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: YVQL2

Calculation Name: 4NN1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NN1

Chain ID: A

ChEMBL ID:

UniProt ID: O86312

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2086533.617907
FMO2-HF: Nuclear repulsion 2006951.2419
FMO2-HF: Total energy -79582.376007
FMO2-MP2: Total energy -79812.013916


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(A:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-14.374-8.7491.611-2.774-4.4630.024
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.016
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].
3A8ALA00.0220.0022.522-3.926-0.8051.312-1.784-2.6490.012
4A9HIS00.0820.0402.966-5.664-3.9450.253-0.673-1.2990.009
5A10ALA0-0.012-0.0094.761-1.581-1.423-0.001-0.029-0.1280.000
6A11ARG11.0151.0146.758-1.218-1.2180.0000.0000.0000.000
7A12ILE0-0.0140.0057.199-0.413-0.4130.0000.0000.0000.000
8A13ARG10.8450.9336.965-0.892-0.8920.0000.0000.0000.000
9A14GLU-1-0.982-0.98610.5790.3330.3330.0000.0000.0000.000
10A15ALA00.0570.02312.453-0.118-0.1180.0000.0000.0000.000
11A16ALA0-0.018-0.01913.747-0.102-0.1020.0000.0000.0000.000
12A17ILE00.0130.01213.954-0.084-0.0840.0000.0000.0000.000
13A18GLU-1-0.770-0.84816.9150.2840.2840.0000.0000.0000.000
14A19GLN0-0.017-0.02318.346-0.070-0.0700.0000.0000.0000.000
15A20PHE0-0.043-0.04016.952-0.031-0.0310.0000.0000.0000.000
16A21GLY00.0320.02820.723-0.033-0.0330.0000.0000.0000.000
17A22ARG10.8210.89021.271-0.297-0.2970.0000.0000.0000.000
18A23HIS0-0.041-0.01823.092-0.037-0.0370.0000.0000.0000.000
19A24GLY00.0340.04124.532-0.013-0.0130.0000.0000.0000.000
20A25PHE00.0680.01320.6420.0250.0250.0000.0000.0000.000
21A26GLY0-0.051-0.01023.3710.0200.0200.0000.0000.0000.000
22A27VAL00.0370.03420.750-0.003-0.0030.0000.0000.0000.000
23A28GLY00.0390.01322.1610.0120.0120.0000.0000.0000.000
24A29LEU00.0780.02416.9820.0200.0200.0000.0000.0000.000
25A30ARG10.9190.95617.463-0.277-0.2770.0000.0000.0000.000
26A31ALA00.0880.05018.9340.0180.0180.0000.0000.0000.000
27A32ILE0-0.0170.00414.2690.0190.0190.0000.0000.0000.000
28A33ALA0-0.045-0.02813.8950.0680.0680.0000.0000.0000.000
29A34GLU-1-0.947-0.96914.6260.3980.3980.0000.0000.0000.000
30A35ALA0-0.013-0.00616.6660.0040.0040.0000.0000.0000.000
31A36ALA0-0.011-0.01411.3130.0100.0100.0000.0000.0000.000
32A37GLY0-0.0170.02012.2200.0690.0690.0000.0000.0000.000
33A38VAL0-0.071-0.0459.1100.0940.0940.0000.0000.0000.000
34A39SER00.0280.01212.606-0.061-0.0610.0000.0000.0000.000
35A40ALA00.0640.00113.3760.0950.0950.0000.0000.0000.000
36A41ALA0-0.017-0.00514.6770.0220.0220.0000.0000.0000.000
37A42LEU00.0240.0117.150-0.047-0.0470.0000.0000.0000.000
38A43VAL00.0450.0219.6650.2510.2510.0000.0000.0000.000
39A44ILE0-0.026-0.01711.5140.0160.0160.0000.0000.0000.000
40A45HIS0-0.031-0.0089.748-0.071-0.0710.0000.0000.0000.000
41A46HIS0-0.063-0.0243.242-0.6040.0230.047-0.288-0.3870.003
42A47PHE0-0.007-0.0188.465-0.146-0.1460.0000.0000.0000.000
43A48GLY00.0190.03511.787-0.139-0.1390.0000.0000.0000.000
44A49SER0-0.025-0.02714.589-0.041-0.0410.0000.0000.0000.000
45A50LYS10.8750.91516.340-0.274-0.2740.0000.0000.0000.000
46A51GLU-1-0.924-0.95718.3480.2390.2390.0000.0000.0000.000
