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: 172ZZ

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2773522.636315
FMO2-HF: Nuclear repulsion 2684240.087965
FMO2-HF: Total energy -89282.548351
FMO2-MP2: Total energy -89544.203504


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.
-11.912-7.598.842-4.259-8.907-0.012
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 : -0.035 / q_NPA : -0.032
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].
3A23PHE00.019-0.0033.451-1.2100.7540.037-0.913-1.0890.001
4A24THR00.0310.0195.6360.0740.0740.0000.0000.0000.000
5A25VAL0-0.0130.0059.3840.0060.0060.0000.0000.0000.000
6A26MET00.0080.00611.8090.0430.0430.0000.0000.0000.000
7A27ILE00.0010.01015.561-0.018-0.0180.0000.0000.0000.000
8A28VAL00.0130.00618.6030.0270.0270.0000.0000.0000.000
9A29GLY00.0770.03521.751-0.014-0.0140.0000.0000.0000.000
10A30GLN0-0.0470.09325.1860.0070.0070.0000.0000.0000.000
11A31SER00.008-0.00328.185-0.007-0.0070.0000.0000.0000.000
12A32GLY0-0.027-0.01930.323-0.005-0.0050.0000.0000.0000.000
13A33SER0-0.084-0.02629.4410.0040.0040.0000.0000.0000.000
14A34GLY00.0530.00228.6900.0040.0040.0000.0000.0000.000
15A35ARG10.8720.93924.1750.0340.0340.0000.0000.0000.000
16A36SER0-0.019-0.01923.684-0.006-0.0060.0000.0000.0000.000
17A37THR0-0.024-0.02424.830-0.002-0.0020.0000.0000.0000.000
18A38PHE00.0400.03118.711-0.009-0.0090.0000.0000.0000.000
19A39ILE00.0540.02917.907-0.023-0.0230.0000.0000.0000.000
20A40ASN0-0.019-0.01619.090-0.031-0.0310.0000.0000.0000.000
21A41THR0-0.096-0.01521.479-0.004-0.0040.0000.0000.0000.000
22A42LEU0-0.020-0.00715.010-0.023-0.0230.0000.0000.0000.000
23A68LEU0-0.046-0.03319.219-0.004-0.0040.0000.0000.0000.000
24A69ARG10.8200.91119.1890.0020.0020.0000.0000.0000.000
25A70GLU-1-0.901-0.94513.6640.0980.0980.0000.0000.0000.000
26A71GLU-1-0.893-0.95815.090-0.039-0.0390.0000.0000.0000.000
27A72THR00.0130.0189.672-0.055-0.0550.0000.0000.0000.000
28A73VAL0-0.109-0.04210.3310.0410.0410.0000.0000.0000.000
29A74GLU-1-0.747-0.9028.788-0.297-0.2970.0000.0000.0000.000
30A75LEU0-0.098-0.05410.4410.0910.0910.0000.0000.0000.000
31A76GLU-1-0.881-0.9096.138-0.564-0.5640.0000.0000.0000.000
32A77ASP-1-0.806-0.8946.894-1.457-1.4570.0000.0000.0000.000
33A78ASP-1-0.842-0.9154.938-1.617-1.6170.0000.0000.0000.000
34A79GLU-1-0.999-0.9967.055-0.486-0.4860.0000.0000.0000.000
35A80GLY0-0.068-0.0449.1710.1630.1630.0000.0000.0000.000
36A81VAL0-0.049-0.0263.516-0.0900.2120.014-0.050-0.2670.000
37A82LYS10.7840.9004.7140.8800.982-0.001-0.013-0.0880.000
38A83ILE0-0.065-0.0572.367-6.850-4.0422.786-1.799-3.795-0.019
39A84GLN0-0.023-0.0093.5281.4591.8430.001-0.049-0.3350.000
