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: R8138

Calculation Name: 4URP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4URP

Chain ID: A

ChEMBL ID:

UniProt ID: P37261

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1716751.784429
FMO2-HF: Nuclear repulsion 1648978.432484
FMO2-HF: Total energy -67773.351945
FMO2-MP2: Total energy -67974.199607


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:3:PRO)


Summations of interaction energy for fragment #1(A:3: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.
-3.968-0.7822.604-2.651-3.1390.001
Interaction energy analysis for fragmet #1(A:3:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.004
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].
3A5GLY00.0680.0503.810-1.3480.790-0.029-1.071-1.0380.002
4A6ASN0-0.069-0.0482.151-1.550-0.6482.632-1.529-2.006-0.001
5A7TYR00.0700.0144.232-0.1420.0040.001-0.051-0.0950.000
6A8LEU00.0310.0117.314-0.059-0.0590.0000.0000.0000.000
7A9ASN00.0200.0105.345-0.148-0.1480.0000.0000.0000.000
8A10ALA00.0010.0128.003-0.179-0.1790.0000.0000.0000.000
9A11ILE0-0.035-0.01210.427-0.125-0.1250.0000.0000.0000.000
10A12THR0-0.033-0.03510.819-0.003-0.0030.0000.0000.0000.000
11A13ASN0-0.076-0.02010.134-0.094-0.0940.0000.0000.0000.000
12A14ARG10.9721.02613.396-0.386-0.3860.0000.0000.0000.000
13A15ARG10.8610.90216.571-0.264-0.2640.0000.0000.0000.000
14A16THR0-0.060-0.01420.270-0.015-0.0150.0000.0000.0000.000
15A17ILE00.0190.02121.1740.0080.0080.0000.0000.0000.000
16A18TYR00.012-0.00724.497-0.014-0.0140.0000.0000.0000.000
17A19ASN00.0000.00825.049-0.022-0.0220.0000.0000.0000.000
18A20LEU00.0030.00425.7060.0050.0050.0000.0000.0000.000
19A21LYS10.9530.97727.065-0.102-0.1020.0000.0000.0000.000
20A22PRO0-0.0140.00528.5840.0000.0000.0000.0000.0000.000
21A23GLU-1-0.890-0.88924.5580.0710.0710.0000.0000.0000.000
22A24LEU0-0.095-0.02526.3510.0010.0010.0000.0000.0000.000
23A25PRO00.0430.02021.707-0.002-0.0020.0000.0000.0000.000
24A26GLN00.061-0.01121.966-0.019-0.0190.0000.0000.0000.000
25A27GLY0-0.0140.00521.474-0.003-0.0030.0000.0000.0000.000
26A28VAL0-0.016-0.00320.544-0.020-0.0200.0000.0000.0000.000
27A29GLY00.0430.03122.6560.0130.0130.0000.0000.0000.000
28A30LEU00.0500.02225.0220.0060.0060.0000.0000.0000.000
29A31ASP-1-0.858-0.97826.286-0.046-0.0460.0000.0000.0000.000
30A32ASP-1-0.890-0.94821.393-0.109-0.1090.0000.0000.0000.000
31A33VAL00.0440.02222.312-0.006-0.0060.0000.0000.0000.000
32A34LYS10.8860.94723.3580.0490.0490.0000.0000.0000.000
33A35ARG10.9050.96121.1700.1150.1150.0000.0000.0000.000
34A36THR00.0160.02018.275-0.009-0.0090.0000.0000.0000.000
35A37VAL00.0730.04220.6380.0060.0060.0000.0000.0000.000
36A38HIS0-0.020-0.00223.1910.0030.0030.0000.0000.0000.000
37A39VAL0-0.054-0.04619.376-0.001-0.0010.0000.0000.0000.000
