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: 72Z6K

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 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 -2413004.865255
FMO2-HF: Nuclear repulsion 2326049.036832
FMO2-HF: Total energy -86955.828423
FMO2-MP2: Total energy -87208.894147


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.
-13.453-1.6854.267-5.598-10.438-0.036
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 : 0.017
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].
3H4LEU00.0160.0053.229-1.4801.871-0.011-1.636-1.7050.007
4H5VAL00.0030.0065.570-0.055-0.0550.0000.0000.0000.000
5H6GLN00.003-0.0369.2540.1100.1100.0000.0000.0000.000
6H7SER00.0360.03612.1480.0000.0000.0000.0000.0000.000
7H8GLY0-0.030-0.01915.841-0.026-0.0260.0000.0000.0000.000
8H9ALA00.001-0.00318.3560.0180.0180.0000.0000.0000.000
9H10GLU-1-0.867-0.93220.652-0.126-0.1260.0000.0000.0000.000
10H11VAL0-0.0110.00323.793-0.004-0.0040.0000.0000.0000.000
11H12LYS10.8170.91324.3250.1250.1250.0000.0000.0000.000
12H13LYS10.9510.98328.3630.0830.0830.0000.0000.0000.000
13H14PRO00.0270.01530.9330.0000.0000.0000.0000.0000.000
14H15GLY0-0.016-0.01131.8630.0040.0040.0000.0000.0000.000
15H16SER0-0.067-0.03229.4310.0020.0020.0000.0000.0000.000
16H17SER00.0400.00426.0910.0000.0000.0000.0000.0000.000
17H18VAL0-0.038-0.01221.138-0.002-0.0020.0000.0000.0000.000
18H19LYS10.8780.92719.4340.0470.0470.0000.0000.0000.000
19H20VAL0-0.051-0.00714.945-0.010-0.0100.0000.0000.0000.000
20H21SER00.0220.00314.3930.0160.0160.0000.0000.0000.000
21H22CYS0-0.016-0.0048.584-0.049-0.0490.0000.0000.0000.000
22H23LYS10.9480.9999.2760.2280.2280.0000.0000.0000.000
23H24ALA00.0110.0094.239-0.294-0.240-0.001-0.010-0.0430.000
24H25SER0-0.044-0.0244.475-0.0770.069-0.001-0.020-0.1240.000
25H26GLY00.0390.0182.674-5.007-2.6160.950-1.541-1.801-0.017
26H33GLY00.0740.0347.961-0.011-0.0110.0000.0000.0000.000
27H33ASP-1-0.858-0.9204.8451.6761.6760.0000.0000.0000.000
28H33THR0-0.013-0.0162.959-0.537-0.0980.038-0.110-0.3670.000
29H33PHE00.002-0.0195.961-0.226-0.2260.0000.0000.0000.000
30H33SER00.0200.0149.242-0.145-0.1450.0000.0000.0000.000
31H33ASN0-0.085-0.0508.953-0.177-0.1770.0000.0000.0000.000
32H33TYR0-0.112-0.0445.468-0.150-0.1500.0000.0000.0000.000
33H33ALA00.0680.0409.020-0.014-0.0140.0000.0000.0000.000
34H34ILE0-0.047-0.0326.624-0.039-0.0390.0000.0000.0000.000
35H35SER00.001-0.01510.0240.0230.0230.0000.0000.0000.000
36H36TRP00.0010.00011.565-0.072-0.0720.0000.0000.0000.000
37H37VAL0-0.019-0.00513.6480.0370.0370.0000.0000.0000.000
38H38ARG10.8060.89415.5150.1090.1090.0000.0000.0000.000
39H39GLN00.0090.01317.959-0.020-0.0200.0000.0000.0000.000
40H40ALA00.0460.02919.808-0.008-0.0080.0000.0000.0000.000
41H41PRO00.021-0.00723.163-0.010-0.0100.0000.0000.0000.000
