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: 76VRK

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287309.512643
FMO2-HF: Nuclear repulsion 2207426.864527
FMO2-HF: Total energy -79882.648116
FMO2-MP2: Total energy -80112.574648


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.
-9.8250.3175.03-5.631-9.54-0.038
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 : 0.017 / q_NPA : -0.005
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].
3A6TYR0-0.075-0.0713.329-0.6391.2490.031-0.891-1.0270.002
4A7LYS10.9330.9443.1960.3861.6040.143-0.431-0.930-0.003
5A8ALA00.0320.0064.8650.1290.160-0.001-0.004-0.0270.000
6A9ASP-1-0.830-0.9007.479-0.819-0.8190.0000.0000.0000.000
7A10ILE00.0140.00010.0090.1120.1120.0000.0000.0000.000
8A11GLY00.0680.02212.0350.0660.0660.0000.0000.0000.000
9A12GLY0-0.073-0.02814.0130.0480.0480.0000.0000.0000.000
10A13GLY00.017-0.00815.9400.0430.0430.0000.0000.0000.000
11A14SER0-0.057-0.04117.460-0.031-0.0310.0000.0000.0000.000
12A15LEU0-0.011-0.00119.430-0.007-0.0070.0000.0000.0000.000
13A16LYS10.8070.88821.5120.1680.1680.0000.0000.0000.000
14A17LEU00.0580.03624.2730.0080.0080.0000.0000.0000.000
15A18PRO00.021-0.00326.4790.0040.0040.0000.0000.0000.000
16A19GLU-1-0.758-0.84725.478-0.139-0.1390.0000.0000.0000.000
17A20SER00.0380.00323.068-0.001-0.0010.0000.0000.0000.000
18A21ARG10.7740.88924.9590.1040.1040.0000.0000.0000.000
19A22ILE00.0000.01028.2920.0050.0050.0000.0000.0000.000
20A23ILE0-0.040-0.01622.0320.0050.0050.0000.0000.0000.000
21A24ALA00.0190.00625.3800.0020.0020.0000.0000.0000.000
22A25GLY0-0.022-0.01226.2940.0070.0070.0000.0000.0000.000
23A26LEU00.0220.00726.4690.0030.0030.0000.0000.0000.000
24A27LEU0-0.049-0.02921.6800.0040.0040.0000.0000.0000.000
25A28LEU0-0.077-0.03525.9760.0050.0050.0000.0000.0000.000
26A29GLU-1-0.976-0.97529.391-0.059-0.0590.0000.0000.0000.000
27A30GLY0-0.0120.01028.5510.0050.0050.0000.0000.0000.000
28A31VAL0-0.039-0.02026.3640.0050.0050.0000.0000.0000.000
29A32THR00.0600.03126.810-0.004-0.0040.0000.0000.0000.000
30A33GLU-1-0.882-0.95322.364-0.043-0.0430.0000.0000.0000.000
31A34ASP-1-0.907-0.96124.051-0.038-0.0380.0000.0000.0000.000
32A35GLN0-0.015-0.02026.5690.0000.0000.0000.0000.0000.000
33A36TRP00.000-0.00120.727-0.009-0.0090.0000.0000.0000.000
34A37ARG10.8570.88921.9850.0560.0560.0000.0000.0000.000
35A38HIS0-0.009-0.02425.327-0.001-0.0010.0000.0000.0000.000
36A39ALA00.0840.05028.106-0.001-0.0010.0000.0000.0000.000
37A40ILE0-0.094-0.04822.894-0.005-0.0050.0000.0000.0000.000
38A41GLU-1-0.885-0.91423.933-0.080-0.0800.0000.0000.0000.000
39A42VAL0-0.053-0.01627.7810.0020.0020.0000.0000.0000.000
40A43GLU-1-0.828-0.88231.527-0.052-0.0520.0000.0000.0000.000
41A44ASN0-0.078-0.03130.081-0.007-0.0070.0000.0000.0000.000
42A45VAL00.1070.04228.958-0.002-0.0020.0000.0000.0000.000
43A46LEU0-0.050-0.02724.781-0.002-0.0020.0000.0000.0000.000
44A47GLN0-0.0120.00529.259-0.002-0.0020.0000.0000.0000.000
45A48ARG10.8030.90324.2620.1300.1300.0000.0000.0000.000
