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

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FMODB ID: 8978Y

Calculation Name: 3DLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q746M7

Base Structure: X-ray

Registration Date: 2023-09-22

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 640
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -13946982.630159
FMO2-HF: Nuclear repulsion 13701613.797581
FMO2-HF: Total energy -245368.832578
FMO2-MP2: Total energy -246102.977902


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:3:HIS)


Summations of interaction energy for fragment #1(A:3:HIS)
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.
-46.266-46.33725.163-10.232-14.8590.059
Interaction energy analysis for fragmet #1(A:3:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.010
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].
3A5GLY0-0.0250.0003.170-1.9810.5910.000-1.312-1.2590.001
4A6LYS10.8820.9445.175-2.138-2.086-0.001-0.001-0.0490.000
5A7THR0-0.031-0.0318.3070.6050.6050.0000.0000.0000.000
6A8GLU-1-0.838-0.89310.2091.4371.4370.0000.0000.0000.000
7A9VAL0-0.026-0.01912.9960.1070.1070.0000.0000.0000.000
8A10PHE00.0280.00115.197-0.117-0.1170.0000.0000.0000.000
9A11LEU00.0310.03216.8820.0060.0060.0000.0000.0000.000
10A12ASN0-0.104-0.05419.9240.0130.0130.0000.0000.0000.000
11A13ARG10.9820.99021.696-0.305-0.3050.0000.0000.0000.000
12A14PHE0-0.013-0.01224.7780.0390.0390.0000.0000.0000.000
13A15ALA00.0250.02327.042-0.025-0.0250.0000.0000.0000.000
14A16LEU0-0.037-0.01828.7250.0000.0000.0000.0000.0000.000
15A17ARG10.8160.91132.482-0.133-0.1330.0000.0000.0000.000
16A18PRO00.0780.00833.780-0.003-0.0030.0000.0000.0000.000
17A19LEU0-0.051-0.01534.763-0.004-0.0040.0000.0000.0000.000
18A20ASN0-0.0280.00337.514-0.004-0.0040.0000.0000.0000.000
19A21PRO00.0950.01340.898-0.003-0.0030.0000.0000.0000.000
20A22GLU-1-0.872-0.94642.8640.0840.0840.0000.0000.0000.000
21A23GLU-1-0.788-0.89940.1580.1100.1100.0000.0000.0000.000
22A24LEU00.0050.00336.892-0.003-0.0030.0000.0000.0000.000
23A25ARG10.8730.94240.674-0.084-0.0840.0000.0000.0000.000
24A26PRO00.0450.04441.905-0.001-0.0010.0000.0000.0000.000
25A27TRP00.0450.01744.795-0.005-0.0050.0000.0000.0000.000
26A28ARG10.9370.94947.140-0.022-0.0220.0000.0000.0000.000
27A29LEU0-0.051-0.03048.5250.0000.0000.0000.0000.0000.000
28A30GLU-1-0.784-0.85750.1420.0120.0120.0000.0000.0000.000
29A31VAL0-0.0030.00150.5120.0020.0020.0000.0000.0000.000
30A32VAL00.0140.00753.278-0.002-0.0020.0000.0000.0000.000
31A33LEU0-0.035-0.03051.7810.0020.0020.0000.0000.0000.000
32A34ASP-1-0.886-0.90256.422-0.002-0.0020.0000.0000.0000.000
33A35PRO00.0590.00659.6710.0010.0010.0000.0000.0000.000
34A36PRO0-0.006-0.01756.7950.0000.0000.0000.0000.0000.000
