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: 6NRYZ

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2437680.4948
FMO2-HF: Nuclear repulsion 2350349.073762
FMO2-HF: Total energy -87331.421039
FMO2-MP2: Total energy -87585.93252


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.
-3.735-1.2640.031-0.927-1.5740.005
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 : -0.011 / q_NPA : -0.026
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].
3H3GLN0-0.007-0.0023.105-3.563-1.2590.033-0.875-1.4620.005
4H4LEU0-0.022-0.0165.8230.2460.2460.0000.0000.0000.000
5H5VAL00.0310.0169.2420.0100.0100.0000.0000.0000.000
6H6GLN0-0.013-0.02611.599-0.030-0.0300.0000.0000.0000.000
7H7SER00.0450.02515.1270.0280.0280.0000.0000.0000.000
8H8GLY0-0.021-0.02718.373-0.021-0.0210.0000.0000.0000.000
9H9ALA0-0.022-0.02020.300-0.009-0.0090.0000.0000.0000.000
10H10GLU-1-0.905-0.95022.8460.0970.0970.0000.0000.0000.000
11H11VAL0-0.022-0.01926.217-0.012-0.0120.0000.0000.0000.000
12H12LYS10.9100.97229.334-0.061-0.0610.0000.0000.0000.000
13H13LYS10.9360.96032.162-0.042-0.0420.0000.0000.0000.000
14H14PRO00.006-0.01235.2150.0020.0020.0000.0000.0000.000
15H15GLY0-0.0220.00236.5670.0010.0010.0000.0000.0000.000
16H16GLU-1-0.874-0.92633.7160.0520.0520.0000.0000.0000.000
17H17SER00.0120.01832.164-0.002-0.0020.0000.0000.0000.000
18H18LEU0-0.025-0.02326.0680.0020.0020.0000.0000.0000.000
19H19LYS10.9450.97823.950-0.114-0.1140.0000.0000.0000.000
20H20ILE00.0030.02920.9180.0080.0080.0000.0000.0000.000
21H21SER0-0.009-0.02418.5130.0090.0090.0000.0000.0000.000
22H22CYS0-0.026-0.02013.700-0.012-0.0120.0000.0000.0000.000
23H23LYS10.9180.97712.335-0.416-0.4160.0000.0000.0000.000
24H24VAL00.0170.0179.173-0.015-0.0150.0000.0000.0000.000
25H25SER0-0.033-0.0216.2110.1790.1790.0000.0000.0000.000
26H26GLY00.0720.0253.973-0.831-0.789-0.001-0.0440.0030.000
27H27TYR00.011-0.0054.6071.2401.365-0.001-0.008-0.1150.000
28H28ASN00.0270.0147.631-0.184-0.1840.0000.0000.0000.000
29H29PHE00.0570.04611.329-0.029-0.0290.0000.0000.0000.000
30H30ALA0-0.017-0.02012.911-0.033-0.0330.0000.0000.0000.000
31H31SER0-0.079-0.04713.305-0.005-0.0050.0000.0000.0000.000
32H32GLU-1-0.797-0.88012.1860.2670.2670.0000.0000.0000.000
33H33TRP0-0.0260.00015.361-0.013-0.0130.0000.0000.0000.000
34H34ILE0-0.019-0.01313.173-0.005-0.0050.0000.0000.0000.000
35H35GLY00.0370.01216.2780.0090.0090.0000.0000.0000.000
36H36TRP0-0.0220.00417.504-0.016-0.0160.0000.0000.0000.000
37H37VAL00.003-0.00819.1360.0000.0000.0000.0000.0000.000
38H38ARG10.8480.89621.1560.0210.0210.0000.0000.0000.000
39H39GLN0-0.004-0.00321.829-0.017-0.0170.0000.0000.0000.000
40H40MET00.0010.00524.4400.0070.0070.0000.0000.0000.000