42H42GLY0-0.0050.01123.7930.0150.0150.0000.0000.0000.000
43H43GLN0-0.044-0.03023.8540.0120.0120.0000.0000.0000.000
44H44GLY00.0280.02321.722-0.019-0.0190.0000.0000.0000.000
45H45PHE00.013-0.00315.671-0.001-0.0010.0000.0000.0000.000
46H46GLU-1-0.772-0.85819.578-0.099-0.0990.0000.0000.0000.000
47H47TRP00.0070.01115.086-0.011-0.0110.0000.0000.0000.000
48H48MET0-0.044-0.03817.7530.0100.0100.0000.0000.0000.000
49H49GLY00.0600.01417.4840.0200.0200.0000.0000.0000.000
50H50GLY0-0.032-0.00214.713-0.032-0.0320.0000.0000.0000.000
51H51ILE0-0.046-0.01713.1770.0040.0040.0000.0000.0000.000
52H52ILE00.0560.03613.027-0.002-0.0020.0000.0000.0000.000
53H52PRO0-0.087-0.04410.385-0.018-0.0180.0000.0000.0000.000
54H53ILE00.0960.06613.666-0.023-0.0230.0000.0000.0000.000
55H54PHE0-0.038-0.01815.434-0.016-0.0160.0000.0000.0000.000
56H55GLY0-0.0190.00117.038-0.019-0.0190.0000.0000.0000.000
57H56THR0-0.034-0.00318.596-0.018-0.0180.0000.0000.0000.000
58H57ALA00.036-0.00118.0090.0040.0040.0000.0000.0000.000
59H58ASN0-0.0520.00018.7720.0060.0060.0000.0000.0000.000
60H59TYR00.0770.02019.465-0.012-0.0120.0000.0000.0000.000
61H60ALA0-0.009-0.00621.7850.0070.0070.0000.0000.0000.000
62H61GLN00.0700.01623.466-0.002-0.0020.0000.0000.0000.000
63H62LYS10.7940.88825.0620.1010.1010.0000.0000.0000.000
64H63PHE0-0.024-0.01522.259-0.003-0.0030.0000.0000.0000.000
65H64GLN00.0160.02125.6850.0000.0000.0000.0000.0000.000
66H65GLY00.0090.00026.8810.0010.0010.0000.0000.0000.000
67H66ARG10.7530.85426.9330.0820.0820.0000.0000.0000.000
68H67VAL0-0.0010.00020.736-0.009-0.0090.0000.0000.0000.000
69H68THR0-0.032-0.00721.2870.0130.0130.0000.0000.0000.000
70H69ILE0-0.009-0.00215.448-0.017-0.0170.0000.0000.0000.000
71H70THR0-0.014-0.00516.8920.0150.0150.0000.0000.0000.000
72H71ALA00.014-0.00912.815-0.018-0.0180.0000.0000.0000.000
73H72ASP-1-0.802-0.85113.8470.1300.1300.0000.0000.0000.000
74H73GLU-1-0.856-0.94712.6390.3420.3420.0000.0000.0000.000
75H74SER0-0.095-0.05113.0660.0500.0500.0000.0000.0000.000
76H75THR0-0.055-0.05913.661-0.007-0.0070.0000.0000.0000.000
77H76SER0-0.0180.0068.1570.0190.0190.0000.0000.0000.000
78H77THR0-0.039-0.0259.086-0.077-0.0770.0000.0000.0000.000
79H78ALA00.0180.02010.9270.0370.0370.0000.0000.0000.000
80H79TYR00.004-0.02912.393-0.072-0.0720.0000.0000.0000.000
81H80MET0-0.0230.01315.5550.0240.0240.0000.0000.0000.000
82H81GLU-1-0.840-0.91217.633-0.064-0.0640.0000.0000.0000.000
83H82LEU00.0270.01321.3050.0080.0080.0000.0000.0000.000
84H82SER0-0.010-0.01723.483-0.002-0.0020.0000.0000.0000.000
85H82SER00.007-0.00827.221-0.001-0.0010.0000.0000.0000.000
86H82LEU0-0.055-0.01724.797-0.002-0.0020.0000.0000.0000.000
87H83ARG11.0171.01228.7250.0730.0730.0000.0000.0000.000
88H84SER00.0490.02028.896-0.008-0.0080.0000.0000.0000.000
89H85GLU-1-0.874-0.94628.886-0.097-0.0970.0000.0000.0000.000
