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: NN12Q

Calculation Name: 1BVO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BVO

Chain ID: A

ChEMBL ID:

UniProt ID: Q17034

Base Structure: X-ray

Registration Date: 2023-09-21

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1830490.783295
FMO2-HF: Nuclear repulsion 1761404.100852
FMO2-HF: Total energy -69086.682443
FMO2-MP2: Total energy -69287.036599


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:48:PRO)


Summations of interaction energy for fragment #1(A:48: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.
-7.302-0.7929.373-6.099-9.785-0.041
Interaction energy analysis for fragmet #1(A:48: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 : -0.024
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].
3A50VAL00.0220.0033.871-0.9340.977-0.020-1.040-0.8510.002
4A51GLU-1-0.793-0.8887.1150.3670.3670.0000.0000.0000.000
5A52ILE0-0.022-0.0129.978-0.006-0.0060.0000.0000.0000.000
6A53THR0-0.036-0.02512.6840.0350.0350.0000.0000.0000.000
7A54GLU-1-0.746-0.81515.086-0.014-0.0140.0000.0000.0000.000
8A55GLN00.0860.02317.640-0.051-0.0510.0000.0000.0000.000
9A56PRO0-0.021-0.01619.2760.0080.0080.0000.0000.0000.000
10A57HIS00.0300.01222.1270.0040.0040.0000.0000.0000.000
11A58PRO00.0500.02225.580-0.005-0.0050.0000.0000.0000.000
12A59LYS10.8960.94527.1080.0430.0430.0000.0000.0000.000
13A60ALA00.0060.01928.7870.0030.0030.0000.0000.0000.000
14A61LEU0-0.001-0.00227.8940.0030.0030.0000.0000.0000.000
15A62ARG10.8340.93530.9590.0480.0480.0000.0000.0000.000
16A63PHE00.028-0.00228.213-0.003-0.0030.0000.0000.0000.000
17A64ARG10.8140.89431.9080.0610.0610.0000.0000.0000.000
18A65TYR00.0550.01533.217-0.005-0.0050.0000.0000.0000.000
19A66GLU-1-0.925-0.95834.551-0.077-0.0770.0000.0000.0000.000
20A67CYS0-0.015-0.01735.7120.0010.0010.0000.0000.0000.000
21A68GLU-1-0.828-0.90537.349-0.052-0.0520.0000.0000.0000.000
22A69GLY00.0200.01937.9200.0020.0020.0000.0000.0000.000
23A70ARG10.8930.95435.2300.0510.0510.0000.0000.0000.000
24A71SER00.0280.00431.715-0.002-0.0020.0000.0000.0000.000
25A72ALA0-0.018-0.00729.363-0.005-0.0050.0000.0000.0000.000
26A73GLY0-0.042-0.02330.3100.0060.0060.0000.0000.0000.000
27A74SER0-0.018-0.02526.413-0.006-0.0060.0000.0000.0000.000
28A75ILE0-0.023-0.00523.0510.0090.0090.0000.0000.0000.000
29A76PRO00.0020.00524.438-0.005-0.0050.0000.0000.0000.000
30A77GLY00.0240.00022.970-0.008-0.0080.0000.0000.0000.000
31A78VAL0-0.028-0.03422.1720.0060.0060.0000.0000.0000.000
32A79ASN0-0.048-0.04022.3190.0140.0140.0000.0000.0000.000
33A80THR0-0.079-0.00725.6790.0030.0030.0000.0000.0000.000
34A81THR00.024-0.00527.8770.0030.0030.0000.0000.0000.000
35A82ALA0-0.040-0.01731.151-0.004-0.0040.0000.0000.0000.000
36A83GLU-1-0.885-0.95134.006-0.017-0.0170.0000.0000.0000.000