47A52GLY00.0030.00115.794-0.009-0.0090.0000.0000.0000.000
48A53LEU00.0000.00212.5170.0310.0310.0000.0000.0000.000
49A54ARG10.9050.96714.766-0.219-0.2190.0000.0000.0000.000
50A55LYS10.9350.95216.185-0.205-0.2050.0000.0000.0000.000
51A56ALA0-0.0080.00311.269-0.028-0.0280.0000.0000.0000.000
52A57CYS0-0.065-0.03112.7050.0370.0370.0000.0000.0000.000
53A58ASP-1-0.769-0.87914.8730.2000.2000.0000.0000.0000.000
54A59ASP-1-0.845-0.90814.3160.1490.1490.0000.0000.0000.000
55A60PHE00.0570.01911.3750.0030.0030.0000.0000.0000.000
56A61VAL00.0550.02713.995-0.040-0.0400.0000.0000.0000.000
57A62ALA0-0.006-0.00917.330-0.028-0.0280.0000.0000.0000.000
58A63GLU-1-0.813-0.87514.244-0.048-0.0480.0000.0000.0000.000
59A64GLU-1-0.916-0.95013.7320.0240.0240.0000.0000.0000.000
60A65ILE0-0.011-0.01116.995-0.018-0.0180.0000.0000.0000.000
61A66ARG10.7100.82317.8250.0260.0260.0000.0000.0000.000
62A67SER0-0.027-0.02217.080-0.014-0.0140.0000.0000.0000.000
63A68SER0-0.0050.01719.425-0.007-0.0070.0000.0000.0000.000
64A69LYS10.9720.96521.614-0.035-0.0350.0000.0000.0000.000
65A70ALA00.0310.00622.559-0.005-0.0050.0000.0000.0000.000
66A71ALA0-0.0100.00521.786-0.008-0.0080.0000.0000.0000.000
67A72ALA0-0.010-0.00123.877-0.004-0.0040.0000.0000.0000.000
68A73LEU0-0.010-0.00227.1080.0010.0010.0000.0000.0000.000
69A74LYS10.8510.91724.1920.0720.0720.0000.0000.0000.000
70A75SER0-0.037-0.00127.384-0.004-0.0040.0000.0000.0000.000
71A76ASN00.006-0.00129.4130.0080.0080.0000.0000.0000.000
72A77ASP-1-0.829-0.90430.071-0.041-0.0410.0000.0000.0000.000
73A78PRO00.0350.00430.7620.0000.0000.0000.0000.0000.000
74A79THR0-0.013-0.02930.3820.0060.0060.0000.0000.0000.000
75A80THR0-0.012-0.00626.1830.0050.0050.0000.0000.0000.000
76A81TRP00.0020.01026.9150.0080.0080.0000.0000.0000.000
77A82LEU0-0.023-0.00829.3300.0070.0070.0000.0000.0000.000
78A83ALA00.004-0.00126.1000.0050.0050.0000.0000.0000.000
79A84GLN0-0.006-0.01423.7660.0100.0100.0000.0000.0000.000
80A85MET0-0.030-0.01026.0080.0120.0120.0000.0000.0000.000
81A86ALA0-0.0180.00427.1270.0070.0070.0000.0000.0000.000
82A87GLU-1-0.877-0.93722.4100.0310.0310.0000.0000.0000.000
83A88ILE00.0180.02124.1090.0130.0130.0000.0000.0000.000
84A89GLU-1-0.797-0.88425.7390.0750.0750.0000.0000.0000.000
85A90SER0-0.095-0.06420.8170.0180.0180.0000.0000.0000.000
86A91TYR00.008-0.00120.5350.0200.0200.0000.0000.0000.000
87A92ALA00.003-0.00322.0260.0120.0120.0000.0000.0000.000
88A93PRO0-0.017-0.01018.4870.0100.0100.0000.0000.0000.000
89A94LEU00.0280.01016.9590.0200.0200.0000.0000.0000.000
90A95MET00.0170.01320.0510.0050.0050.0000.0000.0000.000
91A96ALA00.0360.03022.773-0.002-0.0020.0000.0000.0000.000
92A97TYR0-0.054-0.06318.7830.0170.0170.0000.0000.0000.000
93A98LEU0-0.025-0.02621.834-0.004-0.0040.0000.0000.0000.000
94A99VAL00.018-0.00123.522-0.009-0.0090.0000.0000.0000.000
95A100ARG10.8260.91924.174-0.188-0.1880.0000.0000.0000.000
96A101SER00.0120.00322.5340.0000.0000.0000.0000.0000.000
97A102MET0-0.0250.00125.363-0.006-0.0060.0000.0000.0000.000
98A103GLN00.0580.02728.8950.0030.0030.0000.0000.0000.000
99A104SER0-0.045-0.01026.766-0.001-0.0010.0000.0000.0000.000
100A105GLY00.0340.03327.6970.0090.0090.0000.0000.0000.000
