FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: P767K

Calculation Name: 3BPV-A-Xray22

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BPV

Chain ID: A

ChEMBL ID:

UniProt ID: O26413

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1535551.033254
FMO2-HF: Nuclear repulsion 1471164.656984
FMO2-HF: Total energy -64386.376269
FMO2-MP2: Total energy -64573.072473


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:5:ILE)


Summations of interaction energy for fragment #1(A:5:ILE)
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.
-9.879-13.5720.539-7.83-9.017-0.012
Interaction energy analysis for fragmet #1(A:5:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.004
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].
3A7LEU00.1210.0612.325-2.809-1.7892.483-1.400-2.103-0.013
4A8LYS10.9750.9784.771-0.217-0.056-0.001-0.013-0.1460.000
5A9GLY0-0.009-0.0102.479-0.0980.1631.351-0.749-0.8640.002
6A10LEU00.0840.0352.538-0.6200.4311.1560.201-2.408-0.002
7A11LEU00.0570.0253.9840.2810.4260.008-0.010-0.1420.000
8A12SER0-0.016-0.0106.2110.2150.2150.0000.0000.0000.000
9A13ILE00.0030.0082.832-0.3940.1330.141-0.109-0.5590.000
10A14ILE00.0570.0386.9670.0550.0550.0000.0000.0000.000
11A15LEU00.0530.0309.6030.0810.0810.0000.0000.0000.000
12A16ARG10.7210.8635.998-0.248-0.2480.0000.0000.0000.000
13A17SER0-0.010-0.00111.6440.0240.0240.0000.0000.0000.000
14A18HIS10.8390.90413.5110.1820.1820.0000.0000.0000.000
15A19ARG10.9460.96912.633-0.013-0.0130.0000.0000.0000.000
16A20VAL0-0.014-0.00215.2040.0180.0180.0000.0000.0000.000
17A21PHE00.0480.01217.5270.0070.0070.0000.0000.0000.000
18A22ILE00.0280.02319.3910.0100.0100.0000.0000.0000.000
19A23GLY0-0.029-0.00920.6250.0090.0090.0000.0000.0000.000
20A24ARG10.9410.97021.0370.0590.0590.0000.0000.0000.000
21A25GLU-1-0.807-0.89223.404-0.104-0.1040.0000.0000.0000.000
22A26LEU0-0.022-0.01624.6620.0030.0030.0000.0000.0000.000
23A27GLY00.0240.02426.4920.0080.0080.0000.0000.0000.000
24A28HIS0-0.0160.01127.3860.0090.0090.0000.0000.0000.000
25A29LEU0-0.019-0.01029.7870.0030.0030.0000.0000.0000.000
26A30ASN0-0.019-0.01228.8880.0030.0030.0000.0000.0000.000
27A31LEU00.0240.03626.0620.0050.0050.0000.0000.0000.000
28A32THR0-0.012-0.02721.868-0.001-0.0010.0000.0000.0000.000
29A33ASP-1-0.816-0.89617.346-0.098-0.0980.0000.0000.0000.000
30A34ALA00.0470.00920.450-0.005-0.0050.0000.0000.0000.000
31A35GLN0-0.021-0.01921.565-0.001-0.0010.0000.0000.0000.000
32A36VAL00.0550.03822.826-0.001-0.0010.0000.0000.0000.000
33A37ALA0-0.0010.00520.994-0.005-0.0050.0000.0000.0000.000
34A38CYS0-0.038-0.02423.1110.0020.0020.0000.0000.0000.000
35A39LEU00.0410.03026.0810.0000.0000.0000.0000.0000.000
36A40LEU00.0130.00724.024-0.001-0.0010.0000.0000.0000.000
37A41ARG10.7460.86625.0320.0520.0520.0000.0000.0000.000
38A42ILE00.0200.00727.4000.0010.0010.0000.0000.0000.000
39A43HIS00.0310.03430.3080.0050.0050.0000.0000.0000.000
40A44ARG10.8910.95127.1660.0790.0790.0000.0000.0000.000
