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: 98V62

Calculation Name: 3BHW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BHW

Chain ID: A

ChEMBL ID:

UniProt ID: Q2W5N3

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2281151.466222
FMO2-HF: Nuclear repulsion 2201270.315071
FMO2-HF: Total energy -79881.151151
FMO2-MP2: Total energy -80111.268137


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-12.413-0.7582.176-5.988-7.845-0.029
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.016
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].
3A6TYR0-0.078-0.0873.514-1.0001.275-0.005-1.066-1.2050.007
4A7LYS11.0200.9972.801-1.4050.7020.171-0.822-1.456-0.002
5A8ALA00.019-0.0064.8880.1270.167-0.001-0.003-0.0360.000
6A9ASP-1-0.881-0.9307.610-0.280-0.2800.0000.0000.0000.000
7A10ILE0-0.009-0.0029.6710.0840.0840.0000.0000.0000.000
8A11GLY00.028-0.00111.9560.0500.0500.0000.0000.0000.000
9A12GLY0-0.070-0.02513.6240.0410.0410.0000.0000.0000.000
10A13GLY0-0.035-0.03015.3790.0350.0350.0000.0000.0000.000
11A14SER0-0.0090.00617.485-0.023-0.0230.0000.0000.0000.000
12A15LEU0-0.033-0.02119.561-0.002-0.0020.0000.0000.0000.000
13A16LYS10.8590.94821.6810.1240.1240.0000.0000.0000.000
14A17LEU00.0840.03824.3710.0030.0030.0000.0000.0000.000
15A18PRO00.0170.00626.6450.0030.0030.0000.0000.0000.000
16A19GLU-1-0.827-0.93724.842-0.092-0.0920.0000.0000.0000.000
17A20SER0-0.008-0.00422.894-0.001-0.0010.0000.0000.0000.000
18A21ARG10.7860.89124.7530.0850.0850.0000.0000.0000.000
19A22ILE0-0.0200.01127.9850.0040.0040.0000.0000.0000.000
20A23ILE0-0.035-0.02321.9290.0040.0040.0000.0000.0000.000
21A24ALA00.0310.00625.2570.0020.0020.0000.0000.0000.000
22A25GLY0-0.014-0.01126.0780.0040.0040.0000.0000.0000.000
23A26LEU00.0210.00926.4750.0030.0030.0000.0000.0000.000
24A27LEU0-0.061-0.03021.5280.0030.0030.0000.0000.0000.000
25A28LEU0-0.077-0.03625.7380.0030.0030.0000.0000.0000.000
26A29GLU-1-0.999-0.97428.910-0.040-0.0400.0000.0000.0000.000
27A30GLY00.0090.02527.8290.0030.0030.0000.0000.0000.000
28A31VAL0-0.025-0.02126.4120.0040.0040.0000.0000.0000.000
29A32THR00.0430.01326.344-0.003-0.0030.0000.0000.0000.000
30A33GLU-1-0.889-0.95622.138-0.018-0.0180.0000.0000.0000.000
31A34ASP-1-0.919-0.96424.023-0.006-0.0060.0000.0000.0000.000
32A35GLN0-0.0080.00126.4950.0010.0010.0000.0000.0000.000
33A36TRP0-0.0110.00220.515-0.007-0.0070.0000.0000.0000.000
34A37ARG10.8290.87421.2760.0130.0130.0000.0000.0000.000
35A38HIS00.0460.02524.9220.0000.0000.0000.0000.0000.000
36A39ALA00.0730.03927.896-0.001-0.0010.0000.0000.0000.000
37A40ILE0-0.111-0.05522.379-0.003-0.0030.0000.0000.0000.000
38A41GLU-1-0.819-0.89523.553-0.029-0.0290.0000.0000.0000.000
39A42VAL0-0.046-0.00827.2520.0020.0020.0000.0000.0000.000
40A43GLU-1-0.871-0.93430.942-0.031-0.0310.0000.0000.0000.000
41A44ASN0-0.039-0.00929.779-0.005-0.0050.0000.0000.0000.000
42A45VAL00.0780.03328.284-0.003-0.0030.0000.0000.0000.000
43A46LEU0-0.049-0.03324.322-0.004-0.0040.0000.0000.0000.000
44A47GLN0-0.0090.01328.9310.0000.0000.0000.0000.0000.000
