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: 898LY

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2535528.096426
FMO2-HF: Nuclear repulsion 2450793.575944
FMO2-HF: Total energy -84734.520482
FMO2-MP2: Total energy -84976.987253


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.
-8.467-1.8642.56-2.913-6.2520.004
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 : 0.037 / q_NPA : 0.009
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].
3A4SER00.007-0.0023.220-4.075-1.7100.051-0.985-1.4320.000
4A5MET00.016-0.0042.843-0.8200.3060.141-0.346-0.9220.000
5A6ALA00.0250.0303.685-1.0280.3310.076-0.523-0.9110.003
6A7ALA00.0280.0095.697-0.264-0.097-0.001-0.010-0.1550.000
7A8GLN0-0.0250.0067.1760.0340.0340.0000.0000.0000.000
8A9MET0-0.001-0.0037.7990.0110.0110.0000.0000.0000.000
9A10SER0-0.023-0.0359.2060.0520.0520.0000.0000.0000.000
10A11GLU-1-0.851-0.93211.396-0.029-0.0290.0000.0000.0000.000
11A12ALA00.0180.00813.1290.0230.0230.0000.0000.0000.000
12A13VAL0-0.057-0.01613.0940.0260.0260.0000.0000.0000.000
13A14ALA00.0340.00615.8040.0220.0220.0000.0000.0000.000
14A15GLU-1-0.944-0.96416.966-0.127-0.1270.0000.0000.0000.000
15A16LYS10.8620.92717.2810.2800.2800.0000.0000.0000.000
16A17MET0-0.0280.01619.0620.0130.0130.0000.0000.0000.000
17A18LEU0-0.020-0.01121.6180.0150.0150.0000.0000.0000.000
18A19GLN00.001-0.01123.7200.0110.0110.0000.0000.0000.000
19A20TYR0-0.019-0.01121.6940.0030.0030.0000.0000.0000.000
20A21ARG10.7890.88425.9910.0670.0670.0000.0000.0000.000
21A22ARG10.9060.95326.1700.0660.0660.0000.0000.0000.000
22A23ASP-1-0.867-0.92128.617-0.091-0.0910.0000.0000.0000.000
23A24THR00.019-0.00831.2640.0000.0000.0000.0000.0000.000
24A25ALA00.0190.01933.7610.0020.0020.0000.0000.0000.000
25A26GLY0-0.032-0.01233.111-0.005-0.0050.0000.0000.0000.000
26A27TRP0-0.022-0.03327.932-0.001-0.0010.0000.0000.0000.000
27A28LYS10.8850.95434.5290.0780.0780.0000.0000.0000.000
28A29ILE00.0190.01536.187-0.005-0.0050.0000.0000.0000.000
29A30CYS0-0.106-0.02834.484-0.001-0.0010.0000.0000.0000.000
30A31ARG10.8900.94336.8670.0680.0680.0000.0000.0000.000
31A32GLU-1-0.857-0.94738.399-0.052-0.0520.0000.0000.0000.000
32A33GLY0-0.0390.00140.0760.0000.0000.0000.0000.0000.000
33A34ASN00.013-0.01241.2340.0010.0010.0000.0000.0000.000
34A35GLY0-0.0190.01238.424-0.002-0.0020.0000.0000.0000.000
35A36VAL0-0.038-0.02033.661-0.001-0.0010.0000.0000.0000.000
36A37SER00.0220.01635.1430.0020.0020.0000.0000.0000.000
37A38VAL0-0.031-0.01532.689-0.004-0.0040.0000.0000.0000.000
38A39SER00.0210.00332.9170.0030.0030.0000.0000.0000.000
