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: 6NRJZ

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2453454.100705
FMO2-HF: Nuclear repulsion 2365849.758806
FMO2-HF: Total energy -87604.341898
FMO2-MP2: Total energy -87858.720805


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.
-13.348-4.11511.042-6.88-13.396-0.043
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 : -0.042 / q_NPA : -0.024
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].
3H4LEU00.0120.0132.953-1.3410.8310.090-0.760-1.5020.003
4H5ARG10.8580.9195.269-0.376-0.343-0.001-0.002-0.0300.000
5H6GLU-1-0.732-0.8588.987-0.271-0.2710.0000.0000.0000.000
6H7SER0-0.091-0.03711.9090.0480.0480.0000.0000.0000.000
7H8GLY00.0580.00015.257-0.018-0.0180.0000.0000.0000.000
8H9PRO00.0170.01618.4420.0120.0120.0000.0000.0000.000
9H10GLY00.0070.01921.3650.0090.0090.0000.0000.0000.000
10H11LEU0-0.038-0.02222.878-0.005-0.0050.0000.0000.0000.000
11H12VAL0-0.008-0.01224.4210.0010.0010.0000.0000.0000.000
12H13LYS10.9090.96827.2600.0190.0190.0000.0000.0000.000
13H14PRO00.025-0.00130.438-0.004-0.0040.0000.0000.0000.000
14H15SER0-0.070-0.03331.6250.0040.0040.0000.0000.0000.000
15H16GLU-1-0.900-0.94529.473-0.028-0.0280.0000.0000.0000.000
16H17THR0-0.050-0.04425.807-0.005-0.0050.0000.0000.0000.000
17H18LEU0-0.0040.01420.1380.0060.0060.0000.0000.0000.000
18H19SER00.009-0.00420.048-0.004-0.0040.0000.0000.0000.000
19H20LEU0-0.0440.00315.7780.0110.0110.0000.0000.0000.000
20H21SER0-0.049-0.03114.2370.0000.0000.0000.0000.0000.000
21H22CYS0-0.041-0.0048.241-0.020-0.0200.0000.0000.0000.000
22H23THR0-0.0150.0058.7780.0110.0110.0000.0000.0000.000
23H24VAL00.0350.0203.400-0.347-0.0680.025-0.062-0.2420.000
24H25SER00.0370.0164.140-0.355-0.139-0.001-0.065-0.1500.000
25H26GLN00.014-0.0022.143-3.461-1.7883.793-2.662-2.804-0.018
26H27ASP-1-0.782-0.8842.262-6.565-3.2373.337-2.674-3.992-0.020
27H28SER0-0.014-0.0113.1131.0210.5500.0740.674-0.2780.000
28H29ARG10.9310.9725.6520.3840.3840.0000.0000.0000.000
29H30PRO00.0380.0206.132-0.054-0.0540.0000.0000.0000.000
30H31SER00.014-0.0087.4420.0060.0060.0000.0000.0000.000
31H32ASP-1-0.903-0.9589.068-0.289-0.2890.0000.0000.0000.000
32H33HIS0-0.0040.0045.893-0.004-0.0040.0000.0000.0000.000
33H34SER00.000-0.0029.1060.0590.0590.0000.0000.0000.000
34H35TRP0-0.088-0.0383.644-0.319-0.1050.003-0.039-0.1790.000
35H36THR0-0.012-0.0289.7530.0680.0680.0000.0000.0000.000
36H37TRP0-0.003-0.00611.102-0.029-0.0290.0000.0000.0000.000
37H38VAL00.0210.00913.6310.0160.0160.0000.0000.0000.000
38H39ARG10.7950.87715.5870.1160.1160.0000.0000.0000.000
39H40GLN00.0010.00418.199-0.015-0.0150.0000.0000.0000.000
40H41SER00.0480.03320.4960.0060.0060.0000.0000.0000.000
41H42PRO00.0330.00423.988-0.005-0.0050.0000.0000.0000.000
42H43GLY00.0170.01524.7680.0060.0060.0000.0000.0000.000
