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: QV2MY

Calculation Name: 1B77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B77

Chain ID: A

ChEMBL ID:

UniProt ID: O80164

Base Structure: X-ray

Registration Date: 2023-09-24

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2602919.628573
FMO2-HF: Nuclear repulsion 2514770.966612
FMO2-HF: Total energy -88148.661961
FMO2-MP2: Total energy -88405.851262


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-17.53-29.30963.228-22.133-29.315-0.094
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.030
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].
3A3LEU0-0.031-0.0142.091-2.748-0.2776.355-3.390-5.4360.014
4A4SER00.0360.0114.1700.1130.2540.001-0.043-0.0980.000
5A5LYS11.0050.9647.8170.6040.6040.0000.0000.0000.000
6A6ASP-1-0.905-0.93810.641-0.144-0.1440.0000.0000.0000.000
7A7THR0-0.028-0.0384.8660.2170.2170.0000.0000.0000.000
8A8ILE0-0.019-0.0087.1690.2250.2250.0000.0000.0000.000
9A9ALA0-0.030-0.0178.8940.1050.1050.0000.0000.0000.000
10A10ILE00.0190.01210.2010.0510.0510.0000.0000.0000.000
11A11LEU00.0130.0025.0980.0740.0740.0000.0000.0000.000
12A12LYS10.9400.9709.781-0.034-0.0340.0000.0000.0000.000
13A13ASN0-0.0170.02012.9120.0190.0190.0000.0000.0000.000
14A14PHE00.0550.04011.085-0.002-0.0020.0000.0000.0000.000
15A15ALA00.0220.02612.9410.0010.0010.0000.0000.0000.000
16A16SER0-0.113-0.07014.426-0.038-0.0380.0000.0000.0000.000
17A17ILE0-0.072-0.05116.492-0.034-0.0340.0000.0000.0000.000
18A18ASN0-0.069-0.05415.552-0.033-0.0330.0000.0000.0000.000
19A19SER00.0280.02615.1500.0270.0270.0000.0000.0000.000
20A20GLY00.0130.01713.7240.0110.0110.0000.0000.0000.000
21A21ILE0-0.048-0.0308.724-0.050-0.0500.0000.0000.0000.000
22A22LEU0-0.021-0.00610.5230.0460.0460.0000.0000.0000.000
23A23LEU0-0.0160.0023.745-0.525-0.2330.007-0.047-0.2510.000
24A24SER0-0.021-0.0287.226-0.080-0.0800.0000.0000.0000.000
25A25GLN0-0.043-0.0366.6130.1030.1030.0000.0000.0000.000
26A26GLY00.0090.0266.690-0.548-0.5480.0000.0000.0000.000
27A27LYS10.9190.9726.1130.0970.0970.0000.0000.0000.000
28A28PHE0-0.029-0.0237.818-0.233-0.2330.0000.0000.0000.000
29A29ILE00.0230.0326.1200.2970.2970.0000.0000.0000.000
30A30MET0-0.004-0.0018.968-0.233-0.2330.0000.0000.0000.000
31A31THR0-0.0070.00011.7550.1030.1030.0000.0000.0000.000
32A32ARG10.9430.96814.155-0.402-0.4020.0000.0000.0000.000
33A33ALA00.0110.03717.8600.0220.0220.0000.0000.0000.000
34A34VAL00.0680.03020.2520.0000.0000.0000.0000.0000.000
35A35ASN00.0040.01922.0810.0060.0060.0000.0000.0000.000
36A36GLY0-0.071-0.04422.921-0.014-0.0140.0000.0000.0000.000
37A37THR00.012-0.01823.939-0.001-0.0010.0000.0000.0000.000
38A38THR00.0390.02019.801-0.015-0.0150.0000.0000.0000.000
39A39TYR0-0.068-0.07316.6450.0460.0460.0000.0000.0000.000
40A40ALA00.0180.00515.269-0.046-0.0460.0000.0000.0000.000
