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: MN17Z

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 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 -2280884.405257
FMO2-HF: Nuclear repulsion 2201002.183284
FMO2-HF: Total energy -79882.221973
FMO2-MP2: Total energy -80112.220388


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.
-8.4481.3733.005-4.996-7.831-0.029
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 : -0.007
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].
3A6TYR0-0.070-0.0623.777-0.5841.058-0.010-0.680-0.9510.004
4A7LYS10.9860.9883.3760.8711.7970.056-0.306-0.677-0.002
5A8ALA00.028-0.0014.9570.1870.224-0.001-0.003-0.0330.000
6A9ASP-1-0.861-0.9327.855-0.869-0.8690.0000.0000.0000.000
7A10ILE0-0.011-0.00610.0120.1240.1240.0000.0000.0000.000
8A11GLY00.0470.00711.9810.0760.0760.0000.0000.0000.000
9A12GLY0-0.079-0.03113.8210.0540.0540.0000.0000.0000.000
10A13GLY0-0.005-0.01615.7000.0470.0470.0000.0000.0000.000
11A14SER0-0.054-0.03217.499-0.033-0.0330.0000.0000.0000.000
12A15LEU0-0.030-0.01719.629-0.008-0.0080.0000.0000.0000.000
13A16LYS10.8000.89721.6710.1750.1750.0000.0000.0000.000
14A17LEU00.0850.03924.5120.0020.0020.0000.0000.0000.000
15A18PRO00.0290.00926.7980.0030.0030.0000.0000.0000.000
16A19GLU-1-0.732-0.85325.425-0.151-0.1510.0000.0000.0000.000
17A20SER00.0220.01223.309-0.004-0.0040.0000.0000.0000.000
18A21ARG10.7780.88225.2130.1130.1130.0000.0000.0000.000
19A22ILE0-0.0340.00028.4660.0050.0050.0000.0000.0000.000
20A23ILE0-0.026-0.01522.3010.0040.0040.0000.0000.0000.000
21A24ALA00.0270.00625.7490.0020.0020.0000.0000.0000.000
22A25GLY0-0.010-0.01326.5530.0060.0060.0000.0000.0000.000
23A26LEU00.0270.01526.9860.0030.0030.0000.0000.0000.000
24A27LEU0-0.067-0.03322.0300.0020.0020.0000.0000.0000.000
25A28LEU0-0.079-0.04226.2240.0060.0060.0000.0000.0000.000
26A29GLU-1-1.000-0.97829.451-0.073-0.0730.0000.0000.0000.000
27A30GLY00.0130.02728.2990.0060.0060.0000.0000.0000.000
28A31VAL0-0.030-0.02626.6290.0050.0050.0000.0000.0000.000
29A32THR00.0450.01626.712-0.005-0.0050.0000.0000.0000.000
30A33GLU-1-0.878-0.95122.488-0.072-0.0720.0000.0000.0000.000
31A34ASP-1-0.919-0.96624.257-0.059-0.0590.0000.0000.0000.000
32A35GLN0-0.015-0.01626.6270.0010.0010.0000.0000.0000.000
33A36TRP0-0.016-0.00520.716-0.008-0.0080.0000.0000.0000.000
34A37ARG10.8670.88721.7610.0830.0830.0000.0000.0000.000
35A38HIS00.006-0.00825.2830.0010.0010.0000.0000.0000.000
36A39ALA00.0890.04928.2690.0000.0000.0000.0000.0000.000
37A40ILE0-0.110-0.05422.860-0.003-0.0030.0000.0000.0000.000
38A41GLU-1-0.864-0.90424.251-0.099-0.0990.0000.0000.0000.000
39A42VAL0-0.039-0.00827.9200.0030.0030.0000.0000.0000.000
40A43GLU-1-0.851-0.89931.561-0.066-0.0660.0000.0000.0000.000
41A44ASN0-0.056-0.01430.474-0.006-0.0060.0000.0000.0000.000
42A45VAL00.0860.03228.827-0.001-0.0010.0000.0000.0000.000
43A46LEU0-0.053-0.03024.991-0.004-0.0040.0000.0000.0000.000
44A47GLN0-0.0090.01529.6680.0010.0010.0000.0000.0000.000