41H41PRO00.0330.00627.460-0.011-0.0110.0000.0000.0000.000
42H42GLY00.0070.00627.8560.0030.0030.0000.0000.0000.000
43H43LYS10.9090.96528.0110.0550.0550.0000.0000.0000.000
44H44GLY00.0400.01726.006-0.010-0.0100.0000.0000.0000.000
45H45LEU0-0.011-0.00220.4320.0070.0070.0000.0000.0000.000
46H46GLU-1-0.770-0.86524.183-0.031-0.0310.0000.0000.0000.000
47H47TRP0-0.016-0.00420.6060.0040.0040.0000.0000.0000.000
48H48MET0-0.060-0.01222.4550.0080.0080.0000.0000.0000.000
49H49GLY00.0530.01223.0460.0060.0060.0000.0000.0000.000
50H50ILE0-0.085-0.03119.270-0.004-0.0040.0000.0000.0000.000
51H51ILE0-0.003-0.00819.4300.0020.0020.0000.0000.0000.000
52H52TYR00.0350.02318.3710.0110.0110.0000.0000.0000.000
53H52PRO00.0060.00316.387-0.001-0.0010.0000.0000.0000.000
54H53GLY0-0.014-0.00519.3140.0050.0050.0000.0000.0000.000
55H54ASP-1-0.882-0.94320.5140.1140.1140.0000.0000.0000.000
56H55SER0-0.063-0.03722.733-0.008-0.0080.0000.0000.0000.000
57H56ASP-1-0.851-0.90824.0780.0600.0600.0000.0000.0000.000
58H57THR0-0.051-0.02923.8900.0010.0010.0000.0000.0000.000
59H58LYS10.8950.93824.845-0.054-0.0540.0000.0000.0000.000
60H59TYR00.0750.04325.311-0.002-0.0020.0000.0000.0000.000
61H60SER00.0370.02527.622-0.001-0.0010.0000.0000.0000.000
62H61PRO00.0360.00729.1540.0040.0040.0000.0000.0000.000
63H62SER0-0.027-0.01531.3850.0000.0000.0000.0000.0000.000
64H63PHE00.000-0.01428.3470.0000.0000.0000.0000.0000.000
65H64GLN00.0490.03330.8200.0050.0050.0000.0000.0000.000
66H65GLY0-0.022-0.02032.070-0.002-0.0020.0000.0000.0000.000
67H66GLN0-0.093-0.03831.991-0.001-0.0010.0000.0000.0000.000
68H67VAL0-0.021-0.00127.3450.0010.0010.0000.0000.0000.000
69H68ILE0-0.021-0.00227.2510.0000.0000.0000.0000.0000.000
70H69ILE00.0010.00621.9720.0020.0020.0000.0000.0000.000
71H70SER0-0.001-0.00323.2170.0060.0060.0000.0000.0000.000
72H71ALA0-0.003-0.02319.3960.0000.0000.0000.0000.0000.000
73H72ASP-1-0.792-0.86919.7600.1940.1940.0000.0000.0000.000
74H73LYS10.8730.91917.366-0.168-0.1680.0000.0000.0000.000
75H74SER0-0.060-0.02616.8980.0280.0280.0000.0000.0000.000
76H75ILE00.0280.02016.3920.0310.0310.0000.0000.0000.000
77H76ASN0-0.054-0.03410.5950.0090.0090.0000.0000.0000.000
78H77THR0-0.016-0.00713.925-0.008-0.0080.0000.0000.0000.000
79H78ALA00.0200.02016.564-0.007-0.0070.0000.0000.0000.000
80H79TYR00.001-0.03218.2220.0030.0030.0000.0000.0000.000
81H80LEU00.0160.01821.354-0.008-0.0080.0000.0000.0000.000
82H81GLN0-0.023-0.02523.6270.0090.0090.0000.0000.0000.000
83H82TRP00.0900.00524.869-0.003-0.0030.0000.0000.0000.000
84H82SER0-0.0170.02730.3040.0050.0050.0000.0000.0000.000
85H82SER0-0.008-0.03033.8470.0010.0010.0000.0000.0000.000
86H82LEU0-0.0540.01229.629-0.004-0.0040.0000.0000.0000.000
