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: KGR13

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1719235.020043
FMO2-HF: Nuclear repulsion 1651459.483506
FMO2-HF: Total energy -67775.536537
FMO2-MP2: Total energy -67976.202764


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.
-4.731-0.7011.564-2.549-3.045-0.015
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 : -0.016 / q_NPA : -0.031
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].
3A5GLY00.0910.0493.872-1.8080.400-0.025-1.148-1.035-0.002
4A6ASN0-0.024-0.0182.699-2.235-0.4981.590-1.388-1.939-0.013
5A7TYR00.0310.0124.612-0.353-0.268-0.001-0.013-0.0710.000
6A8LEU00.0310.0047.969-0.071-0.0710.0000.0000.0000.000
7A9ASN00.0170.0005.9070.2160.2160.0000.0000.0000.000
8A10ALA00.0190.0208.488-0.131-0.1310.0000.0000.0000.000
9A11ILE0-0.030-0.00910.630-0.054-0.0540.0000.0000.0000.000
10A12THR0-0.026-0.03111.4460.0000.0000.0000.0000.0000.000
11A13ASN0-0.077-0.01610.1960.0120.0120.0000.0000.0000.000
12A14ARG10.9350.99813.703-0.221-0.2210.0000.0000.0000.000
13A15ARG10.8570.91116.688-0.125-0.1250.0000.0000.0000.000
14A16THR0-0.045-0.01720.408-0.009-0.0090.0000.0000.0000.000
15A17ILE00.0230.04620.5080.0010.0010.0000.0000.0000.000
16A18TYR00.0580.00324.352-0.004-0.0040.0000.0000.0000.000
17A19ASN0-0.0090.01625.045-0.010-0.0100.0000.0000.0000.000
18A20LEU0-0.0010.01425.657-0.004-0.0040.0000.0000.0000.000
19A21LYS10.9240.94327.297-0.011-0.0110.0000.0000.0000.000
20A22PRO0-0.0120.00528.553-0.002-0.0020.0000.0000.0000.000
21A23GLU-1-0.878-0.90024.689-0.022-0.0220.0000.0000.0000.000
22A24LEU0-0.062-0.02026.3220.0030.0030.0000.0000.0000.000
23A25PRO00.0260.01921.0880.0010.0010.0000.0000.0000.000
24A26GLN0-0.012-0.04221.923-0.011-0.0110.0000.0000.0000.000
25A27GLY00.0030.00921.119-0.010-0.0100.0000.0000.0000.000
26A28VAL0-0.0220.00120.066-0.015-0.0150.0000.0000.0000.000
27A29GLY00.0610.02822.3650.0110.0110.0000.0000.0000.000
28A30LEU00.0420.01324.5060.0000.0000.0000.0000.0000.000
29A31ASP-1-0.819-0.91926.372-0.057-0.0570.0000.0000.0000.000
30A32ASP-1-0.798-0.86821.010-0.118-0.1180.0000.0000.0000.000
31A33VAL00.0300.03722.0290.0000.0000.0000.0000.0000.000
32A34LYS10.8350.88923.3640.0560.0560.0000.0000.0000.000
33A35ARG10.8450.90621.7220.1140.1140.0000.0000.0000.000
34A36THR0-0.004-0.01018.422-0.004-0.0040.0000.0000.0000.000
35A37VAL00.0340.01220.8600.0060.0060.0000.0000.0000.000
36A38HIS00.0320.03123.3360.0090.0090.0000.0000.0000.000
37A39VAL0-0.027-0.01819.1590.0040.0040.0000.0000.0000.000
38A40ILE00.0400.04118.4890.0030.0030.0000.0000.0000.000
39A41LEU0-0.017-0.00321.6660.0080.0080.0000.0000.0000.000
40A42LYS10.8350.92024.6030.0560.0560.0000.0000.0000.000
41A43ASN0-0.061-0.03421.131-0.007-0.0070.0000.0000.0000.000
