FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2J5NR

Calculation Name: 4NWU-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NWU

Chain ID: H

ChEMBL ID:

UniProt ID: P01857

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2413431.515785
FMO2-HF: Nuclear repulsion 2326475.149907
FMO2-HF: Total energy -86956.365878
FMO2-MP2: Total energy -87209.477306


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.
-14.849-6.20712.936-7.927-13.651-0.054
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 : -0.002 / q_NPA : 0.009
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].
3H4LEU00.0110.0043.319-0.7262.031-0.001-1.311-1.4440.007
4H5VAL0-0.0040.0015.506-0.069-0.0690.0000.0000.0000.000
5H6GLN00.021-0.0189.2290.1070.1070.0000.0000.0000.000
6H7SER00.0010.02212.2140.0040.0040.0000.0000.0000.000
7H8GLY0-0.003-0.00215.967-0.025-0.0250.0000.0000.0000.000
8H9ALA00.0250.01318.3460.0200.0200.0000.0000.0000.000
9H10GLU-1-0.863-0.93320.972-0.123-0.1230.0000.0000.0000.000
10H11VAL0-0.0080.00124.162-0.005-0.0050.0000.0000.0000.000
11H12LYS10.8240.91724.8060.1260.1260.0000.0000.0000.000
12H13LYS10.8790.93728.8240.0860.0860.0000.0000.0000.000
13H14PRO00.0360.01531.6190.0000.0000.0000.0000.0000.000
14H15GLY0-0.0100.00532.6430.0040.0040.0000.0000.0000.000
15H16SER0-0.050-0.03530.1700.0020.0020.0000.0000.0000.000
16H17SER00.026-0.00726.4880.0000.0000.0000.0000.0000.000
17H18VAL0-0.027-0.01621.430-0.003-0.0030.0000.0000.0000.000
18H19LYS10.8890.93619.6020.0530.0530.0000.0000.0000.000
19H20VAL0-0.0290.00715.250-0.008-0.0080.0000.0000.0000.000
20H21SER00.0290.00114.7370.0210.0210.0000.0000.0000.000
21H22CYS0-0.016-0.0088.781-0.062-0.0620.0000.0000.0000.000
22H23LYS10.9541.0089.2100.1860.1860.0000.0000.0000.000
23H24ALA00.0210.0144.170-0.312-0.243-0.001-0.011-0.0570.000
24H25SER0-0.043-0.0194.297-0.264-0.068-0.001-0.049-0.1460.000
25H26GLY00.0580.0322.055-6.657-6.8267.916-3.828-3.919-0.033
26H33GLY00.0950.0467.717-0.022-0.0220.0000.0000.0000.000
27H33ASP-1-0.857-0.9284.3741.9592.138-0.001-0.022-0.1570.000
28H33THR0-0.023-0.0262.628-0.810-0.1520.162-0.210-0.6110.000
29H33PHE0-0.018-0.0125.605-0.272-0.2720.0000.0000.0000.000
30H33SER00.0050.0019.148-0.123-0.1230.0000.0000.0000.000
31H33ASN0-0.051-0.0368.232-0.194-0.1940.0000.0000.0000.000
32H33TYR0-0.079-0.0345.051-0.226-0.2260.0000.0000.0000.000
33H33ALA00.0510.0409.2110.0110.0110.0000.0000.0000.000
34H34ILE0-0.052-0.0327.132-0.056-0.0560.0000.0000.0000.000
35H35SER00.0340.01010.2860.0370.0370.0000.0000.0000.000
36H36TRP0-0.036-0.01911.834-0.074-0.0740.0000.0000.0000.000
37H37VAL0-0.012-0.00213.7790.0340.0340.0000.0000.0000.000
38H38ARG10.7830.87615.9000.1270.1270.0000.0000.0000.000
39H39GLN00.0060.01518.404-0.020-0.0200.0000.0000.0000.000
40H40ALA00.0490.03920.356-0.004-0.0040.0000.0000.0000.000