87H83LYS10.9890.98533.694-0.012-0.0120.0000.0000.0000.000
88H84ALA00.0700.01733.6970.0000.0000.0000.0000.0000.000
89H85SER0-0.013-0.02133.632-0.002-0.0020.0000.0000.0000.000
90H86ASP-1-0.883-0.92429.7940.0070.0070.0000.0000.0000.000
91H87THR0-0.0030.01728.6470.0030.0030.0000.0000.0000.000
92H88ALA0-0.034-0.02225.734-0.008-0.0080.0000.0000.0000.000
93H89ILE0-0.0220.01020.1950.0120.0120.0000.0000.0000.000
94H90TYR0-0.021-0.04121.100-0.007-0.0070.0000.0000.0000.000
95H91TYR00.0310.03115.9970.0080.0080.0000.0000.0000.000
96H92CYS0-0.0230.01315.0390.0180.0180.0000.0000.0000.000
97H93ALA00.0610.01113.015-0.036-0.0360.0000.0000.0000.000
98H94ARG10.8160.8877.819-0.354-0.3540.0000.0000.0000.000
99H95GLN00.013-0.00112.711-0.028-0.0280.0000.0000.0000.000
100H96ASN00.0110.00810.7290.0530.0530.0000.0000.0000.000
101H97HIS10.8260.88413.807-0.241-0.2410.0000.0000.0000.000
102H98TYR00.0090.00311.6110.0240.0240.0000.0000.0000.000
103H99GLY00.0310.01317.297-0.018-0.0180.0000.0000.0000.000
104H100SER0-0.040-0.02319.6260.0220.0220.0000.0000.0000.000
105H100GLY00.0610.01821.972-0.015-0.0150.0000.0000.0000.000
106H100SER0-0.0280.00324.6280.0130.0130.0000.0000.0000.000
107H100TYR00.0210.00424.7430.0050.0050.0000.0000.0000.000
108H100PHE0-0.017-0.01426.7330.0010.0010.0000.0000.0000.000
109H100TYR00.0120.00429.271-0.006-0.0060.0000.0000.0000.000
110H100ARG10.9370.97327.178-0.065-0.0650.0000.0000.0000.000
111H100THR00.0470.03024.204-0.007-0.0070.0000.0000.0000.000
112H100ALA0-0.023-0.01025.4410.0050.0050.0000.0000.0000.000
113H100TYR0-0.031-0.01520.215-0.001-0.0010.0000.0000.0000.000
114H100TYR00.0280.02419.893-0.010-0.0100.0000.0000.0000.000
115H100TYR00.015-0.00217.9790.0150.0150.0000.0000.0000.000
116H100ALA0-0.018-0.01515.683-0.021-0.0210.0000.0000.0000.000
117H100MET0-0.049-0.02414.3950.0190.0190.0000.0000.0000.000
118H101ASP-1-0.741-0.8169.7210.0270.0270.0000.0000.0000.000
119H102VAL0-0.014-0.0026.371-0.123-0.1230.0000.0000.0000.000
120H103TRP00.003-0.0139.4210.1220.1220.0000.0000.0000.000
121H104GLY00.0130.00810.253-0.056-0.0560.0000.0000.0000.000
122H105GLN0-0.016-0.01012.028-0.054-0.0540.0000.0000.0000.000
123H106GLY0-0.0020.00713.495-0.011-0.0110.0000.0000.0000.000
124H107THR0-0.071-0.03916.9010.0210.0210.0000.0000.0000.000
125H108THR0-0.010-0.01019.726-0.011-0.0110.0000.0000.0000.000
126H109VAL00.0080.00923.0000.0140.0140.0000.0000.0000.000
127H110THR0-0.010-0.01125.989-0.012-0.0120.0000.0000.0000.000
128H111VAL00.0120.01229.4390.0070.0070.0000.0000.0000.000
129H112SER0-0.008-0.01232.595-0.005-0.0050.0000.0000.0000.000
130H113SER00.0220.01035.3920.0040.0040.0000.0000.0000.000
