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: 5J6LZ

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2301931.432583
FMO2-HF: Nuclear repulsion 2225192.503375
FMO2-HF: Total energy -76738.929207
FMO2-MP2: Total energy -76965.269579


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.
-66.162-63.5380.151-1.481-1.2950
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 : -0.938 / q_NPA : -0.971
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].
3A3SER0-0.012-0.0043.0290.5583.1820.151-1.481-1.2950.000
4A4VAL00.0400.0165.658-2.616-2.6160.0000.0000.0000.000
5A5LYS10.9130.9597.009-26.144-26.1440.0000.0000.0000.000
6A6LEU00.0220.01611.700-0.696-0.6960.0000.0000.0000.000
7A7ILE0-0.042-0.01414.8200.0700.0700.0000.0000.0000.000
8A8THR00.0170.00517.413-0.605-0.6050.0000.0000.0000.000
9A9ASN00.0280.00319.832-0.911-0.9110.0000.0000.0000.000
10A10THR00.024-0.00120.9390.2070.2070.0000.0000.0000.000
11A11ASN0-0.056-0.03522.780-0.270-0.2700.0000.0000.0000.000
12A12VAL00.0310.02020.335-0.362-0.3620.0000.0000.0000.000
13A13ALA00.0250.03821.7670.3100.3100.0000.0000.0000.000
14A14PRO00.018-0.00616.9680.1630.1630.0000.0000.0000.000
15A15TYR00.039-0.02014.390-0.584-0.5840.0000.0000.0000.000
16A16SER0-0.013-0.01820.727-0.186-0.1860.0000.0000.0000.000
17A17GLY0-0.0010.00623.188-0.534-0.5340.0000.0000.0000.000
18A18VAL0-0.0180.00020.313-0.137-0.1370.0000.0000.0000.000
19A19THR0-0.033-0.05123.788-0.226-0.2260.0000.0000.0000.000
20A20TRP0-0.033-0.00423.8060.4960.4960.0000.0000.0000.000
21A21MET00.0070.00527.229-0.413-0.4130.0000.0000.0000.000
22A22GLY00.0490.03529.120-0.339-0.3390.0000.0000.0000.000
23A23ALA0-0.027-0.02728.5760.0620.0620.0000.0000.0000.000
24A24GLY00.0260.01625.0380.2650.2650.0000.0000.0000.000
25A25THR0-0.036-0.01021.451-0.238-0.2380.0000.0000.0000.000
26A26GLY00.0520.03924.430-0.282-0.2820.0000.0000.0000.000
27A27PHE0-0.010-0.00723.0200.3430.3430.0000.0000.0000.000
28A28VAL0-0.0140.00625.455-0.343-0.3430.0000.0000.0000.000
29A29VAL00.0320.01226.6260.2560.2560.0000.0000.0000.000
30A30GLY00.005-0.00728.923-0.183-0.1830.0000.0000.0000.000
31A31ASN0-0.121-0.07732.2660.1370.1370.0000.0000.0000.000
32A32HIS10.8690.93534.900-7.816-7.8160.0000.0000.0000.000
33A33THR00.022-0.00832.263-0.192-0.1920.0000.0000.0000.000
34A34ILE0-0.027-0.01828.4870.2440.2440.0000.0000.0000.000
35A35ILE00.0210.02526.361-0.299-0.2990.0000.0000.0000.000
36A36THR00.018-0.02026.4570.3050.3050.0000.0000.0000.000
37A37ASN0-0.040-0.03924.3810.2170.2170.0000.0000.0000.000
38A38LYS10.9210.96928.154-9.423-9.4230.0000.0000.0000.000
39A39HIS0-0.076-0.06725.073-0.080-0.0800.0000.0000.0000.000
40A40VAL0-0.058-0.01826.720-0.101-0.1010.0000.0000.0000.000
41A41THR0-0.003-0.05029.984-0.074-0.0740.0000.0000.0000.000
42A42TYR0-0.0210.01833.401-0.304-0.3040.0000.0000.0000.000
43A43HIS00.017-0.00234.782-0.385-0.3850.0000.0000.0000.000
44A44MET0-0.0350.01633.285-0.048-0.0480.0000.0000.0000.000
45A45LYS10.8260.90836.841-8.060-8.0600.0000.0000.0000.000
46A46VAL00.014-0.00539.6110.1160.1160.0000.0000.0000.000
47A47GLY0-0.0080.00141.234-0.133-0.1330.0000.0000.0000.000