101A106GLY0-0.059-0.04928.143-0.008-0.0080.0000.0000.0000.000
102A107GLU-1-0.802-0.89927.4040.1030.1030.0000.0000.0000.000
103A108LEU00.012-0.00220.783-0.005-0.0050.0000.0000.0000.000
104A109ALA0-0.0040.00823.5990.0030.0030.0000.0000.0000.000
105A110LYS10.8430.90225.586-0.099-0.0990.0000.0000.0000.000
106A111MET0-0.027-0.01623.065-0.008-0.0080.0000.0000.0000.000
107A112LEU0-0.0200.01020.484-0.004-0.0040.0000.0000.0000.000
108A113TRP00.0420.00723.675-0.013-0.0130.0000.0000.0000.000
109A114GLN00.0120.00926.649-0.012-0.0120.0000.0000.0000.000
110A115LYS10.9140.97017.012-0.114-0.1140.0000.0000.0000.000
111A116MET0-0.039-0.02722.491-0.007-0.0070.0000.0000.0000.000
112A117ILE0-0.029-0.01124.473-0.010-0.0100.0000.0000.0000.000
113A118ASP-1-0.806-0.89025.3420.0280.0280.0000.0000.0000.000
114A119ASN0-0.013-0.01520.137-0.013-0.0130.0000.0000.0000.000
115A120ALA0-0.0020.00624.528-0.008-0.0080.0000.0000.0000.000
116A121GLU-1-0.849-0.93427.6140.0010.0010.0000.0000.0000.000
117A122GLU-1-0.882-0.91622.777-0.035-0.0350.0000.0000.0000.000
118A123TYR00.0540.00524.080-0.007-0.0070.0000.0000.0000.000
119A124LEU0-0.017-0.00826.963-0.003-0.0030.0000.0000.0000.000
120A125ASP-1-0.829-0.89030.132-0.030-0.0300.0000.0000.0000.000
121A126GLU-1-0.811-0.88424.824-0.067-0.0670.0000.0000.0000.000
122A127GLY00.0190.01929.182-0.005-0.0050.0000.0000.0000.000
123A128VAL0-0.064-0.03431.2930.0000.0000.0000.0000.0000.000
124A129ARG10.7200.83528.0920.0410.0410.0000.0000.0000.000
125A130ALA0-0.051-0.01630.658-0.002-0.0020.0000.0000.0000.000
126A131GLY0-0.0140.00332.804-0.001-0.0010.0000.0000.0000.000
127A132THR0-0.058-0.03431.9310.0040.0040.0000.0000.0000.000
128A133VAL0-0.024-0.00933.1000.0050.0050.0000.0000.0000.000
129A134LYS11.0091.00636.1170.0010.0010.0000.0000.0000.000
130A135PRO00.0870.05238.0320.0020.0020.0000.0000.0000.000
131A136SER0-0.015-0.02138.4200.0030.0030.0000.0000.0000.000
132A137ARG10.9040.95340.171-0.008-0.0080.0000.0000.0000.000
133A138ASP-1-0.824-0.92439.6250.0090.0090.0000.0000.0000.000
134A139PRO00.0060.00535.2110.0030.0030.0000.0000.0000.000
135A140ARG10.8370.91229.684-0.018-0.0180.0000.0000.0000.000
136A141ALA00.0180.01234.8660.0050.0050.0000.0000.0000.000
137A142ARG10.8250.90335.2670.0030.0030.0000.0000.0000.000
138A143ALA00.0410.01031.2660.0020.0020.0000.0000.0000.000
139A144ARG10.9270.96932.653-0.038-0.0380.0000.0000.0000.000
140A145PHE00.0180.00433.9440.0050.0050.0000.0000.0000.000
141A146LEU00.0300.02033.5790.0030.0030.0000.0000.0000.000
142A147ALA0-0.0110.01129.8900.0030.0030.0000.0000.0000.000
143A148ILE0-0.051-0.03331.5960.0060.0060.0000.0000.0000.000
144A149THR0-0.009-0.01733.8760.0040.0040.0000.0000.0000.000
145A150GLY00.0390.03632.6520.0020.0020.0000.0000.0000.000
146A151GLY0-0.032-0.02230.3540.0030.0030.0000.0000.0000.000
147A152GLY0-0.011-0.01730.9860.0060.0060.0000.0000.0000.000
148A153GLY00.0220.01633.7720.0010.0010.0000.0000.0000.000
149A154PHE00.0100.00127.8860.0030.0030.0000.0000.0000.000
150A155LEU0-0.058-0.03328.8620.0050.0050.0000.0000.0000.000
151A156LEU00.000-0.00332.4970.0020.0020.0000.0000.0000.000
152A157TYR0-0.083-0.06034.0670.0020.0020.0000.0000.0000.000
153A158LEU00.013-0.00729.7000.0010.0010.0000.0000.0000.000