38A40ILE00.0530.05518.744-0.008-0.0080.0000.0000.0000.000
39A41LEU0-0.0180.03221.9130.0040.0040.0000.0000.0000.000
40A42LYS10.8950.96024.6470.0850.0850.0000.0000.0000.000
41A43ASN0-0.077-0.05620.992-0.020-0.0200.0000.0000.0000.000
42A44THR0-0.045-0.06222.1210.0040.0040.0000.0000.0000.000
43A45PRO00.0080.00622.672-0.002-0.0020.0000.0000.0000.000
44A46THR0-0.0330.02625.8620.0110.0110.0000.0000.0000.000
45A47ALA00.038-0.00629.218-0.007-0.0070.0000.0000.0000.000
46A48PHE0-0.018-0.02430.9520.0000.0000.0000.0000.0000.000
47A49ASN00.0190.01530.7560.0000.0000.0000.0000.0000.000
48A50SER00.0060.02132.705-0.002-0.0020.0000.0000.0000.000
49A51GLN0-0.043-0.04031.075-0.006-0.0060.0000.0000.0000.000
50A52VAL00.0540.02032.508-0.001-0.0010.0000.0000.0000.000
51A53ASN00.0130.02228.1570.0100.0100.0000.0000.0000.000
52A54ARG10.9030.94530.630-0.005-0.0050.0000.0000.0000.000
53A55ALA0-0.010-0.01328.9270.0080.0080.0000.0000.0000.000
54A56VAL00.0210.02130.914-0.008-0.0080.0000.0000.0000.000
55A57ILE0-0.0130.00626.5100.0070.0070.0000.0000.0000.000
56A58ILE0-0.0120.01231.011-0.006-0.0060.0000.0000.0000.000
57A59VAL00.0670.01030.9550.0050.0050.0000.0000.0000.000
58A60GLY00.0450.02233.903-0.002-0.0020.0000.0000.0000.000
59A61ASP-1-0.907-0.96936.4980.0190.0190.0000.0000.0000.000
60A62THR0-0.013-0.01337.7880.0000.0000.0000.0000.0000.000
61A63HIS0-0.057-0.02132.639-0.001-0.0010.0000.0000.0000.000
62A64LYS10.9490.95636.606-0.024-0.0240.0000.0000.0000.000
63A65ARG10.9360.97639.010-0.013-0.0130.0000.0000.0000.000
64A66ILE00.0300.03438.4160.0010.0010.0000.0000.0000.000
65A67TRP00.000-0.01033.2480.0050.0050.0000.0000.0000.000
66A68ASP-1-0.938-0.96739.2980.0370.0370.0000.0000.0000.000
67A69ALA00.0440.03042.5840.0000.0000.0000.0000.0000.000
68A70VAL00.001-0.00339.7490.0010.0010.0000.0000.0000.000
69A71ALA0-0.038-0.03141.5070.0020.0020.0000.0000.0000.000
70A72SER0-0.014-0.00443.178-0.001-0.0010.0000.0000.0000.000
71A73ALA0-0.029-0.00145.144-0.001-0.0010.0000.0000.0000.000
72A74MET0-0.072-0.01440.5510.0020.0020.0000.0000.0000.000
73A75PRO0-0.002-0.01145.497-0.001-0.0010.0000.0000.0000.000
74A76THR00.052-0.02545.372-0.001-0.0010.0000.0000.0000.000
75A77ALA0-0.0050.05145.4210.0020.0020.0000.0000.0000.000
76A78GLU-1-0.875-0.96442.4750.0710.0710.0000.0000.0000.000
77A79ALA0-0.062-0.03041.1180.0050.0050.0000.0000.0000.000
78A80LYS10.8660.93041.036-0.051-0.0510.0000.0000.0000.000
79A81LYS10.9941.01137.680-0.068-0.0680.0000.0000.0000.000
80A82ARG10.8910.98031.749-0.108-0.1080.0000.0000.0000.000
81A83PRO00.0350.01135.5190.0000.0000.0000.0000.0000.000
82A84GLU-1-0.855-0.96037.3890.0540.0540.0000.0000.0000.000
83A85SER0-0.039-0.04434.528-0.002-0.0020.0000.0000.0000.000
84A86CYS0-0.033-0.00733.1020.0060.0060.0000.0000.0000.000
85A87ARG10.8850.97434.069-0.047-0.0470.0000.0000.0000.000