48A48ASP-1-0.806-0.89037.0118.0798.0790.0000.0000.0000.000
49A49GLU-1-0.835-0.89836.3507.8427.8420.0000.0000.0000.000
50A50ILE00.0090.02331.4430.2260.2260.0000.0000.0000.000
51A51LYS10.8710.92929.471-9.884-9.8840.0000.0000.0000.000
52A52ALA00.0180.01328.9470.3670.3670.0000.0000.0000.000
53A53HIS10.8500.93724.501-10.901-10.9010.0000.0000.0000.000
54A54PRO0-0.0400.00126.013-0.049-0.0490.0000.0000.0000.000
55A55ASN00.0010.00923.0390.8170.8170.0000.0000.0000.000
56A56GLY00.0720.03624.879-0.208-0.2080.0000.0000.0000.000
57A57PHE0-0.025-0.01525.968-0.343-0.3430.0000.0000.0000.000
58A58TYR00.007-0.01228.673-0.220-0.2200.0000.0000.0000.000
59A59ASN00.0050.02428.579-0.149-0.1490.0000.0000.0000.000
60A60ASN00.033-0.00630.3060.2640.2640.0000.0000.0000.000
61A61GLY00.0660.05929.100-0.025-0.0250.0000.0000.0000.000
62A62GLY0-0.011-0.01629.561-0.304-0.3040.0000.0000.0000.000
63A63GLY0-0.039-0.02331.197-0.350-0.3500.0000.0000.0000.000
64A64LEU0-0.032-0.00833.0280.2690.2690.0000.0000.0000.000
65A65TYR0-0.011-0.01233.573-0.301-0.3010.0000.0000.0000.000
66A66LYS10.9000.95336.598-7.225-7.2250.0000.0000.0000.000
67A67VAL00.0120.00535.852-0.013-0.0130.0000.0000.0000.000
68A68THR0-0.010-0.01538.482-0.155-0.1550.0000.0000.0000.000
69A69LYS10.8890.95838.996-7.833-7.8330.0000.0000.0000.000
70A70ILE00.0440.02535.6200.2320.2320.0000.0000.0000.000
71A71VAL0-0.045-0.02336.003-0.251-0.2510.0000.0000.0000.000
72A72ASP-1-0.791-0.88534.5439.0449.0440.0000.0000.0000.000
73A73TYR0-0.063-0.02232.079-0.335-0.3350.0000.0000.0000.000
74A74PRO00.009-0.00834.5450.0490.0490.0000.0000.0000.000
75A75GLY00.0090.02234.547-0.092-0.0920.0000.0000.0000.000
76A76LYS10.8760.90430.261-9.814-9.8140.0000.0000.0000.000
77A77GLU-1-0.787-0.86827.84010.31410.3140.0000.0000.0000.000
78A78ASP-1-0.721-0.85426.79210.63010.6300.0000.0000.0000.000
79A79ILE0-0.051-0.02027.0330.4030.4030.0000.0000.0000.000
80A80ALA00.0310.01729.143-0.395-0.3950.0000.0000.0000.000
81A81VAL0-0.036-0.01330.3750.3030.3030.0000.0000.0000.000
82A82VAL00.0050.00232.463-0.253-0.2530.0000.0000.0000.000
83A83GLN0-0.090-0.05133.780-0.046-0.0460.0000.0000.0000.000
84A84VAL00.0270.01434.568-0.056-0.0560.0000.0000.0000.000
85A85GLU-1-0.901-0.95737.4067.0497.0490.0000.0000.0000.000
86A86GLU-1-0.843-0.91738.4377.5377.5370.0000.0000.0000.000
87A87LYS10.8090.91338.859-7.088-7.0880.0000.0000.0000.000
88A88SER00.010-0.01737.690-0.021-0.0210.0000.0000.0000.000
89A89THR0-0.029-0.03038.980-0.290-0.2900.0000.0000.0000.000
90A90GLN00.0220.02938.109-0.296-0.2960.0000.0000.0000.000
91A91PRO00.0280.00936.4360.2520.2520.0000.0000.0000.000
92A92LYS10.9330.97139.440-6.995-6.9950.0000.0000.0000.000
93A93GLY00.0270.00441.5950.0140.0140.0000.0000.0000.000
94A94ARG10.8660.94233.160-8.635-8.6350.0000.0000.0000.000
95A95LYS10.8630.92237.812-7.346-7.3460.0000.0000.0000.000
96A96PHE00.1050.04230.9580.1390.1390.0000.0000.0000.000
97A97LYS10.8410.90233.125-7.544-7.5440.0000.0000.0000.000
98A98ASP-1-0.844-0.89733.0538.0028.0020.0000.0000.0000.000
99A99PHE0-0.014-0.00931.5860.0840.0840.0000.0000.0000.000
100A100THR0-0.037-0.01028.4360.3260.3260.0000.0000.0000.000
