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

tag_button

FMODB ID: G6L91

Calculation Name: 5AR1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5AR1

Chain ID: A

ChEMBL ID:

UniProt ID: P32458

Base Structure: X-ray

Registration Date: 2023-06-21

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2776477.818223
FMO2-HF: Nuclear repulsion 2687193.336897
FMO2-HF: Total energy -89284.481326
FMO2-MP2: Total energy -89546.070615


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:21:ILE)


Summations of interaction energy for fragment #1(A:21: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.
-11.327-4.0414.027-3.553-7.759-0.019
Interaction energy analysis for fragmet #1(A:21:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.027
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].
3A23PHE00.0230.0103.124-2.560-0.2700.093-1.117-1.266-0.001
4A24THR00.0180.0265.3680.1970.232-0.001-0.002-0.0310.000
5A25VAL0-0.0110.0069.049-0.009-0.0090.0000.0000.0000.000
6A26MET00.0140.01111.7500.0600.0600.0000.0000.0000.000
7A27ILE00.0060.01215.425-0.017-0.0170.0000.0000.0000.000
8A28VAL00.0270.00518.5970.0280.0280.0000.0000.0000.000
9A29GLY00.0660.03421.687-0.013-0.0130.0000.0000.0000.000
10A30GLN0-0.0060.02525.1950.0110.0110.0000.0000.0000.000
11A31SER00.0450.00928.244-0.005-0.0050.0000.0000.0000.000
12A32GLY0-0.028-0.01330.344-0.004-0.0040.0000.0000.0000.000
13A33SER0-0.095-0.03329.6500.0050.0050.0000.0000.0000.000
14A34GLY00.048-0.00128.8680.0060.0060.0000.0000.0000.000
15A35ARG10.8810.94624.2080.0430.0430.0000.0000.0000.000
16A36SER0-0.025-0.02023.772-0.006-0.0060.0000.0000.0000.000
17A37THR0-0.007-0.02024.9410.0010.0010.0000.0000.0000.000
18A38PHE00.0300.02719.157-0.006-0.0060.0000.0000.0000.000
19A39ILE00.0640.03317.942-0.020-0.0200.0000.0000.0000.000
20A40ASN0-0.034-0.02019.361-0.018-0.0180.0000.0000.0000.000
21A41THR0-0.090-0.01321.5630.0000.0000.0000.0000.0000.000
22A42LEU0-0.013-0.00315.287-0.020-0.0200.0000.0000.0000.000
23A68LEU0-0.055-0.03318.897-0.002-0.0020.0000.0000.0000.000
24A69ARG10.7900.87818.855-0.011-0.0110.0000.0000.0000.000
25A70GLU-1-0.875-0.92913.7480.1060.1060.0000.0000.0000.000
26A71GLU-1-0.869-0.92715.0470.0000.0000.0000.0000.0000.000
27A72THR00.0000.0039.599-0.050-0.0500.0000.0000.0000.000
28A73VAL0-0.115-0.04610.3720.0370.0370.0000.0000.0000.000
29A74GLU-1-0.741-0.8998.820-0.039-0.0390.0000.0000.0000.000
30A75LEU0-0.102-0.05810.4970.0760.0760.0000.0000.0000.000
31A76GLU-1-0.875-0.9106.184-0.170-0.1700.0000.0000.0000.000
32A77ASP-1-0.804-0.8876.940-0.995-0.9950.0000.0000.0000.000
33A78ASP-1-0.845-0.9255.165-1.530-1.5300.0000.0000.0000.000
34A79GLU-1-0.997-0.9977.308-0.434-0.4340.0000.0000.0000.000
35A80GLY0-0.064-0.0409.7070.1380.1380.0000.0000.0000.000
