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: 221YR

Calculation Name: 5FWH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FWH

Chain ID: A

ChEMBL ID:

UniProt ID: A4IKE7

Base Structure: X-ray

Registration Date: 2023-06-20

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2130701.76691
FMO2-HF: Nuclear repulsion 2053228.905551
FMO2-HF: Total energy -77472.861359
FMO2-MP2: Total energy -77697.812271


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.
-11.684-4.5947.915-5.201-9.803-0.024
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 : 0.026 / q_NPA : 0.022
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].
3A3GLN00.0450.0012.4450.1662.2353.540-1.628-3.981-0.002
4A4LEU0-0.030-0.0095.594-0.923-0.894-0.001-0.015-0.0120.000
5A5TRP00.0020.0007.7030.1670.1670.0000.0000.0000.000
6A6VAL00.026-0.00711.118-0.039-0.0390.0000.0000.0000.000
7A7LEU00.0030.00613.931-0.016-0.0160.0000.0000.0000.000
8A8TYR00.0690.03016.1550.0110.0110.0000.0000.0000.000
9A9GLU-1-0.849-0.90619.868-0.015-0.0150.0000.0000.0000.000
10A10THR00.0240.03121.408-0.004-0.0040.0000.0000.0000.000
11A11TYR0-0.044-0.02016.977-0.012-0.0120.0000.0000.0000.000
12A12CYS0-0.013-0.00511.9030.0000.0000.0000.0000.0000.000
13A13GLN0-0.055-0.02811.5560.0040.0040.0000.0000.0000.000
14A14LEU0-0.020-0.0035.586-0.003-0.0030.0000.0000.0000.000
15A15PHE00.0310.0086.945-0.065-0.0650.0000.0000.0000.000
16A16SER00.005-0.0132.465-3.848-2.7992.098-1.229-1.918-0.006
17A17LEU0-0.041-0.0325.047-0.665-0.549-0.001-0.021-0.0940.000
18A18THR0-0.022-0.0315.756-0.229-0.2290.0000.0000.0000.000
19A19ASN0-0.076-0.0536.1550.2050.2050.0000.0000.0000.000
20A20GLU-1-0.876-0.8948.3521.1191.1190.0000.0000.0000.000
21A21GLU-1-0.853-0.89910.3710.3280.3280.0000.0000.0000.000
22A22LYS10.9020.93111.640-0.316-0.3160.0000.0000.0000.000
23A23VAL0-0.008-0.00913.923-0.061-0.0610.0000.0000.0000.000
24A24ILE0-0.0260.00412.2320.0140.0140.0000.0000.0000.000
25A25VAL00.000-0.01515.538-0.054-0.0540.0000.0000.0000.000
26A26ILE00.0040.00514.7920.0210.0210.0000.0000.0000.000
27A27GLY00.0460.00317.400-0.023-0.0230.0000.0000.0000.000
28A28ASN0-0.045-0.01419.5940.0090.0090.0000.0000.0000.000
29A29GLN0-0.033-0.00721.639-0.012-0.0120.0000.0000.0000.000
30A30LEU0-0.010-0.02119.4450.0090.0090.0000.0000.0000.000
31A31GLU-1-0.956-0.96818.3540.1400.1400.0000.0000.0000.000
32A32HIS0-0.055-0.02417.8980.0200.0200.0000.0000.0000.000
33A33HIS00.0300.02512.693-0.032-0.0320.0000.0000.0000.000
34A34VAL0-0.014-0.00311.5490.0150.0150.0000.0000.0000.000
35A35THR0-0.003-0.01514.201-0.016-0.0160.0000.0000.0000.000
36A36VAL00.001-0.00317.331-0.015-0.0150.0000.0000.0000.000
37A37SER00.003-0.02319.379-0.002-0.0020.0000.0000.0000.000
38A38SER0-0.039-0.03622.5400.0020.0020.0000.0000.0000.000
39A39PHE0-0.0100.00822.773-0.005-0.0050.0000.0000.0000.000
40A40SER0-0.043-0.04824.9440.0090.0090.0000.0000.0000.000
41A41PHE00.0430.01220.2640.0060.0060.0000.0000.0000.000
42A42ARG10.8360.90626.188-0.013-0.0130.0000.0000.0000.000
43A43ASN0-0.091-0.05927.4580.0040.0040.0000.0000.0000.000