39A40TRP00.0210.01131.267-0.007-0.0070.0000.0000.0000.000
40A41ARG10.8600.93026.9930.1170.1170.0000.0000.0000.000
41A42PRO00.0420.02629.608-0.006-0.0060.0000.0000.0000.000
42A43SER0-0.0010.02223.5000.0000.0000.0000.0000.0000.000
43A44VAL00.001-0.01523.2940.0070.0070.0000.0000.0000.000
44A45GLU-1-0.910-0.95119.414-0.254-0.2540.0000.0000.0000.000
45A46PHE0-0.039-0.02321.299-0.015-0.0150.0000.0000.0000.000
46A47PRO0-0.004-0.00523.6830.0100.0100.0000.0000.0000.000
47A48GLY00.0010.02326.3990.0100.0100.0000.0000.0000.000
48A49ASN0-0.010-0.01127.8570.0010.0010.0000.0000.0000.000
49A50LEU0-0.0100.00724.023-0.008-0.0080.0000.0000.0000.000
50A51TYR0-0.002-0.03126.6680.0110.0110.0000.0000.0000.000
51A52ARG10.8920.92527.1290.0660.0660.0000.0000.0000.000
52A53GLY0-0.001-0.01128.8060.0060.0060.0000.0000.0000.000
53A54GLU-1-0.819-0.88729.970-0.059-0.0590.0000.0000.0000.000
54A55GLY00.0480.00932.5440.0020.0020.0000.0000.0000.000
55A56ILE00.0040.01833.016-0.001-0.0010.0000.0000.0000.000
56A57VAL0-0.013-0.01030.8330.0000.0000.0000.0000.0000.000
57A58TYR0-0.043-0.03534.2680.0040.0040.0000.0000.0000.000
58A59GLY00.0590.01633.7960.0010.0010.0000.0000.0000.000
59A60THR00.0000.03931.9360.0000.0000.0000.0000.0000.000
60A61LEU00.0770.02526.994-0.004-0.0040.0000.0000.0000.000
61A62GLU-1-0.931-0.98725.643-0.008-0.0080.0000.0000.0000.000
62A63GLU-1-0.815-0.89026.894-0.024-0.0240.0000.0000.0000.000
63A64VAL0-0.024-0.02127.297-0.006-0.0060.0000.0000.0000.000
64A65TRP00.011-0.01118.497-0.012-0.0120.0000.0000.0000.000
65A66ASP-1-0.888-0.94323.446-0.043-0.0430.0000.0000.0000.000
66A67CYS0-0.148-0.05424.131-0.005-0.0050.0000.0000.0000.000
67A68VAL0-0.025-0.04322.444-0.009-0.0090.0000.0000.0000.000
68A69LYS10.9090.98518.6090.0350.0350.0000.0000.0000.000
69A70PRO00.0160.03214.969-0.003-0.0030.0000.0000.0000.000
70A71ALA00.002-0.04115.1300.0000.0000.0000.0000.0000.000
71A72VAL00.0090.01414.8220.0180.0180.0000.0000.0000.000
72A73GLY00.003-0.00217.1820.0100.0100.0000.0000.0000.000
73A74GLY00.0020.00018.504-0.001-0.0010.0000.0000.0000.000
74A75LEU00.0440.00521.9210.0000.0000.0000.0000.0000.000
75A76ARG10.9470.98720.4190.1340.1340.0000.0000.0000.000
76A77VAL0-0.003-0.00922.0080.0000.0000.0000.0000.0000.000
77A78LYS10.9120.97224.4850.0530.0530.0000.0000.0000.000
78A79TRP0-0.028-0.02125.4200.0000.0000.0000.0000.0000.000
79A80ASP-1-0.843-0.92825.258-0.103-0.1030.0000.0000.0000.000
80A81GLU-1-0.949-0.96927.467-0.080-0.0800.0000.0000.0000.000
81A82ASN0-0.034-0.02825.975-0.002-0.0020.0000.0000.0000.000
82A83VAL0-0.028-0.01722.039-0.014-0.0140.0000.0000.0000.000
83A84THR0-0.029-0.02623.9840.0040.0040.0000.0000.0000.000
