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

tag_button

FMODB ID: GY5Z1

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2098703.946094
FMO2-HF: Nuclear repulsion 2020509.230938
FMO2-HF: Total energy -78194.715156
FMO2-MP2: Total energy -78416.469598


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.
-0.00500000000000041.172-0.004-0.582-0.5910.003
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 : 0.034 / 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].
3A2PRO00.0150.0063.8660.2341.411-0.004-0.582-0.5910.003
4A3LYS10.9650.9796.3111.1351.1350.0000.0000.0000.000
5A4LEU00.0230.0128.5410.1790.1790.0000.0000.0000.000
6A5VAL00.0340.0278.2180.1500.1500.0000.0000.0000.000
7A6ASP-1-0.737-0.8518.166-0.408-0.4080.0000.0000.0000.000
8A7HIS0-0.072-0.0659.8590.2760.2760.0000.0000.0000.000
9A8ASP-1-0.809-0.90813.134-0.546-0.5460.0000.0000.0000.000
10A9GLU-1-0.935-0.9699.977-1.019-1.0190.0000.0000.0000.000
11A10ARG10.8390.92211.6660.4640.4640.0000.0000.0000.000
12A11ARG10.7770.86715.2370.4930.4930.0000.0000.0000.000
13A12ARG10.8190.86016.4750.4950.4950.0000.0000.0000.000
14A13SER0-0.040-0.03116.3360.0530.0530.0000.0000.0000.000
15A14ILE0-0.044-0.02418.6770.0420.0420.0000.0000.0000.000
16A15THR0-0.036-0.00321.2010.0180.0180.0000.0000.0000.000
17A16ALA00.0390.01921.9830.0210.0210.0000.0000.0000.000
18A17ALA0-0.074-0.01823.6770.0190.0190.0000.0000.0000.000
19A18ALA00.011-0.00125.3490.0100.0100.0000.0000.0000.000
20A19TRP0-0.011-0.00526.6910.0090.0090.0000.0000.0000.000
21A20ARG10.8610.90127.9190.1290.1290.0000.0000.0000.000
22A21LEU0-0.0080.01231.0870.0080.0080.0000.0000.0000.000
23A22ILE0-0.033-0.03228.8030.0070.0070.0000.0000.0000.000
24A23ALA00.0040.02232.8690.0050.0050.0000.0000.0000.000
25A24ALA0-0.0010.00434.8950.0060.0060.0000.0000.0000.000
26A25ARG10.8070.88835.2800.0800.0800.0000.0000.0000.000
27A26GLY00.0810.05836.8360.0040.0040.0000.0000.0000.000
28A27ILE00.016-0.00631.5670.0030.0030.0000.0000.0000.000
29A28GLU-1-0.816-0.90234.970-0.109-0.1090.0000.0000.0000.000
30A29ALA0-0.0110.01137.6870.0040.0040.0000.0000.0000.000
31A30ALA0-0.0340.00032.5450.0040.0040.0000.0000.0000.000
32A31ASN0-0.030-0.02932.985-0.003-0.0030.0000.0000.0000.000
33A32MET00.0630.02327.621-0.004-0.0040.0000.0000.0000.000
34A33ARG10.8870.93628.4680.0540.0540.0000.0000.0000.000
35A34ASP-1-0.815-0.85829.936-0.062-0.0620.0000.0000.0000.000
36A35ILE00.0450.02526.0580.0020.0020.0000.0000.0000.000
37A36ALA0-0.023-0.00325.246-0.006-0.0060.0000.0000.0000.000
38A37THR0-0.037-0.04225.7700.0070.0070.0000.0000.0000.000
39A38GLU-1-0.881-0.95327.807-0.090-0.0900.0000.0000.0000.000
40A39ALA00.0140.01322.704-0.002-0.0020.0000.0000.0000.000
41A40GLY0-0.0180.00822.714-0.003-0.0030.0000.0000.0000.000
42A41TYR0-0.031-0.01717.087-0.004-0.0040.0000.0000.0000.000
43A42THR00.011-0.00222.7690.0020.0020.0000.0000.0000.000
44A43ASN00.035-0.01023.830-0.010-0.0100.0000.0000.0000.000
45A44GLY00.0180.01523.905-0.012-0.0120.0000.0000.0000.000