45A48ARG10.8560.94323.5560.0800.0800.0000.0000.0000.000
46A49ARG10.9240.95030.0970.0480.0480.0000.0000.0000.000
47A50SER00.0370.01929.2610.0030.0030.0000.0000.0000.000
48A51PRO00.0830.03326.734-0.005-0.0050.0000.0000.0000.000
49A52GLY00.0090.00924.795-0.003-0.0030.0000.0000.0000.000
50A53THR0-0.062-0.04120.096-0.007-0.0070.0000.0000.0000.000
51A54ALA0-0.029-0.00920.252-0.007-0.0070.0000.0000.0000.000
52A55LYS10.9490.96520.2090.0180.0180.0000.0000.0000.000
53A56ARG11.0091.01613.5450.1140.1140.0000.0000.0000.000
54A57GLN00.0010.00316.508-0.015-0.0150.0000.0000.0000.000
55A58SER00.1010.04518.477-0.011-0.0110.0000.0000.0000.000
56A59SER0-0.031-0.02515.9400.0030.0030.0000.0000.0000.000
57A60LEU0-0.046-0.00512.860-0.010-0.0100.0000.0000.0000.000
58A61MET0-0.040-0.01315.512-0.013-0.0130.0000.0000.0000.000
59A62ARG11.0371.01818.7000.0690.0690.0000.0000.0000.000
60A63ASN00.027-0.00113.0570.0120.0120.0000.0000.0000.000
61A64ARG10.8420.89814.8960.2550.2550.0000.0000.0000.000
62A65LEU00.0080.01716.116-0.008-0.0080.0000.0000.0000.000
63A66GLU-1-0.952-0.94615.183-0.116-0.1160.0000.0000.0000.000
64A67THR0-0.056-0.02513.465-0.006-0.0060.0000.0000.0000.000
65A68MET0-0.063-0.01216.237-0.005-0.0050.0000.0000.0000.000
66A69GLY00.0590.03219.9480.0080.0080.0000.0000.0000.000
67A70PRO00.0570.01123.166-0.004-0.0040.0000.0000.0000.000
68A71GLU-1-0.857-0.93226.500-0.085-0.0850.0000.0000.0000.000
69A72LEU00.005-0.00522.4380.0010.0010.0000.0000.0000.000
70A73TRP00.004-0.01721.3020.0050.0050.0000.0000.0000.000
71A74GLN00.0460.01625.9240.0050.0050.0000.0000.0000.000
72A75MET0-0.028-0.00227.6430.0000.0000.0000.0000.0000.000
73A76VAL0-0.061-0.02624.2470.0010.0010.0000.0000.0000.000
74A77ARG10.8090.87127.6540.0650.0650.0000.0000.0000.000
75A78ASP-1-0.786-0.86830.193-0.061-0.0610.0000.0000.0000.000
76A79GLY00.0080.03231.6850.0030.0030.0000.0000.0000.000
77A80SER00.0500.01432.992-0.002-0.0020.0000.0000.0000.000
78A81THR00.029-0.00131.829-0.005-0.0050.0000.0000.0000.000
79A82GLN00.0260.00929.839-0.013-0.0130.0000.0000.0000.000
80A83VAL00.0250.01429.465-0.009-0.0090.0000.0000.0000.000
81A84ALA00.0570.03828.311-0.009-0.0090.0000.0000.0000.000
82A85ILE0-0.012-0.01025.189-0.010-0.0100.0000.0000.0000.000
83A86GLN00.0260.01724.606-0.014-0.0140.0000.0000.0000.000
84A87ALA00.0570.04223.934-0.014-0.0140.0000.0000.0000.000
85A88VAL00.002-0.00221.283-0.016-0.0160.0000.0000.0000.000
86A89PHE0-0.034-0.02619.469-0.025-0.0250.0000.0000.0000.000
87A90ALA00.0210.01219.165-0.031-0.0310.0000.0000.0000.000
88A91ALA00.0400.02317.925-0.029-0.0290.0000.0000.0000.000
89A92ALA0-0.057-0.03615.972-0.036-0.0360.0000.0000.0000.000
90A93ILE0-0.051-0.03914.443-0.063-0.0630.0000.0000.0000.000
91A94LYS10.7740.85513.7180.1580.1580.0000.0000.0000.000
92A95HIS0-0.0120.01311.013-0.088-0.0880.0000.0000.0000.000
93A96SER0-0.022-0.0139.773-0.149-0.1490.0000.0000.0000.000
94A97THR00.0730.0357.7360.1280.1280.0000.0000.0000.000
95A98LEU0-0.0310.0067.9190.0610.0610.0000.0000.0000.000
