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: G6M51

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2167765.974615
FMO2-HF: Nuclear repulsion 2092031.698225
FMO2-HF: Total energy -75734.276389
FMO2-MP2: Total energy -75954.180792


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.
-33.588-32.9421.402-10.27-11.78-0.062
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 : -0.033 / q_NPA : -0.022
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].
3A0ALA0-0.018-0.0123.697-0.1322.670-0.008-1.539-1.2560.008
4A1MET0-0.021-0.0175.932-0.278-0.2780.0000.0000.0000.000
5A2ILE0-0.0070.0098.2210.2020.2020.0000.0000.0000.000
6A3ARG10.6850.7938.509-0.906-0.9060.0000.0000.0000.000
7A4GLN00.0310.01012.6190.0200.0200.0000.0000.0000.000
8A5ALA0-0.0100.01213.7410.0800.0800.0000.0000.0000.000
9A6ARG10.9420.9668.409-0.915-0.9150.0000.0000.0000.000
10A7PRO00.0670.03215.5610.0120.0120.0000.0000.0000.000
11A8GLU-1-0.892-0.95313.5810.4720.4720.0000.0000.0000.000
12A9ASP-1-0.780-0.84712.0520.7670.7670.0000.0000.0000.000
13A10ARG10.8990.93514.666-0.345-0.3450.0000.0000.0000.000
14A11PHE00.0350.03116.582-0.025-0.0250.0000.0000.0000.000
15A12ASP-1-0.904-0.94712.8060.4420.4420.0000.0000.0000.000
16A13ILE0-0.001-0.00715.938-0.053-0.0530.0000.0000.0000.000
17A14ALA00.0690.03917.921-0.040-0.0400.0000.0000.0000.000
18A15LYS10.8420.91716.085-0.322-0.3220.0000.0000.0000.000
19A16LEU0-0.054-0.03315.632-0.034-0.0340.0000.0000.0000.000
20A17VAL00.0240.01020.054-0.024-0.0240.0000.0000.0000.000
21A18TYR00.0630.03623.204-0.019-0.0190.0000.0000.0000.000
22A19MET0-0.087-0.05020.467-0.012-0.0120.0000.0000.0000.000
23A20VAL00.0090.01923.480-0.012-0.0120.0000.0000.0000.000
24A21TRP00.046-0.00126.050-0.004-0.0040.0000.0000.0000.000
25A22ASP-1-0.819-0.90827.9510.0290.0290.0000.0000.0000.000
26A23ASP-1-0.947-0.96826.946-0.011-0.0110.0000.0000.0000.000
27A24MET0-0.085-0.05430.075-0.002-0.0020.0000.0000.0000.000
28A25GLU-1-0.974-0.98132.3180.0040.0040.0000.0000.0000.000
29A26LEU0-0.0060.01331.4710.0000.0000.0000.0000.0000.000
30A27GLU-1-0.849-0.92834.5920.0260.0260.0000.0000.0000.000
31A28LEU0-0.0010.00531.9370.0010.0010.0000.0000.0000.000
32A29VAL0-0.058-0.03230.1550.0060.0060.0000.0000.0000.000
33A30LYS10.8100.90332.600-0.018-0.0180.0000.0000.0000.000
34A31HIS0-0.064-0.02535.453-0.001-0.0010.0000.0000.0000.000
35A32LEU0-0.0330.01233.9540.0020.0020.0000.0000.0000.000
36A33PRO0-0.0030.00032.6120.0000.0000.0000.0000.0000.000
37A34LYS10.8760.90827.698-0.045-0.0450.0000.0000.0000.000
38A35ASP-1-0.951-0.96427.4110.1320.1320.0000.0000.0000.000
39A36MET0-0.0010.00927.9430.0120.0120.0000.0000.0000.000
40A37VAL00.0100.00128.1850.0050.0050.0000.0000.0000.000
41A38LEU0-0.035-0.01522.5380.0050.0050.0000.0000.0000.000
42A39ASP-1-0.783-0.86524.8860.1590.1590.0000.0000.0000.000
43A40ALA00.0190.00426.5000.0080.0080.0000.0000.0000.000
