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: VKQJ1

Calculation Name: 2NX4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NX4

Chain ID: A

ChEMBL ID:

UniProt ID: Q0SCU8

Base Structure: X-ray

Registration Date: 2023-09-27

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2088296.676903
FMO2-HF: Nuclear repulsion 2010103.108493
FMO2-HF: Total energy -78193.56841
FMO2-MP2: Total energy -78415.444888


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
0.0620.756-0.005-0.277-0.4130.001
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / 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].
3A2PRO00.0150.0103.8031.4252.119-0.005-0.277-0.4130.001
4A3LYS10.9880.9856.386-0.024-0.0240.0000.0000.0000.000
5A4LEU00.0010.0018.6340.0560.0560.0000.0000.0000.000
6A5VAL00.0590.0378.2060.0510.0510.0000.0000.0000.000
7A6ASP-1-0.887-0.9437.475-0.036-0.0360.0000.0000.0000.000
8A7HIS0-0.066-0.0589.4500.2100.2100.0000.0000.0000.000
9A8ASP-1-0.863-0.91612.852-0.419-0.4190.0000.0000.0000.000
10A9GLU-1-0.933-0.9729.648-0.731-0.7310.0000.0000.0000.000
11A10ARG10.8810.93012.3110.0700.0700.0000.0000.0000.000
12A11ARG10.8380.88615.0070.2100.2100.0000.0000.0000.000
13A12ARG10.8710.92216.2070.3370.3370.0000.0000.0000.000
14A13SER0-0.021-0.00416.0600.0300.0300.0000.0000.0000.000
15A14ILE0-0.048-0.02418.6010.0240.0240.0000.0000.0000.000
16A15THR0-0.033-0.00920.9380.0160.0160.0000.0000.0000.000
17A16ALA00.0000.00721.8110.0100.0100.0000.0000.0000.000
18A17ALA0-0.057-0.02623.0990.0100.0100.0000.0000.0000.000
19A18ALA00.0250.02024.8870.0100.0100.0000.0000.0000.000
20A19TRP0-0.015-0.00326.3470.0080.0080.0000.0000.0000.000
21A20ARG10.8580.90228.2920.0780.0780.0000.0000.0000.000
22A21LEU0-0.0170.03130.4060.0050.0050.0000.0000.0000.000
23A22ILE0-0.053-0.04928.4650.0050.0050.0000.0000.0000.000
24A23ALA0-0.0070.00632.4890.0030.0030.0000.0000.0000.000
25A24ALA0-0.033-0.01034.5680.0030.0030.0000.0000.0000.000
26A25ARG10.8810.94135.2380.0220.0220.0000.0000.0000.000
27A26GLY00.0500.03836.1730.0030.0030.0000.0000.0000.000
28A27ILE0-0.001-0.01731.0920.0040.0040.0000.0000.0000.000
29A28GLU-1-0.934-0.97934.769-0.031-0.0310.0000.0000.0000.000
30A29ALA0-0.006-0.00537.4650.0040.0040.0000.0000.0000.000
31A30ALA0-0.0070.02332.4050.0040.0040.0000.0000.0000.000
32A31ASN0-0.014-0.02632.7090.0030.0030.0000.0000.0000.000
33A32MET00.0770.03127.4660.0000.0000.0000.0000.0000.000
34A33ARG10.9390.98028.367-0.013-0.0130.0000.0000.0000.000
35A34ASP-1-0.876-0.93029.8120.0010.0010.0000.0000.0000.000
36A35ILE00.0470.02425.7420.0000.0000.0000.0000.0000.000
37A36ALA0-0.037-0.01625.164-0.002-0.0020.0000.0000.0000.000
38A37THR0-0.067-0.04925.7390.0060.0060.0000.0000.0000.000
39A38GLU-1-0.870-0.95027.620-0.030-0.0300.0000.0000.0000.000
40A39ALA00.0090.01822.571-0.004-0.0040.0000.0000.0000.000
41A40GLY0-0.0250.00022.5310.0020.0020.0000.0000.0000.000
42A41TYR0-0.030-0.01317.1780.0190.0190.0000.0000.0000.000
43A42THR00.0140.00222.484-0.005-0.0050.0000.0000.0000.000
