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: Z6RVN

Calculation Name: 3NBI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NBI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H9A7

Base Structure: X-ray

Registration Date: 2023-06-21

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015537.098021
FMO2-HF: Nuclear repulsion 1939355.752787
FMO2-HF: Total energy -76181.345234
FMO2-MP2: Total energy -76404.725476


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-9.868-5.5340.851-1.783-3.4020.007
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.011
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].
3A4THR00.0610.0103.656-1.2720.493-0.005-0.760-1.0000.000
4A5SER0-0.095-0.0353.235-0.1360.4620.036-0.177-0.4570.000
5A6ILE00.000-0.0062.743-1.5430.0740.820-0.789-1.6480.007
6A7ALA00.0810.0406.130-0.338-0.3380.0000.0000.0000.000
7A8LEU00.0490.0318.0490.0060.0060.0000.0000.0000.000
8A9ARG10.8790.9386.675-2.958-2.9580.0000.0000.0000.000
9A10ALA00.0370.02410.394-0.094-0.0940.0000.0000.0000.000
10A11GLU-1-0.913-0.96112.1950.2140.2140.0000.0000.0000.000
11A12THR0-0.044-0.03713.154-0.069-0.0690.0000.0000.0000.000
12A13TRP0-0.009-0.00714.752-0.046-0.0460.0000.0000.0000.000
13A14LEU00.0220.01016.092-0.055-0.0550.0000.0000.0000.000
14A15LEU00.0480.03718.140-0.041-0.0410.0000.0000.0000.000
15A16ALA0-0.043-0.02219.155-0.033-0.0330.0000.0000.0000.000
16A17ALA0-0.052-0.02820.241-0.030-0.0300.0000.0000.0000.000
17A18TRP0-0.020-0.02019.606-0.047-0.0470.0000.0000.0000.000
18A19HIS10.7720.88822.795-0.225-0.2250.0000.0000.0000.000
19A20VAL00.0330.03020.171-0.016-0.0160.0000.0000.0000.000
20A21LYS10.9020.94819.846-0.112-0.1120.0000.0000.0000.000
21A22VAL00.0360.02316.034-0.017-0.0170.0000.0000.0000.000
22A23PRO00.0610.05417.4830.0250.0250.0000.0000.0000.000
23A24PRO00.034-0.00212.149-0.016-0.0160.0000.0000.0000.000
24A25MET00.0060.00112.608-0.007-0.0070.0000.0000.0000.000
25A26TRP00.0710.03214.490-0.030-0.0300.0000.0000.0000.000
26A27LEU0-0.0180.00111.377-0.034-0.0340.0000.0000.0000.000
27A28GLU-1-0.812-0.9127.0390.2950.2950.0000.0000.0000.000
28A29ALA0-0.0060.02010.438-0.183-0.1830.0000.0000.0000.000
29A30CYS0-0.035-0.00313.064-0.092-0.0920.0000.0000.0000.000
30A31ILE0-0.012-0.0207.3650.0000.0000.0000.0000.0000.000
31A32ASN0-0.052-0.0418.030-0.457-0.4570.0000.0000.0000.000
32A33TRP00.0480.0289.752-0.108-0.1080.0000.0000.0000.000
33A34ILE0-0.018-0.01010.9860.0020.0020.0000.0000.0000.000
34A35GLN0-0.083-0.0624.3290.2520.337-0.001-0.012-0.0720.000
35A36GLU-1-0.950-0.9749.605-0.790-0.7900.0000.0000.0000.000
36A37GLU-1-0.850-0.91412.470-0.325-0.3250.0000.0000.0000.000
37A38ASN0-0.102-0.05811.5820.0930.0930.0000.0000.0000.000
38A39ASN0-0.075-0.03613.1020.0030.0030.0000.0000.0000.000
39A40ASN0-0.035-0.0188.845-0.310-0.3100.0000.0000.0000.000
40A41VAL00.0350.0213.734-0.161-0.0340.002-0.030-0.0990.000
41A42ASN0-0.051-0.0204.464-2.391-2.249-0.001-0.015-0.1260.000
42A43LEU00.0400.0355.8190.6600.6600.0000.0000.0000.000
