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: 8N5JY

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 OptH
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 -5130061.00468
FMO2-HF: Nuclear repulsion 5000994.507794
FMO2-HF: Total energy -129066.496886
FMO2-MP2: Total energy -129437.836804


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.
-19.173-13.9724.798-9.78-20.224-0.05
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 : 0.014 / q_NPA : -0.002
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].
3A3MET00.0000.0093.802-1.1110.744-0.021-0.912-0.9220.003
4A4LEU0-0.027-0.0166.0030.2450.2450.0000.0000.0000.000
5A5THR00.019-0.0088.9910.0940.0940.0000.0000.0000.000
6A6LYS10.8500.92611.2220.1640.1640.0000.0000.0000.000
7A7PHE00.0470.02814.1470.0170.0170.0000.0000.0000.000
8A8GLU-1-0.827-0.91215.316-0.286-0.2860.0000.0000.0000.000
9A9SER0-0.0280.01917.6340.0120.0120.0000.0000.0000.000
10A10ARG10.8880.92517.4080.1810.1810.0000.0000.0000.000
11A11SER0-0.022-0.03322.5670.0120.0120.0000.0000.0000.000
12A12SER00.0170.01124.188-0.008-0.0080.0000.0000.0000.000
13A13ARG10.9300.97922.7420.0850.0850.0000.0000.0000.000
14A14ALA00.0140.01720.3070.0120.0120.0000.0000.0000.000
15A15LYS10.7930.90421.0430.0520.0520.0000.0000.0000.000
16A16GLY00.0870.05319.7950.0030.0030.0000.0000.0000.000
17A17VAL0-0.044-0.02416.944-0.010-0.0100.0000.0000.0000.000
18A18ALA00.0000.00118.6440.0150.0150.0000.0000.0000.000
19A19PHE0-0.010-0.00113.436-0.010-0.0100.0000.0000.0000.000
20A20HIS00.0290.02718.9260.0100.0100.0000.0000.0000.000
21A21PRO0-0.013-0.01320.5290.0100.0100.0000.0000.0000.000
22A22THR0-0.036-0.03721.3380.0070.0070.0000.0000.0000.000
23A23GLN00.0070.02423.474-0.007-0.0070.0000.0000.0000.000
24A24PRO0-0.0290.01020.5410.0070.0070.0000.0000.0000.000
25A25TRP00.015-0.02621.486-0.010-0.0100.0000.0000.0000.000
26A26ILE0-0.043-0.03117.3550.0120.0120.0000.0000.0000.000
27A27LEU00.0280.02720.790-0.008-0.0080.0000.0000.0000.000
28A28THR0-0.016-0.02720.2950.0040.0040.0000.0000.0000.000
29A29SER00.0250.01822.5670.0010.0010.0000.0000.0000.000
30A30LEU00.0080.00623.694-0.008-0.0080.0000.0000.0000.000
31A31HIS00.0550.00325.9220.0040.0040.0000.0000.0000.000
32A32ASN0-0.033-0.03127.5590.0050.0050.0000.0000.0000.000
33A33GLY00.0750.05729.6340.0020.0020.0000.0000.0000.000
34A34ARG10.8120.90329.7790.0290.0290.0000.0000.0000.000
35A35ILE00.0290.01126.340-0.003-0.0030.0000.0000.0000.000
36A36GLN00.0070.02224.297-0.002-0.0020.0000.0000.0000.000
37A37LEU00.0150.02024.7910.0050.0050.0000.0000.0000.000
38A38TRP0-0.012-0.02221.719-0.005-0.0050.0000.0000.0000.000
39A39ASP-1-0.774-0.88922.6880.0050.0050.0000.0000.0000.000
40A40TYR0-0.029-0.03017.444-0.003-0.0030.0000.0000.0000.000
