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: 16NRZ

Calculation Name: 3B77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B77

Chain ID: A

ChEMBL ID:

UniProt ID: B1YJX4

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptH
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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1994993.875372
FMO2-HF: Nuclear repulsion 1918297.36321
FMO2-HF: Total energy -76696.512163
FMO2-MP2: Total energy -76922.814522


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:14:ASP)


Summations of interaction energy for fragment #1(A:14:ASP)
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.
75.98987.9482.879-6.73-8.1090.033
Interaction energy analysis for fragmet #1(A:14:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.915 / q_NPA : -0.963
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].
3A16GLY0-0.011-0.0123.6966.4188.6700.011-1.096-1.1670.005
4A17GLN0-0.076-0.0466.104-1.402-1.4020.0000.0000.0000.000
5A18VAL0-0.003-0.0029.245-0.520-0.5200.0000.0000.0000.000
6A19ILE0-0.065-0.03011.203-0.014-0.0140.0000.0000.0000.000
7A20HIS00.0200.01314.408-0.552-0.5520.0000.0000.0000.000
8A21PRO00.038-0.01818.0790.1950.1950.0000.0000.0000.000
9A22ASP-1-0.895-0.93820.78012.90312.9030.0000.0000.0000.000
10A23ASP-1-0.982-0.99417.17316.52416.5240.0000.0000.0000.000
11A24PHE0-0.046-0.02616.7340.8430.8430.0000.0000.0000.000
12A25ASP-1-0.836-0.92318.48614.41414.4140.0000.0000.0000.000
13A26LYS10.8120.92817.949-14.951-14.9510.0000.0000.0000.000
14A27ALA0-0.112-0.04714.3501.1741.1740.0000.0000.0000.000
15A28ALA00.0470.02313.480-0.865-0.8650.0000.0000.0000.000
16A29ALA0-0.023-0.04013.854-0.942-0.9420.0000.0000.0000.000
17A30ASP-1-0.892-0.95315.70813.47313.4730.0000.0000.0000.000
18A31ASP-1-0.889-0.93818.93914.32814.3280.0000.0000.0000.000
19A32TYR0-0.125-0.06816.809-0.722-0.7220.0000.0000.0000.000
20A33VAL0-0.068-0.02319.288-0.134-0.1340.0000.0000.0000.000
21A34LEU0-0.025-0.01121.659-0.295-0.2950.0000.0000.0000.000
22A35HIS00.006-0.00922.619-0.833-0.8330.0000.0000.0000.000
23A36GLU-1-0.970-0.98326.90510.56310.5630.0000.0000.0000.000
24A37ASP-1-0.975-0.98628.5069.7449.7440.0000.0000.0000.000
25A38GLY0-0.049-0.02429.325-0.093-0.0930.0000.0000.0000.000
26A39GLU-1-0.832-0.86522.18013.29313.2930.0000.0000.0000.000
27A40LYS10.9790.98724.091-11.943-11.9430.0000.0000.0000.000
28A41ILE00.012-0.00417.6260.1210.1210.0000.0000.0000.000
29A42TYR0-0.048-0.04319.858-0.450-0.4500.0000.0000.0000.000
30A43PHE00.012-0.00613.7530.0280.0280.0000.0000.0000.000
31A44LEU00.0090.02712.1890.0860.0860.0000.0000.0000.000
32A45ILE00.0180.0217.763-0.012-0.0120.0000.0000.0000.000
33A46LYS10.9280.9698.232-24.988-24.9880.0000.0000.0000.000
34A47SER00.0900.0451.9852.9383.7551.517-0.994-1.341-0.002
35A48LYS10.9190.9662.918-87.643-81.6320.625-3.453-3.1830.035
36A49THR0-0.026-0.0232.808-4.602-2.5940.725-0.963-1.770-0.004
37A50ASP-1-0.799-0.8854.37132.16932.396-0.001-0.019-0.2070.000
38A51GLU-1-0.843-0.9386.09025.64625.6460.0000.0000.0000.000
