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: 2J53R

Calculation Name: 5D1X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1X

Chain ID: B

ChEMBL ID:

UniProt ID: Q2FZF0

Base Structure: X-ray

Registration Date: 2023-06-26

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2088603.356573
FMO2-HF: Nuclear repulsion 2008149.890721
FMO2-HF: Total energy -80453.465852
FMO2-MP2: Total energy -80687.973289


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(B:1:GLN)


Summations of interaction energy for fragment #1(B:1:GLN)
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.
0.8493.5940.051-1.104-1.6910.001
Interaction energy analysis for fragmet #1(B:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.012
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].
3B3GLN0-0.039-0.0253.730-0.6310.997-0.001-0.705-0.9210.002
4B4LEU00.006-0.0076.4390.0460.0460.0000.0000.0000.000
5B5VAL00.0040.0059.6070.1390.1390.0000.0000.0000.000
6B6GLN0-0.011-0.02912.6360.0420.0420.0000.0000.0000.000
7B7SER0-0.0080.00115.902-0.019-0.0190.0000.0000.0000.000
8B8GLY00.0280.02619.492-0.012-0.0120.0000.0000.0000.000
9B9SER0-0.072-0.04620.7480.0110.0110.0000.0000.0000.000
10B10GLU-1-0.754-0.86823.902-0.184-0.1840.0000.0000.0000.000
11B11VAL0-0.085-0.04326.5280.0210.0210.0000.0000.0000.000
12B12LYS10.8060.90928.9370.1460.1460.0000.0000.0000.000
13B13LYS10.8500.90832.8350.0810.0810.0000.0000.0000.000
14B14PRO00.0440.00135.564-0.005-0.0050.0000.0000.0000.000
15B15GLY0-0.0080.02436.4820.0000.0000.0000.0000.0000.000
16B16SER0-0.031-0.02334.411-0.008-0.0080.0000.0000.0000.000
17B17SER00.0450.01231.2730.0110.0110.0000.0000.0000.000
18B18VAL0-0.054-0.01925.937-0.008-0.0080.0000.0000.0000.000
19B19THR00.0210.01024.8100.0110.0110.0000.0000.0000.000
20B20LEU00.0160.02820.468-0.029-0.0290.0000.0000.0000.000
21B21SER00.012-0.00219.129-0.020-0.0200.0000.0000.0000.000
22B22CYS0-0.041-0.01813.409-0.005-0.0050.0000.0000.0000.000
23B23LYS10.8780.95511.8300.9860.9860.0000.0000.0000.000
24B24ALA00.0430.02110.029-0.058-0.0580.0000.0000.0000.000
25B25SER0-0.011-0.0146.7260.2590.2590.0000.0000.0000.000
26B26GLY00.0360.0163.413-0.615-0.5040.013-0.080-0.0450.000
27B27ASP-1-0.784-0.8623.7010.7401.2820.008-0.185-0.365-0.001
28B28THR0-0.005-0.0086.510-0.239-0.2390.0000.0000.0000.000
29B29PHE0-0.0150.00010.3250.2430.2430.0000.0000.0000.000
30B30ASN00.0420.00711.8170.0820.0820.0000.0000.0000.000
31B31THR0-0.006-0.00612.7860.0320.0320.0000.0000.0000.000
32B32HIS0-0.015-0.0029.9020.2900.2900.0000.0000.0000.000
33B33THR00.027-0.03314.048-0.095-0.0950.0000.0000.0000.000
34B34TYR0-0.107-0.06711.1690.0370.0370.0000.0000.0000.000
35B35SER00.0110.00514.929-0.017-0.0170.0000.0000.0000.000
