FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: N293Q

Calculation Name: 4J87-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J87

Chain ID: A

ChEMBL ID:

UniProt ID: Q96WV5

Base Structure: X-ray

Registration Date: 2023-09-26

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 316
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5130719.293949
FMO2-HF: Nuclear repulsion 5001651.98433
FMO2-HF: Total energy -129067.309619
FMO2-MP2: Total energy -129438.707375


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-24.725-11.46916.243-9.826-19.673-0.063
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : 0.004
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].
3A3MET0-0.0060.0063.802-1.6550.452-0.019-1.052-1.0360.005
4A4LEU0-0.019-0.0155.9440.1900.1900.0000.0000.0000.000
5A5THR00.028-0.0048.9760.0470.0470.0000.0000.0000.000
6A6LYS10.8410.92311.3390.3760.3760.0000.0000.0000.000
7A7PHE00.0480.03014.4160.0180.0180.0000.0000.0000.000
8A8GLU-1-0.788-0.86615.749-0.109-0.1090.0000.0000.0000.000
9A9SER0-0.0280.00917.9700.0030.0030.0000.0000.0000.000
10A10ARG10.8480.89617.9340.0830.0830.0000.0000.0000.000
11A11SER0-0.011-0.02122.9280.0010.0010.0000.0000.0000.000
12A12SER00.0420.02124.5260.0000.0000.0000.0000.0000.000
13A13ARG10.8280.91523.078-0.027-0.0270.0000.0000.0000.000
14A14ALA00.0000.01320.5390.0000.0000.0000.0000.0000.000
15A15LYS10.7850.90121.434-0.048-0.0480.0000.0000.0000.000
16A16GLY00.0900.05320.1960.0130.0130.0000.0000.0000.000
17A17VAL0-0.046-0.02717.175-0.013-0.0130.0000.0000.0000.000
18A18ALA0-0.0040.00218.7930.0130.0130.0000.0000.0000.000
19A19PHE0-0.0030.00113.155-0.016-0.0160.0000.0000.0000.000
20A20HIS00.0370.04218.7600.0050.0050.0000.0000.0000.000
21A21PRO0-0.012-0.01620.150-0.007-0.0070.0000.0000.0000.000
22A22THR0-0.020-0.03520.776-0.006-0.0060.0000.0000.0000.000
23A23GLN0-0.0100.01622.938-0.009-0.0090.0000.0000.0000.000
24A24PRO0-0.0320.00620.4500.0000.0000.0000.0000.0000.000
25A25TRP0-0.001-0.03421.4390.0010.0010.0000.0000.0000.000
26A26ILE0-0.034-0.02517.4370.0010.0010.0000.0000.0000.000
27A27LEU00.0230.02620.813-0.003-0.0030.0000.0000.0000.000
28A28THR0-0.019-0.02620.4190.0050.0050.0000.0000.0000.000
29A29SER00.0140.00622.787-0.003-0.0030.0000.0000.0000.000
30A30LEU00.0080.00624.0600.0040.0040.0000.0000.0000.000
31A31HIS00.0750.01126.2340.0050.0050.0000.0000.0000.000
32A32ASN0-0.032-0.03227.9500.0010.0010.0000.0000.0000.000
33A33GLY00.0640.05429.988-0.001-0.0010.0000.0000.0000.000
34A34ARG10.8070.92230.154-0.006-0.0060.0000.0000.0000.000
35A35ILE00.0240.00526.4760.0020.0020.0000.0000.0000.000
36A36GLN00.0100.02324.475-0.004-0.0040.0000.0000.0000.000
37A37LEU00.0180.02324.9670.0030.0030.0000.0000.0000.000
