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: 14GMZ

Calculation Name: 5BNF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BNF

Chain ID: A

ChEMBL ID:

UniProt ID: F1S5D9

Base Structure: X-ray

Registration Date: 2023-06-20

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2685276.515179
FMO2-HF: Nuclear repulsion 2595270.898199
FMO2-HF: Total energy -90005.616981
FMO2-MP2: Total energy -90263.380818


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:54:TRP)


Summations of interaction energy for fragment #1(A:54:TRP)
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.
-30.414-15.05519.933-9.961-25.33-0.011
Interaction energy analysis for fragmet #1(A:54:TRP)
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 : -0.021
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].
3A56GLY00.0210.0162.608-2.2110.6290.158-1.360-1.6380.000
4A57LYS10.9550.9774.102-1.278-1.1260.000-0.050-0.1020.000
5A58GLY00.0460.0325.923-0.313-0.3130.0000.0000.0000.000
6A59SER0-0.038-0.0596.7510.8850.8850.0000.0000.0000.000
7A60THR0-0.033-0.0139.4200.0610.0610.0000.0000.0000.000
8A61VAL00.0410.00312.945-0.026-0.0260.0000.0000.0000.000
9A62ASP-1-0.836-0.91714.892-0.624-0.6240.0000.0000.0000.000
10A63PHE0-0.0150.00313.9360.0770.0770.0000.0000.0000.000
11A64GLN00.046-0.00215.7130.0830.0830.0000.0000.0000.000
12A65GLU-1-0.908-0.95218.579-0.442-0.4420.0000.0000.0000.000
13A66ILE0-0.042-0.01717.7240.0790.0790.0000.0000.0000.000
14A67ILE00.0130.00518.1610.0680.0680.0000.0000.0000.000
15A68LEU0-0.033-0.00921.0940.0460.0460.0000.0000.0000.000
16A69ARG10.9590.97923.9400.3870.3870.0000.0000.0000.000
17A70ARG10.8260.92419.6490.3820.3820.0000.0000.0000.000
18A71CYS00.0790.02824.8880.0290.0290.0000.0000.0000.000
19A72TYR00.0450.00226.4810.0210.0210.0000.0000.0000.000
20A73THR0-0.058-0.04328.5320.0170.0170.0000.0000.0000.000
21A74TYR00.014-0.01628.2540.0180.0180.0000.0000.0000.000
22A75ILE0-0.013-0.00630.1990.0120.0120.0000.0000.0000.000
23A76ARG10.9230.97232.7070.2000.2000.0000.0000.0000.000
24A77VAL0-0.036-0.01733.7820.0070.0070.0000.0000.0000.000
25A78VAL0-0.0390.00030.0580.0090.0090.0000.0000.0000.000
26A79GLN0-0.045-0.03332.8480.0140.0140.0000.0000.0000.000
27A80PRO00.0040.02534.946-0.004-0.0040.0000.0000.0000.000
28A81GLU-1-0.874-0.94037.016-0.096-0.0960.0000.0000.0000.000
29A82LEU0-0.052-0.03031.4380.0030.0030.0000.0000.0000.000
30A83GLY00.0120.00634.005-0.011-0.0110.0000.0000.0000.000
31A84ASP-1-0.867-0.91435.576-0.126-0.1260.0000.0000.0000.000
32A85ARG10.7870.89330.1490.1250.1250.0000.0000.0000.000
33A86ASP-1-0.805-0.90830.240-0.229-0.2290.0000.0000.0000.000
34A88GLN00.0630.05024.482-0.040-0.0400.0000.0000.0000.000