40A85LEU0-0.048-0.0275.639-0.151-0.1510.0000.0000.0000.000
41A86ASN00.0340.0088.2090.3430.3430.0000.0000.0000.000
42A87ILE00.007-0.00310.5520.0460.0460.0000.0000.0000.000
43A88ILE0-0.021-0.01013.2410.0650.0650.0000.0000.0000.000
44A89ASP-1-0.810-0.90116.202-0.089-0.0890.0000.0000.0000.000
45A90THR00.007-0.01219.7160.0300.0300.0000.0000.0000.000
46A91PRO0-0.022-0.01222.628-0.011-0.0110.0000.0000.0000.000
47A92GLY00.0310.02626.474-0.001-0.0010.0000.0000.0000.000
48A93PHE0-0.0080.00325.6510.0050.0050.0000.0000.0000.000
49A94GLY00.039-0.03430.690-0.006-0.0060.0000.0000.0000.000
50A95ASP-1-0.875-0.98432.871-0.031-0.0310.0000.0000.0000.000
51A96SER0-0.034-0.05133.0240.0000.0000.0000.0000.0000.000
52A97LEU0-0.009-0.00133.9500.0020.0020.0000.0000.0000.000
53A98ASP-1-0.925-0.96635.838-0.004-0.0040.0000.0000.0000.000
54A99ASN0-0.039-0.00832.4970.0090.0090.0000.0000.0000.000
55A100SER00.0650.02932.561-0.001-0.0010.0000.0000.0000.000
56A101PRO00.0380.01631.3820.0020.0020.0000.0000.0000.000
57A102SER0-0.089-0.05228.6730.0000.0000.0000.0000.0000.000
58A103PHE0-0.004-0.00626.2940.0000.0000.0000.0000.0000.000
59A104GLU-1-0.894-0.94425.9380.0400.0400.0000.0000.0000.000
60A105ILE00.0540.01825.2610.0080.0080.0000.0000.0000.000
61A106ILE0-0.0270.00820.9940.0120.0120.0000.0000.0000.000
62A107SER0-0.007-0.02521.3850.0120.0120.0000.0000.0000.000
63A108ASP-1-0.928-0.94922.6330.0960.0960.0000.0000.0000.000
64A109TYR0-0.044-0.02014.9950.0200.0200.0000.0000.0000.000
65A110ILE00.000-0.01617.5230.0250.0250.0000.0000.0000.000
66A111ARG10.9840.98817.954-0.050-0.0500.0000.0000.0000.000
67A112HIS00.0280.01519.6140.0040.0040.0000.0000.0000.000
68A113GLN0-0.025-0.01114.6460.0670.0670.0000.0000.0000.000
69A114TYR0-0.068-0.04914.8470.0610.0610.0000.0000.0000.000
70A115ASP-1-0.857-0.91117.0600.1750.1750.0000.0000.0000.000
71A116GLU-1-0.982-0.99415.7650.3830.3830.0000.0000.0000.000
72A117ILE0-0.035-0.00512.8560.0340.0340.0000.0000.0000.000
73A118LEU00.0130.00916.0400.0040.0040.0000.0000.0000.000
74A119LEU0-0.040-0.00619.178-0.011-0.0110.0000.0000.0000.000
75A120GLU-1-1.001-1.03114.8360.5900.5900.0000.0000.0000.000
76A121GLU-1-0.961-0.96315.5610.4340.4340.0000.0000.0000.000
77A122SER0-0.073-0.03919.366-0.038-0.0380.0000.0000.0000.000
78A123ARG10.8250.93818.717-0.387-0.3870.0000.0000.0000.000
79A133GLY00.0450.02010.7530.0350.0350.0000.0000.0000.000
80A134ARG10.9310.96910.048-0.561-0.5610.0000.0000.0000.000
81A135VAL0-0.030-0.02310.3990.0030.0030.0000.0000.0000.000
82A136HIS00.0050.0127.0930.0280.0280.0000.0000.0000.000
83A137CYS0-0.006-0.00510.831-0.023-0.0230.0000.0000.0000.000
84A138CYS0-0.0070.01213.0260.0070.0070.0000.0000.0000.000
