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: Z6GVN

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2438501.420614
FMO2-HF: Nuclear repulsion 2351169.452241
FMO2-HF: Total energy -87331.968373
FMO2-MP2: Total energy -87586.524519


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.
-5.66-1.6130.249-1.799-2.4950.012
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 : 0.031 / q_NPA : 0.010
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].
3H3GLN0-0.0130.0002.732-5.260-1.3830.251-1.743-2.3850.012
4H4LEU0-0.021-0.0095.702-0.153-0.1530.0000.0000.0000.000
5H5VAL00.0260.0099.1990.1800.1800.0000.0000.0000.000
6H6GLN00.011-0.01511.466-0.121-0.1210.0000.0000.0000.000
7H7SER00.0410.02515.0080.0590.0590.0000.0000.0000.000
8H8GLY0-0.011-0.01418.2420.0020.0020.0000.0000.0000.000
9H9ALA0-0.036-0.02020.183-0.022-0.0220.0000.0000.0000.000
10H10GLU-1-0.879-0.94522.7470.1410.1410.0000.0000.0000.000
11H11VAL0-0.033-0.02526.111-0.009-0.0090.0000.0000.0000.000
12H12LYS10.8340.93129.478-0.084-0.0840.0000.0000.0000.000
13H13LYS10.8930.93032.054-0.078-0.0780.0000.0000.0000.000
14H14PRO00.010-0.01235.110-0.001-0.0010.0000.0000.0000.000
15H15GLY0-0.0200.00336.4700.0000.0000.0000.0000.0000.000
16H16GLU-1-0.827-0.89633.6040.0760.0760.0000.0000.0000.000
17H17SER00.0180.02032.054-0.001-0.0010.0000.0000.0000.000
18H18LEU0-0.021-0.01625.7730.0070.0070.0000.0000.0000.000
19H19LYS10.9150.97523.934-0.058-0.0580.0000.0000.0000.000
20H20ILE00.0070.03220.8320.0160.0160.0000.0000.0000.000
21H21SER00.008-0.02218.515-0.013-0.0130.0000.0000.0000.000
22H22CYS0-0.029-0.00513.5770.0460.0460.0000.0000.0000.000
23H23LYS10.9140.96312.196-0.255-0.2550.0000.0000.0000.000
24H24VAL00.0140.0179.3160.0630.0630.0000.0000.0000.000
25H25SER0-0.025-0.0196.5660.2210.2210.0000.0000.0000.000
26H26GLY00.0660.0244.116-0.590-0.544-0.001-0.040-0.0040.000
27H27TYR00.011-0.0104.478-0.385-0.261-0.001-0.016-0.1060.000
28H28ASN00.0240.0187.1710.2450.2450.0000.0000.0000.000
29H29PHE00.0720.04810.9340.0350.0350.0000.0000.0000.000
30H30ALA0-0.016-0.01512.6550.0450.0450.0000.0000.0000.000
31H31SER0-0.063-0.04612.6640.0200.0200.0000.0000.0000.000
32H32GLU-1-0.808-0.88811.715-0.450-0.4500.0000.0000.0000.000
33H33TRP0-0.0300.00114.8270.0270.0270.0000.0000.0000.000
34H34ILE0-0.021-0.01013.155-0.046-0.0460.0000.0000.0000.000
35H35GLY00.0430.01316.2890.0330.0330.0000.0000.0000.000
36H36TRP0-0.0120.00517.5180.0060.0060.0000.0000.0000.000
37H37VAL0-0.013-0.00919.096-0.008-0.0080.0000.0000.0000.000
38H38ARG10.8340.87621.1190.0150.0150.0000.0000.0000.000
39H39GLN00.0160.01221.937-0.004-0.0040.0000.0000.0000.000
40H40MET00.0060.01024.4240.0150.0150.0000.0000.0000.000