35A89LYS10.8540.90825.2040.1710.1710.0000.0000.0000.000
36A90ILE00.0220.01822.958-0.015-0.0150.0000.0000.0000.000
37A91LYS10.9350.96420.7210.4170.4170.0000.0000.0000.000
38A92LYS10.7820.88520.2090.3910.3910.0000.0000.0000.000
39A93ALA00.0400.02320.053-0.032-0.0320.0000.0000.0000.000
40A94PHE0-0.014-0.01115.550-0.018-0.0180.0000.0000.0000.000
41A95THR00.001-0.02515.682-0.047-0.0470.0000.0000.0000.000
42A96ASP-1-0.827-0.89715.223-0.550-0.5500.0000.0000.0000.000
43A97ALA0-0.0180.01015.875-0.009-0.0090.0000.0000.0000.000
44A98PHE0-0.021-0.01010.3420.0280.0280.0000.0000.0000.000
45A99ILE00.0170.01610.642-0.242-0.2420.0000.0000.0000.000
46A100SER0-0.057-0.03110.8050.1710.1710.0000.0000.0000.000
47A101LYS10.8160.9089.8840.6060.6060.0000.0000.0000.000
48A102ASP-1-0.830-0.9185.124-1.964-1.847-0.001-0.002-0.1140.000
49A103PRO0-0.017-0.0112.692-0.6950.6700.349-0.431-1.2840.001
50A104CYS0-0.016-0.0203.4730.5182.4871.752-0.808-2.9130.007
51A105SER0-0.032-0.0115.621-0.049-0.0490.0000.0000.0000.000
52A106ALA0-0.0200.0108.826-0.108-0.1080.0000.0000.0000.000
53A107ARG10.8390.88611.1030.1230.1230.0000.0000.0000.000
54A108GLU-1-0.826-0.91414.6650.0470.0470.0000.0000.0000.000
55A109GLU-1-0.701-0.85317.8560.0110.0110.0000.0000.0000.000
56A110ASP-1-0.867-0.90014.062-0.236-0.2360.0000.0000.0000.000
57A111TYR0-0.045-0.06113.755-0.105-0.1050.0000.0000.0000.000
58A112ASP-1-0.880-0.93319.391-0.070-0.0700.0000.0000.0000.000
59A113LEU0-0.040-0.02822.3670.0020.0020.0000.0000.0000.000
60A114LEU00.020-0.00219.0140.0050.0050.0000.0000.0000.000
61A115MET00.002-0.00320.7920.0080.0080.0000.0000.0000.000
62A116LYS10.9070.96424.4490.1230.1230.0000.0000.0000.000
63A117LEU0-0.042-0.03425.4070.0070.0070.0000.0000.0000.000
64A118GLY00.0330.00826.108-0.006-0.0060.0000.0000.0000.000
65A119HIS0-0.0270.01327.1420.0090.0090.0000.0000.0000.000
66A120GLN00.025-0.00629.307-0.012-0.0120.0000.0000.0000.000
67A121THR0-0.028-0.00531.1750.0080.0080.0000.0000.0000.000
68A122VAL0-0.035-0.00431.336-0.003-0.0030.0000.0000.0000.000
69A123PRO00.0200.00834.3300.0060.0060.0000.0000.0000.000
70A124CYS00.0480.00633.5760.0060.0060.0000.0000.0000.000
71A125ASP-1-0.874-0.94038.146-0.015-0.0150.0000.0000.0000.000
72A126LYS10.8070.89935.7110.0300.0300.0000.0000.0000.000
73A127THR00.0250.02430.752-0.003-0.0030.0000.0000.0000.000
74A128VAL0-0.038-0.02030.3940.0090.0090.0000.0000.0000.000
75A129PHE00.0190.00226.246-0.005-0.0050.0000.0000.0000.000
76A130TRP0-0.030-0.01120.1400.0160.0160.0000.0000.0000.000
77A131SER00.0320.01524.1420.0080.0080.0000.0000.0000.000
78A132LYS10.9120.95120.503-0.058-0.0580.0000.0000.0000.000
79A133THR00.002-0.01023.4070.0000.0000.0000.0000.0000.000
80A134LYS10.8460.94519.8230.1220.1220.0000.0000.0000.000
