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: QYKGY

Calculation Name: 1CBY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CBY

Chain ID: A

ChEMBL ID:

UniProt ID: Q04470

Base Structure: X-ray

Registration Date: 2023-06-22

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 227
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2784193.968367
FMO2-HF: Nuclear repulsion 2695832.432865
FMO2-HF: Total energy -88361.535502
FMO2-MP2: Total energy -88623.658078


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:19:CYM)


Summations of interaction energy for fragment #1(A:19:CYM)
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.
9.83111.43-0.011-0.833-0.7550.005
Interaction energy analysis for fragmet #1(A:19:CYM)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.910 / q_NPA : -0.955
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].
3A21ALA00.0180.0073.803-0.6110.988-0.011-0.833-0.7550.005
4A22PRO0-0.004-0.0056.124-1.804-1.8040.0000.0000.0000.000
5A23ILE00.0150.0038.832-1.403-1.4030.0000.0000.0000.000
6A24ILE0-0.0040.00412.078-0.834-0.8340.0000.0000.0000.000
7A25ARG10.9610.97314.895-16.296-16.2960.0000.0000.0000.000
8A26LYS10.9180.96918.588-11.511-11.5110.0000.0000.0000.000
9A27PRO00.0150.01320.910-0.122-0.1220.0000.0000.0000.000
10A28PHE00.0450.00422.528-0.541-0.5410.0000.0000.0000.000
11A29LYS10.9440.97524.685-10.681-10.6810.0000.0000.0000.000
12A30HIS00.0460.02226.579-0.127-0.1270.0000.0000.0000.000
13A31ILE0-0.022-0.02728.2160.2080.2080.0000.0000.0000.000
14A32VAL00.0360.03431.165-0.144-0.1440.0000.0000.0000.000
15A33LEU0-0.023-0.02133.6990.0250.0250.0000.0000.0000.000
16A34THR00.0420.03636.722-0.053-0.0530.0000.0000.0000.000
17A35VAL0-0.024-0.01739.7780.0520.0520.0000.0000.0000.000
18A36PRO0-0.028-0.01342.281-0.066-0.0660.0000.0000.0000.000
19A37SER00.0310.00646.0890.0300.0300.0000.0000.0000.000
20A38SER0-0.004-0.00548.010-0.107-0.1070.0000.0000.0000.000
21A39ASP-1-0.826-0.91050.7195.6175.6170.0000.0000.0000.000
22A40LEU0-0.043-0.02150.8020.1220.1220.0000.0000.0000.000
23A41ASP-1-0.813-0.90045.4886.8606.8600.0000.0000.0000.000
24A42ASN0-0.044-0.02048.2150.0320.0320.0000.0000.0000.000
25A43PHE0-0.002-0.02244.914-0.032-0.0320.0000.0000.0000.000
26A44ASN0-0.0090.02639.1800.1740.1740.0000.0000.0000.000
27A45THR00.003-0.01539.943-0.009-0.0090.0000.0000.0000.000
28A46VAL0-0.020-0.00234.9290.2500.2500.0000.0000.0000.000
29A47PHE00.000-0.01736.247-0.130-0.1300.0000.0000.0000.000
30A48TYR0-0.0190.00729.2410.4890.4890.0000.0000.0000.000
31A49VAL00.0330.01634.357-0.122-0.1220.0000.0000.0000.000
32A50GLN00.0050.01833.4640.1530.1530.0000.0000.0000.000
33A51PRO00.032-0.00333.545-0.206-0.2060.0000.0000.0000.000
