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: 17QNZ

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 OptH
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 -2164897.21009
FMO2-HF: Nuclear repulsion 2089163.816493
FMO2-HF: Total energy -75733.393597
FMO2-MP2: Total energy -75953.179869


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.
-16.302-9.6626.574-4.864-8.349-0.008
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 : 0.007 / q_NPA : 0.001
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].
3A0ALA0-0.011-0.0063.810-1.1131.399-0.001-1.348-1.1620.006
4A1MET0-0.024-0.0266.017-0.029-0.0290.0000.0000.0000.000
5A2ILE0-0.0100.0108.340-0.001-0.0010.0000.0000.0000.000
6A3ARG10.7090.8318.0581.1681.1680.0000.0000.0000.000
7A4GLN00.0400.01212.6910.0130.0130.0000.0000.0000.000
8A5ALA0-0.0090.01313.581-0.083-0.0830.0000.0000.0000.000
9A6ARG10.9470.9669.0170.9660.9660.0000.0000.0000.000
10A7PRO00.0650.02715.173-0.011-0.0110.0000.0000.0000.000
11A8GLU-1-0.897-0.96012.866-0.381-0.3810.0000.0000.0000.000
12A9ASP-1-0.787-0.86911.163-0.808-0.8080.0000.0000.0000.000
13A10ARG10.8920.93913.6590.2590.2590.0000.0000.0000.000
14A11PHE00.0200.02415.8740.0190.0190.0000.0000.0000.000
15A12ASP-1-0.961-0.98111.772-0.432-0.4320.0000.0000.0000.000
16A13ILE0-0.006-0.01615.0590.0270.0270.0000.0000.0000.000
17A14ALA00.0600.03616.9980.0250.0250.0000.0000.0000.000
18A15LYS10.9290.96915.8860.2360.2360.0000.0000.0000.000
19A16LEU0-0.046-0.02914.9090.0190.0190.0000.0000.0000.000
20A17VAL00.0190.01319.2690.0140.0140.0000.0000.0000.000
21A18TYR00.0610.02622.3610.0190.0190.0000.0000.0000.000
22A19MET0-0.066-0.04619.7180.0090.0090.0000.0000.0000.000
23A20VAL00.0140.02322.7750.0080.0080.0000.0000.0000.000
24A21TRP00.041-0.00325.3130.0110.0110.0000.0000.0000.000
25A22ASP-1-0.960-0.97727.201-0.082-0.0820.0000.0000.0000.000
26A23ASP-1-0.916-0.95626.489-0.108-0.1080.0000.0000.0000.000
27A24MET0-0.094-0.05729.4160.0040.0040.0000.0000.0000.000
28A25GLU-1-1.011-1.00131.596-0.065-0.0650.0000.0000.0000.000
29A26LEU00.0090.01830.7110.0040.0040.0000.0000.0000.000
30A27GLU-1-0.893-0.95033.789-0.064-0.0640.0000.0000.0000.000
31A28LEU00.0120.00030.9530.0020.0020.0000.0000.0000.000
32A29VAL0-0.037-0.02029.370-0.001-0.0010.0000.0000.0000.000
33A30LYS10.8350.92731.9550.0820.0820.0000.0000.0000.000
34A31HIS0-0.038-0.01334.7000.0050.0050.0000.0000.0000.000
35A32LEU0-0.0350.01533.1100.0030.0030.0000.0000.0000.000
36A33PRO00.0030.00231.734-0.003-0.0030.0000.0000.0000.000
37A34LYS10.9630.95726.7200.0770.0770.0000.0000.0000.000
38A35ASP-1-0.933-0.96226.622-0.096-0.0960.0000.0000.0000.000
39A36MET00.0210.01527.099-0.006-0.0060.0000.0000.0000.000
40A37VAL00.0020.00227.179-0.006-0.0060.0000.0000.0000.000
41A38LEU0-0.044-0.02021.920-0.010-0.0100.0000.0000.0000.000
42A39ASP-1-0.779-0.86723.968-0.128-0.1280.0000.0000.0000.000