43H44LYS10.8450.92124.7270.0830.0830.0000.0000.0000.000
44H45ALA00.0380.02422.814-0.008-0.0080.0000.0000.0000.000
45H46LEU00.0020.00016.0810.0040.0040.0000.0000.0000.000
46H47GLU-1-0.784-0.87319.339-0.117-0.1170.0000.0000.0000.000
47H48TRP0-0.0020.00815.1580.0040.0040.0000.0000.0000.000
48H49ILE00.001-0.00517.2340.0220.0220.0000.0000.0000.000
49H50GLY00.0620.00716.7980.0220.0220.0000.0000.0000.000
50H51ASP-1-0.883-0.90513.178-0.278-0.2780.0000.0000.0000.000
51H52ILE00.0030.00912.8970.0330.0330.0000.0000.0000.000
52H53HIS00.0530.03612.518-0.016-0.0160.0000.0000.0000.000
53H54TYR00.0800.0349.6410.0090.0090.0000.0000.0000.000
54H55ASN0-0.033-0.01314.3080.0120.0120.0000.0000.0000.000
55H56GLY0-0.004-0.00516.7310.0160.0160.0000.0000.0000.000
56H57ALA0-0.051-0.01818.3390.0070.0070.0000.0000.0000.000
57H58THR0-0.012-0.01617.306-0.014-0.0140.0000.0000.0000.000
58H59THR0-0.060-0.03117.8370.0140.0140.0000.0000.0000.000
59H60TYR00.030-0.00618.842-0.008-0.0080.0000.0000.0000.000
60H61ASN00.0150.02321.2400.0160.0160.0000.0000.0000.000
61H62PRO00.012-0.00422.8440.0070.0070.0000.0000.0000.000
62H63SER0-0.053-0.03625.9730.0080.0080.0000.0000.0000.000
63H64LEU00.008-0.00622.2360.0050.0050.0000.0000.0000.000
64H65ARG10.9650.99624.6590.0980.0980.0000.0000.0000.000
65H66SER0-0.026-0.01325.7680.0000.0000.0000.0000.0000.000
66H67ARG10.7970.87826.3510.0820.0820.0000.0000.0000.000
67H68VAL0-0.026-0.00421.2500.0000.0000.0000.0000.0000.000
68H69ARG10.8760.93421.3820.0730.0730.0000.0000.0000.000
69H70ILE00.0010.00615.0760.0000.0000.0000.0000.0000.000
70H71GLU-1-0.849-0.91916.900-0.066-0.0660.0000.0000.0000.000
71H72LEU00.004-0.00111.362-0.018-0.0180.0000.0000.0000.000
72H73ASP-1-0.792-0.85513.863-0.005-0.0050.0000.0000.0000.000
73H74GLN00.031-0.02012.3540.0030.0030.0000.0000.0000.000
74H75SER0-0.071-0.04112.5760.0110.0110.0000.0000.0000.000
75H76ILE0-0.070-0.00710.5170.0270.0270.0000.0000.0000.000
76H77PRO00.0020.0137.3380.0480.0480.0000.0000.0000.000
77H78ARG10.8930.9178.9970.0110.0110.0000.0000.0000.000
78H79PHE00.0050.0117.5800.0100.0100.0000.0000.0000.000
79H80SER0-0.021-0.02712.660-0.001-0.0010.0000.0000.0000.000
80H81LEU00.0320.02415.414-0.012-0.0120.0000.0000.0000.000
81H82LYS10.8830.93517.6110.0740.0740.0000.0000.0000.000
82H83MET00.0230.01521.342-0.005-0.0050.0000.0000.0000.000
83H84THR00.014-0.00523.6600.0070.0070.0000.0000.0000.000
84H85SER00.0160.00727.369-0.002-0.0020.0000.0000.0000.000
85H86MET0-0.0400.01223.770-0.004-0.0040.0000.0000.0000.000
86H87THR00.0370.00628.4890.0070.0070.0000.0000.0000.000
87H88ALA00.0490.01228.682-0.004-0.0040.0000.0000.0000.000
88H89ALA0-0.0060.00428.999-0.003-0.0030.0000.0000.0000.000
89H90ASP-1-0.753-0.84024.832-0.085-0.0850.0000.0000.0000.000
90H91THR00.0000.01724.008-0.004-0.0040.0000.0000.0000.000