41A41ARG10.8790.93216.423-0.044-0.0440.0000.0000.0000.000
42A42MET0-0.0120.00120.674-0.004-0.0040.0000.0000.0000.000
43A43GLY0-0.015-0.00122.039-0.007-0.0070.0000.0000.0000.000
44A44THR00.0070.00722.865-0.003-0.0030.0000.0000.0000.000
45A45LEU0-0.021-0.01525.4600.0020.0020.0000.0000.0000.000
46A46LEU0-0.050-0.02626.2180.0020.0020.0000.0000.0000.000
47A47ASP-1-0.822-0.92328.858-0.005-0.0050.0000.0000.0000.000
48A48ARG10.8600.92629.1680.0270.0270.0000.0000.0000.000
49A49PHE0-0.0070.00029.1770.0030.0030.0000.0000.0000.000
50A50ASP-1-0.877-0.94131.854-0.022-0.0220.0000.0000.0000.000
51A51GLY00.0210.00333.8640.0020.0020.0000.0000.0000.000
52A52HIS0-0.062-0.00331.7320.0050.0050.0000.0000.0000.000
53A53ASP-1-0.911-0.93434.681-0.018-0.0180.0000.0000.0000.000
54A54GLY00.008-0.00333.4470.0010.0010.0000.0000.0000.000
55A55PRO0-0.072-0.03928.0270.0010.0010.0000.0000.0000.000
56A56VAL00.0180.02626.9200.0040.0040.0000.0000.0000.000
57A57ARG10.7490.84124.3720.0240.0240.0000.0000.0000.000
58A58GLY00.0220.02323.2910.0030.0030.0000.0000.0000.000
59A59ILE0-0.011-0.02321.949-0.004-0.0040.0000.0000.0000.000
60A60ALA00.0090.01022.5130.0080.0080.0000.0000.0000.000
61A61PHE00.0250.00422.492-0.008-0.0080.0000.0000.0000.000
62A62HIS00.0620.05124.8790.0070.0070.0000.0000.0000.000
63A63PRO00.002-0.00824.5260.0000.0000.0000.0000.0000.000
64A64THR0-0.008-0.02625.7930.0010.0010.0000.0000.0000.000
65A65GLN00.0200.02029.048-0.007-0.0070.0000.0000.0000.000
66A66PRO0-0.033-0.00930.1120.0010.0010.0000.0000.0000.000
67A67ILE0-0.019-0.02730.479-0.005-0.0050.0000.0000.0000.000
68A68PHE0-0.031-0.01727.0440.0050.0050.0000.0000.0000.000
69A69VAL0-0.0090.00027.167-0.003-0.0030.0000.0000.0000.000
70A70SER00.004-0.03527.2310.0010.0010.0000.0000.0000.000
71A71GLY00.0330.01527.9710.0020.0020.0000.0000.0000.000
72A72GLY00.0060.00028.454-0.003-0.0030.0000.0000.0000.000
73A73ASP-1-0.711-0.84029.931-0.022-0.0220.0000.0000.0000.000
74A74ASP-1-0.792-0.89032.345-0.008-0.0080.0000.0000.0000.000
75A75TYR0-0.025-0.00634.0620.0020.0020.0000.0000.0000.000
76A76LYS10.9220.98034.8630.0070.0070.0000.0000.0000.000
77A77VAL00.0310.00731.0740.0000.0000.0000.0000.0000.000
78A78ASN00.0170.03332.2790.0020.0020.0000.0000.0000.000
79A79VAL00.0280.01731.9500.0030.0030.0000.0000.0000.000
80A80TRP00.0340.00631.395-0.003-0.0030.0000.0000.0000.000
81A81ASN00.0340.02332.8130.0030.0030.0000.0000.0000.000
82A82TYR00.0400.01928.722-0.002-0.0020.0000.0000.0000.000
83A83LYS10.9420.96632.127-0.030-0.0300.0000.0000.0000.000
84A84SER0-0.044-0.02234.533-0.002-0.0020.0000.0000.0000.000
85A85ARG10.9020.97130.287-0.005-0.0050.0000.0000.0000.000
86A86LYS10.9941.00135.568-0.011-0.0110.0000.0000.0000.000
87A87LEU00.0210.01935.4130.0030.0030.0000.0000.0000.000
