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: VRL51

Calculation Name: 1Y0K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y0K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HVP2

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptAll
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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1991272.570459
FMO2-HF: Nuclear repulsion 1920300.996016
FMO2-HF: Total energy -70971.574443
FMO2-MP2: Total energy -71182.504972


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.
-7.34-1.6686.109-2.566-9.214-0.008
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 : 0.034 / q_NPA : 0.028
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].
3A3GLU-1-0.786-0.9072.551-4.590-1.1040.977-2.099-2.364-0.006
4A4ALA0-0.007-0.0034.9470.9511.122-0.001-0.007-0.1620.000
5A5ASP-1-0.809-0.8892.828-0.4040.3780.262-0.215-0.8290.000
6A6TYR00.0400.0252.468-0.3442.1433.784-2.287-3.9850.000
7A7LEU00.0010.0013.5921.349-0.6840.0572.394-0.418-0.001
8A8ARG10.8610.9226.603-0.380-0.3800.0000.0000.0000.000
9A9LEU0-0.040-0.0152.422-1.648-0.8691.030-0.352-1.456-0.001
10A10LEU00.0230.0036.124-0.727-0.7270.0000.0000.0000.000
11A11THR0-0.044-0.0328.675-0.378-0.3780.0000.0000.0000.000
12A12ARG10.9811.0014.871-1.354-1.3540.0000.0000.0000.000
13A13GLN00.0110.0179.419-0.063-0.0630.0000.0000.0000.000
14A14ALA00.0280.01611.195-0.114-0.1140.0000.0000.0000.000
15A15GLU-1-0.852-0.92513.3160.3990.3990.0000.0000.0000.000
16A16GLN00.0380.01110.9440.0180.0180.0000.0000.0000.000
17A17ALA0-0.0020.01315.357-0.046-0.0460.0000.0000.0000.000
18A18ASN00.0350.00717.285-0.040-0.0400.0000.0000.0000.000
19A19ASP-1-0.890-0.92117.6870.2670.2670.0000.0000.0000.000
20A20PHE0-0.029-0.00819.562-0.029-0.0290.0000.0000.0000.000
21A21LEU0-0.033-0.02521.359-0.028-0.0280.0000.0000.0000.000
22A22SER0-0.049-0.03322.933-0.023-0.0230.0000.0000.0000.000
23A23ASN0-0.028-0.01723.569-0.027-0.0270.0000.0000.0000.000
24A24ALA0-0.0200.01625.465-0.011-0.0110.0000.0000.0000.000
25A25ARG10.9660.96927.330-0.125-0.1250.0000.0000.0000.000
26A26LYS10.7780.87230.197-0.091-0.0910.0000.0000.0000.000
27A27TRP00.0580.01430.9470.0090.0090.0000.0000.0000.000
28A28ASP-1-0.875-0.92128.5460.1470.1470.0000.0000.0000.000
29A29ARG10.9050.95325.564-0.140-0.1400.0000.0000.0000.000
30A30GLU-1-0.801-0.90326.6460.1220.1220.0000.0000.0000.000
31A31ARG10.8330.91528.468-0.133-0.1330.0000.0000.0000.000
32A32TRP00.0170.00619.3090.0040.0040.0000.0000.0000.000
33A33VAL0-0.008-0.00223.8800.0140.0140.0000.0000.0000.000
34A34CYS0-0.044-0.01824.9170.0020.0020.0000.0000.0000.000
35A35GLN0-0.009-0.00625.332-0.006-0.0060.0000.0000.0000.000
36A36ARG10.8670.91319.436-0.235-0.2350.0000.0000.0000.000
37A37PHE0-0.010-0.00921.9600.0080.0080.0000.0000.0000.000
38A38LEU00.001-0.00524.147-0.004-0.0040.0000.0000.0000.000