36B36TRP0-0.024-0.01215.991-0.024-0.0240.0000.0000.0000.000
37B37VAL00.006-0.00117.5620.0250.0250.0000.0000.0000.000
38B38ARG10.7950.86619.559-0.020-0.0200.0000.0000.0000.000
39B39GLN00.0050.00221.1320.0220.0220.0000.0000.0000.000
40B40ALA00.0530.04623.560-0.015-0.0150.0000.0000.0000.000
41B41PRO00.021-0.02126.5210.0130.0130.0000.0000.0000.000
42B42GLY00.0140.02527.1380.0020.0020.0000.0000.0000.000
43B43GLN0-0.044-0.01526.7770.0050.0050.0000.0000.0000.000
44B44ARG10.9850.99024.852-0.096-0.0960.0000.0000.0000.000
45B45LEU00.0210.00918.215-0.012-0.0120.0000.0000.0000.000
46B46GLU-1-0.798-0.86422.6740.0330.0330.0000.0000.0000.000
47B47TRP0-0.006-0.00819.182-0.018-0.0180.0000.0000.0000.000
48B48ILE0-0.010-0.00121.800-0.008-0.0080.0000.0000.0000.000
49B49GLY00.0760.02121.701-0.010-0.0100.0000.0000.0000.000
50B50GLY0-0.014-0.00319.6150.0140.0140.0000.0000.0000.000
51B51ILE0-0.033-0.01218.518-0.015-0.0150.0000.0000.0000.000
52B52MET00.0400.04117.0910.0070.0070.0000.0000.0000.000
53B52PRO0-0.012-0.00616.653-0.018-0.0180.0000.0000.0000.000
54B53ILE0-0.057-0.03618.349-0.027-0.0270.0000.0000.0000.000
55B54PHE00.0110.00320.1400.0000.0000.0000.0000.0000.000
56B55ALA0-0.043-0.01022.7200.0060.0060.0000.0000.0000.000
57B56ALA00.0360.03923.5260.0070.0070.0000.0000.0000.000
58B57SER00.002-0.02222.9630.0020.0020.0000.0000.0000.000
59B58LYS10.8770.93923.9080.0080.0080.0000.0000.0000.000
60B59SER00.0650.02124.249-0.006-0.0060.0000.0000.0000.000
61B60ALA00.0030.00425.9580.0090.0090.0000.0000.0000.000
62B61PRO00.009-0.00827.470-0.009-0.0090.0000.0000.0000.000
63B62HIS0-0.014-0.01028.073-0.005-0.0050.0000.0000.0000.000
64B63LEU0-0.011-0.01227.422-0.005-0.0050.0000.0000.0000.000
65B64GLN0-0.068-0.04330.492-0.010-0.0100.0000.0000.0000.000
66B65ASP-1-0.914-0.94031.596-0.030-0.0300.0000.0000.0000.000
67B66ARG10.8070.87931.8150.0300.0300.0000.0000.0000.000
68B67LEU0-0.0070.00025.144-0.008-0.0080.0000.0000.0000.000
69B68THR00.0290.02527.3460.0130.0130.0000.0000.0000.000
70B69ILE0-0.0060.00021.283-0.013-0.0130.0000.0000.0000.000
71B70THR00.0060.01022.503-0.001-0.0010.0000.0000.0000.000
72B71ALA00.026-0.00118.470-0.018-0.0180.0000.0000.0000.000
73B72ASN0-0.0130.00719.017-0.017-0.0170.0000.0000.0000.000
74B73LYS10.9510.95617.1510.2130.2130.0000.0000.0000.000
75B74ALA00.0470.03716.324-0.089-0.0890.0000.0000.0000.000
76B75THR00.0030.00316.619-0.128-0.1280.0000.0000.0000.000
77B76ARG10.9100.9559.6661.6471.6470.0000.0000.0000.000
78B77THR0-0.021-0.00713.525-0.129-0.1290.0000.0000.0000.000
79B78ALA00.0220.01215.8560.0710.0710.0000.0000.0000.000
80B79TYR00.012-0.02817.524-0.059-0.0590.0000.0000.0000.000
81B80MET0-0.0210.00320.4960.0380.0380.0000.0000.0000.000
