FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

tag_button

FMODB ID: 1NJ6Z

Calculation Name: 3IBX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IBX

Chain ID: A

ChEMBL ID:

UniProt ID: A8KRL3

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:

Apendix: None


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 221
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2829054.724917
FMO2-HF: Nuclear repulsion 2739037.647107
FMO2-HF: Total energy -90017.07781
FMO2-MP2: Total energy -90277.854972


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:-3:ASP)


Summations of interaction energy for fragment #1(A:-3:ASP)
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.
83.69378.9424.5243.567-3.34-0.001
Interaction energy analysis for fragmet #1(A:-3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.927 / q_NPA : -0.966
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].
3A-1PHE0-0.046-0.0242.832-0.068-4.512-0.1165.482-0.921-0.003
4A0THR0-0.0100.0102.169-8.913-9.6054.642-1.895-2.0550.002
5A1MET0-0.022-0.0014.5922.1852.324-0.001-0.009-0.1290.000
6A2GLN00.0210.0104.6943.1763.422-0.001-0.011-0.2350.000
7A3VAL00.052-0.0036.882-5.116-5.1160.0000.0000.0000.000
8A4SER0-0.015-0.0298.491-3.916-3.9160.0000.0000.0000.000
9A5GLN0-0.002-0.0039.116-4.554-4.5540.0000.0000.0000.000
10A6TYR0-0.053-0.04211.273-2.534-2.5340.0000.0000.0000.000
11A7LEU0-0.023-0.00613.266-1.985-1.9850.0000.0000.0000.000
12A8TYR00.0010.00214.312-1.243-1.2430.0000.0000.0000.000
13A9GLN0-0.003-0.01114.993-2.339-2.3390.0000.0000.0000.000
14A10ASN0-0.084-0.05217.008-1.802-1.8020.0000.0000.0000.000
15A11ALA00.0360.03219.176-0.820-0.8200.0000.0000.0000.000
16A12GLN0-0.040-0.01418.972-1.008-1.0080.0000.0000.0000.000
17A13SER00.006-0.00221.895-0.549-0.5490.0000.0000.0000.000
18A14ILE00.0430.03324.238-0.375-0.3750.0000.0000.0000.000
19A15TRP00.019-0.01418.129-0.182-0.1820.0000.0000.0000.000
20A16GLY0-0.0030.00825.081-0.260-0.2600.0000.0000.0000.000
21A17ASP-1-0.878-0.94027.01810.30810.3080.0000.0000.0000.000
22A18CYS0-0.095-0.04727.527-0.370-0.3700.0000.0000.0000.000
23A19ILE0-0.015-0.00625.248-0.371-0.3710.0000.0000.0000.000
24A20SER0-0.069-0.03229.569-0.426-0.4260.0000.0000.0000.000
25A21HIS00.0260.01532.545-0.342-0.3420.0000.0000.0000.000
26A22PRO00.001-0.01434.489-0.001-0.0010.0000.0000.0000.000
27A23PHE00.0200.00434.917-0.138-0.1380.0000.0000.0000.000
28A24VAL00.0480.02730.560-0.082-0.0820.0000.0000.0000.000
29A25GLN0-0.018-0.01632.661-0.266-0.2660.0000.0000.0000.000
30A26GLY0-0.012-0.00835.638-0.156-0.1560.0000.0000.0000.000
31A27ILE0-0.033-0.01633.919-0.201-0.2010.0000.0000.0000.000
32A28GLY00.0080.01134.604-0.052-0.0520.0000.0000.0000.000
33A29ARG10.8780.93735.252-8.544-8.5440.0000.0000.0000.000
34A30GLY00.0420.01038.793-0.137-0.1370.0000.0000.0000.000