81A135GLU-1-0.867-0.92121.691-0.101-0.1010.0000.0000.0000.000
82A145LYS10.9960.99135.4470.0820.0820.0000.0000.0000.000
83A146GLY00.0160.00935.9850.0040.0040.0000.0000.0000.000
84A147LEU0-0.068-0.03934.2650.0060.0060.0000.0000.0000.000
85A148PHE00.0380.01630.812-0.005-0.0050.0000.0000.0000.000
86A149THR00.003-0.00627.0720.0100.0100.0000.0000.0000.000
87A150LEU00.0530.02721.267-0.012-0.0120.0000.0000.0000.000
88A151GLU-1-0.754-0.88821.845-0.081-0.0810.0000.0000.0000.000
89A152ASN0-0.056-0.00124.413-0.007-0.0070.0000.0000.0000.000
90A153THR0-0.0170.00725.597-0.005-0.0050.0000.0000.0000.000
91A154LEU00.0450.01426.233-0.015-0.0150.0000.0000.0000.000
92A155LEU00.007-0.01222.232-0.023-0.0230.0000.0000.0000.000
93A156GLY00.0340.01521.460-0.024-0.0240.0000.0000.0000.000
94A157TYR0-0.0200.00821.853-0.025-0.0250.0000.0000.0000.000
95A158ILE0-0.059-0.04120.831-0.025-0.0250.0000.0000.0000.000
96A159ALA00.0190.01117.442-0.046-0.0460.0000.0000.0000.000
97A160ASP-1-0.891-0.95517.149-0.262-0.2620.0000.0000.0000.000
98A161ASP-1-0.940-0.97116.240-0.380-0.3800.0000.0000.0000.000
99A162LEU0-0.084-0.01114.549-0.092-0.0920.0000.0000.0000.000
100A163SER0-0.081-0.0498.9610.0870.0870.0000.0000.0000.000
101A164TRP00.0100.0079.756-0.117-0.1170.0000.0000.0000.000
102A165CYS0-0.028-0.0092.976-5.455-2.5560.615-1.304-2.210-0.011
103A166GLY00.0360.0337.797-0.248-0.2480.0000.0000.0000.000
104A167LYS10.8690.9235.4793.3573.3570.0000.0000.0000.000
105A168VAL00.0420.0347.1100.5410.5410.0000.0000.0000.000
106A169GLY00.0040.0079.450-0.055-0.0550.0000.0000.0000.000
107A170SER0-0.0140.00710.1230.1980.1980.0000.0000.0000.000
108A171SER00.018-0.00111.986-0.002-0.0020.0000.0000.0000.000
109A172GLU-1-0.978-0.99112.758-0.907-0.9070.0000.0000.0000.000
110A173ILE0-0.041-0.02910.245-0.193-0.1930.0000.0000.0000.000
111A174ASN0-0.032-0.0273.6911.4141.5930.000-0.018-0.1600.000
112A175LEU00.0340.0087.055-0.297-0.2970.0000.0000.0000.000
113A176GLU-1-0.843-0.8924.420-5.811-5.622-0.001-0.014-0.1730.000
114A177SER00.0150.0042.120-6.498-5.9925.459-2.685-3.280-0.019
115A179PRO00.0070.0232.039-5.191-1.5168.930-3.659-8.9460.016
116A180ASP-1-0.837-0.9272.9120.706-1.1560.1282.423-0.6890.001
117A181ARG10.9530.9605.6620.1950.1950.0000.0000.0000.000
118A182ARG10.9070.9407.761-0.911-0.9110.0000.0000.0000.000
119A183ASN0-0.0140.0082.611-4.221-0.8912.544-2.053-3.821-0.006
120A185ASN00.0140.0095.878-0.251-0.2510.0000.0000.0000.000
121A186SER0-0.041-0.0138.128-0.131-0.1310.0000.0000.0000.000
122A187ASN00.0500.0417.232-0.620-0.6200.0000.0000.0000.000
123A188PHE00.067-0.0068.339-0.207-0.2070.0000.0000.0000.000
124A189VAL00.0290.0519.559-0.078-0.0780.0000.0000.0000.000
125A190SER0-0.015-0.02510.086-0.011-0.0110.0000.0000.0000.000
