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

tag_button

FMODB ID: R9QG8

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 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 227
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2782719.291112
FMO2-HF: Nuclear repulsion 2694358.965642
FMO2-HF: Total energy -88360.32547
FMO2-MP2: Total energy -88622.508624


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.
9.36510.931-0.01-0.798-0.7580.004
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 : -0.909 / 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].
3A21ALA00.0120.0123.803-0.5890.977-0.010-0.798-0.7580.004
4A22PRO0-0.016-0.0076.166-1.670-1.6700.0000.0000.0000.000
5A23ILE00.0270.0058.881-1.487-1.4870.0000.0000.0000.000
6A24ILE0-0.0050.00511.949-0.804-0.8040.0000.0000.0000.000
7A25ARG10.9590.97014.941-16.503-16.5030.0000.0000.0000.000
8A26LYS10.9610.98618.636-11.660-11.6600.0000.0000.0000.000
9A27PRO0-0.0020.00921.037-0.122-0.1220.0000.0000.0000.000
10A28PHE00.0330.00022.573-0.481-0.4810.0000.0000.0000.000
11A29LYS10.9320.96724.732-10.684-10.6840.0000.0000.0000.000
12A30HIS00.0450.02326.662-0.135-0.1350.0000.0000.0000.000
13A31ILE0-0.019-0.02428.2630.2160.2160.0000.0000.0000.000
14A32VAL00.0410.03531.210-0.146-0.1460.0000.0000.0000.000
15A33LEU0-0.010-0.01833.7450.0260.0260.0000.0000.0000.000
16A34THR00.0140.02236.767-0.109-0.1090.0000.0000.0000.000
17A35VAL0-0.031-0.01739.8220.0550.0550.0000.0000.0000.000
18A36PRO0-0.020-0.01242.324-0.066-0.0660.0000.0000.0000.000
19A37SER00.0430.01646.1320.0290.0290.0000.0000.0000.000
20A38SER00.0000.00148.054-0.116-0.1160.0000.0000.0000.000
21A39ASP-1-0.815-0.92350.7645.6015.6010.0000.0000.0000.000
22A40LEU0-0.076-0.03250.8480.1230.1230.0000.0000.0000.000
23A41ASP-1-0.818-0.91645.8316.8646.8640.0000.0000.0000.000
24A42ASN0-0.028-0.00948.1540.0720.0720.0000.0000.0000.000
25A43PHE00.000-0.01744.683-0.037-0.0370.0000.0000.0000.000
26A44ASN0-0.0010.02739.0540.1500.1500.0000.0000.0000.000
27A45THR0-0.002-0.01640.173-0.023-0.0230.0000.0000.0000.000
28A46VAL0-0.0160.00134.7510.2510.2510.0000.0000.0000.000
29A47PHE0-0.005-0.01936.202-0.133-0.1330.0000.0000.0000.000
30A48TYR0-0.031-0.00828.5500.3490.3490.0000.0000.0000.000
31A49VAL00.0390.01734.316-0.124-0.1240.0000.0000.0000.000
32A50GLN0-0.0140.00433.4640.2660.2660.0000.0000.0000.000
33A51PRO00.027-0.00733.590-0.205-0.2050.0000.0000.0000.000
34A52GLN00.0130.01236.566-0.005-0.0050.0000.0000.0000.000
35A53TYR00.0470.01538.212-0.271-0.2710.0000.0000.0000.000
36A54ILE00.0130.02036.178-0.073-0.0730.0000.0000.0000.000
37A55ASN00.0370.01140.375-0.138-0.1380.0000.0000.0000.000
38A56GLN00.0260.01543.6510.0080.0080.0000.0000.0000.000
39A57ALA00.005-0.00441.201-0.112-0.1120.0000.0000.0000.000
40A58LEU00.013-0.00142.692-0.048-0.0480.0000.0000.0000.000