44A43ASN00.059-0.00523.760-0.007-0.0070.0000.0000.0000.000
45A44GLY0-0.0080.00123.713-0.007-0.0070.0000.0000.0000.000
46A45ALA0-0.001-0.00119.218-0.002-0.0020.0000.0000.0000.000
47A46LEU00.0290.01519.816-0.011-0.0110.0000.0000.0000.000
48A47SER0-0.016-0.01921.753-0.016-0.0160.0000.0000.0000.000
49A48HIS0-0.081-0.01614.4990.0370.0370.0000.0000.0000.000
50A49TYR0-0.038-0.02313.3160.0010.0010.0000.0000.0000.000
51A50PHE0-0.0100.00318.833-0.030-0.0300.0000.0000.0000.000
52A51ALA00.0220.00722.3620.0170.0170.0000.0000.0000.000
53A52GLY00.006-0.00625.0540.0120.0120.0000.0000.0000.000
54A53LYS10.8550.92127.0000.0200.0200.0000.0000.0000.000
55A54ASP-1-0.866-0.93729.166-0.083-0.0830.0000.0000.0000.000
56A55GLU-1-0.730-0.82622.143-0.123-0.1230.0000.0000.0000.000
57A56ILE0-0.003-0.01224.459-0.011-0.0110.0000.0000.0000.000
58A57LEU0-0.0120.00926.029-0.005-0.0050.0000.0000.0000.000
59A58ARG10.9060.95922.0050.1680.1680.0000.0000.0000.000
60A59THR00.000-0.02421.609-0.004-0.0040.0000.0000.0000.000
61A60SER00.002-0.02624.345-0.007-0.0070.0000.0000.0000.000
62A61TYR0-0.021-0.05926.8840.0000.0000.0000.0000.0000.000
63A62GLU-1-0.872-0.94022.154-0.222-0.2220.0000.0000.0000.000
64A63HIS0-0.009-0.00222.893-0.012-0.0120.0000.0000.0000.000
65A64ILE00.001-0.00425.155-0.002-0.0020.0000.0000.0000.000
66A65SER0-0.0190.01227.4530.0060.0060.0000.0000.0000.000
67A66GLU-1-0.823-0.89221.806-0.267-0.2670.0000.0000.0000.000
68A67ALA0-0.055-0.02325.718-0.001-0.0010.0000.0000.0000.000
69A68THR00.020-0.00327.3080.0070.0070.0000.0000.0000.000
70A69ASP-1-0.872-0.93927.237-0.161-0.1610.0000.0000.0000.000
71A70ARG10.8550.93324.1790.1580.1580.0000.0000.0000.000
72A71ARG10.7560.85827.5150.1050.1050.0000.0000.0000.000
73A72ILE00.0230.02230.8700.0060.0060.0000.0000.0000.000
74A73ALA0-0.031-0.02528.3670.0040.0040.0000.0000.0000.000
75A74GLU-1-0.998-1.01326.872-0.142-0.1420.0000.0000.0000.000
76A75ALA0-0.019-0.00130.8240.0060.0060.0000.0000.0000.000
77A76LEU0-0.062-0.02933.5630.0050.0050.0000.0000.0000.000
78A77GLY00.0030.01434.2110.0060.0060.0000.0000.0000.000
79A78ASP-1-0.999-1.00735.567-0.089-0.0890.0000.0000.0000.000
80A79ALA00.0050.01638.2600.0030.0030.0000.0000.0000.000
81A80THR0-0.023-0.01339.506-0.005-0.0050.0000.0000.0000.000
82A81GLY00.0560.02142.0940.0030.0030.0000.0000.0000.000
83A82LEU0-0.010-0.02943.452-0.003-0.0030.0000.0000.0000.000
84A83ASP-1-0.926-0.94143.351-0.066-0.0660.0000.0000.0000.000
85A84ALA00.0040.00039.194-0.001-0.0010.0000.0000.0000.000
86A85LEU0-0.010-0.00939.738-0.003-0.0030.0000.0000.0000.000
87A86ARG10.8740.92841.3290.0590.0590.0000.0000.0000.000
88A87ILE0-0.037-0.00536.7960.0010.0010.0000.0000.0000.000
89A88LEU00.0420.02435.903-0.002-0.0020.0000.0000.0000.000
90A89CYS0-0.025-0.04337.552-0.001-0.0010.0000.0000.0000.000
91A90ARG10.9000.95139.8580.0670.0670.0000.0000.0000.000
92A91GLU-1-0.856-0.91234.268-0.091-0.0910.0000.0000.0000.000
93A92VAL00.0010.00635.494-0.001-0.0010.0000.0000.0000.000
94A93MET0-0.0130.00537.0920.0040.0040.0000.0000.0000.000
