Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: MV94Z

Calculation Name: 4FGP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FGP

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZXA4

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2118099.160904
FMO2-HF: Nuclear repulsion 2044276.280626
FMO2-HF: Total energy -73822.880278
FMO2-MP2: Total energy -74039.922351


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:56:ALA)


Summations of interaction energy for fragment #1(A:56:ALA)
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.
0.7013.1030.138-1.002-1.5390.004
Interaction energy analysis for fragmet #1(A:56:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.032
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].
3A58LEU00.0180.0043.885-0.1731.377-0.010-0.780-0.7600.004
4A59ILE0-0.0010.0076.4150.3730.3730.0000.0000.0000.000
5A60SER0-0.008-0.0369.795-0.010-0.0100.0000.0000.0000.000
6A61VAL00.0370.02512.5610.0300.0300.0000.0000.0000.000
7A62GLU-1-0.845-0.90014.714-0.571-0.5710.0000.0000.0000.000
8A63LYS10.9040.9568.9541.6751.6750.0000.0000.0000.000
9A64ILE00.0200.02114.5350.0630.0630.0000.0000.0000.000
10A65GLN00.004-0.00717.3120.0360.0360.0000.0000.0000.000
11A66LYS10.8650.92718.0530.4940.4940.0000.0000.0000.000
12A67LEU00.0320.03215.2420.0300.0300.0000.0000.0000.000
13A68ALA00.0070.00619.7520.0380.0380.0000.0000.0000.000
14A69GLN0-0.022-0.01722.7680.0390.0390.0000.0000.0000.000
15A70SER0-0.045-0.02921.9100.0170.0170.0000.0000.0000.000
16A71TYR00.0690.04819.4410.0320.0320.0000.0000.0000.000
17A72GLN00.014-0.00425.5040.0090.0090.0000.0000.0000.000
18A73GLY00.0390.01528.321-0.003-0.0030.0000.0000.0000.000
19A74ASP-1-0.829-0.95028.942-0.142-0.1420.0000.0000.0000.000
20A75THR00.0290.02623.759-0.003-0.0030.0000.0000.0000.000
21A76ARG10.8410.93324.0820.1860.1860.0000.0000.0000.000
22A77LYS10.8920.97024.7670.1240.1240.0000.0000.0000.000
23A78ARG10.8740.95422.5880.1800.1800.0000.0000.0000.000
24A79PHE00.0290.01817.294-0.017-0.0170.0000.0000.0000.000
25A80THR0-0.041-0.04220.471-0.021-0.0210.0000.0000.0000.000
26A81ALA0-0.019-0.00822.516-0.005-0.0050.0000.0000.0000.000
27A82TRP00.0490.01513.131-0.005-0.0050.0000.0000.0000.000
28A83GLY00.0150.00117.903-0.024-0.0240.0000.0000.0000.000
29A84ASN00.009-0.01218.961-0.013-0.0130.0000.0000.0000.000
30A85LEU0-0.0220.01118.2070.0130.0130.0000.0000.0000.000
31A86ILE00.0380.02213.9000.0150.0150.0000.0000.0000.000
32A87ASP-1-0.782-0.89817.464-0.334-0.3340.0000.0000.0000.000
33A88SER0-0.119-0.06419.8900.0290.0290.0000.0000.0000.000
34A89LEU00.000-0.00218.4860.0290.0290.0000.0000.0000.000
35A90LYS10.9080.96415.3190.4380.4380.0000.0000.0000.000
36A91LYS10.9200.95918.1320.2160.2160.0000.0000.0000.000
37A92LYS10.8380.93620.0330.2050.2050.0000.0000.0000.000
38A93PRO00.0330.00320.534-0.002-0.0020.0000.0000.0000.000
39A94VAL00.0950.04917.474-0.005-0.0050.0000.0000.0000.000
40A95LYS10.8860.95519.8400.0410.0410.0000.0000.0000.000
41A96ILE00.000-0.00722.473-0.002-0.0020.0000.0000.0000.000