42A44THR00.005-0.01721.9250.0100.0100.0000.0000.0000.000
43A45PRO0-0.012-0.01222.840-0.002-0.0020.0000.0000.0000.000
44A46THR0-0.0380.01625.8320.0060.0060.0000.0000.0000.000
45A47ALA00.0520.01629.215-0.003-0.0030.0000.0000.0000.000
46A48PHE00.002-0.01530.969-0.003-0.0030.0000.0000.0000.000
47A49ASN0-0.0140.00831.051-0.004-0.0040.0000.0000.0000.000
48A50SER0-0.003-0.00632.570-0.004-0.0040.0000.0000.0000.000
49A51GLN0-0.018-0.01631.460-0.004-0.0040.0000.0000.0000.000
50A52VAL00.0530.02032.171-0.003-0.0030.0000.0000.0000.000
51A53ASN00.0270.02627.9840.0060.0060.0000.0000.0000.000
52A54ARG10.8270.91030.274-0.008-0.0080.0000.0000.0000.000
53A55ALA00.0080.00128.6870.0060.0060.0000.0000.0000.000
54A56VAL00.0110.01230.656-0.005-0.0050.0000.0000.0000.000
55A57ILE0-0.0300.00326.4890.0040.0040.0000.0000.0000.000
56A58ILE0-0.0180.00230.534-0.003-0.0030.0000.0000.0000.000
57A59VAL00.0770.02430.5340.0020.0020.0000.0000.0000.000
58A60GLY00.0650.04233.3510.0000.0000.0000.0000.0000.000
59A61ASP-1-0.826-0.92435.961-0.006-0.0060.0000.0000.0000.000
60A62THR0-0.012-0.00237.0320.0010.0010.0000.0000.0000.000
61A63HIS00.0010.00632.4110.0010.0010.0000.0000.0000.000
62A64LYS10.8830.91836.4340.0090.0090.0000.0000.0000.000
63A65ARG10.9090.95138.6970.0070.0070.0000.0000.0000.000
64A66ILE00.0100.02437.7170.0020.0020.0000.0000.0000.000
65A67TRP00.013-0.01132.8830.0050.0050.0000.0000.0000.000
66A68ASP-1-0.825-0.89238.8830.0110.0110.0000.0000.0000.000
67A69ALA00.0280.02642.2740.0010.0010.0000.0000.0000.000
68A70VAL0-0.028-0.01939.0910.0020.0020.0000.0000.0000.000
69A71ALA00.005-0.00841.2350.0020.0020.0000.0000.0000.000
70A72SER0-0.044-0.01042.8450.0000.0000.0000.0000.0000.000
71A73ALA0-0.036-0.01044.6550.0000.0000.0000.0000.0000.000
72A74MET0-0.027-0.00241.4150.0020.0020.0000.0000.0000.000
73A75PRO0-0.027-0.01345.137-0.001-0.0010.0000.0000.0000.000
74A76THR0-0.030-0.03645.539-0.002-0.0020.0000.0000.0000.000
75A77ALA00.0380.00945.2080.0010.0010.0000.0000.0000.000
76A78GLU-1-0.847-0.91942.2600.0310.0310.0000.0000.0000.000
77A79ALA0-0.040-0.01640.8760.0030.0030.0000.0000.0000.000
78A80LYS10.9090.95141.220-0.019-0.0190.0000.0000.0000.000
79A81LYS10.8260.92037.680-0.021-0.0210.0000.0000.0000.000
80A82ARG10.8660.94231.243-0.050-0.0500.0000.0000.0000.000
81A83PRO00.0240.00935.586-0.001-0.0010.0000.0000.0000.000
82A84GLU-1-0.822-0.91737.4690.0150.0150.0000.0000.0000.000
83A85SER00.0210.01334.132-0.002-0.0020.0000.0000.0000.000
84A86CYS0-0.082-0.03333.127-0.001-0.0010.0000.0000.0000.000
85A87ARG10.7430.85234.048-0.013-0.0130.0000.0000.0000.000
86A88ASP-1-0.862-0.91336.6100.0050.0050.0000.0000.0000.000
87A89GLU-1-0.884-0.95932.4340.0190.0190.0000.0000.0000.000
