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: 6N99Z

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 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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2497295.886449
FMO2-HF: Nuclear repulsion 2414338.720773
FMO2-HF: Total energy -82957.165676
FMO2-MP2: Total energy -83199.725013


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.
-0.3780.97-0.007-0.598-0.7430.002
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 : -0.014 / q_NPA : -0.020
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].
3A3ARG10.8200.8763.8391.4532.801-0.007-0.598-0.7430.002
4A4SER0-0.066-0.0236.0170.2450.2450.0000.0000.0000.000
5A5VAL0-0.015-0.0129.433-0.023-0.0230.0000.0000.0000.000
6A6LEU00.0100.01412.0140.0460.0460.0000.0000.0000.000
7A7VAL0-0.005-0.00815.573-0.003-0.0030.0000.0000.0000.000
8A8THR00.0290.00618.1000.0100.0100.0000.0000.0000.000
9A9GLY00.0200.00921.777-0.001-0.0010.0000.0000.0000.000
10A10GLY00.0210.00020.1100.0000.0000.0000.0000.0000.000
11A11ASN00.0330.01120.844-0.004-0.0040.0000.0000.0000.000
12A12ARG10.9770.98523.4050.0220.0220.0000.0000.0000.000
13A13GLY0-0.006-0.00424.357-0.002-0.0020.0000.0000.0000.000
14A14ILE00.0740.02522.119-0.003-0.0030.0000.0000.0000.000
15A15GLY00.0360.02320.998-0.005-0.0050.0000.0000.0000.000
16A16LEU0-0.0200.00519.421-0.009-0.0090.0000.0000.0000.000
17A17ALA00.0310.01018.599-0.009-0.0090.0000.0000.0000.000
18A18ILE0-0.028-0.01916.004-0.005-0.0050.0000.0000.0000.000
19A19ALA00.0040.00514.883-0.020-0.0200.0000.0000.0000.000
20A20ARG10.9070.93513.8980.0340.0340.0000.0000.0000.000
21A21ALA00.0320.04213.452-0.014-0.0140.0000.0000.0000.000
22A22PHE0-0.073-0.0579.6070.0180.0180.0000.0000.0000.000
23A23ALA00.0200.0178.941-0.098-0.0980.0000.0000.0000.000
24A24ASP-1-0.918-0.9559.654-0.158-0.1580.0000.0000.0000.000
25A25ALA0-0.119-0.0547.4310.0240.0240.0000.0000.0000.000
26A26GLY00.0240.0215.338-0.101-0.1010.0000.0000.0000.000
27A27ASP-1-0.817-0.8625.578-1.576-1.5760.0000.0000.0000.000
28A28LYS10.9140.9666.394-0.105-0.1050.0000.0000.0000.000
29A29VAL0-0.014-0.0039.837-0.004-0.0040.0000.0000.0000.000
30A30ALA00.0310.02612.8340.0390.0390.0000.0000.0000.000
31A31ILE0-0.026-0.02016.296-0.018-0.0180.0000.0000.0000.000
32A32THR00.0260.02319.3620.0080.0080.0000.0000.0000.000
33A33TYR0-0.050-0.03522.963-0.004-0.0040.0000.0000.0000.000
34A34ARG10.9270.97125.9640.0090.0090.0000.0000.0000.000
35A35SER0-0.045-0.03729.7570.0020.0020.0000.0000.0000.000
36A36GLY0-0.008-0.01129.636-0.002-0.0020.0000.0000.0000.000
37A37GLU-1-0.911-0.95027.288-0.006-0.0060.0000.0000.0000.000
38A38PRO0-0.042-0.01823.022-0.003-0.0030.0000.0000.0000.000
39A39PRO0-0.025-0.01421.0890.0010.0010.0000.0000.0000.000
