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: MV2NZ

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 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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2412281.696081
FMO2-HF: Nuclear repulsion 2325326.773796
FMO2-HF: Total energy -86954.922285
FMO2-MP2: Total energy -87208.051981


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.
-7.2862.5853.616-4.385-9.101-0.029
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 : -0.023 / q_NPA : -0.014
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].
3H4LEU00.0160.0003.284-0.5621.728-0.018-0.965-1.3070.002
4H5VAL00.0140.0135.462-0.089-0.0890.0000.0000.0000.000
5H6GLN0-0.005-0.0349.1360.0080.0080.0000.0000.0000.000
6H7SER00.0380.03112.0480.0290.0290.0000.0000.0000.000
7H8GLY0-0.028-0.01415.738-0.035-0.0350.0000.0000.0000.000
8H9ALA00.0020.00218.2480.0010.0010.0000.0000.0000.000
9H10GLU-1-0.942-0.96720.553-0.022-0.0220.0000.0000.0000.000
10H11VAL0-0.0060.00123.701-0.011-0.0110.0000.0000.0000.000
11H12LYS10.8790.95224.9430.0400.0400.0000.0000.0000.000
12H13LYS10.9891.00128.2880.0250.0250.0000.0000.0000.000
13H14PRO00.0230.01130.8720.0000.0000.0000.0000.0000.000
14H15GLY0-0.011-0.01131.8230.0050.0050.0000.0000.0000.000
15H16SER0-0.079-0.03529.2500.0040.0040.0000.0000.0000.000
16H17SER00.0460.00826.084-0.005-0.0050.0000.0000.0000.000
17H18VAL0-0.032-0.01821.2810.0060.0060.0000.0000.0000.000
18H19LYS10.9981.00819.234-0.034-0.0340.0000.0000.0000.000
19H20VAL0-0.0290.00214.7620.0080.0080.0000.0000.0000.000
20H21SER0-0.008-0.00814.4330.0170.0170.0000.0000.0000.000
21H22CYS0-0.028-0.0128.590-0.045-0.0450.0000.0000.0000.000
22H23LYS10.9671.0059.280-0.439-0.4390.0000.0000.0000.000
23H24ALA00.0080.0034.258-0.184-0.130-0.001-0.009-0.0450.000
24H25SER0-0.046-0.0254.472-0.0580.073-0.001-0.019-0.1110.000
25H26GLY00.0310.0182.8081.5573.4900.679-1.146-1.466-0.009
26H33GLY00.0380.0018.1980.0500.0500.0000.0000.0000.000
27H33ASP-1-0.833-0.9135.1520.2690.2690.0000.0000.0000.000
28H33THR0-0.049-0.0293.070-0.548-0.1630.026-0.098-0.3120.000
29H33PHE0-0.009-0.0306.034-0.168-0.1680.0000.0000.0000.000
30H33SER00.0410.0339.311-0.089-0.0890.0000.0000.0000.000
31H33ASN0-0.104-0.0519.023-0.081-0.0810.0000.0000.0000.000
32H33TYR0-0.061-0.0085.665-0.220-0.2200.0000.0000.0000.000
33H33ALA00.0490.0319.1290.0680.0680.0000.0000.0000.000
34H34ILE0-0.037-0.0276.937-0.091-0.0910.0000.0000.0000.000
35H35SER0-0.009-0.02510.0360.0670.0670.0000.0000.0000.000
36H36TRP00.0040.00611.578-0.061-0.0610.0000.0000.0000.000
37H37VAL0-0.017-0.00613.8510.0310.0310.0000.0000.0000.000
38H38ARG10.8230.90615.4970.1340.1340.0000.0000.0000.000
39H39GLN0-0.017-0.00518.006-0.025-0.0250.0000.0000.0000.000
40H40ALA00.0410.02619.7830.0070.0070.0000.0000.0000.000