126A191VAL00.0030.02012.449-0.063-0.0630.0000.0000.0000.000
127A192PHE00.0280.02814.419-0.048-0.0480.0000.0000.0000.000
128A193TRP00.0270.01514.0290.0200.0200.0000.0000.0000.000
129A194ASN0-0.085-0.05415.2600.0090.0090.0000.0000.0000.000
130A195LEU0-0.0130.01118.137-0.007-0.0070.0000.0000.0000.000
131A196LEU00.0120.00419.999-0.011-0.0110.0000.0000.0000.000
132A197SER0-0.005-0.02121.065-0.006-0.0060.0000.0000.0000.000
133A198LYS10.8020.89921.841-0.099-0.0990.0000.0000.0000.000
134A199ARG10.8370.89024.163-0.018-0.0180.0000.0000.0000.000
135A200PHE0-0.020-0.00425.659-0.006-0.0060.0000.0000.0000.000
136A201ALA0-0.008-0.00626.949-0.002-0.0020.0000.0000.0000.000
137A202GLU-1-0.790-0.85827.4660.0300.0300.0000.0000.0000.000
138A203ASN0-0.066-0.05829.612-0.007-0.0070.0000.0000.0000.000
139A204ALA00.0250.03331.804-0.007-0.0070.0000.0000.0000.000
140A206GLY0-0.0050.00437.368-0.003-0.0030.0000.0000.0000.000
141A207MET0-0.079-0.03938.8720.0070.0070.0000.0000.0000.000
142A208VAL00.0700.03233.291-0.005-0.0050.0000.0000.0000.000
143A209GLN00.0310.01033.7910.0060.0060.0000.0000.0000.000
144A210VAL00.0260.01228.794-0.001-0.0010.0000.0000.0000.000
145A211PHE0-0.035-0.01630.0580.0000.0000.0000.0000.0000.000
146A212LEU00.004-0.01228.7160.0060.0060.0000.0000.0000.000
147A213ASN00.0690.04727.177-0.013-0.0130.0000.0000.0000.000
148A214GLY00.0940.03430.1210.0110.0110.0000.0000.0000.000
149A215SER0-0.036-0.03730.4550.0050.0050.0000.0000.0000.000
150A216ILE0-0.043-0.02625.9530.0060.0060.0000.0000.0000.000
151A217SER00.000-0.02029.366-0.002-0.0020.0000.0000.0000.000
152A218ASN0-0.0020.00327.757-0.008-0.0080.0000.0000.0000.000
153A219ALA0-0.0090.00727.7030.0080.0080.0000.0000.0000.000
154A220PHE0-0.0120.00227.901-0.002-0.0020.0000.0000.0000.000
155A221ASP-1-0.761-0.86322.0770.2390.2390.0000.0000.0000.000
156A222LYS10.9600.97824.892-0.159-0.1590.0000.0000.0000.000
157A223THR0-0.080-0.05719.9230.0230.0230.0000.0000.0000.000
158A224SER0-0.034-0.00919.7980.0240.0240.0000.0000.0000.000
159A225THR00.028-0.01518.5640.0240.0240.0000.0000.0000.000
160A226PHE00.0530.03320.796-0.004-0.0040.0000.0000.0000.000
161A227GLY00.0020.00824.305-0.008-0.0080.0000.0000.0000.000
162A228ARG10.8910.96417.490-0.327-0.3270.0000.0000.0000.000
163A229VAL0-0.039-0.03220.4060.0050.0050.0000.0000.0000.000
164A230GLU-1-0.814-0.90023.6440.0440.0440.0000.0000.0000.000
165A231VAL00.0150.00726.011-0.012-0.0120.0000.0000.0000.000
166A232HIS0-0.023-0.02726.221-0.018-0.0180.0000.0000.0000.000
167A233SER0-0.032-0.01626.529-0.003-0.0030.0000.0000.0000.000
168A234LEU0-0.0400.00629.100-0.013-0.0130.0000.0000.0000.000
169A235GLN00.0670.03032.1740.0090.0090.0000.0000.0000.000
