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: 2J66R

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 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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2494951.655782
FMO2-HF: Nuclear repulsion 2411995.511936
FMO2-HF: Total energy -82956.143846
FMO2-MP2: Total energy -83198.744772


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.
-1.2940.154-0.002-0.639-0.8060.001
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 : -0.027 / q_NPA : -0.022
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].
3A3ARG10.8330.9043.8290.2051.653-0.002-0.639-0.8060.001
4A4SER0-0.046-0.0066.387-0.366-0.3660.0000.0000.0000.000
5A5VAL0-0.013-0.0109.6470.1800.1800.0000.0000.0000.000
6A6LEU0-0.0010.00812.207-0.055-0.0550.0000.0000.0000.000
7A7VAL0-0.012-0.00815.7660.0380.0380.0000.0000.0000.000
8A8THR00.0180.00218.251-0.013-0.0130.0000.0000.0000.000
9A9GLY00.0230.00821.9320.0050.0050.0000.0000.0000.000
10A10GLY00.0270.00420.2830.0020.0020.0000.0000.0000.000
11A11ASN00.0360.01421.029-0.014-0.0140.0000.0000.0000.000
12A12ARG10.9700.97423.6010.0280.0280.0000.0000.0000.000
13A13GLY0-0.013-0.00424.5030.0080.0080.0000.0000.0000.000
14A14ILE00.0760.02522.254-0.011-0.0110.0000.0000.0000.000
15A15GLY00.0450.03121.100-0.001-0.0010.0000.0000.0000.000
16A16LEU0-0.0170.00619.533-0.011-0.0110.0000.0000.0000.000
17A17ALA00.0350.00918.750-0.027-0.0270.0000.0000.0000.000
18A18ILE0-0.024-0.01615.907-0.013-0.0130.0000.0000.0000.000
19A19ALA00.0070.00414.996-0.020-0.0200.0000.0000.0000.000
20A20ARG10.9400.96314.0680.1670.1670.0000.0000.0000.000
21A21ALA00.0340.04213.601-0.050-0.0500.0000.0000.0000.000
22A22PHE0-0.069-0.0579.7150.0170.0170.0000.0000.0000.000
23A23ALA00.0150.0179.099-0.158-0.1580.0000.0000.0000.000
24A24ASP-1-0.919-0.9569.860-0.544-0.5440.0000.0000.0000.000
25A25ALA0-0.130-0.0577.395-0.033-0.0330.0000.0000.0000.000
26A26GLY00.0160.0155.548-0.289-0.2890.0000.0000.0000.000
27A27ASP-1-0.814-0.8995.850-1.601-1.6010.0000.0000.0000.000
28A28LYS10.8970.9516.8130.5710.5710.0000.0000.0000.000
29A29VAL0-0.0060.0039.8680.1700.1700.0000.0000.0000.000
30A30ALA00.0230.02413.063-0.009-0.0090.0000.0000.0000.000
31A31ILE0-0.020-0.01916.3750.0260.0260.0000.0000.0000.000
32A32THR00.0270.02119.5720.0020.0020.0000.0000.0000.000
33A33TYR0-0.055-0.03823.1130.0000.0000.0000.0000.0000.000
34A34ARG11.0231.01926.1730.0070.0070.0000.0000.0000.000
35A35SER0-0.036-0.03029.967-0.002-0.0020.0000.0000.0000.000
36A36GLY0-0.027-0.01729.857-0.002-0.0020.0000.0000.0000.000
37A37GLU-1-0.897-0.94427.345-0.107-0.1070.0000.0000.0000.000
38A38PRO0-0.064-0.03023.2930.0030.0030.0000.0000.0000.000
39A39PRO0-0.033-0.01021.241-0.004-0.0040.0000.0000.0000.000
