FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: YZG22

Calculation Name: 4F15-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F15

Chain ID: A

ChEMBL ID:

UniProt ID: C5MQE6

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2838760.400309
FMO2-HF: Nuclear repulsion 2746779.829914
FMO2-HF: Total energy -91980.570395
FMO2-MP2: Total energy -92249.519604


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:43:LYS)


Summations of interaction energy for fragment #1(A:43: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.
23.13524.887-0.021-0.835-0.897-0.001
Interaction energy analysis for fragmet #1(A:43:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.996 / q_NPA : 0.978
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].
3A45ARG10.9740.9833.86827.13928.891-0.021-0.835-0.897-0.001
4A46GLY00.0100.0126.1722.6652.6650.0000.0000.0000.000
5A47VAL0-0.006-0.0158.9041.0261.0260.0000.0000.0000.000
6A48ALA00.0340.04111.6451.2591.2590.0000.0000.0000.000
7A49PRO00.012-0.00314.402-0.257-0.2570.0000.0000.0000.000
8A50LEU0-0.0200.00017.962-0.317-0.3170.0000.0000.0000.000
9A51HIS00.0120.00613.598-0.078-0.0780.0000.0000.0000.000
10A52LEU0-0.003-0.01219.2110.6440.6440.0000.0000.0000.000
11A53GLY0-0.001-0.00421.369-0.271-0.2710.0000.0000.0000.000
12A54LYS10.8260.92822.27912.43312.4330.0000.0000.0000.000
13A55CYS0-0.120-0.00824.873-0.486-0.4860.0000.0000.0000.000
14A56ASN00.0430.02623.8930.0380.0380.0000.0000.0000.000
15A57ILE00.016-0.00721.5820.5330.5330.0000.0000.0000.000
16A58ALA0-0.0080.01025.6450.4510.4510.0000.0000.0000.000
17A59GLY00.0650.02428.6440.4080.4080.0000.0000.0000.000
18A60TRP0-0.038-0.04325.5630.3090.3090.0000.0000.0000.000
19A61ILE0-0.0090.00228.8680.3540.3540.0000.0000.0000.000
20A62LEU00.0140.01830.7930.4000.4000.0000.0000.0000.000
21A63GLY0-0.018-0.00932.8450.3560.3560.0000.0000.0000.000
22A64ASN0-0.019-0.04331.8230.5770.5770.0000.0000.0000.000
23A65PRO00.005-0.00833.723-0.190-0.1900.0000.0000.0000.000
24A66GLU-1-0.840-0.88828.964-10.911-10.9110.0000.0000.0000.000
25A68GLU-1-0.831-0.91630.025-9.026-9.0260.0000.0000.0000.000
26A69SER00.0290.01527.651-0.142-0.1420.0000.0000.0000.000
27A70LEU0-0.030-0.02722.521-0.029-0.0290.0000.0000.0000.000
28A71SER00.0020.01025.812-0.099-0.0990.0000.0000.0000.000
29A72THR0-0.007-0.00527.661-0.060-0.0600.0000.0000.0000.000
30A73ALA00.0280.02130.0890.2350.2350.0000.0000.0000.000
31A74SER0-0.049-0.04125.053-0.377-0.3770.0000.0000.0000.000
32A75SER0-0.0140.00824.8080.2340.2340.0000.0000.0000.000
33A76TRP0-0.061-0.05520.095-0.357-0.3570.0000.0000.0000.000
34A77SER00.0250.02215.9160.2280.2280.0000.0000.0000.000