45A48ARG10.8160.90124.3870.1420.1420.0000.0000.0000.000
46A49ARG10.9230.94330.8980.0850.0850.0000.0000.0000.000
47A50SER00.0380.01729.6650.0030.0030.0000.0000.0000.000
48A51PRO00.0720.03027.235-0.008-0.0080.0000.0000.0000.000
49A52GLY0-0.0030.00325.367-0.008-0.0080.0000.0000.0000.000
50A53THR0-0.039-0.02520.545-0.011-0.0110.0000.0000.0000.000
51A54ALA0-0.023-0.01120.992-0.015-0.0150.0000.0000.0000.000
52A55LYS10.9810.97620.9110.0860.0860.0000.0000.0000.000
53A56ARG10.9931.00313.7510.2700.2700.0000.0000.0000.000
54A57GLN0-0.010-0.00217.365-0.020-0.0200.0000.0000.0000.000
55A58SER00.0790.03619.222-0.011-0.0110.0000.0000.0000.000
56A59SER0-0.017-0.01216.4270.0060.0060.0000.0000.0000.000
57A60LEU0-0.047-0.00313.349-0.018-0.0180.0000.0000.0000.000
58A61MET0-0.036-0.00816.162-0.012-0.0120.0000.0000.0000.000
59A62ARG10.9090.93919.0180.1630.1630.0000.0000.0000.000
60A63ASN00.006-0.01013.0540.0300.0300.0000.0000.0000.000
61A64ARG10.8290.89614.6360.3760.3760.0000.0000.0000.000
62A65LEU00.0110.02216.609-0.001-0.0010.0000.0000.0000.000
63A66GLU-1-0.841-0.88316.537-0.195-0.1950.0000.0000.0000.000
64A67THR0-0.061-0.03314.2070.0000.0000.0000.0000.0000.000
65A68MET0-0.067-0.01816.9360.0100.0100.0000.0000.0000.000
66A69GLY00.0870.04920.5950.0050.0050.0000.0000.0000.000
67A70PRO00.0490.01023.835-0.006-0.0060.0000.0000.0000.000
68A71GLU-1-0.856-0.93227.179-0.103-0.1030.0000.0000.0000.000
69A72LEU0-0.019-0.01322.7890.0000.0000.0000.0000.0000.000
70A73TRP00.004-0.01621.9380.0050.0050.0000.0000.0000.000
71A74GLN00.0510.02626.5320.0040.0040.0000.0000.0000.000
72A75MET0-0.045-0.00628.3470.0000.0000.0000.0000.0000.000
73A76VAL0-0.072-0.03324.7520.0010.0010.0000.0000.0000.000
74A77ARG10.8270.88228.2000.0920.0920.0000.0000.0000.000
75A78ASP-1-0.790-0.86130.704-0.084-0.0840.0000.0000.0000.000
76A79GLY00.0110.03432.2400.0050.0050.0000.0000.0000.000
77A80SER00.0450.01533.452-0.003-0.0030.0000.0000.0000.000
78A81THR00.0360.00231.778-0.006-0.0060.0000.0000.0000.000
79A82GLN00.0120.00329.714-0.016-0.0160.0000.0000.0000.000
80A83VAL00.0250.01529.486-0.010-0.0100.0000.0000.0000.000
81A84ALA00.0560.03528.545-0.010-0.0100.0000.0000.0000.000
82A85ILE0-0.014-0.01025.283-0.015-0.0150.0000.0000.0000.000
83A86GLN00.0340.02424.612-0.015-0.0150.0000.0000.0000.000
84A87ALA00.0610.04423.998-0.016-0.0160.0000.0000.0000.000
85A88VAL00.005-0.00221.228-0.021-0.0210.0000.0000.0000.000
86A89PHE0-0.035-0.02819.811-0.035-0.0350.0000.0000.0000.000
87A90ALA00.0180.00919.188-0.036-0.0360.0000.0000.0000.000
88A91ALA00.0460.02318.443-0.032-0.0320.0000.0000.0000.000
89A92ALA0-0.054-0.02816.052-0.053-0.0530.0000.0000.0000.000
90A93ILE0-0.049-0.03814.442-0.082-0.0820.0000.0000.0000.000
91A94LYS10.7820.86813.8000.1820.1820.0000.0000.0000.000
92A95HIS00.0000.01511.069-0.069-0.0690.0000.0000.0000.000
93A96SER0-0.032-0.0239.773-0.228-0.2280.0000.0000.0000.000
94A97THR00.0720.0377.8540.0110.0110.0000.0000.0000.000
95A98LEU0-0.0250.0078.0920.1130.1130.0000.0000.0000.000
96A99LEU00.0080.0129.8170.1390.1390.0000.0000.0000.000