86A88ASP-1-0.891-0.95336.2250.0390.0390.0000.0000.0000.000
87A89GLU-1-0.949-0.98031.9880.0810.0810.0000.0000.0000.000
88A90ALA0-0.0030.00530.1740.0030.0030.0000.0000.0000.000
89A91TYR0-0.026-0.00828.708-0.009-0.0090.0000.0000.0000.000
90A92GLY0-0.011-0.02130.039-0.009-0.0090.0000.0000.0000.000
91A93SER0-0.057-0.02129.4080.0100.0100.0000.0000.0000.000
92A94VAL00.0090.00225.876-0.010-0.0100.0000.0000.0000.000
93A95ILE00.0070.01728.9020.0110.0110.0000.0000.0000.000
94A96PHE0-0.004-0.00624.973-0.007-0.0070.0000.0000.0000.000
95A97PHE00.040-0.00130.7880.0030.0030.0000.0000.0000.000
96A98THR00.0140.00132.1780.0030.0030.0000.0000.0000.000
97A99ASP-1-0.883-0.95334.4210.0050.0050.0000.0000.0000.000
98A100LEU00.0130.00537.2100.0000.0000.0000.0000.0000.000
99A101GLY00.0670.04739.6740.0000.0000.0000.0000.0000.000
100A102PRO0-0.030-0.02037.1380.0000.0000.0000.0000.0000.000
101A103THR0-0.001-0.01137.2150.0000.0000.0000.0000.0000.000
102A104GLU-1-0.877-0.92839.2310.0180.0180.0000.0000.0000.000
103A105LYS10.8570.92940.7800.0020.0020.0000.0000.0000.000
104A106LEU0-0.057-0.03237.466-0.001-0.0010.0000.0000.0000.000
105A107GLN0-0.003-0.00741.4750.0000.0000.0000.0000.0000.000
106A108ARG10.9380.99443.542-0.005-0.0050.0000.0000.0000.000
107A109ASP-1-0.897-0.95743.9530.0000.0000.0000.0000.0000.000
108A110PHE0-0.058-0.02541.574-0.001-0.0010.0000.0000.0000.000
109A111PRO00.0530.02743.9760.0030.0030.0000.0000.0000.000
110A112ALA0-0.014-0.00945.1000.0020.0020.0000.0000.0000.000
111A113LEU00.0050.00338.9770.0030.0030.0000.0000.0000.000
112A114ALA00.0400.01840.5250.0020.0020.0000.0000.0000.000
113A115ALA0-0.048-0.02740.7850.0010.0010.0000.0000.0000.000
114A116ALA00.0290.00835.7450.0050.0050.0000.0000.0000.000
115A117PHE00.0240.01835.4950.0030.0030.0000.0000.0000.000
116A118PRO00.0500.01835.9830.0000.0000.0000.0000.0000.000
117A119THR00.0170.01132.8890.0050.0050.0000.0000.0000.000
118A120CYS0-0.049-0.02331.5510.0060.0060.0000.0000.0000.000
119A121ALA0-0.0070.00330.865-0.001-0.0010.0000.0000.0000.000
120A122ALA00.0320.00331.1050.0010.0010.0000.0000.0000.000
121A123HIS0-0.044-0.02827.4730.0120.0120.0000.0000.0000.000
122A124THR00.013-0.00326.3170.0060.0060.0000.0000.0000.000
123A125THR00.0100.01626.354-0.005-0.0050.0000.0000.0000.000
124A126GLY0-0.0090.00226.0220.0020.0020.0000.0000.0000.000
125A127ALA00.0090.00422.5540.0190.0190.0000.0000.0000.000
126A128VAL00.0330.02821.6350.0020.0020.0000.0000.0000.000
127A129GLN0-0.0380.01622.994-0.009-0.0090.0000.0000.0000.000
128A130ILE00.0570.02418.4930.0030.0030.0000.0000.0000.000
129A131GLN0-0.0120.04217.4290.0190.0190.0000.0000.0000.000
130A132SER00.011-0.02518.140-0.010-0.0100.0000.0000.0000.000
131A133TRP0-0.038-0.02420.0030.0000.0000.0000.0000.0000.000
132A134THR0-0.069-0.10614.2340.0120.0120.0000.0000.0000.000
