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: 6GYZZ

Calculation Name: 1YQ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQ1

Chain ID: A

ChEMBL ID:

UniProt ID: Q93698

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2413167.760002
FMO2-HF: Nuclear repulsion 2332219.804306
FMO2-HF: Total energy -80947.955696
FMO2-MP2: Total energy -81189.849458


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.
-1.612-0.759-0.009-0.405-0.4370.001
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 : -0.035 / q_NPA : -0.040
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].
3A3SER0-0.029-0.0103.896-1.112-0.200-0.008-0.393-0.5100.001
4A4TYR0-0.010-0.0276.6610.8470.8470.0000.0000.0000.000
5A5LYS10.9350.9869.8890.6220.6220.0000.0000.0000.000
6A6LEU00.0310.02212.9570.1140.1140.0000.0000.0000.000
7A7THR0-0.0100.01116.584-0.030-0.0300.0000.0000.0000.000
8A8TYR00.039-0.00119.3390.0490.0490.0000.0000.0000.000
9A9PHE00.0090.04222.723-0.018-0.0180.0000.0000.0000.000
10A10PHE00.0330.00925.083-0.012-0.0120.0000.0000.0000.000
11A11PHE00.0040.01326.529-0.003-0.0030.0000.0000.0000.000
12A12ARG10.9480.97226.7250.1160.1160.0000.0000.0000.000
13A13GLY0-0.075-0.04026.864-0.003-0.0030.0000.0000.0000.000
14A14LEU00.031-0.00726.6000.0040.0040.0000.0000.0000.000
15A15GLY00.0440.02423.3510.0060.0060.0000.0000.0000.000
16A16GLU-1-0.752-0.82822.537-0.222-0.2220.0000.0000.0000.000
17A17PRO0-0.011-0.00423.358-0.013-0.0130.0000.0000.0000.000
18A18ILE00.0190.00418.2090.0050.0050.0000.0000.0000.000
19A19ARG10.7700.87418.9550.2330.2330.0000.0000.0000.000
20A20LEU0-0.023-0.02119.466-0.019-0.0190.0000.0000.0000.000
21A21LEU00.0190.01518.0340.0040.0040.0000.0000.0000.000
22A22PHE00.0380.01012.2700.0010.0010.0000.0000.0000.000
23A23HIS0-0.067-0.02515.676-0.064-0.0640.0000.0000.0000.000
24A24LEU0-0.060-0.01618.2140.0020.0020.0000.0000.0000.000
25A25ALA0-0.038-0.01315.7460.0200.0200.0000.0000.0000.000
26A26GLY00.0190.01615.3320.0220.0220.0000.0000.0000.000
27A27VAL0-0.086-0.02910.248-0.056-0.0560.0000.0000.0000.000
28A28GLN0-0.017-0.0238.247-0.085-0.0850.0000.0000.0000.000
29A29PHE0-0.022-0.0189.585-0.137-0.1370.0000.0000.0000.000
30A30GLU-1-0.913-0.95310.781-1.086-1.0860.0000.0000.0000.000
31A31GLU-1-0.873-0.94113.171-0.278-0.2780.0000.0000.0000.000
32A32VAL0-0.001-0.01216.073-0.007-0.0070.0000.0000.0000.000
33A33ARG10.9300.96018.5730.3830.3830.0000.0000.0000.000
34A34MET00.0200.00221.2340.0100.0100.0000.0000.0000.000
35A35ASN00.0730.00824.4640.0060.0060.0000.0000.0000.000
36A36PRO0-0.038-0.01528.0310.0070.0070.0000.0000.0000.000
37A37ASP-1-0.899-0.94230.445-0.096-0.0960.0000.0000.0000.000
38A38GLN0-0.066-0.04929.0670.0050.0050.0000.0000.0000.000
39A39THR0-0.066-0.02327.767-0.005-0.0050.0000.0000.0000.000
40A40TRP00.0280.02428.0630.0150.0150.0000.0000.0000.000
41A41LEU00.0200.01429.000-0.001-0.0010.0000.0000.0000.000
42A42ASP-1-0.813-0.92828.957-0.043-0.0430.0000.0000.0000.000
43A43ILE0-0.065-0.03323.8240.0020.0020.0000.0000.0000.000
44A44LYS10.8740.93025.0600.0570.0570.0000.0000.0000.000
45A45ASP-1-0.881-0.94726.833-0.006-0.0060.0000.0000.0000.000
46A46SER0-0.028-0.00323.4770.0080.0080.0000.0000.0000.000
