FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 8591Y

Calculation Name: 2YMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YMO

Chain ID: A

ChEMBL ID:

UniProt ID: C6KSX0

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:

Apendix: None


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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2657285.486071
FMO2-HF: Nuclear repulsion 2563551.023406
FMO2-HF: Total energy -93734.462665
FMO2-MP2: Total energy -94000.044678


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:29:LEU)


Summations of interaction energy for fragment #1(A:29:LEU)
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.
-12.614-6.95611.484-4.572-12.568-0.03
Interaction energy analysis for fragmet #1(A:29:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.002
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].
3A31CYS0-0.072-0.0043.7510.5672.462-0.042-0.765-1.0870.003
4A32ASP-1-0.757-0.8896.5210.6050.6050.0000.0000.0000.000
5A33PHE0-0.001-0.0169.5830.0770.0770.0000.0000.0000.000
6A34ASN0-0.0150.00612.617-0.125-0.1250.0000.0000.0000.000
7A35ASP-1-0.904-0.96213.1560.5680.5680.0000.0000.0000.000
8A36VAL0-0.063-0.0238.8350.0260.0260.0000.0000.0000.000
9A37TYR0-0.072-0.0457.395-0.413-0.4130.0000.0000.0000.000
10A38LYS10.9280.97212.718-0.732-0.7320.0000.0000.0000.000
11A39LEU00.0360.00715.143-0.030-0.0300.0000.0000.0000.000
12A40GLU-1-0.952-0.96018.1220.3930.3930.0000.0000.0000.000
13A41PHE0-0.064-0.05021.3000.0040.0040.0000.0000.0000.000
14A42HIS00.0340.02721.806-0.022-0.0220.0000.0000.0000.000
15A43PRO0-0.025-0.03126.432-0.017-0.0170.0000.0000.0000.000
16A44ASN0-0.041-0.02630.2060.0060.0060.0000.0000.0000.000
17A45GLN00.0240.00924.2110.0130.0130.0000.0000.0000.000
18A46GLN00.0330.02029.184-0.007-0.0070.0000.0000.0000.000
19A47THR0-0.013-0.00426.241-0.014-0.0140.0000.0000.0000.000
20A48SER0-0.0060.01322.6700.0110.0110.0000.0000.0000.000
21A49VAL00.0120.00719.0530.0060.0060.0000.0000.0000.000
22A50THR0-0.002-0.00417.055-0.007-0.0070.0000.0000.0000.000
23A51LYS10.8830.95013.568-0.731-0.7310.0000.0000.0000.000
24A52LEU00.0320.01112.317-0.049-0.0490.0000.0000.0000.000
25A54ASN00.0350.0107.546-0.242-0.2420.0000.0000.0000.000
26A55LEU0-0.010-0.0092.153-0.944-0.2253.406-1.289-2.836-0.003
27A56THR00.016-0.0033.419-0.3410.0660.017-0.104-0.3190.000
28A57PRO0-0.0170.0112.156-2.176-1.2902.675-1.095-2.467-0.001
29A58ASN0-0.011-0.0132.9972.6101.3000.1641.373-0.2270.000
30A59VAL00.029-0.0056.152-0.156-0.1560.0000.0000.0000.000
31A60LEU0-0.060-0.0338.588-0.099-0.0990.0000.0000.0000.000
32A61GLU-1-0.827-0.9042.277-10.949-9.2662.453-1.527-2.609-0.024
33A62LYS10.8750.9465.0161.4631.4630.0000.0000.0000.000
34A63VAL00.0370.0282.124-3.018-1.9202.804-1.158-2.744-0.005
35A64THR0-0.059-0.0313.5100.4080.7360.0080.002-0.3370.000
36A65ILE00.004-0.0045.7870.5290.481-0.001-0.0090.0580.000
37A66LYS10.9330.9748.400-0.892-0.8920.0000.0000.0000.000
38A67CYS0-0.083-0.01211.0960.0900.0900.0000.0000.0000.000
39A68GLY00.0610.03314.135-0.074-0.0740.0000.0000.0000.000
40A69SER0-0.059-0.06116.8350.0030.0030.0000.0000.0000.000
41A70ASP-1-0.832-0.91219.4270.1950.1950.0000.0000.0000.000