35A78TYR00.004-0.01210.920-0.433-0.4330.0000.0000.0000.000
36A79ILE00.0050.01817.931-0.103-0.1030.0000.0000.0000.000
37A80VAL00.0020.00014.817-0.813-0.8130.0000.0000.0000.000
38A81GLU-1-0.742-0.85617.759-13.052-13.0520.0000.0000.0000.000
39A82THR0-0.0040.02518.695-0.940-0.9400.0000.0000.0000.000
40A83SER00.019-0.00120.0060.8460.8460.0000.0000.0000.000
41A84SER0-0.004-0.01021.9560.1050.1050.0000.0000.0000.000
42A85SER0-0.017-0.03024.6060.3120.3120.0000.0000.0000.000
43A86ASP-1-0.895-0.92326.343-11.520-11.5200.0000.0000.0000.000
44A87ASN0-0.076-0.04427.9100.7730.7730.0000.0000.0000.000
45A88GLY00.0170.00128.6340.3340.3340.0000.0000.0000.000
46A89THR0-0.032-0.00729.5260.0580.0580.0000.0000.0000.000
47A90CYS0-0.0050.01332.901-0.084-0.0840.0000.0000.0000.000
48A91TYR0-0.007-0.01835.3130.1650.1650.0000.0000.0000.000
49A92PRO00.0170.02836.241-0.187-0.1870.0000.0000.0000.000
50A93GLY00.039-0.00235.9090.3310.3310.0000.0000.0000.000
51A94ASP-1-0.846-0.90034.116-8.952-8.9520.0000.0000.0000.000
52A95PHE0-0.005-0.01030.7840.2100.2100.0000.0000.0000.000
53A96ILE0-0.023-0.01031.619-0.220-0.2200.0000.0000.0000.000
54A97ASP-1-0.856-0.94731.033-8.890-8.8900.0000.0000.0000.000
55A98TYR0-0.0180.00024.559-0.102-0.1020.0000.0000.0000.000
56A99GLU-1-0.795-0.90522.771-13.131-13.1310.0000.0000.0000.000
57A100GLU-1-0.939-0.95724.311-9.918-9.9180.0000.0000.0000.000
58A101LEU0-0.011-0.00626.168-0.108-0.1080.0000.0000.0000.000
59A102ARG10.8140.87519.78113.66613.6660.0000.0000.0000.000
60A103GLU-1-0.798-0.86121.521-12.419-12.4190.0000.0000.0000.000
61A104GLN00.0080.00522.780-0.101-0.1010.0000.0000.0000.000
62A105LEU00.0210.00624.5480.2120.2120.0000.0000.0000.000
63A106SER0-0.046-0.01819.475-0.546-0.5460.0000.0000.0000.000
64A107SER0-0.010-0.03021.197-0.150-0.1500.0000.0000.0000.000
65A108VAL0-0.0320.02122.4230.3740.3740.0000.0000.0000.000
66A109SER00.0040.00124.793-0.339-0.3390.0000.0000.0000.000
67A110SER0-0.029-0.05426.7370.0990.0990.0000.0000.0000.000
68A111PHE00.0300.00228.216-0.110-0.1100.0000.0000.0000.000
69A112GLU-1-0.864-0.89930.355-8.141-8.1410.0000.0000.0000.000
70A113ARG10.9230.97233.8438.8138.8130.0000.0000.0000.000
71A114PHE00.0130.01335.7290.1740.1740.0000.0000.0000.000
72A115GLU-1-0.794-0.90839.500-7.313-7.3130.0000.0000.0000.000
73A116ILE0-0.054-0.01040.5750.1780.1780.0000.0000.0000.000
74A117PHE00.039-0.00443.0060.1790.1790.0000.0000.0000.000
75A118PRO00.0040.02645.706-0.099-0.0990.0000.0000.0000.000
76A119LYS10.8990.93946.1976.9226.9220.0000.0000.0000.000
77A120THR00.0110.00948.0840.0590.0590.0000.0000.0000.000
78A121SER00.033-0.00151.7730.0430.0430.0000.0000.0000.000
79A122SER0-0.013-0.01249.1670.1130.1130.0000.0000.0000.000