88A88LEU0-0.096-0.05535.9960.0000.0000.0000.0000.0000.000
89A89PHE00.002-0.01836.960-0.001-0.0010.0000.0000.0000.000
90A90SER00.004-0.01836.9730.0000.0000.0000.0000.0000.000
91A91LEU0-0.062-0.01834.3430.0000.0000.0000.0000.0000.000
92A92CYS0-0.005-0.01636.672-0.001-0.0010.0000.0000.0000.000
93A93GLY00.029-0.00238.6630.0020.0020.0000.0000.0000.000
94A94HIS0-0.0410.01432.9510.0030.0030.0000.0000.0000.000
95A95MET0-0.041-0.02936.696-0.001-0.0010.0000.0000.0000.000
96A96ASP-1-0.783-0.88734.521-0.013-0.0130.0000.0000.0000.000
97A97TYR0-0.076-0.03830.1960.0020.0020.0000.0000.0000.000
98A98VAL0-0.0410.00028.5380.0030.0030.0000.0000.0000.000
99A99ARG10.7230.82425.1800.0140.0140.0000.0000.0000.000
100A100VAL0-0.015-0.01122.242-0.001-0.0010.0000.0000.0000.000
101A101CYS0-0.027-0.00224.813-0.003-0.0030.0000.0000.0000.000
102A102THR0-0.037-0.00922.3530.0040.0040.0000.0000.0000.000
103A103PHE00.0010.00025.361-0.006-0.0060.0000.0000.0000.000
104A104HIS00.0510.04725.6560.0060.0060.0000.0000.0000.000
105A105HIS0-0.041-0.02424.677-0.003-0.0030.0000.0000.0000.000
106A106GLU-1-0.975-0.98226.7160.0720.0720.0000.0000.0000.000
107A107TYR0-0.030-0.03930.297-0.006-0.0060.0000.0000.0000.000
108A108PRO0-0.0030.01431.7080.0010.0010.0000.0000.0000.000
109A109TRP0-0.041-0.04231.396-0.004-0.0040.0000.0000.0000.000
110A110ILE0-0.030-0.02329.4880.0030.0030.0000.0000.0000.000
111A111LEU0-0.0270.01425.522-0.003-0.0030.0000.0000.0000.000
112A112SER0-0.013-0.04528.0800.0000.0000.0000.0000.0000.000
113A113CYS0-0.0220.01626.6000.0030.0030.0000.0000.0000.000
114A114SER00.0140.00729.111-0.003-0.0030.0000.0000.0000.000
115A115ASP-1-0.672-0.81229.855-0.011-0.0110.0000.0000.0000.000
116A116ASP-1-0.763-0.84932.0060.0070.0070.0000.0000.0000.000
117A117GLN0-0.033-0.01932.8210.0030.0030.0000.0000.0000.000
118A118THR0-0.100-0.06533.6870.0040.0040.0000.0000.0000.000
119A119ILE00.0190.00028.9130.0000.0000.0000.0000.0000.000
120A120ARG10.9070.95331.674-0.014-0.0140.0000.0000.0000.000
121A121ILE00.0380.02231.5670.0030.0030.0000.0000.0000.000
122A122TRP0-0.018-0.02832.644-0.004-0.0040.0000.0000.0000.000
123A123ASN00.0340.03234.3410.0030.0030.0000.0000.0000.000
124A124TRP00.003-0.00832.018-0.005-0.0050.0000.0000.0000.000
125A125GLN0-0.031-0.02236.2610.0000.0000.0000.0000.0000.000
126A126SER0-0.018-0.01939.217-0.002-0.0020.0000.0000.0000.000
127A127ARG10.9200.96539.059-0.017-0.0170.0000.0000.0000.000
128A128ASN00.0440.04140.124-0.003-0.0030.0000.0000.0000.000
129A129CYS0-0.042-0.00936.9520.0020.0020.0000.0000.0000.000
130A130ILE0-0.055-0.03535.797-0.001-0.0010.0000.0000.0000.000
131A131ALA00.0190.00535.7200.0010.0010.0000.0000.0000.000
132A132ILE00.002-0.00536.2780.0000.0000.0000.0000.0000.000