35A37PRO0-0.0150.01752.622-0.001-0.0010.0000.0000.0000.000
36A38GLY00.0760.04252.711-0.001-0.0010.0000.0000.0000.000
37A39ARG11.0000.97947.7840.0320.0320.0000.0000.0000.000
38A40GLU-1-0.935-0.96946.678-0.024-0.0240.0000.0000.0000.000
39A41GLU-1-0.800-0.89046.826-0.010-0.0100.0000.0000.0000.000
40A42VAL00.0310.01448.2810.0040.0040.0000.0000.0000.000
41A43TYR0-0.033-0.03441.7020.0040.0040.0000.0000.0000.000
42A44PRO0-0.042-0.02944.3170.0050.0050.0000.0000.0000.000
43A45LEU00.0330.02145.6730.0040.0040.0000.0000.0000.000
44A46LEU00.0320.02446.5470.0040.0040.0000.0000.0000.000
45A47ALA0-0.046-0.01143.6350.0050.0050.0000.0000.0000.000
46A48GLN0-0.050-0.04045.3050.0050.0050.0000.0000.0000.000
47A49VAL00.0470.02448.4110.0030.0030.0000.0000.0000.000
48A50ALA00.0010.00545.7770.0030.0030.0000.0000.0000.000
49A51ARG10.8170.90341.748-0.042-0.0420.0000.0000.0000.000
50A52ARG10.8490.93448.300-0.019-0.0190.0000.0000.0000.000
51A53ALA00.0430.03350.6000.0010.0010.0000.0000.0000.000
52A54GLY00.0090.01349.8750.0020.0020.0000.0000.0000.000
53A55GLY00.0440.01648.8850.0000.0000.0000.0000.0000.000
54A56VAL0-0.072-0.04942.6270.0010.0010.0000.0000.0000.000
55A57THR00.0020.00545.2160.0000.0000.0000.0000.0000.000
56A58VAL0-0.023-0.02140.084-0.001-0.0010.0000.0000.0000.000
57A59ARG10.9200.97440.183-0.010-0.0100.0000.0000.0000.000
58A60MET0-0.053-0.03341.6740.0040.0040.0000.0000.0000.000
59A61GLY00.0020.00942.104-0.001-0.0010.0000.0000.0000.000
60A62ASP-1-0.806-0.91143.678-0.005-0.0050.0000.0000.0000.000
61A63GLY0-0.007-0.00246.4430.0000.0000.0000.0000.0000.000
62A64LEU0-0.033-0.00346.1640.0010.0010.0000.0000.0000.000
63A65ALA00.0490.01243.2920.0000.0000.0000.0000.0000.000
64A66SER0-0.013-0.00245.1010.0020.0020.0000.0000.0000.000
65A67TRP00.020-0.01437.7090.0020.0020.0000.0000.0000.000
66A68SER0-0.0240.01145.5530.0040.0040.0000.0000.0000.000
67A69PRO00.019-0.01048.645-0.002-0.0020.0000.0000.0000.000
68A70PRO00.020-0.00751.639-0.001-0.0010.0000.0000.0000.000
69A71GLU-1-0.896-0.93553.6020.0390.0390.0000.0000.0000.000
70A72VAL0-0.079-0.04352.5720.0000.0000.0000.0000.0000.000
71A73LEU0-0.075-0.01950.3790.0000.0000.0000.0000.0000.000
72A74VAL00.0200.03154.109-0.001-0.0010.0000.0000.0000.000
73A75LEU00.023-0.01655.366-0.002-0.0020.0000.0000.0000.000
74A76GLU-1-0.801-0.88156.9540.0160.0160.0000.0000.0000.000
75A77GLY00.0320.02357.5510.0020.0020.0000.0000.0000.000
76A78THR00.0160.01358.049-0.001-0.0010.0000.0000.0000.000
77A79LEU0-0.029-0.01151.9280.0030.0030.0000.0000.0000.000
78A80ALA00.0140.00853.745-0.002-0.0020.0000.0000.0000.000
79A81ARG10.8260.90445.7310.0140.0140.0000.0000.0000.000
80A82MET0-0.012-0.00750.773-0.002-0.0020.0000.0000.0000.000
81A83GLY00.0340.03752.792-0.002-0.0020.0000.0000.0000.000