82B81GLU-1-0.900-0.94322.874-0.152-0.1520.0000.0000.0000.000
83B82LEU0-0.024-0.00126.5330.0150.0150.0000.0000.0000.000
84B82THR00.0200.00028.505-0.007-0.0070.0000.0000.0000.000
85B82SER00.0110.00032.2730.0100.0100.0000.0000.0000.000
86B82LEU0-0.051-0.01229.5010.0070.0070.0000.0000.0000.000
87B83THR00.0440.01933.3560.0020.0020.0000.0000.0000.000
88B84SER00.016-0.02233.042-0.005-0.0050.0000.0000.0000.000
89B85ASP-1-0.882-0.91832.472-0.005-0.0050.0000.0000.0000.000
90B86ASP-1-0.777-0.83029.365-0.027-0.0270.0000.0000.0000.000
91B87SER0-0.071-0.02928.064-0.008-0.0080.0000.0000.0000.000
92B88GLY00.0320.00626.0150.0150.0150.0000.0000.0000.000
93B89VAL0-0.050-0.01319.534-0.025-0.0250.0000.0000.0000.000
94B90TYR00.007-0.02620.4350.0210.0210.0000.0000.0000.000
95B91TYR0-0.026-0.02215.267-0.038-0.0380.0000.0000.0000.000
96B93ALA00.0400.01511.4910.0160.0160.0000.0000.0000.000
97B94ARG10.8000.8866.105-1.306-1.3060.0000.0000.0000.000
98B95ASP-1-0.757-0.84210.2330.5110.5110.0000.0000.0000.000
99B96GLY0-0.062-0.0288.9210.1450.1450.0000.0000.0000.000
100B97ARG10.9280.9569.452-1.395-1.3950.0000.0000.0000.000
101B98GLY00.000-0.00911.224-0.109-0.1090.0000.0000.0000.000
102B99ALA00.0040.00913.884-0.080-0.0800.0000.0000.0000.000
103B100LEU0-0.027-0.02412.5200.0430.0430.0000.0000.0000.000
104B101GLN00.0290.0456.011-0.046-0.0460.0000.0000.0000.000
105B102TYR0-0.006-0.0123.2290.7881.2520.031-0.134-0.3600.000
106B103TRP00.043-0.0047.719-0.220-0.2200.0000.0000.0000.000
107B104GLY00.0230.0168.685-0.111-0.1110.0000.0000.0000.000
108B105GLN0-0.020-0.00511.1840.0620.0620.0000.0000.0000.000
109B106GLY00.0360.03013.3780.0540.0540.0000.0000.0000.000
110B107THR0-0.066-0.05316.480-0.073-0.0730.0000.0000.0000.000
111B108LEU0-0.0050.01819.8100.0220.0220.0000.0000.0000.000
112B109VAL00.0240.01123.279-0.025-0.0250.0000.0000.0000.000
113B110THR0-0.020-0.01325.9810.0210.0210.0000.0000.0000.000
114B111VAL00.0310.01429.637-0.010-0.0100.0000.0000.0000.000
115B112SER00.0230.01132.7920.0100.0100.0000.0000.0000.000
116B113SER00.0750.02536.178-0.007-0.0070.0000.0000.0000.000
117B114ALA0-0.0080.02638.231-0.003-0.0030.0000.0000.0000.000
118B119SER00.019-0.00338.190-0.007-0.0070.0000.0000.0000.000
119B120THR0-0.036-0.01635.9320.0050.0050.0000.0000.0000.000
120B121LYS10.8440.92937.8900.0450.0450.0000.0000.0000.000
121B122GLY00.0560.02838.303-0.001-0.0010.0000.0000.0000.000
122B123PRO0-0.014-0.00137.2590.0040.0040.0000.0000.0000.000
123B124SER0-0.030-0.01340.099-0.002-0.0020.0000.0000.0000.000
124B125VAL0-0.012-0.00640.4430.0030.0030.0000.0000.0000.000
125B126PHE0-0.001-0.00743.214-0.001-0.0010.0000.0000.0000.000
126B127PRO00.0420.02044.6140.0020.0020.0000.0000.0000.000