36A81VAL0-0.045-0.0233.804-0.0640.2140.005-0.041-0.2410.000
37A82LYS10.7640.8944.7410.4830.585-0.001-0.013-0.0880.000
38A83ILE0-0.045-0.0452.404-6.301-3.3712.364-1.702-3.593-0.018
39A84GLN0-0.029-0.0133.5651.2091.5880.000-0.046-0.3340.000
40A85LEU0-0.047-0.0245.678-0.253-0.2530.0000.0000.0000.000
41A86ASN00.020-0.0048.3170.3710.3710.0000.0000.0000.000
42A87ILE00.0140.00610.3580.0050.0050.0000.0000.0000.000
43A88ILE0-0.017-0.00913.1710.0720.0720.0000.0000.0000.000
44A89ASP-1-0.826-0.91215.969-0.097-0.0970.0000.0000.0000.000
45A90THR0-0.004-0.00919.5510.0290.0290.0000.0000.0000.000
46A91PRO0-0.018-0.01322.386-0.007-0.0070.0000.0000.0000.000
47A92GLY00.0210.02326.257-0.003-0.0030.0000.0000.0000.000
48A93PHE00.0540.02425.5920.0060.0060.0000.0000.0000.000
49A94GLY0-0.092-0.06230.5530.0000.0000.0000.0000.0000.000
50A95ASP-1-0.875-0.94632.062-0.044-0.0440.0000.0000.0000.000
51A96SER0-0.020-0.00932.861-0.002-0.0020.0000.0000.0000.000
52A97LEU00.0160.01933.7880.0010.0010.0000.0000.0000.000
53A98ASP-1-0.913-0.96135.647-0.017-0.0170.0000.0000.0000.000
54A99ASN0-0.0400.00032.3670.0080.0080.0000.0000.0000.000
55A100SER00.0360.00632.295-0.002-0.0020.0000.0000.0000.000
56A101PRO00.0190.00631.0250.0000.0000.0000.0000.0000.000
57A102SER0-0.087-0.04428.4620.0010.0010.0000.0000.0000.000
58A103PHE00.0150.00025.961-0.002-0.0020.0000.0000.0000.000
59A104GLU-1-0.887-0.94125.5950.0110.0110.0000.0000.0000.000
60A105ILE00.0430.01725.0850.0060.0060.0000.0000.0000.000
61A106ILE0-0.0360.00320.5940.0090.0090.0000.0000.0000.000
62A107SER0-0.002-0.01621.1090.0040.0040.0000.0000.0000.000
63A108ASP-1-0.894-0.93422.4650.0450.0450.0000.0000.0000.000
64A109TYR0-0.022-0.00914.5430.0160.0160.0000.0000.0000.000
65A110ILE0-0.003-0.02117.2020.0170.0170.0000.0000.0000.000
66A111ARG10.9370.96317.890-0.010-0.0100.0000.0000.0000.000
67A112HIS0-0.033-0.01518.943-0.005-0.0050.0000.0000.0000.000
68A113GLN0-0.069-0.04514.4310.0490.0490.0000.0000.0000.000
69A114TYR0-0.075-0.05414.1930.0370.0370.0000.0000.0000.000
70A115ASP-1-0.836-0.89917.2000.1060.1060.0000.0000.0000.000
71A116GLU-1-0.893-0.94116.3260.2740.2740.0000.0000.0000.000
72A117ILE0-0.049-0.00712.9820.0390.0390.0000.0000.0000.000
73A118LEU00.0520.02316.1160.0100.0100.0000.0000.0000.000
74A119LEU0-0.058-0.01419.193-0.003-0.0030.0000.0000.0000.000
75A120GLU-1-0.888-0.95114.8190.4560.4560.0000.0000.0000.000
76A121GLU-1-0.923-0.93915.4500.2570.2570.0000.0000.0000.000
77A122SER0-0.047-0.01819.148-0.030-0.0300.0000.0000.0000.000
78A123ARG10.7430.87818.185-0.328-0.3280.0000.0000.0000.000
79A133GLY00.0330.01210.8130.0180.0180.0000.0000.0000.000
80A134ARG10.9010.94310.380-0.311-0.3110.0000.0000.0000.000
81A135VAL0-0.013-0.01710.238-0.035-0.0350.0000.0000.0000.000
82A136HIS00.0280.0206.712-0.022-0.0220.0000.0000.0000.000