41H41PRO0-0.012-0.03223.701-0.011-0.0110.0000.0000.0000.000
42H42GLY00.0080.01524.2660.0140.0140.0000.0000.0000.000
43H43GLN0-0.028-0.00624.3260.0120.0120.0000.0000.0000.000
44H44GLY00.0320.02022.166-0.019-0.0190.0000.0000.0000.000
45H45PHE00.001-0.01216.1070.0030.0030.0000.0000.0000.000
46H46GLU-1-0.770-0.86219.961-0.112-0.1120.0000.0000.0000.000
47H47TRP00.0090.00915.157-0.010-0.0100.0000.0000.0000.000
48H48MET0-0.037-0.02818.0580.0130.0130.0000.0000.0000.000
49H49GLY00.0410.00517.8110.0220.0220.0000.0000.0000.000
50H50GLY0-0.024-0.00715.013-0.035-0.0350.0000.0000.0000.000
51H51ILE0-0.040-0.00513.3870.0070.0070.0000.0000.0000.000
52H52ILE00.0560.03913.122-0.012-0.0120.0000.0000.0000.000
53H52PRO0-0.068-0.03210.529-0.009-0.0090.0000.0000.0000.000
54H53ILE00.0760.05713.547-0.028-0.0280.0000.0000.0000.000
55H54PHE0-0.032-0.01315.435-0.010-0.0100.0000.0000.0000.000
56H55GLY0-0.033-0.00517.219-0.021-0.0210.0000.0000.0000.000
57H56THR0-0.026-0.01518.213-0.018-0.0180.0000.0000.0000.000
58H57ALA00.0360.01117.8440.0020.0020.0000.0000.0000.000
59H58ASN0-0.050-0.00718.9280.0070.0070.0000.0000.0000.000
60H59TYR00.0760.02219.642-0.014-0.0140.0000.0000.0000.000
61H60ALA00.0310.02621.9820.0070.0070.0000.0000.0000.000
62H61GLN00.0440.00123.732-0.003-0.0030.0000.0000.0000.000
63H62LYS10.8110.89825.4290.1140.1140.0000.0000.0000.000
64H63PHE0-0.024-0.01822.655-0.005-0.0050.0000.0000.0000.000
65H64GLN00.0200.01825.9010.0000.0000.0000.0000.0000.000
66H65GLY00.0090.01026.7600.0010.0010.0000.0000.0000.000
67H66ARG10.7560.85427.2950.0890.0890.0000.0000.0000.000
68H67VAL0-0.013-0.00221.279-0.008-0.0080.0000.0000.0000.000
69H68THR0-0.020-0.01021.4420.0150.0150.0000.0000.0000.000
70H69ILE0-0.0230.00015.654-0.018-0.0180.0000.0000.0000.000
71H70THR00.0030.00016.8370.0170.0170.0000.0000.0000.000
72H71ALA00.012-0.00712.996-0.022-0.0220.0000.0000.0000.000
73H72ASP-1-0.785-0.83413.7810.1480.1480.0000.0000.0000.000
74H73GLU-1-0.827-0.93412.1370.3630.3630.0000.0000.0000.000
75H74SER0-0.102-0.06212.6430.0570.0570.0000.0000.0000.000
76H75THR0-0.054-0.05513.572-0.003-0.0030.0000.0000.0000.000
77H76SER0-0.036-0.0158.1480.0330.0330.0000.0000.0000.000
78H77THR0-0.033-0.0198.940-0.081-0.0810.0000.0000.0000.000
79H78ALA00.0170.01410.9010.0370.0370.0000.0000.0000.000
80H79TYR0-0.020-0.03312.493-0.074-0.0740.0000.0000.0000.000
81H80MET0-0.0190.01315.5260.0210.0210.0000.0000.0000.000
82H81GLU-1-0.852-0.91617.835-0.067-0.0670.0000.0000.0000.000
83H82LEU00.0100.00821.5220.0080.0080.0000.0000.0000.000
84H82SER0-0.014-0.02423.9670.0010.0010.0000.0000.0000.000
85H82SER00.008-0.00627.751-0.001-0.0010.0000.0000.0000.000
86H82LEU0-0.044-0.00925.323-0.002-0.0020.0000.0000.0000.000
87H83ARG10.9830.99429.0820.0790.0790.0000.0000.0000.000
88H84SER00.0520.01629.307-0.007-0.0070.0000.0000.0000.000