34A52GLN00.0140.01836.450-0.030-0.0300.0000.0000.0000.000
35A53TYR00.0440.00938.185-0.280-0.2800.0000.0000.0000.000
36A54ILE00.0180.02036.060-0.079-0.0790.0000.0000.0000.000
37A55ASN00.0310.00240.329-0.138-0.1380.0000.0000.0000.000
38A56GLN00.005-0.00543.5990.0230.0230.0000.0000.0000.000
39A57ALA00.011-0.00241.166-0.116-0.1160.0000.0000.0000.000
40A58LEU00.0090.00043.079-0.049-0.0490.0000.0000.0000.000
41A59HIS0-0.036-0.01044.682-0.240-0.2400.0000.0000.0000.000
42A60LEU0-0.014-0.01545.259-0.118-0.1180.0000.0000.0000.000
43A61ALA00.001-0.00544.454-0.081-0.0810.0000.0000.0000.000
44A62ASN00.008-0.00346.5830.0110.0110.0000.0000.0000.000
45A63ALA0-0.0080.00149.554-0.132-0.1320.0000.0000.0000.000
46A64PHE0-0.029-0.02848.467-0.133-0.1330.0000.0000.0000.000
47A65GLN00.0420.02747.645-0.097-0.0970.0000.0000.0000.000
48A66GLY0-0.0150.00951.873-0.079-0.0790.0000.0000.0000.000
49A67ALA0-0.007-0.01052.821-0.138-0.1380.0000.0000.0000.000
50A68ILE0-0.027-0.00650.524-0.042-0.0420.0000.0000.0000.000
51A69ASP-1-0.864-0.92754.4845.1935.1930.0000.0000.0000.000
52A70PRO00.005-0.01157.3250.0410.0410.0000.0000.0000.000
53A71LEU0-0.032-0.00458.450-0.008-0.0080.0000.0000.0000.000
54A72ASN0-0.067-0.05059.094-0.047-0.0470.0000.0000.0000.000
55A73LEU00.0100.01353.6070.0690.0690.0000.0000.0000.000
56A74ASN0-0.0020.00053.6990.2200.2200.0000.0000.0000.000
57A75PHE00.0140.02050.099-0.071-0.0710.0000.0000.0000.000
58A76ASN00.0140.00453.753-0.043-0.0430.0000.0000.0000.000
59A77PHE00.025-0.00452.4480.0290.0290.0000.0000.0000.000
60A78GLU-1-0.853-0.93155.7245.3395.3390.0000.0000.0000.000
61A79LYS10.8730.92257.959-5.402-5.4020.0000.0000.0000.000
62A80ALA00.0430.02752.9190.0220.0220.0000.0000.0000.000
63A81LEU00.0300.00954.5930.0650.0650.0000.0000.0000.000
64A82GLN0-0.046-0.01156.3740.0170.0170.0000.0000.0000.000
65A83ILE0-0.0200.00453.736-0.037-0.0370.0000.0000.0000.000
66A84ALA00.0160.00653.1170.0340.0340.0000.0000.0000.000
67A85ASN0-0.107-0.06654.2710.0490.0490.0000.0000.0000.000
68A86GLY00.0150.01456.502-0.099-0.0990.0000.0000.0000.000
69A87ILE0-0.039-0.00750.849-0.011-0.0110.0000.0000.0000.000
70A88PRO00.0180.01953.561-0.018-0.0180.0000.0000.0000.000
71A89ASN0-0.023-0.02451.8330.0500.0500.0000.0000.0000.000
72A90SER00.010-0.00450.4480.1630.1630.0000.0000.0000.000
73A91ALA00.0130.00550.427-0.132-0.1320.0000.0000.0000.000
74A92ILE00.0070.00349.9950.1470.1470.0000.0000.0000.000
75A93VAL0-0.025-0.00245.918-0.069-0.0690.0000.0000.0000.000
76A94LYS10.9000.94947.641-6.435-6.4350.0000.0000.0000.000
77A95THR00.0200.01649.1370.0620.0620.0000.0000.0000.000
78A96LEU00.001-0.00947.5960.0020.0020.0000.0000.0000.000
79A97ASN00.0290.00651.0340.0500.0500.0000.0000.0000.000
80A98GLN0-0.030-0.00151.354-0.137-0.1370.0000.0000.0000.000