41A59HIS0-0.039-0.00944.730-0.243-0.2430.0000.0000.0000.000
42A60LEU0-0.004-0.00945.179-0.116-0.1160.0000.0000.0000.000
43A61ALA0-0.001-0.00444.475-0.079-0.0790.0000.0000.0000.000
44A62ASN00.0330.00746.561-0.005-0.0050.0000.0000.0000.000
45A63ALA0-0.0140.00149.594-0.132-0.1320.0000.0000.0000.000
46A64PHE0-0.028-0.02848.475-0.133-0.1330.0000.0000.0000.000
47A65GLN00.0340.03747.785-0.105-0.1050.0000.0000.0000.000
48A66GLY0-0.0200.00351.773-0.076-0.0760.0000.0000.0000.000
49A67ALA0-0.021-0.02452.638-0.130-0.1300.0000.0000.0000.000
50A68ILE0-0.031-0.01050.350-0.040-0.0400.0000.0000.0000.000
51A69ASP-1-0.890-0.94754.2925.2005.2000.0000.0000.0000.000
52A70PRO0-0.014-0.01657.1420.0460.0460.0000.0000.0000.000
53A71LEU0-0.030-0.00858.275-0.009-0.0090.0000.0000.0000.000
54A72ASN0-0.030-0.02258.919-0.021-0.0210.0000.0000.0000.000
55A73LEU00.0200.01353.2500.0690.0690.0000.0000.0000.000
56A74ASN00.0020.01253.5200.2070.2070.0000.0000.0000.000
57A75PHE00.0110.01050.377-0.066-0.0660.0000.0000.0000.000
58A76ASN00.0400.01753.563-0.048-0.0480.0000.0000.0000.000
59A77PHE00.041-0.00152.1080.0160.0160.0000.0000.0000.000
60A78GLU-1-0.882-0.94455.5245.2885.2880.0000.0000.0000.000
61A79LYS10.8940.94257.692-5.383-5.3830.0000.0000.0000.000
62A80ALA00.0430.02452.7600.0220.0220.0000.0000.0000.000
63A81LEU00.0180.00254.2700.0660.0660.0000.0000.0000.000
64A82GLN0-0.067-0.02456.162-0.018-0.0180.0000.0000.0000.000
65A83ILE0-0.043-0.01153.758-0.038-0.0380.0000.0000.0000.000
66A84ALA00.0080.00652.9870.0340.0340.0000.0000.0000.000
67A85ASN0-0.063-0.04254.0640.0970.0970.0000.0000.0000.000
68A86GLY00.0090.01256.363-0.099-0.0990.0000.0000.0000.000
69A87ILE0-0.040-0.01150.857-0.014-0.0140.0000.0000.0000.000
70A88PRO00.0120.01753.499-0.014-0.0140.0000.0000.0000.000
71A89ASN0-0.021-0.02451.7160.0450.0450.0000.0000.0000.000
72A90SER00.011-0.00350.4230.1570.1570.0000.0000.0000.000
73A91ALA00.0060.00050.241-0.131-0.1310.0000.0000.0000.000
74A92ILE00.0090.00849.7720.1520.1520.0000.0000.0000.000
75A93VAL0-0.030-0.00245.734-0.068-0.0680.0000.0000.0000.000
76A94LYS10.9160.97047.397-6.521-6.5210.0000.0000.0000.000
77A95THR00.0030.01348.9260.0630.0630.0000.0000.0000.000
78A96LEU0-0.004-0.02647.2800.0070.0070.0000.0000.0000.000
79A97ASN00.0560.01350.8350.0780.0780.0000.0000.0000.000
80A98GLN0-0.050-0.01351.343-0.166-0.1660.0000.0000.0000.000
81A99SER00.0320.02151.2200.0970.0970.0000.0000.0000.000
82A100VAL0-0.059-0.03346.251-0.015-0.0150.0000.0000.0000.000
83A101ILE0-0.027-0.01544.4590.1100.1100.0000.0000.0000.000
84A102GLN00.0250.01648.368-0.125-0.1250.0000.0000.0000.000
85A103GLN0-0.060-0.05546.787-0.034-0.0340.0000.0000.0000.000
86A104THR00.0210.01947.1920.0000.0000.0000.0000.0000.000
87A105VAL0-0.041-0.01843.3720.0220.0220.0000.0000.0000.000
88A106GLU-1-0.855-0.90237.2208.2508.2500.0000.0000.0000.000
