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: Z633N

Calculation Name: 2NM0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NM0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9S274

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 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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2506505.438927
FMO2-HF: Nuclear repulsion 2423547.753469
FMO2-HF: Total energy -82957.685458
FMO2-MP2: Total energy -83200.197734


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-0.4360.926-0.009-0.579-0.7730.001
Interaction energy analysis for fragmet #1(A:1:MET)
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 : -0.014
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].
3A3ARG10.8360.8953.8601.3352.697-0.009-0.579-0.7730.001
4A4SER0-0.058-0.0306.0140.1970.1970.0000.0000.0000.000
5A5VAL0-0.006-0.0129.411-0.028-0.0280.0000.0000.0000.000
6A6LEU00.0130.01712.0180.0400.0400.0000.0000.0000.000
7A7VAL00.002-0.00115.5880.0000.0000.0000.0000.0000.000
8A8THR00.0120.00018.1010.0100.0100.0000.0000.0000.000
9A9GLY00.0440.02321.7180.0000.0000.0000.0000.0000.000
10A10GLY0-0.011-0.01319.912-0.001-0.0010.0000.0000.0000.000
11A11ASN00.0300.00720.598-0.005-0.0050.0000.0000.0000.000
12A12ARG10.9520.97423.2740.0240.0240.0000.0000.0000.000
13A13GLY00.0100.00523.941-0.002-0.0020.0000.0000.0000.000
14A14ILE00.0610.02721.714-0.005-0.0050.0000.0000.0000.000
15A15GLY00.0420.02920.403-0.007-0.0070.0000.0000.0000.000
16A16LEU0-0.0120.00819.059-0.010-0.0100.0000.0000.0000.000
17A17ALA00.0290.00318.364-0.011-0.0110.0000.0000.0000.000
18A18ILE0-0.022-0.01315.360-0.010-0.0100.0000.0000.0000.000
19A19ALA00.0170.00914.463-0.027-0.0270.0000.0000.0000.000
20A20ARG10.8530.91813.8220.0530.0530.0000.0000.0000.000
21A21ALA00.0500.02913.020-0.031-0.0310.0000.0000.0000.000
22A22PHE0-0.063-0.0439.2320.0080.0080.0000.0000.0000.000
23A23ALA00.0260.0208.822-0.129-0.1290.0000.0000.0000.000
24A24ASP-1-0.909-0.9619.784-0.204-0.2040.0000.0000.0000.000
25A25ALA0-0.093-0.0397.4450.0140.0140.0000.0000.0000.000
26A26GLY00.0250.0225.514-0.267-0.2670.0000.0000.0000.000
27A27ASP-1-0.796-0.8535.715-1.604-1.6040.0000.0000.0000.000
28A28LYS10.8460.9165.566-0.083-0.0830.0000.0000.0000.000
29A29VAL0-0.0200.0029.8230.0140.0140.0000.0000.0000.000
30A30ALA00.0250.03312.6830.0480.0480.0000.0000.0000.000
31A31ILE0-0.039-0.02016.179-0.019-0.0190.0000.0000.0000.000
32A32THR00.0110.02019.3340.0090.0090.0000.0000.0000.000
33A33TYR0-0.044-0.03222.956-0.006-0.0060.0000.0000.0000.000
34A34ARG10.9000.94526.1010.0060.0060.0000.0000.0000.000
35A35SER0-0.031-0.04029.7960.0020.0020.0000.0000.0000.000
36A36GLY0-0.011-0.00929.825-0.002-0.0020.0000.0000.0000.000
37A37GLU-1-0.904-0.94727.408-0.004-0.0040.0000.0000.0000.000