83A137CYS0-0.012-0.00410.610-0.014-0.0140.0000.0000.0000.000
84A138CYS00.0280.02513.0350.0210.0210.0000.0000.0000.000
85A139LEU00.0250.00814.904-0.008-0.0080.0000.0000.0000.000
86A140TYR0-0.054-0.05518.3400.0200.0200.0000.0000.0000.000
87A141LEU0-0.011-0.01521.965-0.002-0.0020.0000.0000.0000.000
88A142ILE0-0.0020.00124.2800.0150.0150.0000.0000.0000.000
89A143ASN0-0.058-0.04227.5890.0010.0010.0000.0000.0000.000
90A144PRO00.0600.04130.5420.0030.0030.0000.0000.0000.000
91A145THR0-0.026-0.00732.7560.0050.0050.0000.0000.0000.000
92A146GLY0-0.063-0.05736.1580.0020.0020.0000.0000.0000.000
93A147HIS0-0.035-0.01935.844-0.001-0.0010.0000.0000.0000.000
94A148GLY00.0050.01834.0950.0030.0030.0000.0000.0000.000
95A149LEU0-0.022-0.01128.638-0.003-0.0030.0000.0000.0000.000
96A150LYS10.8110.88832.5840.0630.0630.0000.0000.0000.000
97A151GLU-1-0.882-0.95132.848-0.040-0.0400.0000.0000.0000.000
98A152ILE0-0.041-0.01830.3370.0010.0010.0000.0000.0000.000
99A153ASP-1-0.771-0.86328.705-0.073-0.0730.0000.0000.0000.000
100A154VAL0-0.0010.00128.192-0.005-0.0050.0000.0000.0000.000
101A155GLU-1-0.849-0.95629.313-0.032-0.0320.0000.0000.0000.000
102A156PHE0-0.0040.01422.3170.0030.0030.0000.0000.0000.000
103A157ILE00.004-0.01623.8820.0000.0000.0000.0000.0000.000
104A158ARG10.8160.92624.8010.0430.0430.0000.0000.0000.000
105A159GLN0-0.068-0.03026.3860.0060.0060.0000.0000.0000.000
106A160LEU00.004-0.00921.6070.0030.0030.0000.0000.0000.000
107A161GLY00.0550.03420.837-0.005-0.0050.0000.0000.0000.000
108A162SER0-0.060-0.02521.137-0.008-0.0080.0000.0000.0000.000
109A163LEU00.0230.01019.4510.0050.0050.0000.0000.0000.000
110A164VAL00.0030.00014.8970.0020.0020.0000.0000.0000.000
111A165ASN00.0520.02012.6590.0290.0290.0000.0000.0000.000
112A166ILE0-0.0290.00016.152-0.027-0.0270.0000.0000.0000.000
113A167ILE00.0490.02615.7320.0000.0000.0000.0000.0000.000
114A168PRO0-0.032-0.01219.1250.0020.0020.0000.0000.0000.000
115A169VAL00.0250.00619.951-0.012-0.0120.0000.0000.0000.000
116A170ILE0-0.0040.00923.1470.0180.0180.0000.0000.0000.000
117A171SER0-0.003-0.00226.367-0.002-0.0020.0000.0000.0000.000
118A172LYS10.9620.95027.4140.0780.0780.0000.0000.0000.000
119A173SER00.0450.03327.5560.0040.0040.0000.0000.0000.000
120A174ASP-1-0.910-0.94829.852-0.111-0.1110.0000.0000.0000.000
121A175SER0-0.108-0.05432.0990.0080.0080.0000.0000.0000.000
122A176LEU0-0.0140.00233.4220.0070.0070.0000.0000.0000.000
123A177THR0-0.038-0.04935.541-0.004-0.0040.0000.0000.0000.000
124A178ARG10.9240.93033.5830.1120.1120.0000.0000.0000.000
125A179ASP-1-0.916-0.95435.627-0.086-0.0860.0000.0000.0000.000
126A180GLU-1-0.807-0.86936.868-0.074-0.0740.0000.0000.0000.000
127A181LEU00.0300.02330.1380.0000.0000.0000.0000.0000.000
128A182LYS10.8450.91932.7510.0910.0910.0000.0000.0000.000