40A40GLU-1-0.839-0.92820.628-0.018-0.0180.0000.0000.0000.000
41A41GLY00.0040.00516.873-0.010-0.0100.0000.0000.0000.000
42A42PHE0-0.038-0.01914.828-0.011-0.0110.0000.0000.0000.000
43A43LEU00.0310.03316.3100.0100.0100.0000.0000.0000.000
44A44ALA0-0.012-0.00818.103-0.011-0.0110.0000.0000.0000.000
45A45VAL00.0490.02720.6040.0060.0060.0000.0000.0000.000
46A46LYS10.9190.96223.414-0.005-0.0050.0000.0000.0000.000
47A47CYS0-0.030-0.02625.1730.0020.0020.0000.0000.0000.000
48A48ASP-1-0.818-0.88328.060-0.009-0.0090.0000.0000.0000.000
49A49ILE00.020-0.00624.8150.0010.0010.0000.0000.0000.000
50A50THR0-0.014-0.02827.8140.0000.0000.0000.0000.0000.000
51A51ASP-1-0.820-0.87430.3680.0050.0050.0000.0000.0000.000
52A52THR0-0.008-0.03628.789-0.001-0.0010.0000.0000.0000.000
53A53GLU-1-0.860-0.92228.0000.0110.0110.0000.0000.0000.000
54A54GLN0-0.045-0.03928.1960.0010.0010.0000.0000.0000.000
55A55VAL0-0.025-0.00323.5930.0000.0000.0000.0000.0000.000
56A56GLU-1-0.763-0.84123.5060.0190.0190.0000.0000.0000.000
57A57GLN00.0340.00723.4620.0050.0050.0000.0000.0000.000
58A58ALA00.0350.02622.3270.0050.0050.0000.0000.0000.000
59A59TYR0-0.043-0.05917.552-0.004-0.0040.0000.0000.0000.000
60A60LYS10.8450.93218.699-0.026-0.0260.0000.0000.0000.000
61A61GLU-1-0.845-0.91819.5390.0380.0380.0000.0000.0000.000
62A62ILE0-0.003-0.01514.9800.0100.0100.0000.0000.0000.000
63A63GLU-1-0.878-0.91214.7830.0450.0450.0000.0000.0000.000
64A64GLU-1-0.963-0.98114.9650.1140.1140.0000.0000.0000.000
65A65THR0-0.072-0.02015.2150.0250.0250.0000.0000.0000.000
66A66HIS0-0.021-0.02311.3070.0840.0840.0000.0000.0000.000
67A67GLY00.0330.02410.1560.0760.0760.0000.0000.0000.000
68A68PRO0-0.047-0.03511.300-0.059-0.0590.0000.0000.0000.000
69A69VAL00.0010.00011.041-0.027-0.0270.0000.0000.0000.000
70A70GLU-1-0.838-0.9186.211-0.703-0.7030.0000.0000.0000.000
71A71VAL0-0.037-0.0239.8050.0130.0130.0000.0000.0000.000
72A72LEU00.0010.01212.4820.0120.0120.0000.0000.0000.000
73A73ILE0-0.036-0.02114.8410.0110.0110.0000.0000.0000.000
74A74ALA00.0180.01018.2620.0040.0040.0000.0000.0000.000
75A75ASN0-0.029-0.02221.8270.0060.0060.0000.0000.0000.000
76A76ALA0-0.0030.01123.5330.0030.0030.0000.0000.0000.000
77A77GLY00.0150.01626.6530.0030.0030.0000.0000.0000.000
78A78VAL0-0.031-0.01028.5790.0000.0000.0000.0000.0000.000
79A79THR0-0.049-0.04028.4070.0000.0000.0000.0000.0000.000
80A80LYS10.8440.89630.0170.0130.0130.0000.0000.0000.000
81A81ASP-1-0.758-0.88632.802-0.009-0.0090.0000.0000.0000.000
82A82GLN00.0640.04432.3970.0000.0000.0000.0000.0000.000
83A83LEU00.0630.05934.9060.0010.0010.0000.0000.0000.000
84A84LEU0-0.072-0.05235.7450.0000.0000.0000.0000.0000.000
85A85MET0-0.0100.00638.3420.0000.0000.0000.0000.0000.000
86A86ARG10.8190.90139.7520.0080.0080.0000.0000.0000.000
