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

tag_button

FMODB ID: 94MZ2

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2113264.885715
FMO2-HF: Nuclear repulsion 2039442.386499
FMO2-HF: Total energy -73822.499216
FMO2-MP2: Total energy -74039.580058


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.
0.8072.5930.002-0.745-1.0420.005
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 : 0.054 / q_NPA : 0.027
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].
3A58LEU00.0200.0043.830-0.2851.093-0.018-0.657-0.7030.005
4A59ILE00.0170.0236.5800.4550.4550.0000.0000.0000.000
5A60SER0-0.016-0.04410.187-0.047-0.0470.0000.0000.0000.000
6A61VAL00.0480.02412.5430.0480.0480.0000.0000.0000.000
7A62GLU-1-0.837-0.90014.810-0.588-0.5880.0000.0000.0000.000
8A63LYS10.8600.9188.1581.7231.7230.0000.0000.0000.000
9A64ILE00.0090.01514.8320.0560.0560.0000.0000.0000.000
10A65GLN0-0.002-0.00517.0900.0460.0460.0000.0000.0000.000
11A66LYS10.9120.95417.3320.4900.4900.0000.0000.0000.000
12A67LEU00.0270.02415.0890.0360.0360.0000.0000.0000.000
13A68ALA00.0140.01819.4520.0390.0390.0000.0000.0000.000
14A69GLN0-0.024-0.01222.5620.0300.0300.0000.0000.0000.000
15A70SER0-0.071-0.03721.7420.0210.0210.0000.0000.0000.000
16A71TYR00.0650.04419.6320.0290.0290.0000.0000.0000.000
17A72GLN00.001-0.02225.6460.0070.0070.0000.0000.0000.000
18A73GLY00.0270.01028.646-0.002-0.0020.0000.0000.0000.000
19A74ASP-1-0.813-0.93429.283-0.146-0.1460.0000.0000.0000.000
20A75THR00.0210.01223.905-0.007-0.0070.0000.0000.0000.000
21A76ARG10.8890.96424.3200.1760.1760.0000.0000.0000.000
22A77LYS10.9150.96324.8780.1280.1280.0000.0000.0000.000
23A78ARG10.8750.95123.1390.1870.1870.0000.0000.0000.000
24A79PHE00.0280.01817.440-0.020-0.0200.0000.0000.0000.000
25A80THR0-0.054-0.03820.880-0.024-0.0240.0000.0000.0000.000
26A81ALA0-0.013-0.00122.850-0.007-0.0070.0000.0000.0000.000
27A82TRP00.0470.01913.548-0.004-0.0040.0000.0000.0000.000
28A83GLY00.0260.00718.142-0.026-0.0260.0000.0000.0000.000
29A84ASN0-0.004-0.01419.207-0.014-0.0140.0000.0000.0000.000
30A85LEU0-0.0190.01018.5290.0100.0100.0000.0000.0000.000
31A86ILE00.0140.00014.0830.0110.0110.0000.0000.0000.000
32A87ASP-1-0.783-0.89917.587-0.375-0.3750.0000.0000.0000.000
33A88SER0-0.122-0.05319.8250.0280.0280.0000.0000.0000.000
34A89LEU00.0190.00618.6580.0320.0320.0000.0000.0000.000
35A90LYS10.9210.97315.2860.4810.4810.0000.0000.0000.000
36A91LYS10.9300.95318.5990.2580.2580.0000.0000.0000.000
37A92LYS10.8310.93820.4010.2410.2410.0000.0000.0000.000
38A93PRO00.0370.00820.905-0.006-0.0060.0000.0000.0000.000
39A94VAL00.1120.05317.946-0.007-0.0070.0000.0000.0000.000
40A95LYS10.9210.97820.2920.0750.0750.0000.0000.0000.000
41A96ILE00.0100.00022.855-0.001-0.0010.0000.0000.0000.000
42A97GLN0-0.048-0.02916.8260.0060.0060.0000.0000.0000.000
43A98LEU00.0340.01217.123-0.014-0.0140.0000.0000.0000.000
44A99GLU-1-0.863-0.95119.682-0.107-0.1070.0000.0000.0000.000
