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: R9K88

Calculation Name: 4NRX-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NRX

Chain ID: H

ChEMBL ID:

UniProt ID: Q9QQN5

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2437328.739309
FMO2-HF: Nuclear repulsion 2349996.535453
FMO2-HF: Total energy -87332.203856
FMO2-MP2: Total energy -87586.77836


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:1:GLN)


Summations of interaction energy for fragment #1(H: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.
-10.072-6.9563.252-2.596-3.7720.024
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.021
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].
3H3GLN0-0.030-0.0082.148-9.255-6.4673.254-2.469-3.5740.024
4H4LEU0-0.006-0.0015.315-0.565-0.550-0.001-0.002-0.0120.000
5H5VAL00.0150.0078.8960.2760.2760.0000.0000.0000.000
6H6GLN00.000-0.02711.333-0.175-0.1750.0000.0000.0000.000
7H7SER00.0330.02315.0020.0660.0660.0000.0000.0000.000
8H8GLY0-0.001-0.00618.3050.0270.0270.0000.0000.0000.000
9H9ALA0-0.027-0.00620.507-0.018-0.0180.0000.0000.0000.000
10H10GLU-1-0.871-0.94822.7450.2420.2420.0000.0000.0000.000
11H11VAL0-0.042-0.03326.245-0.006-0.0060.0000.0000.0000.000
12H12LYS10.8320.92329.243-0.162-0.1620.0000.0000.0000.000
13H13LYS10.8690.92432.021-0.139-0.1390.0000.0000.0000.000
14H14PRO0-0.014-0.02335.4080.0000.0000.0000.0000.0000.000
15H15GLY00.0120.01436.523-0.004-0.0040.0000.0000.0000.000
16H16GLU-1-0.820-0.89133.3500.1400.1400.0000.0000.0000.000
17H17SER00.0130.02432.0920.0030.0030.0000.0000.0000.000
18H18LEU0-0.032-0.01425.6670.0080.0080.0000.0000.0000.000
19H19LYS10.8710.95123.657-0.136-0.1360.0000.0000.0000.000
20H20ILE00.0120.04320.9140.0180.0180.0000.0000.0000.000
21H21SER00.001-0.02718.495-0.017-0.0170.0000.0000.0000.000
22H22CYS0-0.019-0.00813.4000.0900.0900.0000.0000.0000.000
23H23LYS10.9130.97411.966-0.388-0.3880.0000.0000.0000.000
24H24VAL0-0.0040.0029.4420.1480.1480.0000.0000.0000.000
25H25SER0-0.029-0.0206.1330.1110.1110.0000.0000.0000.000
26H26GLY00.0730.0244.102-0.460-0.2840.000-0.108-0.0680.000
27H27TYR0-0.008-0.0114.550-0.361-0.224-0.001-0.017-0.1180.000
28H28ASN00.0380.0247.3700.2770.2770.0000.0000.0000.000
29H29PHE00.0520.02711.1430.0630.0630.0000.0000.0000.000
30H30ALA0-0.012-0.00312.8140.0590.0590.0000.0000.0000.000
31H31SER0-0.054-0.03712.9430.0090.0090.0000.0000.0000.000
32H32GLU-1-0.795-0.87511.984-0.388-0.3880.0000.0000.0000.000
33H33TRP0-0.0120.00214.8850.0330.0330.0000.0000.0000.000
34H34ILE0-0.036-0.01413.289-0.026-0.0260.0000.0000.0000.000
35H35GLY00.0430.01316.3400.0060.0060.0000.0000.0000.000
36H36TRP0-0.024-0.00217.5870.0440.0440.0000.0000.0000.000
37H37VAL00.001-0.00119.282-0.027-0.0270.0000.0000.0000.000