87A87MET00.0080.00540.0510.0000.0000.0000.0000.0000.000
88A88SER00.0070.01344.0340.0000.0000.0000.0000.0000.000
89A89GLU-1-0.763-0.90842.774-0.007-0.0070.0000.0000.0000.000
90A90GLU-1-0.891-0.96043.153-0.005-0.0050.0000.0000.0000.000
91A91ASP-1-0.845-0.89744.836-0.004-0.0040.0000.0000.0000.000
92A92PHE0-0.035-0.01835.6810.0000.0000.0000.0000.0000.000
93A93THR00.0140.00839.299-0.001-0.0010.0000.0000.0000.000
94A94SER0-0.035-0.02039.062-0.001-0.0010.0000.0000.0000.000
95A95VAL00.0270.01635.0890.0000.0000.0000.0000.0000.000
96A96VAL0-0.037-0.01234.887-0.001-0.0010.0000.0000.0000.000
97A97GLU-1-0.907-0.97034.368-0.007-0.0070.0000.0000.0000.000
98A98THR0-0.0150.00234.084-0.001-0.0010.0000.0000.0000.000
99A99ASN0-0.050-0.03230.5580.0000.0000.0000.0000.0000.000
100A100LEU0-0.0190.00429.576-0.002-0.0020.0000.0000.0000.000
101A101THR00.0230.02029.758-0.001-0.0010.0000.0000.0000.000
102A102GLY00.0250.00628.6390.0000.0000.0000.0000.0000.000
103A103THR0-0.033-0.03024.808-0.003-0.0030.0000.0000.0000.000
104A104PHE0-0.019-0.02025.106-0.003-0.0030.0000.0000.0000.000
105A105ARG10.8910.94726.0040.0030.0030.0000.0000.0000.000
106A106VAL00.0040.00421.7800.0010.0010.0000.0000.0000.000
107A107VAL00.0150.01921.062-0.004-0.0040.0000.0000.0000.000
108A108LYS10.8880.95221.3420.0110.0110.0000.0000.0000.000
109A109ARG10.6960.80718.953-0.013-0.0130.0000.0000.0000.000
110A110ALA00.0220.01117.0940.0040.0040.0000.0000.0000.000
111A111ASN00.033-0.00417.368-0.009-0.0090.0000.0000.0000.000
112A112ARG10.8700.94518.894-0.013-0.0130.0000.0000.0000.000
113A113ALA0-0.008-0.01514.9450.0070.0070.0000.0000.0000.000
114A114MET00.0220.02813.7620.0040.0040.0000.0000.0000.000
115A115LEU0-0.005-0.01215.213-0.001-0.0010.0000.0000.0000.000
116A116ARG10.8840.94316.540-0.026-0.0260.0000.0000.0000.000
117A117ALA0-0.0010.01511.4570.0120.0120.0000.0000.0000.000
118A118LYS10.8890.95112.917-0.004-0.0040.0000.0000.0000.000
119A119LYS10.9100.9337.7730.2110.2110.0000.0000.0000.000
120A120GLY00.0310.01612.484-0.007-0.0070.0000.0000.0000.000
121A121ARG10.7790.90411.7790.0790.0790.0000.0000.0000.000
122A122VAL00.0520.03014.564-0.012-0.0120.0000.0000.0000.000
123A123VAL0-0.028-0.02016.5520.0130.0130.0000.0000.0000.000
124A124LEU0-0.018-0.00919.294-0.003-0.0030.0000.0000.0000.000
125A125ILE00.0010.00419.9750.0030.0030.0000.0000.0000.000
126A126SER00.0590.01824.0640.0010.0010.0000.0000.0000.000
127A127SER0-0.006-0.02627.294-0.002-0.0020.0000.0000.0000.000
128A128VAL0-0.0220.00427.9470.0010.0010.0000.0000.0000.000
129A129VAL0-0.0220.00230.0700.0010.0010.0000.0000.0000.000
130A130GLY00.018-0.00133.4660.0000.0000.0000.0000.0000.000
131A131LEU0-0.053-0.02036.4070.0000.0000.0000.0000.0000.000
132A132LEU0-0.023-0.00737.3090.0000.0000.0000.0000.0000.000