89H85GLU-1-0.870-0.93129.237-0.101-0.1010.0000.0000.0000.000
90H86ASP-1-0.773-0.84325.375-0.112-0.1120.0000.0000.0000.000
91H87THR0-0.0160.00424.469-0.012-0.0120.0000.0000.0000.000
92H88ALA0-0.0050.00021.3460.0020.0020.0000.0000.0000.000
93H89VAL0-0.0010.00616.3770.0020.0020.0000.0000.0000.000
94H90TYR0-0.022-0.03816.7860.0110.0110.0000.0000.0000.000
95H91TYR00.013-0.01211.896-0.032-0.0320.0000.0000.0000.000
96H93ALA00.025-0.0068.122-0.140-0.1400.0000.0000.0000.000
97H94ARG10.8120.8973.034-2.723-0.7051.093-0.826-2.285-0.008
98H95GLY00.0400.0096.474-0.167-0.1670.0000.0000.0000.000
99H96PRO0-0.0120.0237.7680.1000.1000.0000.0000.0000.000
100H97GLU-1-0.836-0.9419.9070.1370.1370.0000.0000.0000.000
101H98TYR0-0.103-0.06313.5140.0150.0150.0000.0000.0000.000
102H99TYR0-0.003-0.00516.942-0.006-0.0060.0000.0000.0000.000
103H100ASP-1-0.790-0.88620.0500.0210.0210.0000.0000.0000.000
104H100TYR00.014-0.01822.6380.0010.0010.0000.0000.0000.000
105H100VAL0-0.040-0.01026.019-0.002-0.0020.0000.0000.0000.000
106H100TRP0-0.042-0.03122.995-0.006-0.0060.0000.0000.0000.000
107H100GLY00.0010.02326.1580.0010.0010.0000.0000.0000.000
108H100SER0-0.029-0.01721.0300.0110.0110.0000.0000.0000.000
109H100TYR00.0310.02116.221-0.009-0.0090.0000.0000.0000.000
110H100ARG10.8320.92217.675-0.021-0.0210.0000.0000.0000.000
111H100TYR00.037-0.00513.5850.0100.0100.0000.0000.0000.000
112H100ASN0-0.016-0.00513.082-0.025-0.0250.0000.0000.0000.000
113H100TYR0-0.0270.0029.5850.0030.0030.0000.0000.0000.000
114H100PHE00.002-0.0219.1030.0270.0270.0000.0000.0000.000
115H101ASP-1-0.815-0.9014.922-1.088-0.936-0.001-0.007-0.1430.000
116H102TYR0-0.0140.0062.773-4.608-1.8983.771-1.662-4.820-0.020
117H103TRP00.015-0.0085.0990.3570.429-0.001-0.001-0.0690.000
118H104GLY00.0310.0166.721-0.289-0.2890.0000.0000.0000.000
119H105GLN0-0.033-0.0178.373-0.021-0.0210.0000.0000.0000.000
120H106GLY00.0080.01411.2790.0780.0780.0000.0000.0000.000
121H107THR0-0.068-0.04713.825-0.004-0.0040.0000.0000.0000.000
122H108LEU0-0.036-0.00516.7880.0220.0220.0000.0000.0000.000
123H109VAL0-0.007-0.00220.2040.0090.0090.0000.0000.0000.000
124H110THR00.012-0.00122.7470.0020.0020.0000.0000.0000.000
125H111VAL0-0.012-0.00126.4220.0060.0060.0000.0000.0000.000
126H112SER00.012-0.00229.1930.0050.0050.0000.0000.0000.000
127H113SER00.0490.01832.6250.0000.0000.0000.0000.0000.000
128H114GLY00.0300.03335.2930.0040.0040.0000.0000.0000.000
129H115SER0-0.004-0.02433.686-0.002-0.0020.0000.0000.0000.000
130H116ALA0-0.0130.00730.461-0.002-0.0020.0000.0000.0000.000
131H117SER0-0.023-0.00732.1740.0080.0080.0000.0000.0000.000
132H118ALA00.0300.00631.871-0.011-0.0110.0000.0000.0000.000
133H119PRO0-0.035-0.00229.9500.0030.0030.0000.0000.0000.000
134H120THR00.0240.00833.0930.0040.0040.0000.0000.0000.000
135H121LEU00.0050.00231.792-0.002-0.0020.0000.0000.0000.000