39A39GLU-1-0.776-0.83021.4350.2110.2110.0000.0000.0000.000
40A40ALA0-0.010-0.00220.7110.0030.0030.0000.0000.0000.000
41A41LEU0-0.085-0.03421.648-0.010-0.0100.0000.0000.0000.000
42A42ASN0-0.050-0.01824.087-0.007-0.0070.0000.0000.0000.000
43A43VAL0-0.011-0.00725.408-0.014-0.0140.0000.0000.0000.000
44A44PRO0-0.0040.00528.4320.0060.0060.0000.0000.0000.000
45A45TYR0-0.073-0.07125.100-0.013-0.0130.0000.0000.0000.000
46A46ARG10.8450.90930.758-0.086-0.0860.0000.0000.0000.000
47A47GLN0-0.014-0.00729.4170.0080.0080.0000.0000.0000.000
48A48GLU-1-0.753-0.87532.4790.0930.0930.0000.0000.0000.000
49A49ASP-1-0.820-0.90133.6170.0880.0880.0000.0000.0000.000
50A50PHE0-0.055-0.03229.3900.0000.0000.0000.0000.0000.000
51A51ALA00.0120.00534.954-0.001-0.0010.0000.0000.0000.000
52A52ALA00.0110.00837.2890.0020.0020.0000.0000.0000.000
53A53PRO0-0.0130.00438.304-0.004-0.0040.0000.0000.0000.000
54A54GLY0-0.026-0.02241.3300.0010.0010.0000.0000.0000.000
55A55GLU-1-0.892-0.95143.5260.0520.0520.0000.0000.0000.000
56A56GLN00.0000.02738.0510.0070.0070.0000.0000.0000.000
57A57PRO0-0.0120.02938.959-0.002-0.0020.0000.0000.0000.000
58A58PRO00.0180.00037.003-0.003-0.0030.0000.0000.0000.000
59A59ASP-1-0.817-0.90933.7350.0940.0940.0000.0000.0000.000
60A60VAL0-0.066-0.04531.6260.0010.0010.0000.0000.0000.000
61A61LEU00.0120.02034.889-0.001-0.0010.0000.0000.0000.000
62A62PHE00.030-0.01131.8810.0040.0040.0000.0000.0000.000
63A63LYS10.7710.89933.402-0.094-0.0940.0000.0000.0000.000
64A64GLY00.0300.02637.421-0.002-0.0020.0000.0000.0000.000
65A65ALA0-0.014-0.00834.414-0.003-0.0030.0000.0000.0000.000
66A66GLY00.0390.01436.4620.0000.0000.0000.0000.0000.000
67A67PHE0-0.004-0.01031.0090.0000.0000.0000.0000.0000.000
68A68GLU-1-0.701-0.81533.7110.0790.0790.0000.0000.0000.000
69A69VAL0-0.029-0.01728.4870.0040.0040.0000.0000.0000.000
70A70PHE0-0.019-0.03228.856-0.008-0.0080.0000.0000.0000.000
71A71PHE00.0380.01824.4890.0110.0110.0000.0000.0000.000
72A72VAL0-0.028-0.01323.739-0.015-0.0150.0000.0000.0000.000
73A73LEU00.0250.01221.6550.0220.0220.0000.0000.0000.000
74A74ASP-1-0.830-0.92619.6910.2140.2140.0000.0000.0000.000
75A75GLU-1-0.815-0.88420.7550.2080.2080.0000.0000.0000.000
76A105ARG10.9700.97410.5400.1430.1430.0000.0000.0000.000
77A106PRO0-0.0280.00011.110-0.073-0.0730.0000.0000.0000.000
78A107GLN00.0080.00712.841-0.032-0.0320.0000.0000.0000.000
79A108ARG10.8750.9229.0630.0390.0390.0000.0000.0000.000
80A109ILE0-0.042-0.01714.960-0.032-0.0320.0000.0000.0000.000
81A110ALA00.0690.03418.2540.0150.0150.0000.0000.0000.000
82A111ALA00.0310.00620.4050.0220.0220.0000.0000.0000.000
83A112ALA00.0060.00022.0770.0120.0120.0000.0000.0000.000
84A113GLU-1-0.862-0.94822.9340.0130.0130.0000.0000.0000.000
85A114LEU0-0.042-0.01519.0880.0130.0130.0000.0000.0000.000
86A115GLN00.015-0.01022.5880.0160.0160.0000.0000.0000.000