42A97GLN0-0.043-0.03216.7100.0080.0080.0000.0000.0000.000
43A98LEU00.0420.01916.731-0.013-0.0130.0000.0000.0000.000
44A99GLU-1-0.817-0.92719.384-0.065-0.0650.0000.0000.0000.000
45A100LYS10.9250.98021.9060.1220.1220.0000.0000.0000.000
46A101VAL00.0240.01915.710-0.007-0.0070.0000.0000.0000.000
47A102ASN00.0160.01919.129-0.001-0.0010.0000.0000.0000.000
48A103SER0-0.026-0.03920.896-0.001-0.0010.0000.0000.0000.000
49A104PHE0-0.020-0.00420.0110.0010.0010.0000.0000.0000.000
50A105PHE00.041-0.00816.590-0.005-0.0050.0000.0000.0000.000
51A106ASN00.0350.01621.127-0.002-0.0020.0000.0000.0000.000
52A107GLN0-0.096-0.03623.9440.0150.0150.0000.0000.0000.000
53A108PHE0-0.070-0.02521.403-0.003-0.0030.0000.0000.0000.000
54A109ASN0-0.022-0.02025.3100.0190.0190.0000.0000.0000.000
55A110TYR00.0360.00523.978-0.006-0.0060.0000.0000.0000.000
56A111GLU-1-0.865-0.92524.198-0.103-0.1030.0000.0000.0000.000
57A112THR0-0.005-0.01925.6990.0040.0040.0000.0000.0000.000
58A113ASP-1-0.716-0.82727.187-0.009-0.0090.0000.0000.0000.000
59A114PRO0-0.072-0.03528.5580.0030.0030.0000.0000.0000.000
60A115ILE0-0.076-0.03531.7570.0020.0020.0000.0000.0000.000
61A116THR0-0.103-0.08229.8660.0050.0050.0000.0000.0000.000
62A117GLY00.0040.01531.2750.0030.0030.0000.0000.0000.000
63A118ALA0-0.0260.00326.949-0.001-0.0010.0000.0000.0000.000
64A119SER0-0.028-0.05422.246-0.009-0.0090.0000.0000.0000.000
65A120ASP-1-0.899-0.95022.910-0.032-0.0320.0000.0000.0000.000
66A121ASP-1-0.909-0.93821.3270.0490.0490.0000.0000.0000.000
67A122TYR0-0.063-0.04917.1690.0210.0210.0000.0000.0000.000
68A123TRP0-0.009-0.01112.6010.0020.0020.0000.0000.0000.000
69A124LYS10.7570.85015.3480.1110.1110.0000.0000.0000.000
70A125SER0-0.028-0.04911.497-0.035-0.0350.0000.0000.0000.000
71A126PRO0-0.003-0.03110.7450.0310.0310.0000.0000.0000.000
72A127VAL00.001-0.00413.2080.0370.0370.0000.0000.0000.000
73A128GLU-1-0.708-0.79514.864-0.246-0.2460.0000.0000.0000.000
74A129PHE00.0600.05216.9320.0210.0210.0000.0000.0000.000
75A130ILE0-0.021-0.00917.6950.0270.0270.0000.0000.0000.000
76A131VAL0-0.039-0.03219.8140.0230.0230.0000.0000.0000.000
77A132ASP-1-0.812-0.89221.568-0.145-0.1450.0000.0000.0000.000
78A133GLY0-0.088-0.04622.5630.0150.0150.0000.0000.0000.000
79A134GLY00.005-0.00322.4500.0150.0150.0000.0000.0000.000
80A135GLY00.0540.02520.762-0.020-0.0200.0000.0000.0000.000
81A136ASP-1-0.721-0.82220.406-0.035-0.0350.0000.0000.0000.000
82A137CYS0-0.080-0.04120.836-0.012-0.0120.0000.0000.0000.000
83A138GLU-1-0.800-0.90717.6150.0460.0460.0000.0000.0000.000
84A139ASP-1-0.757-0.88316.393-0.130-0.1300.0000.0000.0000.000
85A140PHE0-0.066-0.03616.253-0.037-0.0370.0000.0000.0000.000
86A141ALA0-0.042-0.01315.924-0.021-0.0210.0000.0000.0000.000
87A142ILE00.0470.01611.146-0.027-0.0270.0000.0000.0000.000
88A143ILE0-0.034-0.00611.713-0.089-0.0890.0000.0000.0000.000
89A144LYS10.7730.89313.3970.0420.0420.0000.0000.0000.000
90A145TYR0-0.002-0.0115.931-0.024-0.0240.0000.0000.0000.000
