FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: K3V83

Calculation Name: 3DR5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DR5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NRD3

Base Structure: X-ray

Registration Date: 2023-03-14

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2358287.231433
FMO2-HF: Nuclear repulsion 2277460.63314
FMO2-HF: Total energy -80826.598294
FMO2-MP2: Total energy -81064.601618


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:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-20.868-13.6154.844-5.961-6.136-0.059
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.030
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].
3A5PHE00.0420.0293.101-2.4990.733-0.004-1.554-1.6740.002
4A6GLU-1-0.769-0.8982.078-18.934-15.2524.849-4.378-4.153-0.061
5A7TYR0-0.0040.0324.5430.5010.840-0.001-0.029-0.3090.000
6A8LEU0-0.0110.0046.879-0.002-0.0020.0000.0000.0000.000
7A9ARG10.8930.9287.4400.8510.8510.0000.0000.0000.000
8A10THR0-0.016-0.0178.2330.1420.1420.0000.0000.0000.000
9A11TYR0-0.053-0.00110.6080.0100.0100.0000.0000.0000.000
10A12VAL00.0400.00412.523-0.018-0.0180.0000.0000.0000.000
11A13GLU-1-0.859-0.91612.540-0.229-0.2290.0000.0000.0000.000
12A14SER0-0.132-0.09214.0640.0260.0260.0000.0000.0000.000
13A15THR0-0.051-0.02816.1760.0170.0170.0000.0000.0000.000
14A16THR0-0.049-0.01117.650-0.017-0.0170.0000.0000.0000.000
15A17GLU-1-0.991-0.99019.9900.0340.0340.0000.0000.0000.000
16A18THR0-0.024-0.01322.092-0.008-0.0080.0000.0000.0000.000
17A19ASP-1-0.793-0.89224.001-0.008-0.0080.0000.0000.0000.000
18A20ALA0-0.005-0.01425.978-0.003-0.0030.0000.0000.0000.000
19A21ALA00.0200.01128.165-0.003-0.0030.0000.0000.0000.000
20A22VAL0-0.006-0.01322.892-0.005-0.0050.0000.0000.0000.000
21A23ALA0-0.021-0.01423.465-0.009-0.0090.0000.0000.0000.000
22A24ARG10.7930.86624.5310.0100.0100.0000.0000.0000.000
23A25ALA00.0060.00225.831-0.004-0.0040.0000.0000.0000.000
24A26ARG10.7980.87118.1280.1030.1030.0000.0000.0000.000
25A27GLU-1-0.916-0.94922.600-0.021-0.0210.0000.0000.0000.000
26A28ASP-1-0.850-0.92224.508-0.027-0.0270.0000.0000.0000.000
27A29ALA0-0.040-0.03323.073-0.003-0.0030.0000.0000.0000.000
28A30ALA0-0.0040.00821.290-0.008-0.0080.0000.0000.0000.000
29A31GLU-1-0.957-0.97222.816-0.018-0.0180.0000.0000.0000.000
30A32PHE0-0.098-0.05026.2210.0040.0040.0000.0000.0000.000
31A33GLY0-0.042-0.00623.223-0.002-0.0020.0000.0000.0000.000
32A34LEU0-0.081-0.04023.713-0.008-0.0080.0000.0000.0000.000
33A35PRO0-0.006-0.01020.299-0.009-0.0090.0000.0000.0000.000
34A36ALA00.0230.00719.3980.0140.0140.0000.0000.0000.000
35A37PRO00.0040.01117.194-0.024-0.0240.0000.0000.0000.000
36A38ASP-1-0.778-0.86512.685-0.281-0.2810.0000.0000.0000.000
