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: 6Y9LZ

Calculation Name: 3LRA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LRA

Chain ID: A

ChEMBL ID:

UniProt ID: Q12959

Base Structure: X-ray

Registration Date: 2023-09-24

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 254
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3197822.050601
FMO2-HF: Nuclear repulsion 3097264.892481
FMO2-HF: Total energy -100557.15812
FMO2-MP2: Total energy -100856.665594


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:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-5.535-1.2421.084-2.006-3.373-0.01
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : -0.007
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].
3A4ARG10.8780.9193.8090.7392.121-0.012-0.467-0.9040.003
4A5LYS10.8740.9265.4681.2281.2280.0000.0000.0000.000
5A6GLN00.0090.0028.6800.0880.0880.0000.0000.0000.000
6A7ASP-1-0.771-0.8527.577-0.876-0.8760.0000.0000.0000.000
7A8THR0-0.004-0.0138.4730.2010.2010.0000.0000.0000.000
8A9GLN0-0.004-0.00711.1540.1140.1140.0000.0000.0000.000
9A10ARG10.7910.87113.5480.2590.2590.0000.0000.0000.000
10A11ALA0-0.014-0.01513.0590.0580.0580.0000.0000.0000.000
11A12LEU0-0.0240.00115.0430.0540.0540.0000.0000.0000.000
12A13HIS00.0170.01017.0030.0150.0150.0000.0000.0000.000
13A14LEU0-0.011-0.01316.6560.0250.0250.0000.0000.0000.000
14A15LEU0-0.035-0.01017.0240.0220.0220.0000.0000.0000.000
15A16GLU-1-0.872-0.96720.116-0.054-0.0540.0000.0000.0000.000
16A17GLU-1-0.892-0.93122.742-0.040-0.0400.0000.0000.0000.000
17A18TYR00.011-0.00721.4110.0120.0120.0000.0000.0000.000
18A19ARG10.8850.96924.430-0.014-0.0140.0000.0000.0000.000
19A20SER0-0.077-0.04926.2310.0040.0040.0000.0000.0000.000
20A21LYS10.8540.93726.4540.0200.0200.0000.0000.0000.000
21A22LEU00.0190.01127.5160.0060.0060.0000.0000.0000.000
22A23SER0-0.075-0.03431.542-0.005-0.0050.0000.0000.0000.000
23A24GLN00.0420.01634.4780.0020.0020.0000.0000.0000.000
24A25THR0-0.064-0.02835.6550.0040.0040.0000.0000.0000.000
25A26GLU-1-0.889-0.94630.6910.0680.0680.0000.0000.0000.000
26A27ASP-1-0.698-0.85330.3680.0440.0440.0000.0000.0000.000
27A28ARG10.8450.90630.423-0.045-0.0450.0000.0000.0000.000
28A29GLN0-0.025-0.03328.7730.0080.0080.0000.0000.0000.000
29A30LEU00.1160.06724.5500.0060.0060.0000.0000.0000.000
30A31ARG10.9150.96125.312-0.023-0.0230.0000.0000.0000.000
31A32SER0-0.064-0.03225.7910.0010.0010.0000.0000.0000.000
32A33SER00.0000.00823.0740.0070.0070.0000.0000.0000.000
33A34ILE00.0500.01121.4500.0080.0080.0000.0000.0000.000
34A35GLU-1-0.885-0.92921.4860.0110.0110.0000.0000.0000.000
35A36ARG10.8640.93320.989-0.100-0.1000.0000.0000.0000.000