97A100GLY00.0700.02412.9620.0740.0740.0000.0000.0000.000
98A101ASP-1-0.713-0.81511.032-0.597-0.5970.0000.0000.0000.000
99A102PHE0-0.0040.01313.8080.0720.0720.0000.0000.0000.000
100A103LEU00.0020.00015.6020.0550.0550.0000.0000.0000.000
101A104ASP-1-0.802-0.89116.539-0.206-0.2060.0000.0000.0000.000
102A105LEU0-0.044-0.02313.8530.0330.0330.0000.0000.0000.000
103A106VAL0-0.0200.00617.2280.0220.0220.0000.0000.0000.000
104A107VAL0-0.019-0.01519.7020.0270.0270.0000.0000.0000.000
105A108ARG10.8090.87820.7360.2090.2090.0000.0000.0000.000
106A109ASP-1-0.925-0.96123.018-0.102-0.1020.0000.0000.0000.000
107A110GLN00.0450.00824.0350.0170.0170.0000.0000.0000.000
108A111PHE0-0.093-0.05425.5720.0130.0130.0000.0000.0000.000
109A112ARG10.9450.97928.4020.0870.0870.0000.0000.0000.000
110A113MET0-0.038-0.00129.5050.0060.0060.0000.0000.0000.000
111A114PHE00.0480.01131.8230.0000.0000.0000.0000.0000.000
112A115ARG10.8730.93034.1330.0700.0700.0000.0000.0000.000
113A116PRO00.0410.04628.760-0.001-0.0010.0000.0000.0000.000
114A117ASP-1-0.853-0.92328.460-0.113-0.1130.0000.0000.0000.000
115A118LEU00.0400.02320.914-0.005-0.0050.0000.0000.0000.000
116A119PRO00.0460.04024.287-0.010-0.0100.0000.0000.0000.000
117A120ARG10.8980.91720.9530.1850.1850.0000.0000.0000.000
118A121LYS10.9380.97720.8660.1070.1070.0000.0000.0000.000
119A122MET0-0.023-0.00720.638-0.004-0.0040.0000.0000.0000.000
120A123TRP00.001-0.00612.547-0.035-0.0350.0000.0000.0000.000
121A124ASP-1-0.857-0.94016.166-0.237-0.2370.0000.0000.0000.000
122A125GLN00.0610.03616.160-0.005-0.0050.0000.0000.0000.000
123A126TYR0-0.042-0.04211.995-0.009-0.0090.0000.0000.0000.000
124A127LEU00.0190.01110.857-0.057-0.0570.0000.0000.0000.000
125A128GLU-1-0.912-0.95211.497-0.179-0.1790.0000.0000.0000.000
126A129GLN0-0.015-0.01812.7600.0360.0360.0000.0000.0000.000
127A130CYS0-0.086-0.0468.503-0.001-0.0010.0000.0000.0000.000
128A131ARG10.8690.9046.9790.4310.4310.0000.0000.0000.000
129A132ASN0-0.058-0.0118.8410.1070.1070.0000.0000.0000.000
130A133ARG10.8960.9519.2220.4820.4820.0000.0000.0000.000
131A134ASP-1-0.831-0.9193.162-4.395-1.3040.257-1.786-1.563-0.014
132A135PRO00.0300.0115.754-0.145-0.1450.0000.0000.0000.000
133A136LEU0-0.0060.0072.372-1.1590.2501.143-0.796-1.756-0.004
134A137MET0-0.054-0.0032.622-3.690-1.4731.362-1.468-2.111-0.014
135A138PRO00.0140.0102.8960.0120.4960.1990.045-0.7280.001
136A139VAL00.0250.0135.2690.0730.088-0.001-0.002-0.0120.000
137A140TRP0-0.0090.0038.988-0.098-0.0980.0000.0000.0000.000
138A141GLN00.0770.04111.7310.0400.0400.0000.0000.0000.000
139A142ASP-1-0.818-0.90115.115-0.189-0.1890.0000.0000.0000.000
140A143SER0-0.052-0.04317.656-0.020-0.0200.0000.0000.0000.000
141A144THR0-0.015-0.02212.0970.0090.0090.0000.0000.0000.000
142A145ALA00.0410.03014.104-0.032-0.0320.0000.0000.0000.000
143A146ASN00.005-0.01315.025-0.003-0.0030.0000.0000.0000.000
144A147LYS10.9540.98017.2050.1960.1960.0000.0000.0000.000
145A148LEU0-0.023-0.00410.900-0.003-0.0030.0000.0000.0000.000