101A101SER00.0350.03824.728-0.155-0.1550.0000.0000.0000.000
102A102LYS10.8950.94527.111-8.995-8.9950.0000.0000.0000.000
103A103PHE0-0.018-0.00819.9520.1220.1220.0000.0000.0000.000
104A104ASN00.0010.01024.446-0.580-0.5800.0000.0000.0000.000
105A105ILE0-0.022-0.01923.6630.4720.4720.0000.0000.0000.000
106A106ALA00.0370.02520.817-0.254-0.2540.0000.0000.0000.000
107A107SER0-0.043-0.03122.894-0.223-0.2230.0000.0000.0000.000
108A108GLU-1-0.916-0.93921.90411.24311.2430.0000.0000.0000.000
109A109ALA00.0050.00217.6610.3790.3790.0000.0000.0000.000
110A110LYS10.8790.92415.521-16.290-16.2900.0000.0000.0000.000
111A111GLU-1-0.907-0.96515.02717.62117.6210.0000.0000.0000.000
112A112ASN0-0.016-0.01611.1421.7941.7940.0000.0000.0000.000
113A113GLU-1-0.866-0.89510.70716.95916.9590.0000.0000.0000.000
114A114PRO00.0110.0048.4190.6710.6710.0000.0000.0000.000
115A115ILE0-0.062-0.0329.457-1.869-1.8690.0000.0000.0000.000
116A116SER0-0.066-0.0619.7481.4871.4870.0000.0000.0000.000
117A117VAL00.0410.02111.966-1.370-1.3700.0000.0000.0000.000
118A118ILE0-0.024-0.01214.2900.6170.6170.0000.0000.0000.000
119A119GLY00.0400.00816.855-0.825-0.8250.0000.0000.0000.000
120A120TYR0-0.052-0.04718.6390.3950.3950.0000.0000.0000.000
121A121PRO00.0160.02615.467-0.556-0.5560.0000.0000.0000.000
122A122ASN00.0240.01718.484-0.912-0.9120.0000.0000.0000.000
123A123PRO00.0390.02920.493-0.072-0.0720.0000.0000.0000.000
124A124ASN00.0350.00823.272-0.477-0.4770.0000.0000.0000.000
125A125GLY00.001-0.00321.739-0.314-0.3140.0000.0000.0000.000
126A126ASN00.0180.00717.1640.1740.1740.0000.0000.0000.000
127A127LYS10.8770.94921.113-11.941-11.9410.0000.0000.0000.000
128A128LEU0-0.014-0.01523.640-0.293-0.2930.0000.0000.0000.000
129A129GLN0-0.0020.00220.172-0.321-0.3210.0000.0000.0000.000
130A130MET0-0.0300.00218.6080.3060.3060.0000.0000.0000.000
131A131TYR0-0.002-0.02613.7750.1610.1610.0000.0000.0000.000
132A132GLU-1-0.746-0.82211.29717.86017.8600.0000.0000.0000.000
133A133SER0-0.027-0.0229.9932.1382.1380.0000.0000.0000.000
134A134THR00.022-0.0035.368-1.201-1.2010.0000.0000.0000.000
135A135GLY00.0480.0166.4162.5332.5330.0000.0000.0000.000
136A136LYS10.8800.9426.940-30.153-30.1530.0000.0000.0000.000
137A137VAL00.0060.0239.291-0.238-0.2380.0000.0000.0000.000
138A138LEU0-0.054-0.02310.0720.2430.2430.0000.0000.0000.000
139A139SER00.008-0.00413.642-0.960-0.9600.0000.0000.0000.000
140A140VAL00.0230.00617.3520.2900.2900.0000.0000.0000.000
141A141ASN00.0000.01520.171-0.800-0.8000.0000.0000.0000.000
142A142GLY00.0320.01523.411-0.039-0.0390.0000.0000.0000.000
143A143ASN0-0.074-0.04925.1360.2730.2730.0000.0000.0000.000
144A144ILE00.0070.00620.6590.0710.0710.0000.0000.0000.000
145A145VAL00.0020.01216.2000.1240.1240.0000.0000.0000.000
146A146THR0-0.0050.00214.858-0.036-0.0360.0000.0000.0000.000
147A147SER0-0.014-0.03211.2660.6660.6660.0000.0000.0000.000
148A148ASP-1-0.817-0.9257.51531.63431.6340.0000.0000.0000.000
149A149ALA0-0.0010.0198.9782.0942.0940.0000.0000.0000.000
150A150VAL00.0080.0298.581-2.023-2.0230.0000.0000.0000.000
151A151VAL00.0060.00211.257-1.155-1.1550.0000.0000.0000.000
152A152GLN0-0.002-0.01714.079-0.874-0.8740.0000.0000.0000.000