41H41PRO00.0280.00227.453-0.002-0.0020.0000.0000.0000.000
42H42GLY00.0080.00527.857-0.005-0.0050.0000.0000.0000.000
43H43LYS10.9070.96428.006-0.009-0.0090.0000.0000.0000.000
44H44GLY00.0420.02026.0340.0020.0020.0000.0000.0000.000
45H45LEU0-0.007-0.00120.2690.0070.0070.0000.0000.0000.000
46H46GLU-1-0.761-0.84424.197-0.014-0.0140.0000.0000.0000.000
47H47TRP0-0.0030.00020.7200.0140.0140.0000.0000.0000.000
48H48MET0-0.047-0.00822.8440.0090.0090.0000.0000.0000.000
49H49GLY00.0510.01523.0590.0050.0050.0000.0000.0000.000
50H50ILE0-0.088-0.03419.285-0.006-0.0060.0000.0000.0000.000
51H51ILE00.004-0.00419.4620.0170.0170.0000.0000.0000.000
52H52TYR00.0240.02217.529-0.029-0.0290.0000.0000.0000.000
53H52PRO00.0060.00116.1640.0270.0270.0000.0000.0000.000
54H53GLY00.0010.00818.8540.0180.0180.0000.0000.0000.000
55H54ASP-1-0.872-0.94020.111-0.108-0.1080.0000.0000.0000.000
56H55SER0-0.072-0.03222.3530.0180.0180.0000.0000.0000.000
57H56ASP-1-0.774-0.86823.750-0.087-0.0870.0000.0000.0000.000
58H57THR0-0.024-0.02423.636-0.009-0.0090.0000.0000.0000.000
59H58LYS10.7900.89524.8530.1020.1020.0000.0000.0000.000
60H59TYR00.0780.04325.323-0.003-0.0030.0000.0000.0000.000
61H60SER00.0330.02327.609-0.001-0.0010.0000.0000.0000.000
62H61PRO00.0330.00429.1670.0050.0050.0000.0000.0000.000
63H62SER0-0.017-0.00931.2810.0030.0030.0000.0000.0000.000
64H63PHE0-0.002-0.01828.5520.0060.0060.0000.0000.0000.000
65H64GLN00.0370.02730.834-0.001-0.0010.0000.0000.0000.000
66H65GLY0-0.018-0.01432.0830.0030.0030.0000.0000.0000.000
67H66GLN0-0.079-0.02731.8870.0080.0080.0000.0000.0000.000
68H67VAL0-0.032-0.00827.2970.0060.0060.0000.0000.0000.000
69H68ILE0-0.026-0.00627.422-0.007-0.0070.0000.0000.0000.000
70H69ILE00.0120.00921.8940.0090.0090.0000.0000.0000.000
71H70SER0-0.009-0.01123.236-0.003-0.0030.0000.0000.0000.000
72H71ALA00.002-0.01919.366-0.004-0.0040.0000.0000.0000.000
73H72ASP-1-0.796-0.85819.9120.0110.0110.0000.0000.0000.000
74H73LYS10.8510.89717.4810.1100.1100.0000.0000.0000.000
75H74SER0-0.059-0.03917.065-0.017-0.0170.0000.0000.0000.000
76H75ILE00.0340.02016.5090.0190.0190.0000.0000.0000.000
77H76ASN0-0.064-0.02210.7950.0720.0720.0000.0000.0000.000
78H77THR0-0.011-0.01014.0650.0190.0190.0000.0000.0000.000
79H78ALA00.0270.02216.619-0.019-0.0190.0000.0000.0000.000
80H79TYR00.011-0.02818.2220.0470.0470.0000.0000.0000.000
81H80LEU00.0190.01821.263-0.021-0.0210.0000.0000.0000.000
82H81GLN0-0.014-0.02123.5210.0150.0150.0000.0000.0000.000
83H82TRP00.0970.01324.783-0.008-0.0080.0000.0000.0000.000
84H82SER0-0.0080.02530.1980.0050.0050.0000.0000.0000.000
85H82SER00.005-0.01333.7340.0030.0030.0000.0000.0000.000
86H82LEU0-0.058-0.00329.483-0.004-0.0040.0000.0000.0000.000