81A99SER00.024-0.00451.4000.0970.0970.0000.0000.0000.000
82A100VAL0-0.052-0.02846.620-0.015-0.0150.0000.0000.0000.000
83A101ILE0-0.017-0.00844.4770.1060.1060.0000.0000.0000.000
84A102GLN0-0.042-0.03648.527-0.101-0.1010.0000.0000.0000.000
85A103GLN0-0.042-0.02247.356-0.045-0.0450.0000.0000.0000.000
86A104THR00.0150.01047.3940.0080.0080.0000.0000.0000.000
87A105VAL0-0.050-0.02143.4670.0240.0240.0000.0000.0000.000
88A106GLU-1-0.820-0.86637.2278.2438.2430.0000.0000.0000.000
89A107ILE0-0.009-0.02638.2620.0420.0420.0000.0000.0000.000
90A108SER0-0.065-0.06135.1750.0190.0190.0000.0000.0000.000
91A109VAL00.0470.02536.7990.0490.0490.0000.0000.0000.000
92A110MET0-0.0340.00138.825-0.113-0.1130.0000.0000.0000.000
93A111VAL0-0.011-0.01435.074-0.030-0.0300.0000.0000.0000.000
94A112GLU-1-0.933-0.96434.4358.8178.8170.0000.0000.0000.000
95A113GLN00.007-0.00137.2910.0360.0360.0000.0000.0000.000
96A114LEU00.0170.00740.422-0.067-0.0670.0000.0000.0000.000
97A115LYS10.8650.92830.895-9.628-9.6280.0000.0000.0000.000
98A116LYS10.8560.93038.081-7.583-7.5830.0000.0000.0000.000
99A117ILE0-0.005-0.01239.452-0.114-0.1140.0000.0000.0000.000
100A118ILE0-0.010-0.00439.309-0.102-0.1020.0000.0000.0000.000
101A119GLN0-0.007-0.00536.030-0.186-0.1860.0000.0000.0000.000
102A120GLU-1-0.913-0.94439.5397.1787.1780.0000.0000.0000.000
103A121VAL0-0.047-0.03442.938-0.122-0.1220.0000.0000.0000.000
104A122LEU0-0.0090.01438.331-0.101-0.1010.0000.0000.0000.000
105A123GLY00.0160.02742.579-0.069-0.0690.0000.0000.0000.000
106A124LEU0-0.053-0.03740.1510.0810.0810.0000.0000.0000.000
107A125VAL00.0010.00036.6140.1090.1090.0000.0000.0000.000
108A126ILE0-0.0020.00332.9440.0740.0740.0000.0000.0000.000
109A127ASN0-0.064-0.04530.1530.2610.2610.0000.0000.0000.000
110A128SER00.032-0.01928.1120.3140.3140.0000.0000.0000.000
111A129THR0-0.0030.00123.815-0.060-0.0600.0000.0000.0000.000
112A130SER00.0220.00025.353-0.025-0.0250.0000.0000.0000.000
113A131PHE00.0530.04727.215-0.159-0.1590.0000.0000.0000.000
114A132TRP00.0480.00530.140-0.260-0.2600.0000.0000.0000.000
115A133ASN0-0.031-0.01625.109-0.300-0.3000.0000.0000.0000.000
116A134SER0-0.020-0.01129.352-0.100-0.1000.0000.0000.0000.000
117A135VAL0-0.0080.01631.752-0.200-0.2000.0000.0000.0000.000
118A136GLU-1-0.813-0.88630.7189.7319.7310.0000.0000.0000.000
119A137ALA0-0.037-0.01930.740-0.148-0.1480.0000.0000.0000.000
120A138THR00.030-0.00832.766-0.162-0.1620.0000.0000.0000.000
121A139ILE0-0.0090.00336.182-0.201-0.2010.0000.0000.0000.000
122A140LYS10.8940.94030.508-9.990-9.9900.0000.0000.0000.000
123A141GLY00.0240.03136.466-0.126-0.1260.0000.0000.0000.000
124A142THR0-0.0050.01537.745-0.208-0.2080.0000.0000.0000.000
