FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 3JY1L

Calculation Name: 4RL9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RL9

Chain ID: A

ChEMBL ID:

UniProt ID: A6XB80

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 OptAll
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 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2046170.478213
FMO2-HF: Nuclear repulsion 1968615.816417
FMO2-HF: Total energy -77554.661796
FMO2-MP2: Total energy -77784.127658


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:17:ILE)


Summations of interaction energy for fragment #1(A:17:ILE)
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.
-11.124-8.6844.628-2.778-4.2910.016
Interaction energy analysis for fragmet #1(A:17:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.015
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].
3A19VAL0-0.019-0.0173.000-3.229-1.0740.157-1.061-1.251-0.005
4A20GLY00.009-0.0175.2720.2850.378-0.001-0.003-0.0890.000
5A21ALA0-0.021-0.0027.8030.1590.1590.0000.0000.0000.000
6A22ARG10.8040.90010.633-0.156-0.1560.0000.0000.0000.000
7A23ALA00.0080.01714.4230.0580.0580.0000.0000.0000.000
8A24GLU-1-0.763-0.84617.6340.1340.1340.0000.0000.0000.000
9A25VAL00.0360.01120.4890.0150.0150.0000.0000.0000.000
10A26GLY00.0220.00123.942-0.010-0.0100.0000.0000.0000.000
11A27THR00.0050.01326.2090.0010.0010.0000.0000.0000.000
12A28THR00.0020.02823.571-0.003-0.0030.0000.0000.0000.000
13A29GLY00.1040.06824.6430.0180.0180.0000.0000.0000.000
14A30TYR0-0.030-0.03123.028-0.012-0.0120.0000.0000.0000.000
15A31GLY00.0160.00519.4660.0200.0200.0000.0000.0000.000
16A32GLY0-0.011-0.01015.782-0.045-0.0450.0000.0000.0000.000
17A33ALA00.0000.01212.9260.0620.0620.0000.0000.0000.000
18A34LEU0-0.0120.0016.928-0.133-0.1330.0000.0000.0000.000
19A35LEU00.0170.0058.2630.1720.1720.0000.0000.0000.000
20A36TRP0-0.011-0.0142.226-10.184-10.1364.473-1.701-2.8200.021
21A37GLN0-0.041-0.0396.5600.1880.1880.0000.0000.0000.000
22A38ALA00.0080.0197.566-0.245-0.2450.0000.0000.0000.000
23A39ASN00.0240.0058.482-0.067-0.0670.0000.0000.0000.000
24A40PRO00.002-0.00911.7620.0370.0370.0000.0000.0000.000
25A41TYR00.0010.00914.3700.0160.0160.0000.0000.0000.000
26A42VAL0-0.0120.01011.9810.0490.0490.0000.0000.0000.000
27A43GLY00.0210.00210.129-0.108-0.1080.0000.0000.0000.000
28A44LEU0-0.046-0.0168.0690.0880.0880.0000.0000.0000.000
29A45ALA00.0460.0239.679-0.008-0.0080.0000.0000.0000.000
30A46LEU00.0110.0099.5420.0530.0530.0000.0000.0000.000
31A47GLY00.001-0.01311.685-0.004-0.0040.0000.0000.0000.000
32A48TYR0-0.038-0.01314.4070.0140.0140.0000.0000.0000.000
33A49ASN0-0.110-0.06817.681-0.037-0.0370.0000.0000.0000.000
34A50GLY00.0900.03921.0130.0140.0140.0000.0000.0000.000
35A51GLY00.0130.01023.906-0.012-0.0120.0000.0000.0000.000
36A52ASP-1-0.883-0.93726.9790.1110.1110.0000.0000.0000.000
37A53ILE0-0.106-0.05128.366-0.007-0.0070.0000.0000.0000.000
38A54SER00.015-0.01532.6110.0020.0020.0000.0000.0000.000
39A55TRP0-0.098-0.04531.853-0.002-0.0020.0000.0000.0000.000
40A56THR0-0.012-0.02038.5600.0020.0020.0000.0000.0000.000
41A57ASP-1-0.969-0.98441.6510.0240.0240.0000.0000.0000.000
42A65LYS10.7740.87547.793-0.025-0.0250.0000.0000.0000.000
43A66TYR0-0.058-0.05643.8840.0010.0010.0000.0000.0000.000