45A100LYS10.9350.97722.1360.1600.1600.0000.0000.0000.000
46A101VAL00.0260.02516.013-0.004-0.0040.0000.0000.0000.000
47A102ASN00.0140.02019.407-0.003-0.0030.0000.0000.0000.000
48A103SER0-0.018-0.04121.1940.0030.0030.0000.0000.0000.000
49A104PHE0-0.028-0.00420.5240.0060.0060.0000.0000.0000.000
50A105PHE00.053-0.00416.9330.0000.0000.0000.0000.0000.000
51A106ASN00.0200.01121.6680.0000.0000.0000.0000.0000.000
52A107GLN0-0.095-0.03324.4800.0190.0190.0000.0000.0000.000
53A108PHE0-0.067-0.02522.100-0.001-0.0010.0000.0000.0000.000
54A109ASN0-0.006-0.00225.6320.0180.0180.0000.0000.0000.000
55A110TYR00.0240.00224.741-0.007-0.0070.0000.0000.0000.000
56A111GLU-1-0.869-0.92824.473-0.110-0.1100.0000.0000.0000.000
57A112THR00.000-0.01026.1460.0010.0010.0000.0000.0000.000
58A113ASP-1-0.737-0.85927.581-0.019-0.0190.0000.0000.0000.000
59A114PRO0-0.074-0.03529.1500.0030.0030.0000.0000.0000.000
60A115ILE0-0.064-0.03232.1550.0030.0030.0000.0000.0000.000
61A116THR0-0.074-0.05629.7640.0030.0030.0000.0000.0000.000
62A117GLY0-0.0100.01131.6200.0020.0020.0000.0000.0000.000
63A118ALA0-0.031-0.01627.455-0.003-0.0030.0000.0000.0000.000
64A119SER0-0.046-0.04222.545-0.005-0.0050.0000.0000.0000.000
65A120ASP-1-0.903-0.95523.216-0.042-0.0420.0000.0000.0000.000
66A121ASP-1-0.902-0.94221.9700.0340.0340.0000.0000.0000.000
67A122TYR0-0.070-0.05017.2470.0250.0250.0000.0000.0000.000
68A123TRP0-0.002-0.00512.8600.0070.0070.0000.0000.0000.000
69A124LYS10.7520.84515.4320.1250.1250.0000.0000.0000.000
70A125SER0-0.031-0.05311.735-0.047-0.0470.0000.0000.0000.000
71A126PRO00.012-0.01611.1290.0320.0320.0000.0000.0000.000
72A127VAL00.015-0.00713.3540.0410.0410.0000.0000.0000.000
73A128GLU-1-0.703-0.78715.096-0.218-0.2180.0000.0000.0000.000
74A129PHE00.0540.05916.9980.0220.0220.0000.0000.0000.000
75A130ILE0-0.032-0.01717.9940.0270.0270.0000.0000.0000.000
76A131VAL0-0.041-0.03519.8640.0260.0260.0000.0000.0000.000
77A132ASP-1-0.819-0.89121.530-0.145-0.1450.0000.0000.0000.000
78A133GLY0-0.092-0.03522.8130.0160.0160.0000.0000.0000.000
79A134GLY00.003-0.01422.6260.0130.0130.0000.0000.0000.000
80A135GLY00.0410.02321.188-0.014-0.0140.0000.0000.0000.000
81A136ASP-1-0.693-0.81020.637-0.065-0.0650.0000.0000.0000.000
82A137CYS0-0.049-0.03021.126-0.014-0.0140.0000.0000.0000.000
83A138GLU-1-0.806-0.91617.812-0.008-0.0080.0000.0000.0000.000
84A139ASP-1-0.750-0.87716.751-0.162-0.1620.0000.0000.0000.000
85A140PHE0-0.089-0.04116.929-0.046-0.0460.0000.0000.0000.000
86A141ALA0-0.046-0.01816.373-0.031-0.0310.0000.0000.0000.000
87A142ILE00.0540.02111.555-0.046-0.0460.0000.0000.0000.000
88A143ILE0-0.036-0.00312.215-0.103-0.1030.0000.0000.0000.000
89A144LYS10.8060.90513.7780.0910.0910.0000.0000.0000.000
90A145TYR00.004-0.0116.388-0.028-0.0280.0000.0000.0000.000
91A146PHE00.0590.0095.503-0.040-0.0400.0000.0000.0000.000
92A147THR0-0.055-0.0319.850-0.106-0.1060.0000.0000.0000.000
93A148LEU0-0.006-0.01512.839-0.001-0.0010.0000.0000.0000.000