38H38ARG10.8160.88021.145-0.080-0.0800.0000.0000.0000.000
39H39GLN00.0210.01622.2570.0130.0130.0000.0000.0000.000
40H40MET00.0060.01024.6770.0130.0130.0000.0000.0000.000
41H41PRO00.0170.00327.7580.0040.0040.0000.0000.0000.000
42H42GLY00.0250.01728.253-0.013-0.0130.0000.0000.0000.000
43H43LYS10.8630.93528.146-0.119-0.1190.0000.0000.0000.000
44H44GLY00.0560.03026.1280.0120.0120.0000.0000.0000.000
45H45LEU00.0010.00320.0860.0080.0080.0000.0000.0000.000
46H46GLU-1-0.757-0.85324.0560.0860.0860.0000.0000.0000.000
47H47TRP0-0.004-0.01120.8200.0180.0180.0000.0000.0000.000
48H48MET0-0.0330.00022.941-0.005-0.0050.0000.0000.0000.000
49H49GLY00.0360.01823.387-0.008-0.0080.0000.0000.0000.000
50H50ILE0-0.073-0.02819.4730.0120.0120.0000.0000.0000.000
51H51ILE00.0100.00019.4040.0070.0070.0000.0000.0000.000
52H52TYR00.0100.00617.650-0.017-0.0170.0000.0000.0000.000
53H52PRO0-0.007-0.00816.3520.0160.0160.0000.0000.0000.000
54H53GLY00.0220.02319.1090.0040.0040.0000.0000.0000.000
55H54ASP-1-0.904-0.95820.122-0.092-0.0920.0000.0000.0000.000
56H55SER0-0.048-0.01722.7640.0200.0200.0000.0000.0000.000
57H56ASP-1-0.786-0.87624.186-0.042-0.0420.0000.0000.0000.000
58H57THR0-0.032-0.02623.9660.0000.0000.0000.0000.0000.000
59H58LYS10.7920.88925.0940.0500.0500.0000.0000.0000.000
60H59TYR00.0740.03325.3580.0080.0080.0000.0000.0000.000
61H60SER00.0250.01927.662-0.008-0.0080.0000.0000.0000.000
62H61PRO00.0360.00429.2490.0050.0050.0000.0000.0000.000
63H62SER0-0.021-0.00931.373-0.001-0.0010.0000.0000.0000.000
64H63PHE00.001-0.01528.6490.0080.0080.0000.0000.0000.000
65H64GLN00.0300.01830.7360.0010.0010.0000.0000.0000.000
66H65GLY0-0.009-0.00231.897-0.001-0.0010.0000.0000.0000.000
67H66GLN0-0.069-0.02131.8210.0060.0060.0000.0000.0000.000
68H67VAL0-0.050-0.02127.2680.0090.0090.0000.0000.0000.000
69H68ILE0-0.025-0.00827.372-0.011-0.0110.0000.0000.0000.000
70H69ILE00.0100.00721.7450.0180.0180.0000.0000.0000.000
71H70SER0-0.008-0.01522.973-0.010-0.0100.0000.0000.0000.000
72H71ALA0-0.020-0.02819.1570.0130.0130.0000.0000.0000.000
73H72ASP-1-0.812-0.87819.5590.0230.0230.0000.0000.0000.000
74H73LYS10.8780.91717.3180.1120.1120.0000.0000.0000.000
75H74SER0-0.053-0.03217.321-0.025-0.0250.0000.0000.0000.000
76H75ILE00.0260.01716.7350.0070.0070.0000.0000.0000.000
77H76ASN0-0.039-0.01110.9820.0850.0850.0000.0000.0000.000
78H77THR00.002-0.00613.8350.0850.0850.0000.0000.0000.000
79H78ALA00.0300.02016.167-0.041-0.0410.0000.0000.0000.000
80H79TYR00.019-0.02117.9790.0680.0680.0000.0000.0000.000
81H80LEU00.0260.02120.846-0.025-0.0250.0000.0000.0000.000
82H81GLN0-0.006-0.00423.2500.0150.0150.0000.0000.0000.000
83H82TRP00.0800.03024.574-0.008-0.0080.0000.0000.0000.000