41H41PRO00.023-0.00323.129-0.014-0.0140.0000.0000.0000.000
42H42GLY00.0020.01623.7520.0120.0120.0000.0000.0000.000
43H43GLN0-0.031-0.02623.8360.0040.0040.0000.0000.0000.000
44H44GLY00.0180.01721.720-0.020-0.0200.0000.0000.0000.000
45H45PHE00.0180.00115.9760.0020.0020.0000.0000.0000.000
46H46GLU-1-0.759-0.85619.589-0.133-0.1330.0000.0000.0000.000
47H47TRP00.0010.00615.2510.0050.0050.0000.0000.0000.000
48H48MET0-0.039-0.03917.7720.0210.0210.0000.0000.0000.000
49H49GLY00.0620.02217.4530.0270.0270.0000.0000.0000.000
50H50GLY0-0.034-0.00314.712-0.040-0.0400.0000.0000.0000.000
51H51ILE0-0.039-0.01513.3270.0240.0240.0000.0000.0000.000
52H52ILE00.0500.03013.071-0.026-0.0260.0000.0000.0000.000
53H52PRO0-0.086-0.04210.4610.0100.0100.0000.0000.0000.000
54H53ILE00.0980.06513.7330.0020.0020.0000.0000.0000.000
55H54PHE0-0.033-0.01515.5070.0000.0000.0000.0000.0000.000
56H55GLY0-0.022-0.00117.111-0.002-0.0020.0000.0000.0000.000
57H56THR0-0.038-0.00818.672-0.007-0.0070.0000.0000.0000.000
58H57ALA00.0450.00618.059-0.009-0.0090.0000.0000.0000.000
59H58ASN0-0.053-0.00818.7980.0040.0040.0000.0000.0000.000
60H59TYR00.0650.01719.471-0.011-0.0110.0000.0000.0000.000
61H60ALA0-0.008-0.00621.7830.0040.0040.0000.0000.0000.000
62H61GLN00.0820.02323.4490.0030.0030.0000.0000.0000.000
63H62LYS10.7700.87625.3900.1320.1320.0000.0000.0000.000
64H63PHE0-0.024-0.01422.4360.0040.0040.0000.0000.0000.000
65H64GLN00.0220.02325.6940.0020.0020.0000.0000.0000.000
66H65GLY00.001-0.00426.8640.0030.0030.0000.0000.0000.000
67H66ARG10.7660.88026.7010.0850.0850.0000.0000.0000.000
68H67VAL0-0.010-0.01320.723-0.002-0.0020.0000.0000.0000.000
69H68THR0-0.0140.00021.2220.0060.0060.0000.0000.0000.000
70H69ILE0-0.012-0.00515.526-0.005-0.0050.0000.0000.0000.000
71H70THR0-0.028-0.00916.8990.0160.0160.0000.0000.0000.000
72H71ALA00.017-0.01212.871-0.013-0.0130.0000.0000.0000.000
73H72ASP-1-0.861-0.91113.8930.2170.2170.0000.0000.0000.000
74H73GLU-1-0.842-0.94612.6870.2990.2990.0000.0000.0000.000
75H74SER0-0.085-0.03113.1090.0720.0720.0000.0000.0000.000
76H75THR0-0.029-0.02113.6830.0370.0370.0000.0000.0000.000
77H76SER0-0.028-0.0018.2220.0970.0970.0000.0000.0000.000
78H77THR0-0.027-0.0119.1100.0180.0180.0000.0000.0000.000
79H78ALA00.0190.01911.034-0.009-0.0090.0000.0000.0000.000
80H79TYR0-0.004-0.03312.430-0.022-0.0220.0000.0000.0000.000
81H80MET0-0.0210.01315.585-0.003-0.0030.0000.0000.0000.000
82H81GLU-1-0.940-0.97917.606-0.006-0.0060.0000.0000.0000.000
83H82LEU00.0130.00421.271-0.004-0.0040.0000.0000.0000.000
84H82SER0-0.006-0.01223.4520.0060.0060.0000.0000.0000.000
85H82SER00.002-0.00827.188-0.005-0.0050.0000.0000.0000.000
86H82LEU0-0.051-0.01524.784-0.006-0.0060.0000.0000.0000.000
87H83ARG10.9960.99928.6860.0740.0740.0000.0000.0000.000
