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: NNV4Q

Calculation Name: 2R55-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R55

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NSY2

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2537360.375978
FMO2-HF: Nuclear repulsion 2452624.539446
FMO2-HF: Total energy -84735.836531
FMO2-MP2: Total energy -84978.290906


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:PHE)


Summations of interaction energy for fragment #1(A:2:PHE)
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.
-10.555-2.82.656-3.07-7.3420.004
Interaction energy analysis for fragmet #1(A:2:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.012
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].
3A4SER00.000-0.0023.230-3.993-1.6770.056-0.895-1.4780.000
4A5MET00.006-0.0082.653-1.2040.1130.395-0.491-1.222-0.001
5A6ALA00.0290.0293.344-1.4440.1820.279-0.661-1.2440.004
6A7ALA00.0320.0095.495-0.405-0.227-0.001-0.013-0.1640.000
7A8GLN0-0.0250.0097.3740.0040.0040.0000.0000.0000.000
8A9MET0-0.005-0.0087.855-0.004-0.0040.0000.0000.0000.000
9A10SER0-0.013-0.0328.6920.0410.0410.0000.0000.0000.000
10A11GLU-1-0.783-0.87910.965-0.061-0.0610.0000.0000.0000.000
11A12ALA00.0150.00513.1180.0240.0240.0000.0000.0000.000
12A13VAL0-0.045-0.01112.7520.0240.0240.0000.0000.0000.000
13A14ALA00.0420.01215.3740.0220.0220.0000.0000.0000.000
14A15GLU-1-0.953-0.96417.336-0.120-0.1200.0000.0000.0000.000
15A16LYS10.8170.88817.9210.2770.2770.0000.0000.0000.000
16A17MET0-0.0400.01918.6830.0150.0150.0000.0000.0000.000
17A18LEU0-0.015-0.01221.2000.0160.0160.0000.0000.0000.000
18A19GLN00.0150.00323.3250.0140.0140.0000.0000.0000.000
19A20TYR0-0.035-0.02221.3090.0050.0050.0000.0000.0000.000
20A21ARG10.7580.85825.5820.0780.0780.0000.0000.0000.000
21A22ARG10.8850.94325.4640.0790.0790.0000.0000.0000.000
22A23ASP-1-0.820-0.88128.725-0.098-0.0980.0000.0000.0000.000
23A24THR00.0250.00030.866-0.001-0.0010.0000.0000.0000.000
24A25ALA00.0160.01433.4940.0020.0020.0000.0000.0000.000
25A26GLY00.0090.01032.904-0.006-0.0060.0000.0000.0000.000
26A27TRP0-0.011-0.02127.3520.0000.0000.0000.0000.0000.000
27A28LYS10.8300.91834.1850.0830.0830.0000.0000.0000.000
28A29ILE00.0380.01235.824-0.005-0.0050.0000.0000.0000.000
29A30CYS0-0.089-0.01934.953-0.001-0.0010.0000.0000.0000.000
30A31ARG10.8840.91836.4880.0740.0740.0000.0000.0000.000
31A32GLU-1-0.868-0.94938.055-0.057-0.0570.0000.0000.0000.000
32A33GLY0-0.0340.00439.7380.0000.0000.0000.0000.0000.000
33A34ASN00.004-0.01640.9020.0010.0010.0000.0000.0000.000
34A35GLY0-0.0050.01838.107-0.003-0.0030.0000.0000.0000.000
35A36VAL0-0.038-0.02233.352-0.001-0.0010.0000.0000.0000.000