35A31THR0-0.077-0.05040.629-0.156-0.1560.0000.0000.0000.000
36A32LEU0-0.0320.02138.157-0.172-0.1720.0000.0000.0000.000
37A33GLU-1-0.792-0.87241.7467.3367.3360.0000.0000.0000.000
38A34ARG10.9440.96743.605-7.160-7.1600.0000.0000.0000.000
39A35ASP-1-0.921-0.96744.0907.0057.0050.0000.0000.0000.000
40A36LYS10.9110.95941.843-7.281-7.2810.0000.0000.0000.000
41A37PHE00.0120.00336.0350.1650.1650.0000.0000.0000.000
42A38ARG10.7770.86239.903-6.825-6.8250.0000.0000.0000.000
43A39PHE0-0.010-0.00140.4610.0700.0700.0000.0000.0000.000
44A40TYR00.0520.01932.0030.0080.0080.0000.0000.0000.000
45A41ILE0-0.0130.00036.7340.2080.2080.0000.0000.0000.000
46A42ILE0-0.020-0.00437.8750.1000.1000.0000.0000.0000.000
47A43GLN00.0100.00337.2720.2530.2530.0000.0000.0000.000
48A44ASP-1-0.790-0.89932.11710.29310.2930.0000.0000.0000.000
49A45TYR00.0010.00633.9480.2270.2270.0000.0000.0000.000
50A46LEU0-0.035-0.02635.6450.1160.1160.0000.0000.0000.000
51A47TYR0-0.015-0.03327.0330.0570.0570.0000.0000.0000.000
52A48LEU00.006-0.01029.3280.3270.3270.0000.0000.0000.000
53A49LEU00.0010.01231.3470.2400.2400.0000.0000.0000.000
54A50GLU-1-0.872-0.92832.5189.3559.3550.0000.0000.0000.000
55A51TYR00.010-0.00622.8170.1480.1480.0000.0000.0000.000
56A52ALA00.0340.01027.6110.4410.4410.0000.0000.0000.000
57A53LYS10.7830.87228.707-9.269-9.2690.0000.0000.0000.000
58A54VAL0-0.0060.00624.3600.0840.0840.0000.0000.0000.000
59A55PHE00.0300.00921.5340.4520.4520.0000.0000.0000.000
60A56ALA0-0.007-0.00325.1530.2750.2750.0000.0000.0000.000
61A57LEU0-0.020-0.01625.712-0.029-0.0290.0000.0000.0000.000
62A58GLY00.0250.01322.6370.2690.2690.0000.0000.0000.000
63A59VAL0-0.041-0.01922.9500.3770.3770.0000.0000.0000.000
64A60VAL0-0.058-0.03225.170-0.012-0.0120.0000.0000.0000.000
65A61LYS10.7590.86923.050-12.702-12.7020.0000.0000.0000.000
66A62ALA00.0070.02720.3430.6750.6750.0000.0000.0000.000
67A63CYS0-0.067-0.04019.188-0.626-0.6260.0000.0000.0000.000
68A64ASP-1-0.777-0.90817.45518.65618.6560.0000.0000.0000.000
69A65GLU-1-0.834-0.89619.79012.79912.7990.0000.0000.0000.000
70A66ALA0-0.020-0.00317.582-0.516-0.5160.0000.0000.0000.000
71A67VAL00.0640.02215.700-0.329-0.3290.0000.0000.0000.000
72A68MET0-0.074-0.01618.876-0.654-0.6540.0000.0000.0000.000
73A69ARG10.8250.88721.882-14.318-14.3180.0000.0000.0000.000
74A70GLU-1-0.868-0.92017.13518.53418.5340.0000.0000.0000.000
75A71PHE00.0280.01119.276-0.312-0.3120.0000.0000.0000.000
76A72SER0-0.026-0.02023.026-0.695-0.6950.0000.0000.0000.000
77A73ASN0-0.049-0.04023.404-0.910-0.9100.0000.0000.0000.000
78A74ALA00.0460.03823.033-0.365-0.3650.0000.0000.0000.000
79A75ILE0-0.025-0.00625.142-0.466-0.4660.0000.0000.0000.000
80A76GLN0-0.021-0.01428.421-0.688-0.6880.0000.0000.0000.000
81A77ASP-1-0.851-0.91626.45411.53911.5390.0000.0000.0000.000
82A78ILE0-0.092-0.03427.297-0.257-0.2570.0000.0000.0000.000
