Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: G5QY1

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:


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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2841211.662585
FMO2-HF: Nuclear repulsion 2751194.262182
FMO2-HF: Total energy -90017.400403
FMO2-MP2: Total energy -90278.151842


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.
80.36775.6481.6786.708-3.666-0.005
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 : -0.912 / q_NPA : -0.937
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-1PHE0-0.065-0.0332.6064.314-2.1620.0497.941-1.514-0.007
4A0THR00.012-0.0012.265-10.268-8.9421.632-1.213-1.7440.002
5A1MET0-0.027-0.0024.7430.4560.523-0.001-0.003-0.0630.000
6A2GLN00.000-0.0034.4660.4340.663-0.001-0.013-0.2150.000
7A3VAL00.0550.0096.670-5.456-5.4560.0000.0000.0000.000
8A4SER0-0.044-0.0478.554-3.833-3.8330.0000.0000.0000.000
9A5GLN00.0140.0048.764-4.872-4.8720.0000.0000.0000.000
10A6TYR0-0.039-0.03511.059-2.625-2.6250.0000.0000.0000.000
11A7LEU0-0.030-0.01113.043-2.019-2.0190.0000.0000.0000.000
12A8TYR00.0010.00514.207-1.247-1.2470.0000.0000.0000.000
13A9GLN00.004-0.00314.658-2.404-2.4040.0000.0000.0000.000
14A10ASN0-0.093-0.06016.664-1.902-1.9020.0000.0000.0000.000
15A11ALA00.0380.02819.281-0.819-0.8190.0000.0000.0000.000
16A12GLN0-0.043-0.02518.898-1.013-1.0130.0000.0000.0000.000
17A13SER0-0.041-0.00621.851-0.497-0.4970.0000.0000.0000.000
18A14ILE00.0680.04324.123-0.300-0.3000.0000.0000.0000.000
19A15TRP00.022-0.00418.173-0.132-0.1320.0000.0000.0000.000
20A16GLY00.0200.01724.957-0.255-0.2550.0000.0000.0000.000
21A17ASP-1-0.867-0.93527.00210.48910.4890.0000.0000.0000.000
22A18CYS0-0.075-0.03927.491-0.414-0.4140.0000.0000.0000.000
23A19ILE0-0.025-0.01024.976-0.362-0.3620.0000.0000.0000.000
24A20SER0-0.071-0.04329.391-0.448-0.4480.0000.0000.0000.000
25A21HIS00.0190.01332.351-0.365-0.3650.0000.0000.0000.000
26A22PRO0-0.003-0.01634.336-0.018-0.0180.0000.0000.0000.000
27A23PHE00.0210.00735.171-0.142-0.1420.0000.0000.0000.000
28A24VAL00.0270.02030.472-0.095-0.0950.0000.0000.0000.000
29A25GLN00.015-0.00432.631-0.277-0.2770.0000.0000.0000.000
30A26GLY00.0120.00935.519-0.112-0.1120.0000.0000.0000.000
31A27ILE0-0.042-0.01933.599-0.213-0.2130.0000.0000.0000.000
32A28GLY00.0260.01634.603-0.066-0.0660.0000.0000.0000.000
33A29ARG10.8430.90635.344-8.598-8.5980.0000.0000.0000.000
34A30GLY00.0170.00938.662-0.193-0.1930.0000.0000.0000.000
35A31THR0-0.058-0.04640.357-0.166-0.1660.0000.0000.0000.000
36A32LEU0-0.0360.01338.151-0.153-0.1530.0000.0000.0000.000
37A33GLU-1-0.765-0.85041.6787.3687.3680.0000.0000.0000.000
38A34ARG10.9260.95743.399-7.176-7.1760.0000.0000.0000.000
39A35ASP-1-0.885-0.94744.1047.0617.0610.0000.0000.0000.000