36A37VAL00.0530.02415.810-0.001-0.0010.0000.0000.0000.000
37A38ILE00.0100.04817.367-0.015-0.0150.0000.0000.0000.000
38A39ASN0-0.056-0.04118.834-0.020-0.0200.0000.0000.0000.000
39A40ILE0-0.019-0.01214.870-0.019-0.0190.0000.0000.0000.000
40A41PHE0-0.020-0.02911.890-0.010-0.0100.0000.0000.0000.000
41A42GLN0-0.033-0.01515.448-0.035-0.0350.0000.0000.0000.000
42A43SER0-0.057-0.00917.158-0.022-0.0220.0000.0000.0000.000
43A44ASN00.021-0.00416.898-0.036-0.0360.0000.0000.0000.000
44A45LEU0-0.024-0.00115.743-0.024-0.0240.0000.0000.0000.000
45A46PHE00.0500.01310.7380.0000.0000.0000.0000.0000.000
46A47GLN0-0.004-0.00711.893-0.064-0.0640.0000.0000.0000.000
47A48ALA00.0400.01812.238-0.081-0.0810.0000.0000.0000.000
48A49LEU0-0.020-0.0069.934-0.035-0.0350.0000.0000.0000.000
49A50ILE0-0.0020.0037.036-0.010-0.0100.0000.0000.0000.000
50A51ASP-1-0.754-0.8367.038-0.844-0.8440.0000.0000.0000.000
51A52ILE0-0.016-0.0028.663-0.104-0.1040.0000.0000.0000.000
52A53GLN0-0.037-0.0292.642-1.0150.5931.085-1.295-1.399-0.013
53A54GLU-1-0.838-0.9183.709-2.832-2.4300.006-0.089-0.3190.000
54A55PHE0-0.066-0.0404.801-0.237-0.154-0.001-0.002-0.0800.000
55A56TYR0-0.059-0.0367.3790.0760.0760.0000.0000.0000.000
56A57GLU-1-0.977-0.9773.827-1.701-1.4650.002-0.054-0.1830.000
57A58VAL0-0.0200.0094.8620.3680.413-0.001-0.006-0.0380.000
58A59THR0-0.058-0.0564.5990.4790.763-0.001-0.010-0.2730.000
59A60LEU0-0.044-0.0116.520-0.261-0.2610.0000.0000.0000.000
60A61LEU0-0.053-0.0277.968-0.162-0.1620.0000.0000.0000.000
61A62ASP-1-0.810-0.8936.0980.1490.1490.0000.0000.0000.000
62A63ASN0-0.025-0.0279.046-0.116-0.1160.0000.0000.0000.000
63A64PRO00.0340.01311.4710.0630.0630.0000.0000.0000.000
64A65LYS10.7610.87213.755-0.112-0.1120.0000.0000.0000.000
65A66LEU00.0400.01910.284-0.024-0.0240.0000.0000.0000.000
66A67GLU-1-0.837-0.92213.8460.6710.6710.0000.0000.0000.000
67A68VAL0-0.038-0.01815.914-0.014-0.0140.0000.0000.0000.000
68A69LEU0-0.059-0.03414.274-0.035-0.0350.0000.0000.0000.000
69A70PHE0-0.054-0.01311.557-0.009-0.0090.0000.0000.0000.000
70A71GLN00.001-0.00717.710-0.037-0.0370.0000.0000.0000.000
71A72GLY00.0240.02221.462-0.013-0.0130.0000.0000.0000.000
72A73PRO0-0.030-0.03123.4480.0160.0160.0000.0000.0000.000
73A74GLY00.0480.03121.859-0.006-0.0060.0000.0000.0000.000
74A75SER00.0260.00619.3550.0160.0160.0000.0000.0000.000
75A76ASP-1-0.851-0.92319.4210.3800.3800.0000.0000.0000.000
76A77THR0-0.084-0.04220.168-0.021-0.0210.0000.0000.0000.000
77A78GLY00.0380.03521.477-0.023-0.0230.0000.0000.0000.000
78A79LEU0-0.059-0.04515.6410.0130.0130.0000.0000.0000.000
79A80TYR0-0.049-0.01514.255-0.006-0.0060.0000.0000.0000.000
80A81GLU-1-0.846-0.94017.3910.3340.3340.0000.0000.0000.000