87A116ALA00.0020.01125.6570.0000.0000.0000.0000.0000.000
88A117ARG10.9040.95521.437-0.118-0.1180.0000.0000.0000.000
89A118LEU00.0260.01525.1870.0040.0040.0000.0000.0000.000
90A119ALA00.0190.02228.492-0.002-0.0020.0000.0000.0000.000
91A120PRO0-0.022-0.01930.066-0.004-0.0040.0000.0000.0000.000
92A121THR00.008-0.00230.197-0.005-0.0050.0000.0000.0000.000
93A122LEU00.0010.01530.968-0.002-0.0020.0000.0000.0000.000
94A123ARG10.8470.88234.041-0.042-0.0420.0000.0000.0000.000
95A124LYS10.9310.97635.250-0.061-0.0610.0000.0000.0000.000
96A125LYS10.8400.91933.015-0.090-0.0900.0000.0000.0000.000
97A126ALA00.0430.01937.939-0.003-0.0030.0000.0000.0000.000
98A127HIS0-0.045-0.00839.871-0.003-0.0030.0000.0000.0000.000
99A128ASN00.014-0.01440.300-0.004-0.0040.0000.0000.0000.000
100A129TYR0-0.059-0.06637.585-0.001-0.0010.0000.0000.0000.000
101A130SER00.0170.00143.413-0.002-0.0020.0000.0000.0000.000
102A131GLU-1-0.913-0.94345.9050.0320.0320.0000.0000.0000.000
103A132ARG10.7730.87842.965-0.054-0.0540.0000.0000.0000.000
104A133GLY0-0.0070.00547.8850.0000.0000.0000.0000.0000.000
105A134ILE0-0.072-0.03642.9440.0000.0000.0000.0000.0000.000
106A135ASP-1-0.857-0.92345.1530.0390.0390.0000.0000.0000.000
107A136HIS0-0.041-0.03740.3950.0030.0030.0000.0000.0000.000
108A137GLY00.0260.01040.2800.0040.0040.0000.0000.0000.000
109A138GLU-1-0.884-0.93441.5610.0490.0490.0000.0000.0000.000
110A139LEU0-0.055-0.01737.5630.0050.0050.0000.0000.0000.000
111A140ASP-1-0.750-0.84333.6380.0690.0690.0000.0000.0000.000
112A141LEU0-0.026-0.01231.8730.0080.0080.0000.0000.0000.000
113A142LEU0-0.003-0.00826.1830.0030.0030.0000.0000.0000.000
114A143ALA0-0.0050.00625.8720.0030.0030.0000.0000.0000.000
115A144PHE00.0420.00218.7370.0140.0140.0000.0000.0000.000
116A145VAL0-0.042-0.03419.947-0.009-0.0090.0000.0000.0000.000
117A146ASN0-0.054-0.06116.5880.0830.0830.0000.0000.0000.000
118A147LEU0-0.036-0.00417.140-0.035-0.0350.0000.0000.0000.000
119A148LYS10.8750.93515.585-0.289-0.2890.0000.0000.0000.000
120A149ARG10.7600.85315.639-0.170-0.1700.0000.0000.0000.000
121A150ALA0-0.027-0.02015.668-0.047-0.0470.0000.0000.0000.000
122A151VAL00.0240.01810.8640.0610.0610.0000.0000.0000.000
123A152PRO00.0300.01214.043-0.074-0.0740.0000.0000.0000.000
124A153ASP-1-0.843-0.90214.041-0.114-0.1140.0000.0000.0000.000
125A154PHE00.003-0.00812.830-0.015-0.0150.0000.0000.0000.000
126A155ASN0-0.054-0.01714.356-0.020-0.0200.0000.0000.0000.000
127A156THR0-0.028-0.01518.204-0.001-0.0010.0000.0000.0000.000
128A157PRO00.0040.00721.2430.0200.0200.0000.0000.0000.000
129A158PHE00.0500.00020.4770.0030.0030.0000.0000.0000.000
130A159PRO0-0.0070.01725.617-0.005-0.0050.0000.0000.0000.000
131A160PRO00.0640.01729.1350.0090.0090.0000.0000.0000.000
132A161PRO00.0440.04330.784-0.003-0.0030.0000.0000.0000.000
133A162THR0-0.019-0.02632.4910.0020.0020.0000.0000.0000.000