127B128LEU0-0.063-0.02742.6870.0010.0010.0000.0000.0000.000
128B129ALA00.0560.02546.2560.0020.0020.0000.0000.0000.000
129B130PRO00.0090.02347.6820.0020.0020.0000.0000.0000.000
130B136SER0-0.014-0.02249.383-0.002-0.0020.0000.0000.0000.000
131B137SER0-0.043-0.00851.7650.0020.0020.0000.0000.0000.000
132B137LYS10.9260.96054.242-0.017-0.0170.0000.0000.0000.000
133B137SER00.0280.01752.9310.0020.0020.0000.0000.0000.000
134B137THR0-0.013-0.02148.959-0.002-0.0020.0000.0000.0000.000
135B137SER0-0.011-0.02247.1850.0010.0010.0000.0000.0000.000
136B137GLY00.0240.03746.4940.0000.0000.0000.0000.0000.000
137B138GLY0-0.0030.01443.9870.0040.0040.0000.0000.0000.000
138B139THR0-0.014-0.02944.993-0.002-0.0020.0000.0000.0000.000
139B140ALA00.0610.03246.032-0.003-0.0030.0000.0000.0000.000
140B141ALA0-0.0310.00042.8340.0030.0030.0000.0000.0000.000
141B142LEU00.0140.03542.494-0.002-0.0020.0000.0000.0000.000
142B143GLY00.029-0.00741.4010.0030.0030.0000.0000.0000.000
143B144CYS0-0.0220.02938.394-0.005-0.0050.0000.0000.0000.000
144B145LEU00.0170.01839.7750.0010.0010.0000.0000.0000.000
145B146VAL0-0.013-0.01836.759-0.005-0.0050.0000.0000.0000.000
146B147LYS10.8930.91938.7830.0170.0170.0000.0000.0000.000
147B148ASP-1-0.785-0.87041.088-0.028-0.0280.0000.0000.0000.000
148B149TYR0-0.021-0.01133.103-0.004-0.0040.0000.0000.0000.000
149B150PHE00.0680.03234.4260.0030.0030.0000.0000.0000.000
150B151PRO0-0.028-0.02231.103-0.006-0.0060.0000.0000.0000.000
151B152GLU-1-0.752-0.89429.145-0.029-0.0290.0000.0000.0000.000
152B153PRO0-0.054-0.01627.0800.0040.0040.0000.0000.0000.000
153B154VAL00.0110.01529.031-0.011-0.0110.0000.0000.0000.000
154B155THR0-0.037-0.02127.3980.0030.0030.0000.0000.0000.000
155B156VAL00.009-0.01730.612-0.003-0.0030.0000.0000.0000.000
156B157SER0-0.024-0.00131.5830.0060.0060.0000.0000.0000.000
157B158TRP00.0700.02033.517-0.003-0.0030.0000.0000.0000.000
158B159ASN00.0190.00235.713-0.002-0.0020.0000.0000.0000.000
159B160SER0-0.041-0.02834.189-0.002-0.0020.0000.0000.0000.000
160B161GLY0-0.018-0.00231.982-0.008-0.0080.0000.0000.0000.000
161B162ALA0-0.037-0.00832.5120.0070.0070.0000.0000.0000.000
162B163LEU0-0.029-0.00535.0540.0060.0060.0000.0000.0000.000
163B164THR00.0270.00430.373-0.002-0.0020.0000.0000.0000.000
164B165SER00.012-0.00133.3010.0080.0080.0000.0000.0000.000
165B166GLY00.0470.01735.249-0.006-0.0060.0000.0000.0000.000
166B167VAL0-0.028-0.01133.632-0.004-0.0040.0000.0000.0000.000
167B168HIS0-0.0040.00233.3580.0070.0070.0000.0000.0000.000
168B169THR0-0.0010.00131.408-0.006-0.0060.0000.0000.0000.000
169B170PHE0-0.0050.01331.5440.0060.0060.0000.0000.0000.000
170B171PRO00.004-0.00329.837-0.008-0.0080.0000.0000.0000.000