38A38TRP00.003-0.01421.940-0.005-0.0050.0000.0000.0000.000
39A39ASP-1-0.749-0.87822.821-0.064-0.0640.0000.0000.0000.000
40A40TYR0-0.043-0.03417.136-0.014-0.0140.0000.0000.0000.000
41A41ARG10.8920.93916.6250.1000.1000.0000.0000.0000.000
42A42MET0-0.018-0.00320.837-0.004-0.0040.0000.0000.0000.000
43A43GLY0-0.0110.00322.2940.0000.0000.0000.0000.0000.000
44A44THR00.0030.00223.1220.0050.0050.0000.0000.0000.000
45A45LEU0-0.028-0.01625.6680.0010.0010.0000.0000.0000.000
46A46LEU0-0.035-0.01926.7380.0010.0010.0000.0000.0000.000
47A47ASP-1-0.791-0.89029.022-0.011-0.0110.0000.0000.0000.000
48A48ARG10.8780.93929.3400.0080.0080.0000.0000.0000.000
49A49PHE0-0.008-0.00229.0750.0000.0000.0000.0000.0000.000
50A50ASP-1-0.876-0.95332.0860.0050.0050.0000.0000.0000.000
51A51GLY00.0340.00834.169-0.001-0.0010.0000.0000.0000.000
52A52HIS0-0.064-0.01432.0300.0010.0010.0000.0000.0000.000
53A53ASP-1-0.885-0.93135.0600.0110.0110.0000.0000.0000.000
54A54GLY00.0190.00633.9400.0020.0020.0000.0000.0000.000
55A55PRO0-0.059-0.03128.514-0.001-0.0010.0000.0000.0000.000
56A56VAL00.0160.02227.3500.0010.0010.0000.0000.0000.000
57A57ARG10.7720.84924.845-0.047-0.0470.0000.0000.0000.000
58A58GLY00.0200.02323.6640.0070.0070.0000.0000.0000.000
59A59ILE0-0.006-0.02022.003-0.008-0.0080.0000.0000.0000.000
60A60ALA00.0040.00722.6080.0060.0060.0000.0000.0000.000
61A61PHE00.0170.00222.288-0.006-0.0060.0000.0000.0000.000
62A62HIS00.0570.04724.6490.0030.0030.0000.0000.0000.000
63A63PRO00.004-0.00523.948-0.005-0.0050.0000.0000.0000.000
64A64THR0-0.009-0.02425.361-0.005-0.0050.0000.0000.0000.000
65A65GLN00.0250.02428.563-0.005-0.0050.0000.0000.0000.000
66A66PRO0-0.053-0.02229.7780.0000.0000.0000.0000.0000.000
67A67ILE0-0.016-0.03230.225-0.001-0.0010.0000.0000.0000.000
68A68PHE0-0.017-0.00926.999-0.001-0.0010.0000.0000.0000.000
69A69VAL0-0.0050.00327.246-0.001-0.0010.0000.0000.0000.000
70A70SER00.014-0.03227.3130.0000.0000.0000.0000.0000.000
71A71GLY00.0340.01928.232-0.001-0.0010.0000.0000.0000.000
72A72GLY00.0140.00328.8040.0020.0020.0000.0000.0000.000
73A73ASP-1-0.731-0.84030.4600.0400.0400.0000.0000.0000.000
74A74ASP-1-0.742-0.85232.8460.0210.0210.0000.0000.0000.000
75A75TYR0-0.0310.00234.479-0.002-0.0020.0000.0000.0000.000
76A76LYS10.8170.92635.177-0.016-0.0160.0000.0000.0000.000
77A77VAL00.018-0.00431.1110.0020.0020.0000.0000.0000.000
78A78ASN00.0140.02032.450-0.002-0.0020.0000.0000.0000.000
79A79VAL00.0240.01632.0270.0010.0010.0000.0000.0000.000
80A80TRP00.0440.01631.535-0.004-0.0040.0000.0000.0000.000
81A81ASN00.0420.03032.713-0.001-0.0010.0000.0000.0000.000
82A82TYR00.0610.03228.428-0.004-0.0040.0000.0000.0000.000
83A83LYS10.9310.97032.0070.0080.0080.0000.0000.0000.000
84A84SER0-0.030-0.03034.333-0.001-0.0010.0000.0000.0000.000
