Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4JZMN

Calculation Name: 4INK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4INK

Chain ID: A

ChEMBL ID:

UniProt ID: Q2FXC5

Base Structure: X-ray

Registration Date: 2023-09-23

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2300384.23439
FMO2-HF: Nuclear repulsion 2223645.886967
FMO2-HF: Total energy -76738.347423
FMO2-MP2: Total energy -76964.690923


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:1:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-63.49-61.1340.308-1.348-1.316-0.004
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.943 / q_NPA : -0.978
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].
3A3SER0-0.009-0.0042.8621.3313.6870.308-1.348-1.316-0.004
4A4VAL00.0420.0165.483-2.771-2.7710.0000.0000.0000.000
5A5LYS10.9180.9607.288-26.206-26.2060.0000.0000.0000.000
6A6LEU00.0120.00811.517-0.722-0.7220.0000.0000.0000.000
7A7ILE0-0.038-0.01014.7170.0800.0800.0000.0000.0000.000
8A8THR00.0110.00017.251-0.637-0.6370.0000.0000.0000.000
9A9ASN00.0270.00819.699-0.870-0.8700.0000.0000.0000.000
10A10THR00.030-0.00120.8500.2320.2320.0000.0000.0000.000
11A11ASN0-0.061-0.03422.686-0.343-0.3430.0000.0000.0000.000
12A12VAL00.0290.02220.274-0.375-0.3750.0000.0000.0000.000
13A13ALA00.0160.02921.7580.3090.3090.0000.0000.0000.000
14A14PRO00.021-0.00417.0660.1720.1720.0000.0000.0000.000
15A15TYR00.029-0.03414.305-0.594-0.5940.0000.0000.0000.000
16A16SER0-0.012-0.02220.702-0.181-0.1810.0000.0000.0000.000
17A17GLY0-0.0030.00623.194-0.546-0.5460.0000.0000.0000.000
18A18VAL0-0.0160.00220.335-0.140-0.1400.0000.0000.0000.000
19A19THR0-0.026-0.04823.762-0.211-0.2110.0000.0000.0000.000
20A20TRP0-0.032-0.01223.6950.4760.4760.0000.0000.0000.000
21A21MET00.0130.01127.070-0.405-0.4050.0000.0000.0000.000
22A22GLY00.0400.03328.956-0.339-0.3390.0000.0000.0000.000
23A23ALA0-0.020-0.02328.4130.0600.0600.0000.0000.0000.000
24A24GLY00.0220.01824.8940.2630.2630.0000.0000.0000.000
25A25THR0-0.039-0.01421.360-0.233-0.2330.0000.0000.0000.000
26A26GLY00.0500.03724.286-0.289-0.2890.0000.0000.0000.000
27A27PHE0-0.008-0.00623.1370.3450.3450.0000.0000.0000.000
28A28VAL0-0.0130.00425.485-0.352-0.3520.0000.0000.0000.000
29A29VAL00.0390.01426.6740.2610.2610.0000.0000.0000.000
30A30GLY00.0130.00828.961-0.182-0.1820.0000.0000.0000.000
31A31ASN0-0.109-0.05032.3340.0590.0590.0000.0000.0000.000
32A32HIS10.8700.91434.928-7.852-7.8520.0000.0000.0000.000
33A33THR00.0440.01232.233-0.192-0.1920.0000.0000.0000.000
34A34ILE0-0.025-0.01728.4360.2450.2450.0000.0000.0000.000
35A35ILE00.0140.01926.494-0.300-0.3000.0000.0000.0000.000
36A36THR00.010-0.02126.4730.3150.3150.0000.0000.0000.000
37A37ASN0-0.037-0.02824.4090.2070.2070.0000.0000.0000.000
38A38LYS10.8830.96328.156-9.491-9.4910.0000.0000.0000.000
39A39HIS0-0.104-0.09125.087-0.071-0.0710.0000.0000.0000.000
40A40VAL0-0.053-0.01626.631-0.094-0.0940.0000.0000.0000.000
41A41THR0-0.013-0.05629.858-0.087-0.0870.0000.0000.0000.000
42A42TYR0-0.0150.01533.300-0.306-0.3060.0000.0000.0000.000
43A43HIS0-0.015-0.01334.377-0.389-0.3890.0000.0000.0000.000
44A44MET0-0.061-0.00633.155-0.008-0.0080.0000.0000.0000.000