47A47THR00.0030.01922.051-0.010-0.0100.0000.0000.0000.000
48A48PRO00.0190.02519.9500.0120.0120.0000.0000.0000.000
49A49MET0-0.030-0.01722.9070.0120.0120.0000.0000.0000.000
50A50LYS10.8680.93426.056-0.004-0.0040.0000.0000.0000.000
51A51GLN0-0.030-0.03425.665-0.013-0.0130.0000.0000.0000.000
52A52LEU0-0.0140.05322.608-0.006-0.0060.0000.0000.0000.000
53A53PRO0-0.068-0.04921.0660.0110.0110.0000.0000.0000.000
54A54VAL00.014-0.00817.4980.0290.0290.0000.0000.0000.000
55A55LEU00.0080.01813.393-0.047-0.0470.0000.0000.0000.000
56A56ASN0-0.024-0.02312.3200.0410.0410.0000.0000.0000.000
57A57ILE00.0080.0068.195-0.140-0.1400.0000.0000.0000.000
58A58ASP-1-0.795-0.8895.177-1.171-1.230-0.001-0.0120.0730.000
59A59GLY0-0.038-0.0078.6050.3000.3000.0000.0000.0000.000
60A60PHE00.0090.02611.5110.1260.1260.0000.0000.0000.000
61A61GLU-1-0.901-0.99013.087-0.143-0.1430.0000.0000.0000.000
62A62LEU0-0.0450.00916.1910.0480.0480.0000.0000.0000.000
63A63PRO00.0430.00518.509-0.038-0.0380.0000.0000.0000.000
64A64GLN00.0320.01221.973-0.009-0.0090.0000.0000.0000.000
65A65SER00.0310.03122.6560.0030.0030.0000.0000.0000.000
66A66GLY00.0510.02523.172-0.004-0.0040.0000.0000.0000.000
67A67ALA0-0.006-0.00122.2970.0090.0090.0000.0000.0000.000
68A68ILE0-0.024-0.04817.8450.0150.0150.0000.0000.0000.000
69A69LEU0-0.0030.00618.932-0.003-0.0030.0000.0000.0000.000
70A70ARG10.9210.94920.120-0.035-0.0350.0000.0000.0000.000
71A71TYR0-0.030-0.01413.7060.0230.0230.0000.0000.0000.000
72A72LEU0-0.003-0.00413.9830.0320.0320.0000.0000.0000.000
73A73ALA00.0440.02416.5660.0220.0220.0000.0000.0000.000
74A74ARG10.9430.97819.073-0.115-0.1150.0000.0000.0000.000
75A75LYS10.8950.95710.634-0.190-0.1900.0000.0000.0000.000
76A76PHE0-0.078-0.05511.9200.0040.0040.0000.0000.0000.000
77A77GLY00.0280.04116.195-0.011-0.0110.0000.0000.0000.000
78A78PHE00.014-0.00518.158-0.012-0.0120.0000.0000.0000.000
79A79ALA0-0.005-0.01422.052-0.014-0.0140.0000.0000.0000.000
80A80GLY00.0790.03523.685-0.003-0.0030.0000.0000.0000.000
81A81LYS10.8460.93525.372-0.021-0.0210.0000.0000.0000.000
82A82THR00.0340.03126.8500.0100.0100.0000.0000.0000.000
83A83PRO00.0710.02928.457-0.006-0.0060.0000.0000.0000.000
84A84GLU-1-0.906-0.96229.6970.0710.0710.0000.0000.0000.000
85A85GLU-1-0.831-0.92929.7210.0240.0240.0000.0000.0000.000
86A86GLU-1-0.912-0.96424.7530.0950.0950.0000.0000.0000.000
87A87ALA00.0090.01428.521-0.008-0.0080.0000.0000.0000.000
88A88TRP0-0.012-0.00931.217-0.010-0.0100.0000.0000.0000.000
89A89VAL0-0.0100.00326.645-0.010-0.0100.0000.0000.0000.000
90A90ASP-1-0.869-0.93427.3650.0380.0380.0000.0000.0000.000
91A91ALA00.0250.02029.789-0.006-0.0060.0000.0000.0000.000
92A92VAL0-0.015-0.00831.230-0.006-0.0060.0000.0000.0000.000
93A93HIS0-0.057-0.03727.158-0.007-0.0070.0000.0000.0000.000
94A94ASP-1-0.880-0.94830.9890.0100.0100.0000.0000.0000.000
95A95LEU00.0050.02233.268-0.004-0.0040.0000.0000.0000.000
96A96PHE00.003-0.00529.898-0.007-0.0070.0000.0000.0000.000
97A97LYS10.8950.95429.0000.0220.0220.0000.0000.0000.000
98A98ASP-1-0.870-0.92633.930-0.005-0.0050.0000.0000.0000.000
99A99PHE0-0.005-0.01336.830-0.003-0.0030.0000.0000.0000.000
100A100LEU0-0.068-0.03032.346-0.005-0.0050.0000.0000.0000.000