37A39GLU-1-0.730-0.83615.540-0.045-0.0450.0000.0000.0000.000
38A40MET00.0020.00911.940-0.001-0.0010.0000.0000.0000.000
39A41THR0-0.022-0.04115.0260.0200.0200.0000.0000.0000.000
40A42GLY00.0000.00017.0820.0190.0190.0000.0000.0000.000
41A43GLN0-0.008-0.01818.4980.0090.0090.0000.0000.0000.000
42A44LEU0-0.0100.00718.3050.0120.0120.0000.0000.0000.000
43A45LEU0-0.032-0.02220.5800.0090.0090.0000.0000.0000.000
44A46THR00.000-0.01623.2280.0060.0060.0000.0000.0000.000
45A47THR0-0.031-0.01822.7290.0080.0080.0000.0000.0000.000
46A48LEU00.0020.01623.1020.0050.0050.0000.0000.0000.000
47A49ALA0-0.0210.01026.4460.0040.0040.0000.0000.0000.000
48A50ALA00.0100.01228.2740.0040.0040.0000.0000.0000.000
49A51THR0-0.099-0.05927.6280.0020.0020.0000.0000.0000.000
50A52THR0-0.060-0.03729.4570.0030.0030.0000.0000.0000.000
51A53ASN00.0360.00631.8630.0040.0040.0000.0000.0000.000
52A54GLY00.0520.03335.6560.0000.0000.0000.0000.0000.000
53A55ASN0-0.066-0.04637.3920.0020.0020.0000.0000.0000.000
54A56GLY0-0.027-0.01340.562-0.001-0.0010.0000.0000.0000.000
55A57SER0-0.072-0.03536.351-0.001-0.0010.0000.0000.0000.000
56A58THR00.000-0.01439.0430.0020.0020.0000.0000.0000.000
57A59GLY00.0250.01535.8830.0010.0010.0000.0000.0000.000
58A60ALA0-0.0150.00230.801-0.002-0.0020.0000.0000.0000.000
59A61ILE0-0.024-0.01631.6260.0030.0030.0000.0000.0000.000
60A62ALA00.0090.01628.349-0.004-0.0040.0000.0000.0000.000
61A63ILE0-0.037-0.03128.6150.0050.0050.0000.0000.0000.000
62A64THR00.0490.01024.598-0.007-0.0070.0000.0000.0000.000
63A65PRO00.0640.03525.7310.0060.0060.0000.0000.0000.000
64A66ALA00.0270.02724.4630.0070.0070.0000.0000.0000.000
65A67ALA0-0.026-0.02826.050-0.002-0.0020.0000.0000.0000.000
66A68GLY00.0290.01228.6220.0020.0020.0000.0000.0000.000
67A69LEU00.0400.02820.8670.0030.0030.0000.0000.0000.000
68A70VAL0-0.001-0.00622.9500.0020.0020.0000.0000.0000.000
69A71GLY00.022-0.01825.0160.0020.0020.0000.0000.0000.000
70A72LEU00.0080.00726.9250.0040.0040.0000.0000.0000.000
71A73TYR0-0.031-0.01820.367-0.002-0.0020.0000.0000.0000.000
72A74ILE0-0.013-0.00425.6390.0030.0030.0000.0000.0000.000
73A75LEU0-0.057-0.04227.9810.0030.0030.0000.0000.0000.000
74A76ASN00.0030.01426.5370.0050.0050.0000.0000.0000.000
75A77GLY0-0.0030.00929.2320.0030.0030.0000.0000.0000.000
76A78LEU0-0.063-0.02330.0770.0010.0010.0000.0000.0000.000
77A79ALA00.0430.03232.7930.0030.0030.0000.0000.0000.000
78A80ASP-1-0.846-0.94036.303-0.017-0.0170.0000.0000.0000.000
79A81ASN0-0.119-0.04638.7060.0000.0000.0000.0000.0000.000
80A82THR0-0.016-0.01236.516-0.002-0.0020.0000.0000.0000.000
81A83THR0-0.040-0.02537.5910.0010.0010.0000.0000.0000.000
82A84LEU00.0300.03630.734-0.002-0.0020.0000.0000.0000.000