44A41ILE0-0.012-0.00523.3420.0040.0040.0000.0000.0000.000
45A42GLU-1-0.897-0.96121.1240.2440.2440.0000.0000.0000.000
46A43LYS10.8110.88623.305-0.128-0.1280.0000.0000.0000.000
47A44SER00.000-0.00225.9640.0000.0000.0000.0000.0000.000
48A45CYS0-0.116-0.04521.186-0.003-0.0030.0000.0000.0000.000
49A46VAL0-0.097-0.06121.0540.0170.0170.0000.0000.0000.000
50A47ASP-1-0.842-0.92123.8870.1770.1770.0000.0000.0000.000
51A48ALA0-0.0050.00127.536-0.012-0.0120.0000.0000.0000.000
52A49THR0-0.093-0.03627.5010.0050.0050.0000.0000.0000.000
53A50TYR00.029-0.00727.358-0.010-0.0100.0000.0000.0000.000
54A51ARG10.8030.87227.537-0.043-0.0430.0000.0000.0000.000
55A52THR00.0110.00023.377-0.004-0.0040.0000.0000.0000.000
56A53PHE0-0.0150.01323.0500.0210.0210.0000.0000.0000.000
57A54TYR00.0680.01218.609-0.004-0.0040.0000.0000.0000.000
58A55GLN0-0.032-0.01219.510-0.008-0.0080.0000.0000.0000.000
59A56HIS10.7700.89121.864-0.121-0.1210.0000.0000.0000.000
60A57ILE00.0030.00717.258-0.016-0.0160.0000.0000.0000.000
61A58LEU0-0.0060.02315.9170.0240.0240.0000.0000.0000.000
62A59VAL00.013-0.00611.348-0.025-0.0250.0000.0000.0000.000
63A60TYR0-0.010-0.0209.475-0.043-0.0430.0000.0000.0000.000
64A61GLU-1-0.829-0.8995.4211.7531.7530.0000.0000.0000.000
65A62VAL0-0.006-0.0325.549-0.367-0.3670.0000.0000.0000.000
66A63GLU-1-0.849-0.9131.866-31.714-34.73519.030-9.156-6.853-0.072
67A64ASN0-0.047-0.0272.464-1.647-0.9522.3760.487-3.5580.002
68A65LYS10.9991.0114.349-2.074-1.9020.004-0.062-0.1130.000
69A66VAL00.0230.0237.590-0.029-0.0290.0000.0000.0000.000
70A67ALA0-0.017-0.0119.779-0.145-0.1450.0000.0000.0000.000
71A68GLY0-0.005-0.02511.459-0.117-0.1170.0000.0000.0000.000
72A69CYS0-0.011-0.00113.9570.0710.0710.0000.0000.0000.000
73A70ILE0-0.043-0.00716.657-0.041-0.0410.0000.0000.0000.000
74A71ILE00.0280.01919.7740.0230.0230.0000.0000.0000.000
75A72SER0-0.002-0.00622.603-0.021-0.0210.0000.0000.0000.000
76A73TYR0-0.052-0.05325.1100.0100.0100.0000.0000.0000.000
77A74SER0-0.025-0.03027.911-0.006-0.0060.0000.0000.0000.000
78A75GLY00.0540.00731.4470.0040.0040.0000.0000.0000.000
79A76GLU-1-0.851-0.88834.1110.0420.0420.0000.0000.0000.000
80A77ASN0-0.064-0.04133.3760.0050.0050.0000.0000.0000.000
81A78GLU-1-0.750-0.84333.0290.0370.0370.0000.0000.0000.000
82A79LEU00.0440.00334.0110.0050.0050.0000.0000.0000.000
83A80LYS10.8600.93534.033-0.062-0.0620.0000.0000.0000.000
84A81TYR0-0.029-0.02330.4190.0090.0090.0000.0000.0000.000
85A82GLU-1-0.712-0.80532.2490.0700.0700.0000.0000.0000.000
86A83LYS10.8600.90633.828-0.053-0.0530.0000.0000.0000.000
87A84ALA0-0.005-0.00131.8550.0010.0010.0000.0000.0000.000
88A85TRP00.0590.02128.5640.0080.0080.0000.0000.0000.000
89A86GLU-1-0.868-0.92733.1250.0630.0630.0000.0000.0000.000
90A87LEU0-0.093-0.05033.315-0.002-0.0020.0000.0000.0000.000
91A88LEU0-0.0210.02329.1010.0060.0060.0000.0000.0000.000