95A94PRO0-0.0090.01639.318-0.001-0.0010.0000.0000.0000.000
96A95ILE00.011-0.00140.3420.0050.0050.0000.0000.0000.000
97A96ASN0-0.026-0.01637.4100.0030.0030.0000.0000.0000.000
98A97GLU-1-0.869-0.95238.260-0.048-0.0480.0000.0000.0000.000
99A98GLU-1-0.767-0.86531.359-0.078-0.0780.0000.0000.0000.000
100A99GLN00.018-0.01235.008-0.004-0.0040.0000.0000.0000.000
101A100LEU0-0.0030.01536.611-0.001-0.0010.0000.0000.0000.000
102A101LEU0-0.068-0.03234.3230.0000.0000.0000.0000.0000.000
103A102GLU-1-0.808-0.89531.572-0.102-0.1020.0000.0000.0000.000
104A103ALA00.0520.03634.139-0.002-0.0020.0000.0000.0000.000
105A104ARG10.8780.94836.6270.0460.0460.0000.0000.0000.000
106A105ILE0-0.060-0.01730.3410.0020.0020.0000.0000.0000.000
107A106ALA00.0370.01233.790-0.002-0.0020.0000.0000.0000.000
108A107ALA0-0.004-0.00334.9290.0000.0000.0000.0000.0000.000
109A108SER0-0.073-0.03334.9510.0040.0040.0000.0000.0000.000
110A109LEU0-0.015-0.00630.7910.0020.0020.0000.0000.0000.000
111A110TRP00.0300.00534.0640.0030.0030.0000.0000.0000.000
112A111PRO0-0.005-0.00736.8240.0000.0000.0000.0000.0000.000
113A112ARG10.9030.94432.9220.0610.0610.0000.0000.0000.000
114A113ALA00.0510.02833.630-0.001-0.0010.0000.0000.0000.000
115A114MET0-0.092-0.02934.8630.0000.0000.0000.0000.0000.000
116A115TYR0-0.082-0.03537.0200.0050.0050.0000.0000.0000.000
117A116ASP-1-0.890-0.95631.175-0.096-0.0960.0000.0000.0000.000
118A117GLU-1-0.835-0.89831.261-0.099-0.0990.0000.0000.0000.000
119A118GLN0-0.081-0.04124.248-0.029-0.0290.0000.0000.0000.000
120A119MET0-0.087-0.05028.355-0.008-0.0080.0000.0000.0000.000
121A120ALA00.0840.05430.1330.0000.0000.0000.0000.0000.000
122A121ALA0-0.081-0.04227.633-0.005-0.0050.0000.0000.0000.000
123A122THR0-0.017-0.02725.2200.0000.0000.0000.0000.0000.000
124A123ASN00.0990.11028.084-0.002-0.0020.0000.0000.0000.000
125A124ARG10.9010.93631.7550.1200.1200.0000.0000.0000.000
126A125ARG10.9530.98525.4990.2020.2020.0000.0000.0000.000
127A126THR00.0430.03429.491-0.005-0.0050.0000.0000.0000.000
128A127MET0-0.046-0.02731.2140.0070.0070.0000.0000.0000.000
129A128ASP-1-0.827-0.91933.567-0.113-0.1130.0000.0000.0000.000
130A129ASN00.0080.02030.3060.0010.0010.0000.0000.0000.000
131A130TRP00.017-0.00831.9700.0100.0100.0000.0000.0000.000
132A131ARG10.7850.84935.4040.0990.0990.0000.0000.0000.000
133A132GLU-1-0.953-0.97433.461-0.137-0.1370.0000.0000.0000.000
134A133GLN0-0.021-0.01132.9330.0000.0000.0000.0000.0000.000
135A134MET0-0.016-0.00736.8270.0050.0050.0000.0000.0000.000
136A135ALA00.0220.00240.1230.0050.0050.0000.0000.0000.000
137A136ILE0-0.0250.00036.7260.0030.0030.0000.0000.0000.000
138A137PHE0-0.009-0.00636.5570.0030.0030.0000.0000.0000.000
139A138LEU00.004-0.01342.1270.0050.0050.0000.0000.0000.000
140A139GLU-1-0.862-0.92644.252-0.068-0.0680.0000.0000.0000.000
141A140GLN00.0380.02040.4110.0030.0030.0000.0000.0000.000
142A141ALA00.0260.00745.6610.0030.0030.0000.0000.0000.000
143A142ARG10.7720.88648.1950.0660.0660.0000.0000.0000.000
144A143GLU-1-1.000-0.99947.559-0.071-0.0710.0000.0000.0000.000