41A41GLU-1-0.848-0.89813.2440.4810.4810.0000.0000.0000.000
42A42ALA00.020-0.00211.382-0.082-0.0820.0000.0000.0000.000
43A43ASN00.0010.01510.7400.1690.1690.0000.0000.0000.000
44A44ILE0-0.009-0.0054.861-0.078-0.0780.0000.0000.0000.000
45A45SER0-0.017-0.0248.7640.0430.0430.0000.0000.0000.000
46A46ASP-1-0.780-0.8453.532-1.271-1.0700.006-0.036-0.1710.000
47A47GLU-1-0.888-0.9744.4141.0081.267-0.001-0.057-0.2010.000
48A48ILE0-0.069-0.0262.311-3.544-1.5275.836-2.708-5.145-0.009
49A49ASP-1-0.829-0.9322.1357.6257.7896.297-1.062-5.399-0.025
50A50PHE0-0.048-0.0271.940-1.843-0.9582.544-1.014-2.4150.002
51A51ASP-1-0.850-0.9165.4682.9433.110-0.001-0.008-0.1590.000
52A52VAL0-0.013-0.0085.992-0.492-0.4920.0000.0000.0000.000
53A53ALA0-0.0130.0018.5310.2120.2120.0000.0000.0000.000
54A54LEU00.0060.0047.300-0.158-0.1580.0000.0000.0000.000
55A55TYR00.009-0.00111.469-0.074-0.0740.0000.0000.0000.000
56A56ASP-1-0.851-0.92314.2350.2440.2440.0000.0000.0000.000
57A57LEU00.0230.0088.475-0.014-0.0140.0000.0000.0000.000
58A58ASN00.0490.00911.481-0.048-0.0480.0000.0000.0000.000
59A59SER0-0.032-0.02913.934-0.087-0.0870.0000.0000.0000.000
60A60PHE00.0300.0235.997-0.083-0.0830.0000.0000.0000.000
61A61LEU00.000-0.0117.897-0.148-0.1480.0000.0000.0000.000
62A62SER0-0.074-0.04010.589-0.150-0.1500.0000.0000.0000.000
63A63ILE00.0170.04011.040-0.079-0.0790.0000.0000.0000.000
64A64LEU00.0080.0086.418-0.103-0.1030.0000.0000.0000.000
65A65SER0-0.151-0.09010.459-0.113-0.1130.0000.0000.0000.000
66A66LEU0-0.047-0.03013.3840.0090.0090.0000.0000.0000.000
67A67VAL0-0.0420.00010.0320.0040.0040.0000.0000.0000.000
68A68SER0-0.033-0.05811.9130.1030.1030.0000.0000.0000.000
69A69ASP-1-0.942-0.97410.553-0.953-0.9530.0000.0000.0000.000
70A70ASP-1-0.993-0.9978.705-1.739-1.7390.0000.0000.0000.000
71A71ALA0-0.007-0.0017.696-0.435-0.4350.0000.0000.0000.000
72A72GLU-1-0.882-0.9071.716-12.619-21.63816.955-5.117-2.818-0.034
73A73ILE0-0.023-0.0211.9092.3221.1967.132-2.225-3.7810.000
74A74SER00.0140.0201.723-5.762-14.14818.097-6.366-3.345-0.042
75A75MET00.0020.0064.2290.5090.6640.000-0.060-0.0960.000
76A76HIS0-0.025-0.0157.604-0.255-0.2550.0000.0000.0000.000
77A77THR0-0.009-0.02510.5890.1270.1270.0000.0000.0000.000
78A78ASP-1-0.894-0.95913.8890.0540.0540.0000.0000.0000.000
79A79GLY0-0.0120.00712.6220.0410.0410.0000.0000.0000.000
80A80ASN0-0.010-0.00211.7490.2590.2590.0000.0000.0000.000
81A81ILE00.0130.0156.062-0.059-0.0590.0000.0000.0000.000
82A82LYS10.9110.9577.4191.1451.1450.0000.0000.0000.000
83A83ILE00.0120.0096.418-0.638-0.6380.0000.0000.0000.000
84A84ALA0-0.034-0.0337.1390.5010.5010.0000.0000.0000.000
85A85ASP-1-0.736-0.8229.004-1.267-1.2670.0000.0000.0000.000
86A86THR0-0.038-0.02811.7460.0880.0880.0000.0000.0000.000
87A87ARG10.9060.94114.3970.5440.5440.0000.0000.0000.000
88A88SER0-0.0150.00114.9630.0800.0800.0000.0000.0000.000