45A45LYS10.9080.95836.703-7.879-7.8790.0000.0000.0000.000
46A46VAL00.004-0.01139.4680.1160.1160.0000.0000.0000.000
47A47GLY0-0.031-0.01441.085-0.135-0.1350.0000.0000.0000.000
48A48ASP-1-0.829-0.90036.9188.0618.0610.0000.0000.0000.000
49A49GLU-1-0.856-0.93136.2017.8717.8710.0000.0000.0000.000
50A50ILE00.0030.02131.3250.2350.2350.0000.0000.0000.000
51A51LYS10.9130.94729.328-9.922-9.9220.0000.0000.0000.000
52A52ALA00.0190.01728.8870.3640.3640.0000.0000.0000.000
53A53HIS10.8540.93124.480-10.921-10.9210.0000.0000.0000.000
54A54PRO0-0.046-0.00525.926-0.033-0.0330.0000.0000.0000.000
55A55ASN00.0020.00822.8330.7510.7510.0000.0000.0000.000
56A56GLY00.0790.03724.703-0.202-0.2020.0000.0000.0000.000
57A57PHE0-0.046-0.02925.782-0.340-0.3400.0000.0000.0000.000
58A58TYR00.007-0.00528.488-0.338-0.3380.0000.0000.0000.000
59A59ASN00.0030.02328.405-0.093-0.0930.0000.0000.0000.000
60A60ASN00.025-0.01130.1260.2380.2380.0000.0000.0000.000
61A61GLY00.0450.04528.982-0.013-0.0130.0000.0000.0000.000
62A62GLY0-0.016-0.02629.499-0.294-0.2940.0000.0000.0000.000
63A63GLY0-0.040-0.02131.125-0.352-0.3520.0000.0000.0000.000
64A64LEU0-0.022-0.00532.9410.2690.2690.0000.0000.0000.000
65A65TYR0-0.016-0.01333.489-0.314-0.3140.0000.0000.0000.000
66A66LYS10.9220.97036.443-7.178-7.1780.0000.0000.0000.000
67A67VAL00.0170.01335.792-0.015-0.0150.0000.0000.0000.000
68A68THR0-0.010-0.01838.407-0.155-0.1550.0000.0000.0000.000
69A69LYS10.9460.97539.020-7.624-7.6240.0000.0000.0000.000
70A70ILE00.0450.02635.6590.2280.2280.0000.0000.0000.000
71A71VAL0-0.053-0.02236.019-0.245-0.2450.0000.0000.0000.000
72A72ASP-1-0.790-0.88234.5479.0539.0530.0000.0000.0000.000
73A73TYR0-0.057-0.02732.034-0.327-0.3270.0000.0000.0000.000
74A74PRO00.0250.00934.5490.0530.0530.0000.0000.0000.000
75A75GLY00.0080.02334.537-0.093-0.0930.0000.0000.0000.000
76A76LYS10.8950.91529.970-9.847-9.8470.0000.0000.0000.000
77A77GLU-1-0.801-0.88527.96110.24610.2460.0000.0000.0000.000
78A78ASP-1-0.678-0.83526.66010.68110.6810.0000.0000.0000.000
79A79ILE0-0.052-0.02227.1080.3960.3960.0000.0000.0000.000
80A80ALA00.0320.01629.147-0.393-0.3930.0000.0000.0000.000
81A81VAL0-0.028-0.01230.3900.3140.3140.0000.0000.0000.000
82A82VAL00.0030.00232.492-0.250-0.2500.0000.0000.0000.000
83A83GLN0-0.088-0.04533.806-0.041-0.0410.0000.0000.0000.000
84A84VAL00.0180.01134.542-0.058-0.0580.0000.0000.0000.000
85A85GLU-1-0.904-0.96137.4007.0947.0940.0000.0000.0000.000
86A86GLU-1-0.865-0.92838.4237.4737.4730.0000.0000.0000.000
87A87LYS10.8270.93138.849-7.064-7.0640.0000.0000.0000.000
88A88SER0-0.002-0.02637.661-0.025-0.0250.0000.0000.0000.000
89A89THR0-0.012-0.00838.889-0.322-0.3220.0000.0000.0000.000
90A90GLN00.0150.01337.903-0.297-0.2970.0000.0000.0000.000
91A91PRO00.0420.01536.3140.2520.2520.0000.0000.0000.000
92A92LYS10.9470.99439.330-7.021-7.0210.0000.0000.0000.000
93A93GLY00.0220.00041.5140.0140.0140.0000.0000.0000.000
94A94ARG10.8750.95933.109-8.640-8.6400.0000.0000.0000.000
95A95LYS10.8450.90137.793-7.376-7.3760.0000.0000.0000.000
96A96PHE00.1020.04030.9780.1410.1410.0000.0000.0000.000
97A97LYS10.8560.90833.132-7.590-7.5900.0000.0000.0000.000
98A98ASP-1-0.846-0.89233.0948.0518.0510.0000.0000.0000.000