83A85THR0-0.040-0.02934.3430.0030.0030.0000.0000.0000.000
84A86CYS0-0.0130.00632.482-0.004-0.0040.0000.0000.0000.000
85A87ILE0-0.027-0.02232.3100.0040.0040.0000.0000.0000.000
86A88ASP-1-0.741-0.86830.940-0.060-0.0600.0000.0000.0000.000
87A89PRO0-0.013-0.00833.0150.0040.0040.0000.0000.0000.000
88A90GLU-1-0.869-0.92533.414-0.041-0.0410.0000.0000.0000.000
89A91SER0-0.030-0.02635.4570.0000.0000.0000.0000.0000.000
90A92GLU-1-0.845-0.94132.392-0.037-0.0370.0000.0000.0000.000
91A93HIS10.9240.95230.9110.0520.0520.0000.0000.0000.000
92A94GLN00.0310.04433.0160.0010.0010.0000.0000.0000.000
93A95ARG10.8600.91735.7750.0190.0190.0000.0000.0000.000
94A96GLN00.0400.01730.614-0.001-0.0010.0000.0000.0000.000
95A97ALA00.0070.01231.7270.0010.0010.0000.0000.0000.000
96A98LYS10.8840.92232.6850.0270.0270.0000.0000.0000.000
97A99ALA0-0.060-0.01634.5770.0030.0030.0000.0000.0000.000
98A100LEU00.0740.05328.7320.0020.0020.0000.0000.0000.000
99A101PHE0-0.016-0.01530.5540.0020.0020.0000.0000.0000.000
100A102ARG10.9220.96234.2130.0140.0140.0000.0000.0000.000
101A103GLU-1-0.908-0.93233.505-0.008-0.0080.0000.0000.0000.000
102A104ALA00.0440.03931.9680.0030.0030.0000.0000.0000.000
103A105GLY0-0.007-0.00433.8650.0000.0000.0000.0000.0000.000
104A106TYR0-0.036-0.01831.3040.0000.0000.0000.0000.0000.000
105A107SER00.002-0.00337.2200.0010.0010.0000.0000.0000.000
106A108PRO00.024-0.02139.334-0.002-0.0020.0000.0000.0000.000
107A109SER0-0.047-0.00941.016-0.001-0.0010.0000.0000.0000.000
108A110ARG10.8940.96835.5590.0220.0220.0000.0000.0000.000
109A111VAL00.0070.01835.065-0.003-0.0030.0000.0000.0000.000
110A112ARG10.9010.95736.9670.0330.0330.0000.0000.0000.000
111A113PHE0-0.001-0.01632.999-0.002-0.0020.0000.0000.0000.000
112A114LEU0-0.025-0.00636.9000.0030.0030.0000.0000.0000.000
113A115LEU0-0.027-0.01237.081-0.002-0.0020.0000.0000.0000.000
114A116SER0-0.042-0.02137.1270.0020.0020.0000.0000.0000.000
115A117ARG10.9550.96635.3390.0410.0410.0000.0000.0000.000
116A118PRO00.0730.01031.4530.0030.0030.0000.0000.0000.000
117A119LEU00.004-0.01132.7330.0030.0030.0000.0000.0000.000
118A120ASP-1-0.860-0.88936.032-0.038-0.0380.0000.0000.0000.000
119A121VAL00.003-0.01937.2470.0020.0020.0000.0000.0000.000
120A122MET00.0250.03032.9710.0010.0010.0000.0000.0000.000
121A123SER0-0.0350.00438.1840.0020.0020.0000.0000.0000.000
122A124ARG10.8460.89641.3660.0330.0330.0000.0000.0000.000
123A125LEU0-0.0330.01037.4580.0020.0020.0000.0000.0000.000
124A126ALA00.0130.00841.5020.0000.0000.0000.0000.0000.000
125A127ASN00.033-0.00640.589-0.003-0.0030.0000.0000.0000.000
126A128ASP-1-0.886-0.95339.280-0.031-0.0310.0000.0000.0000.000
127A129SER0-0.0170.00239.2440.0020.0020.0000.0000.0000.000