39A52TYR00.001-0.0055.615-1.686-1.6860.0000.0000.0000.000
40A53CYS00.0040.00110.936-0.537-0.5370.0000.0000.0000.000
41A54PHE00.0160.01012.352-0.564-0.5640.0000.0000.0000.000
42A55THR00.064-0.00217.085-0.411-0.4110.0000.0000.0000.000
43A56ASN00.0190.03420.7000.4470.4470.0000.0000.0000.000
44A57LEU0-0.004-0.00323.365-0.381-0.3810.0000.0000.0000.000
45A58ALA0-0.012-0.01520.229-0.292-0.2920.0000.0000.0000.000
46A59LEU0-0.0040.03912.7390.1800.1800.0000.0000.0000.000
47A60VAL0-0.020-0.01715.597-0.279-0.2790.0000.0000.0000.000
48A61HIS0-0.0110.0018.115-1.568-1.5680.0000.0000.0000.000
49A62LEU0-0.019-0.00210.952-1.070-1.0700.0000.0000.0000.000
50A63ASP-1-0.897-0.9598.80529.61029.6100.0000.0000.0000.000
51A64GLY00.0370.0177.602-2.391-2.3910.0000.0000.0000.000
52A65GLU-1-0.833-0.8886.94125.07525.0750.0000.0000.0000.000
53A66SER0-0.094-0.0648.384-2.329-2.3290.0000.0000.0000.000
54A67ALA00.0490.0286.3313.2593.2590.0000.0000.0000.000
55A68VAL0-0.025-0.0247.3851.5081.5080.0000.0000.0000.000
56A69SER0-0.003-0.01310.018-2.665-2.6650.0000.0000.0000.000
57A70SER00.0050.01310.768-1.762-1.7620.0000.0000.0000.000
58A71LYS10.8240.90711.769-20.886-20.8860.0000.0000.0000.000
59A72ARG10.9010.9537.974-31.133-31.1330.0000.0000.0000.000
60A73VAL00.0030.01112.469-1.827-1.8270.0000.0000.0000.000
61A74LEU0-0.0280.00913.3021.0161.0160.0000.0000.0000.000
62A75TYR0-0.020-0.01313.032-1.685-1.6850.0000.0000.0000.000
63A76ARG10.9620.95316.404-12.911-12.9110.0000.0000.0000.000
64A77TYR0-0.038-0.01414.470-0.378-0.3780.0000.0000.0000.000
65A78PRO0-0.001-0.01519.4880.0400.0400.0000.0000.0000.000
66A79TYR00.049-0.00518.858-0.024-0.0240.0000.0000.0000.000
67A80ALA0-0.065-0.04223.000-0.184-0.1840.0000.0000.0000.000
68A81HIS0-0.028-0.00624.793-0.374-0.3740.0000.0000.0000.000
69A82TYR0-0.054-0.02220.2720.0470.0470.0000.0000.0000.000
70A83PRO0-0.016-0.01921.5180.2720.2720.0000.0000.0000.000
71A84ILE00.0380.02818.2820.3740.3740.0000.0000.0000.000
72A85ARG10.9190.95319.342-12.109-12.1090.0000.0000.0000.000
73A86HIS0-0.007-0.01018.5030.5040.5040.0000.0000.0000.000
74A87VAL00.0080.02016.9630.6020.6020.0000.0000.0000.000
75A88MET0-0.068-0.03815.266-0.744-0.7440.0000.0000.0000.000
76A89PHE0-0.014-0.02213.0640.5590.5590.0000.0000.0000.000
77A90GLU-1-0.913-0.92911.85117.66117.6610.0000.0000.0000.000
78A91THR0-0.069-0.04212.8790.8740.8740.0000.0000.0000.000
79A92ALA00.0860.04512.9850.3000.3000.0000.0000.0000.000
80A93GLY00.0050.01114.220-1.216-1.2160.0000.0000.0000.000
81A94THR0-0.096-0.07616.3640.5940.5940.0000.0000.0000.000
82A95VAL0-0.047-0.03514.5500.1850.1850.0000.0000.0000.000
83A96ASP-1-0.844-0.89011.58021.24821.2480.0000.0000.0000.000
84A97LEU0-0.043-0.0619.068-1.217-1.2170.0000.0000.0000.000
85A98ASP-1-0.910-0.9496.37430.67930.6790.0000.0000.0000.000
86A99VAL0-0.040-0.0099.369-2.326-2.3260.0000.0000.0000.000
87A100GLU-1-0.751-0.8697.57423.21823.2180.0000.0000.0000.000
88A101ILE0-0.070-0.0339.392-2.143-2.1430.0000.0000.0000.000
89A102LYS10.9510.96710.084-16.399-16.3990.0000.0000.0000.000
90A103PHE0-0.028-0.02112.275-1.041-1.0410.0000.0000.0000.000