43A40ALA00.0110.00125.588-0.007-0.0070.0000.0000.0000.000
44A41ILE0-0.0040.00322.440-0.007-0.0070.0000.0000.0000.000
45A42GLU-1-0.871-0.92920.297-0.190-0.1900.0000.0000.0000.000
46A43LYS10.8290.89822.3340.0930.0930.0000.0000.0000.000
47A44SER0-0.067-0.06424.369-0.003-0.0030.0000.0000.0000.000
48A45CYS0-0.050-0.02220.206-0.011-0.0110.0000.0000.0000.000
49A46VAL0-0.102-0.06620.340-0.022-0.0220.0000.0000.0000.000
50A47ASP-1-0.837-0.91523.154-0.141-0.1410.0000.0000.0000.000
51A48ALA0-0.013-0.00426.7750.0130.0130.0000.0000.0000.000
52A49THR0-0.094-0.03426.807-0.008-0.0080.0000.0000.0000.000
53A50TYR00.0310.00726.4890.0060.0060.0000.0000.0000.000
54A51ARG10.8290.89626.7300.1100.1100.0000.0000.0000.000
55A52THR0-0.011-0.00322.477-0.007-0.0070.0000.0000.0000.000
56A53PHE0-0.0050.01722.089-0.021-0.0210.0000.0000.0000.000
57A54TYR00.0450.00217.936-0.014-0.0140.0000.0000.0000.000
58A55GLN0-0.024-0.01119.025-0.013-0.0130.0000.0000.0000.000
59A56HIS10.7840.89721.5190.1960.1960.0000.0000.0000.000
60A57ILE00.0030.00716.3450.0010.0010.0000.0000.0000.000
61A58LEU0-0.0010.02415.492-0.027-0.0270.0000.0000.0000.000
62A59VAL00.010-0.00510.4810.0300.0300.0000.0000.0000.000
63A60TYR0-0.015-0.0248.970-0.027-0.0270.0000.0000.0000.000
64A61GLU-1-0.832-0.9014.423-3.482-3.309-0.001-0.014-0.1580.000
65A62VAL0-0.011-0.0315.2440.0560.0560.0000.0000.0000.000
66A63GLU-1-0.920-0.9602.326-5.796-3.4813.418-2.916-2.8170.004
67A64ASN0-0.044-0.0252.117-7.928-6.6753.139-0.422-3.970-0.016
68A65LYS10.9861.0053.4511.1041.4910.019-0.164-0.242-0.002
69A66VAL00.0220.0256.790-0.006-0.0060.0000.0000.0000.000
70A67ALA0-0.013-0.0109.3020.1310.1310.0000.0000.0000.000
71A68GLY0-0.008-0.02910.8330.0900.0900.0000.0000.0000.000
72A69CYS0-0.037-0.00613.169-0.062-0.0620.0000.0000.0000.000
73A70ILE0-0.0170.00015.8570.0330.0330.0000.0000.0000.000
74A71ILE00.0370.02218.989-0.019-0.0190.0000.0000.0000.000
75A72SER0-0.024-0.01621.7420.0170.0170.0000.0000.0000.000
76A73TYR0-0.059-0.08124.547-0.004-0.0040.0000.0000.0000.000
77A74SER0-0.004-0.00127.3780.0030.0030.0000.0000.0000.000
78A75GLY00.0500.00431.0010.0000.0000.0000.0000.0000.000
79A76GLU-1-0.960-0.97133.504-0.093-0.0930.0000.0000.0000.000
80A77ASN0-0.077-0.03932.6700.0090.0090.0000.0000.0000.000
81A78GLU-1-0.760-0.85732.075-0.111-0.1110.0000.0000.0000.000
82A79LEU00.0520.00633.163-0.002-0.0020.0000.0000.0000.000
83A80LYS10.9100.96833.3510.1110.1110.0000.0000.0000.000
84A81TYR0-0.024-0.02329.658-0.002-0.0020.0000.0000.0000.000
85A82GLU-1-0.696-0.79031.362-0.113-0.1130.0000.0000.0000.000
86A83LYS10.9160.95432.8580.0780.0780.0000.0000.0000.000
87A84ALA0-0.005-0.00231.0100.0040.0040.0000.0000.0000.000
88A85TRP00.0520.02127.701-0.004-0.0040.0000.0000.0000.000
89A86GLU-1-0.924-0.97732.127-0.075-0.0750.0000.0000.0000.000
90A87LEU0-0.106-0.05232.5020.0050.0050.0000.0000.0000.000
