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: 2J5ZR

Calculation Name: 5UD9-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5UD9

Chain ID: H

ChEMBL ID:

UniProt ID:

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2453248.315793
FMO2-HF: Nuclear repulsion 2365644.631502
FMO2-HF: Total energy -87603.684292
FMO2-MP2: Total energy -87858.051234


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(H:2:VAL)


Summations of interaction energy for fragment #1(H:2:VAL)
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.
-12.829-4.3811.317-6.449-13.315-0.039
Interaction energy analysis for fragmet #1(H:2:VAL)
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 : -0.019
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].
3H4LEU00.0160.0112.448-1.1810.8730.538-0.743-1.8500.003
4H5ARG10.8580.9135.147-0.387-0.355-0.001-0.002-0.0290.000
5H6GLU-1-0.702-0.8618.854-0.279-0.2790.0000.0000.0000.000
6H7SER0-0.086-0.03211.8040.0460.0460.0000.0000.0000.000
7H8GLY00.0620.00315.149-0.016-0.0160.0000.0000.0000.000
8H9PRO00.0160.01718.3450.0110.0110.0000.0000.0000.000
9H10GLY00.0030.01521.2710.0090.0090.0000.0000.0000.000
10H11LEU0-0.028-0.01922.768-0.006-0.0060.0000.0000.0000.000
11H12VAL0-0.005-0.00824.4160.0020.0020.0000.0000.0000.000
12H13LYS10.9100.96627.1820.0230.0230.0000.0000.0000.000
13H14PRO00.027-0.00230.377-0.003-0.0030.0000.0000.0000.000
14H15SER0-0.062-0.02631.5760.0040.0040.0000.0000.0000.000
15H16GLU-1-0.915-0.95129.598-0.030-0.0300.0000.0000.0000.000
16H17THR0-0.056-0.03725.839-0.005-0.0050.0000.0000.0000.000
17H18LEU00.0100.01419.9700.0060.0060.0000.0000.0000.000
18H19SER0-0.021-0.02420.099-0.003-0.0030.0000.0000.0000.000
19H20LEU0-0.0340.00115.7190.0100.0100.0000.0000.0000.000
20H21SER0-0.031-0.02114.0210.0050.0050.0000.0000.0000.000
21H22CYS0-0.0390.0028.211-0.017-0.0170.0000.0000.0000.000
22H23THR0-0.018-0.0018.6310.0190.0190.0000.0000.0000.000
23H24VAL00.0330.0213.211-0.389-0.0840.040-0.065-0.2800.000
24H25SER00.0410.0244.028-0.426-0.170-0.001-0.080-0.1750.000
25H26GLN00.019-0.0032.088-4.217-2.5914.313-2.935-3.004-0.019
26H27ASP-1-0.786-0.8912.282-5.098-2.3323.182-2.287-3.660-0.015
27H28SER0-0.005-0.0093.0441.0690.4020.0900.858-0.2810.000
28H29ARG10.9350.9705.6810.2510.2510.0000.0000.0000.000
29H30PRO00.0220.0206.298-0.071-0.0710.0000.0000.0000.000
30H31SER00.025-0.0137.528-0.012-0.0120.0000.0000.0000.000
31H32ASP-1-0.921-0.9529.056-0.225-0.2250.0000.0000.0000.000
32H33HIS0-0.0230.0015.920-0.037-0.0370.0000.0000.0000.000
33H34SER00.0240.0289.1880.0550.0550.0000.0000.0000.000
34H35TRP0-0.061-0.0273.796-0.290-0.1120.001-0.028-0.1500.000
35H36THR0-0.0010.0009.6760.0810.0810.0000.0000.0000.000
36H37TRP00.006-0.00411.125-0.035-0.0350.0000.0000.0000.000
37H38VAL00.0140.00513.5390.0170.0170.0000.0000.0000.000
38H39ARG10.8060.88915.5870.1250.1250.0000.0000.0000.000
