FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: N14LQ

Calculation Name: 1B78-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B78

Chain ID: A

ChEMBL ID:

UniProt ID: Q57679

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2040620.989398
FMO2-HF: Nuclear repulsion 1967853.392657
FMO2-HF: Total energy -72767.596741
FMO2-MP2: Total energy -72984.851313


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:10:LYS)


Summations of interaction energy for fragment #1(A:10:LYS)
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.
-172.985-170.56636.158-18.881-19.695-0.2
Interaction energy analysis for fragmet #1(A:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.820 / q_NPA : 0.900
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].
3A12TYR00.0170.0012.479-10.416-6.6463.649-2.423-4.996-0.010
4A13PHE00.0360.0045.1815.1625.194-0.001-0.002-0.0280.000
5A14ALA00.0220.0198.487-0.797-0.7970.0000.0000.0000.000
6A15THR00.0270.00311.3082.7182.7180.0000.0000.0000.000
7A16GLY00.0420.03812.881-1.452-1.4520.0000.0000.0000.000
8A17ASN0-0.015-0.02015.204-0.015-0.0150.0000.0000.0000.000
9A18PRO00.0570.01712.757-0.899-0.8990.0000.0000.0000.000
10A19ASN00.014-0.01013.039-1.766-1.7660.0000.0000.0000.000
11A20LYS10.8760.94913.62517.86317.8630.0000.0000.0000.000
12A21ILE00.0040.0098.0130.0380.0380.0000.0000.0000.000
13A22LYS10.9190.96810.36421.63121.6310.0000.0000.0000.000
14A23GLU-1-0.814-0.88112.519-16.911-16.9110.0000.0000.0000.000
15A24ALA00.0240.00410.3010.4630.4630.0000.0000.0000.000
16A25ASN00.0670.0186.4670.4450.4450.0000.0000.0000.000
17A26ILE0-0.0170.0049.9260.7660.7660.0000.0000.0000.000
18A27ILE0-0.070-0.03713.3631.1101.1100.0000.0000.0000.000
19A28LEU00.017-0.0038.3550.8370.8370.0000.0000.0000.000
20A29LYS10.8460.95710.13016.63116.6310.0000.0000.0000.000
21A30ASP-1-0.830-0.91611.472-16.781-16.7810.0000.0000.0000.000
22A31LEU0-0.048-0.0198.6530.8970.8970.0000.0000.0000.000
23A32LYS10.9030.9398.38717.73317.7330.0000.0000.0000.000
24A33ASP-1-0.923-0.9506.660-22.578-22.5780.0000.0000.0000.000
25A34VAL0-0.041-0.0233.621-2.103-1.7680.002-0.062-0.2750.000
26A35GLU-1-0.909-0.9372.439-39.673-38.3850.567-0.578-1.277-0.002
27A36ILE0-0.015-0.0202.536-11.041-8.0612.038-2.370-2.647-0.028
28A37GLU-1-0.808-0.8901.716-153.099-159.28029.905-13.423-10.302-0.160
29A38GLN0-0.047-0.0314.6243.3973.452-0.001-0.004-0.0500.000
30A39ILE00.0200.0066.027-4.420-4.4200.0000.0000.0000.000
31A40LYS10.9080.9518.06129.75129.7510.0000.0000.0000.000
32A41ILE00.0170.01210.1910.8660.8660.0000.0000.0000.000
33A42SER0-0.009-0.00213.0840.0080.0080.0000.0000.0000.000
34A43TYR0-0.019-0.01815.341-0.676-0.6760.0000.0000.0000.000
35A44PRO00.0100.01018.3860.3070.3070.0000.0000.0000.000
36A45GLU-1-0.857-0.91720.749-14.751-14.7510.0000.0000.0000.000
37A46ILE0-0.040-0.02522.7280.4690.4690.0000.0000.0000.000
38A47GLN00.006-0.00225.7380.1210.1210.0000.0000.0000.000