87H83LYS10.8970.92733.172-0.017-0.0170.0000.0000.0000.000
88H84ALA00.0690.01833.6220.0030.0030.0000.0000.0000.000
89H85SER00.003-0.00733.5730.0030.0030.0000.0000.0000.000
90H86ASP-1-0.841-0.89429.7820.0190.0190.0000.0000.0000.000
91H87THR00.0200.03028.5820.0080.0080.0000.0000.0000.000
92H88ALA0-0.037-0.02125.690-0.009-0.0090.0000.0000.0000.000
93H89ILE0-0.0180.00620.0390.0170.0170.0000.0000.0000.000
94H90TYR0-0.024-0.04121.042-0.026-0.0260.0000.0000.0000.000
95H91TYR00.0180.00716.2010.0370.0370.0000.0000.0000.000
96H92CYS0-0.051-0.01815.034-0.035-0.0350.0000.0000.0000.000
97H93ALA00.0640.01413.0300.0080.0080.0000.0000.0000.000
98H94ARG10.8150.8917.6310.9670.9670.0000.0000.0000.000
99H95GLN0-0.017-0.01512.7230.0260.0260.0000.0000.0000.000
100H96ASN0-0.016-0.00410.7030.0300.0300.0000.0000.0000.000
101H97HIS10.8460.89513.8130.4130.4130.0000.0000.0000.000
102H98TYR00.0160.00511.293-0.019-0.0190.0000.0000.0000.000
103H99GLY00.0370.01617.2990.0270.0270.0000.0000.0000.000
104H100SER0-0.020-0.01019.171-0.015-0.0150.0000.0000.0000.000
105H100GLY00.031-0.00221.3830.0110.0110.0000.0000.0000.000
106H100SER0-0.0390.00523.685-0.004-0.0040.0000.0000.0000.000
107H100TYR00.0170.00023.677-0.005-0.0050.0000.0000.0000.000
108H100PHE0-0.008-0.01125.7250.0030.0030.0000.0000.0000.000
109H100TYR00.0200.00828.2940.0060.0060.0000.0000.0000.000
110H100ARG10.9440.97426.1100.1070.1070.0000.0000.0000.000
111H100THR00.0470.02623.7880.0060.0060.0000.0000.0000.000
112H100ALA0-0.030-0.01225.107-0.005-0.0050.0000.0000.0000.000
113H100TYR0-0.033-0.01720.133-0.005-0.0050.0000.0000.0000.000
114H100TYR00.0270.02419.8480.0110.0110.0000.0000.0000.000
115H100TYR00.014-0.00217.984-0.030-0.0300.0000.0000.0000.000
116H100ALA0-0.016-0.01315.7180.0250.0250.0000.0000.0000.000
117H100MET0-0.047-0.02014.399-0.027-0.0270.0000.0000.0000.000
118H101ASP-1-0.739-0.8199.650-0.677-0.6770.0000.0000.0000.000
119H102VAL0-0.0090.0016.353-0.027-0.0270.0000.0000.0000.000
120H103TRP00.000-0.0229.4350.0460.0460.0000.0000.0000.000
121H104GLY00.0220.01610.2290.0600.0600.0000.0000.0000.000
122H105GLN0-0.028-0.01511.969-0.024-0.0240.0000.0000.0000.000
123H106GLY0-0.0030.00813.446-0.030-0.0300.0000.0000.0000.000
124H107THR0-0.063-0.03816.8440.0400.0400.0000.0000.0000.000
125H108THR0-0.019-0.01319.645-0.018-0.0180.0000.0000.0000.000
126H109VAL00.0080.00822.9300.0120.0120.0000.0000.0000.000
127H110THR0-0.001-0.00925.908-0.013-0.0130.0000.0000.0000.000
128H111VAL00.0110.00929.3620.0040.0040.0000.0000.0000.000
129H112SER00.001-0.00532.512-0.006-0.0060.0000.0000.0000.000
130H113SER00.0350.01635.3070.0040.0040.0000.0000.0000.000
131H114ALA00.0050.01535.8540.0010.0010.0000.0000.0000.000