44A67ASP-1-0.816-0.88542.3560.0350.0350.0000.0000.0000.000
45A68LEU0-0.047-0.02436.2240.0010.0010.0000.0000.0000.000
46A69ASP-1-0.807-0.87636.1610.0550.0550.0000.0000.0000.000
47A70MET0-0.075-0.03030.1460.0030.0030.0000.0000.0000.000
48A71ASP-1-0.826-0.89130.6730.0900.0900.0000.0000.0000.000
49A72ASN0-0.047-0.04826.0730.0050.0050.0000.0000.0000.000
50A73ASN0-0.023-0.00524.0730.0140.0140.0000.0000.0000.000
51A74ASN0-0.023-0.00722.5420.0070.0070.0000.0000.0000.000
52A75VAL00.0000.00516.4680.0100.0100.0000.0000.0000.000
53A76TYR0-0.030-0.04416.519-0.009-0.0090.0000.0000.0000.000
54A77LEU0-0.017-0.01511.5360.0930.0930.0000.0000.0000.000
55A78ASN00.0380.01414.425-0.032-0.0320.0000.0000.0000.000
56A79ALA0-0.0030.00613.2980.0590.0590.0000.0000.0000.000
57A80GLU-1-0.831-0.90413.721-0.031-0.0310.0000.0000.0000.000
58A81ILE00.0080.00414.872-0.035-0.0350.0000.0000.0000.000
59A82ARG10.8410.90715.0990.0850.0850.0000.0000.0000.000
60A83PRO00.0240.00218.563-0.025-0.0250.0000.0000.0000.000
61A84TRP00.0100.00621.603-0.006-0.0060.0000.0000.0000.000
62A85GLY00.0330.01817.661-0.014-0.0140.0000.0000.0000.000
63A86ALA0-0.041-0.01718.038-0.041-0.0410.0000.0000.0000.000
64A87SER0-0.032-0.00419.2860.0000.0000.0000.0000.0000.000
65A88THR0-0.003-0.01421.263-0.013-0.0130.0000.0000.0000.000
66A89ASN00.0310.02223.1060.0010.0010.0000.0000.0000.000
67A90PRO00.034-0.00321.5960.0010.0010.0000.0000.0000.000
68A91TRP00.0170.00922.2920.0030.0030.0000.0000.0000.000
69A92ALA00.0030.00124.2020.0080.0080.0000.0000.0000.000
70A93GLN0-0.018-0.01916.270-0.001-0.0010.0000.0000.0000.000
71A94GLY00.0500.03419.146-0.009-0.0090.0000.0000.0000.000
72A95LEU0-0.038-0.01420.5620.0170.0170.0000.0000.0000.000
73A96TYR0-0.097-0.07918.187-0.030-0.0300.0000.0000.0000.000
74A97ILE0-0.0010.00719.9620.0040.0040.0000.0000.0000.000
75A98ALA0-0.0240.00018.3270.0060.0060.0000.0000.0000.000
76A99ALA00.0130.00118.107-0.012-0.0120.0000.0000.0000.000
77A100GLY00.004-0.00617.5010.0430.0430.0000.0000.0000.000
78A101ALA0-0.030-0.00218.271-0.038-0.0380.0000.0000.0000.000
79A102ALA00.0120.00418.7010.0440.0440.0000.0000.0000.000
80A103TYR0-0.087-0.01820.717-0.015-0.0150.0000.0000.0000.000
81A104LEU0-0.005-0.03422.6270.0000.0000.0000.0000.0000.000
82A105ASP-1-0.801-0.90525.5120.1660.1660.0000.0000.0000.000
83A106ASN0-0.019-0.01425.8530.0050.0050.0000.0000.0000.000
84A107ASP-1-0.747-0.83029.5380.0960.0960.0000.0000.0000.000
85A108TYR0-0.048-0.04329.1940.0020.0020.0000.0000.0000.000
86A109ASP-1-0.766-0.86835.2210.0650.0650.0000.0000.0000.000
87A110LEU0-0.032-0.02038.661-0.003-0.0030.0000.0000.0000.000
88A111ALA0-0.009-0.01141.3730.0000.0000.0000.0000.0000.000
89A112LYS10.8830.94344.738-0.037-0.0370.0000.0000.0000.000
90A113ARG10.8430.89747.724-0.032-0.0320.0000.0000.0000.000
91A114ILE0-0.047-0.00750.667-0.001-0.0010.0000.0000.0000.000
92A115GLY00.0580.02154.1940.0010.0010.0000.0000.0000.000
93A116ASN0-0.035-0.03657.0580.0000.0000.0000.0000.0000.000
94A117GLY0-0.0100.00760.729-0.001-0.0010.0000.0000.0000.000
95A118ASP-1-0.843-0.88954.0830.0210.0210.0000.0000.0000.000
96A119THR0-0.058-0.04855.2150.0010.0010.0000.0000.0000.000
97A120LEU00.0100.00750.5630.0000.0000.0000.0000.0000.000
98A121SER00.0020.00249.9190.0000.0000.0000.0000.0000.000