84A85GLY0-0.009-0.01021.3180.0090.0090.0000.0000.0000.000
85A86PHE0-0.036-0.00215.696-0.017-0.0170.0000.0000.0000.000
86A87GLU-1-0.906-0.95214.970-0.163-0.1630.0000.0000.0000.000
87A88ILE0-0.022-0.02011.188-0.034-0.0340.0000.0000.0000.000
88A89ILE0-0.003-0.0098.0670.0320.0320.0000.0000.0000.000
89A90GLN00.0120.0242.109-1.102-0.6632.069-0.799-1.7100.002
90A91SER00.012-0.0156.642-0.156-0.1560.0000.0000.0000.000
91A92ILE0-0.060-0.0152.800-1.183-0.0770.225-0.248-1.084-0.001
92A93THR0-0.047-0.0255.0000.1770.218-0.001-0.002-0.0380.000
93A94ASP-1-0.883-0.9537.8370.0400.0400.0000.0000.0000.000
94A95THR0-0.026-0.01710.876-0.034-0.0340.0000.0000.0000.000
95A96LEU0-0.032-0.0046.867-0.022-0.0220.0000.0000.0000.000
96A97CYS0-0.042-0.0067.554-0.042-0.0420.0000.0000.0000.000
97A98VAL00.0470.0265.269-0.023-0.0230.0000.0000.0000.000
98A99SER0-0.0090.0038.2940.0520.0520.0000.0000.0000.000
99A100ARG10.9180.97011.9240.1850.1850.0000.0000.0000.000
100A101THR00.005-0.00314.5900.0380.0380.0000.0000.0000.000
101A102SER0-0.067-0.02718.014-0.007-0.0070.0000.0000.0000.000
102A103THR00.0210.03621.2850.0110.0110.0000.0000.0000.000
103A104PRO0-0.0020.00724.3330.0000.0000.0000.0000.0000.000
104A105SER00.004-0.02627.731-0.005-0.0050.0000.0000.0000.000
105A106ALA00.0460.02630.3520.0030.0030.0000.0000.0000.000
106A107ALA0-0.024-0.01932.0830.0010.0010.0000.0000.0000.000
107A108MET00.015-0.00235.1670.0010.0010.0000.0000.0000.000
108A109LYS10.9150.95034.0640.0680.0680.0000.0000.0000.000
109A110LEU00.0150.02834.370-0.002-0.0020.0000.0000.0000.000
110A111ILE0-0.0190.01028.478-0.004-0.0040.0000.0000.0000.000
111A112SER00.0320.00828.1010.0010.0010.0000.0000.0000.000
112A113PRO00.0270.01726.115-0.006-0.0060.0000.0000.0000.000
113A114ARG10.8700.94222.6780.1410.1410.0000.0000.0000.000
114A115ASP-1-0.790-0.88518.317-0.224-0.2240.0000.0000.0000.000
115A116PHE0-0.0110.00816.782-0.005-0.0050.0000.0000.0000.000
116A117VAL00.0310.00710.4290.0220.0220.0000.0000.0000.000
117A118ASP-1-0.821-0.90111.991-0.365-0.3650.0000.0000.0000.000
118A119LEU0-0.046-0.0216.312-0.059-0.0590.0000.0000.0000.000
119A120VAL0-0.010-0.0169.5380.0760.0760.0000.0000.0000.000
120A121LEU00.0100.00511.1310.0010.0010.0000.0000.0000.000
121A122VAL0-0.020-0.00912.7080.0030.0030.0000.0000.0000.000
122A123LYS10.9170.96315.0900.0770.0770.0000.0000.0000.000
123A124ARG10.9630.96717.494-0.010-0.0100.0000.0000.0000.000
124A125TYR0-0.010-0.01220.6630.0070.0070.0000.0000.0000.000
125A126GLU-1-0.904-0.96123.8180.0280.0280.0000.0000.0000.000
126A127ASP-1-0.879-0.87926.769-0.024-0.0240.0000.0000.0000.000