133A133LEU0-0.024-0.00531.5410.0000.0000.0000.0000.0000.000
134A134THR00.0150.00234.317-0.001-0.0010.0000.0000.0000.000
135A135GLY00.0450.00635.1420.0020.0020.0000.0000.0000.000
136A136HIS0-0.063-0.00428.3340.0040.0040.0000.0000.0000.000
137A137SER0-0.009-0.00233.105-0.002-0.0020.0000.0000.0000.000
138A138HIS00.0370.02431.292-0.001-0.0010.0000.0000.0000.000
139A139TYR00.0200.00229.3570.0020.0020.0000.0000.0000.000
140A140VAL0-0.0240.00027.1110.0010.0010.0000.0000.0000.000
141A141MET0-0.024-0.00623.700-0.002-0.0020.0000.0000.0000.000
142A142CYS0-0.063-0.02620.3590.0040.0040.0000.0000.0000.000
143A143ALA00.0540.01523.4170.0000.0000.0000.0000.0000.000
144A144ALA0-0.035-0.01521.0460.0020.0020.0000.0000.0000.000
145A145PHE00.0680.02623.037-0.003-0.0030.0000.0000.0000.000
146A146HIS00.0290.02222.6010.0070.0070.0000.0000.0000.000
147A147PRO0-0.034-0.01819.941-0.007-0.0070.0000.0000.0000.000
148A148SER0-0.033-0.03222.8450.0020.0020.0000.0000.0000.000
149A149GLU-1-0.945-0.95725.6280.0920.0920.0000.0000.0000.000
150A150ASP-1-0.796-0.88227.5860.0670.0670.0000.0000.0000.000
151A151LEU0-0.032-0.02426.131-0.005-0.0050.0000.0000.0000.000
152A152ILE0-0.017-0.00726.0390.0040.0040.0000.0000.0000.000
153A153VAL0-0.027-0.00121.216-0.003-0.0030.0000.0000.0000.000
154A154SER00.018-0.02924.3430.0010.0010.0000.0000.0000.000
155A155ALA00.0260.01622.3310.0020.0020.0000.0000.0000.000
156A156SER00.0230.01324.417-0.005-0.0050.0000.0000.0000.000
157A157LEU00.0210.00825.976-0.002-0.0020.0000.0000.0000.000
158A158ASP-1-0.783-0.86228.2070.0090.0090.0000.0000.0000.000
159A159GLN0-0.022-0.00826.8760.0010.0010.0000.0000.0000.000
160A160THR0-0.071-0.04526.9270.0050.0050.0000.0000.0000.000
161A161VAL00.000-0.01222.2360.0000.0000.0000.0000.0000.000
162A162ARG10.9170.97225.470-0.023-0.0230.0000.0000.0000.000
163A163VAL00.000-0.00125.2570.0060.0060.0000.0000.0000.000
164A164TRP0-0.035-0.03727.801-0.006-0.0060.0000.0000.0000.000
165A165ASP-1-0.855-0.92129.9710.0620.0620.0000.0000.0000.000
166A166ILE00.013-0.01229.729-0.005-0.0050.0000.0000.0000.000
167A167SER0-0.006-0.01533.526-0.002-0.0020.0000.0000.0000.000
168A168GLY00.0230.01335.175-0.001-0.0010.0000.0000.0000.000
169A169LEU00.011-0.00934.542-0.002-0.0020.0000.0000.0000.000
170A170ARG10.9140.96233.418-0.063-0.0630.0000.0000.0000.000
171A171MET0-0.031-0.01036.615-0.001-0.0010.0000.0000.0000.000
172A172LYS10.8870.94939.837-0.029-0.0290.0000.0000.0000.000
173A173ASN0-0.054-0.02938.4080.0000.0000.0000.0000.0000.000
174A174ALA00.0140.01138.622-0.001-0.0010.0000.0000.0000.000
175A175ALA0-0.0170.00940.5890.0000.0000.0000.0000.0000.000
176A176PRO0-0.0130.00844.122-0.002-0.0020.0000.0000.0000.000
177A177VAL00.003-0.00846.6550.0000.0000.0000.0000.0000.000