129A183LEU0-0.061-0.01834.119-0.001-0.0010.0000.0000.0000.000
130A184ASN00.034-0.01432.3930.0020.0020.0000.0000.0000.000
131A185LYS10.8550.94026.7380.1620.1620.0000.0000.0000.000
132A186LYS10.9430.96331.0490.0790.0790.0000.0000.0000.000
133A187LEU0-0.0060.00233.5070.0020.0020.0000.0000.0000.000
134A188ILE00.0390.02327.9650.0020.0020.0000.0000.0000.000
135A189MET00.0070.00426.238-0.001-0.0010.0000.0000.0000.000
136A190GLU-1-0.973-0.97830.232-0.062-0.0620.0000.0000.0000.000
137A191ASP-1-0.814-0.92932.332-0.062-0.0620.0000.0000.0000.000
138A192ILE0-0.020-0.02126.0140.0030.0030.0000.0000.0000.000
139A193ASP-1-0.912-0.93629.713-0.087-0.0870.0000.0000.0000.000
140A194ARG10.8590.94031.7940.0530.0530.0000.0000.0000.000
141A195TRP0-0.056-0.03131.8820.0100.0100.0000.0000.0000.000
142A196ASN0-0.043-0.02530.2170.0000.0000.0000.0000.0000.000
143A197LEU0-0.028-0.00626.8460.0040.0040.0000.0000.0000.000
144A198PRO0-0.0110.00523.161-0.008-0.0080.0000.0000.0000.000
145A199ILE0-0.005-0.00121.400-0.003-0.0030.0000.0000.0000.000
146A200TYR0-0.004-0.00313.5980.0150.0150.0000.0000.0000.000
147A201ASN00.005-0.02018.833-0.023-0.0230.0000.0000.0000.000
148A202PHE00.0330.02015.7340.0120.0120.0000.0000.0000.000
149A203PRO0-0.0360.00216.4580.0110.0110.0000.0000.0000.000
150A204PHE00.0230.00316.605-0.026-0.0260.0000.0000.0000.000
151A205ASP-1-0.891-0.94315.269-0.174-0.1740.0000.0000.0000.000
152A206GLU-1-1.017-1.02018.403-0.130-0.1300.0000.0000.0000.000
153A207ASP-1-0.957-0.97021.238-0.103-0.1030.0000.0000.0000.000
154A208GLU-1-0.973-0.97715.134-0.193-0.1930.0000.0000.0000.000
155A209ILE00.002-0.00713.887-0.004-0.0040.0000.0000.0000.000
156A210SER0-0.029-0.01617.8090.0140.0140.0000.0000.0000.000
157A211ASP-1-0.924-0.99421.433-0.155-0.1550.0000.0000.0000.000
158A212GLU-1-1.005-0.96122.184-0.246-0.2460.0000.0000.0000.000
159A213ASP-1-0.856-0.95117.414-0.334-0.3340.0000.0000.0000.000
160A214TYR0-0.046-0.02119.914-0.008-0.0080.0000.0000.0000.000
161A215GLU-1-0.908-0.96522.293-0.157-0.1570.0000.0000.0000.000
162A216THR0-0.046-0.01918.806-0.004-0.0040.0000.0000.0000.000
163A217ASN0-0.003-0.00918.788-0.024-0.0240.0000.0000.0000.000
164A218MET0-0.064-0.01920.6220.0130.0130.0000.0000.0000.000
165A219TYR0-0.065-0.05422.9800.0030.0030.0000.0000.0000.000
166A220LEU00.0290.00417.1230.0050.0050.0000.0000.0000.000
167A221ARG10.8570.92120.8320.1920.1920.0000.0000.0000.000
168A222THR0-0.061-0.02923.0560.0170.0170.0000.0000.0000.000
169A223LEU0-0.056-0.02022.1370.0110.0110.0000.0000.0000.000
170A224LEU0-0.0150.02621.0680.0030.0030.0000.0000.0000.000
171A225PRO00.009-0.02124.0930.0130.0130.0000.0000.0000.000
172A226PHE00.0070.00917.5160.0050.0050.0000.0000.0000.000
173A227ALA00.0020.00723.0530.0080.0080.0000.0000.0000.000
174A228ILE0-0.057-0.03318.3630.0000.0000.0000.0000.0000.000