127A128GLY00.0140.00727.0230.0010.0010.0000.0000.0000.000
128A129THR0-0.062-0.09624.409-0.004-0.0040.0000.0000.0000.000
129A130ILE0-0.0470.00420.7990.0050.0050.0000.0000.0000.000
130A131SER0-0.0060.01019.797-0.011-0.0110.0000.0000.0000.000
131A132SER00.010-0.01317.5300.0010.0010.0000.0000.0000.000
132A133ASN0-0.034-0.03015.4580.0030.0030.0000.0000.0000.000
133A134ALA00.0310.00913.805-0.023-0.0230.0000.0000.0000.000
134A135THR00.009-0.00311.8170.0460.0460.0000.0000.0000.000
135A136HIS0-0.0340.00312.191-0.071-0.0710.0000.0000.0000.000
136A137VAL0-0.019-0.0216.654-0.058-0.0580.0000.0000.0000.000
137A138GLU-1-0.948-0.9639.507-0.495-0.4950.0000.0000.0000.000
138A139HIS00.044-0.0075.516-0.143-0.1430.0000.0000.0000.000
139A140PRO00.014-0.0027.2110.1440.1440.0000.0000.0000.000
140A141LEU0-0.042-0.0119.5260.0990.0990.0000.0000.0000.000
141A142CYS0-0.073-0.03511.1530.0640.0640.0000.0000.0000.000
142A143PRO00.0640.04412.916-0.033-0.0330.0000.0000.0000.000
143A144PRO0-0.006-0.02315.3720.0170.0170.0000.0000.0000.000
144A145LYS10.9730.99717.8690.1770.1770.0000.0000.0000.000
145A146PRO00.005-0.00220.7050.0020.0020.0000.0000.0000.000
146A147GLY00.000-0.00924.4410.0040.0040.0000.0000.0000.000
147A148PHE0-0.056-0.01321.9530.0060.0060.0000.0000.0000.000
148A149VAL0-0.024-0.00523.081-0.003-0.0030.0000.0000.0000.000
149A150ARG10.8160.91015.2750.3010.3010.0000.0000.0000.000
150A151GLY00.0030.00319.7250.0070.0070.0000.0000.0000.000
151A152PHE0-0.009-0.02615.184-0.028-0.0280.0000.0000.0000.000
152A153ASN0-0.021-0.00816.6020.0500.0500.0000.0000.0000.000
153A154HIS00.0610.02216.567-0.053-0.0530.0000.0000.0000.000
154A155PRO00.0100.00616.8540.0130.0130.0000.0000.0000.000
155A156CYS0-0.0080.00217.9350.0270.0270.0000.0000.0000.000
156A157GLY00.0230.01518.448-0.012-0.0120.0000.0000.0000.000
157A158CYS0-0.054-0.02820.4300.0100.0100.0000.0000.0000.000
158A159PHE00.0310.02322.083-0.001-0.0010.0000.0000.0000.000
159A160CYS0-0.035-0.01324.2470.0010.0010.0000.0000.0000.000
160A161GLU-1-0.713-0.85226.563-0.049-0.0490.0000.0000.0000.000
161A162PRO00.0350.03428.6930.0000.0000.0000.0000.0000.000
162A163LEU0-0.0150.00631.683-0.001-0.0010.0000.0000.0000.000
163A164PRO00.0030.01535.3690.0020.0020.0000.0000.0000.000
164A165GLY00.003-0.03138.1350.0020.0020.0000.0000.0000.000
165A166GLU-1-0.825-0.92738.613-0.022-0.0220.0000.0000.0000.000
166A167PRO00.0180.00537.6810.0000.0000.0000.0000.0000.000
167A168THR0-0.064-0.04136.9900.0000.0000.0000.0000.0000.000
168A169LYS10.7910.92836.1030.0180.0180.0000.0000.0000.000
169A170THR00.023-0.00629.7510.0020.0020.0000.0000.0000.000