101A101ALA0-0.031-0.03136.340-0.004-0.0040.0000.0000.0000.000
102A102GLU-1-0.905-0.96238.186-0.018-0.0180.0000.0000.0000.000
103A103PHE0-0.045-0.01937.010-0.002-0.0020.0000.0000.0000.000
104A104LYS10.8900.94433.6440.0540.0540.0000.0000.0000.000
105A105LYS10.9290.96439.5990.0190.0190.0000.0000.0000.000
106A106PHE00.0080.02542.5970.0010.0010.0000.0000.0000.000
107A107ALA00.008-0.01540.741-0.001-0.0010.0000.0000.0000.000
108A108ALA0-0.050-0.02942.412-0.002-0.0020.0000.0000.0000.000
109A109GLU-1-0.849-0.93243.758-0.028-0.0280.0000.0000.0000.000
110A110ARG10.8370.93444.5550.0520.0520.0000.0000.0000.000
111A111ARG10.8900.93640.4380.0630.0630.0000.0000.0000.000
112A112SER0-0.036-0.01747.601-0.001-0.0010.0000.0000.0000.000
113A113GLY00.0260.05849.1270.0020.0020.0000.0000.0000.000
114A114LYS10.8410.87951.1120.0340.0340.0000.0000.0000.000
115A115SER0-0.043-0.05354.4590.0000.0000.0000.0000.0000.000
116A116ALA0-0.025-0.00857.149-0.002-0.0020.0000.0000.0000.000
117A117GLU-1-0.858-0.90959.702-0.028-0.0280.0000.0000.0000.000
118A118GLU-1-0.822-0.86353.610-0.031-0.0310.0000.0000.0000.000
119A119VAL0-0.029-0.01755.283-0.002-0.0020.0000.0000.0000.000
120A120GLU-1-0.778-0.89553.197-0.024-0.0240.0000.0000.0000.000
121A121LYS10.8050.87652.3180.0290.0290.0000.0000.0000.000
122A122PHE00.0550.04053.2820.0000.0000.0000.0000.0000.000
123A123ARG10.9921.01245.5340.0260.0260.0000.0000.0000.000
124A124SER0-0.005-0.03949.346-0.001-0.0010.0000.0000.0000.000
125A125GLU-1-0.927-0.94850.434-0.026-0.0260.0000.0000.0000.000
126A126PHE0-0.019-0.02447.6220.0020.0020.0000.0000.0000.000
127A127PHE00.024-0.00642.1800.0010.0010.0000.0000.0000.000
128A128LEU00.0450.03546.0080.0000.0000.0000.0000.0000.000
129A129PRO00.0000.02447.4050.0000.0000.0000.0000.0000.000
130A130ALA00.0500.03943.9930.0020.0020.0000.0000.0000.000
131A131ARG10.8630.94442.5190.0350.0350.0000.0000.0000.000
132A132ASN0-0.015-0.03343.359-0.002-0.0020.0000.0000.0000.000
133A133THR00.0130.02243.8800.0010.0010.0000.0000.0000.000
134A134TYR00.0490.01535.6860.0020.0020.0000.0000.0000.000
135A135PHE00.019-0.01339.016-0.001-0.0010.0000.0000.0000.000
136A136ASN00.0250.02842.039-0.002-0.0020.0000.0000.0000.000
137A137ILE0-0.0480.00238.4740.0010.0010.0000.0000.0000.000
138A138LEU00.018-0.01035.8120.0010.0010.0000.0000.0000.000
139A139ASN0-0.052-0.03539.1860.0000.0000.0000.0000.0000.000
140A140GLY00.0330.01841.8700.0010.0010.0000.0000.0000.000
141A141LEU0-0.073-0.03636.0780.0030.0030.0000.0000.0000.000
142A142LEU00.029-0.00436.4920.0000.0000.0000.0000.0000.000
143A143GLU-1-0.994-0.97039.099-0.011-0.0110.0000.0000.0000.000
144A144LYS10.8480.93440.272-0.008-0.0080.0000.0000.0000.000
145A145SER0-0.003-0.00135.6010.0030.0030.0000.0000.0000.000
146A146ASN0-0.012-0.01436.030-0.003-0.0030.0000.0000.0000.000
147A147SER0-0.004-0.04031.997-0.004-0.0040.0000.0000.0000.000
148A148GLY0-0.061-0.03034.400-0.006-0.0060.0000.0000.0000.000
149A149PHE0-0.015-0.00529.430-0.009-0.0090.0000.0000.0000.000
150A150LEU0-0.016-0.00131.9030.0060.0060.0000.0000.0000.000
151A151ILE0-0.052-0.03229.9740.0050.0050.0000.0000.0000.000
152A152GLY00.0940.05430.535-0.001-0.0010.0000.0000.0000.000
153A153SER0-0.038-0.03529.762-0.002-0.0020.0000.0000.0000.000