84H82SER00.019-0.00330.1750.0060.0060.0000.0000.0000.000
85H82SER00.003-0.00633.596-0.002-0.0020.0000.0000.0000.000
86H82LEU0-0.0400.00029.310-0.003-0.0030.0000.0000.0000.000
87H83LYS10.8980.93433.152-0.096-0.0960.0000.0000.0000.000
88H84ALA00.0660.02333.6570.0070.0070.0000.0000.0000.000
89H85SER0-0.009-0.02033.6360.0050.0050.0000.0000.0000.000
90H86ASP-1-0.820-0.88629.8590.1050.1050.0000.0000.0000.000
91H87THR00.0070.02528.6870.0170.0170.0000.0000.0000.000
92H88ALA0-0.035-0.01725.983-0.011-0.0110.0000.0000.0000.000
93H89ILE0-0.0060.01020.3120.0160.0160.0000.0000.0000.000
94H90TYR0-0.019-0.03721.148-0.036-0.0360.0000.0000.0000.000
95H91TYR00.020-0.00116.3270.0610.0610.0000.0000.0000.000
96H92CYS0-0.046-0.01915.006-0.064-0.0640.0000.0000.0000.000
97H93ALA00.0550.01213.1230.0750.0750.0000.0000.0000.000
98H94ARG10.8230.8897.7290.7870.7870.0000.0000.0000.000
99H95GLN00.0010.01012.9730.0230.0230.0000.0000.0000.000
100H96ASN0-0.010-0.01010.996-0.014-0.0140.0000.0000.0000.000
101H97HIS10.8460.90214.1560.3840.3840.0000.0000.0000.000
102H98TYR00.003-0.00311.683-0.019-0.0190.0000.0000.0000.000
103H99GLY00.0290.01317.6020.0290.0290.0000.0000.0000.000
104H100SER0-0.0020.00119.592-0.018-0.0180.0000.0000.0000.000
105H100GLY00.014-0.01721.6150.0150.0150.0000.0000.0000.000
106H100SER0-0.054-0.00123.874-0.009-0.0090.0000.0000.0000.000
107H100TYR00.004-0.00123.795-0.005-0.0050.0000.0000.0000.000
108H100PHE00.009-0.00425.8060.0050.0050.0000.0000.0000.000
109H100TYR00.0340.01328.5230.0090.0090.0000.0000.0000.000
110H100ARG10.9480.96926.0620.0920.0920.0000.0000.0000.000
111H100THR00.0450.03224.4270.0070.0070.0000.0000.0000.000
112H100ALA0-0.017-0.00725.016-0.005-0.0050.0000.0000.0000.000
113H100TYR0-0.032-0.01220.513-0.004-0.0040.0000.0000.0000.000
114H100TYR00.0280.02420.1580.0130.0130.0000.0000.0000.000
115H100TYR0-0.001-0.01618.186-0.032-0.0320.0000.0000.0000.000
116H100ALA0-0.020-0.01015.6950.0260.0260.0000.0000.0000.000
117H100MET0-0.046-0.01214.810-0.020-0.0200.0000.0000.0000.000
118H101ASP-1-0.736-0.82610.086-0.421-0.4210.0000.0000.0000.000
119H102VAL0-0.0100.0026.5930.0310.0310.0000.0000.0000.000
120H103TRP00.005-0.0279.640-0.052-0.0520.0000.0000.0000.000
121H104GLY00.0270.01910.0340.1930.1930.0000.0000.0000.000
122H105GLN0-0.032-0.01711.860-0.021-0.0210.0000.0000.0000.000
123H106GLY0-0.0090.01013.373-0.069-0.0690.0000.0000.0000.000
124H107THR0-0.073-0.04016.8480.0540.0540.0000.0000.0000.000
125H108THR0-0.011-0.01019.732-0.025-0.0250.0000.0000.0000.000
126H109VAL00.0210.01923.1030.0110.0110.0000.0000.0000.000
127H110THR0-0.011-0.01326.090-0.014-0.0140.0000.0000.0000.000
128H111VAL00.0090.00429.6190.0000.0000.0000.0000.0000.000
129H112SER0-0.001-0.00332.723-0.012-0.0120.0000.0000.0000.000