41A45GLU-1-0.844-0.88530.674-0.046-0.0460.0000.0000.0000.000
42A46PRO00.0640.04632.9250.0050.0050.0000.0000.0000.000
43A47GLY00.1070.06235.8870.0000.0000.0000.0000.0000.000
44A48ILE0-0.0400.00929.7620.0040.0040.0000.0000.0000.000
45A49LYS10.8590.91034.0680.0150.0150.0000.0000.0000.000
46A50GLN00.002-0.00831.125-0.003-0.0030.0000.0000.0000.000
47A51ASP-1-0.858-0.90830.3000.0080.0080.0000.0000.0000.000
48A52GLU-1-0.754-0.87529.803-0.012-0.0120.0000.0000.0000.000
49A53LEU00.0310.01826.750-0.004-0.0040.0000.0000.0000.000
50A54ALA0-0.029-0.05025.925-0.001-0.0010.0000.0000.0000.000
51A55THR0-0.0170.00024.8800.0070.0070.0000.0000.0000.000
52A56PHE00.0100.01522.827-0.004-0.0040.0000.0000.0000.000
53A57PHE0-0.036-0.03720.595-0.011-0.0110.0000.0000.0000.000
54A58HIS0-0.0020.03219.8660.0170.0170.0000.0000.0000.000
55A59VAL0-0.0070.02118.8550.0200.0200.0000.0000.0000.000
56A60ASP-1-0.743-0.75521.2360.0910.0910.0000.0000.0000.000
57A61LYS10.9940.95123.479-0.052-0.0520.0000.0000.0000.000
58A62GLY00.0000.01226.498-0.008-0.0080.0000.0000.0000.000
59A63THR00.049-0.04321.175-0.004-0.0040.0000.0000.0000.000
60A64ILE0-0.0030.03624.448-0.008-0.0080.0000.0000.0000.000
61A65ALA0-0.0090.00126.053-0.007-0.0070.0000.0000.0000.000
62A66ARG10.9270.96126.667-0.056-0.0560.0000.0000.0000.000
63A67THR0-0.0020.01324.662-0.003-0.0030.0000.0000.0000.000
64A68LEU00.0690.03927.011-0.005-0.0050.0000.0000.0000.000
65A69ARG10.9631.00830.104-0.030-0.0300.0000.0000.0000.000
66A70ARG10.8830.94724.955-0.012-0.0120.0000.0000.0000.000
67A71LEU00.0030.00627.979-0.003-0.0030.0000.0000.0000.000
68A72GLU-1-0.914-0.96231.4650.0000.0000.0000.0000.0000.000
69A73GLU-1-0.936-0.96134.1930.0030.0030.0000.0000.0000.000
70A74SER0-0.062-0.00432.796-0.002-0.0020.0000.0000.0000.000
71A75GLY00.0480.06534.958-0.004-0.0040.0000.0000.0000.000
72A76PHE0-0.014-0.01831.473-0.004-0.0040.0000.0000.0000.000
73A77ILE0-0.015-0.01531.672-0.004-0.0040.0000.0000.0000.000
74A78GLU-1-0.910-0.94635.185-0.015-0.0150.0000.0000.0000.000
75A79ARG10.8360.88435.738-0.012-0.0120.0000.0000.0000.000
76A80GLU-1-0.880-0.92538.156-0.007-0.0070.0000.0000.0000.000
77A81GLN0-0.050-0.03740.1770.0030.0030.0000.0000.0000.000
78A82ASP-1-0.742-0.86140.032-0.003-0.0030.0000.0000.0000.000
79A83PRO00.0030.00742.0410.0030.0030.0000.0000.0000.000
80A84GLU-1-0.896-0.92743.411-0.005-0.0050.0000.0000.0000.000
81A85ASN0-0.041-0.02740.7560.0040.0040.0000.0000.0000.000
82A86ARG10.9570.96341.987-0.023-0.0230.0000.0000.0000.000
83A87ARG10.7950.89338.902-0.021-0.0210.0000.0000.0000.000
84A88ARG10.7530.87834.7880.0010.0010.0000.0000.0000.000
85A89TYR00.012-0.00136.1090.0010.0010.0000.0000.0000.000
86A90ILE00.0120.02336.1240.0000.0000.0000.0000.0000.000
87A91LEU0-0.039-0.01631.6230.0020.0020.0000.0000.0000.000
88A92GLU-1-0.841-0.92335.530-0.030-0.0300.0000.0000.0000.000
89A93VAL0-0.072-0.02032.7450.0020.0020.0000.0000.0000.000
90A94THR00.0450.02035.517-0.001-0.0010.0000.0000.0000.000