88H84SER00.0710.02628.853-0.004-0.0040.0000.0000.0000.000
89H85GLU-1-0.906-0.95928.840-0.086-0.0860.0000.0000.0000.000
90H86ASP-1-0.802-0.87024.908-0.103-0.1030.0000.0000.0000.000
91H87THR0-0.0040.02123.905-0.006-0.0060.0000.0000.0000.000
92H88ALA0-0.011-0.00420.777-0.006-0.0060.0000.0000.0000.000
93H89VAL0-0.0050.01115.8310.0180.0180.0000.0000.0000.000
94H90TYR0-0.044-0.04616.278-0.014-0.0140.0000.0000.0000.000
95H91TYR00.0350.02511.4180.0080.0080.0000.0000.0000.000
96H93ALA00.0400.0097.591-0.147-0.1470.0000.0000.0000.000
97H94ARG10.8510.9282.695-1.1170.6681.321-0.806-2.300-0.005
98H95GLY00.0240.0186.394-0.234-0.2340.0000.0000.0000.000
99H96PRO00.0050.0267.9480.1320.1320.0000.0000.0000.000
100H97GLU-1-0.848-0.9329.854-0.064-0.0640.0000.0000.0000.000
101H98TYR0-0.068-0.03313.4200.0090.0090.0000.0000.0000.000
102H99TYR00.0210.01316.7550.0110.0110.0000.0000.0000.000
103H100ASP-1-0.849-0.91719.982-0.104-0.1040.0000.0000.0000.000
104H100TYR00.026-0.01422.9310.0080.0080.0000.0000.0000.000
105H100VAL0-0.019-0.01026.0380.0070.0070.0000.0000.0000.000
106H100TRP0-0.081-0.04922.6580.0020.0020.0000.0000.0000.000
107H100GLY0-0.0140.01325.9420.0070.0070.0000.0000.0000.000
108H100SER0-0.028-0.03421.0560.0130.0130.0000.0000.0000.000
109H100TYR00.0420.03816.794-0.011-0.0110.0000.0000.0000.000
110H100ARG10.8450.93517.6450.1380.1380.0000.0000.0000.000
111H100TYR00.0420.00913.578-0.012-0.0120.0000.0000.0000.000
112H100ASN0-0.018-0.02612.236-0.020-0.0200.0000.0000.0000.000
113H100TYR0-0.013-0.0019.782-0.024-0.0240.0000.0000.0000.000
114H100PHE00.0280.0058.9820.0180.0180.0000.0000.0000.000
115H101ASP-1-0.814-0.9305.189-1.783-1.678-0.001-0.002-0.1010.000
116H102TYR0-0.032-0.0032.892-4.568-1.4521.612-1.339-3.389-0.017
117H103TRP00.010-0.0055.1240.4440.516-0.001-0.001-0.0700.000
118H104GLY00.0320.0176.621-0.266-0.2660.0000.0000.0000.000
119H105GLN0-0.010-0.0077.879-0.051-0.0510.0000.0000.0000.000
120H106GLY00.0090.01010.9210.0560.0560.0000.0000.0000.000
121H107THR0-0.030-0.02913.4370.0230.0230.0000.0000.0000.000
122H108LEU0-0.035-0.01216.3650.0000.0000.0000.0000.0000.000
123H109VAL00.0130.01319.7530.0220.0220.0000.0000.0000.000
124H110THR0-0.010-0.02422.198-0.008-0.0080.0000.0000.0000.000
125H111VAL00.0050.01125.8540.0110.0110.0000.0000.0000.000
126H112SER00.0340.00428.4810.0000.0000.0000.0000.0000.000
127H113SER0-0.018-0.01331.8190.0040.0040.0000.0000.0000.000
128H114GLY0-0.0030.00234.2240.0050.0050.0000.0000.0000.000
129H115SER0-0.015-0.02332.934-0.002-0.0020.0000.0000.0000.000
130H116ALA0-0.0020.00929.819-0.003-0.0030.0000.0000.0000.000
131H117SER0-0.020-0.01331.6870.0080.0080.0000.0000.0000.000
132H118ALA0-0.002-0.00631.366-0.006-0.0060.0000.0000.0000.000
133H119PRO0-0.0270.00230.0000.0000.0000.0000.0000.0000.000
134H120THR00.0130.01133.0620.0070.0070.0000.0000.0000.000