85A85ARG10.8040.89730.9730.0150.0150.0000.0000.0000.000
86A86LYS10.9830.99635.5370.0000.0000.0000.0000.0000.000
87A87LEU00.0220.02035.4090.0010.0010.0000.0000.0000.000
88A88LEU0-0.091-0.05236.225-0.001-0.0010.0000.0000.0000.000
89A89PHE00.002-0.02036.888-0.001-0.0010.0000.0000.0000.000
90A90SER00.0260.00137.0550.0000.0000.0000.0000.0000.000
91A91LEU0-0.073-0.02634.499-0.001-0.0010.0000.0000.0000.000
92A92CYS00.001-0.00536.8440.0010.0010.0000.0000.0000.000
93A93GLY00.040-0.00238.9000.0000.0000.0000.0000.0000.000
94A94HIS0-0.067-0.02932.9670.0020.0020.0000.0000.0000.000
95A95MET0-0.037-0.02336.986-0.003-0.0030.0000.0000.0000.000
96A96ASP-1-0.784-0.90435.0360.0370.0370.0000.0000.0000.000
97A97TYR0-0.071-0.02830.9960.0000.0000.0000.0000.0000.000
98A98VAL0-0.0390.00128.8160.0040.0040.0000.0000.0000.000
99A99ARG10.7150.81625.690-0.064-0.0640.0000.0000.0000.000
100A100VAL0-0.014-0.01222.5780.0030.0030.0000.0000.0000.000
101A101CYS0-0.033-0.00525.000-0.005-0.0050.0000.0000.0000.000
102A102THR0-0.021-0.00322.1600.0000.0000.0000.0000.0000.000
103A103PHE0-0.005-0.00225.218-0.004-0.0040.0000.0000.0000.000
104A104HIS00.0430.04925.4020.0010.0010.0000.0000.0000.000
105A105HIS0-0.042-0.02624.204-0.004-0.0040.0000.0000.0000.000
106A106GLU-1-0.972-0.98626.2630.0280.0280.0000.0000.0000.000
107A107TYR0-0.024-0.03529.797-0.004-0.0040.0000.0000.0000.000
108A108PRO00.0070.01731.3510.0010.0010.0000.0000.0000.000
109A109TRP0-0.051-0.05631.2160.0010.0010.0000.0000.0000.000
110A110ILE0-0.031-0.01929.5200.0000.0000.0000.0000.0000.000
111A111LEU0-0.0130.01725.480-0.001-0.0010.0000.0000.0000.000
112A112SER0-0.004-0.02328.122-0.001-0.0010.0000.0000.0000.000
113A113CYS0-0.0310.01226.9150.0020.0020.0000.0000.0000.000
114A114SER00.0200.00829.416-0.002-0.0020.0000.0000.0000.000
115A115ASP-1-0.688-0.81730.2030.0600.0600.0000.0000.0000.000
116A116ASP-1-0.750-0.83432.4830.0420.0420.0000.0000.0000.000
117A117GLN0-0.026-0.01133.186-0.001-0.0010.0000.0000.0000.000
118A118THR0-0.089-0.06033.9940.0010.0010.0000.0000.0000.000
119A119ILE00.013-0.00528.8940.0030.0030.0000.0000.0000.000
120A120ARG10.8710.94331.832-0.038-0.0380.0000.0000.0000.000
121A121ILE00.0320.01631.4160.0020.0020.0000.0000.0000.000
122A122TRP0-0.020-0.02632.730-0.005-0.0050.0000.0000.0000.000
123A123ASN00.0480.03534.202-0.001-0.0010.0000.0000.0000.000
124A124TRP00.0160.00031.787-0.003-0.0030.0000.0000.0000.000
125A125GLN0-0.029-0.01636.093-0.002-0.0020.0000.0000.0000.000
126A126SER0-0.042-0.03538.977-0.001-0.0010.0000.0000.0000.000
127A127ARG10.9080.95838.968-0.013-0.0130.0000.0000.0000.000
128A128ASN00.0470.04240.0350.0000.0000.0000.0000.0000.000
129A129CYS0-0.023-0.00136.7520.0020.0020.0000.0000.0000.000