46A49ARG10.9270.94430.5630.0780.0780.0000.0000.0000.000
47A50SER00.0360.01929.4840.0030.0030.0000.0000.0000.000
48A51PRO00.0640.02727.073-0.007-0.0070.0000.0000.0000.000
49A52GLY0-0.0050.00125.206-0.007-0.0070.0000.0000.0000.000
50A53THR0-0.030-0.01920.778-0.009-0.0090.0000.0000.0000.000
51A54ALA0-0.019-0.00520.925-0.013-0.0130.0000.0000.0000.000
52A55LYS10.9680.96821.1020.0690.0690.0000.0000.0000.000
53A56ARG10.9700.99913.4130.2570.2570.0000.0000.0000.000
54A57GLN00.0040.00017.142-0.009-0.0090.0000.0000.0000.000
55A58SER00.0490.02619.357-0.014-0.0140.0000.0000.0000.000
56A59SER00.0390.00516.5670.0030.0030.0000.0000.0000.000
57A60LEU0-0.077-0.01613.518-0.016-0.0160.0000.0000.0000.000
58A61MET0-0.045-0.02016.096-0.017-0.0170.0000.0000.0000.000
59A62ARG10.8870.91918.7320.1230.1230.0000.0000.0000.000
60A63ASN00.023-0.00113.1700.0270.0270.0000.0000.0000.000
61A64ARG10.8220.92214.4850.3360.3360.0000.0000.0000.000
62A65LEU00.0090.02116.4620.0000.0000.0000.0000.0000.000
63A66GLU-1-0.815-0.86216.896-0.142-0.1420.0000.0000.0000.000
64A67THR0-0.072-0.04614.1260.0030.0030.0000.0000.0000.000
65A68MET0-0.063-0.02016.8040.0090.0090.0000.0000.0000.000
66A69GLY00.0950.04720.4580.0060.0060.0000.0000.0000.000
67A70PRO00.0470.00923.772-0.006-0.0060.0000.0000.0000.000
68A71GLU-1-0.856-0.92427.180-0.080-0.0800.0000.0000.0000.000
69A72LEU00.009-0.00822.727-0.001-0.0010.0000.0000.0000.000
70A73TRP0-0.019-0.02522.0280.0020.0020.0000.0000.0000.000
71A74GLN00.0460.02526.7310.0040.0040.0000.0000.0000.000
72A75MET0-0.054-0.00928.218-0.001-0.0010.0000.0000.0000.000
73A76VAL0-0.060-0.03424.632-0.002-0.0020.0000.0000.0000.000
74A77ARG10.8150.87028.0790.0760.0760.0000.0000.0000.000
75A78ASP-1-0.773-0.84730.600-0.073-0.0730.0000.0000.0000.000
76A79GLY00.0320.03632.2500.0040.0040.0000.0000.0000.000
77A80SER00.0310.01133.262-0.003-0.0030.0000.0000.0000.000
78A81THR00.028-0.00631.324-0.005-0.0050.0000.0000.0000.000
79A82GLN00.0110.00629.373-0.015-0.0150.0000.0000.0000.000
80A83VAL00.0150.01229.172-0.009-0.0090.0000.0000.0000.000
81A84ALA00.0560.03828.033-0.010-0.0100.0000.0000.0000.000
82A85ILE0-0.016-0.01125.039-0.013-0.0130.0000.0000.0000.000
83A86GLN00.0280.02024.202-0.015-0.0150.0000.0000.0000.000
84A87ALA00.0400.02923.541-0.016-0.0160.0000.0000.0000.000
85A88VAL00.0050.00020.788-0.017-0.0170.0000.0000.0000.000
86A89PHE0-0.018-0.01919.483-0.032-0.0320.0000.0000.0000.000
87A90ALA00.0200.00418.783-0.034-0.0340.0000.0000.0000.000
88A91ALA00.0350.02418.079-0.029-0.0290.0000.0000.0000.000
89A92ALA0-0.037-0.02315.661-0.047-0.0470.0000.0000.0000.000
90A93ILE0-0.044-0.03014.087-0.078-0.0780.0000.0000.0000.000
91A94LYS10.7930.87513.4400.1360.1360.0000.0000.0000.000
92A95HIS0-0.0020.00910.662-0.045-0.0450.0000.0000.0000.000
93A96SER0-0.050-0.0269.449-0.229-0.2290.0000.0000.0000.000
94A97THR00.0860.0437.7110.0600.0600.0000.0000.0000.000
95A98LEU0-0.033-0.0017.6840.0910.0910.0000.0000.0000.000
96A99LEU00.0120.0149.4970.1250.1250.0000.0000.0000.000