94A149VAL00.0240.0226.1900.0230.0230.0000.0000.0000.000
95A150ALA0-0.040-0.0109.686-0.028-0.0280.0000.0000.0000.000
96A151VAL0-0.103-0.04211.0320.0520.0520.0000.0000.0000.000
97A152GLY0-0.035-0.02312.3620.0610.0610.0000.0000.0000.000
98A153VAL0-0.043-0.00612.9390.0610.0610.0000.0000.0000.000
99A154PRO00.0280.01710.645-0.084-0.0840.0000.0000.0000.000
100A155SER00.014-0.0156.342-0.036-0.0360.0000.0000.0000.000
101A156ASP-1-0.909-0.9528.6510.0700.0700.0000.0000.0000.000
102A157GLN0-0.062-0.03210.7830.0080.0080.0000.0000.0000.000
103A158LEU0-0.054-0.01510.759-0.008-0.0080.0000.0000.0000.000
104A159ARG10.9280.97011.188-0.118-0.1180.0000.0000.0000.000
105A160ILE00.0460.03111.033-0.030-0.0300.0000.0000.0000.000
106A161THR0-0.047-0.02914.2700.0540.0540.0000.0000.0000.000
107A162TYR00.0630.04917.692-0.014-0.0140.0000.0000.0000.000
108A163ALA00.013-0.01220.0360.0150.0150.0000.0000.0000.000
109A164ALA00.0310.02523.521-0.004-0.0040.0000.0000.0000.000
110A165SER00.0350.02127.095-0.002-0.0020.0000.0000.0000.000
111A166LEU0-0.060-0.05029.1370.0020.0020.0000.0000.0000.000
112A167THR0-0.015-0.01232.2320.0010.0010.0000.0000.0000.000
113A168LEU00.0140.00429.310-0.001-0.0010.0000.0000.0000.000
114A169ASN0-0.085-0.02832.6700.0040.0040.0000.0000.0000.000
115A170GLN00.0380.01928.8760.0050.0050.0000.0000.0000.000
116A171ALA0-0.038-0.01624.2090.0000.0000.0000.0000.0000.000
117A172HIS00.012-0.02124.307-0.004-0.0040.0000.0000.0000.000
118A173MET0-0.0380.01616.9240.0040.0040.0000.0000.0000.000
119A174VAL0-0.0120.00319.480-0.015-0.0150.0000.0000.0000.000
120A175LEU0-0.023-0.00613.3730.0070.0070.0000.0000.0000.000
121A176SER0-0.047-0.02516.340-0.002-0.0020.0000.0000.0000.000
122A177PHE00.018-0.00815.698-0.004-0.0040.0000.0000.0000.000
123A178TYR0-0.001-0.01416.1400.0200.0200.0000.0000.0000.000
124A179PRO0-0.029-0.01217.600-0.006-0.0060.0000.0000.0000.000
125A180THR0-0.007-0.02019.289-0.007-0.0070.0000.0000.0000.000
126A181PRO00.0220.00217.126-0.003-0.0030.0000.0000.0000.000
127A182GLU-1-0.857-0.90919.1920.0670.0670.0000.0000.0000.000
128A183SER0-0.070-0.02521.948-0.009-0.0090.0000.0000.0000.000
129A184GLU-1-0.744-0.83022.5100.0030.0030.0000.0000.0000.000
130A185PRO0-0.0040.00619.824-0.009-0.0090.0000.0000.0000.000
131A186LEU0-0.053-0.03720.8390.0000.0000.0000.0000.0000.000
132A187ILE0-0.003-0.00320.423-0.006-0.0060.0000.0000.0000.000
133A188LEU0-0.006-0.01417.681-0.007-0.0070.0000.0000.0000.000
134A189ASP-1-0.708-0.83120.366-0.057-0.0570.0000.0000.0000.000
135A190SER0-0.003-0.01622.568-0.009-0.0090.0000.0000.0000.000
136A191LEU0-0.0030.01324.188-0.001-0.0010.0000.0000.0000.000
137A192GLU-1-0.792-0.88526.841-0.047-0.0470.0000.0000.0000.000
138A193SER0-0.036-0.01226.488-0.010-0.0100.0000.0000.0000.000
139A194LYS10.7640.87126.9760.0450.0450.0000.0000.0000.000
140A195ILE00.0060.01521.8570.0000.0000.0000.0000.0000.000
141A196LEU0-0.026-0.01425.2740.0040.0040.0000.0000.0000.000