46A45ALA0-0.007-0.00119.607-0.016-0.0160.0000.0000.0000.000
47A46LEU00.0260.01019.750-0.028-0.0280.0000.0000.0000.000
48A47SER00.000-0.01121.536-0.019-0.0190.0000.0000.0000.000
49A48HIS0-0.114-0.03914.6610.0190.0190.0000.0000.0000.000
50A49TYR0-0.075-0.02512.6300.0030.0030.0000.0000.0000.000
51A50PHE00.0090.00618.654-0.031-0.0310.0000.0000.0000.000
52A51ALA00.0090.01622.1740.0230.0230.0000.0000.0000.000
53A52GLY00.011-0.01124.8660.0230.0230.0000.0000.0000.000
54A53LYS10.8220.89027.0310.0950.0950.0000.0000.0000.000
55A54ASP-1-0.811-0.89229.168-0.165-0.1650.0000.0000.0000.000
56A55GLU-1-0.775-0.87322.450-0.317-0.3170.0000.0000.0000.000
57A56ILE00.0010.00524.366-0.010-0.0100.0000.0000.0000.000
58A57LEU0-0.0170.01426.1100.0000.0000.0000.0000.0000.000
59A58ARG10.8650.92522.8130.3030.3030.0000.0000.0000.000
60A59THR0-0.004-0.01921.6810.0000.0000.0000.0000.0000.000
61A60SER0-0.025-0.04524.614-0.002-0.0020.0000.0000.0000.000
62A61TYR00.0400.01027.1730.0080.0080.0000.0000.0000.000
63A62GLU-1-0.801-0.87923.578-0.309-0.3090.0000.0000.0000.000
64A63HIS00.000-0.00123.270-0.005-0.0050.0000.0000.0000.000
65A64ILE00.0030.00225.1320.0040.0040.0000.0000.0000.000
66A65SER0-0.0200.00927.3760.0130.0130.0000.0000.0000.000
67A66GLU-1-0.803-0.85821.472-0.370-0.3700.0000.0000.0000.000
68A67ALA0-0.044-0.01625.7460.0060.0060.0000.0000.0000.000
69A68THR00.0240.00327.4550.0130.0130.0000.0000.0000.000
70A69ASP-1-0.813-0.90427.798-0.192-0.1920.0000.0000.0000.000
71A70ARG10.7360.83824.3960.1700.1700.0000.0000.0000.000
72A71ARG10.7380.84127.7710.1410.1410.0000.0000.0000.000
73A72ILE00.0140.01231.2200.0090.0090.0000.0000.0000.000
74A73ALA0-0.015-0.01228.7240.0070.0070.0000.0000.0000.000
75A74GLU-1-0.885-0.91226.651-0.148-0.1480.0000.0000.0000.000
76A75ALA0-0.027-0.00931.0100.0100.0100.0000.0000.0000.000
77A76LEU0-0.028-0.01233.8500.0070.0070.0000.0000.0000.000
78A77GLY0-0.036-0.01434.6680.0070.0070.0000.0000.0000.000
79A78ASP-1-0.978-0.99335.668-0.083-0.0830.0000.0000.0000.000
80A79ALA0-0.0190.00838.4390.0040.0040.0000.0000.0000.000
81A80THR0-0.046-0.04540.061-0.005-0.0050.0000.0000.0000.000
82A81GLY00.0600.03642.6560.0020.0020.0000.0000.0000.000
83A82LEU00.000-0.02243.971-0.004-0.0040.0000.0000.0000.000
84A83ASP-1-0.875-0.91644.005-0.068-0.0680.0000.0000.0000.000
85A84ALA00.0060.00539.530-0.002-0.0020.0000.0000.0000.000
86A85LEU0-0.007-0.00139.874-0.006-0.0060.0000.0000.0000.000
87A86ARG10.7860.85841.6280.0630.0630.0000.0000.0000.000
88A87ILE0-0.056-0.01937.052-0.001-0.0010.0000.0000.0000.000
89A88LEU00.0390.01736.344-0.003-0.0030.0000.0000.0000.000
90A89CYS0-0.007-0.02637.839-0.003-0.0030.0000.0000.0000.000
91A90ARG10.9070.94940.0730.0780.0780.0000.0000.0000.000
92A91GLU-1-0.872-0.92934.615-0.105-0.1050.0000.0000.0000.000
93A92VAL00.0160.02235.566-0.007-0.0070.0000.0000.0000.000
94A93MET0-0.0190.00937.4200.0020.0020.0000.0000.0000.000
95A94PRO0-0.0140.00739.510-0.001-0.0010.0000.0000.0000.000
96A95ILE00.0040.00440.3300.0060.0060.0000.0000.0000.000