92A89ASP-1-0.903-0.94331.6750.1130.1130.0000.0000.0000.000
93A90LEU0-0.051-0.02830.7220.0060.0060.0000.0000.0000.000
94A91PRO00.0440.01833.408-0.005-0.0050.0000.0000.0000.000
95A92GLU-1-0.860-0.95736.4090.0640.0640.0000.0000.0000.000
96A93GLU-1-0.951-0.98537.6370.0590.0590.0000.0000.0000.000
97A94ILE00.0390.00632.136-0.003-0.0030.0000.0000.0000.000
98A95LYS10.8920.96336.295-0.086-0.0860.0000.0000.0000.000
99A96GLN0-0.055-0.01538.230-0.005-0.0050.0000.0000.0000.000
100A97TYR0-0.030-0.02237.396-0.005-0.0050.0000.0000.0000.000
101A98GLY0-0.0210.01239.186-0.003-0.0030.0000.0000.0000.000
102A99THR0-0.103-0.07535.1830.0020.0020.0000.0000.0000.000
103A100PRO00.012-0.00631.303-0.005-0.0050.0000.0000.0000.000
104A101LEU0-0.009-0.00730.071-0.005-0.0050.0000.0000.0000.000
105A102PRO00.0000.01134.441-0.001-0.0010.0000.0000.0000.000
106A103VAL0-0.043-0.01137.374-0.002-0.0020.0000.0000.0000.000
107A104LYS10.8070.90836.374-0.019-0.0190.0000.0000.0000.000
108A105GLU-1-0.840-0.92331.9070.0240.0240.0000.0000.0000.000
109A106ALA0-0.030-0.00533.464-0.006-0.0060.0000.0000.0000.000
110A107LYS10.8470.90435.5550.0070.0070.0000.0000.0000.000
111A108ASP-1-0.839-0.93936.4140.0220.0220.0000.0000.0000.000
112A109ASP-1-0.852-0.91037.3700.0020.0020.0000.0000.0000.000
113A110GLU-1-0.768-0.85533.438-0.005-0.0050.0000.0000.0000.000
114A111TYR0-0.0040.00025.5770.0070.0070.0000.0000.0000.000
115A112TYR0-0.027-0.02329.675-0.011-0.0110.0000.0000.0000.000
116A113ILE0-0.035-0.03924.3100.0090.0090.0000.0000.0000.000
117A114GLU-1-0.786-0.84926.3420.0630.0630.0000.0000.0000.000
118A115THR00.007-0.01021.916-0.009-0.0090.0000.0000.0000.000
119A116ILE0-0.030-0.02520.1400.0040.0040.0000.0000.0000.000
120A117ALA00.0370.03719.581-0.016-0.0160.0000.0000.0000.000
121A118THR0-0.061-0.04515.104-0.002-0.0020.0000.0000.0000.000
122A119PHE00.0970.05613.679-0.046-0.0460.0000.0000.0000.000
123A120ALA00.016-0.00816.264-0.052-0.0520.0000.0000.0000.000
124A121ALA00.0120.01514.036-0.036-0.0360.0000.0000.0000.000
125A122TYR00.005-0.0148.184-0.110-0.1100.0000.0000.0000.000
126A123ARG10.8940.95213.8200.0430.0430.0000.0000.0000.000
127A124GLY00.0210.01116.995-0.038-0.0380.0000.0000.0000.000
128A125ARG10.9230.9659.9860.7210.7210.0000.0000.0000.000
129A126GLY00.0210.00115.416-0.037-0.0370.0000.0000.0000.000
130A127ILE0-0.0040.00211.9960.0010.0010.0000.0000.0000.000
131A128ALA00.0930.04715.5840.0290.0290.0000.0000.0000.000
132A129THR00.0110.00618.8720.0100.0100.0000.0000.0000.000
133A130LYS10.8970.96714.2620.5010.5010.0000.0000.0000.000
134A131LEU00.0040.01214.4410.0080.0080.0000.0000.0000.000
135A132LEU00.0300.02017.6810.0170.0170.0000.0000.0000.000
136A133THR0-0.051-0.04520.2760.0070.0070.0000.0000.0000.000
137A134SER0-0.023-0.00617.4030.0110.0110.0000.0000.0000.000
138A135LEU00.0250.01419.3770.0140.0140.0000.0000.0000.000