90H86ASP-1-0.801-0.85724.900-0.106-0.1060.0000.0000.0000.000
91H87THR0-0.0120.01623.949-0.013-0.0130.0000.0000.0000.000
92H88ALA0-0.011-0.00220.8420.0020.0020.0000.0000.0000.000
93H89VAL0-0.0130.00315.9440.0030.0030.0000.0000.0000.000
94H90TYR0-0.033-0.05116.3730.0120.0120.0000.0000.0000.000
95H91TYR00.0190.00911.496-0.029-0.0290.0000.0000.0000.000
96H93ALA00.026-0.0017.574-0.147-0.1470.0000.0000.0000.000
97H94ARG10.8320.9073.111-2.614-0.6580.720-0.712-1.964-0.006
98H95GLY00.0260.0146.395-0.201-0.2010.0000.0000.0000.000
99H96PRO0-0.0020.0277.8970.1040.1040.0000.0000.0000.000
100H97GLU-1-0.831-0.9299.7540.1830.1830.0000.0000.0000.000
101H98TYR0-0.059-0.03413.3200.0190.0190.0000.0000.0000.000
102H99TYR00.0170.01016.651-0.008-0.0080.0000.0000.0000.000
103H100ASP-1-0.863-0.92119.8710.0330.0330.0000.0000.0000.000
104H100TYR00.0500.00122.8340.0020.0020.0000.0000.0000.000
105H100VAL0-0.040-0.01925.930-0.003-0.0030.0000.0000.0000.000
106H100TRP0-0.057-0.03322.521-0.004-0.0040.0000.0000.0000.000
107H100GLY0-0.0030.02025.8580.0000.0000.0000.0000.0000.000
108H100SER0-0.033-0.03220.9760.0070.0070.0000.0000.0000.000
109H100TYR00.0370.03616.493-0.008-0.0080.0000.0000.0000.000
110H100ARG10.8230.91017.547-0.036-0.0360.0000.0000.0000.000
111H100TYR00.033-0.00513.6060.0120.0120.0000.0000.0000.000
112H100ASN0-0.021-0.02312.519-0.025-0.0250.0000.0000.0000.000
113H100TYR00.0000.0059.6540.0040.0040.0000.0000.0000.000
114H100PHE00.015-0.0048.9750.0270.0270.0000.0000.0000.000
115H101ASP-1-0.795-0.9024.930-0.903-0.758-0.001-0.006-0.1380.000
116H102TYR0-0.0210.0052.879-4.672-1.4592.574-1.562-4.225-0.020
117H103TRP00.000-0.0085.1450.3410.414-0.001-0.001-0.0710.000
118H104GLY00.0460.0226.677-0.302-0.3020.0000.0000.0000.000
119H105GLN0-0.028-0.0097.952-0.007-0.0070.0000.0000.0000.000
120H106GLY00.0190.01611.0120.0790.0790.0000.0000.0000.000
121H107THR0-0.041-0.02813.513-0.010-0.0100.0000.0000.0000.000
122H108LEU0-0.044-0.01516.4480.0230.0230.0000.0000.0000.000
123H109VAL00.0130.01119.8050.0110.0110.0000.0000.0000.000
124H110THR0-0.013-0.02122.2700.0040.0040.0000.0000.0000.000
125H111VAL00.0160.01625.9270.0060.0060.0000.0000.0000.000
126H112SER00.0230.00228.5450.0050.0050.0000.0000.0000.000
127H113SER00.0250.01331.8900.0000.0000.0000.0000.0000.000
128H114GLY00.000-0.00234.3130.0040.0040.0000.0000.0000.000
129H115SER0-0.014-0.02433.020-0.004-0.0040.0000.0000.0000.000
130H116ALA0-0.0070.00829.873-0.003-0.0030.0000.0000.0000.000
131H117SER0-0.009-0.00931.7880.0090.0090.0000.0000.0000.000
132H118ALA00.0020.00031.481-0.009-0.0090.0000.0000.0000.000
133H119PRO0-0.0280.00230.0410.0050.0050.0000.0000.0000.000
134H120THR00.0240.01633.1770.0040.0040.0000.0000.0000.000
135H121LEU0-0.011-0.01031.591-0.003-0.0030.0000.0000.0000.000
136H122PHE00.005-0.00335.7240.0080.0080.0000.0000.0000.000
