FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LNM19

Calculation Name: 2R3Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R3Y

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEE3

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 285
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3468501.915699
FMO2-HF: Nuclear repulsion 3363702.73276
FMO2-HF: Total energy -104799.182939
FMO2-MP2: Total energy -105108.216336


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:42:MET)


Summations of interaction energy for fragment #1(A:42:MET)
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.
0.2422.642-0.022-1.127-1.250.005
Interaction energy analysis for fragmet #1(A:42:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.006
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].
3A44PRO00.0010.0083.806-0.6101.790-0.022-1.127-1.2500.005
4A45ALA00.0480.0316.1400.1260.1260.0000.0000.0000.000
5A46SER0-0.012-0.0228.4950.0070.0070.0000.0000.0000.000
6A47TYR00.0760.04311.5240.0090.0090.0000.0000.0000.000
7A48ASN00.0520.02113.7020.0040.0040.0000.0000.0000.000
8A49LEU0-0.0070.01014.7530.0310.0310.0000.0000.0000.000
9A50ALA00.0300.01416.4380.0330.0330.0000.0000.0000.000
10A51VAL00.0190.01018.6810.0230.0230.0000.0000.0000.000
11A52ARG10.8640.91614.6750.5500.5500.0000.0000.0000.000
12A53ARG10.8460.91119.3540.2720.2720.0000.0000.0000.000
13A54ALA00.0400.02022.5080.0180.0180.0000.0000.0000.000
14A55ALA00.0020.01323.5690.0160.0160.0000.0000.0000.000
15A56PRO0-0.006-0.00424.2080.0150.0150.0000.0000.0000.000
16A57ALA00.0030.01127.3630.0120.0120.0000.0000.0000.000
17A58VAL0-0.048-0.00428.0640.0120.0120.0000.0000.0000.000
18A59VAL0-0.018-0.00630.620-0.008-0.0080.0000.0000.0000.000
19A60ASN00.0320.02131.999-0.001-0.0010.0000.0000.0000.000
20A61VAL0-0.012-0.01934.9450.0020.0020.0000.0000.0000.000
21A62TYR0-0.036-0.03935.8730.0000.0000.0000.0000.0000.000
22A63ASN0-0.0030.00941.3390.0020.0020.0000.0000.0000.000
23A64ARG10.8890.91844.4320.0650.0650.0000.0000.0000.000
24A65GLY00.0260.01647.3040.0010.0010.0000.0000.0000.000
25A66LEU0-0.011-0.03250.972-0.001-0.0010.0000.0000.0000.000
26A67ASN0-0.044-0.01954.1530.0020.0020.0000.0000.0000.000
27A68THR0-0.0060.00249.7490.0020.0020.0000.0000.0000.000
28A69ASN0-0.013-0.02151.4940.0020.0020.0000.0000.0000.000
29A70SER00.002-0.02454.5590.0000.0000.0000.0000.0000.000
30A71HIS0-0.041-0.00556.0960.0020.0020.0000.0000.0000.000
31A72ASN0-0.028-0.00855.7190.0010.0010.0000.0000.0000.000
32A73GLN0-0.037-0.00352.1440.0010.0010.0000.0000.0000.000
33A74LEU0-0.013-0.00848.7550.0000.0000.0000.0000.0000.000
34A75GLU-1-0.875-0.92547.449-0.051-0.0510.0000.0000.0000.000
35A76ILE0-0.049-0.03141.8490.0000.0000.0000.0000.0000.000
36A77ARG10.8570.94245.1940.0490.0490.0000.0000.0000.000