131H114ALA0-0.0070.00135.9410.0030.0030.0000.0000.0000.000
132H115SER00.0090.00135.4230.0020.0020.0000.0000.0000.000
133H116THR0-0.028-0.02130.217-0.006-0.0060.0000.0000.0000.000
134H117LYS10.8700.93932.521-0.015-0.0150.0000.0000.0000.000
135H118GLY00.0610.03730.893-0.003-0.0030.0000.0000.0000.000
136H119PRO0-0.024-0.01128.811-0.004-0.0040.0000.0000.0000.000
137H120SER0-0.032-0.00432.1430.0060.0060.0000.0000.0000.000
138H121VAL00.007-0.00329.344-0.005-0.0050.0000.0000.0000.000
139H122PHE0-0.020-0.02132.6050.0040.0040.0000.0000.0000.000
140H123PRO00.0130.00733.353-0.005-0.0050.0000.0000.0000.000
141H124LEU0-0.031-0.00332.9310.0020.0020.0000.0000.0000.000
142H125ALA0-0.017-0.01734.615-0.005-0.0050.0000.0000.0000.000
143H126PRO00.0620.05534.5620.0000.0000.0000.0000.0000.000
144H127SER0-0.008-0.02737.0670.0050.0050.0000.0000.0000.000
145H128SER00.0360.00139.957-0.003-0.0030.0000.0000.0000.000
146H129LYS10.9610.97641.8110.0380.0380.0000.0000.0000.000
147H130SER0-0.0110.02740.841-0.001-0.0010.0000.0000.0000.000
148H131THR0-0.013-0.01938.537-0.004-0.0040.0000.0000.0000.000
149H132SER00.0030.00037.9810.0030.0030.0000.0000.0000.000
150H133GLY00.0320.01738.063-0.005-0.0050.0000.0000.0000.000
151H134GLY00.0260.01937.674-0.005-0.0050.0000.0000.0000.000
152H135THR0-0.073-0.02233.458-0.004-0.0040.0000.0000.0000.000
153H136ALA00.0540.01834.0740.0080.0080.0000.0000.0000.000
154H137ALA00.0120.01032.576-0.009-0.0090.0000.0000.0000.000
155H138LEU0-0.0070.01129.1430.0100.0100.0000.0000.0000.000
156H139GLY00.0500.00229.801-0.010-0.0100.0000.0000.0000.000
157H140CYS0-0.108-0.02424.6990.0040.0040.0000.0000.0000.000
158H141LEU00.0140.02130.701-0.005-0.0050.0000.0000.0000.000
159H142VAL0-0.016-0.01028.1300.0080.0080.0000.0000.0000.000
160H143LYS10.9280.95131.5690.0130.0130.0000.0000.0000.000
161H144ASP-1-0.832-0.92734.5500.0000.0000.0000.0000.0000.000
162H145TYR0-0.013-0.01328.3820.0050.0050.0000.0000.0000.000
163H146PHE00.0410.02431.525-0.007-0.0070.0000.0000.0000.000
164H147PRO00.0190.02227.6850.0070.0070.0000.0000.0000.000
165H148GLU-1-0.778-0.87826.190-0.037-0.0370.0000.0000.0000.000
166H149PRO0-0.035-0.03321.9120.0110.0110.0000.0000.0000.000
167H150VAL00.003-0.01124.4780.0170.0170.0000.0000.0000.000
168H151THR0-0.034-0.01719.044-0.012-0.0120.0000.0000.0000.000
169H152VAL0-0.002-0.01221.8730.0180.0180.0000.0000.0000.000
170H153SER0-0.012-0.00218.641-0.016-0.0160.0000.0000.0000.000
171H154TRP00.0120.00220.4550.0260.0260.0000.0000.0000.000
172H155ASN00.010-0.01420.446-0.006-0.0060.0000.0000.0000.000
173H156SER0-0.012-0.01617.828-0.012-0.0120.0000.0000.0000.000
174H157GLY0-0.0050.00315.8960.0100.0100.0000.0000.0000.000