137H123PRO00.0150.01737.447-0.006-0.0060.0000.0000.0000.000
138H124LEU0-0.040-0.01336.2200.0050.0050.0000.0000.0000.000
139H125ALA00.0380.00838.649-0.004-0.0040.0000.0000.0000.000
140H126PRO00.0050.03039.2220.0020.0020.0000.0000.0000.000
141H127SER0-0.014-0.02941.3960.0060.0060.0000.0000.0000.000
142H128SER00.0580.02044.677-0.002-0.0020.0000.0000.0000.000
143H129LYS10.9180.96346.4120.0640.0640.0000.0000.0000.000
144H130SER0-0.0040.00940.7930.0000.0000.0000.0000.0000.000
145H133THR00.0060.00541.055-0.005-0.0050.0000.0000.0000.000
146H134SER0-0.019-0.02442.1870.0040.0040.0000.0000.0000.000
147H135GLY00.0560.04742.121-0.003-0.0030.0000.0000.0000.000
148H136GLY00.009-0.00141.7740.0020.0020.0000.0000.0000.000
149H137THR0-0.033-0.00236.743-0.003-0.0030.0000.0000.0000.000
150H138ALA00.008-0.00238.2150.0050.0050.0000.0000.0000.000
151H139ALA0-0.0100.00936.508-0.007-0.0070.0000.0000.0000.000
152H140LEU00.0100.01133.9610.0080.0080.0000.0000.0000.000
153H141GLY00.0470.00433.929-0.009-0.0090.0000.0000.0000.000
154H142CYS0-0.0350.01430.038-0.008-0.0080.0000.0000.0000.000
155H143LEU0-0.0010.01233.824-0.006-0.0060.0000.0000.0000.000
156H144VAL0-0.015-0.02329.8670.0050.0050.0000.0000.0000.000
157H145LYS10.8780.91033.2090.0950.0950.0000.0000.0000.000
158H146ASP-1-0.786-0.87435.378-0.099-0.0990.0000.0000.0000.000
159H147TYR0-0.018-0.02527.9130.0050.0050.0000.0000.0000.000
160H148PHE00.0280.02030.791-0.001-0.0010.0000.0000.0000.000
161H149PRO00.0170.01826.6460.0050.0050.0000.0000.0000.000
162H150GLU-1-0.764-0.86524.772-0.206-0.2060.0000.0000.0000.000
163H151PRO0-0.014-0.00620.7920.0030.0030.0000.0000.0000.000
164H152VAL0-0.024-0.02623.9670.0080.0080.0000.0000.0000.000
165H153THR0-0.0010.00819.874-0.019-0.0190.0000.0000.0000.000
166H154VAL00.005-0.01723.0870.0200.0200.0000.0000.0000.000
167H156SER0-0.042-0.02323.017-0.024-0.0240.0000.0000.0000.000
168H157TRP00.0560.03224.9230.0240.0240.0000.0000.0000.000
169H162ASN0-0.034-0.04226.131-0.009-0.0090.0000.0000.0000.000
170H163SER00.003-0.01424.2270.0030.0030.0000.0000.0000.000
171H164GLY0-0.0040.00121.686-0.020-0.0200.0000.0000.0000.000
172H165ALA0-0.0190.00722.195-0.015-0.0150.0000.0000.0000.000
173H166LEU0-0.041-0.00524.4420.0100.0100.0000.0000.0000.000
174H167THR00.006-0.00721.0520.0010.0010.0000.0000.0000.000
175H168SER0-0.006-0.01424.367-0.003-0.0030.0000.0000.0000.000
176H169GLY00.0780.04026.4970.0110.0110.0000.0000.0000.000
177H171VAL0-0.043-0.02525.9130.0110.0110.0000.0000.0000.000
178H172HIS00.0040.01527.087-0.015-0.0150.0000.0000.0000.000
179H173THR0-0.011-0.00625.9140.0190.0190.0000.0000.0000.000
180H174PHE0-0.0170.00227.267-0.008-0.0080.0000.0000.0000.000
181H175PRO00.016-0.00927.374-0.005-0.0050.0000.0000.0000.000
182H176ALA00.0000.02228.1790.0120.0120.0000.0000.0000.000