91A104GLU-1-0.891-0.94113.97014.65014.6500.0000.0000.0000.000
92A105ILE00.0190.00715.152-0.631-0.6310.0000.0000.0000.000
93A106GLY0-0.003-0.00717.7300.1820.1820.0000.0000.0000.000
94A107GLY0-0.068-0.03819.566-0.266-0.2660.0000.0000.0000.000
95A108LYS10.8860.96912.158-19.007-19.0070.0000.0000.0000.000
96A109HIS00.0100.00712.6950.2720.2720.0000.0000.0000.000
97A110TYR0-0.048-0.0449.4640.4880.4880.0000.0000.0000.000
98A111SER0-0.054-0.0277.609-0.842-0.8420.0000.0000.0000.000
99A112ILE0-0.011-0.0085.8051.5041.5040.0000.0000.0000.000
100A113ASP-1-0.809-0.8863.64728.34728.9910.002-0.205-0.441-0.001
101A114VAL0-0.070-0.0465.6753.3273.3270.0000.0000.0000.000
102A115ASP-1-0.746-0.8748.42524.28024.2800.0000.0000.0000.000
103A116LYS10.9440.98210.095-21.359-21.3590.0000.0000.0000.000
104A117LYS10.7790.89212.678-24.721-24.7210.0000.0000.0000.000
105A118GLN0-0.028-0.02511.7720.1940.1940.0000.0000.0000.000
106A119LEU00.0430.03715.177-0.363-0.3630.0000.0000.0000.000
107A120GLU-1-0.878-0.94716.06912.85612.8560.0000.0000.0000.000
108A121HIS00.0420.02116.4450.0720.0720.0000.0000.0000.000
109A122VAL00.0300.01612.177-0.393-0.3930.0000.0000.0000.000
110A123LYS10.7870.87715.172-13.706-13.7060.0000.0000.0000.000
111A124ASP-1-0.850-0.92018.04612.75112.7510.0000.0000.0000.000
112A125LEU0-0.0250.00113.658-0.612-0.6120.0000.0000.0000.000
113A126TYR0-0.004-0.00116.566-0.654-0.6540.0000.0000.0000.000
114A127LYS10.9260.96017.799-12.383-12.3830.0000.0000.0000.000
115A128ALA00.0200.01620.055-0.495-0.4950.0000.0000.0000.000
116A129LEU00.0330.01215.333-0.546-0.5460.0000.0000.0000.000
117A130LEU0-0.028-0.00719.858-0.418-0.4180.0000.0000.0000.000
118A131ALA00.0050.00722.039-0.480-0.4800.0000.0000.0000.000
119A132ILE0-0.043-0.01620.943-0.468-0.4680.0000.0000.0000.000
120A133ALA00.0180.00221.779-0.357-0.3570.0000.0000.0000.000
121A134GLU-1-0.942-0.95723.7299.3389.3380.0000.0000.0000.000
122A135LYS10.9480.97727.101-9.379-9.3790.0000.0000.0000.000
123A136GLN0-0.0090.00123.608-0.027-0.0270.0000.0000.0000.000
124A137TYR0-0.022-0.00727.454-0.365-0.3650.0000.0000.0000.000
125A138GLU-1-0.926-0.97528.9748.4268.4260.0000.0000.0000.000
126A139GLY0-0.0070.00231.371-0.304-0.3040.0000.0000.0000.000
127A140GLN0-0.008-0.01229.801-0.345-0.3450.0000.0000.0000.000
128A141LYS10.8540.92832.650-8.387-8.3870.0000.0000.0000.000
129A142MET0-0.003-0.00535.353-0.341-0.3410.0000.0000.0000.000
130A143LEU00.0150.00533.744-0.241-0.2410.0000.0000.0000.000
131A144GLU-1-0.878-0.91735.1227.8607.8600.0000.0000.0000.000
132A145PHE00.006-0.00538.670-0.211-0.2110.0000.0000.0000.000
133A146ALA00.0250.03640.311-0.231-0.2310.0000.0000.0000.000
134A147ASN00.0190.00438.598-0.232-0.2320.0000.0000.0000.000
135A148SER0-0.044-0.02242.469-0.185-0.1850.0000.0000.0000.000
136A149SER0-0.031-0.03244.723-0.193-0.1930.0000.0000.0000.000
137A150LEU0-0.0310.00745.584-0.160-0.1600.0000.0000.0000.000
138A151ASN00.038-0.00545.238-0.177-0.1770.0000.0000.0000.000
139A152HIS00.0040.01047.472-0.215-0.2150.0000.0000.0000.000
140A153SER00.0320.01350.739-0.163-0.1630.0000.0000.0000.000