178A178SER0-0.019-0.00549.7980.0000.0000.0000.0000.0000.000
179A179MET0-0.042-0.03649.7710.0000.0000.0000.0000.0000.000
180A180SER00.0130.01454.5580.0000.0000.0000.0000.0000.000
181A181LYS10.9530.97556.863-0.012-0.0120.0000.0000.0000.000
182A182GLU-1-0.913-0.96758.1430.0120.0120.0000.0000.0000.000
183A183ASP-1-0.871-0.90859.4450.0130.0130.0000.0000.0000.000
184A184GLN0-0.098-0.05953.9010.0010.0010.0000.0000.0000.000
185A185LYS10.9460.96851.973-0.017-0.0170.0000.0000.0000.000
186A186ALA00.0380.02055.7250.0000.0000.0000.0000.0000.000
187A187GLN0-0.029-0.01552.0610.0000.0000.0000.0000.0000.000
188A188ALA00.0020.00749.8040.0000.0000.0000.0000.0000.000
189A200ALA00.002-0.01140.4250.0000.0000.0000.0000.0000.000
190A201ASP-1-0.873-0.93638.4920.0320.0320.0000.0000.0000.000
191A202ALA00.010-0.01334.2530.0040.0040.0000.0000.0000.000
192A203ILE0-0.0250.01235.156-0.004-0.0040.0000.0000.0000.000
193A204VAL00.0080.00631.9750.0040.0040.0000.0000.0000.000
194A205LYS10.8770.93530.229-0.064-0.0640.0000.0000.0000.000
195A206PHE0-0.042-0.03227.7120.0000.0000.0000.0000.0000.000
196A207VAL00.0250.00529.6600.0000.0000.0000.0000.0000.000
197A208LEU0-0.056-0.02523.8020.0010.0010.0000.0000.0000.000
198A209GLU-1-0.908-0.95826.8870.0180.0180.0000.0000.0000.000
199A210GLY00.0490.00325.5290.0040.0040.0000.0000.0000.000
200A211HIS0-0.084-0.03219.5840.0080.0080.0000.0000.0000.000
201A212ASP-1-0.785-0.86024.775-0.036-0.0360.0000.0000.0000.000
202A213ARG10.8130.88324.8410.0470.0470.0000.0000.0000.000
203A214GLY00.0240.01925.7210.0060.0060.0000.0000.0000.000
204A215VAL0-0.037-0.01321.398-0.005-0.0050.0000.0000.0000.000
205A216ASN0-0.038-0.05419.9400.0060.0060.0000.0000.0000.000
206A217TRP00.003-0.02416.159-0.005-0.0050.0000.0000.0000.000
207A218CYS00.0200.01118.585-0.002-0.0020.0000.0000.0000.000
208A219ALA0-0.033-0.00415.3370.0020.0020.0000.0000.0000.000
209A220PHE00.0810.03717.3870.0020.0020.0000.0000.0000.000
210A221HIS00.0080.02013.321-0.022-0.0220.0000.0000.0000.000
211A222PRO0-0.024-0.02314.506-0.024-0.0240.0000.0000.0000.000
212A223THR00.002-0.01517.257-0.011-0.0110.0000.0000.0000.000
213A224LEU00.0140.01615.783-0.022-0.0220.0000.0000.0000.000
214A225PRO00.0010.01819.188-0.001-0.0010.0000.0000.0000.000
215A226LEU0-0.047-0.04215.692-0.011-0.0110.0000.0000.0000.000
216A227ILE00.0260.00418.4870.0040.0040.0000.0000.0000.000
217A228LEU0-0.038-0.00911.8350.0030.0030.0000.0000.0000.000
218A229SER00.009-0.01416.410-0.004-0.0040.0000.0000.0000.000
219A230ALA00.002-0.00415.639-0.002-0.0020.0000.0000.0000.000
220A231GLY00.0680.03517.6980.0040.0040.0000.0000.0000.000
221A232ASP-1-0.805-0.89519.923-0.067-0.0670.0000.0000.0000.000
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