153A153PRO00.0440.02417.530-0.511-0.5110.0000.0000.0000.000
154A154GLY00.0280.01421.0740.0870.0870.0000.0000.0000.000
155A155SER00.0290.00917.370-0.083-0.0830.0000.0000.0000.000
156A156SER0-0.0140.02619.8170.3440.3440.0000.0000.0000.000
157A157GLY00.0650.02922.544-0.331-0.3310.0000.0000.0000.000
158A158SER0-0.053-0.06318.654-0.222-0.2220.0000.0000.0000.000
159A159PRO0-0.0360.00619.2300.0370.0370.0000.0000.0000.000
160A160ILE00.003-0.00214.0830.7800.7800.0000.0000.0000.000
161A161LEU0-0.037-0.01515.346-0.956-0.9560.0000.0000.0000.000
162A162ASN00.0820.02014.2711.1931.1930.0000.0000.0000.000
163A163SER00.0250.00313.188-0.277-0.2770.0000.0000.0000.000
164A164LYS10.9220.97114.535-12.379-12.3790.0000.0000.0000.000
165A165ARG10.7970.88313.330-17.647-17.6470.0000.0000.0000.000
166A166GLU-1-0.876-0.92118.22111.85211.8520.0000.0000.0000.000
167A167ALA0-0.001-0.00618.9860.7000.7000.0000.0000.0000.000
168A168ILE00.022-0.00416.000-0.591-0.5910.0000.0000.0000.000
169A169GLY00.0420.00820.149-0.256-0.2560.0000.0000.0000.000
170A170VAL0-0.048-0.00720.8390.1980.1980.0000.0000.0000.000
171A171MET0-0.0190.00516.079-0.121-0.1210.0000.0000.0000.000
172A172TYR0-0.011-0.00620.311-0.521-0.5210.0000.0000.0000.000
173A173ALA00.0060.01320.709-0.441-0.4410.0000.0000.0000.000
174A174SER00.013-0.00117.6801.2131.2130.0000.0000.0000.000
175A175ASP-1-0.719-0.84715.53719.07819.0780.0000.0000.0000.000
176A176LYS10.8610.93016.064-18.929-18.9290.0000.0000.0000.000
177A177PRO00.0230.01718.9980.0420.0420.0000.0000.0000.000
178A178THR0-0.027-0.02920.573-0.264-0.2640.0000.0000.0000.000
179A179GLY00.0030.00217.5220.4560.4560.0000.0000.0000.000
180A180GLU-1-0.889-0.94511.35124.68124.6810.0000.0000.0000.000
181A181SER00.0040.02012.745-0.115-0.1150.0000.0000.0000.000
182A182THR0-0.053-0.03210.7071.9461.9460.0000.0000.0000.000
183A183ARG10.8540.9199.928-24.405-24.4050.0000.0000.0000.000
184A184SER0-0.010-0.00313.198-1.444-1.4440.0000.0000.0000.000
185A185PHE00.0180.00015.5670.3050.3050.0000.0000.0000.000
186A186ALA00.0290.00418.408-0.332-0.3320.0000.0000.0000.000
187A187VAL00.0190.01120.251-0.154-0.1540.0000.0000.0000.000
188A188TYR0-0.007-0.00821.1840.1840.1840.0000.0000.0000.000
189A189PHE0-0.017-0.00722.923-0.557-0.5570.0000.0000.0000.000
190A190SER00.0580.01124.995-0.102-0.1020.0000.0000.0000.000
191A191PRO00.028-0.00527.041-0.147-0.1470.0000.0000.0000.000
192A192GLU-1-0.860-0.91830.4879.3529.3520.0000.0000.0000.000
193A193ILE00.0150.01527.256-0.208-0.2080.0000.0000.0000.000
194A194LYS10.8390.90225.997-10.832-10.8320.0000.0000.0000.000
195A195LYS10.8830.94030.090-8.007-8.0070.0000.0000.0000.000
196A196PHE00.0020.00831.538-0.242-0.2420.0000.0000.0000.000
197A197ILE00.0370.01027.620-0.154-0.1540.0000.0000.0000.000
198A198ALA0-0.006-0.00532.050-0.176-0.1760.0000.0000.0000.000
199A199ASP-1-0.846-0.93534.2877.5507.5500.0000.0000.0000.000
200A200ASN0-0.067-0.03135.281-0.408-0.4080.0000.0000.0000.000
201A201LEU00.0320.01932.2620.0950.0950.0000.0000.0000.000
202A202ASP-1-0.807-0.87735.3128.3148.3140.0000.0000.0000.000
203A203LYS10.8920.98137.661-7.748-7.7480.0000.0000.0000.000