37A78THR00.023-0.00442.8130.0010.0010.0000.0000.0000.000
38A79LEU0-0.030-0.00936.752-0.002-0.0020.0000.0000.0000.000
39A80GLY0-0.014-0.00436.6860.0030.0030.0000.0000.0000.000
40A81SER0-0.033-0.01532.928-0.009-0.0090.0000.0000.0000.000
41A82GLY00.0530.03934.3790.0080.0080.0000.0000.0000.000
42A83VAL0-0.027-0.00431.846-0.011-0.0110.0000.0000.0000.000
43A84ILE0-0.004-0.00232.9980.0080.0080.0000.0000.0000.000
44A85MET0-0.0030.00233.582-0.008-0.0080.0000.0000.0000.000
45A86ASP-1-0.762-0.85935.267-0.081-0.0810.0000.0000.0000.000
46A87GLN00.0600.00935.0470.0000.0000.0000.0000.0000.000
47A88ARG10.8170.89938.0420.0710.0710.0000.0000.0000.000
48A89GLY00.0230.01239.5330.0030.0030.0000.0000.0000.000
49A90TYR0-0.033-0.00840.4960.0020.0020.0000.0000.0000.000
50A91ILE00.005-0.00537.106-0.006-0.0060.0000.0000.0000.000
51A92ILE00.0110.02337.0110.0060.0060.0000.0000.0000.000
52A93THR00.006-0.02237.362-0.004-0.0040.0000.0000.0000.000
53A94ASN00.024-0.00738.1030.0000.0000.0000.0000.0000.000
54A95LYS10.8470.91240.6860.0400.0400.0000.0000.0000.000
55A96HIS0-0.066-0.06939.570-0.002-0.0020.0000.0000.0000.000
56A97VAL0-0.024-0.00139.1180.0000.0000.0000.0000.0000.000
57A98ILE0-0.041-0.02542.545-0.001-0.0010.0000.0000.0000.000
58A99ASN00.0340.03845.1820.0010.0010.0000.0000.0000.000
59A100ASP-1-0.918-0.96648.435-0.041-0.0410.0000.0000.0000.000
60A101ALA0-0.0230.01047.6520.0000.0000.0000.0000.0000.000
61A102ASP-1-0.815-0.89649.732-0.043-0.0430.0000.0000.0000.000
62A103GLN00.006-0.01946.973-0.002-0.0020.0000.0000.0000.000
63A104ILE0-0.0030.01443.059-0.001-0.0010.0000.0000.0000.000
64A105ILE0-0.024-0.00340.391-0.001-0.0010.0000.0000.0000.000
65A106VAL00.0080.00237.312-0.001-0.0010.0000.0000.0000.000
66A107ALA0-0.0050.00135.6370.0000.0000.0000.0000.0000.000
67A108LEU0-0.011-0.01332.742-0.003-0.0030.0000.0000.0000.000
68A109GLN0-0.018-0.02127.652-0.003-0.0030.0000.0000.0000.000
69A110ASP-1-0.870-0.91529.318-0.149-0.1490.0000.0000.0000.000
70A111GLY00.0210.01030.6470.0020.0020.0000.0000.0000.000
71A112ARG10.7550.86733.4670.1360.1360.0000.0000.0000.000
72A113VAL00.015-0.00536.360-0.002-0.0020.0000.0000.0000.000
73A114PHE0-0.028-0.02037.5900.0020.0020.0000.0000.0000.000
74A115GLU-1-0.831-0.89041.811-0.063-0.0630.0000.0000.0000.000
75A116ALA0-0.068-0.04742.608-0.001-0.0010.0000.0000.0000.000
76A117LEU00.0010.00944.6760.0030.0030.0000.0000.0000.000
77A118LEU00.0290.00446.134-0.003-0.0030.0000.0000.0000.000
78A119VAL0-0.038-0.03346.0740.0020.0020.0000.0000.0000.000
79A120GLY00.0680.03447.4480.0030.0030.0000.0000.0000.000
80A121SER0-0.058-0.03246.415-0.002-0.0020.0000.0000.0000.000
81A122ASP-1-0.698-0.81445.887-0.036-0.0360.0000.0000.0000.000
82A123SER0-0.005-0.01746.323-0.002-0.0020.0000.0000.0000.000