135H121LEU00.0180.00431.544-0.003-0.0030.0000.0000.0000.000
136H122PHE0-0.026-0.02235.6050.0060.0060.0000.0000.0000.000
137H123PRO00.0180.01937.333-0.003-0.0030.0000.0000.0000.000
138H124LEU0-0.058-0.01835.8070.0000.0000.0000.0000.0000.000
139H125ALA00.0320.00238.456-0.001-0.0010.0000.0000.0000.000
140H126PRO0-0.0020.03639.019-0.001-0.0010.0000.0000.0000.000
141H127SER0-0.011-0.02841.2060.0040.0040.0000.0000.0000.000
142H128SER00.0480.01544.503-0.002-0.0020.0000.0000.0000.000
143H129LYS10.9150.95546.2490.0320.0320.0000.0000.0000.000
144H130SER0-0.0070.00240.551-0.001-0.0010.0000.0000.0000.000
145H133THR00.0060.00840.894-0.001-0.0010.0000.0000.0000.000
146H134SER0-0.012-0.02142.0220.0010.0010.0000.0000.0000.000
147H135GLY00.0400.04041.983-0.002-0.0020.0000.0000.0000.000
148H136GLY00.004-0.00541.6300.0020.0020.0000.0000.0000.000
149H137THR0-0.0200.00836.9060.0010.0010.0000.0000.0000.000
150H138ALA0-0.002-0.01138.0470.0010.0010.0000.0000.0000.000
151H139ALA0-0.0060.00936.347-0.003-0.0030.0000.0000.0000.000
152H140LEU0-0.019-0.00233.9160.0050.0050.0000.0000.0000.000
153H141GLY00.015-0.01733.739-0.007-0.0070.0000.0000.0000.000
154H142CYS-1-0.833-0.91332.079-0.040-0.0400.0000.0000.0000.000
155H143LEU0-0.089-0.03933.716-0.007-0.0070.0000.0000.0000.000
156H144VAL00.0320.00329.8110.0060.0060.0000.0000.0000.000
157H145LYS10.9230.94933.0990.0390.0390.0000.0000.0000.000
158H146ASP-1-0.841-0.93235.268-0.040-0.0400.0000.0000.0000.000
159H147TYR0-0.028-0.02627.8690.0060.0060.0000.0000.0000.000
160H148PHE00.0090.01430.691-0.006-0.0060.0000.0000.0000.000
161H149PRO00.0130.01326.5460.0090.0090.0000.0000.0000.000
162H150GLU-1-0.776-0.87724.742-0.116-0.1160.0000.0000.0000.000
163H151PRO0-0.023-0.01020.7560.0030.0030.0000.0000.0000.000
164H152VAL0-0.006-0.02023.8680.0160.0160.0000.0000.0000.000
165H153THR0-0.017-0.00719.719-0.012-0.0120.0000.0000.0000.000
166H154VAL00.0310.00522.9720.0150.0150.0000.0000.0000.000
167H156SER0-0.064-0.03622.831-0.013-0.0130.0000.0000.0000.000
168H157TRP00.0770.04524.7060.0110.0110.0000.0000.0000.000
169H162ASN0-0.039-0.03925.9520.0000.0000.0000.0000.0000.000
170H163SER0-0.003-0.01924.3410.0060.0060.0000.0000.0000.000
171H164GLY0-0.024-0.00821.5800.0070.0070.0000.0000.0000.000
172H165ALA0-0.035-0.00521.984-0.008-0.0080.0000.0000.0000.000
173H166LEU0-0.041-0.00124.297-0.002-0.0020.0000.0000.0000.000
174H167THR00.007-0.00620.928-0.004-0.0040.0000.0000.0000.000
175H168SER0-0.021-0.02424.189-0.014-0.0140.0000.0000.0000.000
176H169GLY00.0790.04126.3450.0090.0090.0000.0000.0000.000
177H171VAL0-0.029-0.01325.7770.0060.0060.0000.0000.0000.000
178H172HIS0-0.0150.00126.947-0.018-0.0180.0000.0000.0000.000
179H173THR00.0030.00125.8050.0170.0170.0000.0000.0000.000