175A229ILE0-0.012-0.01022.8500.0140.0140.0000.0000.0000.000
176A230GLY00.0260.02424.491-0.004-0.0040.0000.0000.0000.000
177A231SER0-0.027-0.00920.925-0.007-0.0070.0000.0000.0000.000
178A232ASN0-0.035-0.03117.157-0.050-0.0500.0000.0000.0000.000
179A233GLU-1-0.862-0.95219.991-0.196-0.1960.0000.0000.0000.000
180A234VAL00.0170.01720.4540.0130.0130.0000.0000.0000.000
181A235TYR0-0.045-0.03523.2630.0110.0110.0000.0000.0000.000
182A236GLU-1-0.834-0.88727.068-0.158-0.1580.0000.0000.0000.000
183A237MET0-0.100-0.07029.1130.0100.0100.0000.0000.0000.000
184A238GLY00.0060.02332.7820.0010.0010.0000.0000.0000.000
185A261ILE00.0390.02128.7480.0040.0040.0000.0000.0000.000
186A262SER0-0.058-0.03927.6360.0020.0020.0000.0000.0000.000
187A263ASP-1-0.815-0.86929.855-0.126-0.1260.0000.0000.0000.000
188A264PHE00.003-0.00625.8080.0050.0050.0000.0000.0000.000
189A265VAL00.0100.01421.522-0.001-0.0010.0000.0000.0000.000
190A266ILE00.0160.01018.505-0.011-0.0110.0000.0000.0000.000
191A267LEU00.010-0.00515.7420.0000.0000.0000.0000.0000.000
192A268ARG10.9700.98915.4380.3200.3200.0000.0000.0000.000
193A269ASN00.0200.00410.150-0.011-0.0110.0000.0000.0000.000
194A270ALA00.0550.02610.120-0.102-0.1020.0000.0000.0000.000
195A271LEU00.0080.00510.340-0.059-0.0590.0000.0000.0000.000
196A272LEU00.0160.01710.8780.0100.0100.0000.0000.0000.000
197A273ILE00.0240.0115.473-0.028-0.0280.0000.0000.0000.000
198A274SER0-0.054-0.0247.358-0.046-0.0460.0000.0000.0000.000
199A275HIS00.1020.0379.2100.0460.0460.0000.0000.0000.000
200A276LEU0-0.042-0.0146.4990.0810.0810.0000.0000.0000.000
201A277HIS00.005-0.0122.160-0.5980.0441.452-0.501-1.592-0.001
202A278ASP-1-0.825-0.8976.437-0.313-0.3130.0000.0000.0000.000
203A279LEU0-0.079-0.0339.6870.1080.1080.0000.0000.0000.000
204A280LYS10.8000.8802.984-0.2890.3410.115-0.131-0.6140.001
205A281ASN0-0.024-0.0107.5370.1770.1770.0000.0000.0000.000
206A282TYR00.0570.0399.5090.0770.0770.0000.0000.0000.000
207A283THR0-0.066-0.04310.4660.0590.0590.0000.0000.0000.000
208A284HIS0-0.0060.00210.2510.0680.0680.0000.0000.0000.000
209A285GLU-1-0.874-0.94812.236-0.117-0.1170.0000.0000.0000.000
210A286ILE0-0.034-0.01514.3790.0140.0140.0000.0000.0000.000
211A287LEU0-0.073-0.03715.7110.0140.0140.0000.0000.0000.000
212A288TYR0-0.035-0.01614.8620.0060.0060.0000.0000.0000.000
213A289GLU-1-0.814-0.89616.8540.0850.0850.0000.0000.0000.000
214A290ARG10.8620.94619.0430.0500.0500.0000.0000.0000.000
215A291TYR0-0.007-0.02819.670-0.005-0.0050.0000.0000.0000.000
216A292ARG10.8830.93219.659-0.069-0.0690.0000.0000.0000.000
217A293THR0-0.135-0.08321.7120.0050.0050.0000.0000.0000.000
218A294GLU-1-0.956-0.96624.6220.0100.0100.0000.0000.0000.000
219A295ALA0-0.012-0.00625.174-0.001-0.0010.0000.0000.0000.000
220A296LEU0-0.101-0.03723.8490.0000.0000.0000.0000.0000.000