91A95ARG10.9670.96737.4550.0320.0320.0000.0000.0000.000
92A96ARG10.9390.97935.0880.0310.0310.0000.0000.0000.000
93A97GLY00.031-0.00134.052-0.003-0.0030.0000.0000.0000.000
94A98GLU-1-0.817-0.87833.482-0.050-0.0500.0000.0000.0000.000
95A99GLU-1-0.906-0.95835.044-0.046-0.0460.0000.0000.0000.000
96A100ILE0-0.0410.00330.596-0.004-0.0040.0000.0000.0000.000
97A101ILE00.0170.01729.672-0.006-0.0060.0000.0000.0000.000
98A102PRO00.000-0.00229.776-0.009-0.0090.0000.0000.0000.000
99A103LEU0-0.0010.00530.273-0.008-0.0080.0000.0000.0000.000
100A104ILE00.0210.01425.216-0.008-0.0080.0000.0000.0000.000
101A105LEU00.0220.01025.511-0.013-0.0130.0000.0000.0000.000
102A106LYS10.9871.01526.1010.1000.1000.0000.0000.0000.000
103A107VAL0-0.036-0.02522.736-0.011-0.0110.0000.0000.0000.000
104A108GLU-1-0.778-0.85320.329-0.178-0.1780.0000.0000.0000.000
105A109GLU-1-0.889-0.91321.493-0.173-0.1730.0000.0000.0000.000
106A110ARG10.8450.89623.0130.1160.1160.0000.0000.0000.000
107A111TRP00.0190.00713.585-0.019-0.0190.0000.0000.0000.000
108A112GLU-1-0.859-0.93918.356-0.284-0.2840.0000.0000.0000.000
109A113ASP-1-0.794-0.87319.231-0.238-0.2380.0000.0000.0000.000
110A114LEU0-0.071-0.03218.877-0.013-0.0130.0000.0000.0000.000
111A115LEU0-0.039-0.01712.517-0.031-0.0310.0000.0000.0000.000
112A116PHE0-0.052-0.03215.542-0.059-0.0590.0000.0000.0000.000
113A117ARG10.9270.96717.6840.2820.2820.0000.0000.0000.000
114A118ASP-1-0.924-0.94416.252-0.368-0.3680.0000.0000.0000.000
115A119PHE0-0.071-0.03613.451-0.047-0.0470.0000.0000.0000.000
116A120THR00.0210.02918.8030.0440.0440.0000.0000.0000.000
117A121GLU-1-0.774-0.91321.490-0.274-0.2740.0000.0000.0000.000
118A122ASP-1-0.806-0.87423.481-0.256-0.2560.0000.0000.0000.000
119A123GLU-1-0.820-0.87618.193-0.490-0.4900.0000.0000.0000.000
120A124ARG10.9310.98618.9590.2270.2270.0000.0000.0000.000
121A125LYS10.9480.97719.8530.2170.2170.0000.0000.0000.000
122A126LEU00.0740.02218.7010.0120.0120.0000.0000.0000.000
123A127PHE00.0350.01611.626-0.013-0.0130.0000.0000.0000.000
124A128ARG10.9240.95216.7820.2580.2580.0000.0000.0000.000
125A129LYS10.8710.92318.9970.2640.2640.0000.0000.0000.000
126A130MET00.0000.00115.1180.0200.0200.0000.0000.0000.000
127A131CYS00.0150.00814.971-0.004-0.0040.0000.0000.0000.000
128A132ARG10.9220.98116.2830.2390.2390.0000.0000.0000.000
129A133ARG10.8930.94518.9620.3410.3410.0000.0000.0000.000
130A134LEU00.0460.02012.7010.0180.0180.0000.0000.0000.000
131A135ALA00.0010.00616.6060.0270.0270.0000.0000.0000.000
132A136GLU-1-0.878-0.94918.037-0.171-0.1710.0000.0000.0000.000
133A137GLU-1-0.866-0.94717.800-0.157-0.1570.0000.0000.0000.000
134A138ALA00.0100.00016.2250.0250.0250.0000.0000.0000.000
135A139VAL0-0.028-0.01018.0240.0290.0290.0000.0000.0000.000
136A140ARG10.8350.91721.5300.1810.1810.0000.0000.0000.000
137A141MET0-0.045-0.00515.5720.0000.0000.0000.0000.0000.000
138A0NME0-0.0160.02620.7260.0220.0220.0000.0000.0000.000