96A99LEU00.0100.0099.6030.1130.1130.0000.0000.0000.000
97A100GLY00.0520.01412.8180.0590.0590.0000.0000.0000.000
98A101ASP-1-0.690-0.80711.128-0.667-0.6670.0000.0000.0000.000
99A102PHE0-0.0150.00713.5550.0660.0660.0000.0000.0000.000
100A103LEU0-0.009-0.00715.3240.0510.0510.0000.0000.0000.000
101A104ASP-1-0.851-0.94216.327-0.265-0.2650.0000.0000.0000.000
102A105LEU0-0.035-0.02413.9610.0280.0280.0000.0000.0000.000
103A106VAL0-0.0280.00716.8960.0210.0210.0000.0000.0000.000
104A107VAL0-0.018-0.01819.3570.0290.0290.0000.0000.0000.000
105A108ARG10.8020.89120.6220.2310.2310.0000.0000.0000.000
106A109ASP-1-0.910-0.95322.712-0.127-0.1270.0000.0000.0000.000
107A110GLN00.0140.00323.5720.0150.0150.0000.0000.0000.000
108A111PHE0-0.096-0.05625.3060.0160.0160.0000.0000.0000.000
109A112ARG10.9530.97828.0960.1040.1040.0000.0000.0000.000
110A113MET0-0.0320.01429.2070.0050.0050.0000.0000.0000.000
111A114PHE00.0320.00631.4940.0010.0010.0000.0000.0000.000
112A115ARG10.8700.92533.8310.0690.0690.0000.0000.0000.000
113A116PRO00.0450.02928.5800.0000.0000.0000.0000.0000.000
114A117ASP-1-0.865-0.94028.154-0.109-0.1090.0000.0000.0000.000
115A118LEU00.0290.02120.697-0.007-0.0070.0000.0000.0000.000
116A119PRO00.0420.03023.990-0.006-0.0060.0000.0000.0000.000
117A120ARG10.9190.93620.6500.1490.1490.0000.0000.0000.000
118A121LYS10.9731.00320.5670.0990.0990.0000.0000.0000.000
119A122MET0-0.008-0.00320.550-0.006-0.0060.0000.0000.0000.000
120A123TRP00.002-0.00712.526-0.036-0.0360.0000.0000.0000.000
121A124ASP-1-0.888-0.94515.917-0.212-0.2120.0000.0000.0000.000
122A125GLN00.0300.00616.230-0.004-0.0040.0000.0000.0000.000
123A126TYR0-0.038-0.03911.493-0.028-0.0280.0000.0000.0000.000
124A127LEU0-0.004-0.00710.475-0.069-0.0690.0000.0000.0000.000
125A128GLU-1-0.902-0.94711.750-0.193-0.1930.0000.0000.0000.000
126A129GLN0-0.005-0.00913.3310.0200.0200.0000.0000.0000.000
127A130CYS0-0.110-0.0528.436-0.033-0.0330.0000.0000.0000.000
128A131ARG10.9020.9267.6640.2780.2780.0000.0000.0000.000
129A132ASN0-0.042-0.0029.1430.0840.0840.0000.0000.0000.000
130A133ARG10.9030.9519.1020.5890.5890.0000.0000.0000.000
131A134ASP-1-0.822-0.9043.103-5.822-2.5470.225-1.894-1.606-0.015
132A135PRO00.0260.0105.877-0.038-0.0380.0000.0000.0000.000
133A136LEU0-0.0090.0012.426-0.8630.4100.700-0.703-1.270-0.002
134A137MET0-0.053-0.0042.593-3.705-1.5210.975-1.405-1.755-0.018
135A138PRO00.0010.0072.974-0.1130.3810.112-0.094-0.5120.001
136A139VAL00.0260.0085.383-0.0040.003-0.001-0.001-0.0050.000
137A140TRP0-0.0080.0079.191-0.086-0.0860.0000.0000.0000.000
138A141GLN00.0390.00511.9740.0340.0340.0000.0000.0000.000
139A142ASP-1-0.798-0.89515.114-0.132-0.1320.0000.0000.0000.000
140A143SER0-0.055-0.02617.611-0.021-0.0210.0000.0000.0000.000
141A144THR00.011-0.01212.0410.0050.0050.0000.0000.0000.000
142A145ALA00.0360.03113.899-0.030-0.0300.0000.0000.0000.000
143A146ASN00.022-0.00814.827-0.014-0.0140.0000.0000.0000.000
144A147LYS10.9460.97917.0630.1150.1150.0000.0000.0000.000
145A148LEU0-0.020-0.00310.714-0.004-0.0040.0000.0000.0000.000
