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: YV8K2

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2299339.197808
FMO2-HF: Nuclear repulsion 2222599.887033
FMO2-HF: Total energy -76739.310775
FMO2-MP2: Total energy -76965.515951


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.
-69.596-67.2530.183-1.278-1.247-0.002
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 : -0.929 / q_NPA : -0.965
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].
3A3SER0-0.0090.0013.0050.4532.7960.183-1.278-1.247-0.002
4A4VAL00.0120.0035.490-2.741-2.7410.0000.0000.0000.000
5A5LYS10.9290.9636.077-27.016-27.0160.0000.0000.0000.000
6A6LEU00.0330.02611.798-0.699-0.6990.0000.0000.0000.000
7A7ILE0-0.031-0.01314.6020.0540.0540.0000.0000.0000.000
8A8THR00.0320.01117.260-0.716-0.7160.0000.0000.0000.000
9A9ASN00.0280.00219.575-0.920-0.9200.0000.0000.0000.000
10A10THR00.006-0.00720.8060.1830.1830.0000.0000.0000.000
11A11ASN0-0.076-0.04722.160-0.401-0.4010.0000.0000.0000.000
12A12VAL00.0370.02320.235-0.405-0.4050.0000.0000.0000.000
13A13ALA00.0370.04021.4280.3270.3270.0000.0000.0000.000
14A14PRO00.018-0.00316.8010.2070.2070.0000.0000.0000.000
15A15TYR00.014-0.02213.919-0.574-0.5740.0000.0000.0000.000
16A16SER0-0.013-0.02520.337-0.169-0.1690.0000.0000.0000.000
17A17GLY00.0100.00522.945-0.533-0.5330.0000.0000.0000.000
18A18VAL0-0.021-0.00319.948-0.169-0.1690.0000.0000.0000.000
19A19THR0-0.042-0.04923.421-0.290-0.2900.0000.0000.0000.000
20A20TRP0-0.0180.00923.6210.4970.4970.0000.0000.0000.000
21A21MET00.0160.01727.179-0.442-0.4420.0000.0000.0000.000
22A22GLY00.0310.01629.557-0.249-0.2490.0000.0000.0000.000
23A23ALA0-0.007-0.02028.8820.0650.0650.0000.0000.0000.000
24A24GLY00.0240.00925.1160.2610.2610.0000.0000.0000.000
25A25THR0-0.0070.00721.067-0.189-0.1890.0000.0000.0000.000
26A26GLY00.0250.02824.033-0.311-0.3110.0000.0000.0000.000
27A27PHE0-0.008-0.00723.1060.3720.3720.0000.0000.0000.000
28A28VAL00.0050.01425.231-0.341-0.3410.0000.0000.0000.000
29A29VAL00.0490.02026.6060.2520.2520.0000.0000.0000.000
30A30GLY0-0.011-0.02328.935-0.212-0.2120.0000.0000.0000.000
31A31ASN0-0.091-0.07431.9700.2160.2160.0000.0000.0000.000
32A32HIS10.7750.86434.745-7.770-7.7700.0000.0000.0000.000
33A33THR00.018-0.00732.337-0.186-0.1860.0000.0000.0000.000
34A34ILE0-0.014-0.01028.4880.2300.2300.0000.0000.0000.000
35A35ILE00.0110.01826.234-0.283-0.2830.0000.0000.0000.000
36A36THR00.024-0.01226.1930.3060.3060.0000.0000.0000.000
37A37ASN0-0.010-0.02724.2520.1840.1840.0000.0000.0000.000
38A38LYS10.8710.93527.873-9.555-9.5550.0000.0000.0000.000
39A39HIS0-0.071-0.04724.914-0.111-0.1110.0000.0000.0000.000
40A40VAL0-0.060-0.01726.766-0.044-0.0440.0000.0000.0000.000
41A41THR00.003-0.05030.029-0.102-0.1020.0000.0000.0000.000
42A42TYR0-0.0250.01033.345-0.273-0.2730.0000.0000.0000.000
43A43HIS00.034-0.00234.045-0.381-0.3810.0000.0000.0000.000
44A44MET0-0.0280.03232.906-0.097-0.0970.0000.0000.0000.000
45A45LYS10.8120.89236.466-8.071-8.0710.0000.0000.0000.000
46A46VAL00.000-0.00139.3320.1180.1180.0000.0000.0000.000
47A47GLY00.0180.01241.074-0.162-0.1620.0000.0000.0000.000