39A48GLY00.0380.02328.4250.1100.1100.0000.0000.0000.000
40A49THR0-0.052-0.06427.313-0.176-0.1760.0000.0000.0000.000
41A50LEU00.020-0.00523.066-0.239-0.2390.0000.0000.0000.000
42A51GLU-1-0.768-0.87322.253-12.263-12.2630.0000.0000.0000.000
43A52GLU-1-0.799-0.85322.091-11.276-11.2760.0000.0000.0000.000
44A53VAL0-0.0030.01420.811-0.437-0.4370.0000.0000.0000.000
45A54ALA00.002-0.00218.052-0.699-0.6990.0000.0000.0000.000
46A55GLU-1-0.826-0.90117.800-14.214-14.2140.0000.0000.0000.000
47A56PHE0-0.038-0.02019.011-0.479-0.4790.0000.0000.0000.000
48A57GLY00.0280.00417.898-0.356-0.3560.0000.0000.0000.000
49A58ALA0-0.013-0.01314.366-0.986-0.9860.0000.0000.0000.000
50A59LYS10.8770.91314.54412.92212.9220.0000.0000.0000.000
51A60TRP00.0010.01216.671-0.107-0.1070.0000.0000.0000.000
52A61VAL00.0270.00011.370-0.441-0.4410.0000.0000.0000.000
53A62TYR0-0.029-0.00510.132-0.669-0.6690.0000.0000.0000.000
54A63ASN0-0.003-0.00413.073-0.130-0.1300.0000.0000.0000.000
55A64ILE0-0.048-0.02313.3250.3020.3020.0000.0000.0000.000
56A65LEU0-0.098-0.0616.634-1.039-1.0390.0000.0000.0000.000
57A66LYS10.8970.95610.64718.43118.4310.0000.0000.0000.000
58A67LYS10.9430.9774.99742.82842.8280.0000.0000.0000.000
59A68PRO00.0190.0104.7970.7530.893-0.001-0.019-0.1200.000
60A69VAL0-0.047-0.0126.363-4.770-4.7700.0000.0000.0000.000
61A70ILE0-0.005-0.0068.4272.6442.6440.0000.0000.0000.000
62A71VAL00.0160.00910.671-1.130-1.1300.0000.0000.0000.000
63A72GLU-1-0.796-0.86413.586-16.360-16.3600.0000.0000.0000.000
64A73ASP-1-0.812-0.89516.301-13.707-13.7070.0000.0000.0000.000
65A74SER0-0.034-0.02820.0190.1970.1970.0000.0000.0000.000
66A75GLY0-0.0040.00822.6500.0910.0910.0000.0000.0000.000
67A76PHE0-0.006-0.00426.405-0.046-0.0460.0000.0000.0000.000
68A77PHE0-0.043-0.01027.3630.0850.0850.0000.0000.0000.000
69A78VAL00.0830.03732.4320.0860.0860.0000.0000.0000.000
70A79GLU-1-0.802-0.89536.086-8.046-8.0460.0000.0000.0000.000
71A80ALA00.0080.01738.2540.1030.1030.0000.0000.0000.000
72A81LEU0-0.028-0.02438.2890.1710.1710.0000.0000.0000.000
73A82ASN0-0.027-0.01538.587-0.078-0.0780.0000.0000.0000.000
74A83GLY0-0.023-0.00834.665-0.116-0.1160.0000.0000.0000.000
75A84PHE00.0200.02433.387-0.369-0.3690.0000.0000.0000.000
76A85PRO0-0.004-0.01431.5710.1190.1190.0000.0000.0000.000
77A86GLY00.0650.01930.030-0.086-0.0860.0000.0000.0000.000
78A87THR0-0.0090.00226.506-0.197-0.1970.0000.0000.0000.000
79A88TYR00.0110.01327.029-0.432-0.4320.0000.0000.0000.000
80A89SER00.024-0.01127.2930.2790.2790.0000.0000.0000.000
81A90LYS10.8420.91921.92113.96713.9670.0000.0000.0000.000
82A91PHE00.0770.03928.1310.2130.2130.0000.0000.0000.000
83A92VAL00.0210.01930.8930.2540.2540.0000.0000.0000.000
84A93GLN0-0.062-0.03630.4640.3780.3780.0000.0000.0000.000
85A94GLU-1-0.953-0.98528.712-10.852-10.8520.0000.0000.0000.000
86A95THR0-0.088-0.03233.2060.2950.2950.0000.0000.0000.000
87A96ILE0-0.011-0.01936.3320.2720.2720.0000.0000.0000.000
88A97GLY00.0340.03634.9660.1710.1710.0000.0000.0000.000