85A139LEU00.0490.01214.916-0.012-0.0120.0000.0000.0000.000
86A140TYR0-0.039-0.03818.1760.0160.0160.0000.0000.0000.000
87A141LEU0-0.013-0.01921.846-0.005-0.0050.0000.0000.0000.000
88A142ILE00.0070.00724.0880.0140.0140.0000.0000.0000.000
89A143ASN0-0.065-0.03627.3610.0010.0010.0000.0000.0000.000
90A144PRO00.0780.04830.2690.0040.0040.0000.0000.0000.000
91A145THR0-0.052-0.02232.4150.0050.0050.0000.0000.0000.000
92A146GLY0-0.050-0.05435.8540.0020.0020.0000.0000.0000.000
93A147HIS0-0.041-0.02035.589-0.001-0.0010.0000.0000.0000.000
94A148GLY00.0270.02633.7870.0030.0030.0000.0000.0000.000
95A149LEU0-0.017-0.00428.394-0.003-0.0030.0000.0000.0000.000
96A150LYS10.8690.94832.4530.0500.0500.0000.0000.0000.000
97A151GLU-1-0.899-0.96132.797-0.018-0.0180.0000.0000.0000.000
98A152ILE0-0.039-0.01230.4610.0030.0030.0000.0000.0000.000
99A153ASP-1-0.799-0.89228.693-0.051-0.0510.0000.0000.0000.000
100A154VAL0-0.017-0.00928.185-0.002-0.0020.0000.0000.0000.000
101A155GLU-1-0.911-0.99229.3660.0020.0020.0000.0000.0000.000
102A156PHE00.0180.02522.4170.0060.0060.0000.0000.0000.000
103A157ILE0-0.003-0.01723.8810.0050.0050.0000.0000.0000.000
104A158ARG10.8460.93124.8870.0150.0150.0000.0000.0000.000
105A159GLN0-0.040-0.01326.5660.0040.0040.0000.0000.0000.000
106A160LEU0-0.005-0.01521.8300.0090.0090.0000.0000.0000.000
107A161GLY00.0550.04021.0750.0030.0030.0000.0000.0000.000
108A162SER0-0.053-0.02121.261-0.002-0.0020.0000.0000.0000.000
109A163LEU00.000-0.00319.5820.0110.0110.0000.0000.0000.000
110A164VAL0-0.0170.00015.2040.0170.0170.0000.0000.0000.000
111A165ASN00.0600.02212.6790.0090.0090.0000.0000.0000.000
112A166ILE0-0.0170.00016.097-0.028-0.0280.0000.0000.0000.000
113A167ILE00.0430.02015.837-0.003-0.0030.0000.0000.0000.000
114A168PRO0-0.021-0.00318.852-0.001-0.0010.0000.0000.0000.000
115A169VAL00.0290.00819.772-0.015-0.0150.0000.0000.0000.000
116A170ILE0-0.019-0.00122.7730.0190.0190.0000.0000.0000.000
117A171SER00.006-0.00725.931-0.005-0.0050.0000.0000.0000.000
118A172LYS10.9510.94627.0630.0780.0780.0000.0000.0000.000
119A173SER00.0370.03227.1580.0030.0030.0000.0000.0000.000
120A174ASP-1-0.887-0.94229.089-0.123-0.1230.0000.0000.0000.000
121A175SER0-0.132-0.06531.5390.0080.0080.0000.0000.0000.000
122A176LEU0-0.0020.00832.7330.0070.0070.0000.0000.0000.000
123A177THR0-0.026-0.01734.955-0.005-0.0050.0000.0000.0000.000
124A178ARG10.9930.99733.5650.1080.1080.0000.0000.0000.000
125A179ASP-1-0.956-0.97534.987-0.080-0.0800.0000.0000.0000.000
126A180GLU-1-0.868-0.93236.409-0.070-0.0700.0000.0000.0000.000
127A181LEU00.0410.01529.0220.0010.0010.0000.0000.0000.000
128A182LYS10.8840.95132.2020.0930.0930.0000.0000.0000.000