132H115SER00.0050.00335.3250.0010.0010.0000.0000.0000.000
133H116THR0-0.022-0.02130.059-0.004-0.0040.0000.0000.0000.000
134H117LYS10.8230.90332.437-0.106-0.1060.0000.0000.0000.000
135H118GLY00.0780.04730.6340.0040.0040.0000.0000.0000.000
136H119PRO0-0.025-0.00628.515-0.011-0.0110.0000.0000.0000.000
137H120SER0-0.024-0.00431.8460.0030.0030.0000.0000.0000.000
138H121VAL00.001-0.00529.366-0.002-0.0020.0000.0000.0000.000
139H122PHE0-0.013-0.01932.709-0.001-0.0010.0000.0000.0000.000
140H123PRO00.0160.01133.5380.0020.0020.0000.0000.0000.000
141H124LEU0-0.030-0.00433.065-0.006-0.0060.0000.0000.0000.000
142H125ALA0-0.012-0.01434.7870.0000.0000.0000.0000.0000.000
143H126PRO00.0670.05734.666-0.004-0.0040.0000.0000.0000.000
144H127SER0-0.012-0.02437.2140.0000.0000.0000.0000.0000.000
145H128SER00.033-0.00640.0830.0000.0000.0000.0000.0000.000
146H129LYS10.9620.97741.924-0.028-0.0280.0000.0000.0000.000
147H130SER0-0.0130.02540.631-0.003-0.0030.0000.0000.0000.000
148H131THR0-0.018-0.02038.7960.0030.0030.0000.0000.0000.000
149H132SER00.0300.01538.044-0.001-0.0010.0000.0000.0000.000
150H133GLY00.0280.01838.1810.0000.0000.0000.0000.0000.000
151H134GLY00.0310.02237.768-0.002-0.0020.0000.0000.0000.000
152H135THR0-0.074-0.02833.5410.0020.0020.0000.0000.0000.000
153H136ALA00.0420.01534.1940.0000.0000.0000.0000.0000.000
154H137ALA00.0090.00832.7260.0000.0000.0000.0000.0000.000
155H138LEU0-0.0060.01129.3180.0000.0000.0000.0000.0000.000
156H139GLY00.0580.00729.9870.0000.0000.0000.0000.0000.000
157H140CYS0-0.102-0.02124.8500.0110.0110.0000.0000.0000.000
158H141LEU00.0220.02730.9210.0000.0000.0000.0000.0000.000
159H142VAL0-0.008-0.00728.2490.0050.0050.0000.0000.0000.000
160H143LYS10.8860.89931.662-0.076-0.0760.0000.0000.0000.000
161H144ASP-1-0.798-0.87034.3660.0820.0820.0000.0000.0000.000
162H145TYR0-0.002-0.01028.4190.0030.0030.0000.0000.0000.000
163H146PHE00.0380.02831.454-0.008-0.0080.0000.0000.0000.000
164H147PRO00.0140.02127.5420.0050.0050.0000.0000.0000.000
165H148GLU-1-0.785-0.87526.1820.1320.1320.0000.0000.0000.000
166H149PRO0-0.026-0.02221.7860.0040.0040.0000.0000.0000.000
167H150VAL00.003-0.01324.3840.0160.0160.0000.0000.0000.000
168H151THR0-0.034-0.01718.949-0.009-0.0090.0000.0000.0000.000
169H152VAL0-0.004-0.01521.9430.0020.0020.0000.0000.0000.000
170H153SER0-0.021-0.00418.7820.0130.0130.0000.0000.0000.000
171H154TRP00.0180.00520.632-0.012-0.0120.0000.0000.0000.000
172H155ASN00.002-0.01920.5850.0090.0090.0000.0000.0000.000
173H156SER0-0.012-0.01817.982-0.005-0.0050.0000.0000.0000.000
174H157GLY00.0030.00716.0480.0540.0540.0000.0000.0000.000
175H158ALA0-0.0310.00016.238-0.024-0.0240.0000.0000.0000.000