139A136LEU0-0.0260.00021.2990.0080.0080.0000.0000.0000.000
140A137GLU-1-0.996-1.00121.309-0.069-0.0690.0000.0000.0000.000
141A138SER0-0.045-0.02521.3250.0110.0110.0000.0000.0000.000
142A139ASN00.020-0.00123.1110.0050.0050.0000.0000.0000.000
143A140THR00.0260.01526.9310.0010.0010.0000.0000.0000.000
144A141HIS0-0.079-0.03429.5170.0000.0000.0000.0000.0000.000
145A142VAL0-0.0090.00529.3530.0050.0050.0000.0000.0000.000
146A143LYS10.8020.91331.996-0.001-0.0010.0000.0000.0000.000
147A144TRP00.0310.01524.6590.0080.0080.0000.0000.0000.000
148A145SER0-0.066-0.06330.562-0.005-0.0050.0000.0000.0000.000
149A146LEU00.0070.01327.2440.0040.0040.0000.0000.0000.000
150A147ASN00.0370.02130.412-0.009-0.0090.0000.0000.0000.000
151A148CYS0-0.043-0.01530.614-0.002-0.0020.0000.0000.0000.000
152A149ASP-1-0.739-0.85431.184-0.034-0.0340.0000.0000.0000.000
153A150ILE0-0.027-0.01733.006-0.007-0.0070.0000.0000.0000.000
154A151ASN0-0.082-0.04434.491-0.005-0.0050.0000.0000.0000.000
155A152ASN0-0.0180.00027.446-0.016-0.0160.0000.0000.0000.000
156A153GLU-1-0.769-0.88931.327-0.091-0.0910.0000.0000.0000.000
157A154ALA00.0090.00027.574-0.005-0.0050.0000.0000.0000.000
158A155ALA00.0100.01227.045-0.009-0.0090.0000.0000.0000.000
159A156LEU00.0550.03228.037-0.003-0.0030.0000.0000.0000.000
160A157LYS10.7770.87430.2650.0970.0970.0000.0000.0000.000
161A158LEU0-0.026-0.00923.092-0.009-0.0090.0000.0000.0000.000
162A159TYR00.044-0.00725.103-0.005-0.0050.0000.0000.0000.000
163A160LYS10.8940.95128.8310.0570.0570.0000.0000.0000.000
164A161LYS10.9050.96826.3000.1740.1740.0000.0000.0000.000
165A162VAL0-0.057-0.03224.779-0.007-0.0070.0000.0000.0000.000
166A163GLY00.0260.02128.1980.0050.0050.0000.0000.0000.000
167A164PHE0-0.016-0.00127.3400.0070.0070.0000.0000.0000.000
168A165ILE0-0.026-0.02432.513-0.005-0.0050.0000.0000.0000.000
169A166SER0-0.013-0.02836.1920.0020.0020.0000.0000.0000.000
170A167ASP-1-0.832-0.89937.905-0.013-0.0130.0000.0000.0000.000
171A168GLY00.0350.02639.6700.0040.0040.0000.0000.0000.000
172A169GLN0-0.009-0.00439.184-0.005-0.0050.0000.0000.0000.000
173A170ILE00.0110.01136.8020.0020.0020.0000.0000.0000.000
174A171GLU-1-0.830-0.90638.591-0.001-0.0010.0000.0000.0000.000
175A172LEU0-0.017-0.00934.5120.0030.0030.0000.0000.0000.000
176A173TYR00.0570.01534.578-0.001-0.0010.0000.0000.0000.000
177A174LYS10.8400.91238.093-0.003-0.0030.0000.0000.0000.000
178A175HIS00.0360.03634.938-0.003-0.0030.0000.0000.0000.000
179A176MET0-0.021-0.00938.0820.0030.0030.0000.0000.0000.000
180A177TYR00.0450.01631.672-0.004-0.0040.0000.0000.0000.000
181A178HIS0-0.065-0.05334.743-0.001-0.0010.0000.0000.0000.000
182A179HIS10.8080.89834.4190.0060.0060.0000.0000.0000.000
183A180LEU0-0.074-0.04131.487-0.006-0.0060.0000.0000.0000.000
184A181ILE00.0460.01033.3770.0050.0050.0000.0000.0000.000
185A182VAL00.0160.01929.356-0.003-0.0030.0000.0000.0000.000