39H40GLN0-0.007-0.00118.171-0.014-0.0140.0000.0000.0000.000
40H41SER00.0440.03020.4540.0050.0050.0000.0000.0000.000
41H42PRO00.0310.00323.933-0.006-0.0060.0000.0000.0000.000
42H43GLY00.0200.01624.6960.0080.0080.0000.0000.0000.000
43H44LYS10.8480.92624.6780.0990.0990.0000.0000.0000.000
44H45ALA00.0430.02122.798-0.010-0.0100.0000.0000.0000.000
45H46LEU0-0.006-0.00416.3600.0040.0040.0000.0000.0000.000
46H47GLU-1-0.822-0.90319.356-0.125-0.1250.0000.0000.0000.000
47H48TRP0-0.0030.00514.9740.0020.0020.0000.0000.0000.000
48H49ILE0-0.010-0.01417.2610.0240.0240.0000.0000.0000.000
49H50GLY00.040-0.00216.7520.0250.0250.0000.0000.0000.000
50H51ASP-1-0.920-0.94513.211-0.271-0.2710.0000.0000.0000.000
51H52ILE0-0.0060.00112.9190.0330.0330.0000.0000.0000.000
52H53HIS00.0550.04112.510-0.020-0.0200.0000.0000.0000.000
53H54TYR00.0800.0289.0510.0370.0370.0000.0000.0000.000
54H55ASN0-0.021-0.00714.3390.0100.0100.0000.0000.0000.000
55H56GLY0-0.010-0.00716.7470.0140.0140.0000.0000.0000.000
56H57ALA0-0.052-0.01918.3340.0050.0050.0000.0000.0000.000
57H58THR0-0.020-0.01617.307-0.014-0.0140.0000.0000.0000.000
58H59THR0-0.047-0.02217.7940.0120.0120.0000.0000.0000.000
59H60TYR00.0430.00418.798-0.009-0.0090.0000.0000.0000.000
60H61ASN00.0190.02221.1860.0170.0170.0000.0000.0000.000
61H62PRO00.019-0.00222.7810.0080.0080.0000.0000.0000.000
62H63SER0-0.051-0.02825.9850.0080.0080.0000.0000.0000.000
63H64LEU00.0230.00122.3350.0050.0050.0000.0000.0000.000
64H65ARG10.9630.99424.6010.0970.0970.0000.0000.0000.000
65H66SER0-0.036-0.01925.6920.0010.0010.0000.0000.0000.000
66H67ARG10.8170.89926.4070.0870.0870.0000.0000.0000.000
67H68VAL0-0.035-0.00821.2710.0000.0000.0000.0000.0000.000
68H69ARG10.9360.97321.2780.0710.0710.0000.0000.0000.000
69H70ILE0-0.0010.00214.9670.0000.0000.0000.0000.0000.000
70H71GLU-1-0.951-0.96816.923-0.056-0.0560.0000.0000.0000.000
71H72LEU0-0.007-0.01211.263-0.019-0.0190.0000.0000.0000.000
72H73ASP-1-0.834-0.87713.8370.0210.0210.0000.0000.0000.000
73H74GLN00.022-0.02512.3660.0090.0090.0000.0000.0000.000
74H75SER0-0.070-0.04612.5860.0190.0190.0000.0000.0000.000
75H76ILE0-0.086-0.00710.4210.0300.0300.0000.0000.0000.000
76H77PRO00.0100.0137.2910.0510.0510.0000.0000.0000.000
77H78ARG10.9530.9498.939-0.018-0.0180.0000.0000.0000.000
78H79PHE00.0120.0177.6980.0070.0070.0000.0000.0000.000
79H80SER0-0.008-0.02012.618-0.004-0.0040.0000.0000.0000.000
80H81LEU00.0370.03215.406-0.012-0.0120.0000.0000.0000.000
81H82LYS10.9330.95617.6050.0670.0670.0000.0000.0000.000
82H83MET00.0190.01521.330-0.005-0.0050.0000.0000.0000.000
83H84THR00.006-0.01323.6470.0060.0060.0000.0000.0000.000
84H85SER00.0300.01827.354-0.003-0.0030.0000.0000.0000.000
85H86MET0-0.0530.00523.710-0.004-0.0040.0000.0000.0000.000
86H87THR00.0530.01528.4490.0070.0070.0000.0000.0000.000
87H88ALA00.0470.01228.630-0.005-0.0050.0000.0000.0000.000