40A36LYS10.8940.96041.843-7.285-7.2850.0000.0000.0000.000
41A37PHE00.0190.00536.2050.1680.1680.0000.0000.0000.000
42A38ARG10.7480.84040.008-6.798-6.7980.0000.0000.0000.000
43A39PHE0-0.011-0.01140.4420.0480.0480.0000.0000.0000.000
44A40TYR00.0310.00832.5730.0410.0410.0000.0000.0000.000
45A41ILE0-0.012-0.00336.4960.2090.2090.0000.0000.0000.000
46A42ILE0-0.0150.00337.8320.1010.1010.0000.0000.0000.000
47A43GLN00.0170.01137.3010.2500.2500.0000.0000.0000.000
48A44ASP-1-0.750-0.86832.02610.32410.3240.0000.0000.0000.000
49A45TYR00.0080.00533.7860.2370.2370.0000.0000.0000.000
50A46LEU0-0.040-0.03435.5460.1160.1160.0000.0000.0000.000
51A47TYR0-0.008-0.02727.0670.0290.0290.0000.0000.0000.000
52A48LEU00.0180.00229.1200.3060.3060.0000.0000.0000.000
53A49LEU0-0.0010.00831.5970.2200.2200.0000.0000.0000.000
54A50GLU-1-0.867-0.90532.5619.2919.2910.0000.0000.0000.000
55A51TYR0-0.012-0.02522.9440.1420.1420.0000.0000.0000.000
56A52ALA00.0370.01527.6320.4310.4310.0000.0000.0000.000
57A53LYS10.7790.85729.070-9.304-9.3040.0000.0000.0000.000
58A54VAL0-0.0040.00624.6360.0860.0860.0000.0000.0000.000
59A55PHE00.0470.01421.8620.4470.4470.0000.0000.0000.000
60A56ALA0-0.015-0.00325.3620.2410.2410.0000.0000.0000.000
61A57LEU0-0.029-0.02626.156-0.037-0.0370.0000.0000.0000.000
62A58GLY00.0100.00922.7080.2810.2810.0000.0000.0000.000
63A59VAL0-0.043-0.02622.9500.3250.3250.0000.0000.0000.000
64A60VAL0-0.038-0.02525.1340.0120.0120.0000.0000.0000.000
65A61LYS10.7790.88122.892-12.775-12.7750.0000.0000.0000.000
66A62ALA0-0.0070.01620.4840.7520.7520.0000.0000.0000.000
67A63CYS0-0.050-0.03618.781-0.501-0.5010.0000.0000.0000.000
68A64ASP-1-0.809-0.91617.90717.72117.7210.0000.0000.0000.000
69A65GLU-1-0.823-0.88219.90412.44212.4420.0000.0000.0000.000
70A66ALA0-0.040-0.01617.799-0.547-0.5470.0000.0000.0000.000
71A67VAL00.0740.02315.964-0.461-0.4610.0000.0000.0000.000
72A68MET0-0.072-0.02219.073-0.673-0.6730.0000.0000.0000.000
73A69ARG10.8200.88821.955-14.121-14.1210.0000.0000.0000.000
74A70GLU-1-0.868-0.92217.56117.96217.9620.0000.0000.0000.000
75A71PHE00.0230.00719.474-0.276-0.2760.0000.0000.0000.000
76A72SER0-0.006-0.00823.181-0.670-0.6700.0000.0000.0000.000
77A73ASN0-0.046-0.03023.800-0.874-0.8740.0000.0000.0000.000
78A74ALA00.0490.03123.506-0.407-0.4070.0000.0000.0000.000
79A75ILE0-0.032-0.00425.636-0.414-0.4140.0000.0000.0000.000
80A76GLN0-0.007-0.00228.983-0.733-0.7330.0000.0000.0000.000
81A77ASP-1-0.870-0.93226.76111.42511.4250.0000.0000.0000.000
82A78ILE0-0.093-0.03227.962-0.174-0.1740.0000.0000.0000.000
83A79LEU0-0.063-0.04531.629-0.362-0.3620.0000.0000.0000.000
84A80ASN0-0.098-0.04933.602-0.578-0.5780.0000.0000.0000.000
85A81ASN00.0540.03130.419-0.227-0.2270.0000.0000.0000.000