128A130TYR0-0.002-0.00434.6120.0010.0010.0000.0000.0000.000
129A131GLN00.0660.05132.4730.0010.0010.0000.0000.0000.000
130A132LEU00.007-0.00126.520-0.002-0.0020.0000.0000.0000.000
131A133VAL0-0.0080.00129.1880.0030.0030.0000.0000.0000.000
132A134PHE00.0430.02721.318-0.002-0.0020.0000.0000.0000.000
133A135GLY00.002-0.00525.2420.0070.0070.0000.0000.0000.000
134A136GLN0-0.044-0.03319.662-0.005-0.0050.0000.0000.0000.000
135A137VAL0-0.035-0.02824.3230.0080.0080.0000.0000.0000.000
136A138SER00.0360.00724.010-0.011-0.0110.0000.0000.0000.000
137A139PRO00.0250.00022.6500.0060.0060.0000.0000.0000.000
138A140MET0-0.021-0.01724.7550.0060.0060.0000.0000.0000.000
139A141ASP-1-0.897-0.92628.019-0.067-0.0670.0000.0000.0000.000
140A142LEU0-0.0080.00422.9560.0040.0040.0000.0000.0000.000
141A143LYS10.8850.94227.5760.0580.0580.0000.0000.0000.000
142A144ALA00.0160.00930.2960.0030.0030.0000.0000.0000.000
143A145LEU00.0170.00327.3830.0040.0040.0000.0000.0000.000
144A146VAL00.0120.00928.3960.0030.0030.0000.0000.0000.000
145A147ASP-1-0.813-0.87231.028-0.049-0.0490.0000.0000.0000.000
146A148ALA0-0.052-0.02534.1770.0030.0030.0000.0000.0000.000
147A149ALA00.020-0.00931.6180.0030.0030.0000.0000.0000.000
148A150TRP00.0020.01830.4360.0020.0020.0000.0000.0000.000
149A151PRO0-0.0070.00334.5080.0020.0020.0000.0000.0000.000
150A152LEU00.0190.01835.7130.0020.0020.0000.0000.0000.000
151A153LEU0-0.0120.01230.6220.0020.0020.0000.0000.0000.000
152A154ARG10.8810.97035.2790.0320.0320.0000.0000.0000.000
153A155ARG10.8710.90134.9370.0340.0340.0000.0000.0000.000
154A156GLY0-0.041-0.01533.0240.0020.0020.0000.0000.0000.000
155A157GLY0-0.028-0.00831.939-0.001-0.0010.0000.0000.0000.000
156A158ALA0-0.004-0.00426.711-0.002-0.0020.0000.0000.0000.000
157A159LEU00.0080.01626.9210.0010.0010.0000.0000.0000.000
158A160VAL0-0.014-0.02321.761-0.003-0.0030.0000.0000.0000.000
159A161LEU0-0.015-0.01422.7280.0020.0020.0000.0000.0000.000
160A162ALA00.0470.00919.193-0.008-0.0080.0000.0000.0000.000
161A163ASP-1-0.830-0.91616.059-0.221-0.2210.0000.0000.0000.000
162A164ALA0-0.0040.00617.6300.0040.0040.0000.0000.0000.000
163A165LEU0-0.042-0.01715.9340.0120.0120.0000.0000.0000.000
164A166LEU0-0.0090.00416.2660.0050.0050.0000.0000.0000.000
165A167ASP-1-0.857-0.94511.194-0.410-0.4100.0000.0000.0000.000
166A168GLY0-0.067-0.02312.1580.0130.0130.0000.0000.0000.000
167A169THR0-0.099-0.05914.5550.0150.0150.0000.0000.0000.000
168A170ILE0-0.046-0.02216.3920.0130.0130.0000.0000.0000.000
169A171ALA0-0.008-0.00918.6270.0020.0020.0000.0000.0000.000
170A172ASP-1-0.734-0.83818.074-0.128-0.1280.0000.0000.0000.000
171A173GLN0-0.036-0.02020.620-0.002-0.0020.0000.0000.0000.000