82A84GLN0-0.005-0.00454.2730.0010.0010.0000.0000.0000.000
83A85THR0-0.059-0.04155.8550.0020.0020.0000.0000.0000.000
84A86TYR0-0.006-0.01054.256-0.001-0.0010.0000.0000.0000.000
85A87ALA00.0330.01158.0020.0030.0030.0000.0000.0000.000
86A88TYR0-0.038-0.02954.978-0.002-0.0020.0000.0000.0000.000
87A89ARG10.8810.91956.927-0.015-0.0150.0000.0000.0000.000
88A90LEU0-0.065-0.02652.432-0.001-0.0010.0000.0000.0000.000
89A91TYR00.004-0.01054.8300.0000.0000.0000.0000.0000.000
90A92PRO00.007-0.00753.8930.0000.0000.0000.0000.0000.000
91A93LYS10.8530.91552.583-0.017-0.0170.0000.0000.0000.000
92A94GLY00.0350.03152.3170.0000.0000.0000.0000.0000.000
93A95ARG10.7990.91746.557-0.065-0.0650.0000.0000.0000.000
94A96ARG10.8960.94141.545-0.035-0.0350.0000.0000.0000.000
95A97PRO0-0.025-0.01542.3100.0020.0020.0000.0000.0000.000
96A98LEU0-0.036-0.01338.194-0.006-0.0060.0000.0000.0000.000
97A99ASP-1-0.784-0.90034.6480.0800.0800.0000.0000.0000.000
98A100PRO0-0.057-0.03331.961-0.006-0.0060.0000.0000.0000.000
99A101LYS10.8900.94030.430-0.086-0.0860.0000.0000.0000.000
100A102ASP-1-0.776-0.86830.6950.0130.0130.0000.0000.0000.000
101A103PRO0-0.017-0.02229.0420.0060.0060.0000.0000.0000.000
102A104GLY00.0330.02731.1770.0020.0020.0000.0000.0000.000
103A105GLU-1-0.810-0.89234.5860.0450.0450.0000.0000.0000.000
104A106ARG10.8010.87925.878-0.112-0.1120.0000.0000.0000.000
105A107SER0-0.098-0.06132.6780.0080.0080.0000.0000.0000.000
106A108VAL00.0160.00133.6010.0020.0020.0000.0000.0000.000
107A109LEU00.0160.01335.3670.0040.0040.0000.0000.0000.000
108A110SER0-0.019-0.01632.3440.0130.0130.0000.0000.0000.000
109A111ALA0-0.0160.00634.4660.0040.0040.0000.0000.0000.000
110A112LEU0-0.014-0.00237.0200.0000.0000.0000.0000.0000.000
111A113ALA00.0360.01735.0590.0020.0020.0000.0000.0000.000
112A114ARG10.9861.00434.465-0.062-0.0620.0000.0000.0000.000
113A115ARG10.8750.94136.516-0.057-0.0570.0000.0000.0000.000
114A116LEU00.0080.00939.038-0.002-0.0020.0000.0000.0000.000
115A117LEU00.0050.00434.6110.0010.0010.0000.0000.0000.000
116A118GLN0-0.020-0.01638.703-0.006-0.0060.0000.0000.0000.000
117A119GLU-1-0.763-0.86040.9540.0650.0650.0000.0000.0000.000
118A120ARG10.9060.95741.190-0.113-0.1130.0000.0000.0000.000
119A121LEU00.001-0.00437.6570.0010.0010.0000.0000.0000.000
120A122ARG10.8110.88542.201-0.066-0.0660.0000.0000.0000.000
121A123ARG10.8370.91945.442-0.077-0.0770.0000.0000.0000.000
122A124LEU0-0.036-0.00441.3550.0040.0040.0000.0000.0000.000
123A125GLU-1-0.923-0.95346.0130.0980.0980.0000.0000.0000.000
124A126GLY0-0.0070.00046.9120.0040.0040.0000.0000.0000.000
125A127VAL0-0.031-0.02142.0710.0080.0080.0000.0000.0000.000
126A128TRP00.0210.01341.951-0.006-0.0060.0000.0000.0000.000
127A129VAL00.0200.01040.9370.0050.0050.0000.0000.0000.000