38A38PRO0-0.028-0.00823.004-0.003-0.0030.0000.0000.0000.000
39A39PRO0-0.029-0.01621.2830.0010.0010.0000.0000.0000.000
40A40GLU-1-0.811-0.91920.773-0.017-0.0170.0000.0000.0000.000
41A41GLY00.0030.01617.062-0.015-0.0150.0000.0000.0000.000
42A42PHE0-0.036-0.02814.800-0.016-0.0160.0000.0000.0000.000
43A43LEU00.0360.03215.9990.0110.0110.0000.0000.0000.000
44A44ALA0-0.017-0.01418.030-0.010-0.0100.0000.0000.0000.000
45A45VAL00.0640.03920.2110.0050.0050.0000.0000.0000.000
46A46LYS10.8820.94222.997-0.006-0.0060.0000.0000.0000.000
47A47CYS0-0.036-0.01924.8920.0020.0020.0000.0000.0000.000
48A48ASP-1-0.815-0.88227.761-0.007-0.0070.0000.0000.0000.000
49A49ILE00.0320.00824.8560.0020.0020.0000.0000.0000.000
50A50THR0-0.002-0.02227.6940.0010.0010.0000.0000.0000.000
51A51ASP-1-0.838-0.87830.3340.0090.0090.0000.0000.0000.000
52A52THR0-0.007-0.02728.903-0.001-0.0010.0000.0000.0000.000
53A53GLU-1-0.846-0.92227.9180.0160.0160.0000.0000.0000.000
54A54GLN0-0.038-0.03727.8210.0020.0020.0000.0000.0000.000
55A55VAL0-0.0150.00523.5900.0000.0000.0000.0000.0000.000
56A56GLU-1-0.773-0.84023.4300.0260.0260.0000.0000.0000.000
57A57GLN00.020-0.00323.4550.0060.0060.0000.0000.0000.000
58A58ALA00.0340.01722.3430.0050.0050.0000.0000.0000.000
59A59TYR0-0.043-0.06517.452-0.004-0.0040.0000.0000.0000.000
60A60LYS10.8540.94318.480-0.032-0.0320.0000.0000.0000.000
61A61GLU-1-0.830-0.91519.1520.0450.0450.0000.0000.0000.000
62A62ILE0-0.009-0.00214.5600.0120.0120.0000.0000.0000.000
63A63GLU-1-0.867-0.91214.7660.0580.0580.0000.0000.0000.000
64A64GLU-1-0.963-0.98014.9190.1150.1150.0000.0000.0000.000
65A65THR0-0.079-0.03015.2880.0280.0280.0000.0000.0000.000
66A66HIS0-0.034-0.04211.2220.0910.0910.0000.0000.0000.000
67A67GLY00.0250.0309.9800.0690.0690.0000.0000.0000.000
68A68PRO0-0.022-0.02411.513-0.054-0.0540.0000.0000.0000.000
69A69VAL0-0.011-0.00711.131-0.024-0.0240.0000.0000.0000.000
70A70GLU-1-0.819-0.8976.067-0.576-0.5760.0000.0000.0000.000
71A71VAL0-0.058-0.0339.9470.0190.0190.0000.0000.0000.000
72A72LEU0-0.0080.00612.5690.0030.0030.0000.0000.0000.000
73A73ILE0-0.024-0.01514.6140.0100.0100.0000.0000.0000.000
74A74ALA00.0370.01518.0850.0040.0040.0000.0000.0000.000
75A75ASN0-0.051-0.04121.7780.0060.0060.0000.0000.0000.000
76A76ALA00.0150.02023.2740.0020.0020.0000.0000.0000.000
77A77GLY00.0200.02826.3650.0030.0030.0000.0000.0000.000
78A78VAL0-0.026-0.01328.2940.0000.0000.0000.0000.0000.000
79A79THR0-0.037-0.03628.000-0.001-0.0010.0000.0000.0000.000
80A80LYS10.8250.87230.2020.0130.0130.0000.0000.0000.000
81A81ASP-1-0.759-0.85132.334-0.009-0.0090.0000.0000.0000.000
82A82GLN00.0680.03932.020-0.001-0.0010.0000.0000.0000.000
83A83LEU00.0400.03034.4480.0010.0010.0000.0000.0000.000
84A84LEU0-0.016-0.00835.7190.0000.0000.0000.0000.0000.000