83A79LEU0-0.069-0.04230.947-0.376-0.3760.0000.0000.0000.000
84A80ASN0-0.095-0.04333.100-0.583-0.5830.0000.0000.0000.000
85A81ASN00.0680.03030.077-0.246-0.2460.0000.0000.0000.000
86A82GLU-1-0.905-0.93334.0398.9088.9080.0000.0000.0000.000
87A83MET0-0.014-0.01533.878-0.321-0.3210.0000.0000.0000.000
88A84SER0-0.0250.00432.0590.1330.1330.0000.0000.0000.000
89A85ILE00.007-0.00629.136-0.367-0.3670.0000.0000.0000.000
90A86HIS10.8660.91231.581-10.155-10.1550.0000.0000.0000.000
91A87ASN00.005-0.01235.476-0.458-0.4580.0000.0000.0000.000
92A88HIS0-0.064-0.01736.932-0.128-0.1280.0000.0000.0000.000
93A89TYR00.015-0.04135.464-0.133-0.1330.0000.0000.0000.000
94A90ILE00.0000.01538.859-0.226-0.2260.0000.0000.0000.000
95A91ARG10.8900.95139.063-8.335-8.3350.0000.0000.0000.000
96A92GLU-1-0.906-0.93842.1417.3357.3350.0000.0000.0000.000
97A93LEU0-0.057-0.03041.593-0.176-0.1760.0000.0000.0000.000
98A94GLN0-0.029-0.03045.201-0.197-0.1970.0000.0000.0000.000
99A95ILE0-0.0270.00442.392-0.142-0.1420.0000.0000.0000.000
100A96THR0-0.020-0.00645.7690.0230.0230.0000.0000.0000.000
101A97GLN00.0850.02043.0930.1660.1660.0000.0000.0000.000
102A98LYS10.9700.98046.184-6.024-6.0240.0000.0000.0000.000
103A99GLU-1-0.809-0.87646.2256.8576.8570.0000.0000.0000.000
104A100LEU00.0100.00941.1470.0490.0490.0000.0000.0000.000
105A101GLN0-0.045-0.02543.4470.0960.0960.0000.0000.0000.000
106A102ASN0-0.038-0.02245.4190.0090.0090.0000.0000.0000.000
107A103ALA0-0.0080.02743.106-0.074-0.0740.0000.0000.0000.000
108A104CYS0-0.013-0.00543.4440.0530.0530.0000.0000.0000.000
109A105PRO00.0160.02238.5020.0070.0070.0000.0000.0000.000
110A106THR00.022-0.03838.807-0.110-0.1100.0000.0000.0000.000
111A107LEU00.030-0.00638.6710.1660.1660.0000.0000.0000.000
112A108ALA00.0210.03435.6610.1830.1830.0000.0000.0000.000
113A109ASN0-0.002-0.01034.3210.5210.5210.0000.0000.0000.000
114A110LYS10.9490.96834.014-7.619-7.6190.0000.0000.0000.000
115A111SER0-0.032-0.01234.3600.0900.0900.0000.0000.0000.000
116A112TYR00.000-0.02726.0400.2800.2800.0000.0000.0000.000
117A113THR00.0180.00129.6970.3090.3090.0000.0000.0000.000
118A114SER0-0.038-0.03830.6390.1220.1220.0000.0000.0000.000
119A115TYR0-0.0030.00725.1820.2110.2110.0000.0000.0000.000
120A116MET00.0200.02125.3820.4270.4270.0000.0000.0000.000
121A117LEU00.0040.00726.4610.3410.3410.0000.0000.0000.000
122A118ALA0-0.030-0.01128.6260.1370.1370.0000.0000.0000.000
123A119GLU-1-0.799-0.88524.55512.00712.0070.0000.0000.0000.000
124A120GLY00.0270.01924.1840.4320.4320.0000.0000.0000.000
125A121PHE0-0.058-0.03125.2580.1690.1690.0000.0000.0000.000
126A122LYS10.8020.87327.502-11.516-11.5160.0000.0000.0000.000
127A123GLY0-0.0210.01723.4450.0560.0560.0000.0000.0000.000
128A124SER0-0.061-0.04719.922-0.166-0.1660.0000.0000.0000.000
129A125ILE00.0820.02217.313-0.155-0.1550.0000.0000.0000.000