170A171ASN0-0.057-0.01031.524-0.001-0.0010.0000.0000.0000.000
171A172LEU0-0.0070.00526.207-0.001-0.0010.0000.0000.0000.000
172A173VAL00.0100.02427.896-0.001-0.0010.0000.0000.0000.000
173A174THR00.015-0.00125.117-0.004-0.0040.0000.0000.0000.000
174A175PHE00.0290.00823.1880.0030.0030.0000.0000.0000.000
175A176PHE0-0.031-0.00722.888-0.010-0.0100.0000.0000.0000.000
176A177HIS00.011-0.01720.9580.0150.0150.0000.0000.0000.000
177A178THR00.0030.00421.318-0.014-0.0140.0000.0000.0000.000
178A179ASP-1-0.851-0.91621.108-0.184-0.1840.0000.0000.0000.000
179A180LEU0-0.025-0.03422.153-0.009-0.0090.0000.0000.0000.000
180A181SER00.0460.05821.8870.0040.0040.0000.0000.0000.000
181A182GLY0-0.048-0.04124.2910.0140.0140.0000.0000.0000.000
182A183TYR0-0.023-0.02426.280-0.002-0.0020.0000.0000.0000.000
183A184LEU0-0.010-0.00428.7280.0090.0090.0000.0000.0000.000
184A185PRO00.0190.01431.435-0.002-0.0020.0000.0000.0000.000
185A186GLN00.0970.03831.099-0.007-0.0070.0000.0000.0000.000
186A187ASN00.0240.01034.035-0.004-0.0040.0000.0000.0000.000
187A188VAL00.0090.02732.9000.0020.0020.0000.0000.0000.000
188A189VAL00.0330.01229.1250.0010.0010.0000.0000.0000.000
189A190ASP-1-0.904-0.95832.029-0.099-0.0990.0000.0000.0000.000
190A191SER0-0.080-0.05734.0960.0050.0050.0000.0000.0000.000
191A192PHE0-0.072-0.03827.7060.0050.0050.0000.0000.0000.000
192A193PHE00.0980.03725.9260.0040.0040.0000.0000.0000.000
193A194PRO00.0310.02230.7550.0020.0020.0000.0000.0000.000
194A195ARG10.9100.94233.4580.0710.0710.0000.0000.0000.000
195A196SER00.0140.01428.5520.0040.0040.0000.0000.0000.000
196A197MET00.0420.04227.3500.0020.0020.0000.0000.0000.000
197A198THR0-0.033-0.02330.7510.0050.0050.0000.0000.0000.000
198A199ARG10.9360.96332.8290.0700.0700.0000.0000.0000.000
199A200PHE00.0470.04025.2880.0020.0020.0000.0000.0000.000
200A201TYR0-0.018-0.04529.5440.0000.0000.0000.0000.0000.000
201A202ALA0-0.0080.00532.1600.0040.0040.0000.0000.0000.000
202A203ASN0-0.075-0.04131.025-0.001-0.0010.0000.0000.0000.000
203A204LEU00.0510.02228.0460.0040.0040.0000.0000.0000.000
204A205GLN0-0.004-0.00630.9120.0040.0040.0000.0000.0000.000
205A206LYS10.9140.96734.3960.0470.0470.0000.0000.0000.000
206A207ALA0-0.011-0.00530.6190.0030.0030.0000.0000.0000.000
207A208VAL00.0320.01531.4150.0030.0030.0000.0000.0000.000
208A209LYS10.9450.96433.3740.0320.0320.0000.0000.0000.000
209A210GLN0-0.002-0.00734.150-0.001-0.0010.0000.0000.0000.000
210A211PHE0-0.0200.00229.7780.0010.0010.0000.0000.0000.000
211A212HIS0-0.103-0.04535.4500.0020.0020.0000.0000.0000.000
212A213GLU-1-1.000-0.98738.689-0.023-0.0230.0000.0000.0000.000