37A84GLN0-0.085-0.03127.0870.0010.0010.0000.0000.0000.000
38A85LYS10.9760.99528.7180.0380.0380.0000.0000.0000.000
39A86THR00.011-0.01523.364-0.001-0.0010.0000.0000.0000.000
40A87PHE0-0.007-0.02222.217-0.001-0.0010.0000.0000.0000.000
41A88PRO00.0110.01918.9290.0020.0020.0000.0000.0000.000
42A89SER0-0.010-0.00316.390-0.006-0.0060.0000.0000.0000.000
43A90ILE0-0.042-0.00810.4690.0080.0080.0000.0000.0000.000
44A91GLN00.020-0.0059.4510.0580.0580.0000.0000.0000.000
45A92VAL00.0180.0173.899-0.241-0.0920.002-0.031-0.1210.000
46A93HIS10.7770.8754.561-0.2040.048-0.001-0.073-0.1780.000
47A94GLY00.0660.0252.312-1.271-0.7625.828-3.330-3.007-0.026
48A95TYR0-0.007-0.0242.561-3.835-1.6891.789-0.845-3.090-0.014
49A96ARG10.8950.9263.8630.1780.2940.005-0.027-0.0940.000
50A97GLY00.0390.0347.501-0.007-0.0070.0000.0000.0000.000
51A98ARG10.7690.8609.5890.2740.2740.0000.0000.0000.000
52A99ALA00.0300.0167.560-0.081-0.0810.0000.0000.0000.000
53A100VAL00.0050.0239.5410.0820.0820.0000.0000.0000.000
54A101VAL00.000-0.0089.832-0.114-0.1140.0000.0000.0000.000
55A102VAL00.0070.01611.8800.0700.0700.0000.0000.0000.000
56A103VAL00.002-0.00414.011-0.032-0.0320.0000.0000.0000.000
57A104SER00.0220.00116.6620.0330.0330.0000.0000.0000.000
58A105CYS0-0.0020.01619.363-0.002-0.0020.0000.0000.0000.000
59A106VAL00.0050.00018.863-0.004-0.0040.0000.0000.0000.000
60A107THR00.000-0.00721.8900.0080.0080.0000.0000.0000.000
61A108LYS10.8060.89622.7700.0530.0530.0000.0000.0000.000
62A109GLU-1-0.794-0.91124.144-0.077-0.0770.0000.0000.0000.000
63A110GLY00.0380.02323.661-0.013-0.0130.0000.0000.0000.000
64A111PRO00.0050.01318.864-0.005-0.0050.0000.0000.0000.000
65A112GLU-1-0.860-0.93418.634-0.180-0.1800.0000.0000.0000.000
66A113HIS10.8000.89918.0690.1540.1540.0000.0000.0000.000
67A114LYS10.9140.95120.4800.1040.1040.0000.0000.0000.000
68A115PRO00.0320.01521.1770.0020.0020.0000.0000.0000.000
69A116HIS00.0090.00722.9620.0110.0110.0000.0000.0000.000
70A117PRO00.000-0.00125.583-0.007-0.0070.0000.0000.0000.000
71A118HIS0-0.012-0.01427.137-0.003-0.0030.0000.0000.0000.000
72A119ASN00.0140.01925.954-0.020-0.0200.0000.0000.0000.000
73A120LEU0-0.020-0.00520.3490.0090.0090.0000.0000.0000.000
74A121VAL0-0.024-0.01924.421-0.002-0.0020.0000.0000.0000.000
75A122GLY00.0790.01224.9840.0000.0000.0000.0000.0000.000
76A123LYS10.8400.91525.9950.0850.0850.0000.0000.0000.000
77A124GLU-1-0.823-0.89620.931-0.148-0.1480.0000.0000.0000.000
78A125GLY00.0810.02920.428-0.007-0.0070.0000.0000.0000.000
79A126CYS0-0.131-0.03321.334-0.014-0.0140.0000.0000.0000.000
80A127LYS10.9640.96523.5470.1590.1590.0000.0000.0000.000
81A128LYS10.8960.94124.1640.1170.1170.0000.0000.0000.000
82A129GLY00.0200.02325.372-0.003-0.0030.0000.0000.0000.000
83A130VAL0-0.0270.00319.191-0.006-0.0060.0000.0000.0000.000