43A44SER0-0.045-0.0456.8380.5040.5040.0000.0000.0000.000
44A45GLN00.007-0.0337.3920.7050.7050.0000.0000.0000.000
45A46ALA00.0030.0059.515-0.184-0.1840.0000.0000.0000.000
46A47GLN00.0460.03711.491-0.037-0.0370.0000.0000.0000.000
47A48MET00.0320.0447.955-0.069-0.0690.0000.0000.0000.000
48A49ASN00.0110.00610.8330.0150.0150.0000.0000.0000.000
49A50LYS10.8180.90113.442-0.161-0.1610.0000.0000.0000.000
50A51GLN00.0250.01412.964-0.054-0.0540.0000.0000.0000.000
51A52VAL00.0370.02212.150-0.027-0.0270.0000.0000.0000.000
52A53PHE0-0.032-0.02115.109-0.015-0.0150.0000.0000.0000.000
53A54GLU-1-0.842-0.91318.4020.0370.0370.0000.0000.0000.000
54A55GLN00.0680.02916.657-0.010-0.0100.0000.0000.0000.000
55A56TRP00.0070.00719.1330.0010.0010.0000.0000.0000.000
56A57LEU0-0.064-0.04820.847-0.004-0.0040.0000.0000.0000.000
57A58LEU0-0.0060.01222.439-0.001-0.0010.0000.0000.0000.000
58A59THR0-0.037-0.00521.456-0.020-0.0200.0000.0000.0000.000
59A60ASP-1-0.704-0.80323.8910.0120.0120.0000.0000.0000.000
60A61LEU0-0.021-0.01824.8410.0010.0010.0000.0000.0000.000
61A62ARG10.7830.85026.0050.0070.0070.0000.0000.0000.000
62A63ASP-1-0.872-0.92623.651-0.046-0.0460.0000.0000.0000.000
63A64LEU0-0.111-0.06020.5650.0000.0000.0000.0000.0000.000
64A65GLU-1-0.929-0.96522.2500.0000.0000.0000.0000.0000.000
65A66HIS0-0.020-0.01519.5690.0010.0010.0000.0000.0000.000
66A67PRO0-0.0040.01223.6970.0030.0030.0000.0000.0000.000
67A68LEU0-0.100-0.05423.8970.0160.0160.0000.0000.0000.000
68A69LEU0-0.046-0.03527.0800.0090.0090.0000.0000.0000.000
69A70PRO0-0.051-0.02930.5950.0000.0000.0000.0000.0000.000
70A71ASP-1-0.812-0.90132.5890.0440.0440.0000.0000.0000.000
71A72GLY00.0170.01034.1110.0020.0020.0000.0000.0000.000
72A73ILE0-0.073-0.03935.398-0.002-0.0020.0000.0000.0000.000
73A74LEU0-0.022-0.02037.374-0.002-0.0020.0000.0000.0000.000
74A75GLU-1-0.947-0.96140.2370.0320.0320.0000.0000.0000.000
75A76ILE0-0.029-0.00839.778-0.001-0.0010.0000.0000.0000.000
76A77PRO00.012-0.00343.4640.0000.0000.0000.0000.0000.000
77A78LYS10.9120.93045.890-0.043-0.0430.0000.0000.0000.000
78A79GLY00.0030.01942.6850.0000.0000.0000.0000.0000.000
79A80GLU-1-0.892-0.93140.8750.0610.0610.0000.0000.0000.000
80A81LEU00.0010.02533.6880.0030.0030.0000.0000.0000.000
81A82ASN00.006-0.00935.5160.0030.0030.0000.0000.0000.000
82A83GLY00.0050.02631.4250.0020.0020.0000.0000.0000.000
83A84PHE0-0.028-0.03327.969-0.001-0.0010.0000.0000.0000.000
84A85TYR0-0.036-0.03328.0360.0080.0080.0000.0000.0000.000
85A86ALA00.0030.00725.280-0.007-0.0070.0000.0000.0000.000
86A87LEU00.0050.01026.930-0.003-0.0030.0000.0000.0000.000
87A88GLN00.0330.00228.7330.0040.0040.0000.0000.0000.000
88A89ILE0-0.039-0.02530.8490.0000.0000.0000.0000.0000.000
89A90ASN00.0380.03033.391-0.004-0.0040.0000.0000.0000.000
90A91SER00.0690.03935.183-0.003-0.0030.0000.0000.0000.000
91A92LEU0-0.022-0.01738.3440.0060.0060.0000.0000.0000.000
92A93VAL00.0680.04441.036-0.003-0.0030.0000.0000.0000.000
93A94ASP-1-0.763-0.88444.6940.0220.0220.0000.0000.0000.000
94A95VAL00.0350.00847.446-0.002-0.0020.0000.0000.0000.000
