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

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FMODB ID: NN32Q

Calculation Name: 3IB6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IB6

Chain ID: A

ChEMBL ID:

UniProt ID:

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1994549.191078
FMO2-HF: Nuclear repulsion 1924379.460668
FMO2-HF: Total energy -70169.73041
FMO2-MP2: Total energy -70377.122222


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:2:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-28.494-12.54512.055-8.38-19.622-0.039
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.032
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].
3A4HIS00.0030.0153.654-1.1062.144-0.036-1.551-1.662-0.002
4A5VAL0-0.002-0.0034.353-0.855-0.5380.000-0.033-0.2840.000
5A6ILE0-0.041-0.0316.3580.2540.2540.0000.0000.0000.000
6A7TRP00.006-0.0278.7580.0340.0340.0000.0000.0000.000
7A8ASP-1-0.715-0.86511.515-0.333-0.3330.0000.0000.0000.000
8A9MET0-0.073-0.04614.5370.0140.0140.0000.0000.0000.000
9A10GLY00.037-0.00917.7550.0230.0230.0000.0000.0000.000
10A11GLU-1-0.878-0.94319.086-0.166-0.1660.0000.0000.0000.000
11A12THR00.0030.00213.827-0.003-0.0030.0000.0000.0000.000
12A13LEU0-0.0030.00514.1290.0360.0360.0000.0000.0000.000
13A14ASN0-0.050-0.04117.5130.0110.0110.0000.0000.0000.000
14A15THR0-0.0190.01921.201-0.010-0.0100.0000.0000.0000.000
15A16VAL0-0.0010.01423.115-0.011-0.0110.0000.0000.0000.000
16A17PRO00.0060.00025.6170.0110.0110.0000.0000.0000.000
17A18ASN0-0.028-0.01829.1840.0010.0010.0000.0000.0000.000
18A19THR0-0.060-0.03431.4420.0040.0040.0000.0000.0000.000
19A20ARG10.8860.96925.1340.1390.1390.0000.0000.0000.000
20A21TYR00.032-0.00626.509-0.013-0.0130.0000.0000.0000.000
21A22ASP-1-0.760-0.85626.493-0.167-0.1670.0000.0000.0000.000
22A23HIS00.0260.00229.128-0.001-0.0010.0000.0000.0000.000
23A24HIS0-0.0100.00832.1420.0030.0030.0000.0000.0000.000
24A25PRO00.0360.00830.110-0.008-0.0080.0000.0000.0000.000
25A26LEU00.0680.03723.8470.0080.0080.0000.0000.0000.000
26A27ASP-1-0.842-0.91328.209-0.121-0.1210.0000.0000.0000.000
27A28THR0-0.097-0.06529.6740.0100.0100.0000.0000.0000.000
28A29TYR00.0120.01729.9450.0060.0060.0000.0000.0000.000
29A30PRO0-0.003-0.00830.647-0.003-0.0030.0000.0000.0000.000
30A31GLU-1-0.844-0.91530.166-0.091-0.0910.0000.0000.0000.000
31A32VAL0-0.017-0.00325.313-0.003-0.0030.0000.0000.0000.000
32A33VAL00.002-0.01025.9790.0010.0010.0000.0000.0000.000
33A34LEU00.0210.00220.857-0.009-0.0090.0000.0000.0000.000
34A35ARG10.7940.87618.0860.1390.1390.0000.0000.0000.000
35A36LYS10.7680.85521.1350.0650.0650.0000.0000.0000.000
36A37ASN00.008-0.00218.1170.0060.0060.0000.0000.0000.000
37A38ALA00.0340.05016.9340.0020.0020.0000.0000.0000.000
38A39LYS10.9500.96416.5970.0740.0740.0000.0000.0000.000