44A44GLY00.0010.01326.6910.0000.0000.0000.0000.0000.000
45A45TYR00.0230.00621.578-0.003-0.0030.0000.0000.0000.000
46A46ILE0-0.010-0.00618.492-0.010-0.0100.0000.0000.0000.000
47A47GLN0-0.024-0.00518.8420.0170.0170.0000.0000.0000.000
48A48ILE00.011-0.00113.295-0.038-0.0380.0000.0000.0000.000
49A49GLU-1-0.911-0.95215.0040.1690.1690.0000.0000.0000.000
50A50LYS10.8510.9238.398-0.015-0.0150.0000.0000.0000.000
51A51LYN0-0.031-0.00913.0570.0240.0240.0000.0000.0000.000
52A52SER0-0.018-0.01812.3760.0490.0490.0000.0000.0000.000
53A53ASP-1-0.910-0.97313.952-0.045-0.0450.0000.0000.0000.000
54A54GLY0-0.0220.02211.0250.0330.0330.0000.0000.0000.000
55A55SER0-0.011-0.04011.1080.0400.0400.0000.0000.0000.000
56A56THR0-0.040-0.00711.682-0.110-0.1100.0000.0000.0000.000
57A57LEU00.0090.0079.8910.0490.0490.0000.0000.0000.000
58A58ALA00.0380.02813.795-0.020-0.0200.0000.0000.0000.000
59A59VAL00.0130.00516.9110.0310.0310.0000.0000.0000.000
60A60LEU00.003-0.01318.997-0.018-0.0180.0000.0000.0000.000
61A61GLN0-0.0200.00921.9230.0040.0040.0000.0000.0000.000
62A62GLY00.0310.00224.3100.0050.0050.0000.0000.0000.000
63A63GLY0-0.0090.00524.9680.0000.0000.0000.0000.0000.000
64A64ARG10.9010.94825.950-0.025-0.0250.0000.0000.0000.000
65A65GLN0-0.0020.00021.4120.0140.0140.0000.0000.0000.000
66A66ILE0-0.060-0.03222.408-0.004-0.0040.0000.0000.0000.000
67A67GLY0-0.007-0.01021.104-0.011-0.0110.0000.0000.0000.000
68A68GLU-1-0.899-0.94617.504-0.056-0.0560.0000.0000.0000.000
69A69LEU0-0.0450.00113.918-0.017-0.0170.0000.0000.0000.000
70A70LYS10.9310.94613.4330.2380.2380.0000.0000.0000.000
71A71PRO00.044-0.0039.4620.0030.0030.0000.0000.0000.000
72A72ARG10.8070.90610.1330.7260.7260.0000.0000.0000.000
73A73CYS0-0.082-0.00612.1620.0940.0940.0000.0000.0000.000
74A74SER00.0500.00614.3150.0000.0000.0000.0000.0000.000
75A75ILE0-0.030-0.01516.691-0.002-0.0020.0000.0000.0000.000
76A76THR00.0160.01819.3780.0100.0100.0000.0000.0000.000
77A77ILE0-0.026-0.00720.8530.0020.0020.0000.0000.0000.000
78A78ASP-1-0.867-0.93623.794-0.013-0.0130.0000.0000.0000.000
79A79VAL00.0030.00223.4150.0070.0070.0000.0000.0000.000
80A80ASP-1-0.789-0.86126.4380.0160.0160.0000.0000.0000.000
81A81GLY0-0.0310.00428.738-0.003-0.0030.0000.0000.0000.000
82A82GLN0-0.037-0.03724.948-0.010-0.0100.0000.0000.0000.000
83A83GLN0-0.0480.00124.338-0.003-0.0030.0000.0000.0000.000
84A84MET00.0370.01618.6210.0080.0080.0000.0000.0000.000
85A85THR0-0.007-0.01517.326-0.007-0.0070.0000.0000.0000.000
86A86ILE0-0.025-0.00313.9370.0230.0230.0000.0000.0000.000
87A87ALA00.0360.01413.068-0.045-0.0450.0000.0000.0000.000
88A88TRP0-0.022-0.0116.9560.0110.0110.0000.0000.0000.000
89A89SER00.0540.0315.6370.3890.3890.0000.0000.0000.000
90A90GLY00.023-0.0057.383-0.156-0.1560.0000.0000.0000.000
91A91GLU-1-0.902-0.9454.149-1.426-1.317-0.001-0.038-0.0690.000
92A92GLU-1-0.888-0.9182.512-5.598-4.2411.519-1.308-1.569-0.013
93A93GLN0-0.042-0.0432.387-1.1460.9080.763-0.943-1.874-0.003
94A94ARG10.8230.9094.3891.0051.261-0.001-0.018-0.2370.000
95A95LYS10.9750.9556.9530.7100.7100.0000.0000.0000.000