130A126LYS10.8640.93814.368-21.526-21.5260.0000.0000.0000.000
131A127GLU-1-0.711-0.83417.24516.10316.1030.0000.0000.0000.000
132A128VAL0-0.0050.00320.118-0.298-0.2980.0000.0000.0000.000
133A129ALA0-0.0130.00015.797-0.235-0.2350.0000.0000.0000.000
134A130ALA0-0.004-0.00716.8550.2510.2510.0000.0000.0000.000
135A131ALA0-0.024-0.01517.903-0.395-0.3950.0000.0000.0000.000
136A132VAL0-0.022-0.01019.976-0.650-0.6500.0000.0000.0000.000
137A133LEU00.0090.03414.585-0.234-0.2340.0000.0000.0000.000
138A134SER00.005-0.01418.9520.2790.2790.0000.0000.0000.000
139A135CYS0-0.0350.04421.087-0.323-0.3230.0000.0000.0000.000
140A136GLY00.0560.01921.478-0.320-0.3200.0000.0000.0000.000
141A137TRP00.025-0.00812.7300.0390.0390.0000.0000.0000.000
142A138SER00.019-0.01219.764-0.322-0.3220.0000.0000.0000.000
143A139TYR00.0370.00822.762-0.619-0.6190.0000.0000.0000.000
144A140LEU0-0.0170.01218.735-0.382-0.3820.0000.0000.0000.000
145A141VAL00.004-0.00320.025-0.349-0.3490.0000.0000.0000.000
146A142ILE0-0.0040.00222.740-0.517-0.5170.0000.0000.0000.000
147A143ALA0-0.0120.00025.954-0.459-0.4590.0000.0000.0000.000
148A144GLN0-0.010-0.02320.378-0.098-0.0980.0000.0000.0000.000
149A145ASN0-0.045-0.01325.486-0.577-0.5770.0000.0000.0000.000
150A146LEU00.022-0.00427.391-0.399-0.3990.0000.0000.0000.000
151A147SER0-0.073-0.02728.157-0.363-0.3630.0000.0000.0000.000
152A148GLN0-0.076-0.03727.254-0.087-0.0870.0000.0000.0000.000
153A149ILE0-0.0110.04731.959-0.030-0.0300.0000.0000.0000.000
154A150PRO00.017-0.01135.150-0.120-0.1200.0000.0000.0000.000
155A151ASN0-0.065-0.06536.525-0.257-0.2570.0000.0000.0000.000
156A152ALA00.0480.03634.204-0.128-0.1280.0000.0000.0000.000
157A153LEU0-0.032-0.01631.2980.0080.0080.0000.0000.0000.000
158A154GLU-1-0.896-0.96235.0068.8368.8360.0000.0000.0000.000
159A155HIS0-0.0090.02738.426-0.236-0.2360.0000.0000.0000.000
160A156ALA00.012-0.00739.5950.1110.1110.0000.0000.0000.000
161A157PHE0-0.027-0.00640.858-0.016-0.0160.0000.0000.0000.000
162A158TYR00.025-0.01937.0740.0800.0800.0000.0000.0000.000
163A159GLY00.0690.05935.7340.2720.2720.0000.0000.0000.000
164A160HIS0-0.010-0.01134.2630.3520.3520.0000.0000.0000.000
165A161TRP00.0270.01129.6460.2940.2940.0000.0000.0000.000
166A162ILE00.0290.02330.2590.4020.4020.0000.0000.0000.000
167A163LYS10.9200.98229.301-9.155-9.1550.0000.0000.0000.000
168A164GLY0-0.002-0.00628.8610.3450.3450.0000.0000.0000.000
169A165TYR00.0050.00026.1270.2250.2250.0000.0000.0000.000
170A166SER00.001-0.02224.6110.5240.5240.0000.0000.0000.000
171A167SER0-0.056-0.00724.7280.4590.4590.0000.0000.0000.000
172A168LYS10.8900.90822.425-11.710-11.7100.0000.0000.0000.000
173A169GLU-1-0.785-0.88521.59413.02313.0230.0000.0000.0000.000
174A170PHE00.0380.03122.2650.4680.4680.0000.0000.0000.000
175A171GLN0-0.018-0.02418.9441.1871.1870.0000.0000.0000.000