89A89THR0-0.030-0.02211.121-0.149-0.1490.0000.0000.0000.000
90A90VAL00.0170.02711.5520.1520.1520.0000.0000.0000.000
91A91TYR00.000-0.00911.023-0.149-0.1490.0000.0000.0000.000
92A92TRP0-0.006-0.00610.303-0.021-0.0210.0000.0000.0000.000
93A93PRO0-0.019-0.00611.5190.0560.0560.0000.0000.0000.000
94A94ALA00.0330.03411.0500.1340.1340.0000.0000.0000.000
95A95ALA0-0.047-0.02812.419-0.122-0.1220.0000.0000.0000.000
96A96ASP-1-0.803-0.88714.3460.5480.5480.0000.0000.0000.000
97A97LYS10.9760.96113.954-0.902-0.9020.0000.0000.0000.000
98A98SER0-0.092-0.04416.602-0.021-0.0210.0000.0000.0000.000
99A99THR0-0.057-0.02717.957-0.037-0.0370.0000.0000.0000.000
100A100ILE00.0020.00613.778-0.014-0.0140.0000.0000.0000.000
101A101VAL0-0.0070.00217.815-0.006-0.0060.0000.0000.0000.000
102A102PHE0-0.013-0.01614.4670.0450.0450.0000.0000.0000.000
103A103PRO00.001-0.00314.656-0.057-0.0570.0000.0000.0000.000
104A104ASN00.0130.00115.8110.0690.0690.0000.0000.0000.000
105A105LYS10.9270.96317.257-0.366-0.3660.0000.0000.0000.000
106A106PRO00.0710.03415.965-0.019-0.0190.0000.0000.0000.000
107A107ILE0-0.050-0.01317.638-0.038-0.0380.0000.0000.0000.000
108A108GLN00.0060.00020.7490.0130.0130.0000.0000.0000.000
109A109PHE0-0.045-0.03223.275-0.010-0.0100.0000.0000.0000.000
110A110PRO00.0000.01325.340-0.004-0.0040.0000.0000.0000.000
111A111VAL00.0010.00328.934-0.001-0.0010.0000.0000.0000.000
112A112ALA0-0.028-0.02330.276-0.002-0.0020.0000.0000.0000.000
113A113SER0-0.0100.00331.894-0.002-0.0020.0000.0000.0000.000
114A114VAL00.0270.00534.006-0.008-0.0080.0000.0000.0000.000
115A115ILE0-0.042-0.01730.6640.0090.0090.0000.0000.0000.000
116A116THR00.0290.03131.634-0.010-0.0100.0000.0000.0000.000
117A117GLU-1-0.956-0.98729.7380.0670.0670.0000.0000.0000.000
118A118ILE00.0080.02727.712-0.005-0.0050.0000.0000.0000.000
119A119LYS10.9990.99628.343-0.031-0.0310.0000.0000.0000.000
120A120ALA00.0300.00726.3890.0030.0030.0000.0000.0000.000
121A121GLU-1-0.945-0.97527.6460.0080.0080.0000.0000.0000.000
122A122ASP-1-0.831-0.91230.6590.0390.0390.0000.0000.0000.000
123A123LEU0-0.016-0.00424.4690.0020.0020.0000.0000.0000.000
124A124GLN0-0.020-0.01927.837-0.001-0.0010.0000.0000.0000.000
125A125GLN00.0200.03428.8800.0020.0020.0000.0000.0000.000
126A126LEU00.0640.04130.1660.0000.0000.0000.0000.0000.000
127A127LEU00.009-0.00225.4130.0010.0010.0000.0000.0000.000
128A128ARG10.8330.92328.062-0.019-0.0190.0000.0000.0000.000
129A129VAL00.0140.00331.681-0.001-0.0010.0000.0000.0000.000
130A130SER00.009-0.00732.0270.0000.0000.0000.0000.0000.000
131A131ARG10.9310.97026.989-0.063-0.0630.0000.0000.0000.000
132A132GLY0-0.0210.00233.554-0.001-0.0010.0000.0000.0000.000
133A133LEU0-0.037-0.00936.868-0.003-0.0030.0000.0000.0000.000
134A134GLN0-0.047-0.02436.4630.0000.0000.0000.0000.0000.000
135A135ILE0-0.0250.00434.8830.0010.0010.0000.0000.0000.000