86A82GLU-1-0.866-0.92134.3238.8908.8900.0000.0000.0000.000
87A83MET0-0.009-0.01034.385-0.283-0.2830.0000.0000.0000.000
88A84SER0-0.0260.00432.2290.0740.0740.0000.0000.0000.000
89A85ILE00.000-0.00529.619-0.366-0.3660.0000.0000.0000.000
90A86HIS10.8650.91831.604-10.142-10.1420.0000.0000.0000.000
91A87ASN00.008-0.00835.908-0.454-0.4540.0000.0000.0000.000
92A88HIS0-0.058-0.02637.198-0.162-0.1620.0000.0000.0000.000
93A89TYR00.009-0.04535.493-0.132-0.1320.0000.0000.0000.000
94A90ILE0-0.0020.00239.172-0.215-0.2150.0000.0000.0000.000
95A91ARG10.8520.93139.051-8.323-8.3230.0000.0000.0000.000
96A92GLU-1-0.890-0.93142.0327.3727.3720.0000.0000.0000.000
97A93LEU0-0.043-0.02041.647-0.149-0.1490.0000.0000.0000.000
98A94GLN0-0.015-0.01145.305-0.208-0.2080.0000.0000.0000.000
99A95ILE0-0.0120.01642.389-0.127-0.1270.0000.0000.0000.000
100A96THR0-0.033-0.01346.147-0.003-0.0030.0000.0000.0000.000
101A97GLN00.0640.01643.3270.1650.1650.0000.0000.0000.000
102A98LYS10.9820.98546.339-6.012-6.0120.0000.0000.0000.000
103A99GLU-1-0.803-0.87246.4136.8176.8170.0000.0000.0000.000
104A100LEU00.0220.01641.2430.0570.0570.0000.0000.0000.000
105A101GLN0-0.049-0.03443.8940.0530.0530.0000.0000.0000.000
106A102ASN0-0.044-0.01945.838-0.006-0.0060.0000.0000.0000.000
107A103ALA00.0040.03143.201-0.070-0.0700.0000.0000.0000.000
108A104CYS0-0.027-0.02443.356-0.006-0.0060.0000.0000.0000.000
109A105PRO00.0020.02538.409-0.008-0.0080.0000.0000.0000.000
110A106THR00.027-0.04138.644-0.089-0.0890.0000.0000.0000.000
111A107LEU00.015-0.00238.8870.1460.1460.0000.0000.0000.000
112A108ALA00.0510.04635.4920.1630.1630.0000.0000.0000.000
113A109ASN00.011-0.00434.5100.5100.5100.0000.0000.0000.000
114A110LYS10.9330.96734.316-7.583-7.5830.0000.0000.0000.000
115A111SER0-0.025-0.00434.3650.0700.0700.0000.0000.0000.000
116A112TYR0-0.012-0.03726.2300.2850.2850.0000.0000.0000.000
117A113THR0-0.004-0.01629.9320.2780.2780.0000.0000.0000.000
118A114SER0-0.032-0.03530.8770.1700.1700.0000.0000.0000.000
119A115TYR00.0020.00825.4560.1960.1960.0000.0000.0000.000
120A116MET00.0080.01825.7790.4510.4510.0000.0000.0000.000
121A117LEU0-0.0020.00126.9880.3200.3200.0000.0000.0000.000
122A118ALA0-0.0180.00029.4130.0720.0720.0000.0000.0000.000
123A119GLU-1-0.798-0.88924.99011.77611.7760.0000.0000.0000.000
124A120GLY00.0260.01924.6490.4450.4450.0000.0000.0000.000
125A121PHE0-0.054-0.02325.7140.1320.1320.0000.0000.0000.000
126A122LYS10.7760.85227.962-11.250-11.2500.0000.0000.0000.000
127A123GLY00.0020.02723.7260.1000.1000.0000.0000.0000.000
128A124SER0-0.070-0.05319.565-0.127-0.1270.0000.0000.0000.000
129A125ILE00.0650.01317.016-0.179-0.1790.0000.0000.0000.000
130A126LYS10.8390.92314.385-21.331-21.3310.0000.0000.0000.000
131A127GLU-1-0.720-0.83617.31816.00416.0040.0000.0000.0000.000