88H89ALA0-0.0100.00228.942-0.004-0.0040.0000.0000.0000.000
89H90ASP-1-0.760-0.86524.813-0.092-0.0920.0000.0000.0000.000
90H91THR00.0000.02023.956-0.005-0.0050.0000.0000.0000.000
91H92GLY00.010-0.01422.396-0.003-0.0030.0000.0000.0000.000
92H93MET0-0.0580.01016.3370.0100.0100.0000.0000.0000.000
93H94TYR0-0.028-0.05216.295-0.009-0.0090.0000.0000.0000.000
94H95TYR00.0750.04011.7400.0090.0090.0000.0000.0000.000
95H97ALA00.051-0.0017.340-0.081-0.0810.0000.0000.0000.000
96H98ARG10.7590.8572.606-0.1231.3410.827-0.577-1.713-0.005
97H99ASN00.0010.0006.288-0.087-0.0870.0000.0000.0000.000
98H100ALA0-0.001-0.0026.6490.0560.0560.0000.0000.0000.000
99H101ILE00.0280.0178.2600.0610.0610.0000.0000.0000.000
100H102ARG10.8120.9206.7850.5950.5950.0000.0000.0000.000
101H103ILE00.0430.00912.6590.0170.0170.0000.0000.0000.000
102H104TYR0-0.040-0.01215.5410.0000.0000.0000.0000.0000.000
103H105GLY00.0220.01218.5540.0140.0140.0000.0000.0000.000
104H106VAL0-0.048-0.02620.351-0.003-0.0030.0000.0000.0000.000
105H107VAL00.0480.01317.950-0.003-0.0030.0000.0000.0000.000
106H108ALA0-0.030-0.01920.721-0.004-0.0040.0000.0000.0000.000
107H109LEU0-0.026-0.01224.0420.0040.0040.0000.0000.0000.000
108H110GLY0-0.0020.00121.7770.0000.0000.0000.0000.0000.000
109H111GLU-1-0.880-0.91021.242-0.106-0.1060.0000.0000.0000.000
110H112TRP0-0.031-0.03115.615-0.010-0.0100.0000.0000.0000.000
111H113PHE00.0100.00814.7770.0060.0060.0000.0000.0000.000
112H114HIS00.012-0.01411.945-0.013-0.0130.0000.0000.0000.000
113H115TYR0-0.054-0.0309.4180.0430.0430.0000.0000.0000.000
114H116GLY00.0520.02211.3430.0240.0240.0000.0000.0000.000
115H117MET0-0.051-0.0349.166-0.067-0.0670.0000.0000.0000.000
116H118ASP-1-0.765-0.8515.912-1.310-1.3100.0000.0000.0000.000
117H119VAL0-0.032-0.0062.187-1.113-0.7802.329-0.588-2.074-0.003
118H120TRP00.007-0.0085.3800.2080.310-0.001-0.002-0.0990.000
119H121GLY0-0.0050.0056.988-0.147-0.1470.0000.0000.0000.000
120H122GLN0-0.039-0.0358.3400.0100.0100.0000.0000.0000.000
121H123GLY00.0400.01811.5180.0380.0380.0000.0000.0000.000
122H124THR0-0.091-0.04713.6880.0540.0540.0000.0000.0000.000
123H125ALA0-0.008-0.00916.294-0.007-0.0070.0000.0000.0000.000
124H126VAL0-0.026-0.01119.6090.0130.0130.0000.0000.0000.000
125H127THR00.000-0.00322.191-0.003-0.0030.0000.0000.0000.000
126H128VAL0-0.0050.00425.9480.0050.0050.0000.0000.0000.000
127H129SER00.010-0.00328.4570.0020.0020.0000.0000.0000.000
128H130SER00.0760.01831.7220.0000.0000.0000.0000.0000.000
129H131ALA0-0.0130.02233.4720.0040.0040.0000.0000.0000.000
130H132SER00.002-0.01632.730-0.002-0.0020.0000.0000.0000.000
131H133THR00.0100.01128.413-0.002-0.0020.0000.0000.0000.000
132H134LYS10.8590.93730.8200.0040.0040.0000.0000.0000.000
133H135GLY00.0640.03929.856-0.003-0.0030.0000.0000.0000.000
134H136PRO0-0.040-0.01528.684-0.001-0.0010.0000.0000.0000.000
135H137SER0-0.021-0.00731.7370.0040.0040.0000.0000.0000.000