96A96TYR0-0.016-0.0088.8730.1010.1010.0000.0000.0000.000
97A97VAL0-0.038-0.04012.525-0.051-0.0510.0000.0000.0000.000
98A98TYR00.0490.01714.6360.0240.0240.0000.0000.0000.000
99A99TYR0-0.028-0.01318.0830.0000.0000.0000.0000.0000.000
100A100VAL00.014-0.01220.4800.0080.0080.0000.0000.0000.000
101A101GLY00.0130.00223.0290.0080.0080.0000.0000.0000.000
102A102GLN0-0.093-0.03725.5230.0110.0110.0000.0000.0000.000
103A103GLN0-0.0210.00624.4160.0100.0100.0000.0000.0000.000
104A104SER00.002-0.01526.8180.0000.0000.0000.0000.0000.000
105A105GLU-1-0.813-0.89026.242-0.132-0.1320.0000.0000.0000.000
106A106VAL00.0090.01420.367-0.002-0.0020.0000.0000.0000.000
107A107LEU0-0.038-0.01223.2240.0000.0000.0000.0000.0000.000
108A108VAL0-0.0020.00917.861-0.013-0.0130.0000.0000.0000.000
109A109SER00.016-0.03021.0900.0100.0100.0000.0000.0000.000
110A110ASN00.0400.01721.860-0.025-0.0250.0000.0000.0000.000
111A111ASP-1-0.822-0.85523.471-0.141-0.1410.0000.0000.0000.000
112A112PRO00.007-0.01425.454-0.008-0.0080.0000.0000.0000.000
113A113GLN0-0.060-0.03427.0690.0010.0010.0000.0000.0000.000
114A114ALA0-0.0280.02122.8490.0040.0040.0000.0000.0000.000
115A115ASP-1-0.785-0.89022.619-0.178-0.1780.0000.0000.0000.000
116A116ILE0-0.064-0.02516.422-0.021-0.0210.0000.0000.0000.000
117A117GLU-1-0.908-0.96119.466-0.203-0.2030.0000.0000.0000.000
118A118THR0-0.048-0.05015.534-0.031-0.0310.0000.0000.0000.000
119A119THR00.0140.01318.2130.0250.0250.0000.0000.0000.000
120A120ASN0-0.065-0.05113.6900.0420.0420.0000.0000.0000.000
121A121ALA0-0.011-0.00816.6880.0110.0110.0000.0000.0000.000
122A122ARG10.8370.87918.7120.1510.1510.0000.0000.0000.000
123A123PHE0-0.035-0.00716.6420.0100.0100.0000.0000.0000.000
124A124SER0-0.051-0.03122.462-0.004-0.0040.0000.0000.0000.000
125A125LEU00.0210.00718.290-0.002-0.0020.0000.0000.0000.000
126A126ARG10.8350.89722.8740.1320.1320.0000.0000.0000.000
127A127LYS10.8580.94425.1310.1390.1390.0000.0000.0000.000
128A128HIS00.012-0.00326.8590.0140.0140.0000.0000.0000.000
129A129ARG10.8780.93028.8770.0760.0760.0000.0000.0000.000
130A130GLY00.0580.02127.6840.0030.0030.0000.0000.0000.000
131A131GLN0-0.038-0.00624.715-0.001-0.0010.0000.0000.0000.000
132A132TRP00.0030.00021.3750.0060.0060.0000.0000.0000.000
133A133VAL0-0.048-0.02923.0980.0020.0020.0000.0000.0000.000
134A134VAL00.0450.03019.510-0.008-0.0080.0000.0000.0000.000
135A135ILE0-0.049-0.03522.2760.0160.0160.0000.0000.0000.000
136A136PRO00.0110.00522.136-0.010-0.0100.0000.0000.0000.000
137A137ASP-1-0.864-0.94623.731-0.119-0.1190.0000.0000.0000.000
138A138ASP-1-0.971-0.97225.115-0.095-0.0950.0000.0000.0000.000
139A139ASP-1-0.943-0.97426.088-0.137-0.1370.0000.0000.0000.000
140A140ALA0-0.027-0.01221.169-0.001-0.0010.0000.0000.0000.000
141A141PRO0-0.038-0.00719.7140.0000.0000.0000.0000.0000.000
142A142LEU00.0160.00616.186-0.019-0.0190.0000.0000.0000.000
143A143PHE0-0.038-0.03714.6350.0240.0240.0000.0000.0000.000
144A144LEU00.0230.01614.950-0.038-0.0380.0000.0000.0000.000
145A145ASN0-0.053-0.05713.197-0.010-0.0100.0000.0000.0000.000