125A143PHE0-0.022-0.02139.977-0.234-0.2340.0000.0000.0000.000
126A144THR0-0.064-0.03336.8890.0420.0420.0000.0000.0000.000
127A145ASN00.0180.00034.170-0.022-0.0220.0000.0000.0000.000
128A146LEU00.0270.01438.635-0.023-0.0230.0000.0000.0000.000
129A147ASP-1-0.852-0.91939.8547.7867.7860.0000.0000.0000.000
130A148THR0-0.112-0.05937.091-0.005-0.0050.0000.0000.0000.000
131A149GLN0-0.020-0.01339.659-0.007-0.0070.0000.0000.0000.000
132A150ILE0-0.061-0.02542.484-0.176-0.1760.0000.0000.0000.000
133A151ASP-1-0.937-0.97645.8956.4296.4290.0000.0000.0000.000
134A152GLU-1-0.919-0.94142.4647.2647.2640.0000.0000.0000.000
135A153ALA00.005-0.00846.252-0.092-0.0920.0000.0000.0000.000
136A154TRP0-0.075-0.02040.934-0.124-0.1240.0000.0000.0000.000
137A155ILE0-0.019-0.01245.4390.0030.0030.0000.0000.0000.000
138A156PHE00.0050.01747.812-0.087-0.0870.0000.0000.0000.000
139A157TRP00.0730.00546.537-0.052-0.0520.0000.0000.0000.000
140A158HIS00.0280.01752.573-0.185-0.1850.0000.0000.0000.000
141A159SER0-0.029-0.03655.3460.0210.0210.0000.0000.0000.000
142A160LEU0-0.0430.00752.7940.0200.0200.0000.0000.0000.000
143A161SER0-0.030-0.01655.974-0.169-0.1690.0000.0000.0000.000
144A162ALA0-0.016-0.01255.7560.0980.0980.0000.0000.0000.000
145A163HIS00.006-0.00755.6410.1230.1230.0000.0000.0000.000
146A164ASN0-0.034-0.01854.245-0.003-0.0030.0000.0000.0000.000
147A165THR00.022-0.00349.833-0.034-0.0340.0000.0000.0000.000
148A166SER0-0.0080.01051.7420.0720.0720.0000.0000.0000.000
149A167TYR0-0.025-0.04344.482-0.047-0.0470.0000.0000.0000.000
150A168TYR0-0.041-0.00850.270-0.020-0.0200.0000.0000.0000.000
151A169TYR00.036-0.00740.7970.0620.0620.0000.0000.0000.000
152A170ASN0-0.032-0.00246.555-0.043-0.0430.0000.0000.0000.000
153A171ILE00.0190.00140.5030.1280.1280.0000.0000.0000.000
154A172LEU00.0030.01542.182-0.152-0.1520.0000.0000.0000.000
155A173PHE00.0000.00636.6330.2190.2190.0000.0000.0000.000
156A174SER00.0210.01139.064-0.201-0.2010.0000.0000.0000.000
157A175ILE0-0.038-0.02034.6000.2600.2600.0000.0000.0000.000
158A176GLN00.036-0.01136.502-0.154-0.1540.0000.0000.0000.000
159A177ASN0-0.043-0.05932.1940.0110.0110.0000.0000.0000.000
160A178GLU-1-0.898-0.94831.0729.6059.6050.0000.0000.0000.000
161A179ASP-1-0.798-0.86133.2719.1649.1640.0000.0000.0000.000
162A180THR0-0.035-0.01836.087-0.124-0.1240.0000.0000.0000.000
163A181GLY00.0070.01638.362-0.242-0.2420.0000.0000.0000.000
164A182ALA0-0.026-0.01640.1360.0230.0230.0000.0000.0000.000
165A183VAL0-0.0060.00142.596-0.183-0.1830.0000.0000.0000.000
166A184MET0-0.0240.01140.2430.2030.2030.0000.0000.0000.000
167A185ALA00.004-0.00340.894-0.195-0.1950.0000.0000.0000.000
168A186VAL0-0.0030.00141.7020.1600.1600.0000.0000.0000.000
169A187LEU0-0.017-0.02241.744-0.096-0.0960.0000.0000.0000.000