84A131CYS0-0.010-0.00319.1760.0110.0110.0000.0000.0000.000
85A132THR0-0.056-0.03915.607-0.035-0.0350.0000.0000.0000.000
86A133VAL00.0180.02215.0240.0270.0270.0000.0000.0000.000
87A134GLU-1-0.791-0.87213.675-0.310-0.3100.0000.0000.0000.000
88A135ILE0-0.039-0.0178.5380.0300.0300.0000.0000.0000.000
89A136ASN00.0530.03012.4400.0080.0080.0000.0000.0000.000
90A137SER00.0480.01311.1790.0000.0000.0000.0000.0000.000
91A138THR00.0130.01511.087-0.001-0.0010.0000.0000.0000.000
92A139THR00.006-0.02811.8790.0230.0230.0000.0000.0000.000
93A140MET0-0.0540.0257.009-0.023-0.0230.0000.0000.0000.000
94A141SER00.0420.0299.464-0.016-0.0160.0000.0000.0000.000
95A142TYR00.003-0.00712.122-0.003-0.0030.0000.0000.0000.000
96A143THR00.0320.01014.776-0.001-0.0010.0000.0000.0000.000
97A144PHE00.0120.00914.5780.0080.0080.0000.0000.0000.000
98A145ASN00.014-0.00419.8700.0020.0020.0000.0000.0000.000
99A146ASN0-0.051-0.02223.1810.0110.0110.0000.0000.0000.000
100A147LEU00.0690.05519.552-0.006-0.0060.0000.0000.0000.000
101A148GLY00.0170.00423.6170.0100.0100.0000.0000.0000.000
102A149ILE00.0020.00325.113-0.009-0.0090.0000.0000.0000.000
103A150GLN00.0130.00827.5370.0060.0060.0000.0000.0000.000
104A151CYS0-0.047-0.01029.866-0.004-0.0040.0000.0000.0000.000
105A152VAL00.0680.03330.7540.0040.0040.0000.0000.0000.000
106A153LYS10.8370.89333.4470.0670.0670.0000.0000.0000.000
107A154LYS10.8680.91335.4890.0580.0580.0000.0000.0000.000
108A155LYS10.9340.96837.1950.0480.0480.0000.0000.0000.000
109A156ASP-1-0.720-0.84134.978-0.068-0.0680.0000.0000.0000.000
110A157VAL0-0.028-0.00231.829-0.005-0.0050.0000.0000.0000.000
111A158GLU-1-0.789-0.89631.910-0.086-0.0860.0000.0000.0000.000
112A159GLU-1-0.840-0.89832.719-0.097-0.0970.0000.0000.0000.000
113A160ALA00.0500.02129.909-0.006-0.0060.0000.0000.0000.000
114A161LEU0-0.020-0.01526.996-0.010-0.0100.0000.0000.0000.000
115A162ARG10.7610.86727.9810.0910.0910.0000.0000.0000.000
116A163LEU0-0.006-0.01028.632-0.009-0.0090.0000.0000.0000.000
117A164ARG10.8380.91322.4700.1450.1450.0000.0000.0000.000
118A165GLN00.0090.00323.881-0.017-0.0170.0000.0000.0000.000
119A166GLU-1-0.854-0.91325.323-0.123-0.1230.0000.0000.0000.000
120A167ILE0-0.061-0.02822.111-0.002-0.0020.0000.0000.0000.000
121A168ARG10.9300.95921.1600.1770.1770.0000.0000.0000.000
122A169VAL0-0.0040.00918.265-0.022-0.0220.0000.0000.0000.000
123A170ASP-1-0.780-0.91019.255-0.190-0.1900.0000.0000.0000.000
124A171PRO0-0.068-0.03815.090-0.020-0.0200.0000.0000.0000.000
125A172PHE00.0520.01215.202-0.052-0.0520.0000.0000.0000.000
126A173ARG10.9020.96714.6820.3530.3530.0000.0000.0000.000
127A174THR00.0520.04519.7850.0300.0300.0000.0000.0000.000
128A175GLY0-0.002-0.00122.5330.0190.0190.0000.0000.0000.000
129A176PHE00.000-0.01923.3150.0070.0070.0000.0000.0000.000