80A123TRP00.0300.01046.8930.0730.0730.0000.0000.0000.000
81A124PRO00.0330.01753.1700.0290.0290.0000.0000.0000.000
82A125ASN00.0040.00656.6300.1000.1000.0000.0000.0000.000
83A126HIS00.0110.00453.6000.0050.0050.0000.0000.0000.000
84A127ASP-1-0.830-0.91054.284-5.870-5.8700.0000.0000.0000.000
85A128SER00.0290.01849.998-0.168-0.1680.0000.0000.0000.000
86A129ASN0-0.058-0.04349.389-0.204-0.2040.0000.0000.0000.000
87A130LYS10.8980.93050.8766.0656.0650.0000.0000.0000.000
88A131GLY00.0230.04447.428-0.031-0.0310.0000.0000.0000.000
89A132VAL0-0.069-0.03444.994-0.155-0.1550.0000.0000.0000.000
90A133THR00.010-0.00241.8730.1100.1100.0000.0000.0000.000
91A134ALA0-0.001-0.01542.760-0.114-0.1140.0000.0000.0000.000
92A135ALA00.0110.01739.219-0.121-0.1210.0000.0000.0000.000
93A137PRO0-0.0150.00038.1220.1740.1740.0000.0000.0000.000
94A138HIS00.0460.02637.443-0.248-0.2480.0000.0000.0000.000
95A139ALA0-0.008-0.01639.0720.0520.0520.0000.0000.0000.000
96A140GLY00.0120.02040.3360.2060.2060.0000.0000.0000.000
97A141ALA0-0.010-0.00443.3140.0780.0780.0000.0000.0000.000
98A142LYS10.9650.97443.0816.5406.5400.0000.0000.0000.000
99A143SER00.0200.01241.0820.2350.2350.0000.0000.0000.000
100A144PHE00.026-0.01241.0770.0400.0400.0000.0000.0000.000
101A145TYR00.011-0.00834.770-0.184-0.1840.0000.0000.0000.000
102A146LYS10.8430.90237.0908.6588.6580.0000.0000.0000.000
103A147ASN0-0.005-0.02334.2360.3680.3680.0000.0000.0000.000
104A148LEU00.0050.03037.7800.1160.1160.0000.0000.0000.000
105A149ILE0-0.045-0.02641.0870.0910.0910.0000.0000.0000.000
106A150TRP00.0130.02143.9500.0010.0010.0000.0000.0000.000
107A151LEU0-0.023-0.01046.0260.1130.1130.0000.0000.0000.000
108A152VAL0-0.0170.00049.512-0.021-0.0210.0000.0000.0000.000
109A153LYS10.8120.90852.5465.6245.6240.0000.0000.0000.000
110A154LYS10.8420.91356.3085.5535.5530.0000.0000.0000.000
111A155GLY00.0140.00858.6250.0710.0710.0000.0000.0000.000
112A156ASN0-0.003-0.01560.7370.0060.0060.0000.0000.0000.000
113A157SER00.0490.03760.8200.0260.0260.0000.0000.0000.000
114A158TYR00.0480.01050.874-0.094-0.0940.0000.0000.0000.000
115A159PRO00.0080.01657.8060.0110.0110.0000.0000.0000.000
116A160LYS10.8410.91954.6715.5805.5800.0000.0000.0000.000
117A161LEU0-0.0340.00349.3470.0420.0420.0000.0000.0000.000
118A162SER00.001-0.01052.025-0.059-0.0590.0000.0000.0000.000
119A163LYS10.9020.94548.4766.1686.1680.0000.0000.0000.000
120A164SER0-0.008-0.02747.392-0.007-0.0070.0000.0000.0000.000
121A165TYR0-0.019-0.01240.9920.0620.0620.0000.0000.0000.000
122A166ILE00.008-0.00945.6550.0120.0120.0000.0000.0000.000
123A167ASN0-0.0150.01240.010-0.149-0.1490.0000.0000.0000.000
124A168ASP-1-0.858-0.92143.341-6.620-6.6200.0000.0000.0000.000