176A172ALA0-0.030-0.00217.7181.2241.2240.0000.0000.0000.000
177A173CYS0-0.020-0.00217.5640.7280.7280.0000.0000.0000.000
178A174VAL00.0340.01616.3110.6990.6990.0000.0000.0000.000
179A175ASN0-0.029-0.03013.6362.2702.2700.0000.0000.0000.000
180A176TRP0-0.067-0.02212.9221.9141.9140.0000.0000.0000.000
181A177ASN00.006-0.00713.9190.3130.3130.0000.0000.0000.000
182A178ILE00.0050.00110.0520.6490.6490.0000.0000.0000.000
183A179ASN0-0.002-0.0109.1064.8394.8390.0000.0000.0000.000
184A180LEU0-0.0210.0139.7472.3512.3510.0000.0000.0000.000
185A181LEU00.0290.00611.8140.6490.6490.0000.0000.0000.000
186A182ASP-1-0.746-0.8436.34939.38039.3800.0000.0000.0000.000
187A183SER0-0.068-0.0297.7901.9161.9160.0000.0000.0000.000
188A184LEU0-0.011-0.0068.892-1.324-1.3240.0000.0000.0000.000
189A185THR0-0.065-0.05810.127-1.367-1.3670.0000.0000.0000.000
190A186LEU00.0150.0205.304-0.470-0.4700.0000.0000.0000.000
191A187ALA0-0.025-0.0138.4590.0620.0620.0000.0000.0000.000
192A188SER0-0.092-0.05611.194-1.889-1.8890.0000.0000.0000.000
193A189SER0-0.047-0.03712.9770.5310.5310.0000.0000.0000.000
194A190LYN00.0930.01715.3900.5090.5090.0000.0000.0000.000
195A191GLN0-0.0040.00016.795-0.102-0.1020.0000.0000.0000.000
196A192GLU-1-0.773-0.84516.61819.42219.4220.0000.0000.0000.000
197A193ILE00.0120.00512.125-0.203-0.2030.0000.0000.0000.000
198A194GLU-1-0.781-0.86815.86316.59816.5980.0000.0000.0000.000
199A195LYS10.8940.94519.156-14.800-14.8000.0000.0000.0000.000
200A196LEU0-0.012-0.01614.989-0.427-0.4270.0000.0000.0000.000
201A197LYS10.8310.90617.378-16.610-16.6100.0000.0000.0000.000
202A198GLU-1-0.925-0.95618.56612.38612.3860.0000.0000.0000.000
203A199ILE0-0.0020.01520.694-0.601-0.6010.0000.0000.0000.000
204A200PHE00.0120.00817.507-0.397-0.3970.0000.0000.0000.000
205A201ILE00.0290.01520.464-0.288-0.2880.0000.0000.0000.000
206A202THR00.0040.00122.840-0.705-0.7050.0000.0000.0000.000
207A203THR0-0.051-0.03222.839-0.354-0.3540.0000.0000.0000.000
208A204SER00.0000.00122.234-0.245-0.2450.0000.0000.0000.000
209A205GLU-1-0.938-0.96824.88910.90210.9020.0000.0000.0000.000
210A206TYR0-0.032-0.03328.122-0.664-0.6640.0000.0000.0000.000
211A207GLU-1-0.748-0.84725.52211.47411.4740.0000.0000.0000.000
212A208TYR00.0000.00228.791-0.358-0.3580.0000.0000.0000.000
213A209LEU0-0.018-0.01730.695-0.418-0.4180.0000.0000.0000.000
214A210PHE0-0.040-0.01131.757-0.436-0.4360.0000.0000.0000.000
215A211TRP00.0220.00628.900-0.516-0.5160.0000.0000.0000.000
216A212ASP-1-0.869-0.91634.1928.2748.2740.0000.0000.0000.000
217A213MET0-0.0640.00736.015-0.449-0.4490.0000.0000.0000.000
218A214ALA0-0.003-0.00136.665-0.235-0.2350.0000.0000.0000.000
219A215TYR0-0.009-0.00738.480-0.241-0.2410.0000.0000.0000.000
220A216GLN0-0.080-0.03740.206-0.328-0.3280.0000.0000.0000.000
221A217SER0-0.043-0.01342.499-0.189-0.1890.0000.0000.0000.000