130A177GLY00.0100.00227.8610.0080.0080.0000.0000.0000.000
131A178HIS00.0480.00526.4700.0110.0110.0000.0000.0000.000
132A179ALA0-0.041-0.01230.4910.0040.0040.0000.0000.0000.000
133A180LYS10.8700.93432.0970.0900.0900.0000.0000.0000.000
134A181GLU-1-0.905-0.93934.210-0.053-0.0530.0000.0000.0000.000
135A182PRO00.0250.00834.295-0.001-0.0010.0000.0000.0000.000
136A183GLY0-0.041-0.02135.2550.0000.0000.0000.0000.0000.000
137A184SER00.001-0.00232.901-0.001-0.0010.0000.0000.0000.000
138A185ILE0-0.025-0.00229.302-0.002-0.0020.0000.0000.0000.000
139A186ASP-1-0.762-0.87730.601-0.056-0.0560.0000.0000.0000.000
140A187LEU0-0.027-0.00630.505-0.007-0.0070.0000.0000.0000.000
141A188ASN0-0.049-0.02632.2780.0010.0010.0000.0000.0000.000
142A189ALA00.0070.00128.1050.0040.0040.0000.0000.0000.000
143A190VAL0-0.0190.00224.030-0.004-0.0040.0000.0000.0000.000
144A191ARG10.8320.93019.9430.1060.1060.0000.0000.0000.000
145A192LEU00.0330.01718.169-0.006-0.0060.0000.0000.0000.000
146A193CYS0-0.025-0.00214.709-0.009-0.0090.0000.0000.0000.000
147A194PHE00.003-0.00111.8110.0180.0180.0000.0000.0000.000
148A195GLN00.0380.00510.515-0.035-0.0350.0000.0000.0000.000
149A196VAL00.0210.0135.9110.0980.0980.0000.0000.0000.000
150A197PHE00.0000.0067.473-0.176-0.1760.0000.0000.0000.000
151A198LEU00.016-0.0013.064-0.5370.1110.133-0.151-0.6300.000
152A199GLU-1-0.861-0.9407.519-0.255-0.2550.0000.0000.0000.000
153A200GLY0-0.0040.0178.970-0.038-0.0380.0000.0000.0000.000
154A201GLN00.006-0.00710.1040.0330.0330.0000.0000.0000.000
155A202GLN00.0440.02713.1530.0360.0360.0000.0000.0000.000
156A203ARG10.9380.95915.0650.1550.1550.0000.0000.0000.000
157A204GLY0-0.005-0.00315.6080.0330.0330.0000.0000.0000.000
158A205ARG10.8610.93715.0220.2340.2340.0000.0000.0000.000
159A206PHE00.004-0.00610.884-0.015-0.0150.0000.0000.0000.000
160A207THR0-0.031-0.01711.1410.0040.0040.0000.0000.0000.000
161A208GLU-1-0.836-0.9156.336-0.671-0.6710.0000.0000.0000.000
162A209PRO0-0.069-0.0137.133-0.121-0.1210.0000.0000.0000.000
163A210LEU00.007-0.0012.352-1.359-0.5801.637-0.602-1.814-0.003
164A211THR0-0.020-0.0165.7040.5690.5690.0000.0000.0000.000
165A212PRO0-0.025-0.0128.287-0.071-0.0710.0000.0000.0000.000
166A213VAL0-0.0050.0099.0160.0460.0460.0000.0000.0000.000
167A214VAL0-0.031-0.02411.8450.0180.0180.0000.0000.0000.000
168A215SER0-0.007-0.00615.5580.0210.0210.0000.0000.0000.000
169A216ASP-1-0.850-0.91617.824-0.048-0.0480.0000.0000.0000.000
170A217ILE0-0.070-0.02321.101-0.013-0.0130.0000.0000.0000.000
171A218ILE00.0050.01522.4190.0090.0090.0000.0000.0000.000
172A219TYR00.019-0.01825.811-0.004-0.0040.0000.0000.0000.000
173A220ASP-1-0.736-0.83029.507-0.054-0.0540.0000.0000.0000.000
174A221LYS10.8220.92531.9510.0460.0460.0000.0000.0000.000
175A222LYS10.9160.92534.3090.0350.0350.0000.0000.0000.000