91H92GLY00.009-0.01522.459-0.002-0.0020.0000.0000.0000.000
92H93MET0-0.0460.01616.4560.0100.0100.0000.0000.0000.000
93H94TYR0-0.021-0.04716.335-0.011-0.0110.0000.0000.0000.000
94H95TYR00.0290.01211.7920.0110.0110.0000.0000.0000.000
95H97ALA00.0410.0047.315-0.069-0.0690.0000.0000.0000.000
96H98ARG10.7840.8692.3550.0971.2651.640-0.713-2.094-0.006
97H99ASN0-0.0030.0006.330-0.066-0.0660.0000.0000.0000.000
98H100ALA0-0.016-0.0076.5020.0490.0490.0000.0000.0000.000
99H101ILE00.0290.0248.1640.0690.0690.0000.0000.0000.000
100H102ARG10.7990.9196.9420.5810.5810.0000.0000.0000.000
101H103ILE00.0360.00212.6050.0200.0200.0000.0000.0000.000
102H104TYR0-0.042-0.01315.502-0.003-0.0030.0000.0000.0000.000
103H105GLY00.0300.01818.4880.0150.0150.0000.0000.0000.000
104H106VAL0-0.050-0.02420.328-0.006-0.0060.0000.0000.0000.000
105H107VAL00.0460.01118.065-0.002-0.0020.0000.0000.0000.000
106H108ALA0-0.030-0.01920.738-0.002-0.0020.0000.0000.0000.000
107H109LEU0-0.031-0.01424.0000.0050.0050.0000.0000.0000.000
108H110GLY0-0.0010.00221.6880.0010.0010.0000.0000.0000.000
109H111GLU-1-0.868-0.91121.218-0.116-0.1160.0000.0000.0000.000
110H112TRP0-0.035-0.03215.558-0.014-0.0140.0000.0000.0000.000
111H113PHE00.0120.01214.9440.0080.0080.0000.0000.0000.000
112H114HIS00.006-0.01211.932-0.013-0.0130.0000.0000.0000.000
113H115TYR0-0.054-0.0299.0080.0450.0450.0000.0000.0000.000
114H116GLY00.0540.02211.2780.0280.0280.0000.0000.0000.000
115H117MET0-0.051-0.0319.183-0.067-0.0670.0000.0000.0000.000
116H118ASP-1-0.772-0.8575.691-1.177-1.1770.0000.0000.0000.000
117H119VAL0-0.027-0.0052.252-1.177-0.6582.083-0.575-2.027-0.002
118H120TRP00.011-0.0155.3670.1600.262-0.001-0.002-0.0980.000
119H121GLY00.0090.0127.089-0.121-0.1210.0000.0000.0000.000
120H122GLN0-0.043-0.0328.4460.0020.0020.0000.0000.0000.000
121H123GLY00.0430.01911.6460.0330.0330.0000.0000.0000.000
122H124THR0-0.038-0.03313.7920.0510.0510.0000.0000.0000.000
123H125ALA0-0.007-0.00516.402-0.008-0.0080.0000.0000.0000.000
124H126VAL0-0.033-0.01419.6950.0110.0110.0000.0000.0000.000
125H127THR00.004-0.00222.280-0.002-0.0020.0000.0000.0000.000
126H128VAL0-0.0020.00526.0390.0040.0040.0000.0000.0000.000
127H129SER00.009-0.00528.5340.0020.0020.0000.0000.0000.000
128H130SER00.0750.02031.8080.0000.0000.0000.0000.0000.000
129H131ALA0-0.0120.01933.5840.0030.0030.0000.0000.0000.000
130H132SER00.007-0.01032.835-0.002-0.0020.0000.0000.0000.000
131H133THR00.0040.00328.281-0.002-0.0020.0000.0000.0000.000
132H134LYS10.8280.91330.955-0.005-0.0050.0000.0000.0000.000
133H135GLY00.0730.04730.002-0.002-0.0020.0000.0000.0000.000
134H136PRO0-0.037-0.01228.779-0.002-0.0020.0000.0000.0000.000
135H137SER0-0.017-0.00231.8920.0030.0030.0000.0000.0000.000
136H138VAL00.003-0.00230.767-0.002-0.0020.0000.0000.0000.000