89A107ILE0-0.008-0.02838.2230.0500.0500.0000.0000.0000.000
90A108SER0-0.051-0.03435.0380.0060.0060.0000.0000.0000.000
91A109VAL00.0550.03036.6640.0550.0550.0000.0000.0000.000
92A110MET0-0.0240.00538.685-0.114-0.1140.0000.0000.0000.000
93A111VAL0-0.015-0.01635.128-0.044-0.0440.0000.0000.0000.000
94A112GLU-1-0.926-0.96034.0948.8888.8880.0000.0000.0000.000
95A113GLN00.0110.00037.1270.0800.0800.0000.0000.0000.000
96A114LEU00.0090.00540.192-0.073-0.0730.0000.0000.0000.000
97A115LYS10.9410.98930.858-9.666-9.6660.0000.0000.0000.000
98A116LYS10.9590.98337.897-7.635-7.6350.0000.0000.0000.000
99A117ILE0-0.022-0.01639.268-0.114-0.1140.0000.0000.0000.000
100A118ILE0-0.0130.00038.905-0.102-0.1020.0000.0000.0000.000
101A119GLN0-0.049-0.02735.675-0.170-0.1700.0000.0000.0000.000
102A120GLU-1-0.970-0.97639.3377.0127.0120.0000.0000.0000.000
103A121VAL0-0.039-0.03342.737-0.128-0.1280.0000.0000.0000.000
104A122LEU0-0.0050.01338.137-0.101-0.1010.0000.0000.0000.000
105A123GLY00.0290.03142.368-0.071-0.0710.0000.0000.0000.000
106A124LEU0-0.057-0.04240.0520.0860.0860.0000.0000.0000.000
107A125VAL00.0020.00636.4240.1150.1150.0000.0000.0000.000
108A126ILE00.0060.00432.6330.0860.0860.0000.0000.0000.000
109A127ASN0-0.041-0.01229.8100.2850.2850.0000.0000.0000.000
110A128SER00.015-0.01727.9010.3480.3480.0000.0000.0000.000
111A129THR0-0.0010.00223.567-0.074-0.0740.0000.0000.0000.000
112A130SER00.014-0.00725.229-0.002-0.0020.0000.0000.0000.000
113A131PHE00.0590.05027.005-0.135-0.1350.0000.0000.0000.000
114A132TRP00.0580.00729.938-0.234-0.2340.0000.0000.0000.000
115A133ASN0-0.012-0.00624.908-0.366-0.3660.0000.0000.0000.000
116A134SER0-0.040-0.01529.160-0.113-0.1130.0000.0000.0000.000
117A135VAL0-0.0070.00731.557-0.192-0.1920.0000.0000.0000.000
118A136GLU-1-0.945-0.98430.2059.7589.7580.0000.0000.0000.000
119A137ALA0-0.030-0.01730.610-0.148-0.1480.0000.0000.0000.000
120A138THR00.0310.00932.592-0.178-0.1780.0000.0000.0000.000
121A139ILE0-0.014-0.00136.003-0.210-0.2100.0000.0000.0000.000
122A140LYS10.9530.97430.144-10.071-10.0710.0000.0000.0000.000
123A141GLY00.0180.03136.300-0.125-0.1250.0000.0000.0000.000
124A142THR0-0.0070.01737.587-0.210-0.2100.0000.0000.0000.000
125A143PHE0-0.025-0.03439.826-0.226-0.2260.0000.0000.0000.000
126A144THR0-0.074-0.03836.7650.0590.0590.0000.0000.0000.000
127A145ASN00.013-0.00234.0920.0050.0050.0000.0000.0000.000
128A146LEU00.0230.00938.504-0.020-0.0200.0000.0000.0000.000
129A147ASP-1-0.882-0.93939.9117.8037.8030.0000.0000.0000.000
130A148THR0-0.097-0.04237.1130.0130.0130.0000.0000.0000.000
131A149GLN0-0.0100.01139.352-0.031-0.0310.0000.0000.0000.000
132A150ILE0-0.047-0.01942.339-0.184-0.1840.0000.0000.0000.000
133A151ASP-1-0.925-0.97145.7556.4576.4570.0000.0000.0000.000
134A152GLU-1-0.943-0.95042.5697.2917.2910.0000.0000.0000.000