85A85MET0-0.016-0.00638.2900.0000.0000.0000.0000.0000.000
86A86ARG10.8130.89539.8850.0080.0080.0000.0000.0000.000
87A87MET00.0160.02540.0140.0000.0000.0000.0000.0000.000
88A88SER00.004-0.00843.9060.0000.0000.0000.0000.0000.000
89A89GLU-1-0.771-0.89942.425-0.006-0.0060.0000.0000.0000.000
90A90GLU-1-0.887-0.96042.807-0.004-0.0040.0000.0000.0000.000
91A91ASP-1-0.817-0.87744.339-0.003-0.0030.0000.0000.0000.000
92A92PHE0-0.057-0.02335.2530.0000.0000.0000.0000.0000.000
93A93THR00.001-0.00139.0140.0000.0000.0000.0000.0000.000
94A94SER0-0.032-0.02939.0780.0000.0000.0000.0000.0000.000
95A95VAL00.0030.00334.6530.0000.0000.0000.0000.0000.000
96A96VAL0-0.025-0.00434.482-0.001-0.0010.0000.0000.0000.000
97A97GLU-1-0.838-0.89934.164-0.003-0.0030.0000.0000.0000.000
98A98THR0-0.013-0.00133.881-0.001-0.0010.0000.0000.0000.000
99A99ASN0-0.024-0.01730.0250.0010.0010.0000.0000.0000.000
100A100LEU0-0.054-0.00329.379-0.002-0.0020.0000.0000.0000.000
101A101THR0-0.004-0.03329.788-0.001-0.0010.0000.0000.0000.000
102A102GLY00.011-0.00329.0040.0010.0010.0000.0000.0000.000
103A103THR0-0.044-0.04524.749-0.002-0.0020.0000.0000.0000.000
104A104PHE0-0.033-0.02925.205-0.001-0.0010.0000.0000.0000.000
105A105ARG10.8640.94226.209-0.001-0.0010.0000.0000.0000.000
106A106VAL00.0300.01721.7610.0010.0010.0000.0000.0000.000
107A107VAL00.0190.02721.088-0.003-0.0030.0000.0000.0000.000
108A108LYS10.8260.90021.2690.0000.0000.0000.0000.0000.000
109A109ARG10.6850.79819.092-0.019-0.0190.0000.0000.0000.000
110A110ALA00.0470.03017.1190.0040.0040.0000.0000.0000.000
111A111ASN00.0410.01017.607-0.004-0.0040.0000.0000.0000.000
112A112ARG10.8620.92319.305-0.020-0.0200.0000.0000.0000.000
113A113ALA0-0.023-0.00215.1240.0100.0100.0000.0000.0000.000
114A114MET00.0200.01813.7800.0070.0070.0000.0000.0000.000
115A115LEU00.003-0.00215.4540.0020.0020.0000.0000.0000.000
116A116ARG10.8460.91616.755-0.033-0.0330.0000.0000.0000.000
117A117ALA00.0100.00911.6580.0080.0080.0000.0000.0000.000
118A118LYS10.8830.95513.169-0.020-0.0200.0000.0000.0000.000
119A119LYS10.8960.9278.091-0.017-0.0170.0000.0000.0000.000
120A120GLY00.0310.01412.543-0.012-0.0120.0000.0000.0000.000
121A121ARG10.7750.88611.928-0.003-0.0030.0000.0000.0000.000
122A122VAL00.0450.02714.780-0.015-0.0150.0000.0000.0000.000
123A123VAL0-0.018-0.00616.6310.0120.0120.0000.0000.0000.000
124A124LEU00.0030.00519.298-0.005-0.0050.0000.0000.0000.000
125A125ILE0-0.005-0.00419.8760.0020.0020.0000.0000.0000.000
126A126SER00.0160.00524.0150.0020.0020.0000.0000.0000.000
127A127SER0-0.006-0.01627.289-0.002-0.0020.0000.0000.0000.000
128A128VAL0-0.0090.00427.8190.0000.0000.0000.0000.0000.000
129A129VAL0-0.0160.00330.1190.0010.0010.0000.0000.0000.000
130A130GLY00.018-0.00433.425-0.001-0.0010.0000.0000.0000.000
131A131LEU0-0.047-0.02436.3200.0010.0010.0000.0000.0000.000