89A98ASN0-0.019-0.03633.851-0.069-0.0690.0000.0000.0000.000
90A99GLU-1-0.864-0.93136.901-7.620-7.6200.0000.0000.0000.000
91A100GLY00.0110.01239.4590.2140.2140.0000.0000.0000.000
92A101ILE0-0.051-0.02835.6390.1100.1100.0000.0000.0000.000
93A102LEU00.0000.00539.1370.1280.1280.0000.0000.0000.000
94A103LYS10.8220.90041.8496.7616.7610.0000.0000.0000.000
95A104LEU0-0.049-0.03640.0570.1510.1510.0000.0000.0000.000
96A105LEU0-0.046-0.02939.9340.1030.1030.0000.0000.0000.000
97A106GLU-1-0.801-0.87543.625-6.442-6.4420.0000.0000.0000.000
98A107GLY0-0.008-0.00146.9680.0710.0710.0000.0000.0000.000
99A108LYS10.8170.92543.9537.1217.1210.0000.0000.0000.000
100A109ASP-1-0.867-0.93346.395-6.369-6.3690.0000.0000.0000.000
101A110ASN0-0.079-0.03740.738-0.142-0.1420.0000.0000.0000.000
102A111ARG10.9180.95041.1797.2457.2450.0000.0000.0000.000
103A112ASN0-0.0210.00237.521-0.199-0.1990.0000.0000.0000.000
104A113ALA0-0.004-0.01234.1690.0040.0040.0000.0000.0000.000
105A114TYR0-0.053-0.02528.835-0.073-0.0730.0000.0000.0000.000
106A115PHE00.0300.04126.242-0.067-0.0670.0000.0000.0000.000
107A116LYS10.8280.88924.24711.43111.4310.0000.0000.0000.000
108A117THR0-0.010-0.01918.526-0.040-0.0400.0000.0000.0000.000
109A118VAL0-0.045-0.03219.4050.2480.2480.0000.0000.0000.000
110A119ILE00.0120.00812.889-0.353-0.3530.0000.0000.0000.000
111A120GLY00.011-0.01015.2580.7780.7780.0000.0000.0000.000
112A121TYR0-0.074-0.0747.334-1.968-1.9680.0000.0000.0000.000
113A122CYS0-0.012-0.01011.2152.2052.2050.0000.0000.0000.000
114A123ASP-1-0.738-0.8238.991-23.911-23.9110.0000.0000.0000.000
115A124GLU-1-0.824-0.8978.545-23.499-23.4990.0000.0000.0000.000
116A125ASN0-0.102-0.05611.7702.0542.0540.0000.0000.0000.000
117A126GLY0-0.0030.01314.2611.0151.0150.0000.0000.0000.000
118A127VAL0-0.017-0.03114.255-0.932-0.9320.0000.0000.0000.000
119A128ARG10.9080.97214.01215.91015.9100.0000.0000.0000.000
120A129LEU0-0.0050.00715.438-0.707-0.7070.0000.0000.0000.000
121A130PHE0-0.0010.00312.9270.4190.4190.0000.0000.0000.000
122A131LYS10.8820.91717.55711.83811.8380.0000.0000.0000.000
123A132GLY00.0450.02520.6240.0230.0230.0000.0000.0000.000
124A133ILE0-0.080-0.05422.031-0.036-0.0360.0000.0000.0000.000
125A134VAL00.0480.04525.619-0.019-0.0190.0000.0000.0000.000
126A135LYS10.9120.93628.1078.7918.7910.0000.0000.0000.000
127A136GLY00.0550.01731.760-0.076-0.0760.0000.0000.0000.000
128A137ARG10.8580.94234.4548.0228.0220.0000.0000.0000.000
129A138VAL0-0.027-0.02336.376-0.191-0.1910.0000.0000.0000.000
130A139SER0-0.018-0.01038.3250.1430.1430.0000.0000.0000.000
131A140GLU-1-0.899-0.96640.366-6.941-6.9410.0000.0000.0000.000
132A141GLU-1-0.877-0.95042.203-7.253-7.2530.0000.0000.0000.000
133A142ILE0-0.0200.01437.780-0.219-0.2190.0000.0000.0000.000
134A143ARG10.8330.91538.1967.9507.9500.0000.0000.0000.000
135A144SER00.000-0.03134.833-0.357-0.3570.0000.0000.0000.000
136A145LYS10.8430.89734.9198.5328.5320.0000.0000.0000.000