83A124LEU0-0.0170.00347.0470.0000.0000.0000.0000.0000.000
84A125THR0-0.020-0.03742.4630.0000.0000.0000.0000.0000.000
85A126ASP-1-0.751-0.85442.162-0.051-0.0510.0000.0000.0000.000
86A127LEU00.0050.03238.868-0.004-0.0040.0000.0000.0000.000
87A128ALA00.019-0.01041.8890.0040.0040.0000.0000.0000.000
88A129VAL0-0.0150.00041.796-0.004-0.0040.0000.0000.0000.000
89A130LEU0-0.0030.00540.8120.0030.0030.0000.0000.0000.000
90A131LYS10.8840.93142.6250.0680.0680.0000.0000.0000.000
91A132ILE00.0220.04338.3650.0030.0030.0000.0000.0000.000
92A133ASN0-0.033-0.03242.9930.0020.0020.0000.0000.0000.000
93A134ALA00.0160.00839.517-0.001-0.0010.0000.0000.0000.000
94A135THR00.0080.00441.2910.0010.0010.0000.0000.0000.000
95A136GLY00.001-0.01238.670-0.003-0.0030.0000.0000.0000.000
96A137GLY00.0040.02436.143-0.006-0.0060.0000.0000.0000.000
97A138LEU0-0.004-0.00734.827-0.002-0.0020.0000.0000.0000.000
98A139PRO00.0000.02029.867-0.001-0.0010.0000.0000.0000.000
99A140THR0-0.007-0.01530.8080.0090.0090.0000.0000.0000.000
100A141ILE00.008-0.00428.274-0.012-0.0120.0000.0000.0000.000
101A142PRO0-0.0140.00225.0460.0090.0090.0000.0000.0000.000
102A143ILE00.0430.01728.0240.0040.0040.0000.0000.0000.000
103A144ASN0-0.038-0.02726.2630.0080.0080.0000.0000.0000.000
104A145ALA00.0360.00329.5840.0040.0040.0000.0000.0000.000
105A146ARG10.9480.96831.1230.0610.0610.0000.0000.0000.000
106A147ARG10.8030.88123.6500.1030.1030.0000.0000.0000.000
107A148VAL0-0.002-0.00429.3720.0000.0000.0000.0000.0000.000
108A149PRO0-0.023-0.02328.2440.0010.0010.0000.0000.0000.000
109A150HIS0-0.0010.00926.5010.0110.0110.0000.0000.0000.000
110A151ILE0-0.012-0.00727.170-0.005-0.0050.0000.0000.0000.000
111A152GLY00.0060.00325.0560.0070.0070.0000.0000.0000.000
112A153ASP-1-0.898-0.93922.890-0.055-0.0550.0000.0000.0000.000
113A154VAL0-0.011-0.00817.863-0.003-0.0030.0000.0000.0000.000
114A155VAL0-0.075-0.04621.095-0.012-0.0120.0000.0000.0000.000
115A156LEU0-0.025-0.02318.811-0.010-0.0100.0000.0000.0000.000
116A157ALA00.0180.01322.9840.0060.0060.0000.0000.0000.000
117A158ILE0-0.052-0.03423.786-0.015-0.0150.0000.0000.0000.000
118A159GLY00.029-0.00626.9430.0130.0130.0000.0000.0000.000
119A160ASN00.0090.00929.179-0.016-0.0160.0000.0000.0000.000
120A161PRO00.0220.02929.0740.0090.0090.0000.0000.0000.000
121A162TYR0-0.025-0.05632.241-0.003-0.0030.0000.0000.0000.000
122A163ASN0-0.0080.01034.112-0.002-0.0020.0000.0000.0000.000
123A164LEU0-0.0100.00329.656-0.001-0.0010.0000.0000.0000.000
124A165GLY00.0340.02929.297-0.009-0.0090.0000.0000.0000.000
125A166GLN0-0.057-0.04525.973-0.014-0.0140.0000.0000.0000.000
126A167THR0-0.038-0.01424.821-0.011-0.0110.0000.0000.0000.000
127A168ILE0-0.028-0.03020.5420.0020.0020.0000.0000.0000.000
128A169THR0-0.020-0.01222.350-0.006-0.0060.0000.0000.0000.000