48A48ASP-1-0.814-0.88936.9498.0078.0070.0000.0000.0000.000
49A49GLU-1-0.826-0.88635.9757.8297.8290.0000.0000.0000.000
50A50ILE0-0.0160.00731.0010.2300.2300.0000.0000.0000.000
51A51LYS10.8340.90729.203-9.886-9.8860.0000.0000.0000.000
52A52ALA00.0270.01028.6890.3660.3660.0000.0000.0000.000
53A53HIS10.8460.93424.070-10.825-10.8250.0000.0000.0000.000
54A54PRO0-0.0310.00625.552-0.018-0.0180.0000.0000.0000.000
55A55ASN00.002-0.00521.5310.7270.7270.0000.0000.0000.000
56A56GLY00.0540.03124.862-0.222-0.2220.0000.0000.0000.000
57A57PHE0-0.015-0.00726.214-0.319-0.3190.0000.0000.0000.000
58A58TYR00.023-0.00428.796-0.192-0.1920.0000.0000.0000.000
59A59ASN00.0070.02628.364-0.154-0.1540.0000.0000.0000.000
60A60ASN00.041-0.00230.3240.2030.2030.0000.0000.0000.000
61A61GLY00.0570.04828.366-0.055-0.0550.0000.0000.0000.000
62A62GLY00.0010.00629.147-0.306-0.3060.0000.0000.0000.000
63A63GLY0-0.029-0.02430.891-0.365-0.3650.0000.0000.0000.000
64A64LEU0-0.0140.00532.5580.2640.2640.0000.0000.0000.000
65A65TYR0-0.026-0.01933.162-0.260-0.2600.0000.0000.0000.000
66A66LYS10.8960.94736.139-7.212-7.2120.0000.0000.0000.000
67A67VAL0-0.0070.00635.6280.0260.0260.0000.0000.0000.000
68A68THR0-0.009-0.01938.192-0.145-0.1450.0000.0000.0000.000
69A69LYS10.8470.92938.495-7.875-7.8750.0000.0000.0000.000
70A70ILE00.0380.01535.6700.2400.2400.0000.0000.0000.000
71A71VAL0-0.024-0.01335.842-0.248-0.2480.0000.0000.0000.000
72A72ASP-1-0.782-0.87734.1039.0169.0160.0000.0000.0000.000
73A73TYR0-0.080-0.03231.887-0.334-0.3340.0000.0000.0000.000
74A74PRO00.002-0.00434.2700.0620.0620.0000.0000.0000.000
75A75GLY00.0130.02934.399-0.108-0.1080.0000.0000.0000.000
76A76LYS10.8730.90530.395-9.749-9.7490.0000.0000.0000.000
77A77GLU-1-0.758-0.86027.72310.29910.2990.0000.0000.0000.000
78A78ASP-1-0.745-0.86126.88510.55110.5510.0000.0000.0000.000
79A79ILE0-0.044-0.01426.7960.4130.4130.0000.0000.0000.000
80A80ALA00.0410.02128.969-0.396-0.3960.0000.0000.0000.000
81A81VAL0-0.041-0.01530.1770.3060.3060.0000.0000.0000.000
82A82VAL00.0060.00232.398-0.246-0.2460.0000.0000.0000.000
83A83GLN0-0.065-0.04333.720-0.037-0.0370.0000.0000.0000.000
84A84VAL00.0370.01934.326-0.027-0.0270.0000.0000.0000.000
85A85GLU-1-0.883-0.94637.2526.9706.9700.0000.0000.0000.000
86A86GLU-1-0.811-0.88538.0317.5907.5900.0000.0000.0000.000
87A87LYS10.7920.90138.661-7.089-7.0890.0000.0000.0000.000
88A88SER0-0.012-0.02637.0420.0060.0060.0000.0000.0000.000
89A89THR0-0.008-0.03638.409-0.251-0.2510.0000.0000.0000.000
90A90GLN00.0000.01337.897-0.290-0.2900.0000.0000.0000.000
91A91PRO00.0150.01135.7950.2540.2540.0000.0000.0000.000
92A92LYS10.9560.98038.832-7.016-7.0160.0000.0000.0000.000
93A93GLY00.0330.01740.6810.0600.0600.0000.0000.0000.000
94A94ARG10.8630.93332.788-8.666-8.6660.0000.0000.0000.000
95A95LYS10.9190.94937.035-7.428-7.4280.0000.0000.0000.000
96A96PHE00.0630.02730.7780.1590.1590.0000.0000.0000.000
97A97LYS10.8550.91932.690-7.552-7.5520.0000.0000.0000.000
98A98ASP-1-0.847-0.89232.6168.0238.0230.0000.0000.0000.000
99A99PHE00.000-0.00531.3690.0460.0460.0000.0000.0000.000
100A100THR0-0.058-0.03028.1590.3170.3170.0000.0000.0000.000