130H113SER00.0450.01235.4230.0050.0050.0000.0000.0000.000
131H114ALA00.0110.02735.617-0.002-0.0020.0000.0000.0000.000
132H115SER00.003-0.00135.7510.0010.0010.0000.0000.0000.000
133H116THR0-0.006-0.01429.689-0.003-0.0030.0000.0000.0000.000
134H117LYS10.8170.91132.137-0.175-0.1750.0000.0000.0000.000
135H118GLY00.0850.05129.7920.0100.0100.0000.0000.0000.000
136H119PRO0-0.063-0.01827.908-0.017-0.0170.0000.0000.0000.000
137H120SER00.0140.00931.1850.0020.0020.0000.0000.0000.000
138H121VAL00.000-0.00328.9820.0000.0000.0000.0000.0000.000
139H122PHE00.008-0.00432.273-0.005-0.0050.0000.0000.0000.000
140H123PRO00.0170.01433.1340.0060.0060.0000.0000.0000.000
141H124LEU0-0.032-0.01632.761-0.009-0.0090.0000.0000.0000.000
142H125ALA0-0.002-0.00934.6560.0010.0010.0000.0000.0000.000
143H126PRO00.0450.04034.632-0.005-0.0050.0000.0000.0000.000
144H127SER00.019-0.00937.265-0.003-0.0030.0000.0000.0000.000
145H128SER00.022-0.00340.5410.0010.0010.0000.0000.0000.000
146H129LYS10.9630.97941.892-0.053-0.0530.0000.0000.0000.000
147H130SER0-0.0280.00940.111-0.003-0.0030.0000.0000.0000.000
148H131THR0-0.032-0.01838.9610.0050.0050.0000.0000.0000.000
149H132SER00.0220.01137.961-0.003-0.0030.0000.0000.0000.000
150H133GLY00.0220.01438.2890.0020.0020.0000.0000.0000.000
151H134GLY00.0330.02838.099-0.001-0.0010.0000.0000.0000.000
152H135THR0-0.056-0.01433.7990.0030.0030.0000.0000.0000.000
153H136ALA00.0500.01734.282-0.003-0.0030.0000.0000.0000.000
154H137ALA00.0060.00632.5460.0040.0040.0000.0000.0000.000
155H138LEU0-0.0060.01629.209-0.005-0.0050.0000.0000.0000.000
156H139GLY00.0520.00229.9100.0080.0080.0000.0000.0000.000
157H140CYS0-0.0800.00124.4810.0110.0110.0000.0000.0000.000
158H141LEU00.0360.04430.4530.0070.0070.0000.0000.0000.000
159H142VAL0-0.004-0.00727.7550.0050.0050.0000.0000.0000.000
160H143LYS10.8790.91031.092-0.131-0.1310.0000.0000.0000.000
161H144ASP-1-0.793-0.86233.7990.1390.1390.0000.0000.0000.000
162H145TYR0-0.022-0.02228.134-0.003-0.0030.0000.0000.0000.000
163H146PHE00.0320.01831.381-0.007-0.0070.0000.0000.0000.000
164H147PRO00.0260.02227.461-0.001-0.0010.0000.0000.0000.000
165H148GLU-1-0.764-0.87026.3830.2750.2750.0000.0000.0000.000
166H149PRO0-0.059-0.02721.6920.0010.0010.0000.0000.0000.000
167H150VAL00.004-0.01023.8530.0170.0170.0000.0000.0000.000
168H151THR0-0.030-0.02218.6000.0030.0030.0000.0000.0000.000
169H152VAL0-0.013-0.01421.400-0.013-0.0130.0000.0000.0000.000
170H153SER0-0.0060.00818.6070.0340.0340.0000.0000.0000.000
171H154TRP00.0200.00620.404-0.035-0.0350.0000.0000.0000.000
172H155ASN0-0.004-0.01920.2460.0220.0220.0000.0000.0000.000
173H156SER0-0.017-0.01818.006-0.008-0.0080.0000.0000.0000.000
174H157GLY00.0090.01115.7120.0730.0730.0000.0000.0000.000