135A153ALA00.008-0.00946.094-0.085-0.0850.0000.0000.0000.000
136A154TRP0-0.066-0.02040.866-0.126-0.1260.0000.0000.0000.000
137A155ILE0-0.015-0.01145.3980.0020.0020.0000.0000.0000.000
138A156PHE00.0020.01747.648-0.089-0.0890.0000.0000.0000.000
139A157TRP00.036-0.00546.552-0.048-0.0480.0000.0000.0000.000
140A158HIS00.0220.01652.422-0.180-0.1800.0000.0000.0000.000
141A159SER0-0.017-0.03155.2010.0220.0220.0000.0000.0000.000
142A160LEU0-0.0450.00252.7070.0220.0220.0000.0000.0000.000
143A161SER0-0.047-0.02055.847-0.167-0.1670.0000.0000.0000.000
144A162ALA00.002-0.00655.6370.0950.0950.0000.0000.0000.000
145A163HIS0-0.004-0.01055.5330.1210.1210.0000.0000.0000.000
146A164ASN0-0.033-0.02254.1210.0030.0030.0000.0000.0000.000
147A165THR00.018-0.01349.851-0.037-0.0370.0000.0000.0000.000
148A166SER0-0.0130.00051.6020.0670.0670.0000.0000.0000.000
149A167TYR0-0.020-0.03044.558-0.029-0.0290.0000.0000.0000.000
150A168TYR0-0.035-0.00150.115-0.016-0.0160.0000.0000.0000.000
151A169TYR00.021-0.02940.7730.0790.0790.0000.0000.0000.000
152A170ASN0-0.037-0.00446.371-0.043-0.0430.0000.0000.0000.000
153A171ILE00.008-0.00540.2760.1300.1300.0000.0000.0000.000
154A172LEU00.0150.01841.986-0.153-0.1530.0000.0000.0000.000
155A173PHE0-0.0150.00036.7080.2260.2260.0000.0000.0000.000
156A174SER00.0180.00838.900-0.208-0.2080.0000.0000.0000.000
157A175ILE0-0.029-0.01534.5680.2640.2640.0000.0000.0000.000
158A176GLN00.0570.00536.286-0.181-0.1810.0000.0000.0000.000
159A177ASN0-0.034-0.03631.924-0.019-0.0190.0000.0000.0000.000
160A178GLU-1-0.919-0.97530.8629.6139.6130.0000.0000.0000.000
161A179ASP-1-0.810-0.89732.9059.2049.2040.0000.0000.0000.000
162A180THR0-0.0370.00035.870-0.183-0.1830.0000.0000.0000.000
163A181GLY00.0030.00438.271-0.238-0.2380.0000.0000.0000.000
164A182ALA0-0.015-0.01140.0840.0230.0230.0000.0000.0000.000
165A183VAL0-0.018-0.00242.527-0.188-0.1880.0000.0000.0000.000
166A184MET0-0.0160.00840.2210.1830.1830.0000.0000.0000.000
167A185ALA00.000-0.00440.653-0.195-0.1950.0000.0000.0000.000
168A186VAL0-0.0010.00241.5260.1670.1670.0000.0000.0000.000
169A187LEU0-0.021-0.02641.233-0.099-0.0990.0000.0000.0000.000
170A188PRO0-0.0020.01643.6910.1130.1130.0000.0000.0000.000
171A189LEU0-0.020-0.01742.053-0.088-0.0880.0000.0000.0000.000
172A190ALA00.0470.02645.6590.0350.0350.0000.0000.0000.000
173A191PHE0-0.013-0.02042.184-0.058-0.0580.0000.0000.0000.000
174A192GLU-1-0.891-0.94347.7155.7615.7610.0000.0000.0000.000
175A193VAL00.002-0.00346.085-0.004-0.0040.0000.0000.0000.000
176A194SER00.0100.01549.442-0.100-0.1000.0000.0000.0000.000
177A195VAL00.0240.00147.4750.0780.0780.0000.0000.0000.000
178A196ASP-1-0.864-0.93450.5066.1226.1220.0000.0000.0000.000
179A197VAL0-0.015-0.00448.230-0.009-0.0090.0000.0000.0000.000
180A198GLU-1-0.912-0.93151.1865.9755.9750.0000.0000.0000.000