154A154ASP-1-0.903-0.90326.105-0.036-0.0360.0000.0000.0000.000
155A155ILE0-0.0210.00724.5960.0010.0010.0000.0000.0000.000
156A156THR00.013-0.00425.3120.0130.0130.0000.0000.0000.000
157A157PHE0-0.033-0.03822.803-0.014-0.0140.0000.0000.0000.000
158A158ALA00.0300.01524.674-0.009-0.0090.0000.0000.0000.000
159A159ASP-1-0.734-0.88128.311-0.039-0.0390.0000.0000.0000.000
160A160LEU0-0.034-0.00322.482-0.006-0.0060.0000.0000.0000.000
161A161VAL0-0.016-0.01826.791-0.007-0.0070.0000.0000.0000.000
162A162VAL0-0.0110.00728.602-0.002-0.0020.0000.0000.0000.000
163A163VAL00.0370.00229.674-0.001-0.0010.0000.0000.0000.000
164A164ASP-1-0.832-0.91628.650-0.124-0.1240.0000.0000.0000.000
165A165ASN00.017-0.01330.7250.0040.0040.0000.0000.0000.000
166A166LEU00.0450.03933.5260.0010.0010.0000.0000.0000.000
167A167LEU0-0.059-0.01331.602-0.001-0.0010.0000.0000.0000.000
168A168THR0-0.061-0.03633.102-0.001-0.0010.0000.0000.0000.000
169A169LEU0-0.021-0.01035.6880.0020.0020.0000.0000.0000.000
170A170LYS10.9470.99038.1470.0740.0740.0000.0000.0000.000
171A171ASN00.0110.01735.5070.0050.0050.0000.0000.0000.000
172A172TYR0-0.086-0.03337.6210.0020.0020.0000.0000.0000.000
173A173GLY0-0.020-0.02341.7680.0040.0040.0000.0000.0000.000
174A174LEU0-0.079-0.03242.1480.0040.0040.0000.0000.0000.000
175A175PHE0-0.039-0.04739.2100.0030.0030.0000.0000.0000.000
176A176ASP-1-0.815-0.87642.943-0.050-0.0500.0000.0000.0000.000
177A177GLU-1-0.888-0.98038.918-0.065-0.0650.0000.0000.0000.000
178A178SER0-0.012-0.01342.6360.0020.0020.0000.0000.0000.000
179A179GLU-1-1.018-1.01146.036-0.029-0.0290.0000.0000.0000.000
180A180PHE00.0280.01343.0370.0030.0030.0000.0000.0000.000
181A181THR00.0490.00942.779-0.002-0.0020.0000.0000.0000.000
182A182LYS10.9520.98241.5170.0190.0190.0000.0000.0000.000
183A183LEU00.0400.00638.020-0.002-0.0020.0000.0000.0000.000
184A184ALA00.0010.02037.569-0.004-0.0040.0000.0000.0000.000
185A185ALA00.0070.00137.600-0.005-0.0050.0000.0000.0000.000
186A186LEU0-0.025-0.00232.670-0.004-0.0040.0000.0000.0000.000
187A187ARG10.9300.93833.3580.0780.0780.0000.0000.0000.000
188A188GLU-1-0.904-0.95132.873-0.094-0.0940.0000.0000.0000.000
189A189LYS10.9620.99831.9090.0380.0380.0000.0000.0000.000
190A190VAL00.0040.01527.406-0.004-0.0040.0000.0000.0000.000
191A191ASN0-0.035-0.02727.810-0.017-0.0170.0000.0000.0000.000
192A192SER0-0.114-0.06528.412-0.014-0.0140.0000.0000.0000.000
193A193TYR0-0.0030.00323.744-0.006-0.0060.0000.0000.0000.000
194A194PRO00.0150.01423.920-0.017-0.0170.0000.0000.0000.000
195A195GLY00.0600.03221.3020.0020.0020.0000.0000.0000.000
196A196ILE0-0.057-0.02721.937-0.026-0.0260.0000.0000.0000.000
197A197LYS10.9470.98623.9690.1180.1180.0000.0000.0000.000
198A198GLU-1-0.888-0.96322.758-0.195-0.1950.0000.0000.0000.000
199A199TYR0-0.048-0.05421.074-0.005-0.0050.0000.0000.0000.000
200A200ILE0-0.038-0.03323.113-0.003-0.0030.0000.0000.0000.000
201A201ALA0-0.042-0.01526.5200.0080.0080.0000.0000.0000.000
202A202LYS10.8990.94820.5480.3550.3550.0000.0000.0000.000
203A203ARG10.8810.96825.0850.1530.1530.0000.0000.0000.000
204A204PRO0-0.032-0.02126.0600.0130.0130.0000.0000.0000.000
205A205VAL00.0110.01029.1690.0110.0110.0000.0000.0000.000