97A100GLY00.0580.01212.6710.0740.0740.0000.0000.0000.000
98A101ASP-1-0.694-0.78610.740-0.624-0.6240.0000.0000.0000.000
99A102PHE0-0.0220.00313.5090.0650.0650.0000.0000.0000.000
100A103LEU00.0210.00015.2110.0540.0540.0000.0000.0000.000
101A104ASP-1-0.794-0.87816.499-0.199-0.1990.0000.0000.0000.000
102A105LEU0-0.038-0.01813.8050.0330.0330.0000.0000.0000.000
103A106VAL0-0.0290.00016.8810.0150.0150.0000.0000.0000.000
104A107VAL0-0.010-0.00919.4480.0270.0270.0000.0000.0000.000
105A108ARG10.7850.87920.4890.2110.2110.0000.0000.0000.000
106A109ASP-1-0.853-0.91522.987-0.103-0.1030.0000.0000.0000.000
107A110GLN00.030-0.00223.6940.0160.0160.0000.0000.0000.000
108A111PHE0-0.047-0.04625.1860.0140.0140.0000.0000.0000.000
109A112ARG10.8590.93727.8280.1010.1010.0000.0000.0000.000
110A113MET0-0.043-0.00229.0370.0060.0060.0000.0000.0000.000
111A114PHE00.0590.01431.5940.0020.0020.0000.0000.0000.000
112A115ARG10.8780.93933.7250.0700.0700.0000.0000.0000.000
113A116PRO00.0300.04628.537-0.002-0.0020.0000.0000.0000.000
114A117ASP-1-0.852-0.92327.926-0.123-0.1230.0000.0000.0000.000
115A118LEU00.0640.03320.432-0.007-0.0070.0000.0000.0000.000
116A119PRO00.0420.03423.526-0.013-0.0130.0000.0000.0000.000
117A120ARG10.8440.88620.8740.1930.1930.0000.0000.0000.000
118A121LYS10.9690.97820.3880.1250.1250.0000.0000.0000.000
119A122MET0-0.032-0.00720.319-0.003-0.0030.0000.0000.0000.000
120A123TRP00.0280.00512.049-0.038-0.0380.0000.0000.0000.000
121A124ASP-1-0.872-0.94915.633-0.269-0.2690.0000.0000.0000.000
122A125GLN00.0620.03315.664-0.012-0.0120.0000.0000.0000.000
123A126TYR0-0.031-0.02211.581-0.017-0.0170.0000.0000.0000.000
124A127LEU00.0110.00910.518-0.073-0.0730.0000.0000.0000.000
125A128GLU-1-0.918-0.95211.016-0.238-0.2380.0000.0000.0000.000
126A129GLN0-0.003-0.00812.1840.0130.0130.0000.0000.0000.000
127A130CYS0-0.093-0.0488.014-0.015-0.0150.0000.0000.0000.000
128A131ARG10.8690.9076.9650.5480.5480.0000.0000.0000.000
129A132ASN0-0.059-0.0218.7080.0860.0860.0000.0000.0000.000
130A133ARG10.8850.9429.1630.5620.5620.0000.0000.0000.000
131A134ASP-1-0.829-0.9152.859-5.530-2.1380.601-2.027-1.966-0.019
132A135PRO00.0260.0035.315-0.254-0.2540.0000.0000.0000.000
133A136LEU0-0.0120.0082.384-1.0400.2481.434-0.803-1.919-0.003
134A137MET0-0.055-0.0032.538-3.686-1.7042.724-1.729-2.976-0.016
135A138PRO00.0110.0133.0030.2610.5880.0990.257-0.6830.001
136A139VAL00.0280.0134.9490.0790.095-0.001-0.003-0.0120.000
137A140TRP0-0.015-0.0038.776-0.098-0.0980.0000.0000.0000.000
138A141GLN00.0810.04511.6670.0470.0470.0000.0000.0000.000
139A142ASP-1-0.813-0.89514.938-0.216-0.2160.0000.0000.0000.000
140A143SER0-0.033-0.03217.769-0.013-0.0130.0000.0000.0000.000
141A144THR0-0.027-0.02512.3260.0110.0110.0000.0000.0000.000
142A145ALA00.0220.01213.817-0.028-0.0280.0000.0000.0000.000
143A146ASN00.007-0.00714.771-0.002-0.0020.0000.0000.0000.000
144A147LYS10.9590.97917.1380.1940.1940.0000.0000.0000.000
145A148LEU0-0.026-0.00110.4990.0000.0000.0000.0000.0000.000
146A149ALA00.0300.02714.835-0.010-0.0100.0000.0000.0000.000