88A90ALA0-0.032-0.00829.9300.0000.0000.0000.0000.0000.000
89A91TYR0-0.018-0.00128.344-0.004-0.0040.0000.0000.0000.000
90A92GLY0-0.006-0.02529.709-0.004-0.0040.0000.0000.0000.000
91A93SER0-0.035-0.01428.9360.0060.0060.0000.0000.0000.000
92A94VAL0-0.0040.00325.645-0.006-0.0060.0000.0000.0000.000
93A95ILE0-0.0160.00328.6390.0080.0080.0000.0000.0000.000
94A96PHE00.0420.00525.006-0.004-0.0040.0000.0000.0000.000
95A97PHE00.0350.00230.7990.0030.0030.0000.0000.0000.000
96A98THR0-0.0050.01032.4360.0010.0010.0000.0000.0000.000
97A99ASP-1-0.809-0.91234.4670.0070.0070.0000.0000.0000.000
98A100LEU00.0480.01337.2920.0020.0020.0000.0000.0000.000
99A101GLY00.0350.04240.0330.0000.0000.0000.0000.0000.000
100A102PRO0-0.022-0.02537.0760.0000.0000.0000.0000.0000.000
101A103THR0-0.023-0.01237.5430.0020.0020.0000.0000.0000.000
102A104GLU-1-0.876-0.94639.2400.0170.0170.0000.0000.0000.000
103A105LYS10.8020.89540.766-0.010-0.0100.0000.0000.0000.000
104A106LEU0-0.006-0.00236.8370.0000.0000.0000.0000.0000.000
105A107GLN0-0.060-0.04441.1860.0000.0000.0000.0000.0000.000
106A108ARG10.9110.97243.366-0.012-0.0120.0000.0000.0000.000
107A109ASP-1-0.839-0.90643.5040.0110.0110.0000.0000.0000.000
108A110PHE0-0.047-0.02340.6630.0000.0000.0000.0000.0000.000
109A111PRO00.0690.03343.8470.0030.0030.0000.0000.0000.000
110A112ALA0-0.028-0.01845.4390.0020.0020.0000.0000.0000.000
111A113LEU0-0.007-0.00739.4590.0030.0030.0000.0000.0000.000
112A114ALA00.0030.00340.6790.0020.0020.0000.0000.0000.000
113A115ALA00.0280.02341.1780.0000.0000.0000.0000.0000.000
114A116ALA00.0080.00636.3750.0030.0030.0000.0000.0000.000
115A117PHE00.0360.01935.8950.0030.0030.0000.0000.0000.000
116A118PRO00.0480.02035.6640.0010.0010.0000.0000.0000.000
117A119THR00.0350.01933.9000.0030.0030.0000.0000.0000.000
118A120CYS0-0.046-0.02031.5660.0050.0050.0000.0000.0000.000
119A121ALA00.0050.00230.8100.0010.0010.0000.0000.0000.000
120A122ALA00.0240.00730.9820.0000.0000.0000.0000.0000.000
121A123HIS0-0.035-0.02527.3350.0110.0110.0000.0000.0000.000
122A124THR0-0.022-0.01326.4140.0050.0050.0000.0000.0000.000
123A125THR0-0.010-0.01826.158-0.004-0.0040.0000.0000.0000.000
124A126GLY0-0.0020.00926.0720.0000.0000.0000.0000.0000.000
125A127ALA00.0110.00122.2880.0080.0080.0000.0000.0000.000
126A128VAL00.0140.00921.6210.0000.0000.0000.0000.0000.000
127A129GLN00.0260.04522.650-0.010-0.0100.0000.0000.0000.000
128A130ILE00.0100.00818.855-0.003-0.0030.0000.0000.0000.000
129A131GLN0-0.0110.00017.3190.0060.0060.0000.0000.0000.000
130A132SER0-0.002-0.02418.055-0.015-0.0150.0000.0000.0000.000
131A133TRP0-0.028-0.03019.8270.0010.0010.0000.0000.0000.000
132A134THR0-0.029-0.04313.8600.0080.0080.0000.0000.0000.000
133A135ALA00.0000.00415.222-0.008-0.0080.0000.0000.0000.000