133A133GLY00.0520.03641.6300.0000.0000.0000.0000.0000.000
134A134SER00.016-0.00943.5990.0000.0000.0000.0000.0000.000
135A135ALA00.0610.04044.1300.0000.0000.0000.0000.0000.000
136A136GLY00.0140.00440.9630.0000.0000.0000.0000.0000.000
137A137GLN0-0.060-0.05439.471-0.001-0.0010.0000.0000.0000.000
138A138ALA00.0060.00939.5050.0000.0000.0000.0000.0000.000
139A139ASN00.0150.00238.4550.0000.0000.0000.0000.0000.000
140A140TYR00.0080.00031.803-0.001-0.0010.0000.0000.0000.000
141A141ALA0-0.015-0.01134.853-0.001-0.0010.0000.0000.0000.000
142A142ALA00.0080.00635.7990.0000.0000.0000.0000.0000.000
143A143SER00.0060.01132.305-0.001-0.0010.0000.0000.0000.000
144A144LYS10.9340.96130.3850.0090.0090.0000.0000.0000.000
145A145ALA00.0080.00630.927-0.001-0.0010.0000.0000.0000.000
146A146GLY00.0530.03432.4810.0000.0000.0000.0000.0000.000
147A147LEU0-0.0010.00326.738-0.001-0.0010.0000.0000.0000.000
148A148VAL0-0.022-0.01027.654-0.001-0.0010.0000.0000.0000.000
149A149GLY0-0.004-0.00828.9350.0000.0000.0000.0000.0000.000
150A150PHE0-0.013-0.00425.1440.0000.0000.0000.0000.0000.000
151A151ALA00.0210.00524.4400.0000.0000.0000.0000.0000.000
152A152ARG10.8940.92625.3420.0090.0090.0000.0000.0000.000
153A153SER0-0.020-0.00727.8570.0010.0010.0000.0000.0000.000
154A154LEU0-0.0130.01223.2760.0010.0010.0000.0000.0000.000
155A155ALA00.0000.00523.5070.0000.0000.0000.0000.0000.000
156A156ARG10.9200.95824.5400.0090.0090.0000.0000.0000.000
157A157GLU-1-0.921-0.95126.537-0.011-0.0110.0000.0000.0000.000
158A158LEU0-0.035-0.02721.1790.0010.0010.0000.0000.0000.000
159A159GLY00.0410.03823.4360.0010.0010.0000.0000.0000.000
160A160SER0-0.025-0.01122.024-0.003-0.0030.0000.0000.0000.000
161A161ARG10.8740.91119.0740.0120.0120.0000.0000.0000.000
162A162ASN0-0.040-0.01815.2190.0000.0000.0000.0000.0000.000
163A163ILE00.0010.01815.116-0.017-0.0170.0000.0000.0000.000
164A164THR0-0.045-0.01216.5880.0060.0060.0000.0000.0000.000
165A165PHE00.0490.01118.181-0.010-0.0100.0000.0000.0000.000
166A166ASN0-0.031-0.02518.8570.0120.0120.0000.0000.0000.000
167A167VAL00.0090.00821.857-0.005-0.0050.0000.0000.0000.000
168A168VAL00.0230.02420.4660.0040.0040.0000.0000.0000.000
169A169ALA0-0.021-0.02723.770-0.002-0.0020.0000.0000.0000.000
170A170PRO0-0.0050.00424.9490.0020.0020.0000.0000.0000.000
171A171GLY00.0650.03127.2860.0010.0010.0000.0000.0000.000
172A172PHE0-0.0030.00730.514-0.001-0.0010.0000.0000.0000.000
173A173VAL0-0.010-0.01525.9970.0000.0000.0000.0000.0000.000
174A174ASP-1-0.822-0.86828.914-0.013-0.0130.0000.0000.0000.000
175A175THR0-0.035-0.01027.542-0.001-0.0010.0000.0000.0000.000
176A185GLN00.0600.01341.8780.0000.0000.0000.0000.0000.000
177A186ARG10.8670.88333.3500.0110.0110.0000.0000.0000.000