132A128VAL0-0.0030.01720.259-0.311-0.3110.0000.0000.0000.000
133A129ALA00.0190.01716.435-0.297-0.2970.0000.0000.0000.000
134A130ALA00.0090.00017.0750.2580.2580.0000.0000.0000.000
135A131ALA0-0.017-0.01518.164-0.372-0.3720.0000.0000.0000.000
136A132VAL0-0.022-0.00820.238-0.526-0.5260.0000.0000.0000.000
137A133LEU00.0080.03314.666-0.305-0.3050.0000.0000.0000.000
138A134SER0-0.003-0.01119.0190.2940.2940.0000.0000.0000.000
139A135CYS0-0.0410.04221.070-0.380-0.3800.0000.0000.0000.000
140A136GLY00.0370.01621.488-0.243-0.2430.0000.0000.0000.000
141A137TRP00.037-0.01012.6750.0250.0250.0000.0000.0000.000
142A138SER00.023-0.00519.851-0.325-0.3250.0000.0000.0000.000
143A139TYR00.028-0.00522.829-0.563-0.5630.0000.0000.0000.000
144A140LEU0-0.0210.00918.953-0.381-0.3810.0000.0000.0000.000
145A141VAL00.0020.00019.992-0.338-0.3380.0000.0000.0000.000
146A142ILE00.0050.00622.785-0.516-0.5160.0000.0000.0000.000
147A143ALA0-0.0180.00026.121-0.433-0.4330.0000.0000.0000.000
148A144GLN0-0.004-0.02220.591-0.112-0.1120.0000.0000.0000.000
149A145ASN0-0.041-0.00525.582-0.536-0.5360.0000.0000.0000.000
150A146LEU00.015-0.00427.430-0.422-0.4220.0000.0000.0000.000
151A147SER0-0.051-0.03228.262-0.412-0.4120.0000.0000.0000.000
152A148GLN0-0.073-0.04326.484-0.089-0.0890.0000.0000.0000.000
153A149ILE0-0.0300.01631.796-0.115-0.1150.0000.0000.0000.000
154A150PRO0-0.0080.00434.820-0.132-0.1320.0000.0000.0000.000
155A151ASN0-0.039-0.04836.172-0.257-0.2570.0000.0000.0000.000
156A152ALA00.0430.03234.326-0.149-0.1490.0000.0000.0000.000
157A153LEU0-0.039-0.01831.3430.0050.0050.0000.0000.0000.000
158A154GLU-1-0.883-0.95735.1268.8188.8180.0000.0000.0000.000
159A155HIS00.0030.03438.385-0.219-0.2190.0000.0000.0000.000
160A156ALA0-0.004-0.01539.6790.1200.1200.0000.0000.0000.000
161A157PHE0-0.0220.00340.735-0.106-0.1060.0000.0000.0000.000
162A158TYR00.026-0.00537.1440.0780.0780.0000.0000.0000.000
163A159GLY00.0640.05235.5500.2780.2780.0000.0000.0000.000
164A160HIS0-0.027-0.01634.2380.3600.3600.0000.0000.0000.000
165A161TRP00.0360.00629.5200.2980.2980.0000.0000.0000.000
166A162ILE00.0180.02330.3190.3990.3990.0000.0000.0000.000
167A163LYS10.9210.97629.335-9.054-9.0540.0000.0000.0000.000
168A164GLY00.0030.00329.2730.2710.2710.0000.0000.0000.000
169A165TYR00.0040.00226.4890.3320.3320.0000.0000.0000.000
170A166SER0-0.008-0.02324.7790.5240.5240.0000.0000.0000.000
171A167SER0-0.038-0.00924.7930.4790.4790.0000.0000.0000.000
172A168LYS10.8700.91122.752-11.568-11.5680.0000.0000.0000.000
173A169GLU-1-0.774-0.88021.79112.96212.9620.0000.0000.0000.000
174A170PHE00.0350.02422.4920.4650.4650.0000.0000.0000.000
175A171GLN0-0.016-0.02419.3011.2131.2130.0000.0000.0000.000
176A172ALA0-0.0100.01018.0561.2001.2000.0000.0000.0000.000