99A122ILE00.0100.00049.2850.0020.0020.0000.0000.0000.000
100A123ASP-1-0.768-0.85448.8080.0320.0320.0000.0000.0000.000
101A124GLY0-0.031-0.00849.909-0.001-0.0010.0000.0000.0000.000
102A125LYS10.8000.90351.504-0.032-0.0320.0000.0000.0000.000
103A126ASN00.012-0.00753.4840.0020.0020.0000.0000.0000.000
104A127TYR0-0.004-0.01654.1760.0000.0000.0000.0000.0000.000
105A128GLN00.0150.01056.789-0.001-0.0010.0000.0000.0000.000
106A129GLN00.022-0.01858.6760.0000.0000.0000.0000.0000.000
107A130ALA0-0.046-0.00859.926-0.001-0.0010.0000.0000.0000.000
108A131VAL0-0.003-0.01661.872-0.001-0.0010.0000.0000.0000.000
109A132PRO00.0110.01062.1560.0010.0010.0000.0000.0000.000
110A133GLY0-0.023-0.00663.627-0.001-0.0010.0000.0000.0000.000
111A134GLN0-0.0080.00058.7100.0000.0000.0000.0000.0000.000
112A135GLU-1-0.781-0.84352.3580.0300.0300.0000.0000.0000.000
113A136GLY00.0200.00555.3520.0000.0000.0000.0000.0000.000
114A137GLY00.009-0.01251.3700.0000.0000.0000.0000.0000.000
115A138VAL0-0.026-0.01647.0140.0000.0000.0000.0000.0000.000
116A139ARG10.8610.91241.289-0.056-0.0560.0000.0000.0000.000
117A140GLY00.0140.00443.541-0.001-0.0010.0000.0000.0000.000
118A141LYS10.8440.94737.031-0.083-0.0830.0000.0000.0000.000
119A142MET0-0.049-0.01436.597-0.001-0.0010.0000.0000.0000.000
120A143SER00.015-0.03034.2730.0000.0000.0000.0000.0000.000
121A144TYR0-0.010-0.02130.219-0.004-0.0040.0000.0000.0000.000
122A145LYS10.8550.92527.471-0.176-0.1760.0000.0000.0000.000
123A146ASN0-0.065-0.04127.477-0.009-0.0090.0000.0000.0000.000
124A147ASP-1-0.840-0.91025.6560.2070.2070.0000.0000.0000.000
125A148ILE0-0.044-0.02721.3310.0320.0320.0000.0000.0000.000
126A149ALA00.0260.02723.672-0.023-0.0230.0000.0000.0000.000
127A150PRO0-0.011-0.01022.9920.0210.0210.0000.0000.0000.000
128A151TYR0-0.042-0.04420.325-0.020-0.0200.0000.0000.0000.000
129A152LEU0-0.020-0.01022.3230.0070.0070.0000.0000.0000.000
130A153GLY00.0480.02422.766-0.008-0.0080.0000.0000.0000.000
131A154PHE0-0.032-0.01522.967-0.001-0.0010.0000.0000.0000.000
132A155GLY00.0560.03122.1830.0060.0060.0000.0000.0000.000
133A156PHE0-0.082-0.03222.667-0.015-0.0150.0000.0000.0000.000
134A157ALA00.0300.00617.8350.0080.0080.0000.0000.0000.000
135A158PRO0-0.0400.00018.767-0.032-0.0320.0000.0000.0000.000
136A159LYS10.9160.94813.1250.3500.3500.0000.0000.0000.000
137A160ILE0-0.001-0.00618.4680.0110.0110.0000.0000.0000.000
138A161SER0-0.011-0.01217.832-0.006-0.0060.0000.0000.0000.000
139A162LYS10.9370.95514.1340.3670.3670.0000.0000.0000.000
140A163ASN0-0.021-0.01112.057-0.013-0.0130.0000.0000.0000.000
141A164TRP00.0450.03114.010-0.006-0.0060.0000.0000.0000.000
142A165GLY00.0190.00516.467-0.006-0.0060.0000.0000.0000.000
143A166VAL00.0010.02318.1050.0100.0100.0000.0000.0000.000
144A167PHE0-0.041-0.02918.758-0.020-0.0200.0000.0000.0000.000
145A168GLY00.0450.03621.2250.0080.0080.0000.0000.0000.000
146A169GLU-1-0.819-0.87719.2770.1180.1180.0000.0000.0000.000
147A170VAL00.003-0.00723.4570.0040.0040.0000.0000.0000.000
148A171GLY00.0320.00925.368-0.003-0.0030.0000.0000.0000.000
149A172ALA0-0.0300.00226.291-0.006-0.0060.0000.0000.0000.000
150A173TYR00.0420.02021.7120.0180.0180.0000.0000.0000.000
151A174TYR0-0.102-0.05926.628-0.009-0.0090.0000.0000.0000.000
