041-0.00837.4640.0000.0000.0000.0000.0000.000
107A104LYS10.7670.87336.9470.0090.0090.0000.0000.0000.000
108A105GLU-1-0.799-0.89132.762-0.025-0.0250.0000.0000.0000.000
109A106ALA0-0.038-0.00533.938-0.007-0.0070.0000.0000.0000.000
110A107LYS10.8200.89936.0730.0410.0410.0000.0000.0000.000
111A108ASP-1-0.838-0.93637.255-0.006-0.0060.0000.0000.0000.000
112A109ASP-1-0.848-0.91338.617-0.023-0.0230.0000.0000.0000.000
113A110GLU-1-0.745-0.83334.122-0.041-0.0410.0000.0000.0000.000
114A111TYR0-0.014-0.00226.2700.0100.0100.0000.0000.0000.000
115A112TYR0-0.018-0.01430.433-0.013-0.0130.0000.0000.0000.000
116A113ILE0-0.041-0.03624.7580.0050.0050.0000.0000.0000.000
117A114GLU-1-0.784-0.83526.509-0.009-0.0090.0000.0000.0000.000
118A115THR00.009-0.01422.367-0.013-0.0130.0000.0000.0000.000
119A116ILE0-0.019-0.02320.793-0.001-0.0010.0000.0000.0000.000
120A117ALA00.0290.02819.916-0.012-0.0120.0000.0000.0000.000
121A118THR0-0.053-0.05215.113-0.031-0.0310.0000.0000.0000.000
122A119PHE00.0810.06313.946-0.023-0.0230.0000.0000.0000.000
123A120ALA00.0250.00316.402-0.064-0.0640.0000.0000.0000.000
124A121ALA00.0140.01013.918-0.031-0.0310.0000.0000.0000.000
125A122TYR00.005-0.0077.989-0.088-0.0880.0000.0000.0000.000
126A123ARG10.9340.97113.9590.1970.1970.0000.0000.0000.000
127A124GLY00.0130.01216.945-0.054-0.0540.0000.0000.0000.000
128A125ARG10.8890.9379.7931.2331.2330.0000.0000.0000.000
129A126GLY00.015-0.00215.493-0.041-0.0410.0000.0000.0000.000
130A127ILE0-0.0040.00212.1350.0150.0150.0000.0000.0000.000
131A128ALA00.0860.04516.0780.0340.0340.0000.0000.0000.000
132A129THR00.0110.00719.4450.0190.0190.0000.0000.0000.000
133A130LYS10.8870.97014.7690.6650.6650.0000.0000.0000.000
134A131LEU00.0260.01614.9670.0160.0160.0000.0000.0000.000
135A132LEU00.0290.02018.2540.0280.0280.0000.0000.0000.000
136A133THR0-0.052-0.04320.8370.0180.0180.0000.0000.0000.000
137A134SER0-0.017-0.01818.0040.0100.0100.0000.0000.0000.000
138A135LEU00.0000.00819.9970.0210.0210.0000.0000.0000.000
139A136LEU0-0.0030.00922.0200.0150.0150.0000.0000.0000.000
140A137GLU-1-1.004-0.99622.179-0.087-0.0870.0000.0000.0000.000
141A138SER0-0.029-0.02721.7580.0180.0180.0000.0000.0000.000
142A139ASN00.018-0.00123.7160.0130.0130.0000.0000.0000.000
143A140THR00.0300.02227.4890.0010.0010.0000.0000.0000.000
144A141HIS0-0.079-0.02929.8890.0030.0030.0000.0000.0000.000
145A142VAL0-0.0080.00130.3960.0070.0070.0000.0000.0000.000
146A143LYS10.7670.89032.5790.0270.0270.0000.0000.0000.000
147A144TRP00.0520.01025.1730.0050.0050.0000.0000.0000.000
148A145SER0-0.080-0.06530.992-0.004-0.0040.0000.0000.0000.000
149A146LEU00.0150.01227.9350.0000.0000.0000.0000.0000.000
150A147ASN00.0300.01231.022-0.001-0.0010.0000.0000.0000.000
151A148CYS0-0.044-0.01431.233-0.008-0.0080.0000.0000.0000.000
152A149ASP-1-0.755-0.86631.868-0.085-0.0850.0000.0000.0000.000
153A150ILE0-0.039-0.02433.712-0.007-0.0070.0000.0000.0000.000
154A151ASN0-0.054-0.03234.584-0.002-0.0020.0000.0000.0000.000
155A152ASN00.0030.01027.483-0.017-0.0170.0000.0000.0000.000
156A153GLU-1-0.782-0.88931.504-0.139-0.1390.0000.0000.0000.000
157A154ALA00.0140.00228.182-0.005-0.0050.0000.0000.0000.000
158A155ALA0-0.0020.00527.597-0.011-0.0110.0000.0000.0000.000
159A156LEU00.0500.02228.5560.0000.0000.0000.0000.0000.000
160A157LYS10.7760.87130.7140.1440.1440.0000.0000.0000.000
161A158LEU0-0.050-0.01623.664-0.007-0.0070.0000.0000.0000.000
162A159TYR00.0670.00825.675-0.006-0.0060.0000.0000.0000.000
163A160LYS10.8890.95229.4180.0960.0960.0000.0000.0000.000
164A161LYS10.9080.96326.1150.2290.2290.0000.0000.0000.000
165A162VAL0-0.056-0.03125.215-0.007-0.0070.0000.0000.0000.000
166A163GLY00.0240.01928.6140.0060.0060.0000.0000.0000.000
167A164PHE0-0.0060.00127.9100.0090.0090.0000.0000.0000.000
168A165ILE0-0.019-0.01833.056-0.003-0.0030.0000.0000.0000.000
169A166SER00.004-0.01836.353-0.002-0.0020.0000.0000.0000.000
170A167ASP-1-0.824-0.89938.265-0.040-0.0400.0000.0000.0000.000
171A168GLY00.0360.02040.0850.0050.0050.0000.0000.0000.000
172A169GLN0-0.028-0.01039.841-0.008-0.0080.0000.0000.0000.000
173A170ILE00.0130.01137.4830.0040.0040.0000.0000.0000.000
174A171GLU-1-0.818-0.90039.108-0.034-0.0340.0000.0000.0000.000
175A172LEU0-0.016-0.00534.6990.0040.0040.0000.0000.0000.000
176A173TYR00.033-0.01534.607-0.002-0.0020.0000.0000.0000.000
177A174LYS10.8200.90538.5940.0270.0270.0000.0000.0000.000
178A175HIS00.0060.02934.751-0.005-0.0050.0000.0000.0000.000
179A176MET0-0.007-0.00938.1710.0040.0040.0000.0000.0000.000
180A177TYR00.0390.01532.160-0.008-0.0080.0000.0000.0000.000
181A178HIS0-0.048-0.03935.6160.0020.0020.0000.0000.0000.000
182A179HIS10.8120.89535.1880.0410.0410.0000.0000.0000.000
183A180LEU0-0.074-0.04132.014-0.003-0.0030.0000.0000.0000.000
184A181ILE00.0210.00633.8600.0040.0040.0000.0000.0000.000
185A182VAL00.0230.02129.842-0.003-0.0030.0000.0000.0000.000