36A37SER00.0200.01734.7980.0020.0020.0000.0000.0000.000
37A38VAL0-0.025-0.01432.396-0.004-0.0040.0000.0000.0000.000
38A39SER00.0010.00432.5570.0040.0040.0000.0000.0000.000
39A40TRP00.0170.00430.904-0.007-0.0070.0000.0000.0000.000
40A41ARG10.7820.87526.8640.1230.1230.0000.0000.0000.000
41A42PRO00.0410.02429.514-0.006-0.0060.0000.0000.0000.000
42A43SER0-0.018-0.02023.666-0.003-0.0030.0000.0000.0000.000
43A44VAL0-0.012-0.01623.2600.0070.0070.0000.0000.0000.000
44A45GLU-1-0.853-0.91119.510-0.255-0.2550.0000.0000.0000.000
45A46PHE0-0.027-0.01321.283-0.015-0.0150.0000.0000.0000.000
46A47PRO0-0.004-0.00923.6650.0100.0100.0000.0000.0000.000
47A48GLY00.0070.02826.3830.0100.0100.0000.0000.0000.000
48A49ASN0-0.010-0.01327.8370.0030.0030.0000.0000.0000.000
49A50LEU0-0.0130.00823.734-0.009-0.0090.0000.0000.0000.000
50A51TYR00.004-0.03126.3210.0120.0120.0000.0000.0000.000
51A52ARG10.8590.92326.7710.0750.0750.0000.0000.0000.000
52A53GLY00.004-0.00828.4450.0070.0070.0000.0000.0000.000
53A54GLU-1-0.758-0.86129.606-0.070-0.0700.0000.0000.0000.000
54A55GLY00.0530.01432.1800.0020.0020.0000.0000.0000.000
55A56ILE00.0110.02032.674-0.002-0.0020.0000.0000.0000.000
56A57VAL0-0.017-0.01030.4850.0000.0000.0000.0000.0000.000
57A58TYR0-0.029-0.02833.9570.0020.0020.0000.0000.0000.000
58A59GLY00.0450.00733.3850.0010.0010.0000.0000.0000.000
59A60THR0-0.022-0.01331.9170.0000.0000.0000.0000.0000.000
60A61LEU00.0590.02026.757-0.004-0.0040.0000.0000.0000.000
61A62GLU-1-0.932-0.98825.377-0.024-0.0240.0000.0000.0000.000
62A63GLU-1-0.796-0.84426.534-0.035-0.0350.0000.0000.0000.000
63A64VAL0-0.014-0.01927.175-0.007-0.0070.0000.0000.0000.000
64A65TRP00.0460.01418.071-0.014-0.0140.0000.0000.0000.000
65A66ASP-1-0.814-0.90423.070-0.069-0.0690.0000.0000.0000.000
66A67CYS0-0.094-0.03023.837-0.005-0.0050.0000.0000.0000.000
67A68VAL0-0.012-0.03722.250-0.009-0.0090.0000.0000.0000.000
68A69LYS10.7800.91718.6900.0500.0500.0000.0000.0000.000
69A70PRO00.0020.03114.7040.0000.0000.0000.0000.0000.000
70A71ALA00.012-0.04015.161-0.003-0.0030.0000.0000.0000.000
71A72VAL00.0150.03114.8510.0220.0220.0000.0000.0000.000
72A73GLY0-0.011-0.02017.2260.0130.0130.0000.0000.0000.000
73A74GLY00.0260.01218.420-0.003-0.0030.0000.0000.0000.000
74A75LEU00.033-0.00221.7560.0030.0030.0000.0000.0000.000
75A76ARG10.8550.92520.5710.1510.1510.0000.0000.0000.000
76A77VAL0-0.030-0.01521.8860.0020.0020.0000.0000.0000.000
77A78LYS10.9230.97824.3700.0640.0640.0000.0000.0000.000
78A79TRP0-0.020-0.01125.1070.0010.0010.0000.0000.0000.000
79A80ASP-1-0.741-0.85725.137-0.120-0.1200.0000.0000.0000.000
80A81GLU-1-0.787-0.85227.303-0.088-0.0880.0000.0000.0000.000