39A40GLU-1-0.891-0.94517.690-0.038-0.0380.0000.0000.0000.000
40A41THR0-0.031-0.02912.0250.0330.0330.0000.0000.0000.000
41A42LEU00.0290.02812.8260.0040.0040.0000.0000.0000.000
42A43GLU-1-0.750-0.82213.329-0.028-0.0280.0000.0000.0000.000
43A44LYS10.8200.89111.681-0.234-0.2340.0000.0000.0000.000
44A45VAL0-0.002-0.0087.7050.0830.0830.0000.0000.0000.000
45A46LYS10.9020.9379.3750.0710.0710.0000.0000.0000.000
46A47GLN0-0.105-0.05611.6290.0800.0800.0000.0000.0000.000
47A48LEU0-0.116-0.0588.0180.0880.0880.0000.0000.0000.000
48A49GLY0-0.025-0.0138.6440.2540.2540.0000.0000.0000.000
49A50PHE0-0.069-0.0192.714-1.1270.0220.373-0.294-1.227-0.001
50A51LYS10.8430.9076.8470.6910.6910.0000.0000.0000.000
51A52GLN00.0150.0067.494-0.247-0.2470.0000.0000.0000.000
52A53ALA00.0130.0199.9440.0750.0750.0000.0000.0000.000
53A54ILE0-0.0160.00311.763-0.009-0.0090.0000.0000.0000.000
54A55LEU00.0040.00012.8290.0150.0150.0000.0000.0000.000
55A56SER00.0220.00914.9230.0030.0030.0000.0000.0000.000
56A57ASN00.0120.00417.840-0.022-0.0220.0000.0000.0000.000
57A58THR0-0.054-0.03320.6790.0030.0030.0000.0000.0000.000
58A59ALA0-0.0030.00423.997-0.004-0.0040.0000.0000.0000.000
59A60THR00.0380.02127.5860.0020.0020.0000.0000.0000.000
60A61SER0-0.061-0.03925.7980.0080.0080.0000.0000.0000.000
61A62ASP-1-0.837-0.90825.570-0.193-0.1930.0000.0000.0000.000
62A63THR00.047-0.00821.3610.0000.0000.0000.0000.0000.000
63A64GLU-1-0.806-0.88723.653-0.213-0.2130.0000.0000.0000.000
64A65VAL0-0.078-0.02226.3930.0100.0100.0000.0000.0000.000
65A66ILE00.0540.02120.5490.0100.0100.0000.0000.0000.000
66A67LYS10.8290.89922.2920.2280.2280.0000.0000.0000.000
67A68ARG10.8660.91923.6570.1440.1440.0000.0000.0000.000
68A69VAL0-0.0030.01023.6340.0120.0120.0000.0000.0000.000
69A70LEU00.0290.01219.0030.0100.0100.0000.0000.0000.000
70A71THR0-0.033-0.03122.5390.0090.0090.0000.0000.0000.000
71A72ASN0-0.017-0.00525.0130.0150.0150.0000.0000.0000.000
72A73PHE0-0.040-0.01521.7790.0120.0120.0000.0000.0000.000
73A74GLY0-0.017-0.00723.8400.0110.0110.0000.0000.0000.000
74A75ILE0-0.043-0.03517.9410.0100.0100.0000.0000.0000.000
75A76ILE00.0130.01318.447-0.028-0.0280.0000.0000.0000.000
76A77ASP-1-0.920-0.96718.602-0.182-0.1820.0000.0000.0000.000
77A78TYR0-0.133-0.08414.2150.0040.0040.0000.0000.0000.000
78A79PHE0-0.038-0.01913.105-0.058-0.0580.0000.0000.0000.000
79A80ASP-1-0.792-0.88412.220-0.521-0.5210.0000.0000.0000.000
80A81PHE0-0.020-0.01413.1660.0170.0170.0000.0000.0000.000
81A82ILE00.0090.00014.764-0.022-0.0220.0000.0000.0000.000
82A83TYR0-0.064-0.02917.0860.0350.0350.0000.0000.0000.000
83A84ALA00.0440.02518.261-0.017-0.0170.0000.0000.0000.000
84A85SER0-0.012-0.02820.9150.0060.0060.0000.0000.0000.000
85A86ASN0-0.034-0.02222.2230.0170.0170.0000.0000.0000.000
86A87SER00.001-0.04124.3360.0020.0020.0000.0000.0000.000