97A96ASN0-0.052-0.03637.4320.0040.0040.0000.0000.0000.000
98A97GLU-1-0.860-0.94038.475-0.080-0.0800.0000.0000.0000.000
99A98GLU-1-0.767-0.85331.325-0.117-0.1170.0000.0000.0000.000
100A99GLN00.0720.03334.966-0.006-0.0060.0000.0000.0000.000
101A100LEU00.0120.02136.522-0.003-0.0030.0000.0000.0000.000
102A101LEU0-0.073-0.03534.446-0.002-0.0020.0000.0000.0000.000
103A102GLU-1-0.817-0.90231.243-0.150-0.1500.0000.0000.0000.000
104A103ALA00.0490.03234.192-0.005-0.0050.0000.0000.0000.000
105A104ARG10.8350.91936.8780.0840.0840.0000.0000.0000.000
106A105ILE0-0.052-0.02030.657-0.001-0.0010.0000.0000.0000.000
107A106ALA00.016-0.00334.070-0.006-0.0060.0000.0000.0000.000
108A107ALA00.0030.00435.402-0.001-0.0010.0000.0000.0000.000
109A108SER0-0.049-0.02334.9930.0050.0050.0000.0000.0000.000
110A109LEU0-0.019-0.00231.026-0.001-0.0010.0000.0000.0000.000
111A110TRP00.006-0.00734.2770.0020.0020.0000.0000.0000.000
112A111PRO00.002-0.01036.933-0.001-0.0010.0000.0000.0000.000
113A112ARG10.7900.86533.8560.1340.1340.0000.0000.0000.000
114A113ALA00.019-0.00133.712-0.004-0.0040.0000.0000.0000.000
115A114MET0-0.067-0.01334.9680.0010.0010.0000.0000.0000.000
116A115TYR0-0.066-0.03036.8780.0070.0070.0000.0000.0000.000
117A116ASP-1-0.788-0.89130.545-0.209-0.2090.0000.0000.0000.000
118A117GLU-1-0.874-0.93331.679-0.175-0.1750.0000.0000.0000.000
119A118GLN0-0.102-0.06025.552-0.034-0.0340.0000.0000.0000.000
120A119MET0-0.063-0.03228.476-0.014-0.0140.0000.0000.0000.000
121A120ALA00.0170.02630.5590.0030.0030.0000.0000.0000.000
122A121ALA0-0.045-0.02028.050-0.001-0.0010.0000.0000.0000.000
123A122THR0-0.078-0.06025.0380.0000.0000.0000.0000.0000.000
124A123ASN00.0740.05128.1240.0040.0040.0000.0000.0000.000
125A124ARG10.8610.90731.6490.1740.1740.0000.0000.0000.000
126A125ARG10.9400.97625.3230.2940.2940.0000.0000.0000.000
127A126THR00.0260.02029.827-0.003-0.0030.0000.0000.0000.000
128A127MET0-0.025-0.00731.3830.0120.0120.0000.0000.0000.000
129A128ASP-1-0.775-0.87233.686-0.153-0.1530.0000.0000.0000.000
130A129ASN0-0.0040.01330.1340.0120.0120.0000.0000.0000.000
131A130TRP0-0.001-0.02532.2250.0120.0120.0000.0000.0000.000
132A131ARG10.8080.86135.8350.1370.1370.0000.0000.0000.000
133A132GLU-1-0.959-0.97634.008-0.162-0.1620.0000.0000.0000.000
134A133GLN0-0.032-0.02932.0730.0140.0140.0000.0000.0000.000
135A134MET0-0.023-0.01137.0400.0060.0060.0000.0000.0000.000
136A135ALA00.0140.00040.3240.0070.0070.0000.0000.0000.000
137A136ILE0-0.024-0.00636.8980.0060.0060.0000.0000.0000.000
138A137PHE00.001-0.00536.5760.0050.0050.0000.0000.0000.000
139A138LEU00.003-0.00842.3220.0060.0060.0000.0000.0000.000
140A139GLU-1-0.830-0.90244.580-0.076-0.0760.0000.0000.0000.000
141A140GLN00.0230.00940.8800.0040.0040.0000.0000.0000.000
142A141ALA00.0230.01245.7840.0040.0040.0000.0000.0000.000
143A142ARG10.7210.84348.2550.0760.0760.0000.0000.0000.000
144A143GLU-1-1.003-1.00147.117-0.074-0.0740.0000.0000.0000.000
145A144GLU-1-0.868-0.91846.555-0.069-0.0690.0000.0000.0000.000