81A82ASN0-0.091-0.05726.172-0.002-0.0020.0000.0000.0000.000
82A83VAL0-0.009-0.01721.750-0.015-0.0150.0000.0000.0000.000
83A84THR0-0.034-0.02723.8120.0050.0050.0000.0000.0000.000
84A85GLY0-0.001-0.00421.2830.0100.0100.0000.0000.0000.000
85A86PHE0-0.025-0.00115.251-0.016-0.0160.0000.0000.0000.000
86A87GLU-1-0.852-0.92215.090-0.184-0.1840.0000.0000.0000.000
87A88ILE00.016-0.00411.119-0.042-0.0420.0000.0000.0000.000
88A89ILE0-0.024-0.0178.7210.0440.0440.0000.0000.0000.000
89A90GLN00.0240.0252.604-1.908-0.7690.633-0.572-1.2000.002
90A91SER00.011-0.0136.594-0.240-0.2400.0000.0000.0000.000
91A92ILE0-0.069-0.0212.330-1.597-0.4671.295-0.435-1.990-0.001
92A93THR0-0.044-0.0284.8080.2320.281-0.001-0.003-0.0440.000
93A94ASP-1-0.913-0.9567.5070.0020.0020.0000.0000.0000.000
94A95THR00.015-0.00210.436-0.025-0.0250.0000.0000.0000.000
95A96LEU0-0.033-0.0035.777-0.013-0.0130.0000.0000.0000.000
96A97CYS0-0.045-0.0137.348-0.084-0.0840.0000.0000.0000.000
97A98VAL00.0550.0345.163-0.016-0.0160.0000.0000.0000.000
98A99SER0-0.0020.0078.1300.0970.0970.0000.0000.0000.000
99A100ARG10.7950.88011.7980.2080.2080.0000.0000.0000.000
100A101THR00.0230.00914.5140.0390.0390.0000.0000.0000.000
101A102SER0-0.057-0.02117.894-0.006-0.0060.0000.0000.0000.000
102A103THR00.0330.03421.1990.0120.0120.0000.0000.0000.000
103A104PRO0-0.0050.01024.2070.0000.0000.0000.0000.0000.000
104A105SER0-0.006-0.02627.630-0.002-0.0020.0000.0000.0000.000
105A106ALA00.0330.01730.1940.0030.0030.0000.0000.0000.000
106A107ALA0-0.008-0.01331.9290.0020.0020.0000.0000.0000.000
107A108MET00.0290.00734.9940.0010.0010.0000.0000.0000.000
108A109LYS10.9050.94333.9550.0760.0760.0000.0000.0000.000
109A110LEU00.0110.02834.269-0.002-0.0020.0000.0000.0000.000
110A111ILE0-0.0160.01028.409-0.004-0.0040.0000.0000.0000.000
111A112SER00.0400.02128.6580.0010.0010.0000.0000.0000.000
112A113PRO00.0240.00826.073-0.005-0.0050.0000.0000.0000.000
113A114ARG10.8710.94222.4120.1540.1540.0000.0000.0000.000
114A115ASP-1-0.787-0.88718.515-0.238-0.2380.0000.0000.0000.000
115A116PHE0-0.0060.01316.547-0.002-0.0020.0000.0000.0000.000
116A117VAL00.024-0.00110.2700.0190.0190.0000.0000.0000.000
117A118ASP-1-0.812-0.89611.746-0.409-0.4090.0000.0000.0000.000
118A119LEU0-0.046-0.0195.874-0.081-0.0810.0000.0000.0000.000
119A120VAL0-0.008-0.0189.2100.1000.1000.0000.0000.0000.000
120A121LEU00.0090.00710.609-0.022-0.0220.0000.0000.0000.000
121A122VAL0-0.009-0.00212.2750.0180.0180.0000.0000.0000.000
122A123LYS10.8580.92014.5320.0950.0950.0000.0000.0000.000
123A124ARG10.9560.97716.9080.0160.0160.0000.0000.0000.000
124A125TYR00.007-0.01020.1390.0090.0090.0000.0000.0000.000