40A40GLU-1-0.855-0.93820.977-0.205-0.2050.0000.0000.0000.000
41A41GLY0-0.012-0.01317.128-0.007-0.0070.0000.0000.0000.000
42A42PHE0-0.034-0.02114.905-0.037-0.0370.0000.0000.0000.000
43A43LEU00.0350.03415.9690.0130.0130.0000.0000.0000.000
44A44ALA0-0.009-0.00817.9780.0250.0250.0000.0000.0000.000
45A45VAL00.0400.02720.5210.0060.0060.0000.0000.0000.000
46A46LYS10.9140.95823.2430.0520.0520.0000.0000.0000.000
47A47CYS0-0.029-0.02625.1960.0080.0080.0000.0000.0000.000
48A48ASP-1-0.880-0.91728.1130.0140.0140.0000.0000.0000.000
49A49ILE0-0.005-0.01225.0230.0050.0050.0000.0000.0000.000
50A50THR0-0.029-0.03728.1880.0110.0110.0000.0000.0000.000
51A51ASP-1-0.836-0.90630.7640.0310.0310.0000.0000.0000.000
52A52THR0-0.005-0.03729.2310.0010.0010.0000.0000.0000.000
53A53GLU-1-0.882-0.92728.3770.0550.0550.0000.0000.0000.000
54A54GLN00.007-0.00128.383-0.008-0.0080.0000.0000.0000.000
55A55VAL0-0.023-0.00324.014-0.004-0.0040.0000.0000.0000.000
56A56GLU-1-0.815-0.90923.7870.1000.1000.0000.0000.0000.000
57A57GLN0-0.004-0.01223.6400.0120.0120.0000.0000.0000.000
58A58ALA00.0400.02522.367-0.008-0.0080.0000.0000.0000.000
59A59TYR0-0.049-0.05617.918-0.004-0.0040.0000.0000.0000.000
60A60LYS10.9180.97718.795-0.051-0.0510.0000.0000.0000.000
61A61GLU-1-0.866-0.91919.416-0.063-0.0630.0000.0000.0000.000
62A62ILE0-0.013-0.01914.956-0.022-0.0220.0000.0000.0000.000
63A63GLU-1-0.876-0.93614.7840.1470.1470.0000.0000.0000.000
64A64GLU-1-0.973-0.98214.7840.0100.0100.0000.0000.0000.000
65A65THR0-0.066-0.01614.648-0.026-0.0260.0000.0000.0000.000
66A66HIS0-0.020-0.02211.165-0.085-0.0850.0000.0000.0000.000
67A67GLY00.0340.0289.9150.0270.0270.0000.0000.0000.000
68A68PRO0-0.035-0.03311.510-0.035-0.0350.0000.0000.0000.000
69A69VAL0-0.014-0.00211.5070.0660.0660.0000.0000.0000.000
70A70GLU-1-0.859-0.9317.3331.4841.4840.0000.0000.0000.000
71A71VAL0-0.047-0.02610.1020.0560.0560.0000.0000.0000.000
72A72LEU00.0120.01512.886-0.080-0.0800.0000.0000.0000.000
73A73ILE0-0.038-0.02114.9670.0220.0220.0000.0000.0000.000
74A74ALA00.0170.00218.318-0.026-0.0260.0000.0000.0000.000
75A75ASN0-0.047-0.03221.9550.0140.0140.0000.0000.0000.000
76A76ALA0-0.0090.01023.631-0.008-0.0080.0000.0000.0000.000
77A77GLY0-0.004-0.00526.746-0.001-0.0010.0000.0000.0000.000
78A78VAL0-0.029-0.00828.670-0.004-0.0040.0000.0000.0000.000
79A79THR0-0.038-0.02428.415-0.008-0.0080.0000.0000.0000.000
80A80LYS10.9420.95329.6920.0510.0510.0000.0000.0000.000
81A81ASP-1-0.816-0.92932.959-0.023-0.0230.0000.0000.0000.000
82A82GLN00.0310.02332.6340.0010.0010.0000.0000.0000.000
83A83LEU00.0660.05634.8380.0020.0020.0000.0000.0000.000
84A84LEU0-0.077-0.05235.826-0.002-0.0020.0000.0000.0000.000