136H138VAL00.0070.00230.646-0.003-0.0030.0000.0000.0000.000
137H139PHE00.001-0.00633.8400.0030.0030.0000.0000.0000.000
138H140PRO0-0.015-0.00435.1390.0000.0000.0000.0000.0000.000
139H141LEU0-0.025-0.01033.959-0.003-0.0030.0000.0000.0000.000
140H142ALA00.0300.01236.1630.0020.0020.0000.0000.0000.000
141H143PRO00.0280.02536.838-0.003-0.0030.0000.0000.0000.000
142H144SER0-0.039-0.02038.4620.0000.0000.0000.0000.0000.000
143H145SER0-0.001-0.00441.4700.0010.0010.0000.0000.0000.000
144H146LYS10.9510.98843.983-0.013-0.0130.0000.0000.0000.000
145H147SER0-0.024-0.01944.651-0.001-0.0010.0000.0000.0000.000
146H148THR00.0500.00841.599-0.001-0.0010.0000.0000.0000.000
147H149SER00.0140.00843.1040.0010.0010.0000.0000.0000.000
148H150GLY00.0190.01940.755-0.001-0.0010.0000.0000.0000.000
149H151GLY00.0430.00938.4570.0020.0020.0000.0000.0000.000
150H152THR0-0.057-0.00833.9170.0020.0020.0000.0000.0000.000
151H153ALA00.0310.02035.304-0.003-0.0030.0000.0000.0000.000
152H154ALA00.0040.01033.7390.0020.0020.0000.0000.0000.000
153H155LEU0-0.0030.00331.535-0.001-0.0010.0000.0000.0000.000
154H156GLY00.0550.00431.391-0.001-0.0010.0000.0000.0000.000
155H157CYS0-0.095-0.01027.1840.0080.0080.0000.0000.0000.000
156H158LEU00.0230.02931.654-0.004-0.0040.0000.0000.0000.000
157H159VAL0-0.006-0.01128.6010.0040.0040.0000.0000.0000.000
158H160LYS10.9730.97631.790-0.005-0.0050.0000.0000.0000.000
159H161ASP-1-0.839-0.90333.762-0.003-0.0030.0000.0000.0000.000
160H162TYR0-0.009-0.00826.9790.0050.0050.0000.0000.0000.000
161H163PHE00.0430.02229.557-0.006-0.0060.0000.0000.0000.000
162H164PRO00.0090.01125.4360.0050.0050.0000.0000.0000.000
163H165GLU-1-0.790-0.89524.049-0.040-0.0400.0000.0000.0000.000
164H166PRO0-0.037-0.02319.999-0.004-0.0040.0000.0000.0000.000
165H167VAL0-0.004-0.02023.2400.0090.0090.0000.0000.0000.000
166H168THR0-0.041-0.01818.470-0.007-0.0070.0000.0000.0000.000
167H169VAL00.011-0.00721.7950.0080.0080.0000.0000.0000.000
168H170SER0-0.029-0.00720.4430.0000.0000.0000.0000.0000.000
169H171TRP00.0300.00422.315-0.004-0.0040.0000.0000.0000.000
170H172ASN00.009-0.00423.5570.0070.0070.0000.0000.0000.000
171H173SER0-0.011-0.01222.2260.0080.0080.0000.0000.0000.000
172H174GLY0-0.016-0.00519.1960.0230.0230.0000.0000.0000.000
173H175ALA0-0.0210.00119.5910.0100.0100.0000.0000.0000.000
174H176LEU0-0.041-0.01021.931-0.004-0.0040.0000.0000.0000.000
175H177THR00.009-0.00818.380-0.010-0.0100.0000.0000.0000.000
176H178SER0-0.004-0.00721.663-0.019-0.0190.0000.0000.0000.000
177H179GLY00.0680.02923.9450.0020.0020.0000.0000.0000.000
178H180VAL0-0.039-0.01023.209-0.003-0.0030.0000.0000.0000.000
179H181HIS00.0080.00724.377-0.006-0.0060.0000.0000.0000.000
180H182THR00.0170.00323.7320.0080.0080.0000.0000.0000.000
181H183PHE0-0.0200.00225.508-0.009-0.0090.0000.0000.0000.000
182H184PRO00.005-0.01425.9980.0020.0020.0000.0000.0000.000