101A101SER00.0430.02324.669-0.091-0.0910.0000.0000.0000.000
102A102LYS10.8200.94025.790-8.792-8.7920.0000.0000.0000.000
103A103PHE00.0190.01019.4220.1030.1030.0000.0000.0000.000
104A104ASN00.0020.00624.023-0.554-0.5540.0000.0000.0000.000
105A105ILE0-0.034-0.01923.3020.4650.4650.0000.0000.0000.000
106A106ALA00.0280.02720.580-0.260-0.2600.0000.0000.0000.000
107A107SER0-0.009-0.03222.693-0.327-0.3270.0000.0000.0000.000
108A108GLU-1-0.921-0.93821.64411.39811.3980.0000.0000.0000.000
109A109ALA0-0.005-0.00117.7690.3980.3980.0000.0000.0000.000
110A110LYS10.8600.91315.820-16.274-16.2740.0000.0000.0000.000
111A111GLU-1-0.841-0.92215.21817.91217.9120.0000.0000.0000.000
112A112ASN0-0.012-0.02211.2672.0452.0450.0000.0000.0000.000
113A113GLU-1-0.870-0.89610.46617.54317.5430.0000.0000.0000.000
114A114PRO00.0050.0037.9710.6790.6790.0000.0000.0000.000
115A115ILE0-0.073-0.0349.218-1.903-1.9030.0000.0000.0000.000
116A116SER0-0.058-0.0599.4681.5461.5460.0000.0000.0000.000
117A117VAL00.0440.02011.739-1.295-1.2950.0000.0000.0000.000
118A118ILE0-0.015-0.00914.0410.6530.6530.0000.0000.0000.000
119A119GLY00.031-0.00116.594-0.804-0.8040.0000.0000.0000.000
120A120TYR0-0.045-0.04318.6980.3180.3180.0000.0000.0000.000
121A121PRO00.0300.03015.326-0.481-0.4810.0000.0000.0000.000
122A122ASN00.0060.01118.209-0.856-0.8560.0000.0000.0000.000
123A123PRO00.0080.01320.508-0.018-0.0180.0000.0000.0000.000
124A124ASN00.0490.01623.200-0.435-0.4350.0000.0000.0000.000
125A125GLY00.0090.01521.501-0.336-0.3360.0000.0000.0000.000
126A126ASN00.027-0.00216.949-0.082-0.0820.0000.0000.0000.000
127A127LYS10.8770.94620.990-11.972-11.9720.0000.0000.0000.000
128A128LEU0-0.001-0.00223.552-0.352-0.3520.0000.0000.0000.000
129A129GLN0-0.017-0.00420.392-0.267-0.2670.0000.0000.0000.000
130A130MET0-0.0330.00918.4060.3280.3280.0000.0000.0000.000
131A131TYR0-0.019-0.03313.6480.3120.3120.0000.0000.0000.000
132A132GLU-1-0.744-0.81111.14717.65917.6590.0000.0000.0000.000
133A133SER0-0.048-0.03610.0021.9061.9060.0000.0000.0000.000
134A134THR00.005-0.0216.265-0.706-0.7060.0000.0000.0000.000
135A135GLY00.0530.0196.0772.8952.8950.0000.0000.0000.000
136A136LYS10.8840.9426.944-30.918-30.9180.0000.0000.0000.000
137A137VAL0-0.0030.0259.259-0.316-0.3160.0000.0000.0000.000
138A138LEU0-0.047-0.0299.998-0.034-0.0340.0000.0000.0000.000
139A139SER0-0.022-0.01613.634-1.047-1.0470.0000.0000.0000.000
140A140VAL00.0460.01317.4190.2750.2750.0000.0000.0000.000
141A141ASN0-0.018-0.00320.250-0.828-0.8280.0000.0000.0000.000
142A142GLY00.0190.01323.552-0.122-0.1220.0000.0000.0000.000
143A143ASN0-0.061-0.03325.6010.1330.1330.0000.0000.0000.000
144A144ILE0-0.0080.00620.8500.0750.0750.0000.0000.0000.000
145A145VAL00.0110.01416.2320.1110.1110.0000.0000.0000.000
146A146THR0-0.026-0.01014.949-0.239-0.2390.0000.0000.0000.000
147A147SER00.006-0.01711.2240.6980.6980.0000.0000.0000.000
148A148ASP-1-0.784-0.9077.91630.95530.9550.0000.0000.0000.000
149A149ALA00.0070.0218.5712.7152.7150.0000.0000.0000.000
150A150VAL00.0120.0338.080-2.267-2.2670.0000.0000.0000.000
151A151VAL00.0040.01010.821-1.204-1.2040.0000.0000.0000.000
152A152GLN00.006-0.01614.116-0.999-0.9990.0000.0000.0000.000