178A187ALA00.0340.00939.1070.0000.0000.0000.0000.0000.000
179A188ASN0-0.0100.00041.4110.0000.0000.0000.0000.0000.000
180A189ILE0-0.0150.01137.0850.0000.0000.0000.0000.0000.000
181A190VAL0-0.008-0.00535.6460.0000.0000.0000.0000.0000.000
182A191SER0-0.052-0.01438.1410.0000.0000.0000.0000.0000.000
183A192GLN00.0280.01038.5530.0000.0000.0000.0000.0000.000
184A193VAL0-0.055-0.02333.5760.0000.0000.0000.0000.0000.000
185A194PRO00.0150.01835.6440.0000.0000.0000.0000.0000.000
186A195LEU0-0.032-0.02030.3000.0000.0000.0000.0000.0000.000
187A196GLY00.0030.02234.4790.0000.0000.0000.0000.0000.000
188A197ARG10.7500.82926.9590.0060.0060.0000.0000.0000.000
189A198TYR00.0250.01131.0530.0000.0000.0000.0000.0000.000
190A199ALA0-0.004-0.00226.3230.0000.0000.0000.0000.0000.000
191A200ARG10.9350.95523.0960.0090.0090.0000.0000.0000.000
192A201PRO00.0280.00822.6680.0010.0010.0000.0000.0000.000
193A202GLU-1-0.844-0.93819.368-0.028-0.0280.0000.0000.0000.000
194A203GLU-1-0.774-0.84019.263-0.004-0.0040.0000.0000.0000.000
195A204ILE0-0.001-0.00220.9440.0030.0030.0000.0000.0000.000
196A205ALA00.0210.00616.549-0.001-0.0010.0000.0000.0000.000
197A206ALA00.0140.01115.883-0.003-0.0030.0000.0000.0000.000
198A207THR00.0000.00516.2820.0150.0150.0000.0000.0000.000
199A208VAL0-0.007-0.00515.5780.0030.0030.0000.0000.0000.000
200A209ARG10.9410.9727.850-0.038-0.0380.0000.0000.0000.000
201A210PHE00.0020.01612.6390.0130.0130.0000.0000.0000.000
202A211LEU00.0160.00814.4240.0090.0090.0000.0000.0000.000
203A212ALA0-0.012-0.01311.829-0.009-0.0090.0000.0000.0000.000
204A213SER0-0.031-0.0179.859-0.047-0.0470.0000.0000.0000.000
205A214ASP-1-0.768-0.8848.380-0.048-0.0480.0000.0000.0000.000
206A215ASP-1-0.888-0.92811.0150.2090.2090.0000.0000.0000.000
207A216ALA0-0.058-0.01613.814-0.025-0.0250.0000.0000.0000.000
208A217SER0-0.034-0.02613.951-0.024-0.0240.0000.0000.0000.000
209A218TYR0-0.031-0.01315.760-0.011-0.0110.0000.0000.0000.000
210A219ILE0-0.0080.01318.745-0.001-0.0010.0000.0000.0000.000
211A220THR00.0460.01019.523-0.009-0.0090.0000.0000.0000.000
212A221GLY00.0070.01821.9920.0030.0030.0000.0000.0000.000
213A222ALA0-0.0030.01123.3790.0030.0030.0000.0000.0000.000
214A223VAL0-0.008-0.02024.565-0.003-0.0030.0000.0000.0000.000
215A224ILE00.0180.00421.3490.0020.0020.0000.0000.0000.000
216A225PRO0-0.0120.01025.347-0.003-0.0030.0000.0000.0000.000
217A226VAL0-0.002-0.00422.9470.0020.0020.0000.0000.0000.000
218A227ASP-1-0.821-0.93826.377-0.008-0.0080.0000.0000.0000.000
219A228GLY00.0180.01229.4690.0000.0000.0000.0000.0000.000
220A229GLY00.0400.00731.3190.0000.0000.0000.0000.0000.000
221A230LEU0-0.070-0.03333.3910.0000.0000.0000.0000.0000.000
222A231GLY00.007-0.00233.9560.0000.0000.0000.0000.0000.000
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