91A146PHE00.0570.0115.006-0.013-0.0130.0000.0000.0000.000
92A147THR0-0.053-0.0279.370-0.097-0.0970.0000.0000.0000.000
93A148LEU00.003-0.00612.4410.0040.0040.0000.0000.0000.000
94A149VAL00.0310.0256.1160.0160.0160.0000.0000.0000.000
95A150ALA0-0.042-0.0139.571-0.023-0.0230.0000.0000.0000.000
96A151VAL0-0.094-0.03810.9400.0360.0360.0000.0000.0000.000
97A152GLY0-0.032-0.02512.3860.0470.0470.0000.0000.0000.000
98A153VAL0-0.041-0.00512.7040.0500.0500.0000.0000.0000.000
99A154PRO00.0280.01210.602-0.053-0.0530.0000.0000.0000.000
100A155SER00.023-0.0216.353-0.086-0.0860.0000.0000.0000.000
101A156ASP-1-0.886-0.9388.6660.2560.2560.0000.0000.0000.000
102A157GLN0-0.040-0.02210.977-0.014-0.0140.0000.0000.0000.000
103A158LEU0-0.059-0.02410.494-0.038-0.0380.0000.0000.0000.000
104A159ARG10.8710.94510.784-0.241-0.2410.0000.0000.0000.000
105A160ILE00.0410.03110.538-0.054-0.0540.0000.0000.0000.000
106A161THR0-0.021-0.04213.9820.0660.0660.0000.0000.0000.000
107A162TYR00.0160.02917.409-0.019-0.0190.0000.0000.0000.000
108A163ALA00.012-0.02319.8050.0170.0170.0000.0000.0000.000
109A164ALA00.0380.02823.445-0.007-0.0070.0000.0000.0000.000
110A165SER00.0130.01027.073-0.002-0.0020.0000.0000.0000.000
111A166LEU0-0.055-0.03928.8300.0000.0000.0000.0000.0000.000
112A167THR0-0.016-0.00631.913-0.001-0.0010.0000.0000.0000.000
113A168LEU00.0300.00528.757-0.002-0.0020.0000.0000.0000.000
114A169ASN0-0.088-0.03432.4540.0020.0020.0000.0000.0000.000
115A170GLN00.0200.01628.6800.0040.0040.0000.0000.0000.000
116A171ALA0-0.029-0.01324.1250.0030.0030.0000.0000.0000.000
117A172HIS00.029-0.00424.014-0.008-0.0080.0000.0000.0000.000
118A173MET0-0.0330.02516.6480.0140.0140.0000.0000.0000.000
119A174VAL00.0150.01519.179-0.019-0.0190.0000.0000.0000.000
120A175LEU00.0050.01513.0750.0190.0190.0000.0000.0000.000
121A176SER0-0.061-0.01515.8780.0010.0010.0000.0000.0000.000
122A177PHE00.0540.01715.3450.0120.0120.0000.0000.0000.000
123A178TYR00.003-0.00115.8900.0060.0060.0000.0000.0000.000
124A179PRO0-0.040-0.02217.7780.0010.0010.0000.0000.0000.000
125A180THR0-0.004-0.01119.452-0.009-0.0090.0000.0000.0000.000
126A181PRO00.005-0.00817.256-0.002-0.0020.0000.0000.0000.000
127A182GLU-1-0.850-0.89919.0920.1380.1380.0000.0000.0000.000
128A183SER0-0.048-0.02222.004-0.017-0.0170.0000.0000.0000.000
129A184GLU-1-0.762-0.83922.5950.0480.0480.0000.0000.0000.000
130A185PRO0-0.0080.00019.631-0.009-0.0090.0000.0000.0000.000
131A186LEU0-0.052-0.03520.545-0.008-0.0080.0000.0000.0000.000
132A187ILE0-0.005-0.00219.971-0.001-0.0010.0000.0000.0000.000
133A188LEU0-0.008-0.01917.312-0.011-0.0110.0000.0000.0000.000
134A189ASP-1-0.719-0.84020.022-0.023-0.0230.0000.0000.0000.000
135A190SER00.0050.00021.860-0.012-0.0120.0000.0000.0000.000
136A191LEU00.0110.01623.475-0.005-0.0050.0000.0000.0000.000
137A192GLU-1-0.795-0.86626.186-0.022-0.0220.0000.0000.0000.000
138A193SER0-0.017-0.02125.809-0.009-0.0090.0000.0000.0000.000
139A194LYS10.7520.85726.4270.0190.0190.0000.0000.0000.000
140A195ILE00.0130.02121.3960.0030.0030.0000.0000.0000.000