139A143HOH00.0000.00019.7150.0010.0010.0000.0000.0000.000
140A144HOH00.021-0.00734.884-0.001-0.0010.0000.0000.0000.000
141A145HOH0-0.014-0.00814.9360.0160.0160.0000.0000.0000.000
142A146HOH0-0.070-0.05824.3310.0010.0010.0000.0000.0000.000
143A147HOH0-0.006-0.01821.8320.0040.0040.0000.0000.0000.000
144A149HOH0-0.061-0.04519.311-0.010-0.0100.0000.0000.0000.000
145A150HOH0-0.040-0.02226.6600.0070.0070.0000.0000.0000.000
146A151HOH0-0.004-0.00919.475-0.007-0.0070.0000.0000.0000.000
147A152HOH0-0.003-0.00438.3140.0010.0010.0000.0000.0000.000
148A153HOH0-0.028-0.02521.9890.0070.0070.0000.0000.0000.000
149A154HOH00.001-0.01825.848-0.006-0.0060.0000.0000.0000.000
150A156HOH0-0.037-0.03636.350-0.002-0.0020.0000.0000.0000.000
151A157HOH00.0400.01631.1560.0000.0000.0000.0000.0000.000
152A158HOH00.0170.0205.848-0.124-0.1240.0000.0000.0000.000
153A160HOH0-0.068-0.06041.766-0.001-0.0010.0000.0000.0000.000
154A161HOH0-0.031-0.01920.2420.0020.0020.0000.0000.0000.000
155A163HOH0-0.002-0.0069.6050.0360.0360.0000.0000.0000.000
156A164HOH0-0.036-0.03023.3200.0030.0030.0000.0000.0000.000
157A166HOH0-0.052-0.04629.805-0.002-0.0020.0000.0000.0000.000
158A167HOH0-0.018-0.01422.745-0.005-0.0050.0000.0000.0000.000
159A168HOH00.0420.02234.6430.0020.0020.0000.0000.0000.000
160A169HOH00.0210.02520.731-0.008-0.0080.0000.0000.0000.000
161A170HOH0-0.006-0.02219.370-0.010-0.0100.0000.0000.0000.000
162A171HOH0-0.029-0.02640.6410.0010.0010.0000.0000.0000.000
163A172HOH0-0.010-0.00931.398-0.001-0.0010.0000.0000.0000.000
164A173HOH0-0.047-0.03118.179-0.007-0.0070.0000.0000.0000.000
165A174HOH0-0.035-0.02028.873-0.002-0.0020.0000.0000.0000.000
166A175HOH00.0040.01036.2550.0010.0010.0000.0000.0000.000
167A176HOH0-0.024-0.01623.4830.0040.0040.0000.0000.0000.000
168A179HOH0-0.020-0.02827.767-0.001-0.0010.0000.0000.0000.000
169A180HOH0-0.034-0.03824.322-0.003-0.0030.0000.0000.0000.000
170A181HOH0-0.037-0.03232.0000.0020.0020.0000.0000.0000.000
171A182HOH0-0.091-0.06726.5500.0000.0000.0000.0000.0000.000
172A184HOH0-0.025-0.01516.123-0.005-0.0050.0000.0000.0000.000
173A185HOH00.0190.01022.950-0.003-0.0030.0000.0000.0000.000
174A186HOH0-0.017-0.01228.922-0.001-0.0010.0000.0000.0000.000
175A188HOH0-0.0080.00323.284-0.006-0.0060.0000.0000.0000.000
176A191HOH00.002-0.02031.3310.0000.0000.0000.0000.0000.000
177A192HOH0-0.039-0.02719.2830.0080.0080.0000.0000.0000.000
178A193HOH0-0.023-0.01448.4440.0000.0000.0000.0000.0000.000
179A194HOH0-0.003-0.01521.3560.0080.0080.0000.0000.0000.000
180A195HOH00.0220.02724.2870.0050.0050.0000.0000.0000.000
181A197HOH0-0.023-0.02234.746-0.002-0.0020.0000.0000.0000.000
182A198HOH0-0.035-0.02139.142-0.001-0.0010.0000.0000.0000.000
183A199HOH00.0390.0368.3160.0470.0470.0000.0000.0000.000
184A200HOH0-0.021-0.03535.941-0.001-0.0010.0000.0000.0000.000
185A201HOH0-0.044-0.0229.8710.0220.0220.0000.0000.0000.000
186A202HOH00.0400.02245.5690.0010.0010.0000.0000.0000.000
187A203HOH00.0040.00033.0100.0020.0020.0000.0000.0000.000