130A130ILE0-0.036-0.02235.505-0.001-0.0010.0000.0000.0000.000
131A131ALA00.0150.00435.6520.0000.0000.0000.0000.0000.000
132A132ILE0-0.002-0.00936.3110.0010.0010.0000.0000.0000.000
133A133LEU0-0.027-0.00431.568-0.001-0.0010.0000.0000.0000.000
134A134THR00.0260.00434.4850.0020.0020.0000.0000.0000.000
135A135GLY00.0440.00535.3440.0000.0000.0000.0000.0000.000
136A136HIS0-0.078-0.02428.5240.0030.0030.0000.0000.0000.000
137A137SER0-0.015-0.00533.429-0.004-0.0040.0000.0000.0000.000
138A138HIS00.0330.01331.853-0.003-0.0030.0000.0000.0000.000
139A139TYR00.0140.00930.0150.0020.0020.0000.0000.0000.000
140A140VAL0-0.0160.00727.3560.0070.0070.0000.0000.0000.000
141A141MET0-0.022-0.00524.189-0.008-0.0080.0000.0000.0000.000
142A142CYS0-0.067-0.03120.6950.0040.0040.0000.0000.0000.000
143A143ALA00.0530.01523.626-0.002-0.0020.0000.0000.0000.000
144A144ALA0-0.041-0.01521.022-0.001-0.0010.0000.0000.0000.000
145A145PHE00.0670.02322.9930.0000.0000.0000.0000.0000.000
146A146HIS00.0260.02522.3040.0060.0060.0000.0000.0000.000
147A147PRO0-0.025-0.01119.490-0.009-0.0090.0000.0000.0000.000
148A148SER0-0.027-0.03122.355-0.006-0.0060.0000.0000.0000.000
149A149GLU-1-0.940-0.95825.0550.0790.0790.0000.0000.0000.000
150A150ASP-1-0.772-0.86027.1840.0480.0480.0000.0000.0000.000
151A151LEU0-0.024-0.02426.0790.0000.0000.0000.0000.0000.000
152A152ILE0-0.015-0.00625.8890.0000.0000.0000.0000.0000.000
153A153VAL0-0.0160.00821.1810.0000.0000.0000.0000.0000.000
154A154SER00.026-0.01424.400-0.003-0.0030.0000.0000.0000.000
155A155ALA00.0120.01222.6260.0050.0050.0000.0000.0000.000
156A156SER00.0260.00324.742-0.008-0.0080.0000.0000.0000.000
157A157LEU00.0140.00526.5480.0060.0060.0000.0000.0000.000
158A158ASP-1-0.760-0.85528.7780.0760.0760.0000.0000.0000.000
159A159GLN0-0.018-0.00227.4020.0000.0000.0000.0000.0000.000
160A160THR0-0.052-0.03827.3780.0070.0070.0000.0000.0000.000
161A161VAL0-0.005-0.01622.4710.0030.0030.0000.0000.0000.000
162A162ARG10.8870.96525.717-0.076-0.0760.0000.0000.0000.000
163A163VAL00.005-0.00225.1810.0050.0050.0000.0000.0000.000
164A164TRP0-0.030-0.03027.771-0.009-0.0090.0000.0000.0000.000
165A165ASP-1-0.814-0.89029.8060.0610.0610.0000.0000.0000.000
166A166ILE00.016-0.00529.289-0.004-0.0040.0000.0000.0000.000
167A167SER0-0.003-0.01733.293-0.005-0.0050.0000.0000.0000.000
168A168GLY00.0280.01534.832-0.003-0.0030.0000.0000.0000.000
169A169LEU00.000-0.00834.342-0.003-0.0030.0000.0000.0000.000
170A170ARG10.8640.92433.147-0.043-0.0430.0000.0000.0000.000
171A171MET0-0.013-0.00136.263-0.003-0.0030.0000.0000.0000.000
172A172LYS10.7950.88239.439-0.032-0.0320.0000.0000.0000.000
173A173ASN0-0.026-0.00938.061-0.001-0.0010.0000.0000.0000.000
174A174ALA00.0060.00738.166-0.001-0.0010.0000.0000.0000.000