132A132LEU0-0.0220.00136.9870.0000.0000.0000.0000.0000.000
133A133GLY00.0530.03241.4020.0000.0000.0000.0000.0000.000
134A134SER00.013-0.00943.0840.0000.0000.0000.0000.0000.000
135A135ALA00.0620.04443.6460.0000.0000.0000.0000.0000.000
136A136GLY00.0090.00640.3100.0000.0000.0000.0000.0000.000
137A137GLN0-0.070-0.05438.8130.0000.0000.0000.0000.0000.000
138A138ALA00.0190.01238.8490.0000.0000.0000.0000.0000.000
139A139ASN00.0280.01237.8430.0000.0000.0000.0000.0000.000
140A140TYR0-0.0100.00431.3700.0000.0000.0000.0000.0000.000
141A141ALA0-0.007-0.01034.2410.0000.0000.0000.0000.0000.000
142A142ALA00.0240.01335.3300.0000.0000.0000.0000.0000.000
143A143SER00.0050.00831.6540.0000.0000.0000.0000.0000.000
144A144LYS10.9170.95130.1000.0070.0070.0000.0000.0000.000
145A145ALA00.001-0.00630.8260.0000.0000.0000.0000.0000.000
146A146GLY00.0340.02532.4380.0010.0010.0000.0000.0000.000
147A147LEU00.0010.00126.6540.0000.0000.0000.0000.0000.000
148A148VAL0-0.010-0.00827.6750.0000.0000.0000.0000.0000.000
149A149GLY00.0020.00028.8740.0010.0010.0000.0000.0000.000
150A150PHE00.0000.00125.2660.0010.0010.0000.0000.0000.000
151A151ALA00.0260.01024.3300.0000.0000.0000.0000.0000.000
152A152ARG10.8900.92725.4330.0000.0000.0000.0000.0000.000
153A153SER0-0.017-0.00727.7970.0020.0020.0000.0000.0000.000
154A154LEU0-0.0240.00323.4960.0010.0010.0000.0000.0000.000
155A155ALA0-0.0050.00123.6750.0010.0010.0000.0000.0000.000
156A156ARG10.8970.94724.7060.0000.0000.0000.0000.0000.000
157A157GLU-1-0.838-0.89626.2540.0010.0010.0000.0000.0000.000
158A158LEU0-0.019-0.02021.2440.0010.0010.0000.0000.0000.000
159A159GLY00.0550.04323.3470.0010.0010.0000.0000.0000.000
160A160SER0-0.013-0.00122.342-0.001-0.0010.0000.0000.0000.000
161A161ARG10.8440.90219.556-0.005-0.0050.0000.0000.0000.000
162A162ASN0-0.029-0.02315.4440.0000.0000.0000.0000.0000.000
163A163ILE0-0.0080.01615.375-0.007-0.0070.0000.0000.0000.000
164A164THR0-0.043-0.01216.7230.0010.0010.0000.0000.0000.000
165A165PHE00.0390.00818.215-0.010-0.0100.0000.0000.0000.000
166A166ASN0-0.027-0.02518.7120.0090.0090.0000.0000.0000.000
167A167VAL0-0.0030.00021.891-0.005-0.0050.0000.0000.0000.000
168A168VAL00.0190.01720.1300.0040.0040.0000.0000.0000.000
169A169ALA0-0.002-0.01723.426-0.002-0.0020.0000.0000.0000.000
170A170PRO0-0.0020.00224.8960.0020.0020.0000.0000.0000.000
171A171GLY00.0660.03327.2810.0020.0020.0000.0000.0000.000
172A172PHE00.0020.00930.400-0.001-0.0010.0000.0000.0000.000
173A173VAL0-0.023-0.01825.6090.0000.0000.0000.0000.0000.000
174A174ASP-1-0.804-0.86628.620-0.019-0.0190.0000.0000.0000.000
175A175THR0-0.062-0.01927.280-0.002-0.0020.0000.0000.0000.000
176A185GLN00.0770.02641.5170.0000.0000.0000.0000.0000.000
177A186ARG10.8390.87232.9520.0170.0170.0000.0000.0000.000
178A187ALA00.0430.01838.6860.0000.0000.0000.0000.0000.000