134A163GLU-1-0.811-0.87335.0450.0370.0370.0000.0000.0000.000
135A164TYR0-0.017-0.03429.341-0.001-0.0010.0000.0000.0000.000
136A165LEU00.0080.01435.2650.0010.0010.0000.0000.0000.000
137A166ARG10.9040.95037.598-0.021-0.0210.0000.0000.0000.000
138A167GLN0-0.044-0.02035.3630.0030.0030.0000.0000.0000.000
139A168GLY00.0360.02739.6910.0020.0020.0000.0000.0000.000
140A169TRP0-0.064-0.02335.6130.0010.0010.0000.0000.0000.000
141A170ARG10.7830.87837.770-0.063-0.0630.0000.0000.0000.000
142A171SER0-0.060-0.07033.3920.0000.0000.0000.0000.0000.000
143A172LEU0-0.0150.00929.6260.0010.0010.0000.0000.0000.000
144A173SER0-0.008-0.00326.936-0.004-0.0040.0000.0000.0000.000
145A174MET0-0.043-0.00322.8180.0030.0030.0000.0000.0000.000
146A175VAL00.0280.01220.9510.0000.0000.0000.0000.0000.000
147A176GLY00.0590.04018.384-0.015-0.0150.0000.0000.0000.000
148A177PRO0-0.009-0.01013.8400.0090.0090.0000.0000.0000.000
149A178THR0-0.014-0.00811.3290.0520.0520.0000.0000.0000.000
150A179PHE0-0.010-0.01413.851-0.032-0.0320.0000.0000.0000.000
151A180ALA00.0520.03117.2360.0000.0000.0000.0000.0000.000
152A181ARG10.8420.91521.015-0.078-0.0780.0000.0000.0000.000
153A182VAL00.0320.03424.0980.0030.0030.0000.0000.0000.000
154A183LEU0-0.079-0.04425.641-0.009-0.0090.0000.0000.0000.000
155A184PHE0-0.009-0.02429.064-0.010-0.0100.0000.0000.0000.000
156A185ALA00.027-0.00532.6960.0070.0070.0000.0000.0000.000
157A186HIS00.0240.03635.050-0.005-0.0050.0000.0000.0000.000
158A187SER0-0.004-0.01438.7160.0030.0030.0000.0000.0000.000
159A188GLY00.0290.01541.0710.0010.0010.0000.0000.0000.000
160A189ALA00.0160.02236.1420.0030.0030.0000.0000.0000.000
161A190PRO00.0280.00734.967-0.003-0.0030.0000.0000.0000.000
162A191GLU-1-0.813-0.89535.4440.0510.0510.0000.0000.0000.000
163A192PHE00.004-0.00430.522-0.001-0.0010.0000.0000.0000.000
164A193LEU00.0160.02130.4360.0070.0070.0000.0000.0000.000
165A194ARG10.8500.90631.457-0.050-0.0500.0000.0000.0000.000
166A195ALA0-0.028-0.01232.248-0.004-0.0040.0000.0000.0000.000
167A196ASN0-0.025-0.01826.9500.0060.0060.0000.0000.0000.000
168A197LEU00.0210.03527.7970.0040.0040.0000.0000.0000.000
169A198GLY00.0050.01928.727-0.003-0.0030.0000.0000.0000.000
170A199ARG10.8850.92924.325-0.097-0.0970.0000.0000.0000.000
171A200SER0-0.024-0.02020.726-0.002-0.0020.0000.0000.0000.000
172A201ILE0-0.0180.01518.598-0.013-0.0130.0000.0000.0000.000
173A202LEU0-0.002-0.00914.1960.0040.0040.0000.0000.0000.000
174A203PHE0-0.036-0.00113.380-0.022-0.0220.0000.0000.0000.000
175A204ASP-1-0.885-0.9379.5310.7540.7540.0000.0000.0000.000
176A205ALA0-0.037-0.0376.226-0.032-0.0320.0000.0000.0000.000
177A206GLY0-0.006-0.0038.116-0.146-0.1460.0000.0000.0000.000
178A207VAL00.0040.00110.590-0.101-0.1010.0000.0000.0000.000
179A208GLY00.0150.00713.292-0.064-0.0640.0000.0000.0000.000
180A209LEU0-0.108-0.04813.329-0.085-0.0850.0000.0000.0000.000