125A169LYS10.7830.88938.7487.8087.8080.0000.0000.0000.000
126A170GLY00.0710.03438.994-0.014-0.0140.0000.0000.0000.000
127A171LYS10.7490.84433.0498.6628.6620.0000.0000.0000.000
128A172GLU-1-0.806-0.90830.914-9.255-9.2550.0000.0000.0000.000
129A173VAL0-0.034-0.01233.916-0.196-0.1960.0000.0000.0000.000
130A174LEU0-0.0020.00730.4130.0450.0450.0000.0000.0000.000
131A175VAL0-0.016-0.01734.4660.0560.0560.0000.0000.0000.000
132A176LEU00.0300.00332.099-0.084-0.0840.0000.0000.0000.000
133A177TRP0-0.071-0.03536.5860.1880.1880.0000.0000.0000.000
134A178GLY00.0630.02838.022-0.253-0.2530.0000.0000.0000.000
135A179ILE0-0.059-0.02940.1850.2390.2390.0000.0000.0000.000
136A180HIS00.0430.03042.246-0.219-0.2190.0000.0000.0000.000
137A181HIS00.0040.02042.1170.3890.3890.0000.0000.0000.000
138A182PRO0-0.051-0.03246.068-0.089-0.0890.0000.0000.0000.000
139A183SER00.0720.02248.493-0.052-0.0520.0000.0000.0000.000
140A184THR00.017-0.02149.4970.1240.1240.0000.0000.0000.000
141A185SER00.0510.00153.294-0.018-0.0180.0000.0000.0000.000
142A186ALA00.0360.02555.9330.0590.0590.0000.0000.0000.000
143A187ASP-1-0.800-0.83851.590-6.208-6.2080.0000.0000.0000.000
144A188GLN00.004-0.00951.773-0.139-0.1390.0000.0000.0000.000
145A189GLN0-0.0060.01053.679-0.007-0.0070.0000.0000.0000.000
146A190SER0-0.021-0.02454.9010.0870.0870.0000.0000.0000.000
147A191LEU0-0.039-0.01450.1410.0240.0240.0000.0000.0000.000
148A192TYR00.0440.00247.884-0.010-0.0100.0000.0000.0000.000
149A193GLN0-0.048-0.00554.5070.0180.0180.0000.0000.0000.000
150A194ASN0-0.065-0.04455.9560.1740.1740.0000.0000.0000.000
151A195ALA00.0460.02255.676-0.117-0.1170.0000.0000.0000.000
152A196ASP-1-0.850-0.90955.165-5.711-5.7110.0000.0000.0000.000
153A197ALA0-0.042-0.01152.0780.0300.0300.0000.0000.0000.000
154A198TYR0-0.028-0.02250.509-0.060-0.0600.0000.0000.0000.000
155A199VAL00.0110.00345.4110.0370.0370.0000.0000.0000.000
156A200PHE0-0.014-0.01047.009-0.052-0.0520.0000.0000.0000.000
157A201VAL00.0310.01841.752-0.027-0.0270.0000.0000.0000.000
158A202GLY0-0.014-0.00645.2140.0930.0930.0000.0000.0000.000
159A203SER0-0.041-0.01842.092-0.195-0.1950.0000.0000.0000.000
160A204SER0-0.052-0.04543.1330.1150.1150.0000.0000.0000.000
161A205ARG10.9160.97033.8258.2488.2480.0000.0000.0000.000
162A206TYR00.0410.01036.589-0.063-0.0630.0000.0000.0000.000
163A207SER0-0.045-0.01940.2570.1630.1630.0000.0000.0000.000
164A208LYS10.9340.97137.0387.9577.9570.0000.0000.0000.000
165A209LYS10.9430.96843.4676.1526.1520.0000.0000.0000.000
166A210PHE00.0160.00840.535-0.077-0.0770.0000.0000.0000.000
167A211LYS10.8690.91046.1156.0516.0510.0000.0000.0000.000
168A212PRO0-0.0130.01547.090-0.136-0.1360.0000.0000.0000.000