146A146GLY00.0310.01913.6920.0260.0260.0000.0000.0000.000
147A147VAL0-0.012-0.00114.3620.0260.0260.0000.0000.0000.000
148A148GLN0-0.028-0.01518.125-0.008-0.0080.0000.0000.0000.000
149A149LEU0-0.027-0.00418.4420.0060.0060.0000.0000.0000.000
150A150SER0-0.025-0.02822.0860.0000.0000.0000.0000.0000.000
151A151ASP-1-0.916-0.94525.408-0.083-0.0830.0000.0000.0000.000
152A152ALA0-0.018-0.01524.904-0.008-0.0080.0000.0000.0000.000
153A153VAL00.0220.01822.1420.0080.0080.0000.0000.0000.000
154A154SER0-0.051-0.02823.133-0.010-0.0100.0000.0000.0000.000
155A155LEU0-0.032-0.00617.9480.0020.0020.0000.0000.0000.000
156A156ARG10.7820.86218.2220.1640.1640.0000.0000.0000.000
157A157ASN00.025-0.00317.194-0.023-0.0230.0000.0000.0000.000
158A158GLY0-0.014-0.00313.1050.0130.0130.0000.0000.0000.000
159A159ASP-1-0.767-0.83113.469-0.190-0.1900.0000.0000.0000.000
160A160VAL0-0.051-0.0318.957-0.056-0.0560.0000.0000.0000.000
161A161LEU00.0220.01512.1500.0560.0560.0000.0000.0000.000
162A162LEU0-0.032-0.0178.634-0.073-0.0730.0000.0000.0000.000
163A163CYS00.0610.04112.3020.0400.0400.0000.0000.0000.000
164A164PRO0-0.010-0.00712.464-0.033-0.0330.0000.0000.0000.000
165A165TYR0-0.006-0.0089.397-0.024-0.0240.0000.0000.0000.000
166A166MET00.0030.0289.156-0.121-0.1210.0000.0000.0000.000
167A167GLN0-0.020-0.0154.839-0.085-0.034-0.001-0.001-0.0490.000
168A168PHE00.0290.0179.667-0.078-0.0780.0000.0000.0000.000
169A169VAL00.000-0.0089.2470.0190.0190.0000.0000.0000.000
170A170PHE00.0470.03412.365-0.007-0.0070.0000.0000.0000.000
171A171ILE0-0.091-0.05411.537-0.014-0.0140.0000.0000.0000.000
172A172GLU-1-0.836-0.90715.116-0.133-0.1330.0000.0000.0000.000
173A173GLU-1-0.887-0.94818.921-0.143-0.1430.0000.0000.0000.000
174A174ASP-1-0.894-0.95821.502-0.161-0.1610.0000.0000.0000.000
175A175LEU0-0.044-0.00917.150-0.003-0.0030.0000.0000.0000.000
176A176LEU00.0290.01914.921-0.020-0.0200.0000.0000.0000.000
177A177ALA0-0.040-0.01710.892-0.008-0.0080.0000.0000.0000.000
178A178VAL00.0510.01911.545-0.005-0.0050.0000.0000.0000.000
179A179THR0-0.054-0.0374.863-0.126-0.1260.0000.0000.0000.000
180A180SER00.0170.0007.3080.1550.1550.0000.0000.0000.000
181A181SER00.0300.0076.974-0.139-0.1390.0000.0000.0000.000
182A182GLU-1-0.879-0.9057.887-0.461-0.4610.0000.0000.0000.000
183A183GLU-1-0.862-0.90510.991-0.445-0.4450.0000.0000.0000.000
184A184VAL0-0.043-0.01011.9250.0180.0180.0000.0000.0000.000
185A185VAL00.0150.01914.5810.0270.0270.0000.0000.0000.000
186A186SER00.012-0.02018.1080.0010.0010.0000.0000.0000.000
187A187SER0-0.0140.00820.0170.0080.0080.0000.0000.0000.000
188A188LEU0-0.0090.00519.5410.0170.0170.0000.0000.0000.000
189A189THR0-0.025-0.01921.8110.0060.0060.0000.0000.0000.000
190A190GLU-1-0.845-0.92316.964-0.294-0.2940.0000.0000.0000.000
191A191THR0-0.017-0.00917.7630.0140.0140.0000.0000.0000.000
192A192MET0-0.104-0.05913.5470.0390.0390.0000.0000.0000.000
193A193PRO0-0.005-0.00115.638-0.022-0.0220.0000.0000.0000.000
194A194PRO00.0600.03812.2810.0000.0000.0000.0000.0000.000
195A195LEU0-0.086-0.0047.2540.0880.0880.0000.0000.0000.000