91A88LEU0-0.0170.02528.214-0.003-0.0030.0000.0000.0000.000
92A89ASP-1-0.906-0.94630.708-0.088-0.0880.0000.0000.0000.000
93A90LEU0-0.045-0.02029.794-0.003-0.0030.0000.0000.0000.000
94A91PRO00.0510.01932.3590.0050.0050.0000.0000.0000.000
95A92GLU-1-0.878-0.96435.481-0.060-0.0600.0000.0000.0000.000
96A93GLU-1-0.976-0.99036.789-0.057-0.0570.0000.0000.0000.000
97A94ILE00.0310.00931.277-0.001-0.0010.0000.0000.0000.000
98A95LYS10.9060.96535.5060.0750.0750.0000.0000.0000.000
99A96GLN0-0.041-0.01437.2760.0000.0000.0000.0000.0000.000
100A97TYR0-0.032-0.02436.5000.0020.0020.0000.0000.0000.000
101A98GLY0-0.0150.01638.2350.0000.0000.0000.0000.0000.000
102A99THR0-0.121-0.09834.185-0.001-0.0010.0000.0000.0000.000
103A100PRO00.023-0.00330.4660.0040.0040.0000.0000.0000.000
104A101LEU0-0.026-0.01229.1040.0010.0010.0000.0000.0000.000
105A102PRO00.0070.01633.535-0.002-0.0020.0000.0000.0000.000
106A103VAL0-0.048-0.02036.5480.0030.0030.0000.0000.0000.000
107A104LYS10.8120.91035.4920.0830.0830.0000.0000.0000.000
108A105GLU-1-0.846-0.90930.994-0.118-0.1180.0000.0000.0000.000
109A106ALA0-0.035-0.00832.6620.0000.0000.0000.0000.0000.000
110A107LYS10.8900.93234.7420.0900.0900.0000.0000.0000.000
111A108ASP-1-0.830-0.92635.814-0.090-0.0900.0000.0000.0000.000
112A109ASP-1-0.877-0.93136.957-0.092-0.0920.0000.0000.0000.000
113A110GLU-1-0.822-0.88132.864-0.106-0.1060.0000.0000.0000.000
114A111TYR00.001-0.00325.580-0.003-0.0030.0000.0000.0000.000
115A112TYR0-0.037-0.04229.152-0.004-0.0040.0000.0000.0000.000
116A113ILE0-0.026-0.03723.625-0.013-0.0130.0000.0000.0000.000
117A114GLU-1-0.800-0.84825.639-0.155-0.1550.0000.0000.0000.000
118A115THR00.0050.00221.3210.0050.0050.0000.0000.0000.000
119A116ILE0-0.010-0.01319.494-0.020-0.0200.0000.0000.0000.000
120A117ALA00.0390.03518.8770.0180.0180.0000.0000.0000.000
121A118THR0-0.064-0.04214.666-0.030-0.0300.0000.0000.0000.000
122A119PHE00.0710.04212.9360.0520.0520.0000.0000.0000.000
123A120ALA00.009-0.01215.9520.0010.0010.0000.0000.0000.000
124A121ALA00.0070.01013.9740.0070.0070.0000.0000.0000.000
125A122TYR0-0.005-0.0158.492-0.016-0.0160.0000.0000.0000.000
126A123ARG10.9240.96413.8070.1420.1420.0000.0000.0000.000
127A124GLY00.0050.00617.1340.0100.0100.0000.0000.0000.000
128A125ARG10.9590.9869.9510.2100.2100.0000.0000.0000.000
129A126GLY00.010-0.00215.220-0.029-0.0290.0000.0000.0000.000
130A127ILE00.0050.00811.697-0.005-0.0050.0000.0000.0000.000
131A128ALA00.0900.04315.227-0.016-0.0160.0000.0000.0000.000
132A129THR0-0.007-0.00218.4010.0040.0040.0000.0000.0000.000
133A130LYS10.8960.95113.7130.3640.3640.0000.0000.0000.000
134A131LEU00.0070.01213.850-0.009-0.0090.0000.0000.0000.000
135A132LEU00.0180.01817.1260.0070.0070.0000.0000.0000.000
136A133THR0-0.041-0.02820.0510.0160.0160.0000.0000.0000.000
137A134SER0-0.026-0.00717.399-0.003-0.0030.0000.0000.0000.000
138A135LEU00.0340.01719.3300.0020.0020.0000.0000.0000.000