172A174THR0-0.056-0.04920.0520.0020.0020.0000.0000.0000.000
173A175ARG10.8940.94015.2280.1750.1750.0000.0000.0000.000
174A176LYS10.8700.94721.7950.0820.0820.0000.0000.0000.000
175A177ASP-1-0.797-0.90323.493-0.113-0.1130.0000.0000.0000.000
176A178ARG10.7570.83724.3380.1020.1020.0000.0000.0000.000
177A179ASP-1-0.763-0.87623.363-0.100-0.1000.0000.0000.0000.000
178A180THR00.0240.02221.299-0.003-0.0030.0000.0000.0000.000
179A181GLN0-0.058-0.02322.8980.0050.0050.0000.0000.0000.000
180A182ALA00.0160.02026.2620.0040.0040.0000.0000.0000.000
181A183ALA00.0480.01121.6520.0020.0020.0000.0000.0000.000
182A184ARG00.0260.02422.254-0.002-0.0020.0000.0000.0000.000
183A185ASP-1-0.929-0.96124.325-0.062-0.0620.0000.0000.0000.000
184A186ALA00.0320.01625.2200.0040.0040.0000.0000.0000.000
185A187ASP-1-0.783-0.86421.999-0.088-0.0880.0000.0000.0000.000
186A188GLU-1-0.869-0.93924.560-0.065-0.0650.0000.0000.0000.000
187A189TYR0-0.036-0.04427.2890.0050.0050.0000.0000.0000.000
188A190ILE0-0.022-0.01325.2270.0030.0030.0000.0000.0000.000
189A191ARG10.6980.82923.6920.0760.0760.0000.0000.0000.000
190A192SER0-0.084-0.04127.8530.0030.0030.0000.0000.0000.000
191A193ILE0-0.030-0.00430.8220.0030.0030.0000.0000.0000.000
192A194GLU-1-0.882-0.94132.377-0.046-0.0460.0000.0000.0000.000
193A195GLY0-0.046-0.02334.8500.0010.0010.0000.0000.0000.000
194A196ALA0-0.011-0.01130.2440.0000.0000.0000.0000.0000.000
195A197HIS0-0.035-0.01127.6820.0020.0020.0000.0000.0000.000
196A198VAL00.0380.00923.284-0.002-0.0020.0000.0000.0000.000
197A199ALA0-0.0130.00221.0370.0010.0010.0000.0000.0000.000
198A200ARG10.8410.90518.0510.0870.0870.0000.0000.0000.000
199A201LEU0-0.003-0.00815.5250.0070.0070.0000.0000.0000.000
200A202PRO00.0010.0039.950-0.006-0.0060.0000.0000.0000.000
201A203LEU0-0.0060.00010.746-0.058-0.0580.0000.0000.0000.000
202A204GLY00.0320.02612.1760.0360.0360.0000.0000.0000.000
203A205ALA00.0230.02011.428-0.057-0.0570.0000.0000.0000.000
204A206GLY0-0.020-0.01613.4310.0360.0360.0000.0000.0000.000
205A207LEU0-0.028-0.00714.7050.0180.0180.0000.0000.0000.000
206A208THR00.0460.01217.5830.0120.0120.0000.0000.0000.000
207A209VAL0-0.024-0.01220.8210.0030.0030.0000.0000.0000.000
208A210VAL00.0210.00723.2700.0030.0030.0000.0000.0000.000
209A211THR0-0.015-0.01626.6150.0020.0020.0000.0000.0000.000
210A212LYS10.8350.91629.1800.0430.0430.0000.0000.0000.000
211A213ALA00.0510.04032.8650.0020.0020.0000.0000.0000.000
212A214LEU00.0190.00933.9960.0020.0020.0000.0000.0000.000
213A215GLU-1-1.030-1.01736.998-0.031-0.0310.0000.0000.0000.000
214A216HIS00.0250.00834.4920.0010.0010.0000.0000.0000.000
215A217HIS00.0050.01539.6290.0010.0010.0000.0000.0000.000
216A218HIS00.0080.00638.095-0.001-0.0010.0000.0000.0000.000