147A150ASP-1-0.816-0.89616.958-0.192-0.1920.0000.0000.0000.000
148A151CYS0-0.173-0.06915.9200.0280.0280.0000.0000.0000.000
149A152VAL00.0450.02614.1800.0110.0110.0000.0000.0000.000
150A153TYR00.001-0.03117.2930.0130.0130.0000.0000.0000.000
151A154ARG10.8750.93819.9020.2370.2370.0000.0000.0000.000
152A155ILE00.0100.00516.9650.0160.0160.0000.0000.0000.000
153A156LEU0-0.006-0.00819.5130.0150.0150.0000.0000.0000.000
154A157VAL0-0.028-0.00422.4280.0160.0160.0000.0000.0000.000
155A158GLU-1-0.766-0.86522.817-0.193-0.1930.0000.0000.0000.000
156A159VAL0-0.020-0.00422.8510.0110.0110.0000.0000.0000.000
157A160GLY0-0.004-0.00325.6530.0080.0080.0000.0000.0000.000
158A161TYR0-0.024-0.02523.1670.0110.0110.0000.0000.0000.000
159A162ILE00.0060.00923.2060.0040.0040.0000.0000.0000.000
160A163THR0-0.011-0.00327.1390.0020.0020.0000.0000.0000.000
161A164ASP-1-0.733-0.84528.753-0.112-0.1120.0000.0000.0000.000
162A165SER0-0.069-0.03229.441-0.003-0.0030.0000.0000.0000.000
163A166LYS10.7890.85929.5380.1260.1260.0000.0000.0000.000
164A167THR00.0120.00030.251-0.004-0.0040.0000.0000.0000.000
165A168TYR0-0.0200.00324.061-0.006-0.0060.0000.0000.0000.000
166A169ARG10.8670.92327.4140.1020.1020.0000.0000.0000.000
167A170LEU00.0120.02024.183-0.004-0.0040.0000.0000.0000.000
168A171LYS10.8640.91628.3210.1200.1200.0000.0000.0000.000
169A172SER00.0670.03628.599-0.008-0.0080.0000.0000.0000.000
170A173VAL0-0.037-0.00526.6350.0100.0100.0000.0000.0000.000
171A174ARG10.8920.95028.5010.0860.0860.0000.0000.0000.000
172A175ILE00.0430.02825.1680.0020.0020.0000.0000.0000.000
173A176SER00.017-0.00328.5940.0120.0120.0000.0000.0000.000
174A177GLY0-0.025-0.02730.158-0.003-0.0030.0000.0000.0000.000
175A178GLU-1-0.819-0.92231.118-0.089-0.0890.0000.0000.0000.000
176A179VAL00.0260.01825.060-0.001-0.0010.0000.0000.0000.000
177A180MET0-0.013-0.01525.074-0.008-0.0080.0000.0000.0000.000
178A181SER0-0.070-0.03327.8380.0040.0040.0000.0000.0000.000
179A182TYR00.0760.02922.583-0.006-0.0060.0000.0000.0000.000
180A183LEU00.010-0.01221.187-0.002-0.0020.0000.0000.0000.000
181A184ARG10.8800.93823.5830.0910.0910.0000.0000.0000.000
182A185GLU-1-0.869-0.90725.936-0.071-0.0710.0000.0000.0000.000
183A186ASN0-0.027-0.00422.2110.0070.0070.0000.0000.0000.000
184A187ASN0-0.032-0.00721.7540.0010.0010.0000.0000.0000.000
185A188GLU-1-0.757-0.85118.349-0.203-0.2030.0000.0000.0000.000
186A189GLN0-0.027-0.03618.902-0.028-0.0280.0000.0000.0000.000
187A190TYR0-0.018-0.03312.450-0.018-0.0180.0000.0000.0000.000
188A191VAL00.0540.02616.609-0.018-0.0180.0000.0000.0000.000
189A192ILE0-0.029-0.01518.4470.0070.0070.0000.0000.0000.000
190A193ARG10.8450.90718.4560.2030.2030.0000.0000.0000.000
191A194CYS0-0.048-0.01216.3350.0000.0000.0000.0000.0000.000
192A195ILE00.0020.01218.9720.0010.0010.0000.0000.0000.000
193A196GLN0-0.018-0.01421.4540.0210.0210.0000.0000.0000.000
194A197VAL0-0.005-0.00120.7550.0060.0060.0000.0000.0000.000
195A198SER00.0030.01024.1640.0050.0050.0000.0000.0000.000