146A149ALA00.0210.02014.982-0.014-0.0140.0000.0000.0000.000
147A150ASP-1-0.829-0.91417.160-0.143-0.1430.0000.0000.0000.000
148A151CYS0-0.174-0.07016.1550.0160.0160.0000.0000.0000.000
149A152VAL00.0670.03214.3850.0040.0040.0000.0000.0000.000
150A153TYR00.006-0.02017.4440.0070.0070.0000.0000.0000.000
151A154ARG10.8920.95420.2030.1740.1740.0000.0000.0000.000
152A155ILE00.0100.00617.1590.0110.0110.0000.0000.0000.000
153A156LEU0-0.005-0.00119.7500.0110.0110.0000.0000.0000.000
154A157VAL0-0.026-0.00822.6620.0120.0120.0000.0000.0000.000
155A158GLU-1-0.825-0.93322.914-0.149-0.1490.0000.0000.0000.000
156A159VAL0-0.051-0.01422.9510.0090.0090.0000.0000.0000.000
157A160GLY00.0190.01625.8580.0070.0070.0000.0000.0000.000
158A161TYR0-0.053-0.04223.3830.0080.0080.0000.0000.0000.000
159A162ILE00.0230.02023.1410.0040.0040.0000.0000.0000.000
160A163THR0-0.014-0.00627.3100.0020.0020.0000.0000.0000.000
161A164ASP-1-0.742-0.84729.221-0.086-0.0860.0000.0000.0000.000
162A165SER0-0.068-0.03629.801-0.002-0.0020.0000.0000.0000.000
163A166LYS10.7930.85729.8460.0980.0980.0000.0000.0000.000
164A167THR00.0200.01530.729-0.003-0.0030.0000.0000.0000.000
165A168TYR0-0.0010.00225.429-0.005-0.0050.0000.0000.0000.000
166A169ARG10.9180.97327.6310.0910.0910.0000.0000.0000.000
167A170LEU0-0.0090.00424.315-0.003-0.0030.0000.0000.0000.000
168A171LYS10.9020.94628.5700.1010.1010.0000.0000.0000.000
169A172SER00.0190.00628.835-0.007-0.0070.0000.0000.0000.000
170A173VAL00.0000.01026.6030.0080.0080.0000.0000.0000.000
171A174ARG10.9660.99428.9830.0870.0870.0000.0000.0000.000
172A175ILE00.0310.01525.4910.0030.0030.0000.0000.0000.000
173A176SER0-0.041-0.02829.0390.0090.0090.0000.0000.0000.000
174A177GLY00.010-0.01830.122-0.005-0.0050.0000.0000.0000.000
175A178GLU-1-0.868-0.93931.316-0.083-0.0830.0000.0000.0000.000
176A179VAL00.0180.01525.330-0.002-0.0020.0000.0000.0000.000
177A180MET0-0.047-0.03825.663-0.009-0.0090.0000.0000.0000.000
178A181SER0-0.036-0.00827.609-0.002-0.0020.0000.0000.0000.000
179A182TYR00.0940.05122.312-0.006-0.0060.0000.0000.0000.000
180A183LEU00.003-0.00421.181-0.004-0.0040.0000.0000.0000.000
181A184ARG10.9050.95023.8790.1050.1050.0000.0000.0000.000
182A185GLU-1-0.904-0.94426.196-0.082-0.0820.0000.0000.0000.000
183A186ASN0-0.045-0.02022.5810.0090.0090.0000.0000.0000.000
184A187ASN0-0.011-0.00121.882-0.006-0.0060.0000.0000.0000.000
185A188GLU-1-0.768-0.85318.210-0.238-0.2380.0000.0000.0000.000
186A189GLN0-0.041-0.04318.768-0.004-0.0040.0000.0000.0000.000
187A190TYR0-0.020-0.02012.686-0.012-0.0120.0000.0000.0000.000
188A191VAL00.0850.02916.826-0.008-0.0080.0000.0000.0000.000
189A192ILE0-0.035-0.00718.7390.0110.0110.0000.0000.0000.000
190A193ARG10.8900.95118.4760.2420.2420.0000.0000.0000.000
191A194CYS0-0.0220.00916.733-0.005-0.0050.0000.0000.0000.000
192A195ILE00.0080.01719.3820.0080.0080.0000.0000.0000.000
193A196GLN0-0.039-0.02321.7540.0200.0200.0000.0000.0000.000
194A197VAL0-0.017-0.00221.0830.0010.0010.0000.0000.0000.000
195A198SER0-0.002-0.00124.5330.0070.0070.0000.0000.0000.000