141A154VAL0-0.0140.01650.121-0.126-0.1260.0000.0000.0000.000
142A155THR0-0.059-0.04652.318-0.117-0.1170.0000.0000.0000.000
143A156ILE0-0.092-0.04354.813-0.106-0.1060.0000.0000.0000.000
144A157LEU0-0.010-0.01555.358-0.103-0.1030.0000.0000.0000.000
145A158GLY0-0.0030.02457.476-0.051-0.0510.0000.0000.0000.000
146A159GLY0-0.067-0.03058.880-0.064-0.0640.0000.0000.0000.000
147A160LEU00.0530.03360.389-0.062-0.0620.0000.0000.0000.000
148A161ARG10.9480.96264.300-4.439-4.4390.0000.0000.0000.000
149A162GLN0-0.003-0.00766.759-0.005-0.0050.0000.0000.0000.000
150A163GLY0-0.042-0.02968.4080.0200.0200.0000.0000.0000.000
151A164ASP-1-0.927-0.95868.4444.5044.5040.0000.0000.0000.000
152A165MET00.0280.03763.6720.0620.0620.0000.0000.0000.000
153A166ASN0-0.011-0.00965.018-0.011-0.0110.0000.0000.0000.000
154A167VAL00.0520.00763.2440.0740.0740.0000.0000.0000.000
155A168PRO00.0160.00661.8030.0820.0820.0000.0000.0000.000
156A169GLN0-0.023-0.00459.5900.0480.0480.0000.0000.0000.000
157A170THR00.0390.01459.3340.0770.0770.0000.0000.0000.000
158A171PHE0-0.032-0.01656.0640.0800.0800.0000.0000.0000.000
159A172LYS10.9671.00255.893-5.300-5.3000.0000.0000.0000.000
160A173ASP-1-0.840-0.93554.4315.4535.4530.0000.0000.0000.000
161A174LEU0-0.0250.00353.7680.0850.0850.0000.0000.0000.000
162A175SER0-0.051-0.05951.7990.1080.1080.0000.0000.0000.000
163A176GLN0-0.051-0.01448.7760.2530.2530.0000.0000.0000.000
164A177GLU-1-0.862-0.92149.0156.0516.0510.0000.0000.0000.000
165A178SER0-0.068-0.02848.1240.1820.1820.0000.0000.0000.000
166A179PHE0-0.002-0.00342.9550.2030.2030.0000.0000.0000.000
167A180ASP-1-0.814-0.92844.3766.5986.5980.0000.0000.0000.000
168A181TRP0-0.068-0.02644.0640.1420.1420.0000.0000.0000.000
169A182LEU0-0.026-0.03341.8380.1840.1840.0000.0000.0000.000
170A183GLN0-0.0140.00240.1110.1630.1630.0000.0000.0000.000
171A184GLY0-0.001-0.00939.2510.2110.2110.0000.0000.0000.000
172A185HIS00.007-0.00139.1280.3350.3350.0000.0000.0000.000
173A186TYR0-0.0220.00332.1270.2640.2640.0000.0000.0000.000
174A187TYR0-0.002-0.02134.3990.3550.3550.0000.0000.0000.000
175A188LYS10.8890.96934.687-7.290-7.2900.0000.0000.0000.000
176A189TRP0-0.045-0.03733.8660.1660.1660.0000.0000.0000.000
177A190ASN0-0.048-0.00730.4890.4040.4040.0000.0000.0000.000
178A191GLN0-0.044-0.02429.203-0.224-0.2240.0000.0000.0000.000
179A192LYS10.9560.95628.045-9.385-9.3850.0000.0000.0000.000
180A193ASP-1-0.798-0.88626.66110.89710.8970.0000.0000.0000.000
181A194PHE0-0.007-0.01324.390-0.382-0.3820.0000.0000.0000.000
182A195GLY00.0730.02625.1820.3560.3560.0000.0000.0000.000
183A196SER00.0040.01326.2780.1610.1610.0000.0000.0000.000
184A197PHE0-0.075-0.04424.936-0.195-0.1950.0000.0000.0000.000
185A198TYR00.0350.00518.8220.3120.3120.0000.0000.0000.000
186A199GLU-1-0.949-0.98023.64810.48210.4820.0000.0000.0000.000
187A200LYS10.8780.94826.744-9.720-9.7200.0000.0000.0000.000
188A201TYR0-0.067-0.05223.383-0.347-0.3470.0000.0000.0000.000
189A202ILE00.0310.03320.0590.2240.2240.0000.0000.0000.000
190A203ASN0-0.056-0.00423.2490.0710.0710.0000.0000.0000.000