95A96SER0-0.061-0.03750.025-0.002-0.0020.0000.0000.0000.000
96A97GLN00.009-0.01551.9270.0000.0000.0000.0000.0000.000
97A98PRO00.0210.00651.008-0.001-0.0010.0000.0000.0000.000
98A99ALA00.0510.03754.225-0.001-0.0010.0000.0000.0000.000
99A100TYR00.018-0.00256.167-0.001-0.0010.0000.0000.0000.000
100A101SER0-0.014-0.00657.306-0.001-0.0010.0000.0000.0000.000
101A102GLN0-0.0070.00258.4560.0000.0000.0000.0000.0000.000
102A103ILE00.0440.01859.095-0.001-0.0010.0000.0000.0000.000
103A104GLN00.0480.01562.0010.0000.0000.0000.0000.0000.000
104A105LYS10.8010.90360.589-0.006-0.0060.0000.0000.0000.000
105A106LEU0-0.011-0.01563.751-0.001-0.0010.0000.0000.0000.000
106A107ARG10.8040.88465.930-0.013-0.0130.0000.0000.0000.000
107A108GLY00.0110.01367.9780.0000.0000.0000.0000.0000.000
108A109LYS10.8980.96967.305-0.005-0.0050.0000.0000.0000.000
109A120ALA00.0440.02487.5880.0000.0000.0000.0000.0000.000
110A121GLN0-0.042-0.03483.9340.0000.0000.0000.0000.0000.000
111A122VAL00.0290.01579.8100.0000.0000.0000.0000.0000.000
112A123THR0-0.014-0.01078.3320.0000.0000.0000.0000.0000.000
113A124PRO00.0370.01174.7670.0000.0000.0000.0000.0000.000
114A125LYS10.9070.95272.018-0.012-0.0120.0000.0000.0000.000
115A126PRO00.0150.01868.8020.0000.0000.0000.0000.0000.000
116A127TRP00.0460.01561.5070.0000.0000.0000.0000.0000.000
117A128GLU-1-0.844-0.88963.7570.0150.0150.0000.0000.0000.000
118A129ALA0-0.029-0.01159.702-0.001-0.0010.0000.0000.0000.000
119A130LYS10.8920.95853.651-0.017-0.0170.0000.0000.0000.000
120A131PRO00.0020.00255.5530.0010.0010.0000.0000.0000.000
121A132SER00.0180.01150.835-0.001-0.0010.0000.0000.0000.000
122A133ARG10.7620.85442.915-0.032-0.0320.0000.0000.0000.000
123A134MET0-0.034-0.02547.4300.0010.0010.0000.0000.0000.000
124A135LEU00.0060.00341.600-0.002-0.0020.0000.0000.0000.000
125A136MET0-0.042-0.01143.6610.0040.0040.0000.0000.0000.000
126A137LEU00.0120.00836.917-0.003-0.0030.0000.0000.0000.000
127A138GLN0-0.033-0.02438.9700.0020.0020.0000.0000.0000.000
128A139LEU0-0.013-0.00834.294-0.001-0.0010.0000.0000.0000.000
129A140THR00.010-0.01930.897-0.004-0.0040.0000.0000.0000.000
130A141ASP-1-0.741-0.88228.5030.0590.0590.0000.0000.0000.000
131A142GLY00.0350.02927.3710.0040.0040.0000.0000.0000.000
132A143ILE0-0.045-0.01227.240-0.007-0.0070.0000.0000.0000.000
133A144VAL0-0.010-0.00430.306-0.004-0.0040.0000.0000.0000.000
134A145GLN0-0.005-0.00733.233-0.001-0.0010.0000.0000.0000.000
135A146ILE0-0.013-0.00135.8060.0000.0000.0000.0000.0000.000
136A147GLN00.0520.03238.247-0.002-0.0020.0000.0000.0000.000
137A148GLY00.024-0.00139.4910.0040.0040.0000.0000.0000.000
138A149MET0-0.020-0.00240.399-0.002-0.0020.0000.0000.0000.000
139A150GLU-1-0.753-0.82643.2620.0370.0370.0000.0000.0000.000
140A151TYR0-0.044-0.02244.453-0.002-0.0020.0000.0000.0000.000
141A152GLN0-0.002-0.00845.3460.0020.0020.0000.0000.0000.000
142A153PRO0-0.002-0.00844.7810.0010.0010.0000.0000.0000.000
143A154ILE00.0220.00939.2490.0030.0030.0000.0000.0000.000