129A183LEU0-0.053-0.01133.5660.0010.0010.0000.0000.0000.000
130A184ASN00.035-0.00231.8860.0030.0030.0000.0000.0000.000
131A185LYS10.8540.94326.1280.1550.1550.0000.0000.0000.000
132A186LYS10.9380.96330.5820.0700.0700.0000.0000.0000.000
133A187LEU0-0.023-0.01133.0750.0020.0020.0000.0000.0000.000
134A188ILE00.0590.03927.6390.0020.0020.0000.0000.0000.000
135A189MET0-0.0010.00025.7820.0010.0010.0000.0000.0000.000
136A190GLU-1-0.970-0.97629.851-0.045-0.0450.0000.0000.0000.000
137A191ASP-1-0.827-0.93832.059-0.045-0.0450.0000.0000.0000.000
138A192ILE0-0.017-0.01826.1030.0050.0050.0000.0000.0000.000
139A193ASP-1-0.907-0.94229.488-0.060-0.0600.0000.0000.0000.000
140A194ARG10.8790.95731.5500.0340.0340.0000.0000.0000.000
141A195TRP0-0.056-0.03531.8280.0090.0090.0000.0000.0000.000
142A196ASN0-0.043-0.01830.1020.0010.0010.0000.0000.0000.000
143A197LEU0-0.031-0.01126.6680.0060.0060.0000.0000.0000.000
144A198PRO0-0.0160.00123.260-0.008-0.0080.0000.0000.0000.000
145A199ILE0-0.0140.00321.3950.0010.0010.0000.0000.0000.000
146A200TYR00.0190.00813.6650.0160.0160.0000.0000.0000.000
147A201ASN00.021-0.01518.598-0.028-0.0280.0000.0000.0000.000
148A202PHE0-0.0020.00515.1340.0050.0050.0000.0000.0000.000
149A203PRO0-0.048-0.01916.5010.0020.0020.0000.0000.0000.000
150A204PHE00.0240.01416.784-0.019-0.0190.0000.0000.0000.000
151A205ASP-1-0.883-0.94315.455-0.081-0.0810.0000.0000.0000.000
152A206GLU-1-1.021-1.02118.487-0.094-0.0940.0000.0000.0000.000
153A207ASP-1-0.957-0.97721.424-0.066-0.0660.0000.0000.0000.000
154A208GLU-1-0.974-0.96615.126-0.148-0.1480.0000.0000.0000.000
155A209ILE0-0.002-0.01113.932-0.012-0.0120.0000.0000.0000.000
156A210SER0-0.037-0.02317.7110.0120.0120.0000.0000.0000.000
157A211ASP-1-0.926-0.98621.293-0.140-0.1400.0000.0000.0000.000
158A212GLU-1-1.008-0.96722.200-0.239-0.2390.0000.0000.0000.000
159A213ASP-1-0.870-0.95717.404-0.314-0.3140.0000.0000.0000.000
160A214TYR0-0.022-0.00219.901-0.004-0.0040.0000.0000.0000.000
161A215GLU-1-0.923-0.97822.192-0.151-0.1510.0000.0000.0000.000
162A216THR0-0.030-0.01119.184-0.005-0.0050.0000.0000.0000.000
163A217ASN0-0.009-0.00418.336-0.028-0.0280.0000.0000.0000.000
164A218MET0-0.076-0.03820.5240.0150.0150.0000.0000.0000.000
165A219TYR0-0.050-0.05822.9930.0020.0020.0000.0000.0000.000
166A220LEU00.027-0.00216.3960.0040.0040.0000.0000.0000.000
167A221ARG10.8790.92221.0690.1460.1460.0000.0000.0000.000
168A222THR0-0.037-0.00222.6400.0170.0170.0000.0000.0000.000
169A223LEU0-0.076-0.02721.4050.0090.0090.0000.0000.0000.000
170A224LEU0-0.0200.02720.2370.0010.0010.0000.0000.0000.000
171A225PRO0-0.012-0.02123.6360.0120.0120.0000.0000.0000.000