99A99PHE0-0.028-0.01731.5710.0900.0900.0000.0000.0000.000
100A100THR0-0.038-0.00728.4370.3270.3270.0000.0000.0000.000
101A101SER00.0310.03424.775-0.159-0.1590.0000.0000.0000.000
102A102LYS10.9160.95127.161-9.022-9.0220.0000.0000.0000.000
103A103PHE0-0.024-0.01020.0750.1330.1330.0000.0000.0000.000
104A104ASN00.0080.01524.514-0.583-0.5830.0000.0000.0000.000
105A105ILE0-0.032-0.02323.7040.4630.4630.0000.0000.0000.000
106A106ALA00.0390.02520.845-0.257-0.2570.0000.0000.0000.000
107A107SER0-0.021-0.02422.930-0.254-0.2540.0000.0000.0000.000
108A108GLU-1-0.982-0.98921.52011.62511.6250.0000.0000.0000.000
109A109ALA0-0.0010.00917.7170.3880.3880.0000.0000.0000.000
110A110LYS10.9370.97215.149-16.878-16.8780.0000.0000.0000.000
111A111GLU-1-0.917-0.97015.02817.11417.1140.0000.0000.0000.000
112A112ASN0-0.031-0.04911.1781.2761.2760.0000.0000.0000.000
113A113GLU-1-0.929-0.95210.72217.11817.1180.0000.0000.0000.000
114A114PRO00.0010.0038.4670.5950.5950.0000.0000.0000.000
115A115ILE0-0.050-0.0219.484-1.841-1.8410.0000.0000.0000.000
116A116SER0-0.033-0.0249.7831.5721.5720.0000.0000.0000.000
117A117VAL00.0410.02212.000-1.413-1.4130.0000.0000.0000.000
118A118ILE0-0.027-0.01414.2900.6530.6530.0000.0000.0000.000
119A119GLY00.0400.00916.813-0.841-0.8410.0000.0000.0000.000
120A120TYR0-0.050-0.04018.4740.3870.3870.0000.0000.0000.000
121A121PRO0-0.0090.00915.320-0.581-0.5810.0000.0000.0000.000
122A122ASN00.0270.01218.322-0.858-0.8580.0000.0000.0000.000
123A123PRO00.0350.02520.328-0.082-0.0820.0000.0000.0000.000
124A124ASN00.014-0.00223.099-0.427-0.4270.0000.0000.0000.000
125A125GLY0-0.021-0.01121.569-0.267-0.2670.0000.0000.0000.000
126A126ASN00.0170.00316.8740.0440.0440.0000.0000.0000.000
127A127LYS10.9160.97120.929-11.615-11.6150.0000.0000.0000.000
128A128LEU0-0.017-0.01723.480-0.307-0.3070.0000.0000.0000.000
129A129GLN0-0.011-0.00120.073-0.339-0.3390.0000.0000.0000.000
130A130MET0-0.0310.00218.5510.3020.3020.0000.0000.0000.000
131A131TYR00.0290.00213.7460.0370.0370.0000.0000.0000.000
132A132GLU-1-0.766-0.84211.21818.24418.2440.0000.0000.0000.000
133A133SER0-0.030-0.0239.8432.1512.1510.0000.0000.0000.000
134A134THR00.0250.0015.373-1.278-1.2780.0000.0000.0000.000
135A135GLY00.0500.0216.4262.3752.3750.0000.0000.0000.000
136A136LYS10.9150.9706.988-30.916-30.9160.0000.0000.0000.000
137A137VAL00.0110.0239.295-0.285-0.2850.0000.0000.0000.000
138A138LEU0-0.051-0.02510.1360.3610.3610.0000.0000.0000.000
139A139SER00.0150.00013.620-0.636-0.6360.0000.0000.0000.000
140A140VAL00.0260.00717.3340.2970.2970.0000.0000.0000.000
141A141ASN00.0110.01920.161-0.700-0.7000.0000.0000.0000.000
142A142GLY00.0200.01023.394-0.038-0.0380.0000.0000.0000.000
143A143ASN0-0.051-0.02825.1300.3110.3110.0000.0000.0000.000
144A144ILE0-0.008-0.00220.6450.0790.0790.0000.0000.0000.000
145A145VAL00.0090.01516.1930.0960.0960.0000.0000.0000.000
146A146THR00.0050.00314.758-0.070-0.0700.0000.0000.0000.000
147A147SER0-0.016-0.01611.1340.6790.6790.0000.0000.0000.000
148A148ASP-1-0.813-0.9197.03031.76831.7680.0000.0000.0000.000
149A149ALA00.0000.0168.8842.0522.0520.0000.0000.0000.000
150A150VAL00.0060.0268.647-2.061-2.0610.0000.0000.0000.000
151A151VAL00.0120.00311.148-1.123-1.1230.0000.0000.0000.000