137H139PHE0-0.001-0.00334.0070.0020.0020.0000.0000.0000.000
138H140PRO0-0.016-0.00235.2380.0010.0010.0000.0000.0000.000
139H141LEU0-0.022-0.00834.093-0.003-0.0030.0000.0000.0000.000
140H142ALA00.0270.00836.2600.0020.0020.0000.0000.0000.000
141H143PRO00.0460.03136.966-0.003-0.0030.0000.0000.0000.000
142H144SER0-0.036-0.03138.557-0.001-0.0010.0000.0000.0000.000
143H145SER00.0100.00341.5630.0010.0010.0000.0000.0000.000
144H146LYS10.9460.99144.093-0.019-0.0190.0000.0000.0000.000
145H147SER0-0.024-0.02244.739-0.001-0.0010.0000.0000.0000.000
146H148THR00.0340.00541.8780.0000.0000.0000.0000.0000.000
147H149SER00.0000.00743.3890.0000.0000.0000.0000.0000.000
148H150GLY00.0390.03640.6940.0000.0000.0000.0000.0000.000
149H151GLY00.0250.00438.537-0.001-0.0010.0000.0000.0000.000
150H152THR0-0.052-0.02634.0900.0030.0030.0000.0000.0000.000
151H153ALA00.0210.01635.396-0.003-0.0030.0000.0000.0000.000
152H154ALA00.0040.01033.8300.0030.0030.0000.0000.0000.000
153H155LEU0-0.0060.00131.671-0.002-0.0020.0000.0000.0000.000
154H156GLY00.0590.00631.4890.0010.0010.0000.0000.0000.000
155H157CYS0-0.090-0.00727.2880.0080.0080.0000.0000.0000.000
156H158LEU00.0200.02631.748-0.003-0.0030.0000.0000.0000.000
157H159VAL0-0.002-0.00628.7420.0030.0030.0000.0000.0000.000
158H160LYS10.9400.94631.952-0.011-0.0110.0000.0000.0000.000
159H161ASP-1-0.835-0.89733.9170.0060.0060.0000.0000.0000.000
160H162TYR0-0.011-0.03027.1670.0050.0050.0000.0000.0000.000
161H163PHE00.0580.02929.681-0.005-0.0050.0000.0000.0000.000
162H164PRO00.0040.01425.4840.0050.0050.0000.0000.0000.000
163H165GLU-1-0.778-0.86824.240-0.020-0.0200.0000.0000.0000.000
164H166PRO0-0.036-0.02120.102-0.004-0.0040.0000.0000.0000.000
165H167VAL00.004-0.01323.3800.0070.0070.0000.0000.0000.000
166H168THR0-0.017-0.00518.573-0.006-0.0060.0000.0000.0000.000
167H169VAL0-0.025-0.02621.9590.0060.0060.0000.0000.0000.000
168H170SER0-0.029-0.00620.5100.0040.0040.0000.0000.0000.000
169H171TRP00.0320.00922.417-0.008-0.0080.0000.0000.0000.000
170H172ASN0-0.002-0.01023.6600.0070.0070.0000.0000.0000.000
171H173SER0-0.009-0.01422.4360.0070.0070.0000.0000.0000.000
172H174GLY0-0.0060.00119.3000.0240.0240.0000.0000.0000.000
173H175ALA0-0.025-0.00219.6920.0130.0130.0000.0000.0000.000
174H176LEU0-0.041-0.00822.032-0.005-0.0050.0000.0000.0000.000
175H177THR00.014-0.00618.435-0.010-0.0100.0000.0000.0000.000
176H178SER00.002-0.00521.755-0.018-0.0180.0000.0000.0000.000
177H179GLY00.0590.02624.0280.0000.0000.0000.0000.0000.000
178H180VAL0-0.040-0.01123.297-0.005-0.0050.0000.0000.0000.000
179H181HIS00.0110.00824.460-0.003-0.0030.0000.0000.0000.000
180H182THR00.0180.00923.8140.0050.0050.0000.0000.0000.000
181H183PHE0-0.027-0.00125.586-0.008-0.0080.0000.0000.0000.000
182H184PRO00.017-0.00926.2290.0020.0020.0000.0000.0000.000
183H185ALA00.0030.00927.6310.0040.0040.0000.0000.0000.000