136H122PHE0-0.009-0.01435.8120.0080.0080.0000.0000.0000.000
137H123PRO00.0070.01337.599-0.006-0.0060.0000.0000.0000.000
138H124LEU0-0.037-0.01536.6690.0050.0050.0000.0000.0000.000
139H125ALA00.0310.00939.467-0.004-0.0040.0000.0000.0000.000
140H126PRO00.0170.02939.6770.0020.0020.0000.0000.0000.000
141H127SER00.021-0.00441.8550.0060.0060.0000.0000.0000.000
142H128SER00.0370.01245.241-0.002-0.0020.0000.0000.0000.000
143H129LYS10.9120.95046.7540.0680.0680.0000.0000.0000.000
144H130SER0-0.024-0.00841.1860.0000.0000.0000.0000.0000.000
145H133THR0-0.0120.00141.654-0.004-0.0040.0000.0000.0000.000
146H134SER0-0.008-0.01442.5160.0040.0040.0000.0000.0000.000
147H135GLY00.0550.03342.674-0.003-0.0030.0000.0000.0000.000
148H136GLY00.0130.00442.0360.0010.0010.0000.0000.0000.000
149H137THR0-0.0220.00437.302-0.003-0.0030.0000.0000.0000.000
150H138ALA00.010-0.00538.7240.0060.0060.0000.0000.0000.000
151H139ALA00.0050.02237.053-0.007-0.0070.0000.0000.0000.000
152H140LEU00.0030.01934.4230.0090.0090.0000.0000.0000.000
153H141GLY00.0510.00334.648-0.009-0.0090.0000.0000.0000.000
154H142CYS0-0.0560.00630.538-0.007-0.0070.0000.0000.0000.000
155H143LEU00.0270.03633.658-0.008-0.0080.0000.0000.0000.000
156H144VAL0-0.011-0.01830.1000.0030.0030.0000.0000.0000.000
157H145LYS10.8560.89133.2280.0940.0940.0000.0000.0000.000
158H146ASP-1-0.753-0.85635.320-0.100-0.1000.0000.0000.0000.000
159H147TYR0-0.015-0.00628.2800.0070.0070.0000.0000.0000.000
160H148PHE00.0200.00531.191-0.001-0.0010.0000.0000.0000.000
161H149PRO00.0070.01426.9490.0040.0040.0000.0000.0000.000
162H150GLU-1-0.747-0.86325.208-0.212-0.2120.0000.0000.0000.000
163H151PRO0-0.018-0.00721.0090.0050.0050.0000.0000.0000.000
164H152VAL0-0.035-0.02224.1320.0080.0080.0000.0000.0000.000
165H153THR0-0.023-0.00320.063-0.021-0.0210.0000.0000.0000.000
166H154VAL0-0.006-0.01723.2580.0170.0170.0000.0000.0000.000
167H156SER0-0.011-0.00723.579-0.025-0.0250.0000.0000.0000.000
168H157TRP00.0240.00925.5780.0260.0260.0000.0000.0000.000
169H162ASN0-0.005-0.01626.466-0.011-0.0110.0000.0000.0000.000
170H163SER0-0.014-0.01624.9430.0030.0030.0000.0000.0000.000
171H164GLY00.0090.01222.074-0.019-0.0190.0000.0000.0000.000
172H165ALA0-0.042-0.01222.803-0.012-0.0120.0000.0000.0000.000
173H166LEU0-0.033-0.00924.9800.0120.0120.0000.0000.0000.000
174H167THR00.0210.00021.622-0.001-0.0010.0000.0000.0000.000
175H168SER00.0290.00824.898-0.001-0.0010.0000.0000.0000.000
176H169GLY00.0480.01926.8130.0090.0090.0000.0000.0000.000
177H171VAL0-0.047-0.01326.5570.0110.0110.0000.0000.0000.000
178H172HIS0-0.0010.00927.735-0.014-0.0140.0000.0000.0000.000
179H173THR00.000-0.01026.2700.0170.0170.0000.0000.0000.000
180H174PHE0-0.0090.01227.517-0.010-0.0100.0000.0000.0000.000
181H175PRO00.0330.00127.619-0.005-0.0050.0000.0000.0000.000
182H176ALA0-0.0180.00828.2630.0120.0120.0000.0000.0000.000