175A175ALA0-0.0170.00940.177-0.002-0.0020.0000.0000.0000.000
176A176PRO0-0.0140.00743.6960.0000.0000.0000.0000.0000.000
177A177VAL00.009-0.00846.2200.0000.0000.0000.0000.0000.000
178A178SER0-0.021-0.00349.408-0.001-0.0010.0000.0000.0000.000
179A179MET0-0.047-0.03849.2510.0010.0010.0000.0000.0000.000
180A180SER00.001-0.01154.240-0.001-0.0010.0000.0000.0000.000
181A181LYS10.9550.97956.882-0.008-0.0080.0000.0000.0000.000
182A182GLU-1-0.902-0.96157.9020.0090.0090.0000.0000.0000.000
183A183ASP-1-0.882-0.90359.1800.0110.0110.0000.0000.0000.000
184A184GLN0-0.086-0.04753.7560.0020.0020.0000.0000.0000.000
185A185LYS10.9420.96252.298-0.019-0.0190.0000.0000.0000.000
186A186ALA00.0400.02355.6330.0000.0000.0000.0000.0000.000
187A187GLN0-0.025-0.01552.3150.0000.0000.0000.0000.0000.000
188A188ALA00.0020.01149.8930.0010.0010.0000.0000.0000.000
189A200ALA00.006-0.01140.3130.0000.0000.0000.0000.0000.000
190A201ASP-1-0.829-0.89638.5920.0340.0340.0000.0000.0000.000
191A202ALA00.023-0.00234.1940.0020.0020.0000.0000.0000.000
192A203ILE0-0.0240.00935.021-0.001-0.0010.0000.0000.0000.000
193A204VAL00.0110.00831.9830.0030.0030.0000.0000.0000.000
194A205LYS10.8450.91929.813-0.070-0.0700.0000.0000.0000.000
195A206PHE0-0.034-0.03327.5050.0010.0010.0000.0000.0000.000
196A207VAL00.0370.01329.7730.0010.0010.0000.0000.0000.000
197A208LEU0-0.060-0.02723.865-0.001-0.0010.0000.0000.0000.000
198A209GLU-1-0.896-0.95027.1730.0810.0810.0000.0000.0000.000
199A210GLY00.038-0.00625.9140.0040.0040.0000.0000.0000.000
200A211HIS0-0.086-0.03020.0630.0100.0100.0000.0000.0000.000
201A212ASP-1-0.771-0.84225.3100.0990.0990.0000.0000.0000.000
202A213ARG10.7890.86025.921-0.110-0.1100.0000.0000.0000.000
203A214GLY00.0340.02626.3410.0050.0050.0000.0000.0000.000
204A215VAL0-0.037-0.01521.8400.0120.0120.0000.0000.0000.000
205A216ASN0-0.057-0.06120.552-0.020-0.0200.0000.0000.0000.000
206A217TRP00.024-0.01516.294-0.014-0.0140.0000.0000.0000.000
207A218CYS00.0160.00818.8220.0070.0070.0000.0000.0000.000
208A219ALA0-0.037-0.00515.373-0.011-0.0110.0000.0000.0000.000
209A220PHE00.0900.03717.3970.0130.0130.0000.0000.0000.000
210A221HIS00.0050.01212.441-0.021-0.0210.0000.0000.0000.000
211A222PRO0-0.028-0.02213.983-0.023-0.0230.0000.0000.0000.000
212A223THR00.003-0.01716.622-0.011-0.0110.0000.0000.0000.000
213A224LEU00.0090.02015.038-0.012-0.0120.0000.0000.0000.000
214A225PRO00.0180.02518.5930.0070.0070.0000.0000.0000.000
215A226LEU0-0.052-0.04215.1390.0040.0040.0000.0000.0000.000
216A227ILE00.019-0.00118.349-0.007-0.0070.0000.0000.0000.000
217A228LEU0-0.042-0.01012.2440.0240.0240.0000.0000.0000.000
218A229SER00.026-0.01016.532-0.026-0.0260.0000.0000.0000.000
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