184H186VAL0-0.025-0.00229.594-0.004-0.0040.0000.0000.0000.000
185H187LEU0-0.010-0.00932.2840.0020.0020.0000.0000.0000.000
186H188GLN0-0.057-0.04333.9040.0010.0010.0000.0000.0000.000
187H189SER00.0520.02237.308-0.001-0.0010.0000.0000.0000.000
188H190SER0-0.019-0.01338.467-0.001-0.0010.0000.0000.0000.000
189H191GLY00.0160.00835.7640.0000.0000.0000.0000.0000.000
190H192LEU0-0.076-0.02133.499-0.001-0.0010.0000.0000.0000.000
191H193TYR00.0330.00828.990-0.002-0.0020.0000.0000.0000.000
192H194SER0-0.016-0.01232.1120.0060.0060.0000.0000.0000.000
193H195LEU0-0.0010.02926.093-0.003-0.0030.0000.0000.0000.000
194H196SER00.0270.00330.6940.0050.0050.0000.0000.0000.000
195H197SER0-0.032-0.01426.018-0.001-0.0010.0000.0000.0000.000
196H198VAL00.020-0.00628.7560.0030.0030.0000.0000.0000.000
197H199VAL00.0080.01027.3270.0000.0000.0000.0000.0000.000
198H200THR0-0.028-0.01129.323-0.003-0.0030.0000.0000.0000.000
199H201VAL00.0290.01629.9870.0050.0050.0000.0000.0000.000
200H202PRO00.0620.02231.329-0.006-0.0060.0000.0000.0000.000
201H203SER00.0410.02034.6000.0020.0020.0000.0000.0000.000
202H204SER0-0.025-0.01137.2300.0000.0000.0000.0000.0000.000
203H205SER0-0.031-0.01633.8480.0020.0020.0000.0000.0000.000
204H206LEU0-0.0040.00335.7480.0020.0020.0000.0000.0000.000
205H207GLY0-0.0130.00137.641-0.001-0.0010.0000.0000.0000.000
206H208THR0-0.006-0.00836.7570.0010.0010.0000.0000.0000.000
207H209GLN0-0.045-0.02030.1810.0060.0060.0000.0000.0000.000
208H210THR0-0.0010.01031.408-0.004-0.0040.0000.0000.0000.000
209H211TYR00.025-0.01129.5940.0090.0090.0000.0000.0000.000
210H212ILE00.013-0.00328.715-0.007-0.0070.0000.0000.0000.000
211H214ASN00.025-0.00323.8020.0020.0020.0000.0000.0000.000
212H215VAL00.0140.00724.491-0.001-0.0010.0000.0000.0000.000
213H216ASN0-0.0080.00120.5870.0100.0100.0000.0000.0000.000
214H217HIS00.0550.03223.528-0.003-0.0030.0000.0000.0000.000
215H218LYS10.9190.96316.8020.0380.0380.0000.0000.0000.000
216H219PRO00.0210.01322.4960.0010.0010.0000.0000.0000.000
217H220SER0-0.015-0.03924.6090.0010.0010.0000.0000.0000.000
218H221ASN0-0.077-0.03424.0240.0080.0080.0000.0000.0000.000
219H222THR00.0090.02225.8620.0060.0060.0000.0000.0000.000
220H223LYS10.8940.92621.574-0.097-0.0970.0000.0000.0000.000
221H224VAL0-0.0080.00626.8160.0000.0000.0000.0000.0000.000
222H225ASP-1-0.819-0.90126.5650.0910.0910.0000.0000.0000.000
223H226LYS10.9050.94829.493-0.044-0.0440.0000.0000.0000.000
224H227ARG10.9130.95031.893-0.059-0.0590.0000.0000.0000.000
225H228VAL0-0.039-0.02432.777-0.006-0.0060.0000.0000.0000.000
226H229GLU-1-0.867-0.92335.1710.0520.0520.0000.0000.0000.000
227H230PRO00.009-0.01038.199-0.003-0.0030.0000.0000.0000.000
228H231LYS10.9230.96640.597-0.022-0.0220.0000.0000.0000.000
229H232SER00.0240.02443.5870.0000.0000.0000.0000.0000.000