169A213GLU-1-0.864-0.91745.178-6.923-6.9230.0000.0000.0000.000
170A214ILE0-0.031-0.02647.599-0.104-0.1040.0000.0000.0000.000
171A215ALA00.0390.02347.6670.1090.1090.0000.0000.0000.000
172A216ILE0-0.0050.00747.492-0.133-0.1330.0000.0000.0000.000
173A217ARG10.7560.87842.3387.0697.0690.0000.0000.0000.000
174A218PRO00.030-0.00140.9180.0670.0670.0000.0000.0000.000
175A219LYS10.8540.93441.7736.7516.7510.0000.0000.0000.000
176A220VAL00.0050.01636.526-0.150-0.1500.0000.0000.0000.000
177A221ARG10.8240.90032.4569.5659.5650.0000.0000.0000.000
178A222ASP-1-0.848-0.91439.832-6.895-6.8950.0000.0000.0000.000
179A223GLN0-0.025-0.01741.5040.2890.2890.0000.0000.0000.000
180A224GLU-1-0.829-0.91642.639-6.832-6.8320.0000.0000.0000.000
181A225GLY00.0330.02845.1030.0320.0320.0000.0000.0000.000
182A226ARG10.8090.87639.2447.7427.7420.0000.0000.0000.000
183A227MET0-0.025-0.01239.2670.2740.2740.0000.0000.0000.000
184A228ASN0-0.053-0.01437.237-0.023-0.0230.0000.0000.0000.000
185A229TYR00.021-0.00134.3280.2220.2220.0000.0000.0000.000
186A230TYR00.0160.00235.348-0.055-0.0550.0000.0000.0000.000
187A231TRP00.004-0.01630.3710.0540.0540.0000.0000.0000.000
188A232THR00.001-0.00434.8540.0880.0880.0000.0000.0000.000
189A233LEU00.0120.01031.945-0.139-0.1390.0000.0000.0000.000
190A234VAL0-0.046-0.02435.3040.2380.2380.0000.0000.0000.000
191A235GLU-1-0.769-0.90835.814-8.269-8.2690.0000.0000.0000.000
192A236PRO00.006-0.00836.9330.1880.1880.0000.0000.0000.000
193A237GLY0-0.0050.01639.6340.1070.1070.0000.0000.0000.000
194A238ASP-1-0.795-0.85641.934-6.742-6.7420.0000.0000.0000.000
195A239LYS10.8580.90243.6336.3856.3850.0000.0000.0000.000
196A240ILE00.0200.02940.2060.0830.0830.0000.0000.0000.000
197A241THR0-0.042-0.01243.9290.1400.1400.0000.0000.0000.000
198A242PHE00.0370.02141.185-0.112-0.1120.0000.0000.0000.000
199A243GLU-1-0.843-0.92047.185-5.710-5.7100.0000.0000.0000.000
200A244ALA00.0260.00849.138-0.080-0.0800.0000.0000.0000.000
201A245THR00.0090.00351.2450.0710.0710.0000.0000.0000.000
202A246GLY00.0530.02651.6060.1090.1090.0000.0000.0000.000
203A247ASN0-0.017-0.01747.5180.0600.0600.0000.0000.0000.000
204A248LEU0-0.0200.00743.984-0.168-0.1680.0000.0000.0000.000
205A249VAL0-0.054-0.02341.9570.1170.1170.0000.0000.0000.000
206A250VAL00.0070.00642.397-0.168-0.1680.0000.0000.0000.000
207A251PRO00.0690.02940.218-0.083-0.0830.0000.0000.0000.000
208A252ARG10.7690.89040.9757.7787.7780.0000.0000.0000.000
209A253TYR0-0.098-0.06637.7320.0050.0050.0000.0000.0000.000
210A254ALA0-0.0150.00636.868-0.054-0.0540.0000.0000.0000.000
211A255PHE00.025-0.00732.336-0.053-0.0530.0000.0000.0000.000
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