87A88GLU-1-0.930-0.96426.734-0.128-0.1280.0000.0000.0000.000
88A89LEU0-0.101-0.02129.4630.0090.0090.0000.0000.0000.000
89A90GLN0-0.042-0.03730.5540.0040.0040.0000.0000.0000.000
90A91PRO00.0350.00530.286-0.009-0.0090.0000.0000.0000.000
91A92GLY0-0.003-0.00528.5590.0010.0010.0000.0000.0000.000
92A93LYS10.8590.96425.1310.2140.2140.0000.0000.0000.000
93A94MET0-0.028-0.00119.901-0.006-0.0060.0000.0000.0000.000
94A95GLU-1-0.834-0.90920.176-0.231-0.2310.0000.0000.0000.000
95A96LYS10.7410.89614.5850.4040.4040.0000.0000.0000.000
96A97PRO00.0190.01016.5230.0250.0250.0000.0000.0000.000
97A98ASP-1-0.908-0.95316.913-0.299-0.2990.0000.0000.0000.000
98A99LYS10.8370.86916.4150.3660.3660.0000.0000.0000.000
99A100THR00.0090.01116.506-0.043-0.0430.0000.0000.0000.000
100A101ILE00.0260.02615.612-0.020-0.0200.0000.0000.0000.000
101A102PHE00.0340.03910.834-0.041-0.0410.0000.0000.0000.000
102A103ASP-1-0.824-0.89712.876-0.531-0.5310.0000.0000.0000.000
103A104PHE0-0.041-0.02814.495-0.031-0.0310.0000.0000.0000.000
104A105THR0-0.019-0.03110.9440.0070.0070.0000.0000.0000.000
105A106LEU0-0.0110.0057.912-0.047-0.0470.0000.0000.0000.000
106A107ASN00.0150.00311.166-0.014-0.0140.0000.0000.0000.000
107A108ALA0-0.040-0.01214.3470.0340.0340.0000.0000.0000.000
108A109LEU0-0.026-0.0129.1270.0510.0510.0000.0000.0000.000
109A110GLN0-0.133-0.06111.310-0.004-0.0040.0000.0000.0000.000
110A111ILE0-0.0190.0046.116-0.058-0.0580.0000.0000.0000.000
111A112ASP-1-0.788-0.8957.572-0.936-0.9360.0000.0000.0000.000
112A113LYS10.9100.9556.6760.2790.2790.0000.0000.0000.000
113A114THR0-0.112-0.0815.272-0.188-0.1880.0000.0000.0000.000
114A115GLU-1-0.895-0.9362.389-4.469-2.7410.940-1.108-1.559-0.005
115A116ALA0-0.007-0.0022.762-4.341-1.9991.739-1.859-2.223-0.025
116A117VAL0-0.036-0.0202.278-1.852-0.3742.186-0.792-2.872-0.005
117A118MET0-0.0430.0103.6450.1980.2460.0130.013-0.0740.000
118A119VAL0-0.009-0.0147.4120.1020.1020.0000.0000.0000.000
119A120GLY00.0350.0099.5950.0140.0140.0000.0000.0000.000
120A121ASN00.030-0.00313.209-0.006-0.0060.0000.0000.0000.000
121A122THR00.0440.04016.2750.0430.0430.0000.0000.0000.000
122A123PHE0-0.030-0.02116.173-0.042-0.0420.0000.0000.0000.000
123A124GLU-1-0.723-0.89316.699-0.220-0.2200.0000.0000.0000.000
124A125SER00.0110.00617.1550.0010.0010.0000.0000.0000.000
125A126ASP-1-0.768-0.89612.671-0.428-0.4280.0000.0000.0000.000
126A127ILE0-0.045-0.01411.543-0.080-0.0800.0000.0000.0000.000
127A128ILE0-0.002-0.00512.504-0.041-0.0410.0000.0000.0000.000
128A129GLY00.0190.00614.342-0.003-0.0030.0000.0000.0000.000
129A130ALA00.0000.0088.633-0.028-0.0280.0000.0000.0000.000
130A131ASN0-0.008-0.01210.506-0.009-0.0090.0000.0000.0000.000
131A132ARG10.9490.97011.8030.2920.2920.0000.0000.0000.000
132A133ALA0-0.040-0.00811.4960.0370.0370.0000.0000.0000.000
133A134GLY0-0.051-0.03010.209-0.071-0.0710.0000.0000.0000.000