136A136ASP-1-0.783-0.89733.5370.0870.0870.0000.0000.0000.000
137A137THR0-0.041-0.01133.3560.0080.0080.0000.0000.0000.000
138A138ILE00.0240.00430.836-0.008-0.0080.0000.0000.0000.000
139A139ALA00.0070.00334.8930.0060.0060.0000.0000.0000.000
140A140ILE0-0.039-0.01531.493-0.005-0.0050.0000.0000.0000.000
141A141THR0-0.024-0.05836.0880.0020.0020.0000.0000.0000.000
142A142ASN00.0050.02239.4680.0000.0000.0000.0000.0000.000
143A143LYS10.9450.95441.794-0.048-0.0480.0000.0000.0000.000
144A144ASP-1-0.927-0.96644.3590.0410.0410.0000.0000.0000.000
145A145GLY00.0370.03045.327-0.002-0.0020.0000.0000.0000.000
146A146LYS10.8770.94041.251-0.041-0.0410.0000.0000.0000.000
147A147ILE0-0.0020.02135.8220.0030.0030.0000.0000.0000.000
148A148VAL0-0.038-0.02938.294-0.003-0.0030.0000.0000.0000.000
149A149ILE00.0190.01032.3430.0060.0060.0000.0000.0000.000
150A150ASN0-0.023-0.00236.648-0.009-0.0090.0000.0000.0000.000
151A151GLY00.0310.00436.8950.0060.0060.0000.0000.0000.000
152A152TYR00.005-0.01437.583-0.006-0.0060.0000.0000.0000.000
153A153ASN00.0490.02737.8500.0060.0060.0000.0000.0000.000
154A154LYS10.9250.94938.049-0.091-0.0910.0000.0000.0000.000
155A155VAL0-0.038-0.01538.734-0.001-0.0010.0000.0000.0000.000
156A156GLU-1-0.957-0.97141.2820.0480.0480.0000.0000.0000.000
157A157ASP-1-0.834-0.94642.9780.0560.0560.0000.0000.0000.000
158A158SER00.0050.00942.9370.0040.0040.0000.0000.0000.000
159A159GLY0-0.001-0.00943.2560.0040.0040.0000.0000.0000.000
160A160LEU0-0.042-0.00838.5870.0010.0010.0000.0000.0000.000
161A161THR0-0.054-0.02942.981-0.002-0.0020.0000.0000.0000.000
162A162ARG10.8580.93244.975-0.054-0.0540.0000.0000.0000.000
163A163PRO0-0.0130.01842.1450.0010.0010.0000.0000.0000.000
164A164LYS10.8830.93840.590-0.052-0.0520.0000.0000.0000.000
165A165TYR0-0.044-0.07835.368-0.002-0.0020.0000.0000.0000.000
166A166SER0-0.011-0.00239.4770.0030.0030.0000.0000.0000.000
167A167LEU00.0140.02733.418-0.004-0.0040.0000.0000.0000.000
168A168THR00.000-0.00637.6830.0040.0040.0000.0000.0000.000
169A169LEU0-0.056-0.02633.167-0.001-0.0010.0000.0000.0000.000
170A170THR0-0.006-0.00734.835-0.004-0.0040.0000.0000.0000.000
171A171ASP-1-0.858-0.92037.6420.0410.0410.0000.0000.0000.000
172A172TYR0-0.079-0.04639.6800.0060.0060.0000.0000.0000.000
173A173ASP-1-0.887-0.94741.5450.0470.0470.0000.0000.0000.000
174A174GLY0-0.072-0.04642.5230.0000.0000.0000.0000.0000.000
175A175SER0-0.030-0.01043.475-0.001-0.0010.0000.0000.0000.000
176A176ASN0-0.013-0.01441.721-0.001-0.0010.0000.0000.0000.000
177A177ASN0-0.012-0.00843.437-0.005-0.0050.0000.0000.0000.000
178A178PHE00.0400.00237.9340.0050.0050.0000.0000.0000.000
179A179ASN00.0050.04139.427-0.008-0.0080.0000.0000.0000.000
180A180PHE00.009-0.00934.0760.0030.0030.0000.0000.0000.000
181A181VAL00.0080.01635.127-0.003-0.0030.0000.0000.0000.000