128A130GLU-1-0.836-0.89639.8210.0520.0520.0000.0000.0000.000
129A131GLY0-0.008-0.00939.297-0.001-0.0010.0000.0000.0000.000
130A132LEU00.000-0.00634.080-0.001-0.0010.0000.0000.0000.000
131A133ALA0-0.0130.00735.6020.0120.0120.0000.0000.0000.000
132A134VAL00.0240.01636.583-0.006-0.0060.0000.0000.0000.000
133A135TYR0-0.028-0.00936.1390.0100.0100.0000.0000.0000.000
134A136ARG10.8250.88336.271-0.177-0.1770.0000.0000.0000.000
135A137ARG10.9760.98538.667-0.154-0.1540.0000.0000.0000.000
136A138GLU-1-0.770-0.87840.9520.0790.0790.0000.0000.0000.000
137A139HIS0-0.092-0.05237.4510.0190.0190.0000.0000.0000.000
138A140ALA00.0760.04741.7140.0000.0000.0000.0000.0000.000
139A141ARG10.7300.82644.238-0.063-0.0630.0000.0000.0000.000
140A142GLY00.1270.08947.412-0.003-0.0030.0000.0000.0000.000
141A143PRO00.018-0.01150.1790.0010.0010.0000.0000.0000.000
142A144GLY00.0220.00451.885-0.002-0.0020.0000.0000.0000.000
143A145TRP00.0350.04443.9910.0020.0020.0000.0000.0000.000
144A146ARG10.8880.92145.666-0.064-0.0640.0000.0000.0000.000
145A147VAL0-0.0180.01539.5240.0000.0000.0000.0000.0000.000
146A148LEU0-0.018-0.01040.9030.0050.0050.0000.0000.0000.000
147A149GLY00.0330.02236.9500.0000.0000.0000.0000.0000.000
148A150GLY0-0.032-0.05635.7830.0000.0000.0000.0000.0000.000
149A151ALA0-0.035-0.00431.6260.0130.0130.0000.0000.0000.000
150A152VAL0-0.0230.00430.313-0.011-0.0110.0000.0000.0000.000
151A153LEU0-0.029-0.02131.0940.0180.0180.0000.0000.0000.000
152A154ASP-1-0.863-0.95629.7080.1010.1010.0000.0000.0000.000
153A155LEU0-0.065-0.01331.1740.0190.0190.0000.0000.0000.000
154A156TRP0-0.031-0.01524.581-0.009-0.0090.0000.0000.0000.000
155A157VAL00.0310.02331.3840.0140.0140.0000.0000.0000.000
156A158SER00.0320.01627.026-0.011-0.0110.0000.0000.0000.000
157A159ASP-1-0.820-0.92525.3020.1490.1490.0000.0000.0000.000
158A160SER0-0.026-0.02126.9750.0020.0020.0000.0000.0000.000
159A161GLY0-0.031-0.01229.468-0.002-0.0020.0000.0000.0000.000
160A162ALA0-0.013-0.00330.516-0.004-0.0040.0000.0000.0000.000
161A163PHE0-0.028-0.01331.030-0.003-0.0030.0000.0000.0000.000
162A164LEU00.0180.01224.8280.0230.0230.0000.0000.0000.000
163A165LEU0-0.021-0.01029.182-0.019-0.0190.0000.0000.0000.000
164A166GLU-1-0.903-0.96125.4020.2370.2370.0000.0000.0000.000
165A167VAL00.016-0.00827.156-0.019-0.0190.0000.0000.0000.000
166A168ASP-1-0.754-0.86526.0820.2550.2550.0000.0000.0000.000
167A169PRO0-0.009-0.00227.753-0.022-0.0220.0000.0000.0000.000
168A170ALA0-0.040-0.01329.945-0.001-0.0010.0000.0000.0000.000
169A171TYR00.0290.00932.6770.0090.0090.0000.0000.0000.000
170A172ARG10.8650.91735.998-0.065-0.0650.0000.0000.0000.000
171A173ILE00.0380.03338.9970.0050.0050.0000.0000.0000.000
172A174LEU0-0.035-0.01041.850-0.005-0.0050.0000.0000.0000.000
173A175CYS00.0180.01445.0310.0000.0000.0000.0000.0000.000