175H158ALA0-0.0280.00016.112-0.059-0.0590.0000.0000.0000.000
176H159LEU0-0.040-0.01017.912-0.025-0.0250.0000.0000.0000.000
177H160THR00.015-0.00416.3790.0230.0230.0000.0000.0000.000
178H161SER00.006-0.00319.8270.0070.0070.0000.0000.0000.000
179H162GLY00.0680.03022.3530.0200.0200.0000.0000.0000.000
180H163VAL0-0.037-0.01422.4300.0220.0220.0000.0000.0000.000
181H164HIS00.0060.01524.229-0.017-0.0170.0000.0000.0000.000
182H165THR0-0.011-0.01223.4100.0190.0190.0000.0000.0000.000
183H166PHE0-0.021-0.00226.014-0.009-0.0090.0000.0000.0000.000
184H167PRO00.0230.00127.8080.0060.0060.0000.0000.0000.000
185H168ALA0-0.0080.01528.6550.0050.0050.0000.0000.0000.000
186H169VAL0-0.014-0.00630.458-0.002-0.0020.0000.0000.0000.000
187H170LEU0-0.029-0.01534.0520.0050.0050.0000.0000.0000.000
188H171GLN0-0.028-0.02535.847-0.004-0.0040.0000.0000.0000.000
189H172SER00.0360.01538.9930.0020.0020.0000.0000.0000.000
190H173SER00.0040.00039.7880.0010.0010.0000.0000.0000.000
191H174GLY00.0140.00738.4080.0030.0030.0000.0000.0000.000
192H175LEU0-0.067-0.01735.6170.0030.0030.0000.0000.0000.000
193H176TYR00.0100.00131.582-0.006-0.0060.0000.0000.0000.000
194H177SER0-0.009-0.01233.2520.0060.0060.0000.0000.0000.000
195H178LEU0-0.0120.01826.951-0.004-0.0040.0000.0000.0000.000
196H179SER00.0470.00730.7260.0080.0080.0000.0000.0000.000
197H180SER0-0.0140.00325.297-0.008-0.0080.0000.0000.0000.000
198H181VAL00.012-0.01027.9380.0120.0120.0000.0000.0000.000
199H182VAL00.0270.01325.718-0.013-0.0130.0000.0000.0000.000
200H183THR0-0.0140.00228.0800.0110.0110.0000.0000.0000.000
201H184VAL0-0.008-0.01028.145-0.013-0.0130.0000.0000.0000.000
202H185PRO00.0460.02129.6410.0070.0070.0000.0000.0000.000
203H186SER00.010-0.00832.8270.0060.0060.0000.0000.0000.000
204H187SER0-0.005-0.00534.5580.0040.0040.0000.0000.0000.000
205H188SER00.012-0.01030.8890.0000.0000.0000.0000.0000.000
206H189LEU0-0.024-0.01032.7060.0040.0040.0000.0000.0000.000
207H190GLY0-0.0180.00134.5260.0020.0020.0000.0000.0000.000
208H191THR0-0.026-0.01033.4970.0020.0020.0000.0000.0000.000
209H192GLN0-0.0130.00828.453-0.003-0.0030.0000.0000.0000.000
210H193THR00.0030.00627.3910.0080.0080.0000.0000.0000.000
211H194TYR00.0310.01926.626-0.008-0.0080.0000.0000.0000.000
212H195ILE00.005-0.01225.1800.0110.0110.0000.0000.0000.000
213H197ASN00.009-0.02621.372-0.002-0.0020.0000.0000.0000.000
214H198VAL00.0100.00522.769-0.010-0.0100.0000.0000.0000.000
215H199ASN0-0.004-0.00320.1970.0390.0390.0000.0000.0000.000
216H200HIS00.0230.01623.465-0.008-0.0080.0000.0000.0000.000
217H201LYS10.9811.00818.901-0.064-0.0640.0000.0000.0000.000
218H202PRO0-0.0130.00523.5070.0120.0120.0000.0000.0000.000
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