125A126GLU-1-0.903-0.95523.2210.0180.0180.0000.0000.0000.000
126A127ASP-1-0.876-0.90226.180-0.034-0.0340.0000.0000.0000.000
127A128GLY00.0140.00526.4870.0020.0020.0000.0000.0000.000
128A129THR0-0.047-0.07123.772-0.006-0.0060.0000.0000.0000.000
129A130ILE0-0.0600.00020.3570.0030.0030.0000.0000.0000.000
130A131SER00.000-0.00519.566-0.009-0.0090.0000.0000.0000.000
131A132SER0-0.011-0.02217.177-0.004-0.0040.0000.0000.0000.000
132A133ASN0-0.035-0.02315.0460.0140.0140.0000.0000.0000.000
133A134ALA00.0310.01213.450-0.034-0.0340.0000.0000.0000.000
134A135THR00.012-0.00611.6140.0550.0550.0000.0000.0000.000
135A136HIS0-0.044-0.00411.880-0.079-0.0790.0000.0000.0000.000
136A137VAL0-0.045-0.0346.706-0.060-0.0600.0000.0000.0000.000
137A138GLU-1-0.938-0.9579.498-0.518-0.5180.0000.0000.0000.000
138A139HIS00.033-0.0145.203-0.090-0.0900.0000.0000.0000.000
139A140PRO00.019-0.0017.2140.1490.1490.0000.0000.0000.000
140A141LEU0-0.034-0.0019.7180.1040.1040.0000.0000.0000.000
141A142CYS0-0.084-0.03611.3760.0720.0720.0000.0000.0000.000
142A143PRO00.0760.05513.028-0.035-0.0350.0000.0000.0000.000
143A144PRO00.005-0.01915.3500.0180.0180.0000.0000.0000.000
144A145LYS10.9380.98517.3470.2140.2140.0000.0000.0000.000
145A146PRO00.0160.00220.7780.0030.0030.0000.0000.0000.000
146A147GLY0-0.009-0.01124.5230.0040.0040.0000.0000.0000.000
147A148PHE0-0.056-0.01321.9570.0070.0070.0000.0000.0000.000
148A149VAL0-0.035-0.01223.158-0.002-0.0020.0000.0000.0000.000
149A150ARG10.8250.91814.7200.3350.3350.0000.0000.0000.000
150A151GLY00.0080.00519.6070.0090.0090.0000.0000.0000.000
151A152PHE0-0.013-0.02615.309-0.030-0.0300.0000.0000.0000.000
152A153ASN0-0.019-0.01316.4150.0550.0550.0000.0000.0000.000
153A154HIS00.0650.03416.364-0.057-0.0570.0000.0000.0000.000
154A155PRO00.0060.00316.4890.0110.0110.0000.0000.0000.000
155A156CYS0-0.003-0.00117.5400.0280.0280.0000.0000.0000.000
156A157GLY00.0410.01718.081-0.017-0.0170.0000.0000.0000.000
157A158CYS0-0.056-0.02920.0780.0160.0160.0000.0000.0000.000
158A159PHE00.0350.02621.719-0.004-0.0040.0000.0000.0000.000
159A160CYS0-0.046-0.02024.0970.0030.0030.0000.0000.0000.000
160A161GLU-1-0.693-0.81726.055-0.062-0.0620.0000.0000.0000.000
161A162PRO00.0360.03228.1620.0000.0000.0000.0000.0000.000
162A163LEU00.002-0.00831.148-0.001-0.0010.0000.0000.0000.000
163A164PRO0-0.0060.01634.8240.0020.0020.0000.0000.0000.000
164A165GLY00.009-0.02237.5850.0020.0020.0000.0000.0000.000
165A166GLU-1-0.818-0.90638.042-0.028-0.0280.0000.0000.0000.000
166A167PRO00.0190.01937.261-0.001-0.0010.0000.0000.0000.000
167A168THR0-0.044-0.01636.4970.0000.0000.0000.0000.0000.000
168A169LYS10.7460.86935.5730.0250.0250.0000.0000.0000.000