137A146GLY0-0.0150.00533.508-0.053-0.0530.0000.0000.0000.000
138A147TYR0-0.023-0.01929.552-0.247-0.2470.0000.0000.0000.000
139A148GLY00.0120.00428.298-0.329-0.3290.0000.0000.0000.000
140A149PHE0-0.098-0.03922.330-0.196-0.1960.0000.0000.0000.000
141A150ALA00.0510.00928.1390.0850.0850.0000.0000.0000.000
142A151TYR00.041-0.00129.4190.2590.2590.0000.0000.0000.000
143A152ASP-1-0.822-0.90527.911-10.993-10.9930.0000.0000.0000.000
144A153SER0-0.048-0.03031.1230.2130.2130.0000.0000.0000.000
145A154ILE00.0230.01934.3870.2470.2470.0000.0000.0000.000
146A155PHE0-0.0290.00530.2100.1160.1160.0000.0000.0000.000
147A156ILE00.0090.01133.723-0.169-0.1690.0000.0000.0000.000
148A157PRO0-0.070-0.01730.7310.0250.0250.0000.0000.0000.000
149A158GLU-1-0.944-1.00730.549-9.542-9.5420.0000.0000.0000.000
150A159GLU-1-0.930-0.95734.077-7.608-7.6080.0000.0000.0000.000
151A160GLU-1-0.828-0.87833.624-8.480-8.4800.0000.0000.0000.000
152A161GLU-1-0.864-0.93836.469-7.190-7.1900.0000.0000.0000.000
153A162ARG10.6880.83034.0219.0189.0180.0000.0000.0000.000
154A163THR00.0480.00834.812-0.202-0.2020.0000.0000.0000.000
155A164PHE00.0540.00527.400-0.146-0.1460.0000.0000.0000.000
156A165ALA0-0.044-0.00530.729-0.256-0.2560.0000.0000.0000.000
157A166GLU-1-0.811-0.87932.433-8.082-8.0820.0000.0000.0000.000
158A167MET0-0.055-0.01030.4880.1000.1000.0000.0000.0000.000
159A168THR00.008-0.02528.792-0.362-0.3620.0000.0000.0000.000
160A169THR00.002-0.01422.421-0.034-0.0340.0000.0000.0000.000
161A170GLU-1-0.858-0.94724.681-12.075-12.0750.0000.0000.0000.000
162A171GLU-1-0.772-0.81625.889-9.512-9.5120.0000.0000.0000.000
163A172LYS10.8640.94625.96111.25111.2510.0000.0000.0000.000
164A173SER0-0.099-0.06122.226-0.327-0.3270.0000.0000.0000.000
165A174GLN0-0.016-0.03321.786-0.739-0.7390.0000.0000.0000.000
166A175ILE00.0680.03823.948-0.140-0.1400.0000.0000.0000.000
167A176SER00.0040.02522.311-0.096-0.0960.0000.0000.0000.000
168A177HIS00.0590.02822.721-0.177-0.1770.0000.0000.0000.000
169A178ARG10.8050.85716.50516.12816.1280.0000.0000.0000.000
170A179LYS10.8560.93318.01313.11513.1150.0000.0000.0000.000
171A180LYS10.8890.93118.33412.26712.2670.0000.0000.0000.000
172A181ALA00.0200.01517.9110.0060.0060.0000.0000.0000.000
173A182PHE00.023-0.00511.693-0.695-0.6950.0000.0000.0000.000
174A183GLU-1-0.809-0.88214.229-15.665-15.6650.0000.0000.0000.000
175A184GLU-1-0.875-0.91116.260-12.794-12.7940.0000.0000.0000.000
176A185PHE0-0.016-0.0138.160-0.125-0.1250.0000.0000.0000.000
177A186LYS10.8860.93111.42415.54315.5430.0000.0000.0000.000
178A187LYS10.8570.93112.51112.91612.9160.0000.0000.0000.000
179A188PHE00.015-0.0019.9880.1710.1710.0000.0000.0000.000
180A189LEU0-0.059-0.0396.763-0.314-0.3140.0000.0000.0000.000
181A190LEU0-0.010-0.01110.101-0.174-0.1740.0000.0000.0000.000
182A191ASP-1-0.948-0.96012.419-13.383-13.3830.0000.0000.0000.000
183A192ARG10.8030.9076.61522.81722.8170.0000.0000.0000.000
184A193ILE0-0.0240.00012.1100.2530.2530.0000.0000.0000.000