171B172ALA0-0.025-0.00631.6140.0010.0010.0000.0000.0000.000
172B173VAL0-0.011-0.00733.7470.0050.0050.0000.0000.0000.000
173B174LEU0-0.022-0.00834.943-0.006-0.0060.0000.0000.0000.000
174B175GLN0-0.025-0.02337.0140.0070.0070.0000.0000.0000.000
175B176SER00.0460.00240.713-0.003-0.0030.0000.0000.0000.000
176B177SER0-0.0130.00443.052-0.001-0.0010.0000.0000.0000.000
177B178GLY00.0100.00939.286-0.004-0.0040.0000.0000.0000.000
178B179LEU0-0.063-0.02738.303-0.006-0.0060.0000.0000.0000.000
179B180TYR00.0170.00931.7280.0020.0020.0000.0000.0000.000
180B181SER00.0040.00037.084-0.004-0.0040.0000.0000.0000.000
181B182LEU00.0230.02832.3730.0040.0040.0000.0000.0000.000
182B183SER00.002-0.00736.1600.0000.0000.0000.0000.0000.000
183B184SER0-0.003-0.00334.8390.0040.0040.0000.0000.0000.000
184B185VAL00.018-0.00236.980-0.003-0.0030.0000.0000.0000.000
185B186VAL00.0140.01537.4510.0030.0030.0000.0000.0000.000
186B187THR0-0.054-0.02839.323-0.001-0.0010.0000.0000.0000.000
187B188VAL00.0460.01441.2150.0010.0010.0000.0000.0000.000
188B189PRO00.0330.01443.6200.0010.0010.0000.0000.0000.000
189B190SER00.0070.00346.766-0.003-0.0030.0000.0000.0000.000
190B191SER0-0.001-0.01949.721-0.002-0.0020.0000.0000.0000.000
191B192SER0-0.038-0.02249.250-0.002-0.0020.0000.0000.0000.000
192B193LEU00.004-0.00345.076-0.002-0.0020.0000.0000.0000.000
193B194GLY00.0070.01148.758-0.002-0.0020.0000.0000.0000.000
194B195THR0-0.018-0.01049.853-0.002-0.0020.0000.0000.0000.000
195B196GLN0-0.065-0.01742.824-0.003-0.0030.0000.0000.0000.000
196B197THR00.0220.02745.1160.0010.0010.0000.0000.0000.000
197B198TYR00.041-0.00441.8510.0020.0020.0000.0000.0000.000
198B199ILE0-0.0110.00939.561-0.002-0.0020.0000.0000.0000.000
199B201ASN0-0.040-0.04135.314-0.002-0.0020.0000.0000.0000.000
200B202VAL00.0530.02734.9180.0010.0010.0000.0000.0000.000
201B203ASN0-0.009-0.01529.634-0.008-0.0080.0000.0000.0000.000
202B204HIS00.0460.02432.096-0.002-0.0020.0000.0000.0000.000
203B205LYS10.9710.98728.7690.1410.1410.0000.0000.0000.000
204B206PRO0-0.030-0.00132.147-0.007-0.0070.0000.0000.0000.000
205B207SER00.005-0.00635.4030.0050.0050.0000.0000.0000.000
206B208ASN0-0.029-0.01633.657-0.004-0.0040.0000.0000.0000.000
207B209THR0-0.004-0.01237.4040.0040.0040.0000.0000.0000.000
208B210LYS10.9260.96237.0140.0590.0590.0000.0000.0000.000
209B211VAL00.0230.02040.868-0.001-0.0010.0000.0000.0000.000
210B212ASP-1-0.810-0.89943.127-0.008-0.0080.0000.0000.0000.000
211B213LYN0-0.053-0.02142.7580.0000.0000.0000.0000.0000.000
212B214LYS10.9120.94446.4600.0150.0150.0000.0000.0000.000
213B215VAL00.0050.00250.0630.0020.0020.0000.0000.0000.000
214B216GLU-1-0.879-0.94752.496-0.007-0.0070.0000.0000.0000.000
215B217PRO0-0.070-0.02155.3130.0030.0030.0000.0000.0000.000