141A196LEU0-0.032-0.01424.8440.0020.0020.0000.0000.0000.000
142A197LYS10.8640.91724.774-0.025-0.0250.0000.0000.0000.000
143A198ALA00.0630.03324.335-0.002-0.0020.0000.0000.0000.000
144A199SER0-0.083-0.08326.074-0.004-0.0040.0000.0000.0000.000
145A200ALA0-0.078-0.03528.999-0.002-0.0020.0000.0000.0000.000
146A201ARG10.7530.82726.434-0.009-0.0090.0000.0000.0000.000
147A202PRO00.0370.02028.4140.0050.0050.0000.0000.0000.000
148A203ASP-1-0.828-0.88029.4950.0180.0180.0000.0000.0000.000
149A204LEU0-0.0040.00324.2670.0010.0010.0000.0000.0000.000
150A205LYS10.9770.98626.944-0.082-0.0820.0000.0000.0000.000
151A206PRO0-0.018-0.01221.5120.0040.0040.0000.0000.0000.000
152A207VAL0-0.027-0.01021.9960.0020.0020.0000.0000.0000.000
153A208TYR0-0.040-0.02115.9950.0270.0270.0000.0000.0000.000
154A209SER0-0.0090.01115.395-0.026-0.0260.0000.0000.0000.000
155A210PHE00.0560.00710.4250.0640.0640.0000.0000.0000.000
156A211ASN00.0330.0177.7990.0340.0340.0000.0000.0000.000
157A212ALA00.0420.0242.870-0.2580.0560.147-0.134-0.3270.000
158A213GLU-1-0.839-0.8754.7141.4241.592-0.001-0.012-0.1550.000
159A214GLY0-0.002-0.0135.9730.0870.0870.0000.0000.0000.000
160A215LEU00.0020.0149.515-0.125-0.1250.0000.0000.0000.000
161A216TRP0-0.013-0.01910.412-0.010-0.0100.0000.0000.0000.000
162A217LEU00.0350.01516.299-0.039-0.0390.0000.0000.0000.000
163A218ALA00.0220.02719.7630.0010.0010.0000.0000.0000.000
164A219LYS10.7610.86721.483-0.198-0.1980.0000.0000.0000.000
165A220THR0-0.031-0.03125.195-0.013-0.0130.0000.0000.0000.000
166A221ARG10.9160.97920.504-0.240-0.2400.0000.0000.0000.000
167A222GLY00.0790.02026.2990.0020.0020.0000.0000.0000.000
168A223GLU-1-0.870-0.93324.4350.1630.1630.0000.0000.0000.000
169A224SER00.0350.03220.2720.0060.0060.0000.0000.0000.000
170A225SER0-0.047-0.02919.220-0.022-0.0220.0000.0000.0000.000
171A226LEU0-0.002-0.01117.5060.0170.0170.0000.0000.0000.000
172A227MET0-0.0350.0189.753-0.065-0.0650.0000.0000.0000.000
173A228GLY0-0.007-0.00214.235-0.002-0.0020.0000.0000.0000.000
174A229ASP-1-0.816-0.9269.4461.4671.4670.0000.0000.0000.000
175A230SER0-0.0040.0096.352-0.229-0.2290.0000.0000.0000.000
176A231LYS10.8620.9135.152-1.672-1.6720.0000.0000.0000.000
177A232SER0-0.046-0.0329.535-0.196-0.1960.0000.0000.0000.000
178A233LEU00.0100.01611.932-0.109-0.1090.0000.0000.0000.000
179A234GLY00.0350.01211.9740.0080.0080.0000.0000.0000.000
180A235LYS10.8070.88612.972-0.084-0.0840.0000.0000.0000.000
181A236TRP00.008-0.0127.448-0.207-0.2070.0000.0000.0000.000
182A237ASP-1-0.758-0.8618.0570.5670.5670.0000.0000.0000.000
183A238ALA00.0000.0048.759-0.132-0.1320.0000.0000.0000.000
184A239LEU0-0.033-0.0089.241-0.127-0.1270.0000.0000.0000.000
185A240MET0-0.034-0.0254.658-0.1770.0260.003-0.069-0.1370.000
186A241LYS10.8340.8976.766-0.810-0.8100.0000.0000.0000.000
187A242ARG10.7930.8908.6270.1310.1310.0000.0000.0000.000
188A243MET0-0.087-0.0237.2440.0680.0680.0000.0000.0000.000
189A244GLU-1-1.010-1.0074.681-1.015-0.848-0.001-0.007-0.1600.000