85A85MET0-0.0100.00538.4830.0000.0000.0000.0000.0000.000
86A86ARG10.8200.90139.9000.0070.0070.0000.0000.0000.000
87A87MET00.0250.01840.0070.0010.0010.0000.0000.0000.000
88A88SER00.0460.05044.1530.0000.0000.0000.0000.0000.000
89A89GLU-1-0.780-0.91842.3720.0170.0170.0000.0000.0000.000
90A90GLU-1-0.924-0.97943.2410.0180.0180.0000.0000.0000.000
91A91ASP-1-0.872-0.93244.9470.0160.0160.0000.0000.0000.000
92A92PHE0-0.050-0.03035.8810.0010.0010.0000.0000.0000.000
93A93THR0-0.043-0.01539.4030.0020.0020.0000.0000.0000.000
94A94SER00.0270.01539.2210.0030.0030.0000.0000.0000.000
95A95VAL00.0550.02535.1990.0010.0010.0000.0000.0000.000
96A96VAL0-0.067-0.02235.0110.0020.0020.0000.0000.0000.000
97A97GLU-1-0.895-0.96834.5470.0450.0450.0000.0000.0000.000
98A98THR0-0.040-0.00734.6110.0020.0020.0000.0000.0000.000
99A99ASN00.002-0.00630.5890.0010.0010.0000.0000.0000.000
100A100LEU0-0.0130.00129.9070.0080.0080.0000.0000.0000.000
101A101THR00.0080.01930.2610.0100.0100.0000.0000.0000.000
102A102GLY00.0340.00729.1280.0050.0050.0000.0000.0000.000
103A103THR0-0.020-0.01825.1760.0070.0070.0000.0000.0000.000
104A104PHE0-0.027-0.02225.7580.0150.0150.0000.0000.0000.000
105A105ARG10.8810.94126.826-0.048-0.0480.0000.0000.0000.000
106A106VAL00.0100.00822.3390.0100.0100.0000.0000.0000.000
107A107VAL00.0210.01921.8810.0180.0180.0000.0000.0000.000
108A108LYS10.9040.95622.232-0.109-0.1090.0000.0000.0000.000
109A109ARG10.7030.84119.443-0.114-0.1140.0000.0000.0000.000
110A110ALA00.0280.01917.9020.0130.0130.0000.0000.0000.000
111A111ASN00.0530.00518.2370.0580.0580.0000.0000.0000.000
112A112ARG10.9110.97419.892-0.120-0.1200.0000.0000.0000.000
113A113ALA0-0.001-0.00815.6000.0140.0140.0000.0000.0000.000
114A114MET00.0240.03014.7570.0570.0570.0000.0000.0000.000
115A115LEU0-0.018-0.01716.2180.0480.0480.0000.0000.0000.000
116A116ARG10.8910.94917.288-0.260-0.2600.0000.0000.0000.000
117A117ALA00.0040.01512.4440.0070.0070.0000.0000.0000.000
118A118LYS10.8820.94813.892-0.472-0.4720.0000.0000.0000.000
119A119LYS10.9040.9308.078-1.717-1.7170.0000.0000.0000.000
120A120GLY00.0340.01913.266-0.019-0.0190.0000.0000.0000.000
121A121ARG10.8100.93312.173-0.689-0.6890.0000.0000.0000.000
122A122VAL00.0550.03314.756-0.039-0.0390.0000.0000.0000.000
123A123VAL0-0.029-0.01916.5510.0040.0040.0000.0000.0000.000
124A124LEU0-0.020-0.01219.311-0.025-0.0250.0000.0000.0000.000
125A125ILE00.0020.00720.0470.0040.0040.0000.0000.0000.000
126A126SER00.0390.01524.104-0.005-0.0050.0000.0000.0000.000
127A127SER00.010-0.02127.342-0.005-0.0050.0000.0000.0000.000
128A128VAL0-0.0200.00327.9300.0040.0040.0000.0000.0000.000
129A129VAL0-0.0230.00430.1230.0000.0000.0000.0000.0000.000
130A130GLY00.0130.00033.503-0.006-0.0060.0000.0000.0000.000