129A170GLN0-0.019-0.02818.171-0.014-0.0140.0000.0000.0000.000
130A171GLY00.0660.03521.5160.0120.0120.0000.0000.0000.000
131A172ILE0-0.0100.00121.964-0.011-0.0110.0000.0000.0000.000
132A173ILE0-0.0340.01324.1910.0000.0000.0000.0000.0000.000
133A174SER00.043-0.00427.5170.0060.0060.0000.0000.0000.000
134A175ALA0-0.034-0.02029.6870.0070.0070.0000.0000.0000.000
135A176THR0-0.002-0.00532.420-0.005-0.0050.0000.0000.0000.000
136A177GLY00.0080.00234.9060.0030.0030.0000.0000.0000.000
137A178ARG10.8870.94835.6600.0150.0150.0000.0000.0000.000
138A179ILE00.0530.02039.120-0.003-0.0030.0000.0000.0000.000
139A180GLY0-0.0120.00039.365-0.002-0.0020.0000.0000.0000.000
140A181LEU0-0.011-0.00840.2500.0010.0010.0000.0000.0000.000
141A182ASN0-0.004-0.00543.3110.0000.0000.0000.0000.0000.000
142A183PRO0-0.0020.00746.2810.0020.0020.0000.0000.0000.000
143A184THR00.0160.00948.1860.0010.0010.0000.0000.0000.000
144A185GLY00.0440.01146.300-0.001-0.0010.0000.0000.0000.000
145A186ARG10.9720.99044.9250.0150.0150.0000.0000.0000.000
146A187GLN0-0.012-0.00942.9840.0000.0000.0000.0000.0000.000
147A188ASN0-0.046-0.01238.959-0.004-0.0040.0000.0000.0000.000
148A189PHE00.0460.02436.875-0.004-0.0040.0000.0000.0000.000
149A190LEU0-0.043-0.02730.2250.0050.0050.0000.0000.0000.000
150A191GLN00.0540.02132.4590.0000.0000.0000.0000.0000.000
151A192THR0-0.053-0.04926.955-0.003-0.0030.0000.0000.0000.000
152A193ASP-1-0.788-0.87825.615-0.033-0.0330.0000.0000.0000.000
153A194ALA0-0.043-0.00925.025-0.003-0.0030.0000.0000.0000.000
154A195SER0-0.022-0.02025.7230.0030.0030.0000.0000.0000.000
155A196ILE0-0.0020.01827.646-0.012-0.0120.0000.0000.0000.000
156A197ASN00.0350.02630.2160.0110.0110.0000.0000.0000.000
157A198HIS00.0950.05433.188-0.004-0.0040.0000.0000.0000.000
158A199GLY00.0670.04334.865-0.005-0.0050.0000.0000.0000.000
159A200ASN0-0.021-0.02229.013-0.002-0.0020.0000.0000.0000.000
160A201SER00.0170.01732.953-0.003-0.0030.0000.0000.0000.000
161A202GLY00.0090.01935.973-0.003-0.0030.0000.0000.0000.000
162A203GLY00.0170.00831.893-0.004-0.0040.0000.0000.0000.000
163A204ALA00.004-0.00528.3660.0060.0060.0000.0000.0000.000
164A205LEU00.0140.03626.481-0.007-0.0070.0000.0000.0000.000
165A206VAL00.016-0.00222.9590.0060.0060.0000.0000.0000.000
166A207ASN00.0970.03222.687-0.018-0.0180.0000.0000.0000.000
167A208SER00.0450.01017.161-0.017-0.0170.0000.0000.0000.000
168A209LEU0-0.051-0.02718.133-0.040-0.0400.0000.0000.0000.000
169A210GLY00.017-0.00120.331-0.008-0.0080.0000.0000.0000.000
170A211GLU-1-0.783-0.82022.597-0.109-0.1090.0000.0000.0000.000
171A212LEU00.0050.00625.5950.0020.0020.0000.0000.0000.000
172A213MET0-0.040-0.01726.4310.0110.0110.0000.0000.0000.000
173A214GLY00.0290.00129.4120.0110.0110.0000.0000.0000.000
174A215ILE0-0.0240.00531.373-0.009-0.0090.0000.0000.0000.000