145A144GLU-1-0.970-0.98946.351-0.068-0.0680.0000.0000.0000.000
146A145GLY0-0.041-0.00650.9700.0030.0030.0000.0000.0000.000
147A146SER0-0.061-0.03349.6250.0020.0020.0000.0000.0000.000
148A147VAL0-0.043-0.01550.1580.0010.0010.0000.0000.0000.000
149A148GLY0-0.008-0.01253.0180.0010.0010.0000.0000.0000.000
150A149ASP-1-0.873-0.93153.597-0.057-0.0570.0000.0000.0000.000
151A150ILE0-0.043-0.02248.8550.0010.0010.0000.0000.0000.000
152A151ASP-1-0.867-0.93950.232-0.063-0.0630.0000.0000.0000.000
153A152VAL00.0500.01244.9280.0000.0000.0000.0000.0000.000
154A153THR00.001-0.00244.582-0.003-0.0030.0000.0000.0000.000
155A154ILE00.0030.00845.873-0.001-0.0010.0000.0000.0000.000
156A155VAL00.0090.01347.3210.0000.0000.0000.0000.0000.000
157A156VAL00.0130.00941.4860.0000.0000.0000.0000.0000.000
158A157GLU-1-0.782-0.85243.044-0.082-0.0820.0000.0000.0000.000
159A158GLN0-0.035-0.02045.0270.0000.0000.0000.0000.0000.000
160A159LEU00.0280.02043.6210.0010.0010.0000.0000.0000.000
161A160LEU00.0300.01538.3500.0000.0000.0000.0000.0000.000
162A161ASN0-0.067-0.05542.2730.0010.0010.0000.0000.0000.000
163A162MET0-0.038-0.00144.4650.0020.0020.0000.0000.0000.000
164A163MET00.0340.02140.1540.0020.0020.0000.0000.0000.000
165A164MET00.0000.00937.816-0.002-0.0020.0000.0000.0000.000
166A165GLY00.0200.00841.5470.0020.0020.0000.0000.0000.000
167A166MET0-0.018-0.01743.2450.0020.0020.0000.0000.0000.000
168A167GLN0-0.035-0.01538.2450.0020.0020.0000.0000.0000.000
169A168ILE0-0.027-0.00641.2790.0020.0020.0000.0000.0000.000
170A169LEU00.014-0.00643.6970.0030.0030.0000.0000.0000.000
171A170GLY00.0300.02344.4900.0030.0030.0000.0000.0000.000
172A171VAL0-0.057-0.02440.7490.0020.0020.0000.0000.0000.000
173A172LEU0-0.059-0.04244.0830.0030.0030.0000.0000.0000.000
174A173THR0-0.074-0.02946.9900.0030.0030.0000.0000.0000.000
175A174PRO00.0480.02446.9190.0000.0000.0000.0000.0000.000
176A175GLY0-0.015-0.00348.8210.0000.0000.0000.0000.0000.000
177A176GLU-1-0.957-0.99052.469-0.032-0.0320.0000.0000.0000.000
178A177THR0-0.048-0.02547.426-0.001-0.0010.0000.0000.0000.000
179A178SER00.0400.03647.602-0.003-0.0030.0000.0000.0000.000
180A179SER00.0240.00444.444-0.002-0.0020.0000.0000.0000.000
181A180GLU-1-0.866-0.95546.544-0.041-0.0410.0000.0000.0000.000
182A181ARG10.9210.96249.5820.0360.0360.0000.0000.0000.000
183A182GLN00.004-0.01643.891-0.003-0.0030.0000.0000.0000.000
184A183LEU0-0.018-0.00944.193-0.002-0.0020.0000.0000.0000.000
185A184GLU-1-0.855-0.90447.757-0.042-0.0420.0000.0000.0000.000
186A185MET0-0.068-0.03249.1500.0000.0000.0000.0000.0000.000
187A186LEU00.0180.01144.334-0.001-0.0010.0000.0000.0000.000
188A187GLU-1-0.873-0.94248.280-0.056-0.0560.0000.0000.0000.000
189A188GLN0-0.090-0.06950.7300.0010.0010.0000.0000.0000.000
190A189PHE0-0.030-0.01048.0850.0010.0010.0000.0000.0000.000
191A190VAL00.002-0.01947.4570.0000.0000.0000.0000.0000.000
192A191ALA0-0.030-0.00450.7780.0000.0000.0000.0000.0000.000
193A192ALA0-0.066-0.02154.2780.0020.0020.0000.0000.0000.000
194A193LEU0-0.0220.01949.3690.0000.0000.0000.0000.0000.000