181A199LYS10.9980.99949.046-6.179-6.1790.0000.0000.0000.000
182A200GLN00.0160.00147.9800.1270.1270.0000.0000.0000.000
183A201LYS10.9300.96646.462-6.230-6.2300.0000.0000.0000.000
184A202VAL00.0180.01944.8610.1500.1500.0000.0000.0000.000
185A203LEU0-0.045-0.03043.7020.1460.1460.0000.0000.0000.000
186A204PHE0-0.030-0.00840.5880.1390.1390.0000.0000.0000.000
187A205PHE00.0210.02940.7270.0800.0800.0000.0000.0000.000
188A206THR0-0.055-0.04635.8580.2870.2870.0000.0000.0000.000
189A207ILE0-0.004-0.02833.170-0.082-0.0820.0000.0000.0000.000
190A208LYS10.9540.96431.742-9.514-9.5140.0000.0000.0000.000
191A209ASP-1-0.798-0.86237.2097.6387.6380.0000.0000.0000.000
192A210SER0-0.019-0.02240.8480.0350.0350.0000.0000.0000.000
193A211ALA0-0.015-0.00143.819-0.071-0.0710.0000.0000.0000.000
194A212ARG10.8850.98047.196-5.860-5.8600.0000.0000.0000.000
195A213TYR00.033-0.00444.009-0.038-0.0380.0000.0000.0000.000
196A214GLU-1-0.898-0.95149.0705.8705.8700.0000.0000.0000.000
197A215VAL00.0060.00145.9910.0510.0510.0000.0000.0000.000
198A216LYS10.9630.99949.275-5.704-5.7040.0000.0000.0000.000
199A217MET0-0.034-0.00544.6570.1120.1120.0000.0000.0000.000
200A218LYS10.7600.88248.975-6.080-6.0800.0000.0000.0000.000
201A219ALA00.0240.00946.2740.1090.1090.0000.0000.0000.000
202A220LEU0-0.015-0.01647.699-0.145-0.1450.0000.0000.0000.000
203A221THR00.0000.00143.7960.1110.1110.0000.0000.0000.000
204A222LEU0-0.0230.00346.369-0.134-0.1340.0000.0000.0000.000
205A223VAL00.0110.00244.2880.1730.1730.0000.0000.0000.000
206A224GLN00.0530.01345.983-0.060-0.0600.0000.0000.0000.000
207A225ALA0-0.026-0.00245.9450.1660.1660.0000.0000.0000.000
208A226LEU0-0.039-0.01640.152-0.018-0.0180.0000.0000.0000.000
209A227HIS0-0.012-0.00744.723-0.109-0.1090.0000.0000.0000.000
210A228SER0-0.039-0.01842.4530.1270.1270.0000.0000.0000.000
211A229SER0-0.019-0.02342.931-0.167-0.1670.0000.0000.0000.000
212A230ASN0-0.026-0.02141.3120.2530.2530.0000.0000.0000.000
213A231ALA0-0.0030.01343.230-0.058-0.0580.0000.0000.0000.000
214A232PRO00.0300.01243.9350.1970.1970.0000.0000.0000.000
215A233ILE00.0390.00939.213-0.065-0.0650.0000.0000.0000.000
216A234VAL00.008-0.00343.2070.0050.0050.0000.0000.0000.000
217A235ASP-1-0.874-0.94245.9616.2646.2640.0000.0000.0000.000
218A236ILE0-0.069-0.03542.716-0.073-0.0730.0000.0000.0000.000
219A237PHE0-0.025-0.02340.3740.0100.0100.0000.0000.0000.000
220A238ASN00.0110.01346.3910.0100.0100.0000.0000.0000.000
221A239VAL0-0.083-0.01649.290-0.153-0.1530.0000.0000.0000.000
222A240ASN00.0060.01550.5360.1090.1090.0000.0000.0000.000
223A241ASN0-0.010-0.02251.6200.1410.1410.0000.0000.0000.000
224A242TYR0-0.070-0.03653.902-0.148-0.1480.0000.0000.0000.000
225A243ASN0-0.073-0.03256.274-0.033-0.0330.0000.0000.0000.000
226A244LEU00.0350.01551.5770.0600.0600.0000.0000.0000.000
227A245TYR0-0.0230.00654.5900.0280.0280.0000.0000.0000.000