134A135ILE0-0.0220.0015.536-0.118-0.1180.0000.0000.0000.000
135A136HIS00.014-0.0012.337-0.1550.4780.656-0.282-1.0070.001
136A137ALA00.0230.0135.809-0.212-0.2120.0000.0000.0000.000
137A138ILE0-0.033-0.0165.0030.1500.1500.0000.0000.0000.000
138A139TRP0-0.011-0.0168.703-0.033-0.0330.0000.0000.0000.000
139A140LEU00.0010.00712.5010.0540.0540.0000.0000.0000.000
140A141GLN0-0.057-0.04414.9410.0120.0120.0000.0000.0000.000
141A142ASN0-0.039-0.03417.8900.0130.0130.0000.0000.0000.000
142A143PRO00.001-0.00120.371-0.013-0.0130.0000.0000.0000.000
143A144GLU-1-0.814-0.84922.758-0.076-0.0760.0000.0000.0000.000
144A145VAL0-0.029-0.02918.562-0.004-0.0040.0000.0000.0000.000
145A146CYS0-0.096-0.00317.866-0.015-0.0150.0000.0000.0000.000
146A147LEU00.0090.00419.5380.0160.0160.0000.0000.0000.000
147A148GLN0-0.043-0.04419.579-0.003-0.0030.0000.0000.0000.000
148A149ASP-1-0.933-0.94621.893-0.123-0.1230.0000.0000.0000.000
149A150GLU-1-0.966-0.99523.468-0.107-0.1070.0000.0000.0000.000
150A151ARG10.8710.94921.6820.0660.0660.0000.0000.0000.000
151A152LEU0-0.0060.00120.1640.0040.0040.0000.0000.0000.000
152A153PRO0-0.016-0.02319.938-0.004-0.0040.0000.0000.0000.000
153A154LEU00.0100.02214.171-0.022-0.0220.0000.0000.0000.000
154A155VAL0-0.060-0.03313.6850.0380.0380.0000.0000.0000.000
155A156ALA0-0.0140.03412.425-0.032-0.0320.0000.0000.0000.000
156A157PRO0-0.055-0.0289.3330.0440.0440.0000.0000.0000.000
157A158PRO00.0150.0087.7360.0210.0210.0000.0000.0000.000
158A159PHE00.005-0.0206.9140.1230.1230.0000.0000.0000.000
159A160VAL00.0510.0208.436-0.125-0.1250.0000.0000.0000.000
160A161ILE0-0.056-0.0287.2320.0940.0940.0000.0000.0000.000
161A162PRO00.0140.01910.000-0.042-0.0420.0000.0000.0000.000
162A163VAL0-0.005-0.00610.3930.0520.0520.0000.0000.0000.000
163A164TRP00.0350.03013.405-0.031-0.0310.0000.0000.0000.000
164A165ASP-1-0.731-0.87215.688-0.117-0.1170.0000.0000.0000.000
165A166LEU0-0.004-0.00313.6740.0090.0090.0000.0000.0000.000
166A167ALA0-0.001-0.00113.3220.0140.0140.0000.0000.0000.000
167A168ASP-1-0.861-0.93713.1810.0800.0800.0000.0000.0000.000
168A169VAL0-0.0160.0018.1360.0400.0400.0000.0000.0000.000
169A170PRO0-0.004-0.0148.0100.0580.0580.0000.0000.0000.000
170A171GLU-1-0.768-0.8837.8020.4920.4920.0000.0000.0000.000
171A172ALA00.0120.0187.5700.1500.1500.0000.0000.0000.000
172A173LEU00.0040.0143.688-0.2760.1210.009-0.066-0.3400.000
173A174LEU0-0.0020.0053.1580.3001.1280.127-0.369-0.585-0.003
174A175LEU0-0.043-0.0115.5380.3440.3440.0000.0000.0000.000
175A176LEU00.0410.0052.366-0.557-0.1781.293-0.332-1.3400.001
176A177LYS10.9240.9662.257-10.587-8.2163.561-1.941-3.9910.003
177A178LYS10.8770.9363.1430.238-0.8060.1011.282-0.3390.001
178A179ILE0-0.053-0.0155.526-0.174-0.1740.0000.0000.0000.000
179A180SER0-0.0120.0092.504-2.945-0.8721.093-1.048-2.119-0.004