81A82LEU0-0.053-0.01719.221-0.004-0.0040.0000.0000.0000.000
82A83LEU00.0610.02113.124-0.013-0.0130.0000.0000.0000.000
83A84ALA00.0100.01016.467-0.003-0.0030.0000.0000.0000.000
84A85ALA0-0.058-0.02817.323-0.022-0.0220.0000.0000.0000.000
85A86LEU00.0170.00118.342-0.037-0.0370.0000.0000.0000.000
86A87PRO0-0.0210.00516.121-0.038-0.0380.0000.0000.0000.000
87A88ALA00.0050.00819.132-0.022-0.0220.0000.0000.0000.000
88A89GLN0-0.031-0.03122.364-0.024-0.0240.0000.0000.0000.000
89A90LEU00.0150.00020.226-0.016-0.0160.0000.0000.0000.000
90A91GLN00.0160.01922.369-0.002-0.0020.0000.0000.0000.000
91A92PRO0-0.097-0.05223.704-0.011-0.0110.0000.0000.0000.000
92A93HIS0-0.039-0.02826.187-0.013-0.0130.0000.0000.0000.000
93A94VAL0-0.0380.01021.346-0.012-0.0120.0000.0000.0000.000
94A95ASP-1-0.927-0.94724.6050.0140.0140.0000.0000.0000.000
95A96SER0-0.028-0.04421.789-0.009-0.0090.0000.0000.0000.000
96A97GLN0-0.056-0.03721.7930.0160.0160.0000.0000.0000.000
97A98GLU-1-0.865-0.91816.574-0.128-0.1280.0000.0000.0000.000
98A99ASP-1-0.772-0.87517.391-0.080-0.0800.0000.0000.0000.000
99A100LEU0-0.0160.01317.3010.0210.0210.0000.0000.0000.000
100A101THR00.000-0.01615.9600.0300.0300.0000.0000.0000.000
101A102PHE00.0670.04010.7930.0490.0490.0000.0000.0000.000
102A103LEU0-0.040-0.03212.8830.0400.0400.0000.0000.0000.000
103A104TRP0-0.061-0.05714.2220.0680.0680.0000.0000.0000.000
104A105ASP-1-0.941-0.94510.0230.2970.2970.0000.0000.0000.000
105A106MET0-0.079-0.0157.0670.1500.1500.0000.0000.0000.000
106A107PHE0-0.008-0.01810.3920.1890.1890.0000.0000.0000.000
107A108GLY00.0430.02013.1870.0040.0040.0000.0000.0000.000
108A109GLU-1-0.856-0.93111.2991.1221.1220.0000.0000.0000.000
109A110LYS10.8600.9027.486-1.124-1.1240.0000.0000.0000.000
110A111SER00.0310.0393.6770.2240.4770.006-0.083-0.1770.000
111A112LEU00.0600.0245.813-0.810-0.8100.0000.0000.0000.000
112A113HIS0-0.0010.0047.577-0.146-0.1460.0000.0000.0000.000
113A114SER0-0.003-0.0028.225-0.120-0.1200.0000.0000.0000.000
114A115LEU0-0.0020.0116.225-0.220-0.2200.0000.0000.0000.000
115A116VAL00.031-0.0039.082-0.177-0.1770.0000.0000.0000.000
116A117LYS10.8710.93812.394-0.564-0.5640.0000.0000.0000.000
117A118ILE00.0250.01810.214-0.081-0.0810.0000.0000.0000.000
118A119HIS0-0.013-0.01613.212-0.111-0.1110.0000.0000.0000.000
119A120GLU-1-0.853-0.93414.8370.1340.1340.0000.0000.0000.000
120A121LYS10.8040.92716.960-0.243-0.2430.0000.0000.0000.000
121A122LEU0-0.008-0.01514.822-0.032-0.0320.0000.0000.0000.000
122A123HIS00.0570.03118.517-0.013-0.0130.0000.0000.0000.000
123A124TYR0-0.078-0.04720.384-0.017-0.0170.0000.0000.0000.000
124A125TYR00.0510.02120.536-0.003-0.0030.0000.0000.0000.000