183H177VAL0-0.012-0.00830.1460.0010.0010.0000.0000.0000.000
184H178LEU0-0.044-0.01832.6160.0010.0010.0000.0000.0000.000
185H179GLN0-0.025-0.04034.1740.0080.0080.0000.0000.0000.000
186H180SER00.024-0.00237.7980.0000.0000.0000.0000.0000.000
187H182SER0-0.016-0.00339.3810.0010.0010.0000.0000.0000.000
188H183GLY00.0260.02236.9450.0020.0020.0000.0000.0000.000
189H184LEU0-0.046-0.01534.604-0.005-0.0050.0000.0000.0000.000
190H185TYR0-0.0020.00529.3630.0030.0030.0000.0000.0000.000
191H186SER00.0190.00233.0480.0050.0050.0000.0000.0000.000
192H187LEU0-0.0160.01427.798-0.001-0.0010.0000.0000.0000.000
193H188SER00.0160.00132.3090.0080.0080.0000.0000.0000.000
194H189SER0-0.014-0.01928.438-0.007-0.0070.0000.0000.0000.000
195H190VAL00.012-0.00731.1130.0110.0110.0000.0000.0000.000
196H191VAL00.0190.01729.883-0.012-0.0120.0000.0000.0000.000
197H192THR00.0090.00531.9500.0100.0100.0000.0000.0000.000
198H193VAL0-0.009-0.00932.406-0.008-0.0080.0000.0000.0000.000
199H194PRO00.0720.03534.0730.0060.0060.0000.0000.0000.000
200H195SER00.0040.00137.3420.0000.0000.0000.0000.0000.000
201H196SER00.009-0.00640.0650.0010.0010.0000.0000.0000.000
202H197SER0-0.011-0.00736.7070.0010.0010.0000.0000.0000.000
203H198LEU00.0130.00238.455-0.002-0.0020.0000.0000.0000.000
204H199GLY0-0.0160.00340.3330.0000.0000.0000.0000.0000.000
205H200THR0-0.037-0.02539.7490.0010.0010.0000.0000.0000.000
206H203GLN0-0.037-0.00932.5030.0010.0010.0000.0000.0000.000
207H205THR0-0.0120.00233.8500.0020.0020.0000.0000.0000.000
208H206TYR00.0340.00032.121-0.011-0.0110.0000.0000.0000.000
209H207ILE00.010-0.00230.7470.0080.0080.0000.0000.0000.000
210H209ASN00.0510.02326.075-0.003-0.0030.0000.0000.0000.000
211H210VAL00.0130.00026.874-0.016-0.0160.0000.0000.0000.000
212H211ASN0-0.036-0.01021.6520.0270.0270.0000.0000.0000.000
213H212HIS10.8480.90124.8950.1530.1530.0000.0000.0000.000
214H213LYS10.9410.95921.0380.1960.1960.0000.0000.0000.000
215H214PRO00.0130.00623.8340.0130.0130.0000.0000.0000.000
216H215SER00.0160.00626.1150.0080.0080.0000.0000.0000.000
217H216ASN0-0.0310.00125.999-0.005-0.0050.0000.0000.0000.000
218H217THR00.0350.02927.7660.0090.0090.0000.0000.0000.000
219H218LYS10.9150.95222.9920.2050.2050.0000.0000.0000.000
220H219VAL00.0020.00428.8540.0120.0120.0000.0000.0000.000
221H220ASP-1-0.809-0.88629.115-0.174-0.1740.0000.0000.0000.000
222H221LYS10.8640.92531.7730.1120.1120.0000.0000.0000.000
223H222LYS10.8920.93934.1520.0830.0830.0000.0000.0000.000
224H225VAL0-0.031-0.01835.3210.0050.0050.0000.0000.0000.000
225H226GLU-1-0.873-0.92237.645-0.084-0.0840.0000.0000.0000.000
226H227PRO00.0330.00440.6690.0000.0000.0000.0000.0000.000
227H228LYS10.8730.93542.9300.0660.0660.0000.0000.0000.000
228H229SER00.0200.01346.0750.0020.0020.0000.0000.0000.000
229H230CYS00.0390.03349.0750.0000.0000.0000.0000.0000.000