182A182ILE00.0150.00028.9550.0100.0100.0000.0000.0000.000
183A183ASN00.0980.05129.540-0.018-0.0180.0000.0000.0000.000
184A184MET00.0060.00229.0470.0070.0070.0000.0000.0000.000
185A185ALA0-0.027-0.00727.7880.0030.0030.0000.0000.0000.000
186A186ASN0-0.037-0.03624.7520.0010.0010.0000.0000.0000.000
187A187MET00.0190.01123.9150.0190.0190.0000.0000.0000.000
188A188LYS10.8470.94020.174-0.222-0.2220.0000.0000.0000.000
189A189ILE00.0020.02319.8120.0180.0180.0000.0000.0000.000
190A190GLN00.0000.01215.799-0.016-0.0160.0000.0000.0000.000
191A191PRO0-0.0140.00419.9900.0000.0000.0000.0000.0000.000
192A192GLY00.0640.02121.193-0.004-0.0040.0000.0000.0000.000
193A193ASN0-0.021-0.00923.3030.0020.0020.0000.0000.0000.000
194A194TYR0-0.055-0.06320.5100.0140.0140.0000.0000.0000.000
195A195LYS10.9961.01325.190-0.129-0.1290.0000.0000.0000.000
196A196VAL0-0.039-0.03826.1270.0130.0130.0000.0000.0000.000
197A197MET0-0.045-0.02224.716-0.007-0.0070.0000.0000.0000.000
198A198LEU00.0410.01728.8330.0120.0120.0000.0000.0000.000
199A199TRP00.029-0.00130.4930.0010.0010.0000.0000.0000.000
200A200GLY00.0680.03032.5250.0040.0040.0000.0000.0000.000
201A201ALA0-0.051-0.01935.227-0.005-0.0050.0000.0000.0000.000
202A202GLY00.0090.00436.9000.0040.0040.0000.0000.0000.000
203A203ASP-1-0.897-0.95137.5030.1320.1320.0000.0000.0000.000
204A204LYS10.9040.96532.209-0.163-0.1630.0000.0000.0000.000
205A205VAL00.0470.02632.941-0.005-0.0050.0000.0000.0000.000
206A206ALA0-0.041-0.02127.5240.0110.0110.0000.0000.0000.000
207A207ALA00.0290.01527.650-0.012-0.0120.0000.0000.0000.000
208A208LYS10.9390.98621.507-0.208-0.2080.0000.0000.0000.000
209A209PHE0-0.010-0.00123.115-0.019-0.0190.0000.0000.0000.000
210A210GLU-1-0.913-0.97020.7500.1960.1960.0000.0000.0000.000
211A211SER00.0230.03219.327-0.025-0.0250.0000.0000.0000.000
212A212SER0-0.050-0.03519.7570.0170.0170.0000.0000.0000.000
213A213GLN00.0190.00115.1980.0120.0120.0000.0000.0000.000
214A214VAL00.0000.00914.0660.0340.0340.0000.0000.0000.000
215A215SER00.0220.01416.441-0.043-0.0430.0000.0000.0000.000
216A216TYR0-0.017-0.03717.3280.0270.0270.0000.0000.0000.000
217A217VAL0-0.033-0.01720.188-0.021-0.0210.0000.0000.0000.000
218A218ILE0-0.035-0.02222.5990.0190.0190.0000.0000.0000.000
219A219ALA0-0.013-0.00225.107-0.011-0.0110.0000.0000.0000.000
220A220MET0-0.030-0.00827.924-0.007-0.0070.0000.0000.0000.000
221A221GLU-1-0.892-0.95031.3400.1430.1430.0000.0000.0000.000
222A222ALA00.0140.01534.277-0.002-0.0020.0000.0000.0000.000
223A223ASP-1-0.912-0.95837.2060.0970.0970.0000.0000.0000.000
224A224SER0-0.027-0.02835.630-0.006-0.0060.0000.0000.0000.000
225A225THR0-0.039-0.01738.235-0.001-0.0010.0000.0000.0000.000
226A226HIS0-0.078-0.04938.516-0.003-0.0030.0000.0000.0000.000
227A227ASP-1-0.825-0.89740.9040.0730.0730.0000.0000.0000.000
228A228PHE0-0.033-0.00738.9060.0000.0000.0000.0000.0000.000