177A173CYS0-0.021-0.00817.7760.8220.8220.0000.0000.0000.000
178A174VAL00.0300.01416.6120.6610.6610.0000.0000.0000.000
179A175ASN0-0.044-0.04213.7362.4912.4910.0000.0000.0000.000
180A176TRP0-0.055-0.01813.2542.0462.0460.0000.0000.0000.000
181A177ASN0-0.010-0.01414.1490.3640.3640.0000.0000.0000.000
182A178ILE00.0050.00310.2060.6190.6190.0000.0000.0000.000
183A179ASN0-0.040-0.0359.0115.1165.1160.0000.0000.0000.000
184A180LEU0-0.0070.0179.9902.2712.2710.0000.0000.0000.000
185A181LEU00.0290.01712.0440.6590.6590.0000.0000.0000.000
186A182ASP-1-0.727-0.8206.63239.66539.6650.0000.0000.0000.000
187A183SER0-0.051-0.0307.8700.8550.8550.0000.0000.0000.000
188A184LEU0-0.013-0.0048.858-0.943-0.9430.0000.0000.0000.000
189A185THR0-0.056-0.05810.260-1.598-1.5980.0000.0000.0000.000
190A186LEU00.0100.0164.787-0.515-0.380-0.001-0.004-0.1300.000
191A187ALA0-0.033-0.0138.1260.6350.6350.0000.0000.0000.000
192A188SER0-0.090-0.06010.946-2.145-2.1450.0000.0000.0000.000
193A189SER0-0.060-0.05012.9440.4780.4780.0000.0000.0000.000
194A190LYN00.0910.01314.9840.3690.3690.0000.0000.0000.000
195A191GLN0-0.0080.00016.552-0.159-0.1590.0000.0000.0000.000
196A192GLU-1-0.751-0.82416.54719.55819.5580.0000.0000.0000.000
197A193ILE00.0120.00712.371-0.181-0.1810.0000.0000.0000.000
198A194GLU-1-0.766-0.86015.91416.95716.9570.0000.0000.0000.000
199A195LYS10.9060.95319.223-14.691-14.6910.0000.0000.0000.000
200A196LEU0-0.021-0.01915.058-0.437-0.4370.0000.0000.0000.000
201A197LYS10.8130.89917.663-17.012-17.0120.0000.0000.0000.000
202A198GLU-1-0.933-0.95918.88212.43212.4320.0000.0000.0000.000
203A199ILE00.0030.01220.946-0.581-0.5810.0000.0000.0000.000
204A200PHE00.0180.02217.344-0.375-0.3750.0000.0000.0000.000
205A201ILE00.0160.01920.723-0.313-0.3130.0000.0000.0000.000
206A202THR00.0090.00123.161-0.618-0.6180.0000.0000.0000.000
207A203THR0-0.058-0.04523.154-0.338-0.3380.0000.0000.0000.000
208A204SER00.0150.00222.415-0.219-0.2190.0000.0000.0000.000
209A205GLU-1-0.938-0.97225.04611.00311.0030.0000.0000.0000.000
210A206TYR0-0.023-0.02728.358-0.689-0.6890.0000.0000.0000.000
211A207GLU-1-0.748-0.84625.57511.45011.4500.0000.0000.0000.000
212A208TYR0-0.012-0.01228.813-0.351-0.3510.0000.0000.0000.000
213A209LEU0-0.025-0.01830.835-0.426-0.4260.0000.0000.0000.000
214A210PHE0-0.043-0.01531.846-0.439-0.4390.0000.0000.0000.000
215A211TRP00.018-0.00629.033-0.565-0.5650.0000.0000.0000.000
216A212ASP-1-0.864-0.91134.1528.3228.3220.0000.0000.0000.000
217A213MET0-0.0510.01035.915-0.446-0.4460.0000.0000.0000.000
218A214ALA0-0.0100.00336.766-0.239-0.2390.0000.0000.0000.000
219A215TYR0-0.053-0.04738.605-0.212-0.2120.0000.0000.0000.000
220A216GLN0-0.045-0.02140.424-0.338-0.3380.0000.0000.0000.000
221A217SER0-0.041-0.00542.523-0.187-0.1870.0000.0000.0000.000