179A188ASN0-0.004-0.00240.8150.0010.0010.0000.0000.0000.000
180A189ILE0-0.0250.00536.5360.0000.0000.0000.0000.0000.000
181A190VAL0-0.010-0.00435.1000.0000.0000.0000.0000.0000.000
182A191SER0-0.069-0.03337.5350.0000.0000.0000.0000.0000.000
183A192GLN00.0300.01638.2350.0000.0000.0000.0000.0000.000
184A193VAL0-0.047-0.01533.0360.0000.0000.0000.0000.0000.000
185A194PRO00.0110.01235.0860.0000.0000.0000.0000.0000.000
186A195LEU0-0.037-0.01429.7150.0000.0000.0000.0000.0000.000
187A196GLY00.0050.01033.928-0.001-0.0010.0000.0000.0000.000
188A197ARG10.7360.82426.3100.0140.0140.0000.0000.0000.000
189A198TYR00.0420.01530.5430.0010.0010.0000.0000.0000.000
190A199ALA00.0300.02825.9560.0000.0000.0000.0000.0000.000
191A200ARG10.8520.89522.4140.0260.0260.0000.0000.0000.000
192A201PRO00.0230.00522.3140.0000.0000.0000.0000.0000.000
193A202GLU-1-0.756-0.88818.638-0.040-0.0400.0000.0000.0000.000
194A203GLU-1-0.769-0.82518.683-0.016-0.0160.0000.0000.0000.000
195A204ILE00.0050.00420.4100.0050.0050.0000.0000.0000.000
196A205ALA00.0250.01316.1930.0010.0010.0000.0000.0000.000
197A206ALA00.0030.00615.245-0.006-0.0060.0000.0000.0000.000
198A207THR0-0.008-0.00715.7110.0160.0160.0000.0000.0000.000
199A208VAL0-0.006-0.01115.3180.0080.0080.0000.0000.0000.000
200A209ARG10.8820.9356.7930.2370.2370.0000.0000.0000.000
201A210PHE00.0150.02112.1630.0270.0270.0000.0000.0000.000
202A211LEU00.0050.00814.3490.0200.0200.0000.0000.0000.000
203A212ALA0-0.024-0.01211.792-0.003-0.0030.0000.0000.0000.000
204A213SER0-0.016-0.01210.077-0.031-0.0310.0000.0000.0000.000
205A214ASP-1-0.765-0.8748.5740.1470.1470.0000.0000.0000.000
206A215ASP-1-0.882-0.92411.1140.2930.2930.0000.0000.0000.000
207A216ALA0-0.029-0.00513.566-0.038-0.0380.0000.0000.0000.000
208A217SER0-0.045-0.03813.648-0.033-0.0330.0000.0000.0000.000
209A218TYR0-0.036-0.01315.440-0.016-0.0160.0000.0000.0000.000
210A219ILE0-0.0170.00618.426-0.008-0.0080.0000.0000.0000.000
211A220THR00.0630.02119.235-0.007-0.0070.0000.0000.0000.000
212A221GLY00.0100.01721.7540.0020.0020.0000.0000.0000.000
213A222ALA00.0060.01422.8230.0000.0000.0000.0000.0000.000
214A223VAL0-0.013-0.02824.498-0.003-0.0030.0000.0000.0000.000
215A224ILE00.0080.01120.8500.0020.0020.0000.0000.0000.000
216A225PRO0-0.0050.00824.888-0.003-0.0030.0000.0000.0000.000
217A226VAL0-0.024-0.02322.6360.0010.0010.0000.0000.0000.000
218A227ASP-1-0.800-0.91626.070-0.008-0.0080.0000.0000.0000.000
219A228GLY00.0240.00929.0810.0000.0000.0000.0000.0000.000
220A229GLY00.0420.00130.8930.0000.0000.0000.0000.0000.000
221A230LEU0-0.062-0.02933.1470.0000.0000.0000.0000.0000.000
222A231GLY00.0020.00133.6030.0000.0000.0000.0000.0000.000
223A232MET0-0.078-0.02633.6290.0010.0010.0000.0000.0000.000
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