174A176GLU-1-0.849-0.91148.3390.0550.0550.0000.0000.0000.000
175A177MET0-0.0270.00651.387-0.002-0.0020.0000.0000.0000.000
176A178SER00.0470.02452.5950.0000.0000.0000.0000.0000.000
177A179LEU0-0.010-0.01851.5330.0000.0000.0000.0000.0000.000
178A180GLU-1-0.761-0.84553.9300.0030.0030.0000.0000.0000.000
179A181ALA00.000-0.00256.533-0.001-0.0010.0000.0000.0000.000
180A182TRP00.009-0.02447.742-0.001-0.0010.0000.0000.0000.000
181A183LEU00.0280.01653.208-0.001-0.0010.0000.0000.0000.000
182A184ALA00.0200.02955.815-0.001-0.0010.0000.0000.0000.000
183A185GLN0-0.081-0.06056.2550.0010.0010.0000.0000.0000.000
184A186GLY00.0380.02156.3630.0010.0010.0000.0000.0000.000
185A187HIS10.7940.91550.765-0.021-0.0210.0000.0000.0000.000
186A188PRO00.0670.03048.573-0.002-0.0020.0000.0000.0000.000
187A189LEU00.0160.00550.4860.0030.0030.0000.0000.0000.000
188A190PRO00.0310.03946.426-0.002-0.0020.0000.0000.0000.000
189A191LYS10.8970.93442.4720.0240.0240.0000.0000.0000.000
190A192ARG10.8350.90541.3170.0140.0140.0000.0000.0000.000
191A193VAL00.0440.02745.0140.0040.0040.0000.0000.0000.000
192A194ARG10.8550.94145.339-0.032-0.0320.0000.0000.0000.000
193A195ASN00.0280.02547.765-0.003-0.0030.0000.0000.0000.000
194A196ALA00.0190.00250.0660.0040.0040.0000.0000.0000.000
195A197TYR00.002-0.01552.4760.0030.0030.0000.0000.0000.000
196A198ASP-1-0.809-0.88849.5390.0180.0180.0000.0000.0000.000
197A199ARG10.8440.88343.702-0.052-0.0520.0000.0000.0000.000
198A200ARG10.8210.92845.0350.0060.0060.0000.0000.0000.000
199A201THR0-0.044-0.02342.7360.0000.0000.0000.0000.0000.000
200A202TRP0-0.015-0.02445.426-0.004-0.0040.0000.0000.0000.000
201A203GLU-1-0.844-0.89143.648-0.030-0.0300.0000.0000.0000.000
202A204LEU00.0280.00146.092-0.001-0.0010.0000.0000.0000.000
203A205LEU0-0.063-0.02648.387-0.003-0.0030.0000.0000.0000.000
204A206ARG10.9200.96250.6280.0200.0200.0000.0000.0000.000
205A207LEU00.0540.02053.8780.0020.0020.0000.0000.0000.000
206A208GLY0-0.055-0.03557.006-0.003-0.0030.0000.0000.0000.000
207A209GLU-1-0.963-0.98160.204-0.014-0.0140.0000.0000.0000.000
208A210GLU-1-0.764-0.87661.580-0.015-0.0150.0000.0000.0000.000
209A211ASP-1-0.811-0.92764.559-0.005-0.0050.0000.0000.0000.000
210A212PRO0-0.016-0.01263.2040.0000.0000.0000.0000.0000.000
211A213LYS10.7480.84964.9780.0030.0030.0000.0000.0000.000
212A214GLU-1-0.815-0.88768.138-0.005-0.0050.0000.0000.0000.000
213A215LEU0-0.0140.01661.294-0.002-0.0020.0000.0000.0000.000
214A216PRO0-0.005-0.00165.3390.0010.0010.0000.0000.0000.000
215A217LEU0-0.039-0.03160.326-0.001-0.0010.0000.0000.0000.000
216A218PRO0-0.013-0.02459.5890.0000.0000.0000.0000.0000.000
217A219GLY0-0.002-0.00362.888-0.001-0.0010.0000.0000.0000.000
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