153A153PRO00.0270.00717.245-0.435-0.4350.0000.0000.0000.000
154A154GLY00.0370.02121.117-0.039-0.0390.0000.0000.0000.000
155A155SER00.0250.01017.267-0.122-0.1220.0000.0000.0000.000
156A156SER00.0040.01819.6020.4180.4180.0000.0000.0000.000
157A157GLY00.0270.02122.545-0.276-0.2760.0000.0000.0000.000
158A158SER0-0.044-0.05318.664-0.192-0.1920.0000.0000.0000.000
159A159PRO0-0.0320.00819.1570.0340.0340.0000.0000.0000.000
160A160ILE00.012-0.00314.0410.7400.7400.0000.0000.0000.000
161A161LEU0-0.054-0.02015.077-0.981-0.9810.0000.0000.0000.000
162A162ASN00.0800.02314.0081.1981.1980.0000.0000.0000.000
163A163SER00.0380.00912.821-0.318-0.3180.0000.0000.0000.000
164A164LYS10.8160.91014.150-12.544-12.5440.0000.0000.0000.000
165A165ARG10.7910.87213.464-17.632-17.6320.0000.0000.0000.000
166A166GLU-1-0.785-0.87117.66711.85611.8560.0000.0000.0000.000
167A167ALA00.000-0.00718.6710.7010.7010.0000.0000.0000.000
168A168ILE00.020-0.00115.855-0.596-0.5960.0000.0000.0000.000
169A169GLY00.035-0.00120.030-0.291-0.2910.0000.0000.0000.000
170A170VAL0-0.046-0.01420.7600.1810.1810.0000.0000.0000.000
171A171MET0-0.0050.01216.060-0.086-0.0860.0000.0000.0000.000
172A172TYR0-0.020-0.00220.258-0.496-0.4960.0000.0000.0000.000
173A173ALA0-0.0020.01020.753-0.390-0.3900.0000.0000.0000.000
174A174SER00.012-0.01317.8021.2611.2610.0000.0000.0000.000
175A175ASP-1-0.737-0.85215.68318.92218.9220.0000.0000.0000.000
176A176LYS10.8200.90816.045-18.334-18.3340.0000.0000.0000.000
177A177PRO00.0340.03219.0890.1130.1130.0000.0000.0000.000
178A178THR0-0.014-0.02421.057-0.273-0.2730.0000.0000.0000.000
179A179GLY00.0100.01217.9220.3640.3640.0000.0000.0000.000
180A180GLU-1-0.859-0.92611.28523.67323.6730.0000.0000.0000.000
181A181SER0-0.024-0.00212.659-0.083-0.0830.0000.0000.0000.000
182A182THR0-0.022-0.01310.7151.8391.8390.0000.0000.0000.000
183A183ARG10.8570.9209.605-24.943-24.9430.0000.0000.0000.000
184A184SER0-0.022-0.01013.188-1.520-1.5200.0000.0000.0000.000
185A185PHE00.0220.00415.5180.2560.2560.0000.0000.0000.000
186A186ALA00.0350.00118.347-0.338-0.3380.0000.0000.0000.000
187A187VAL0-0.0030.00620.158-0.120-0.1200.0000.0000.0000.000
188A188TYR00.0120.00221.1730.1230.1230.0000.0000.0000.000
189A189PHE0-0.034-0.00622.861-0.566-0.5660.0000.0000.0000.000
190A190SER00.044-0.00125.035-0.141-0.1410.0000.0000.0000.000
191A191PRO00.030-0.01027.161-0.139-0.1390.0000.0000.0000.000
192A192GLU-1-0.851-0.91130.7019.3019.3010.0000.0000.0000.000
193A193ILE00.0220.01627.273-0.204-0.2040.0000.0000.0000.000
194A194LYS10.8300.90925.657-10.959-10.9590.0000.0000.0000.000
195A195LYS10.8980.94630.139-7.960-7.9600.0000.0000.0000.000
196A196PHE00.0100.00631.598-0.217-0.2170.0000.0000.0000.000
197A197ILE00.0370.02027.674-0.157-0.1570.0000.0000.0000.000
198A198ALA00.0060.00032.049-0.180-0.1800.0000.0000.0000.000
199A199ASP-1-0.837-0.91234.2077.5027.5020.0000.0000.0000.000
200A200ASN0-0.009-0.01334.896-0.387-0.3870.0000.0000.0000.000
201A201LEU00.0130.01732.0020.0290.0290.0000.0000.0000.000
202A202ASP-1-0.776-0.86334.8168.2838.2830.0000.0000.0000.000
203A203LYS10.8710.96537.214-7.820-7.8200.0000.0000.0000.000