131A131LEU0-0.052-0.02236.4600.0030.0030.0000.0000.0000.000
132A132LEU0-0.011-0.00337.561-0.001-0.0010.0000.0000.0000.000
133A133GLY00.0600.04341.6820.0010.0010.0000.0000.0000.000
134A134SER00.011-0.01243.6420.0010.0010.0000.0000.0000.000
135A135ALA00.0610.03744.1660.0030.0030.0000.0000.0000.000
136A136GLY00.0150.00841.0250.0020.0020.0000.0000.0000.000
137A137GLN0-0.053-0.04939.5200.0050.0050.0000.0000.0000.000
138A138ALA00.0070.01039.5280.0040.0040.0000.0000.0000.000
139A139ASN00.0170.00338.4740.0070.0070.0000.0000.0000.000
140A140TYR0-0.016-0.00531.4770.0060.0060.0000.0000.0000.000
141A141ALA0-0.009-0.00834.8800.0060.0060.0000.0000.0000.000
142A142ALA00.0010.00035.8140.0060.0060.0000.0000.0000.000
143A143SER00.0040.00932.2040.0080.0080.0000.0000.0000.000
144A144LYS10.9630.98030.173-0.068-0.0680.0000.0000.0000.000
145A145ALA00.0020.00030.9430.0100.0100.0000.0000.0000.000
146A146GLY00.0530.03132.5320.0070.0070.0000.0000.0000.000
147A147LEU0-0.0020.00426.7580.0100.0100.0000.0000.0000.000
148A148VAL0-0.026-0.01227.6750.0150.0150.0000.0000.0000.000
149A149GLY0-0.004-0.01028.9570.0110.0110.0000.0000.0000.000
150A150PHE0-0.011-0.00525.6570.0090.0090.0000.0000.0000.000
151A151ALA00.0200.00524.4760.0110.0110.0000.0000.0000.000
152A152ARG10.9040.93625.546-0.120-0.1200.0000.0000.0000.000
153A153SER0-0.010-0.00127.9560.0030.0030.0000.0000.0000.000
154A154LEU0-0.0180.00824.0480.0050.0050.0000.0000.0000.000
155A155ALA0-0.0060.00723.8760.0160.0160.0000.0000.0000.000
156A156ARG10.9200.95524.881-0.136-0.1360.0000.0000.0000.000
157A157GLU-1-0.953-0.96927.3300.1720.1720.0000.0000.0000.000
158A158LEU0-0.047-0.03021.9670.0060.0060.0000.0000.0000.000
159A159GLY00.0420.03224.3070.0140.0140.0000.0000.0000.000
160A160SER0-0.021-0.00922.5400.0140.0140.0000.0000.0000.000
161A161ARG10.8820.92120.007-0.266-0.2660.0000.0000.0000.000
162A162ASN0-0.028-0.00415.671-0.002-0.0020.0000.0000.0000.000
163A163ILE00.0050.01215.6240.0760.0760.0000.0000.0000.000
164A164THR0-0.048-0.01016.784-0.039-0.0390.0000.0000.0000.000
165A165PHE00.0500.01318.341-0.003-0.0030.0000.0000.0000.000
166A166ASN0-0.023-0.02018.776-0.030-0.0300.0000.0000.0000.000
167A167VAL00.0070.00821.874-0.010-0.0100.0000.0000.0000.000
168A168VAL00.0170.01920.4100.0070.0070.0000.0000.0000.000
169A169ALA0-0.014-0.02723.749-0.010-0.0100.0000.0000.0000.000
170A170PRO0-0.0050.00125.2380.0000.0000.0000.0000.0000.000
171A171GLY00.0670.03227.2910.0010.0010.0000.0000.0000.000
172A172PHE00.0130.01030.538-0.004-0.0040.0000.0000.0000.000
173A173VAL0-0.010-0.01726.1280.0000.0000.0000.0000.0000.000
174A174ASP-1-0.944-0.97028.951-0.029-0.0290.0000.0000.0000.000
175A175THR0-0.029-0.01127.665-0.006-0.0060.0000.0000.0000.000