125A126GLU-1-0.834-0.89721.4290.0040.0040.0000.0000.0000.000
126A127LYS10.8540.93723.798-0.097-0.0970.0000.0000.0000.000
127A128GLN0-0.110-0.06726.313-0.004-0.0040.0000.0000.0000.000
128A129SER0-0.0170.00126.190-0.004-0.0040.0000.0000.0000.000
129A130PRO0-0.0150.01028.062-0.002-0.0020.0000.0000.0000.000
130A131VAL0-0.014-0.02030.450-0.004-0.0040.0000.0000.0000.000
131A132PRO0-0.0020.01830.6250.0010.0010.0000.0000.0000.000
132A133ILE0-0.070-0.04132.7930.0000.0000.0000.0000.0000.000
133A134LEU0-0.056-0.03334.4350.0010.0010.0000.0000.0000.000
134A135HIS00.049-0.00130.8190.0010.0010.0000.0000.0000.000
135A136GLY00.0410.04031.962-0.005-0.0050.0000.0000.0000.000
136A137ALA0-0.039-0.04331.8680.0030.0030.0000.0000.0000.000
137A138ALA00.0030.00330.3320.0010.0010.0000.0000.0000.000
138A139ALA00.0410.02432.4890.0000.0000.0000.0000.0000.000
139A140LEU00.0050.01235.4220.0020.0020.0000.0000.0000.000
140A141ALA0-0.025-0.03734.8460.0020.0020.0000.0000.0000.000
141A142ASP-1-0.879-0.94934.839-0.068-0.0680.0000.0000.0000.000
142A143ASP-1-0.891-0.91237.845-0.044-0.0440.0000.0000.0000.000
143A144LEU0-0.076-0.05340.3540.0030.0030.0000.0000.0000.000
144A145ALA00.004-0.01939.3800.0020.0020.0000.0000.0000.000
145A146GLU-1-0.875-0.90941.352-0.048-0.0480.0000.0000.0000.000
146A147GLU-1-0.879-0.96143.358-0.032-0.0320.0000.0000.0000.000
147A148LEU0-0.049-0.03542.7720.0020.0020.0000.0000.0000.000
148A149GLN0-0.045-0.02442.0430.0010.0010.0000.0000.0000.000
149A150ASN0-0.113-0.04546.5050.0010.0010.0000.0000.0000.000
150A151LYS10.8540.92849.4650.0290.0290.0000.0000.0000.000
151A152PRO0-0.014-0.00550.839-0.001-0.0010.0000.0000.0000.000
152A153LEU00.0290.00847.2400.0000.0000.0000.0000.0000.000
153A154ASN00.0990.05349.5610.0010.0010.0000.0000.0000.000
154A155SER0-0.013-0.03748.359-0.002-0.0020.0000.0000.0000.000
155A156GLU-1-0.783-0.87345.889-0.023-0.0230.0000.0000.0000.000
156A157ILE00.0140.01044.565-0.001-0.0010.0000.0000.0000.000
157A158ARG10.9110.95744.0620.0290.0290.0000.0000.0000.000
158A159GLU-1-0.859-0.90840.966-0.032-0.0320.0000.0000.0000.000
159A160LEU00.0600.03939.367-0.002-0.0020.0000.0000.0000.000
160A161LEU00.0210.01939.124-0.003-0.0030.0000.0000.0000.000
161A162LYS10.8890.95738.4330.0380.0380.0000.0000.0000.000
162A163LEU0-0.010-0.00935.703-0.004-0.0040.0000.0000.0000.000
163A164LEU00.0110.01134.260-0.003-0.0030.0000.0000.0000.000
164A165SER00.0050.00733.901-0.005-0.0050.0000.0000.0000.000
165A166LYS10.8070.88831.2530.0500.0500.0000.0000.0000.000
166A167PRO00.000-0.00826.5550.0010.0010.0000.0000.0000.000
167A168ASN00.0620.02926.264-0.005-0.0050.0000.0000.0000.000
168A169VAL0-0.004-0.00327.3180.0020.0020.0000.0000.0000.000