154A159GLN0-0.072-0.02634.2710.0010.0010.0000.0000.0000.000
155A160MET0-0.049-0.03136.3580.0000.0000.0000.0000.0000.000
156A161HIS0-0.030-0.01535.1970.0010.0010.0000.0000.0000.000
157A162GLU-1-0.900-0.94237.7460.0590.0590.0000.0000.0000.000
158A163ASN0-0.004-0.00533.8400.0070.0070.0000.0000.0000.000
159A164PRO00.0250.01233.7370.0060.0060.0000.0000.0000.000
160A165THR0-0.124-0.06730.2350.0100.0100.0000.0000.0000.000
161A166ASP-1-0.868-0.92629.1120.1140.1140.0000.0000.0000.000
162A167LEU0-0.024-0.03126.224-0.007-0.0070.0000.0000.0000.000
163A168ARG10.8680.92524.740-0.103-0.1030.0000.0000.0000.000
164A169ALA00.0130.02628.269-0.009-0.0090.0000.0000.0000.000
165A170ALA00.0460.02530.793-0.006-0.0060.0000.0000.0000.000
166A171LEU0-0.050-0.02825.872-0.005-0.0050.0000.0000.0000.000
167A172ARG10.8160.90429.689-0.051-0.0510.0000.0000.0000.000
168A173ASP-1-0.798-0.89532.3390.0530.0530.0000.0000.0000.000
169A174TYR00.0000.01231.595-0.004-0.0040.0000.0000.0000.000
170A175ALA0-0.042-0.03031.790-0.005-0.0050.0000.0000.0000.000
171A176HIS0-0.066-0.01833.797-0.005-0.0050.0000.0000.0000.000
172A177ASP-1-0.838-0.90837.2290.0400.0400.0000.0000.0000.000
173A178MET0-0.058-0.04235.596-0.003-0.0030.0000.0000.0000.000
174A179VAL0-0.0050.00833.428-0.003-0.0030.0000.0000.0000.000
175A180LEU00.0190.01836.207-0.003-0.0030.0000.0000.0000.000
176A181PRO00.0880.03939.670-0.002-0.0020.0000.0000.0000.000
177A182SER0-0.069-0.03336.461-0.001-0.0010.0000.0000.0000.000
178A183LEU0-0.004-0.01035.262-0.002-0.0020.0000.0000.0000.000
179A184GLU-1-0.905-0.92838.8460.0100.0100.0000.0000.0000.000
180A185VAL00.0280.02441.339-0.002-0.0020.0000.0000.0000.000
181A186TYR0-0.114-0.07635.7130.0000.0000.0000.0000.0000.000
182A187THR0-0.092-0.04339.977-0.004-0.0040.0000.0000.0000.000
183A188GLU-1-0.956-0.98541.917-0.001-0.0010.0000.0000.0000.000
184A189GLY0-0.096-0.02644.092-0.001-0.0010.0000.0000.0000.000
185A190LEU0-0.024-0.02945.3490.0010.0010.0000.0000.0000.000
186A191LEU0-0.033-0.02347.6050.0000.0000.0000.0000.0000.000
187A192ALA00.0360.02450.457-0.001-0.0010.0000.0000.0000.000
188A193ASP-1-0.858-0.94353.3830.0050.0050.0000.0000.0000.000
189A194ARG10.8110.88949.6130.0000.0000.0000.0000.0000.000
190A195ALA00.0530.05252.7720.0000.0000.0000.0000.0000.000
191A196MET00.0290.00352.0100.0000.0000.0000.0000.0000.000
192A197TYR0-0.013-0.01445.4880.0000.0000.0000.0000.0000.000
193A198GLU-1-0.852-0.92850.6970.0020.0020.0000.0000.0000.000
194A199ALA00.0030.01053.4910.0000.0000.0000.0000.0000.000
195A200PHE00.019-0.00350.2010.0000.0000.0000.0000.0000.000
196A201LEU0-0.039-0.01347.4770.0000.0000.0000.0000.0000.000
197A202ALA0-0.009-0.00251.0390.0000.0000.0000.0000.0000.000
198A203GLU-1-0.882-0.93953.3990.0110.0110.0000.0000.0000.000
199A204ALA0-0.033-0.02149.2820.0010.0010.0000.0000.0000.000
200A205GLN0-0.067-0.02849.742-0.001-0.0010.0000.0000.0000.000
201A206GLN0-0.084-0.03752.339-0.001-0.0010.0000.0000.0000.000
202A207GLY00.008-0.00252.9470.0000.0000.0000.0000.0000.000
203A208GLU-1-0.965-0.98847.2980.0060.0060.0000.0000.0000.000
204A209ALA0-0.071-0.01951.599-0.001-0.0010.0000.0000.0000.000
205A210HIS0-0.049-0.01154.7020.0000.0000.0000.0000.0000.000