139A136LEU0-0.033-0.00621.0950.0150.0150.0000.0000.0000.000
140A137GLU-1-0.991-1.00221.808-0.210-0.2100.0000.0000.0000.000
141A138SER0-0.042-0.01821.4900.0090.0090.0000.0000.0000.000
142A139ASN00.019-0.00323.2620.0160.0160.0000.0000.0000.000
143A140THR00.0030.00527.0820.0030.0030.0000.0000.0000.000
144A141HIS0-0.047-0.01329.6740.0150.0150.0000.0000.0000.000
145A142VAL0-0.017-0.00129.1860.0060.0060.0000.0000.0000.000
146A143LYS10.8650.95231.8850.0960.0960.0000.0000.0000.000
147A144TRP00.0370.01524.848-0.003-0.0030.0000.0000.0000.000
148A145SER0-0.054-0.05629.9620.0050.0050.0000.0000.0000.000
149A146LEU00.0090.01226.595-0.010-0.0100.0000.0000.0000.000
150A147ASN00.0460.03229.7100.0130.0130.0000.0000.0000.000
151A148CYS0-0.049-0.01229.986-0.007-0.0070.0000.0000.0000.000
152A149ASP-1-0.781-0.88730.579-0.085-0.0850.0000.0000.0000.000
153A150ILE0-0.022-0.01732.422-0.001-0.0010.0000.0000.0000.000
154A151ASN0-0.036-0.00834.1100.0060.0060.0000.0000.0000.000
155A152ASN0-0.023-0.00426.9390.0020.0020.0000.0000.0000.000
156A153GLU-1-0.856-0.94630.894-0.083-0.0830.0000.0000.0000.000
157A154ALA0-0.023-0.01627.343-0.003-0.0030.0000.0000.0000.000
158A155ALA00.0210.01826.643-0.007-0.0070.0000.0000.0000.000
159A156LEU00.0650.03727.620-0.005-0.0050.0000.0000.0000.000
160A157LYS10.8660.93529.7380.0860.0860.0000.0000.0000.000
161A158LEU0-0.023-0.00522.587-0.004-0.0040.0000.0000.0000.000
162A159TYR00.046-0.00424.545-0.003-0.0030.0000.0000.0000.000
163A160LYS10.9100.96428.4000.0900.0900.0000.0000.0000.000
164A161LYS10.8970.96326.4230.1320.1320.0000.0000.0000.000
165A162VAL0-0.053-0.02824.4800.0000.0000.0000.0000.0000.000
166A163GLY00.0190.01827.854-0.002-0.0020.0000.0000.0000.000
167A164PHE0-0.0200.00026.7340.0040.0040.0000.0000.0000.000
168A165ILE0-0.025-0.03232.0310.0060.0060.0000.0000.0000.000
169A166SER0-0.007-0.02835.645-0.003-0.0030.0000.0000.0000.000
170A167ASP-1-0.871-0.93137.401-0.080-0.0800.0000.0000.0000.000
171A168GLY00.0130.01839.0620.0000.0000.0000.0000.0000.000
172A169GLN0-0.0020.00338.560-0.007-0.0070.0000.0000.0000.000
173A170ILE00.0050.00836.0750.0030.0030.0000.0000.0000.000
174A171GLU-1-0.900-0.96437.895-0.065-0.0650.0000.0000.0000.000
175A172LEU0-0.038-0.02233.7170.0000.0000.0000.0000.0000.000
176A173TYR00.0630.01734.0620.0010.0010.0000.0000.0000.000
177A174LYS10.9440.98837.3550.0580.0580.0000.0000.0000.000
178A175HIS00.0560.04434.866-0.001-0.0010.0000.0000.0000.000
179A176MET0-0.024-0.00837.399-0.001-0.0010.0000.0000.0000.000
180A177TYR00.0480.02031.040-0.005-0.0050.0000.0000.0000.000
181A178HIS0-0.069-0.06134.1690.0050.0050.0000.0000.0000.000
182A179HIS10.8050.89033.7950.0940.0940.0000.0000.0000.000
183A180LEU0-0.077-0.03930.8950.0050.0050.0000.0000.0000.000
184A181ILE00.0500.01132.736-0.005-0.0050.0000.0000.0000.000
185A182VAL00.0140.01629.0020.0030.0030.0000.0000.0000.000