134A136LEU0-0.025-0.01616.409-0.021-0.0210.0000.0000.0000.000
135A137GLU-1-0.768-0.89416.8310.0820.0820.0000.0000.0000.000
136A138LEU0-0.042-0.02210.320-0.003-0.0030.0000.0000.0000.000
137A139LEU0-0.047-0.02213.926-0.035-0.0350.0000.0000.0000.000
138A140GLY0-0.0060.01416.521-0.014-0.0140.0000.0000.0000.000
139A141LEU0-0.046-0.01217.6660.0070.0070.0000.0000.0000.000
140A142GLY00.0350.01619.5080.0120.0120.0000.0000.0000.000
141A143ALA0-0.027-0.02421.998-0.010-0.0100.0000.0000.0000.000
142A144ASN0-0.037-0.02723.7560.0100.0100.0000.0000.0000.000
143A145LEU0-0.0020.00225.990-0.006-0.0060.0000.0000.0000.000
144A146GLN00.0340.02227.7510.0020.0020.0000.0000.0000.000
145A147HIS00.0190.00929.1320.0000.0000.0000.0000.0000.000
146A148TYR00.0430.04134.0260.0000.0000.0000.0000.0000.000
147A149ASN00.022-0.01034.109-0.004-0.0040.0000.0000.0000.000
148A150ASP-1-0.836-0.90337.4400.0290.0290.0000.0000.0000.000
149A151TYR00.007-0.01540.664-0.003-0.0030.0000.0000.0000.000
150A152VAL0-0.004-0.01136.167-0.003-0.0030.0000.0000.0000.000
151A153LYS10.8310.91939.573-0.017-0.0170.0000.0000.0000.000
152A154SER0-0.030-0.01240.940-0.002-0.0020.0000.0000.0000.000
153A155ALA0-0.0170.00041.675-0.001-0.0010.0000.0000.0000.000
154A156LEU0-0.049-0.02937.153-0.002-0.0020.0000.0000.0000.000
155A157PRO0-0.0160.00940.3990.0010.0010.0000.0000.0000.000
156A158GLN00.003-0.02243.3490.0000.0000.0000.0000.0000.000
157A159ASP-1-0.921-0.95041.205-0.006-0.0060.0000.0000.0000.000
158A160VAL0-0.015-0.00138.877-0.001-0.0010.0000.0000.0000.000
159A161PRO0-0.002-0.00239.3650.0020.0020.0000.0000.0000.000
160A162ILE00.0480.02041.1820.0020.0020.0000.0000.0000.000
161A163ALA00.0430.02542.0430.0020.0020.0000.0000.0000.000
162A164TRP0-0.033-0.02536.1000.0020.0020.0000.0000.0000.000
163A165THR00.0210.01537.4680.0000.0000.0000.0000.0000.000
164A166VAL0-0.010-0.00234.6610.0010.0010.0000.0000.0000.000
165A167GLN0-0.005-0.01431.4040.0060.0060.0000.0000.0000.000
166A168SER0-0.033-0.02729.1600.0100.0100.0000.0000.0000.000
167A169GLN0-0.010-0.01530.665-0.005-0.0050.0000.0000.0000.000
168A170LEU0-0.0280.00222.7570.0060.0060.0000.0000.0000.000
169A171VAL00.012-0.00327.204-0.009-0.0090.0000.0000.0000.000
170A172PHE0-0.002-0.00524.3460.0050.0050.0000.0000.0000.000
171A173GLY00.026-0.02124.024-0.003-0.0030.0000.0000.0000.000
172A186ASN0-0.027-0.02921.529-0.009-0.0090.0000.0000.0000.000
173A187ASN0-0.038-0.02219.763-0.014-0.0140.0000.0000.0000.000
174A188VAL00.0500.03223.9180.0060.0060.0000.0000.0000.000
175A189ILE00.0110.00722.4540.0000.0000.0000.0000.0000.000
176A190ASN0-0.026-0.01725.888-0.006-0.0060.0000.0000.0000.000
177A191VAL0-0.011-0.00326.728-0.002-0.0020.0000.0000.0000.000
178A192TYR00.0420.03329.6880.0040.0040.0000.0000.0000.000