183H185ALA00.0080.01327.4940.0050.0050.0000.0000.0000.000
184H186VAL0-0.027-0.00229.455-0.004-0.0040.0000.0000.0000.000
185H187LEU0-0.004-0.00831.9850.0020.0020.0000.0000.0000.000
186H188GLN0-0.059-0.05333.7780.0020.0020.0000.0000.0000.000
187H189SER00.0340.01437.179-0.001-0.0010.0000.0000.0000.000
188H190SER0-0.001-0.00238.088-0.001-0.0010.0000.0000.0000.000
189H191GLY00.0140.00635.6460.0000.0000.0000.0000.0000.000
190H192LEU0-0.079-0.01733.369-0.001-0.0010.0000.0000.0000.000
191H193TYR00.0290.00529.384-0.003-0.0030.0000.0000.0000.000
192H194SER0-0.017-0.01631.9750.0060.0060.0000.0000.0000.000
193H195LEU0-0.0040.02726.037-0.004-0.0040.0000.0000.0000.000
194H196SER00.019-0.00230.5160.0060.0060.0000.0000.0000.000
195H197SER0-0.030-0.00625.999-0.002-0.0020.0000.0000.0000.000
196H198VAL00.019-0.00728.6650.0040.0040.0000.0000.0000.000
197H199VAL00.0110.01227.368-0.001-0.0010.0000.0000.0000.000
198H200THR0-0.037-0.01629.233-0.002-0.0020.0000.0000.0000.000
199H201VAL00.0290.01529.9320.0040.0040.0000.0000.0000.000
200H202PRO00.0520.01331.219-0.005-0.0050.0000.0000.0000.000
201H203SER00.0330.01634.5130.0020.0020.0000.0000.0000.000
202H204SER0-0.027-0.01137.1980.0010.0010.0000.0000.0000.000
203H205SER0-0.025-0.00433.7610.0020.0020.0000.0000.0000.000
204H206LEU0-0.0050.00035.6840.0020.0020.0000.0000.0000.000
205H207GLY0-0.0120.00337.5440.0000.0000.0000.0000.0000.000
206H208THR0-0.005-0.00636.6320.0010.0010.0000.0000.0000.000
207H209GLN0-0.043-0.01430.0020.0060.0060.0000.0000.0000.000
208H210THR0-0.044-0.01632.110-0.003-0.0030.0000.0000.0000.000
209H211TYR00.058-0.00529.5530.0080.0080.0000.0000.0000.000
210H212ILE00.010-0.00228.377-0.006-0.0060.0000.0000.0000.000
211H214ASN00.020-0.00523.7140.0040.0040.0000.0000.0000.000
212H215VAL00.0230.01324.404-0.003-0.0030.0000.0000.0000.000
213H216ASN0-0.007-0.00519.9310.0080.0080.0000.0000.0000.000
214H217HIS00.0590.03523.368-0.004-0.0040.0000.0000.0000.000
215H218LYS10.9180.96916.8780.0570.0570.0000.0000.0000.000
216H219PRO00.0130.00322.3240.0030.0030.0000.0000.0000.000
217H220SER0-0.014-0.03724.4790.0020.0020.0000.0000.0000.000
218H221ASN0-0.082-0.03124.1230.0090.0090.0000.0000.0000.000
219H222THR00.0180.02525.7200.0070.0070.0000.0000.0000.000
220H223LYS10.9020.93521.489-0.081-0.0810.0000.0000.0000.000
221H224VAL0-0.0090.00526.6640.0010.0010.0000.0000.0000.000
222H225ASP-1-0.836-0.91426.7440.0770.0770.0000.0000.0000.000
223H226LYS10.9080.95729.485-0.033-0.0330.0000.0000.0000.000
224H227ARG10.9600.97931.789-0.056-0.0560.0000.0000.0000.000
225H228VAL0-0.043-0.03032.671-0.005-0.0050.0000.0000.0000.000
226H229GLU-1-0.909-0.95135.0680.0430.0430.0000.0000.0000.000
227H230PRO00.001-0.01538.096-0.004-0.0040.0000.0000.0000.000
228H231LYS10.9520.97740.497-0.014-0.0140.0000.0000.0000.000
229H232SER00.0200.02343.4870.0010.0010.0000.0000.0000.000