146A149ALA00.0210.02115.131-0.011-0.0110.0000.0000.0000.000
147A150ASP-1-0.806-0.89117.376-0.186-0.1860.0000.0000.0000.000
148A151CYS0-0.180-0.07016.1680.0240.0240.0000.0000.0000.000
149A152VAL00.0640.03014.6030.0050.0050.0000.0000.0000.000
150A153TYR0-0.004-0.03617.6100.0130.0130.0000.0000.0000.000
151A154ARG10.8850.94520.0170.2420.2420.0000.0000.0000.000
152A155ILE00.0050.00517.2410.0140.0140.0000.0000.0000.000
153A156LEU0-0.010-0.00119.8930.0150.0150.0000.0000.0000.000
154A157VAL0-0.024-0.01022.8220.0160.0160.0000.0000.0000.000
155A158GLU-1-0.792-0.88822.878-0.204-0.2040.0000.0000.0000.000
156A159VAL0-0.043-0.01423.2650.0120.0120.0000.0000.0000.000
157A160GLY00.0160.01725.9600.0100.0100.0000.0000.0000.000
158A161TYR0-0.055-0.03423.2920.0120.0120.0000.0000.0000.000
159A162ILE00.0190.01723.5520.0070.0070.0000.0000.0000.000
160A163THR0-0.0050.00127.5190.0010.0010.0000.0000.0000.000
161A164ASP-1-0.728-0.84229.350-0.108-0.1080.0000.0000.0000.000
162A165SER0-0.071-0.03430.026-0.002-0.0020.0000.0000.0000.000
163A166LYS10.7920.85730.1120.1210.1210.0000.0000.0000.000
164A167THR00.0070.00330.921-0.003-0.0030.0000.0000.0000.000
165A168TYR0-0.0080.00424.854-0.006-0.0060.0000.0000.0000.000
166A169ARG10.8820.93927.9110.1000.1000.0000.0000.0000.000
167A170LEU00.0010.01024.609-0.005-0.0050.0000.0000.0000.000
168A171LYS10.8730.92928.8230.1190.1190.0000.0000.0000.000
169A172SER00.0610.02629.044-0.009-0.0090.0000.0000.0000.000
170A173VAL0-0.0100.00026.8680.0080.0080.0000.0000.0000.000
171A174ARG10.9330.98729.1310.0940.0940.0000.0000.0000.000
172A175ILE00.0390.01825.6660.0020.0020.0000.0000.0000.000
173A176SER0-0.034-0.03229.1230.0110.0110.0000.0000.0000.000
174A177GLY00.002-0.01430.329-0.005-0.0050.0000.0000.0000.000
175A178GLU-1-0.846-0.93531.628-0.099-0.0990.0000.0000.0000.000
176A179VAL00.0420.02625.634-0.003-0.0030.0000.0000.0000.000
177A180MET0-0.042-0.03725.352-0.009-0.0090.0000.0000.0000.000
178A181SER0-0.053-0.04527.6040.0000.0000.0000.0000.0000.000
179A182TYR00.0550.03522.721-0.006-0.0060.0000.0000.0000.000
180A183LEU00.002-0.00821.490-0.004-0.0040.0000.0000.0000.000
181A184ARG10.9270.96123.8030.1030.1030.0000.0000.0000.000
182A185GLU-1-0.880-0.90926.036-0.085-0.0850.0000.0000.0000.000
183A186ASN0-0.039-0.01422.6670.0070.0070.0000.0000.0000.000
184A187ASN0-0.032-0.01021.924-0.003-0.0030.0000.0000.0000.000
185A188GLU-1-0.774-0.85818.486-0.249-0.2490.0000.0000.0000.000
186A189GLN0-0.022-0.03718.750-0.015-0.0150.0000.0000.0000.000
187A190TYR0-0.035-0.02912.705-0.016-0.0160.0000.0000.0000.000
188A191VAL00.0750.02017.033-0.011-0.0110.0000.0000.0000.000
189A192ILE0-0.028-0.00618.6410.0110.0110.0000.0000.0000.000
190A193ARG10.8450.91218.2700.2130.2130.0000.0000.0000.000
191A194CYS0-0.0330.00116.7350.0020.0020.0000.0000.0000.000
192A195ILE00.0040.01219.5360.0040.0040.0000.0000.0000.000
193A196GLN0-0.022-0.02121.8730.0200.0200.0000.0000.0000.000
194A197VAL0-0.015-0.00521.3100.0060.0060.0000.0000.0000.000
195A198SER00.0000.00724.7430.0070.0070.0000.0000.0000.000