176H159LEU0-0.041-0.01018.002-0.037-0.0370.0000.0000.0000.000
177H160THR00.022-0.00216.5280.0110.0110.0000.0000.0000.000
178H161SER00.0100.00019.974-0.010-0.0100.0000.0000.0000.000
179H162GLY00.0640.02922.4780.0070.0070.0000.0000.0000.000
180H163VAL0-0.044-0.02022.5010.0050.0050.0000.0000.0000.000
181H164HIS00.0010.01324.424-0.004-0.0040.0000.0000.0000.000
182H165THR0-0.009-0.00623.6350.0040.0040.0000.0000.0000.000
183H166PHE0-0.0170.00026.252-0.005-0.0050.0000.0000.0000.000
184H167PRO00.024-0.00127.8110.0110.0110.0000.0000.0000.000
185H168ALA0-0.0060.01428.639-0.003-0.0030.0000.0000.0000.000
186H169VAL0-0.015-0.00830.442-0.007-0.0070.0000.0000.0000.000
187H170LEU0-0.034-0.01734.0350.0060.0060.0000.0000.0000.000
188H171GLN0-0.016-0.02035.815-0.007-0.0070.0000.0000.0000.000
189H172SER00.0410.01738.9570.0010.0010.0000.0000.0000.000
190H173SER00.001-0.00139.831-0.001-0.0010.0000.0000.0000.000
191H174GLY00.0100.00538.3540.0010.0010.0000.0000.0000.000
192H175LEU0-0.058-0.01935.5510.0060.0060.0000.0000.0000.000
193H176TYR00.0170.00831.323-0.005-0.0050.0000.0000.0000.000
194H177SER0-0.062-0.03433.1590.0020.0020.0000.0000.0000.000
195H178LEU00.0250.02926.901-0.004-0.0040.0000.0000.0000.000
196H179SER00.0330.00431.0050.0010.0010.0000.0000.0000.000
197H180SER0-0.0050.00125.4880.0010.0010.0000.0000.0000.000
198H181VAL00.015-0.01128.1570.0000.0000.0000.0000.0000.000
199H182VAL00.0200.01225.6990.0020.0020.0000.0000.0000.000
200H183THR0-0.0120.00328.244-0.003-0.0030.0000.0000.0000.000
201H184VAL0-0.010-0.00828.252-0.001-0.0010.0000.0000.0000.000
202H185PRO00.0540.02729.882-0.003-0.0030.0000.0000.0000.000
203H186SER00.008-0.01632.9070.0050.0050.0000.0000.0000.000
204H187SER0-0.007-0.00534.6160.0040.0040.0000.0000.0000.000
205H188SER00.014-0.00830.9320.0020.0020.0000.0000.0000.000
206H189LEU0-0.027-0.01032.7790.0080.0080.0000.0000.0000.000
207H190GLY0-0.018-0.00234.621-0.004-0.0040.0000.0000.0000.000
208H191THR0-0.025-0.01433.6550.0030.0030.0000.0000.0000.000
209H192GLN0-0.0200.00928.4790.0070.0070.0000.0000.0000.000
210H193THR0-0.008-0.00327.5280.0030.0030.0000.0000.0000.000
211H194TYR00.0450.02926.7610.0050.0050.0000.0000.0000.000
212H195ILE00.008-0.00925.397-0.003-0.0030.0000.0000.0000.000
213H197ASN00.015-0.01221.5390.0040.0040.0000.0000.0000.000
214H198VAL00.0130.00622.9820.0090.0090.0000.0000.0000.000
215H199ASN0-0.010-0.00420.2410.0200.0200.0000.0000.0000.000
216H200HIS00.0250.02423.182-0.004-0.0040.0000.0000.0000.000
217H201LYS11.0001.00218.654-0.307-0.3070.0000.0000.0000.000
218H202PRO00.0040.01623.3500.0010.0010.0000.0000.0000.000
219H203SER0-0.017-0.03326.139-0.010-0.0100.0000.0000.0000.000
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