172A226PHE00.0200.01217.2300.0010.0010.0000.0000.0000.000
173A227ALA00.0020.00822.4990.0090.0090.0000.0000.0000.000
174A228ILE0-0.070-0.03617.6060.0000.0000.0000.0000.0000.000
175A229ILE0-0.018-0.01122.2580.0150.0150.0000.0000.0000.000
176A230GLY00.0360.02824.111-0.006-0.0060.0000.0000.0000.000
177A231SER0-0.031-0.01020.975-0.011-0.0110.0000.0000.0000.000
178A232ASN0-0.033-0.03416.325-0.040-0.0400.0000.0000.0000.000
179A233GLU-1-0.858-0.94919.705-0.214-0.2140.0000.0000.0000.000
180A234VAL00.0250.02119.7640.0170.0170.0000.0000.0000.000
181A235TYR0-0.060-0.05122.5790.0100.0100.0000.0000.0000.000
182A236GLU-1-0.823-0.87226.349-0.153-0.1530.0000.0000.0000.000
183A237MET0-0.113-0.10228.3440.0120.0120.0000.0000.0000.000
184A238GLY00.0410.03932.0460.0030.0030.0000.0000.0000.000
185A261ILE0-0.017-0.01328.9040.0040.0040.0000.0000.0000.000
186A262SER0-0.010-0.01127.486-0.001-0.0010.0000.0000.0000.000
187A263ASP-1-0.876-0.90829.440-0.132-0.1320.0000.0000.0000.000
188A264PHE00.005-0.00925.3890.0070.0070.0000.0000.0000.000
189A265VAL0-0.0020.00921.349-0.003-0.0030.0000.0000.0000.000
190A266ILE00.0170.01118.505-0.010-0.0100.0000.0000.0000.000
191A267LEU00.010-0.00714.926-0.002-0.0020.0000.0000.0000.000
192A268ARG10.9730.99415.3790.3360.3360.0000.0000.0000.000
193A269ASN00.015-0.00110.154-0.023-0.0230.0000.0000.0000.000
194A270ALA00.0690.03410.405-0.102-0.1020.0000.0000.0000.000
195A271LEU00.0120.00510.801-0.047-0.0470.0000.0000.0000.000
196A272LEU00.0180.01710.1690.0300.0300.0000.0000.0000.000
197A273ILE00.0180.0135.955-0.003-0.0030.0000.0000.0000.000
198A274SER0-0.064-0.0297.0610.0060.0060.0000.0000.0000.000
199A275HIS00.1160.0389.2610.0840.0840.0000.0000.0000.000
200A276LEU0-0.043-0.0165.8650.1130.1130.0000.0000.0000.000
201A277HIS00.013-0.0111.9920.270-0.5903.657-0.779-2.018-0.001
202A278ASP-1-0.836-0.8986.535-0.113-0.1130.0000.0000.0000.000
203A279LEU0-0.088-0.0379.4400.1050.1050.0000.0000.0000.000
204A280LYS10.8680.9342.014-2.893-3.2712.348-0.656-1.3150.007
205A281ASN0-0.013-0.0107.2390.2250.2250.0000.0000.0000.000
206A282TYR00.0680.0499.5680.0420.0420.0000.0000.0000.000
207A283THR0-0.086-0.04910.5580.0450.0450.0000.0000.0000.000
208A284HIS0-0.025-0.02110.1700.0430.0430.0000.0000.0000.000
209A285GLU-1-0.881-0.94812.1520.0310.0310.0000.0000.0000.000
210A286ILE0-0.042-0.01614.380-0.011-0.0110.0000.0000.0000.000
211A287LEU0-0.063-0.03415.7290.0010.0010.0000.0000.0000.000
212A288TYR00.0430.02714.8040.0060.0060.0000.0000.0000.000
213A289GLU-1-0.837-0.91216.7250.1960.1960.0000.0000.0000.000
214A290ARG10.8690.94719.013-0.042-0.0420.0000.0000.0000.000
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