183H177VAL0-0.005-0.00830.1510.0010.0010.0000.0000.0000.000
184H178LEU0-0.042-0.01533.0480.0020.0020.0000.0000.0000.000
185H179GLN0-0.021-0.02334.5320.0080.0080.0000.0000.0000.000
186H180SER00.0290.00238.143-0.001-0.0010.0000.0000.0000.000
187H182SER0-0.007-0.00139.6200.0020.0020.0000.0000.0000.000
188H183GLY00.0230.01737.5250.0020.0020.0000.0000.0000.000
189H184LEU0-0.049-0.01634.968-0.005-0.0050.0000.0000.0000.000
190H185TYR00.0150.00529.5510.0030.0030.0000.0000.0000.000
191H186SER0-0.015-0.00733.2760.0060.0060.0000.0000.0000.000
192H187LEU00.0130.02927.724-0.002-0.0020.0000.0000.0000.000
193H188SER0-0.009-0.02632.0080.0130.0130.0000.0000.0000.000
194H189SER0-0.0060.00428.726-0.008-0.0080.0000.0000.0000.000
195H190VAL00.008-0.01631.1420.0130.0130.0000.0000.0000.000
196H191VAL00.0200.01130.483-0.012-0.0120.0000.0000.0000.000
197H192THR0-0.020-0.00332.5120.0100.0100.0000.0000.0000.000
198H193VAL00.0150.00733.097-0.007-0.0070.0000.0000.0000.000
199H194PRO00.0720.02834.7010.0060.0060.0000.0000.0000.000
200H195SER0-0.025-0.00137.9540.0000.0000.0000.0000.0000.000
201H196SER00.0230.00340.8920.0010.0010.0000.0000.0000.000
202H197SER0-0.022-0.01437.1630.0010.0010.0000.0000.0000.000
203H198LEU00.005-0.00839.063-0.001-0.0010.0000.0000.0000.000
204H199GLY0-0.0050.00940.9100.0010.0010.0000.0000.0000.000
205H200THR0-0.036-0.01939.9540.0020.0020.0000.0000.0000.000
206H203GLN0-0.040-0.01633.0700.0000.0000.0000.0000.0000.000
207H205THR00.0030.00634.6030.0010.0010.0000.0000.0000.000
208H206TYR00.0270.00132.687-0.011-0.0110.0000.0000.0000.000
209H207ILE00.004-0.01231.3500.0080.0080.0000.0000.0000.000
210H209ASN00.0560.01926.646-0.002-0.0020.0000.0000.0000.000
211H210VAL00.0070.00527.145-0.015-0.0150.0000.0000.0000.000
212H211ASN0-0.010-0.00221.8680.0260.0260.0000.0000.0000.000
213H212HIS10.8370.88525.0330.1530.1530.0000.0000.0000.000
214H213LYS10.9340.97321.0880.1970.1970.0000.0000.0000.000
215H214PRO00.0030.00623.8860.0120.0120.0000.0000.0000.000
216H215SER00.0200.00526.1900.0090.0090.0000.0000.0000.000
217H216ASN0-0.047-0.02525.981-0.004-0.0040.0000.0000.0000.000
218H217THR00.0340.04127.5670.0070.0070.0000.0000.0000.000
219H218LYS10.9080.94123.1820.1990.1990.0000.0000.0000.000
220H219VAL0-0.008-0.00128.9190.0130.0130.0000.0000.0000.000
221H220ASP-1-0.812-0.89129.825-0.172-0.1720.0000.0000.0000.000
222H221LYS10.8650.91732.3430.1140.1140.0000.0000.0000.000
223H222LYS10.8780.94634.6020.0830.0830.0000.0000.0000.000
224H225VAL0-0.053-0.02535.6720.0040.0040.0000.0000.0000.000
225H226GLU-1-0.829-0.91438.006-0.086-0.0860.0000.0000.0000.000
226H227PRO00.0310.00540.9830.0000.0000.0000.0000.0000.000
227H228LYS10.8500.91443.6000.0670.0670.0000.0000.0000.000
228H229SER00.0390.03046.5470.0030.0030.0000.0000.0000.000
229H230CYS00.0230.02649.3600.0000.0000.0000.0000.0000.000