170A236PRO00.0500.02735.137-0.006-0.0060.0000.0000.0000.000
171A237SER0-0.029-0.01038.245-0.003-0.0030.0000.0000.0000.000
172A238LYS10.8100.90134.545-0.005-0.0050.0000.0000.0000.000
173A239VAL0-0.0340.00434.704-0.005-0.0050.0000.0000.0000.000
174A240HIS00.0460.05038.1290.0080.0080.0000.0000.0000.000
175A241THR0-0.049-0.05339.7910.0050.0050.0000.0000.0000.000
176A242LEU00.0120.02232.321-0.003-0.0030.0000.0000.0000.000
177A243LYS10.8340.90536.606-0.012-0.0120.0000.0000.0000.000
178A244ALA00.010-0.00234.225-0.001-0.0010.0000.0000.0000.000
179A245TRP0-0.035-0.02734.252-0.001-0.0010.0000.0000.0000.000
180A246VAL00.0080.00733.6360.0020.0020.0000.0000.0000.000
181A247ILE0-0.029-0.02132.781-0.004-0.0040.0000.0000.0000.000
182A248HIS0-0.038-0.03634.0180.0060.0060.0000.0000.0000.000
183A249ASP-1-0.847-0.92433.8430.0030.0030.0000.0000.0000.000
184A250SER0-0.041-0.03536.7840.0030.0030.0000.0000.0000.000
185A251GLY0-0.0060.00638.4600.0010.0010.0000.0000.0000.000
186A252LYS10.8330.91935.165-0.052-0.0520.0000.0000.0000.000
187A253THR00.0590.01738.2480.0000.0000.0000.0000.0000.000
188A254PRO00.0300.02236.5680.0030.0030.0000.0000.0000.000
189A255ARG10.8300.92631.275-0.098-0.0980.0000.0000.0000.000
190A256ASP-1-0.791-0.89532.5040.0980.0980.0000.0000.0000.000
191A257THR0-0.017-0.01434.755-0.008-0.0080.0000.0000.0000.000
192A258CYS0-0.031-0.01636.7520.0060.0060.0000.0000.0000.000
193A259SER0-0.045-0.01338.4860.0000.0000.0000.0000.0000.000
194A260GLY00.0150.03036.4930.0030.0030.0000.0000.0000.000
195A261SER00.038-0.00434.168-0.003-0.0030.0000.0000.0000.000
196A262SER00.0000.01130.1290.0000.0000.0000.0000.0000.000
197A263ILE00.0750.01332.5210.0010.0010.0000.0000.0000.000
198A264ASN0-0.0090.00534.451-0.009-0.0090.0000.0000.0000.000
199A265GLU-1-0.909-0.96429.9880.1550.1550.0000.0000.0000.000
200A266LEU0-0.054-0.01130.9480.0010.0010.0000.0000.0000.000
201A267GLN00.0470.02833.133-0.008-0.0080.0000.0000.0000.000
202A268LEU0-0.001-0.01435.777-0.005-0.0050.0000.0000.0000.000
203A269ILE0-0.042-0.00129.9090.0010.0010.0000.0000.0000.000
204A270LEU0-0.016-0.00433.936-0.004-0.0040.0000.0000.0000.000
205A271ARG10.9300.94436.437-0.059-0.0590.0000.0000.0000.000
206A272GLY00.0060.02537.186-0.003-0.0030.0000.0000.0000.000
207A273LYS10.8060.90731.817-0.076-0.0760.0000.0000.0000.000
208A274ASN0-0.046-0.03038.415-0.006-0.0060.0000.0000.0000.000
209A275ILE0-0.0260.00536.142-0.005-0.0050.0000.0000.0000.000
210A276LYS10.9330.97140.029-0.021-0.0210.0000.0000.0000.000
211A277PHE00.0630.01635.3580.0000.0000.0000.0000.0000.000
212A278THR0-0.036-0.01239.088-0.003-0.0030.0000.0000.0000.000
213A280GLN00.0240.01938.609-0.003-0.0030.0000.0000.0000.000
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