175H158ALA0-0.039-0.01016.453-0.019-0.0190.0000.0000.0000.000
176H159LEU0-0.031-0.00718.036-0.042-0.0420.0000.0000.0000.000
177H160THR00.020-0.00316.6580.0150.0150.0000.0000.0000.000
178H161SER00.0300.00920.066-0.007-0.0070.0000.0000.0000.000
179H162GLY00.0530.02422.3980.0010.0010.0000.0000.0000.000
180H163VAL0-0.053-0.01322.339-0.002-0.0020.0000.0000.0000.000
181H164HIS00.0030.01124.4240.0070.0070.0000.0000.0000.000
182H165THR0-0.008-0.01423.610-0.006-0.0060.0000.0000.0000.000
183H166PHE0-0.0120.01226.3020.0030.0030.0000.0000.0000.000
184H167PRO00.034-0.00127.7300.0150.0150.0000.0000.0000.000
185H168ALA0-0.0200.01128.470-0.011-0.0110.0000.0000.0000.000
186H169VAL0-0.014-0.00930.208-0.008-0.0080.0000.0000.0000.000
187H170LEU0-0.033-0.01633.9770.0040.0040.0000.0000.0000.000
188H171GLN0-0.013-0.01535.718-0.013-0.0130.0000.0000.0000.000
189H172SER00.0370.00638.7910.0020.0020.0000.0000.0000.000
190H173SER0-0.008-0.00139.506-0.003-0.0030.0000.0000.0000.000
191H174GLY00.0240.01738.8020.0000.0000.0000.0000.0000.000
192H175LEU0-0.047-0.01735.4210.0090.0090.0000.0000.0000.000
193H176TYR00.0160.00631.354-0.006-0.0060.0000.0000.0000.000
194H177SER0-0.066-0.05132.446-0.004-0.0040.0000.0000.0000.000
195H178LEU00.0490.03626.294-0.002-0.0020.0000.0000.0000.000
196H179SER00.004-0.01730.255-0.010-0.0100.0000.0000.0000.000
197H180SER0-0.0040.00625.3230.0060.0060.0000.0000.0000.000
198H181VAL00.018-0.01027.777-0.010-0.0100.0000.0000.0000.000
199H182VAL00.0160.01025.6740.0110.0110.0000.0000.0000.000
200H183THR0-0.0040.00228.071-0.009-0.0090.0000.0000.0000.000
201H184VAL0-0.006-0.00628.5310.0030.0030.0000.0000.0000.000
202H185PRO00.0420.02229.949-0.005-0.0050.0000.0000.0000.000
203H186SER0-0.001-0.03132.9590.0020.0020.0000.0000.0000.000
204H187SER00.0080.00234.8190.0040.0040.0000.0000.0000.000
205H188SER00.0260.01230.908-0.001-0.0010.0000.0000.0000.000
206H189LEU0-0.037-0.01932.9010.0080.0080.0000.0000.0000.000
207H190GLY00.0080.00734.424-0.006-0.0060.0000.0000.0000.000
208H191THR0-0.062-0.03133.8800.0000.0000.0000.0000.0000.000
209H192GLN0-0.0170.00328.3980.0040.0040.0000.0000.0000.000
210H193THR0-0.0110.00027.1320.0040.0040.0000.0000.0000.000
211H194TYR00.0490.03226.8460.0070.0070.0000.0000.0000.000
212H195ILE0-0.005-0.01825.119-0.008-0.0080.0000.0000.0000.000
213H197ASN00.012-0.01821.3460.0020.0020.0000.0000.0000.000
214H198VAL00.0110.00522.5420.0270.0270.0000.0000.0000.000
215H199ASN0-0.016-0.01520.3600.0070.0070.0000.0000.0000.000
216H200HIS00.0140.00223.0130.0010.0010.0000.0000.0000.000
217H201LYS11.0051.00318.245-0.558-0.5580.0000.0000.0000.000
218H202PRO00.0010.00922.555-0.002-0.0020.0000.0000.0000.000
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