133A135ALA00.0130.01815.2290.0200.0200.0000.0000.0000.000
134A136LEU0-0.018-0.02716.453-0.020-0.0200.0000.0000.0000.000
135A137GLU-1-0.827-0.93016.6870.2510.2510.0000.0000.0000.000
136A138LEU0-0.075-0.03111.3060.0250.0250.0000.0000.0000.000
137A139LEU0-0.066-0.03014.414-0.029-0.0290.0000.0000.0000.000
138A140GLY00.0210.01916.885-0.019-0.0190.0000.0000.0000.000
139A141LEU0-0.068-0.02118.1200.0110.0110.0000.0000.0000.000
140A142GLY00.0410.03119.8570.0260.0260.0000.0000.0000.000
141A143ALA00.024-0.00122.218-0.022-0.0220.0000.0000.0000.000
142A144ASN0-0.034-0.01723.5300.0210.0210.0000.0000.0000.000
143A145LEU0-0.019-0.00525.937-0.011-0.0110.0000.0000.0000.000
144A146GLN00.0360.01827.8240.0060.0060.0000.0000.0000.000
145A147HIS00.0730.03429.083-0.003-0.0030.0000.0000.0000.000
146A148TYR00.0190.02833.896-0.001-0.0010.0000.0000.0000.000
147A149ASN00.047-0.00535.014-0.004-0.0040.0000.0000.0000.000
148A150ASP-1-0.853-0.93837.6250.0510.0510.0000.0000.0000.000
149A151TYR00.001-0.00640.495-0.004-0.0040.0000.0000.0000.000
150A152VAL00.005-0.00936.571-0.004-0.0040.0000.0000.0000.000
151A153LYS10.9100.96939.884-0.031-0.0310.0000.0000.0000.000
152A154SER0-0.056-0.02741.215-0.004-0.0040.0000.0000.0000.000
153A155ALA0-0.0010.01141.701-0.002-0.0020.0000.0000.0000.000
154A156LEU0-0.071-0.03037.757-0.002-0.0020.0000.0000.0000.000
155A157PRO0-0.0130.00840.4650.0000.0000.0000.0000.0000.000
156A158GLN00.041-0.00143.6270.0000.0000.0000.0000.0000.000
157A159ASP-1-0.959-0.95241.7390.0010.0010.0000.0000.0000.000
158A160VAL0-0.008-0.01339.008-0.001-0.0010.0000.0000.0000.000
159A161PRO0-0.001-0.00139.5120.0010.0010.0000.0000.0000.000
160A162ILE00.0360.00841.3620.0030.0030.0000.0000.0000.000
161A163ALA00.0160.01241.8100.0030.0030.0000.0000.0000.000
162A164TRP0-0.036-0.02735.6360.0020.0020.0000.0000.0000.000
163A165THR00.0090.01336.8390.0020.0020.0000.0000.0000.000
164A166VAL0-0.029-0.01335.3380.0010.0010.0000.0000.0000.000
165A167GLN0-0.012-0.00931.6250.0080.0080.0000.0000.0000.000
166A168SER0-0.036-0.02829.2130.0130.0130.0000.0000.0000.000
167A169GLN00.007-0.00530.905-0.005-0.0050.0000.0000.0000.000
168A170LEU0-0.0230.00323.1120.0080.0080.0000.0000.0000.000
169A171VAL00.0140.00427.637-0.013-0.0130.0000.0000.0000.000
170A172PHE0-0.0060.00424.5840.0110.0110.0000.0000.0000.000
171A173GLY00.012-0.05224.217-0.004-0.0040.0000.0000.0000.000
172A186ASN0-0.020-0.03121.150-0.009-0.0090.0000.0000.0000.000
173A187ASN0-0.052-0.02619.541-0.036-0.0360.0000.0000.0000.000
174A188VAL00.0660.03823.5210.0110.0110.0000.0000.0000.000
175A189ILE00.0020.00922.127-0.003-0.0030.0000.0000.0000.000
176A190ASN00.0110.00625.5620.0040.0040.0000.0000.0000.000
177A191VAL0-0.070-0.03626.227-0.005-0.0050.0000.0000.0000.000
178A192TYR00.0630.04228.9960.0060.0060.0000.0000.0000.000