180H174PHE0-0.031-0.00727.180-0.012-0.0120.0000.0000.0000.000
181H175PRO00.006-0.01527.3640.0000.0000.0000.0000.0000.000
182H176ALA00.0080.02928.0990.0100.0100.0000.0000.0000.000
183H177VAL0-0.017-0.01230.060-0.005-0.0050.0000.0000.0000.000
184H178LEU0-0.048-0.01732.6820.0040.0040.0000.0000.0000.000
185H179GLN0-0.031-0.03034.0940.0030.0030.0000.0000.0000.000
186H180SER00.009-0.00937.7140.0000.0000.0000.0000.0000.000
187H182SER0-0.022-0.00939.0850.0000.0000.0000.0000.0000.000
188H183GLY00.0270.02536.8650.0020.0020.0000.0000.0000.000
189H184LEU0-0.043-0.01434.509-0.002-0.0020.0000.0000.0000.000
190H185TYR0-0.010-0.00229.817-0.001-0.0010.0000.0000.0000.000
191H186SER00.005-0.00632.9550.0080.0080.0000.0000.0000.000
192H187LEU0-0.0030.01427.789-0.005-0.0050.0000.0000.0000.000
193H188SER00.0240.00832.2120.0100.0100.0000.0000.0000.000
194H189SER0-0.016-0.00528.207-0.007-0.0070.0000.0000.0000.000
195H190VAL00.001-0.01030.9460.0090.0090.0000.0000.0000.000
196H191VAL00.0240.02029.808-0.008-0.0080.0000.0000.0000.000
197H192THR0-0.004-0.01031.7800.0050.0050.0000.0000.0000.000
198H193VAL00.0090.00932.268-0.002-0.0020.0000.0000.0000.000
199H194PRO00.0530.02433.8930.0010.0010.0000.0000.0000.000
200H195SER00.009-0.00437.1760.0030.0030.0000.0000.0000.000
201H196SER0-0.015-0.01939.9210.0020.0020.0000.0000.0000.000
202H197SER00.0060.01436.5010.0030.0030.0000.0000.0000.000
203H198LEU00.0190.00138.3110.0020.0020.0000.0000.0000.000
204H199GLY0-0.0170.00540.1310.0010.0010.0000.0000.0000.000
205H200THR0-0.045-0.03039.5780.0020.0020.0000.0000.0000.000
206H203GLN0-0.043-0.00532.2620.0050.0050.0000.0000.0000.000
207H205THR0-0.023-0.00834.107-0.002-0.0020.0000.0000.0000.000
208H206TYR00.014-0.01731.933-0.001-0.0010.0000.0000.0000.000
209H207ILE0-0.042-0.03030.9320.0020.0020.0000.0000.0000.000
210H208CYS-1-0.775-0.84729.891-0.052-0.0520.0000.0000.0000.000
211H209ASN00.0370.01026.0790.0020.0020.0000.0000.0000.000
212H210VAL00.0520.02026.752-0.012-0.0120.0000.0000.0000.000
213H211ASN0-0.042-0.02921.6700.0230.0230.0000.0000.0000.000
214H212HIS10.8590.91024.7760.0430.0430.0000.0000.0000.000
215H213LYS10.9560.97320.9750.0190.0190.0000.0000.0000.000
216H214PRO00.0190.00823.7020.0110.0110.0000.0000.0000.000
217H215SER00.0060.00626.0080.0020.0020.0000.0000.0000.000
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220H218LYS10.9210.96023.375-0.014-0.0140.0000.0000.0000.000
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223H221LYS10.8960.95531.8590.0220.0220.0000.0000.0000.000
224H222LYS10.9010.95834.0760.0010.0010.0000.0000.0000.000
225H225VAL0-0.012-0.00735.087-0.001-0.0010.0000.0000.0000.000
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228H228LYS10.9340.97642.7200.0250.0250.0000.0000.0000.000
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