175A216ASN0-0.003-0.01029.1790.0120.0120.0000.0000.0000.000
176A217THR0-0.024-0.02333.3310.0000.0000.0000.0000.0000.000
177A218LEU00.0270.00635.9640.0010.0010.0000.0000.0000.000
178A219SER00.0060.00534.3730.0010.0010.0000.0000.0000.000
179A220PHE0-0.0310.00035.7940.0020.0020.0000.0000.0000.000
180A221ASP-1-0.831-0.93936.122-0.042-0.0420.0000.0000.0000.000
181A222LYS10.8820.93638.4280.0260.0260.0000.0000.0000.000
182A223SER00.0720.05841.0380.0010.0010.0000.0000.0000.000
183A224ASN0-0.203-0.12542.706-0.002-0.0020.0000.0000.0000.000
184A225ASP-1-0.876-0.94645.456-0.007-0.0070.0000.0000.0000.000
185A226GLY00.0010.01745.0870.0020.0020.0000.0000.0000.000
186A227GLU-1-0.954-0.96740.175-0.003-0.0030.0000.0000.0000.000
187A228THR0-0.007-0.01636.690-0.002-0.0020.0000.0000.0000.000
188A229PRO0-0.045-0.00936.3360.0020.0020.0000.0000.0000.000
189A230GLU-1-0.916-0.95129.064-0.015-0.0150.0000.0000.0000.000
190A231GLY0-0.002-0.00129.6420.0040.0040.0000.0000.0000.000
191A232ILE0-0.048-0.02030.3060.0020.0020.0000.0000.0000.000
192A233GLY00.0350.03832.034-0.002-0.0020.0000.0000.0000.000
193A234PHE0-0.014-0.01733.0390.0030.0030.0000.0000.0000.000
194A235ALA00.0350.00632.252-0.006-0.0060.0000.0000.0000.000
195A236ILE00.0140.03334.2770.0050.0050.0000.0000.0000.000
196A237PRO00.0160.01333.989-0.007-0.0070.0000.0000.0000.000
197A238PHE00.009-0.00531.2710.0020.0020.0000.0000.0000.000
198A239GLN0-0.0160.00434.3630.0010.0010.0000.0000.0000.000
199A240LEU0-0.0130.00136.8550.0020.0020.0000.0000.0000.000
200A241ALA00.0360.01136.5800.0010.0010.0000.0000.0000.000
201A242THR00.0190.00136.905-0.001-0.0010.0000.0000.0000.000
202A243LYS10.9530.97939.0480.0410.0410.0000.0000.0000.000
203A244ILE0-0.014-0.00342.0580.0020.0020.0000.0000.0000.000
204A245MET00.0140.00639.580-0.001-0.0010.0000.0000.0000.000
205A246ASP-1-0.892-0.95742.045-0.059-0.0590.0000.0000.0000.000
206A247LYS10.7640.85444.4550.0380.0380.0000.0000.0000.000
207A248LEU0-0.0400.00644.6370.0020.0020.0000.0000.0000.000
208A249ILE0-0.054-0.01542.7850.0000.0000.0000.0000.0000.000
209A250ARG10.8250.92747.3130.0440.0440.0000.0000.0000.000
210A251ASP-1-0.885-0.95750.063-0.037-0.0370.0000.0000.0000.000
211A252GLY00.0270.03150.6110.0010.0010.0000.0000.0000.000
212A253ARG10.7690.82850.8510.0330.0330.0000.0000.0000.000
213A254VAL0-0.038-0.01548.0760.0000.0000.0000.0000.0000.000
214A255ILE0-0.034-0.00750.4530.0020.0020.0000.0000.0000.000
215A256ARG10.8140.88647.0430.0340.0340.0000.0000.0000.000
216A257GLY00.0160.03853.7660.0010.0010.0000.0000.0000.000
217A258TYR00.001-0.00256.2870.0000.0000.0000.0000.0000.000
218A259ILE0-0.004-0.01058.6490.0000.0000.0000.0000.0000.000
219A260GLY00.011-0.00861.0550.0000.0000.0000.0000.0000.000
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