176A185GLN00.0490.01241.6180.0010.0010.0000.0000.0000.000
177A186ARG10.9710.97533.5350.0260.0260.0000.0000.0000.000
178A187ALA00.0500.01639.1270.0020.0020.0000.0000.0000.000
179A188ASN00.0150.00041.4230.0040.0040.0000.0000.0000.000
180A189ILE0-0.0270.00337.1600.0020.0020.0000.0000.0000.000
181A190VAL0-0.002-0.00135.7000.0030.0030.0000.0000.0000.000
182A191SER0-0.045-0.00238.1370.0030.0030.0000.0000.0000.000
183A192GLN00.0290.01338.5920.0040.0040.0000.0000.0000.000
184A193VAL0-0.058-0.02333.6110.0040.0040.0000.0000.0000.000
185A194PRO00.0160.02035.539-0.003-0.0030.0000.0000.0000.000
186A195LEU0-0.025-0.01930.338-0.003-0.0030.0000.0000.0000.000
187A196GLY00.0000.01934.415-0.004-0.0040.0000.0000.0000.000
188A197ARG10.7320.82627.008-0.013-0.0130.0000.0000.0000.000
189A198TYR00.0110.01030.9940.0050.0050.0000.0000.0000.000
190A199ALA0-0.008-0.00526.297-0.001-0.0010.0000.0000.0000.000
191A200ARG11.0010.98923.1960.0180.0180.0000.0000.0000.000
192A201PRO00.0260.01122.8140.0110.0110.0000.0000.0000.000
193A202GLU-1-0.846-0.94019.495-0.065-0.0650.0000.0000.0000.000
194A203GLU-1-0.814-0.86919.2660.0190.0190.0000.0000.0000.000
195A204ILE0-0.0050.00120.9160.0200.0200.0000.0000.0000.000
196A205ALA00.0230.00516.5240.0230.0230.0000.0000.0000.000
197A206ALA00.0150.00915.8420.0170.0170.0000.0000.0000.000
198A207THR00.0080.00916.2140.0450.0450.0000.0000.0000.000
199A208VAL0-0.009-0.00715.5840.0410.0410.0000.0000.0000.000
200A209ARG10.9480.9758.154-0.012-0.0120.0000.0000.0000.000
201A210PHE0-0.0040.01412.5560.0840.0840.0000.0000.0000.000
202A211LEU00.0150.00314.4280.0760.0760.0000.0000.0000.000
203A212ALA0-0.009-0.00911.8270.0470.0470.0000.0000.0000.000
204A213SER0-0.029-0.0099.8670.1450.1450.0000.0000.0000.000
205A214ASP-1-0.791-0.9048.2751.7441.7440.0000.0000.0000.000
206A215ASP-1-0.892-0.94211.0270.5850.5850.0000.0000.0000.000
207A216ALA0-0.070-0.01913.965-0.095-0.0950.0000.0000.0000.000
208A217SER0-0.042-0.03113.945-0.057-0.0570.0000.0000.0000.000
209A218TYR0-0.019-0.00715.778-0.032-0.0320.0000.0000.0000.000
210A219ILE0-0.0070.01418.762-0.049-0.0490.0000.0000.0000.000
211A220THR00.0380.00419.5420.0220.0220.0000.0000.0000.000
212A221GLY00.0040.01422.013-0.017-0.0170.0000.0000.0000.000
213A222ALA0-0.0030.00623.393-0.022-0.0220.0000.0000.0000.000
214A223VAL0-0.011-0.02024.580-0.001-0.0010.0000.0000.0000.000
215A224ILE00.013-0.00121.510-0.002-0.0020.0000.0000.0000.000
216A225PRO0-0.0110.00525.289-0.006-0.0060.0000.0000.0000.000
217A226VAL0-0.002-0.00222.9440.0020.0020.0000.0000.0000.000
218A227ASP-1-0.829-0.94526.3320.0470.0470.0000.0000.0000.000
219A228GLY00.0090.00829.409-0.005-0.0050.0000.0000.0000.000
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