170A188PRO00.0000.01743.8960.1120.1120.0000.0000.0000.000
171A189LEU0-0.024-0.01842.041-0.089-0.0890.0000.0000.0000.000
172A190ALA00.0460.02645.8550.0350.0350.0000.0000.0000.000
173A191PHE00.001-0.01542.482-0.060-0.0600.0000.0000.0000.000
174A192GLU-1-0.807-0.87247.8925.7325.7320.0000.0000.0000.000
175A193VAL00.0130.00346.206-0.013-0.0130.0000.0000.0000.000
176A194SER00.004-0.00749.600-0.115-0.1150.0000.0000.0000.000
177A195VAL00.009-0.00247.6230.0760.0760.0000.0000.0000.000
178A196ASP-1-0.859-0.92750.6156.1046.1040.0000.0000.0000.000
179A197VAL00.0010.00148.237-0.013-0.0130.0000.0000.0000.000
180A198GLU-1-0.819-0.87551.1296.0116.0110.0000.0000.0000.000
181A199LYS10.9830.99548.974-6.186-6.1860.0000.0000.0000.000
182A200GLN00.000-0.00548.0960.1240.1240.0000.0000.0000.000
183A201LYS10.8230.90046.555-6.062-6.0620.0000.0000.0000.000
184A202VAL00.0090.01344.9690.1480.1480.0000.0000.0000.000
185A203LEU0-0.036-0.02343.8240.1420.1420.0000.0000.0000.000
186A204PHE0-0.054-0.01640.8880.1210.1210.0000.0000.0000.000
187A205PHE00.0210.02440.8290.0770.0770.0000.0000.0000.000
188A206THR0-0.037-0.04635.9540.2940.2940.0000.0000.0000.000
189A207ILE0-0.007-0.03033.233-0.094-0.0940.0000.0000.0000.000
190A208LYS10.9600.97331.711-9.444-9.4440.0000.0000.0000.000
191A209ASP-1-0.824-0.86337.3157.6297.6290.0000.0000.0000.000
192A210SER00.002-0.01440.9560.0310.0310.0000.0000.0000.000
193A211ALA0-0.0160.00143.931-0.070-0.0700.0000.0000.0000.000
194A212ARG10.8780.96647.315-5.877-5.8770.0000.0000.0000.000
195A213TYR00.027-0.00643.844-0.052-0.0520.0000.0000.0000.000
196A214GLU-1-0.848-0.90849.2115.8095.8090.0000.0000.0000.000
197A215VAL00.000-0.00446.1530.0380.0380.0000.0000.0000.000
198A216LYS10.8570.93649.439-5.735-5.7350.0000.0000.0000.000
199A217MET0-0.0190.00244.2960.0920.0920.0000.0000.0000.000
200A218LYS10.7560.86849.159-6.044-6.0440.0000.0000.0000.000
201A219ALA00.0280.01046.4610.1080.1080.0000.0000.0000.000
202A220LEU0-0.001-0.01147.907-0.143-0.1430.0000.0000.0000.000
203A221THR0-0.011-0.00343.9880.1120.1120.0000.0000.0000.000
204A222LEU0-0.0310.00246.587-0.132-0.1320.0000.0000.0000.000
205A223VAL00.0230.00544.3780.1710.1710.0000.0000.0000.000
206A224GLN00.0420.01146.074-0.063-0.0630.0000.0000.0000.000
207A225ALA0-0.021-0.00145.9520.1680.1680.0000.0000.0000.000
208A226LEU0-0.030-0.00240.052-0.012-0.0120.0000.0000.0000.000
209A227HIS0-0.020-0.00744.677-0.131-0.1310.0000.0000.0000.000
210A228SER0-0.039-0.01942.4860.1220.1220.0000.0000.0000.000
211A229SER0-0.026-0.02242.882-0.186-0.1860.0000.0000.0000.000
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223A241ASN0-0.035-0.03251.4670.1400.1400.0000.0000.0000.000
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