142A197LYS10.8750.92025.2000.0120.0120.0000.0000.0000.000
143A198ALA00.0780.03724.3070.0000.0000.0000.0000.0000.000
144A199SER0-0.077-0.07126.1230.0000.0000.0000.0000.0000.000
145A200ALA0-0.087-0.04129.1550.0010.0010.0000.0000.0000.000
146A201ARG10.7420.82126.4750.0290.0290.0000.0000.0000.000
147A202PRO00.0290.02128.7850.0040.0040.0000.0000.0000.000
148A203ASP-1-0.820-0.88029.700-0.014-0.0140.0000.0000.0000.000
149A204LEU0-0.0030.01224.3490.0010.0010.0000.0000.0000.000
150A205LYS10.9810.98827.142-0.045-0.0450.0000.0000.0000.000
151A206PRO0-0.016-0.01221.7290.0040.0040.0000.0000.0000.000
152A207VAL0-0.032-0.00622.2580.0060.0060.0000.0000.0000.000
153A208TYR0-0.040-0.02216.3310.0230.0230.0000.0000.0000.000
154A209SER0-0.019-0.00415.652-0.025-0.0250.0000.0000.0000.000
155A210PHE00.0570.00810.8060.0610.0610.0000.0000.0000.000
156A211ASN00.0330.0238.2760.0320.0320.0000.0000.0000.000
157A212ALA00.0370.0183.271-0.1000.1020.021-0.065-0.1570.000
158A213GLU-1-0.867-0.9134.3630.6550.861-0.001-0.023-0.1820.000
159A214GLY00.013-0.0016.5010.1120.1120.0000.0000.0000.000
160A215LEU0-0.0030.01110.174-0.096-0.0960.0000.0000.0000.000
161A216TRP0-0.029-0.02710.6670.0000.0000.0000.0000.0000.000
162A217LEU00.0350.01616.699-0.028-0.0280.0000.0000.0000.000
163A218ALA00.0360.03220.2260.0000.0000.0000.0000.0000.000
164A219LYS10.7210.83921.366-0.131-0.1310.0000.0000.0000.000
165A220THR00.0260.01325.227-0.010-0.0100.0000.0000.0000.000
166A221ARG10.9520.96621.144-0.168-0.1680.0000.0000.0000.000
167A222GLY00.010-0.00326.703-0.007-0.0070.0000.0000.0000.000
168A223GLU-1-0.802-0.91924.3720.1180.1180.0000.0000.0000.000
169A224SER0-0.049-0.01120.3330.0020.0020.0000.0000.0000.000
170A225SER0-0.0130.00919.175-0.020-0.0200.0000.0000.0000.000
171A226LEU00.000-0.00218.0710.0110.0110.0000.0000.0000.000
172A227MET0-0.0520.0009.985-0.062-0.0620.0000.0000.0000.000
173A228GLY00.0120.01314.6560.0340.0340.0000.0000.0000.000
174A229ASP-1-0.808-0.9189.9991.1971.1970.0000.0000.0000.000
175A230SER00.0100.0217.027-0.116-0.1160.0000.0000.0000.000
176A231LYS10.8870.9205.808-1.854-1.8540.0000.0000.0000.000
177A232SER0-0.073-0.03910.115-0.131-0.1310.0000.0000.0000.000
178A233LEU00.0010.01112.367-0.088-0.0880.0000.0000.0000.000
179A234GLY00.0370.01012.3670.0190.0190.0000.0000.0000.000
180A235LYS10.8290.89513.352-0.040-0.0400.0000.0000.0000.000
181A236TRP00.0170.0027.886-0.150-0.1500.0000.0000.0000.000
182A237ASP-1-0.760-0.8678.4320.7300.7300.0000.0000.0000.000
183A238ALA0-0.020-0.0108.876-0.035-0.0350.0000.0000.0000.000
184A239LEU0-0.031-0.0039.113-0.109-0.1090.0000.0000.0000.000
185A240MET0-0.034-0.0274.963-0.065-0.0650.0000.0000.0000.000
186A241LYS10.8390.9056.668-0.918-0.9180.0000.0000.0000.000
187A242ARG10.7950.8888.2450.0440.0440.0000.0000.0000.000
188A243MET0-0.091-0.0227.4060.0140.0140.0000.0000.0000.000
189A244GLU-1-1.046-1.0084.879-0.417-0.4170.0000.0000.0000.000