188A204HOH0-0.038-0.02518.6710.0100.0100.0000.0000.0000.000
189A205HOH0-0.053-0.03825.0940.0040.0040.0000.0000.0000.000
190A207HOH0-0.039-0.02422.7050.0070.0070.0000.0000.0000.000
191A209HOH00.0090.01536.4240.0010.0010.0000.0000.0000.000
192A212HOH0-0.050-0.04219.4410.0070.0070.0000.0000.0000.000
193A215HOH0-0.036-0.02332.875-0.001-0.0010.0000.0000.0000.000
194A216HOH0-0.0080.01319.3120.0070.0070.0000.0000.0000.000
195A218HOH0-0.072-0.05527.9470.0040.0040.0000.0000.0000.000
196A219HOH00.0240.02033.2260.0010.0010.0000.0000.0000.000
197A220HOH0-0.026-0.01838.8730.0000.0000.0000.0000.0000.000
198A221HOH0-0.027-0.01728.408-0.001-0.0010.0000.0000.0000.000
199A222HOH0-0.001-0.00710.2100.0340.0340.0000.0000.0000.000
200A224HOH0-0.031-0.02027.6600.0030.0030.0000.0000.0000.000
201A225HOH0-0.027-0.02225.6650.0010.0010.0000.0000.0000.000
202A226HOH0-0.012-0.02634.162-0.002-0.0020.0000.0000.0000.000
203A228HOH0-0.002-0.0091.635-5.592-12.53715.402-5.737-2.7200.001
204A229HOH00.0050.00141.204-0.001-0.0010.0000.0000.0000.000
205A235HOH0-0.037-0.02518.1580.0090.0090.0000.0000.0000.000
206A236HOH0-0.028-0.01434.434-0.001-0.0010.0000.0000.0000.000
207A237HOH0-0.017-0.02324.5620.0000.0000.0000.0000.0000.000
208A238HOH0-0.056-0.04240.3180.0010.0010.0000.0000.0000.000
209A239HOH0-0.005-0.00745.1260.0000.0000.0000.0000.0000.000
210A240HOH0-0.038-0.03224.9340.0020.0020.0000.0000.0000.000
211A242HOH00.0070.00433.1140.0020.0020.0000.0000.0000.000
212A245HOH0-0.032-0.03123.1180.0030.0030.0000.0000.0000.000
213A247HOH0-0.037-0.03119.2220.0050.0050.0000.0000.0000.000
214A248HOH0-0.050-0.03920.8160.0000.0000.0000.0000.0000.000
215A249HOH0-0.0140.00128.1810.0030.0030.0000.0000.0000.000
216A250HOH00.0140.03620.9210.0040.0040.0000.0000.0000.000
217A251HOH0-0.009-0.00933.6300.0000.0000.0000.0000.0000.000
218A253HOH00.0490.02841.814-0.001-0.0010.0000.0000.0000.000
219A254HOH0-0.011-0.00814.540-0.001-0.0010.0000.0000.0000.000
220A255HOH0-0.029-0.01825.4880.0010.0010.0000.0000.0000.000
221A256HOH0-0.010-0.02318.668-0.005-0.0050.0000.0000.0000.000
222A257HOH0-0.039-0.04022.8770.0040.0040.0000.0000.0000.000
223A258HOH00.0780.0523.937-0.083-0.0240.000-0.011-0.0480.000
224A259HOH00.0460.02839.3220.0000.0000.0000.0000.0000.000
225A260HOH0-0.003-0.0284.574-0.097-0.067-0.001-0.002-0.0270.000
226A262HOH0-0.026-0.02025.683-0.008-0.0080.0000.0000.0000.000
227A266HOH0-0.0040.00523.953-0.001-0.0010.0000.0000.0000.000
228A271HOH00.0380.02523.129-0.005-0.0050.0000.0000.0000.000
229A272HOH0-0.047-0.06734.8850.0010.0010.0000.0000.0000.000
230A273HOH00.0130.01333.5340.0020.0020.0000.0000.0000.000
231A281HOH0-0.020-0.01539.5890.0000.0000.0000.0000.0000.000
232A284HOH00.0180.03135.248-0.002-0.0020.0000.0000.0000.000
233A285HOH0-0.013-0.00720.3030.0010.0010.0000.0000.0000.000
234A288HOH0-0.055-0.03030.806-0.002-0.0020.0000.0000.0000.000
235A292HOH00.0450.03843.6610.0010.0010.0000.0000.0000.000