146A145GLY0-0.055-0.01150.9540.0030.0030.0000.0000.0000.000
147A146SER0-0.089-0.06149.3220.0020.0020.0000.0000.0000.000
148A147VAL0-0.028-0.01250.3150.0000.0000.0000.0000.0000.000
149A148GLY00.0230.00753.0350.0010.0010.0000.0000.0000.000
150A149ASP-1-0.871-0.92453.619-0.065-0.0650.0000.0000.0000.000
151A150ILE0-0.030-0.01749.1420.0000.0000.0000.0000.0000.000
152A151ASP-1-0.829-0.91149.832-0.082-0.0820.0000.0000.0000.000
153A152VAL00.0390.01745.079-0.001-0.0010.0000.0000.0000.000
154A153THR0-0.015-0.02045.044-0.005-0.0050.0000.0000.0000.000
155A154ILE0-0.052-0.02346.143-0.003-0.0030.0000.0000.0000.000
156A155VAL00.0140.01147.548-0.001-0.0010.0000.0000.0000.000
157A156VAL00.0080.01641.703-0.001-0.0010.0000.0000.0000.000
158A157GLU-1-0.784-0.85442.838-0.115-0.1150.0000.0000.0000.000
159A158GLN0-0.043-0.02544.9370.0000.0000.0000.0000.0000.000
160A159LEU00.0360.02343.9410.0010.0010.0000.0000.0000.000
161A160LEU00.0260.01738.643-0.001-0.0010.0000.0000.0000.000
162A161ASN0-0.062-0.06042.474-0.002-0.0020.0000.0000.0000.000
163A162MET0-0.0370.00344.5340.0020.0020.0000.0000.0000.000
164A163MET00.0190.01440.3080.0020.0020.0000.0000.0000.000
165A164MET0-0.033-0.00337.910-0.004-0.0040.0000.0000.0000.000
166A165GLY00.0260.00541.7380.0010.0010.0000.0000.0000.000
167A166MET0-0.035-0.02143.5370.0020.0020.0000.0000.0000.000
168A167GLN0-0.047-0.02038.2350.0000.0000.0000.0000.0000.000
169A168ILE0-0.020-0.00641.4690.0010.0010.0000.0000.0000.000
170A169LEU00.013-0.00343.9310.0030.0030.0000.0000.0000.000
171A170GLY00.0380.02844.6260.0040.0040.0000.0000.0000.000
172A171VAL0-0.057-0.02640.9330.0030.0030.0000.0000.0000.000
173A172LEU0-0.079-0.04144.2700.0030.0030.0000.0000.0000.000
174A173THR0-0.086-0.03847.4520.0030.0030.0000.0000.0000.000
175A174PRO00.0630.02647.3470.0000.0000.0000.0000.0000.000
176A175GLY0-0.0010.00349.1100.0010.0010.0000.0000.0000.000
177A176GLU-1-0.970-1.00052.423-0.052-0.0520.0000.0000.0000.000
178A177THR0-0.005-0.00847.2890.0000.0000.0000.0000.0000.000
179A178SER00.005-0.01547.412-0.004-0.0040.0000.0000.0000.000
180A179SER0-0.013-0.02644.279-0.001-0.0010.0000.0000.0000.000
181A180GLU-1-0.812-0.89246.478-0.056-0.0560.0000.0000.0000.000
182A181ARG10.8900.96349.6120.0530.0530.0000.0000.0000.000
183A182GLN00.003-0.02843.694-0.003-0.0030.0000.0000.0000.000
184A183LEU0-0.008-0.00744.287-0.001-0.0010.0000.0000.0000.000
185A184GLU-1-0.867-0.90847.743-0.051-0.0510.0000.0000.0000.000
186A185MET0-0.052-0.03349.3470.0010.0010.0000.0000.0000.000
187A186LEU00.0210.01344.257-0.001-0.0010.0000.0000.0000.000
188A187GLU-1-0.807-0.88648.049-0.065-0.0650.0000.0000.0000.000
189A188GLN0-0.094-0.06950.6700.0010.0010.0000.0000.0000.000
190A189PHE0-0.031-0.01248.1720.0010.0010.0000.0000.0000.000
191A190VAL00.019-0.00947.4600.0000.0000.0000.0000.0000.000
192A191ALA0-0.0140.00450.7610.0010.0010.0000.0000.0000.000
193A192ALA0-0.061-0.02754.3240.0020.0020.0000.0000.0000.000
194A193LEU0-0.076-0.01249.4230.0010.0010.0000.0000.0000.000