144A155PRO0-0.013-0.01041.742-0.002-0.0020.0000.0000.0000.000
145A156ILE0-0.023-0.00835.563-0.002-0.0020.0000.0000.0000.000
146A157LEU00.0090.01936.4360.0000.0000.0000.0000.0000.000
147A158HIS00.008-0.01837.552-0.002-0.0020.0000.0000.0000.000
148A159SER0-0.029-0.05440.4830.0010.0010.0000.0000.0000.000
149A160ASP-1-0.850-0.88740.3030.0060.0060.0000.0000.0000.000
150A161LEU0-0.097-0.04434.7820.0000.0000.0000.0000.0000.000
151A162PRO00.0460.04732.505-0.001-0.0010.0000.0000.0000.000
152A163PRO00.0410.02533.8490.0060.0060.0000.0000.0000.000
153A164GLY00.0700.03630.680-0.005-0.0050.0000.0000.0000.000
154A165THR0-0.051-0.03129.5270.0060.0060.0000.0000.0000.000
155A166LYS10.7940.90725.454-0.015-0.0150.0000.0000.0000.000
156A167ILE0-0.031-0.03329.0410.0030.0030.0000.0000.0000.000
157A168LEU0-0.041-0.00727.6950.0040.0040.0000.0000.0000.000
158A169ILE00.0210.01330.135-0.004-0.0040.0000.0000.0000.000
159A170TYR0-0.064-0.06031.5210.0110.0110.0000.0000.0000.000
160A171GLY00.0290.02633.456-0.006-0.0060.0000.0000.0000.000
161A172ASN0-0.083-0.06135.653-0.001-0.0010.0000.0000.0000.000
162A173ILE00.0260.01736.104-0.003-0.0030.0000.0000.0000.000
163A174SER00.0340.01839.951-0.001-0.0010.0000.0000.0000.000
164A175PHE00.0030.00539.588-0.001-0.0010.0000.0000.0000.000
165A176ARG10.9070.93343.093-0.032-0.0320.0000.0000.0000.000
166A177LEU0-0.031-0.01045.284-0.001-0.0010.0000.0000.0000.000
167A178GLY00.0980.06541.600-0.002-0.0020.0000.0000.0000.000
168A179VAL0-0.045-0.01741.723-0.001-0.0010.0000.0000.0000.000
169A180LEU00.0270.00936.4110.0020.0020.0000.0000.0000.000
170A181LEU0-0.063-0.04041.130-0.003-0.0030.0000.0000.0000.000
171A182LEU00.0120.01937.9050.0030.0030.0000.0000.0000.000
172A183LYS10.8290.89341.022-0.063-0.0630.0000.0000.0000.000
173A184PRO00.0130.00240.2150.0030.0030.0000.0000.0000.000
174A185GLU-1-0.804-0.89038.7270.0670.0670.0000.0000.0000.000
175A186ASN0-0.075-0.03536.8480.0020.0020.0000.0000.0000.000
176A187VAL00.0160.00534.7530.0020.0020.0000.0000.0000.000
177A188LYS10.9270.97526.822-0.140-0.1400.0000.0000.0000.000
178A189VAL00.0150.00631.0480.0030.0030.0000.0000.0000.000
179A190LEU0-0.078-0.04625.4000.0100.0100.0000.0000.0000.000
180A191GLY0-0.0020.01227.1290.0030.0030.0000.0000.0000.000
181A192GLY00.0270.00926.8020.0020.0020.0000.0000.0000.000
182A193GLU-1-0.943-0.97827.534-0.014-0.0140.0000.0000.0000.000
183A194VAL00.014-0.00127.357-0.002-0.0020.0000.0000.0000.000
184A195ASP-1-0.879-0.93328.922-0.061-0.0610.0000.0000.0000.000
185A196ALA00.0510.02130.1340.0030.0030.0000.0000.0000.000
186A197LEU0-0.050-0.02831.8160.0050.0050.0000.0000.0000.000
187A198LEU0-0.041-0.02732.2890.0050.0050.0000.0000.0000.000
188A199GLU-1-0.936-0.97033.755-0.057-0.0570.0000.0000.0000.000
189A200GLU-1-0.922-0.93636.181-0.017-0.0170.0000.0000.0000.000
190A201TYR0-0.038-0.05236.2840.0030.0030.0000.0000.0000.000
191A202ALA0-0.037-0.00739.2800.0020.0020.0000.0000.0000.000
192A203GLN0-0.102-0.04640.916-0.002-0.0020.0000.0000.0000.000
193A204GLU-1-1.036-1.01142.989-0.005-0.0050.0000.0000.0000.000