169A170LYS10.9130.95529.1680.0880.0880.0000.0000.0000.000
170A171ALA00.0340.03023.826-0.002-0.0020.0000.0000.0000.000
171A172LEU00.0010.02025.4960.0000.0000.0000.0000.0000.000
172A173LEU0-0.022-0.01827.0000.0040.0040.0000.0000.0000.000
173A174SER00.002-0.01624.7980.0040.0040.0000.0000.0000.000
174A175VAL00.033-0.00121.732-0.001-0.0010.0000.0000.0000.000
175A176HIS0-0.090-0.05524.2570.0120.0120.0000.0000.0000.000
176A177ASP-1-0.707-0.83927.290-0.053-0.0530.0000.0000.0000.000
177A178THR00.0260.03121.6330.0000.0000.0000.0000.0000.000
178A179VAL0-0.017-0.01722.0160.0020.0020.0000.0000.0000.000
179A180ALA0-0.044-0.01024.4940.0090.0090.0000.0000.0000.000
180A181GLN0-0.102-0.07927.4300.0060.0060.0000.0000.0000.000
181A182LYS10.8300.92724.3020.0090.0090.0000.0000.0000.000
182A183ASN0-0.032-0.02223.5200.0020.0020.0000.0000.0000.000
183A184TYR0-0.038-0.04913.4810.0190.0190.0000.0000.0000.000
184A185ASP-1-0.812-0.91218.751-0.224-0.2240.0000.0000.0000.000
185A186LEU00.0050.02312.4730.0060.0060.0000.0000.0000.000
186A187GLU-1-0.931-0.95915.968-0.193-0.1930.0000.0000.0000.000
187A188VAL0-0.024-0.03918.8320.0070.0070.0000.0000.0000.000
188A189LEU0-0.0250.00111.7980.0220.0220.0000.0000.0000.000
189A190PHE00.0120.00112.8670.0210.0210.0000.0000.0000.000
190A191GLN0-0.0370.01117.1140.0320.0320.0000.0000.0000.000
191A192GLY00.0480.02417.7870.0230.0230.0000.0000.0000.000
192A193PRO00.006-0.00716.5650.0260.0260.0000.0000.0000.000
193A194ALA0-0.058-0.01719.1850.0120.0120.0000.0000.0000.000
194A195LEU0-0.055-0.02721.6720.0150.0150.0000.0000.0000.000
195A196GLY0-0.035-0.00622.4500.0120.0120.0000.0000.0000.000
196A197GLU-1-0.798-0.87923.192-0.019-0.0190.0000.0000.0000.000
197A198PRO00.0730.03422.9310.0000.0000.0000.0000.0000.000
198A199VAL00.0230.00325.6860.0030.0030.0000.0000.0000.000
199A200ARG10.8160.88728.8300.0390.0390.0000.0000.0000.000
200A201LEU00.0220.02425.7410.0010.0010.0000.0000.0000.000
201A202GLU-1-0.832-0.89729.3000.0010.0010.0000.0000.0000.000
202A203ARG10.9370.96531.2020.0100.0100.0000.0000.0000.000
203A204ASP-1-0.799-0.86231.821-0.046-0.0460.0000.0000.0000.000
204A205ILE00.0320.00630.786-0.001-0.0010.0000.0000.0000.000
205A206CYS0-0.026-0.00734.1970.0020.0020.0000.0000.0000.000
206A207ARG10.7760.85536.9990.0240.0240.0000.0000.0000.000
207A208ALA00.009-0.00936.5760.0000.0000.0000.0000.0000.000
208A209ILE00.0160.00536.3860.0000.0000.0000.0000.0000.000
209A210GLU-1-0.886-0.92339.948-0.015-0.0150.0000.0000.0000.000
210A211LEU0-0.091-0.05240.7200.0010.0010.0000.0000.0000.000
211A212LEU00.0040.00639.4740.0000.0000.0000.0000.0000.000
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