152A175THR0-0.031-0.04228.3080.0140.0140.0000.0000.0000.000
153A176GLY00.0150.02330.6610.0010.0010.0000.0000.0000.000
154A177ASN0-0.071-0.04334.2000.0040.0040.0000.0000.0000.000
155A178PRO00.0190.03634.8860.0030.0030.0000.0000.0000.000
156A179LYS10.9150.95136.205-0.095-0.0950.0000.0000.0000.000
157A180VAL00.0350.01138.3680.0000.0000.0000.0000.0000.000
158A181GLU-1-0.923-0.94640.7400.0690.0690.0000.0000.0000.000
159A182LEU00.005-0.02543.329-0.001-0.0010.0000.0000.0000.000
160A183THR0-0.0570.00346.079-0.001-0.0010.0000.0000.0000.000
161A184GLN0-0.005-0.03049.166-0.002-0.0020.0000.0000.0000.000
162A185TYR0-0.010-0.00948.5430.0000.0000.0000.0000.0000.000
163A186ASN0-0.026-0.03254.300-0.001-0.0010.0000.0000.0000.000
164A187LEU00.0230.03153.078-0.001-0.0010.0000.0000.0000.000
165A188ALA00.0040.00457.6100.0000.0000.0000.0000.0000.000
166A189PRO00.0140.01359.0380.0000.0000.0000.0000.0000.000
167A190VAL0-0.0060.00459.007-0.001-0.0010.0000.0000.0000.000
168A191THR0-0.021-0.03061.5080.0000.0000.0000.0000.0000.000
169A192GLY00.0270.01163.901-0.001-0.0010.0000.0000.0000.000
170A193ASN0-0.047-0.01057.2630.0000.0000.0000.0000.0000.000
171A194PRO0-0.013-0.00960.7590.0000.0000.0000.0000.0000.000
172A195THR0-0.036-0.00355.6560.0010.0010.0000.0000.0000.000
173A196SER0-0.001-0.03658.6560.0000.0000.0000.0000.0000.000
174A197ALA00.0430.00455.2790.0010.0010.0000.0000.0000.000
175A198GLN0-0.011-0.00352.7590.0010.0010.0000.0000.0000.000
176A199ASP-1-0.813-0.87453.5750.0320.0320.0000.0000.0000.000
177A200ALA0-0.026-0.00452.4610.0010.0010.0000.0000.0000.000
178A201VAL00.0280.01049.1920.0010.0010.0000.0000.0000.000
179A202ASP-1-0.837-0.91248.7350.0440.0440.0000.0000.0000.000
180A203LYS10.7230.84149.407-0.034-0.0340.0000.0000.0000.000
181A204GLU-1-0.843-0.92845.5030.0420.0420.0000.0000.0000.000
182A205ALA00.0270.00644.6570.0030.0030.0000.0000.0000.000
183A206ASN0-0.020-0.01144.4030.0060.0060.0000.0000.0000.000
184A207GLU-1-0.824-0.89045.2820.0420.0420.0000.0000.0000.000
185A208ILE00.0110.00039.4810.0020.0020.0000.0000.0000.000
186A209ARG10.8340.90640.345-0.054-0.0540.0000.0000.0000.000
187A210ASN0-0.074-0.04141.6250.0040.0040.0000.0000.0000.000
188A211ASP-1-0.828-0.87842.0320.0500.0500.0000.0000.0000.000
189A212ASN00.0710.02838.9460.0010.0010.0000.0000.0000.000
190A213LYS10.7700.87737.525-0.044-0.0440.0000.0000.0000.000
191A214TYR0-0.026-0.01736.4390.0000.0000.0000.0000.0000.000
192A215GLU-1-0.873-0.91334.6270.0870.0870.0000.0000.0000.000
193A216TRP0-0.024-0.01427.4620.0120.0120.0000.0000.0000.000
194A217MET00.0040.02328.550-0.002-0.0020.0000.0000.0000.000
195A218PRO0-0.025-0.01628.9780.0070.0070.0000.0000.0000.000
196A219VAL0-0.004-0.01125.0710.0010.0010.0000.0000.0000.000
197A220GLY00.006-0.00326.800-0.006-0.0060.0000.0000.0000.000
198A221LYS10.8240.91719.237-0.158-0.1580.0000.0000.0000.000
199A222VAL00.005-0.00523.255-0.011-0.0110.0000.0000.0000.000
200A223GLY00.0400.01920.4600.0160.0160.0000.0000.0000.000
201A224VAL0-0.056-0.02217.879-0.019-0.0190.0000.0000.0000.000
202A225ASN0-0.011-0.01114.1990.0330.0330.0000.0000.0000.000
203A226PHE00.000-0.01010.947-0.016-0.0160.0000.0000.0000.000
204A227TYR00.0070.0019.282-0.012-0.0120.0000.0000.0000.000
205A228TRP0-0.0110.0064.0180.3660.510-0.001-0.013-0.1310.000