152A152GLN00.0400.01114.724-0.440-0.4400.0000.0000.0000.000
153A153PRO00.0460.02317.395-0.489-0.4890.0000.0000.0000.000
154A154GLY00.0320.01520.9240.1010.1010.0000.0000.0000.000
155A155SER00.007-0.00517.3910.1300.1300.0000.0000.0000.000
156A156SER00.0010.02519.6790.3500.3500.0000.0000.0000.000
157A157GLY00.0520.01922.424-0.327-0.3270.0000.0000.0000.000
158A158SER0-0.041-0.05018.661-0.223-0.2230.0000.0000.0000.000
159A159PRO0-0.0410.01019.0890.0080.0080.0000.0000.0000.000
160A160ILE00.011-0.00313.9950.7810.7810.0000.0000.0000.000
161A161LEU0-0.043-0.02115.384-0.959-0.9590.0000.0000.0000.000
162A162ASN00.0970.04214.3081.1901.1900.0000.0000.0000.000
163A163SER00.015-0.00313.267-0.342-0.3420.0000.0000.0000.000
164A164LYS10.9370.97114.648-12.683-12.6830.0000.0000.0000.000
165A165ARG10.8040.89213.587-17.797-17.7970.0000.0000.0000.000
166A166GLU-1-0.883-0.92718.38711.73911.7390.0000.0000.0000.000
167A167ALA0-0.009-0.01319.0250.6960.6960.0000.0000.0000.000
168A168ILE00.0300.00116.120-0.591-0.5910.0000.0000.0000.000
169A169GLY00.0370.00520.173-0.267-0.2670.0000.0000.0000.000
170A170VAL0-0.052-0.00720.8580.2040.2040.0000.0000.0000.000
171A171MET0-0.0210.00216.057-0.129-0.1290.0000.0000.0000.000
172A172TYR0-0.023-0.01020.312-0.678-0.6780.0000.0000.0000.000
173A173ALA00.0090.01520.622-0.426-0.4260.0000.0000.0000.000
174A174SER00.0180.01017.5921.1831.1830.0000.0000.0000.000
175A175ASP-1-0.753-0.88315.72918.96318.9630.0000.0000.0000.000
176A176LYS10.9320.96816.264-17.623-17.6230.0000.0000.0000.000
177A177PRO00.0140.01019.0110.0370.0370.0000.0000.0000.000
178A178THR0-0.033-0.03220.448-0.304-0.3040.0000.0000.0000.000
179A179GLY00.0010.00217.3880.4270.4270.0000.0000.0000.000
180A180GLU-1-0.950-0.97811.17425.11925.1190.0000.0000.0000.000
181A181SER0-0.0060.01512.863-0.167-0.1670.0000.0000.0000.000
182A182THR0-0.056-0.02710.8812.2182.2180.0000.0000.0000.000
183A183ARG10.8490.92010.609-23.073-23.0730.0000.0000.0000.000
184A184SER0-0.0090.00113.043-1.382-1.3820.0000.0000.0000.000
185A185PHE00.009-0.00515.4830.2430.2430.0000.0000.0000.000
186A186ALA00.0240.00218.428-0.319-0.3190.0000.0000.0000.000
187A187VAL00.0140.00820.246-0.158-0.1580.0000.0000.0000.000
188A188TYR0-0.006-0.00821.1630.1980.1980.0000.0000.0000.000
189A189PHE0-0.023-0.01022.936-0.562-0.5620.0000.0000.0000.000
190A190SER00.0570.01325.010-0.100-0.1000.0000.0000.0000.000
191A191PRO00.024-0.00927.051-0.148-0.1480.0000.0000.0000.000
192A192GLU-1-0.877-0.92530.5029.3549.3540.0000.0000.0000.000
193A193ILE00.0160.01427.296-0.204-0.2040.0000.0000.0000.000
194A194LYS10.8900.93826.208-10.706-10.7060.0000.0000.0000.000
195A195LYS10.8660.93530.111-8.028-8.0280.0000.0000.0000.000
196A196PHE00.0090.01431.514-0.229-0.2290.0000.0000.0000.000
197A197ILE00.0320.01627.584-0.156-0.1560.0000.0000.0000.000
198A198ALA0-0.012-0.01232.073-0.171-0.1710.0000.0000.0000.000
199A199ASP-1-0.881-0.94334.3157.6897.6890.0000.0000.0000.000
200A200ASN0-0.078-0.04735.208-0.439-0.4390.0000.0000.0000.000
201A201LEU00.0210.00932.1850.0910.0910.0000.0000.0000.000
202A202ASP-1-0.808-0.88335.3438.2718.2710.0000.0000.0000.000
203A203LYS10.9150.98837.695-7.741-7.7410.0000.0000.0000.000