169A170THR00.0140.00029.2530.0020.0020.0000.0000.0000.000
170A171ASN0-0.066-0.02831.471-0.002-0.0020.0000.0000.0000.000
171A172LEU00.0080.01325.947-0.003-0.0030.0000.0000.0000.000
172A173VAL00.0070.03527.5750.0000.0000.0000.0000.0000.000
173A174THR0-0.010-0.02524.759-0.008-0.0080.0000.0000.0000.000
174A175PHE00.0270.00722.8100.0050.0050.0000.0000.0000.000
175A176PHE0-0.0050.00122.542-0.013-0.0130.0000.0000.0000.000
176A177HIS00.0140.01820.7590.0190.0190.0000.0000.0000.000
177A178THR0-0.005-0.00121.008-0.014-0.0140.0000.0000.0000.000
178A179ASP-1-0.843-0.91021.152-0.191-0.1910.0000.0000.0000.000
179A180LEU0-0.028-0.03722.063-0.010-0.0100.0000.0000.0000.000
180A181SER00.0510.05321.6440.0030.0030.0000.0000.0000.000
181A182GLY0-0.044-0.03224.2390.0140.0140.0000.0000.0000.000
182A183TYR0-0.023-0.02426.239-0.001-0.0010.0000.0000.0000.000
183A184LEU0-0.0080.00028.2950.0090.0090.0000.0000.0000.000
184A185PRO00.0190.01331.399-0.002-0.0020.0000.0000.0000.000
185A186GLN00.0350.00330.969-0.009-0.0090.0000.0000.0000.000
186A187ASN00.0400.01633.995-0.004-0.0040.0000.0000.0000.000
187A188VAL0-0.0200.00033.0850.0020.0020.0000.0000.0000.000
188A189VAL00.0460.01628.9470.0010.0010.0000.0000.0000.000
189A190ASP-1-0.866-0.93531.793-0.107-0.1070.0000.0000.0000.000
190A191SER0-0.067-0.03433.8250.0060.0060.0000.0000.0000.000
191A192PHE0-0.078-0.03827.3970.0060.0060.0000.0000.0000.000
192A193PHE00.0970.03825.5020.0030.0030.0000.0000.0000.000
193A194PRO00.0450.02830.4790.0020.0020.0000.0000.0000.000
194A195ARG10.9120.94733.1620.0790.0790.0000.0000.0000.000
195A196SER0-0.0050.01228.6740.0020.0020.0000.0000.0000.000
196A197MET00.0660.04226.5930.0030.0030.0000.0000.0000.000
197A198THR0-0.012-0.00530.4560.0040.0040.0000.0000.0000.000
198A199ARG10.7500.83132.5610.0810.0810.0000.0000.0000.000
199A200PHE00.0790.05524.5580.0030.0030.0000.0000.0000.000
200A201TYR0-0.031-0.04229.2730.0000.0000.0000.0000.0000.000
201A202ALA0-0.0150.00031.8750.0040.0040.0000.0000.0000.000
202A203ASN0-0.078-0.04430.7230.0000.0000.0000.0000.0000.000
203A204LEU00.0430.02127.7390.0040.0040.0000.0000.0000.000
204A205GLN0-0.015-0.00830.6620.0050.0050.0000.0000.0000.000
205A206LYS10.9070.95034.1380.0540.0540.0000.0000.0000.000
206A207ALA0-0.031-0.01830.3800.0040.0040.0000.0000.0000.000
207A208VAL00.0440.02031.0830.0030.0030.0000.0000.0000.000
208A209LYS10.9490.97133.1430.0390.0390.0000.0000.0000.000
209A210GLN00.0240.02534.1610.0000.0000.0000.0000.0000.000
210A211PHE0-0.024-0.00229.3800.0020.0020.0000.0000.0000.000
211A212HIS0-0.116-0.06434.7900.0030.0030.0000.0000.0000.000
212A213GLU-1-1.010-0.99338.382-0.029-0.0290.0000.0000.0000.000