42A71LYS10.8800.94122.219-0.246-0.2460.0000.0000.0000.000
43A72LEU0-0.0250.00817.807-0.008-0.0080.0000.0000.0000.000
44A73ASN00.0260.01520.685-0.012-0.0120.0000.0000.0000.000
45A74TYR0-0.028-0.02416.4850.0140.0140.0000.0000.0000.000
46A75ASN00.0380.02619.218-0.013-0.0130.0000.0000.0000.000
47A76LEU00.011-0.00412.6200.0460.0460.0000.0000.0000.000
48A77TYR0-0.0540.00416.657-0.047-0.0470.0000.0000.0000.000
49A78PRO00.1110.03215.3800.0360.0360.0000.0000.0000.000
50A79PRO00.026-0.00316.212-0.003-0.0030.0000.0000.0000.000
51A80THR00.0320.00914.3010.0110.0110.0000.0000.0000.000
52A81CYS0-0.190-0.07210.939-0.089-0.0890.0000.0000.0000.000
53A82PHE00.0250.0199.511-0.010-0.0100.0000.0000.0000.000
54A83GLU-1-0.968-0.97812.239-0.221-0.2210.0000.0000.0000.000
55A117ILE0-0.022-0.02115.3700.0170.0170.0000.0000.0000.000
56A118ASN0-0.0150.00515.310-0.050-0.0500.0000.0000.0000.000
57A119GLU-1-0.882-0.95810.8300.1910.1910.0000.0000.0000.000
58A120VAL00.0010.01910.018-0.070-0.0700.0000.0000.0000.000
59A121SER00.010-0.0187.884-0.130-0.1300.0000.0000.0000.000
60A122PHE00.0220.0287.2370.0810.0810.0000.0000.0000.000
61A123ARG10.8860.9236.9710.9850.9850.0000.0000.0000.000
62A124ILE00.0080.0384.9790.2410.2410.0000.0000.0000.000
63A125PRO00.0860.0418.678-0.125-0.1250.0000.0000.0000.000
64A126PRO00.014-0.01911.621-0.037-0.0370.0000.0000.0000.000
65A127ASN0-0.052-0.02211.9520.1200.1200.0000.0000.0000.000
66A128MET00.013-0.00715.350-0.021-0.0210.0000.0000.0000.000
67A129MET0-0.0200.00917.2220.0190.0190.0000.0000.0000.000
68A130PRO00.0060.01515.693-0.025-0.0250.0000.0000.0000.000
69A131GLU-1-0.898-0.93913.880-0.255-0.2550.0000.0000.0000.000
70A132LYS10.9010.93414.3950.0540.0540.0000.0000.0000.000
71A133PRO00.0050.00311.178-0.031-0.0310.0000.0000.0000.000
72A134ILE00.0330.03810.6740.0240.0240.0000.0000.0000.000
73A135TYR0-0.045-0.03210.7050.0250.0250.0000.0000.0000.000
74A137PHE00.007-0.00613.2230.0960.0960.0000.0000.0000.000
75A139GLU-1-0.857-0.94415.4800.2270.2270.0000.0000.0000.000
76A140ASN00.005-0.00719.080-0.044-0.0440.0000.0000.0000.000
77A141LYS10.9940.99121.306-0.145-0.1450.0000.0000.0000.000
78A142LYS10.9771.00825.012-0.214-0.2140.0000.0000.0000.000
79A158ASP-1-0.950-0.96529.1390.1240.1240.0000.0000.0000.000
80A159ILE0-0.060-0.02525.8950.0070.0070.0000.0000.0000.000
81A160ILE0-0.037-0.03420.4170.0030.0030.0000.0000.0000.000
82A161ASN0-0.0100.01519.709-0.019-0.0190.0000.0000.0000.000
83A162ARG10.9020.94117.777-0.256-0.2560.0000.0000.0000.000
84A163GLY00.0410.01913.5810.0460.0460.0000.0000.0000.000
85A164ILE0-0.055-0.02712.989-0.081-0.0810.0000.0000.0000.000
86A165VAL00.012-0.0087.4660.1530.1530.0000.0000.0000.000
87A166GLU-1-0.862-0.9338.7960.0880.0880.0000.0000.0000.000
88A167ILE0-0.018-0.0115.4930.1310.1310.0000.0000.0000.000
89A168ILE00.0200.0067.092-0.066-0.0660.0000.0000.0000.000
90A169ILE0-0.001-0.0057.265-0.213-0.2130.0000.0000.0000.000
91A170PRO0-0.0370.0067.1250.0950.0950.0000.0000.0000.000
92A171SER00.0110.0059.7000.0360.0360.0000.0000.0000.000
93A172LEU0-0.034-0.03812.858-0.047-0.0470.0000.0000.0000.000
94A173ASN00.003-0.00915.0900.0670.0670.0000.0000.0000.000
95A174GLU-1-0.978-0.97917.998-0.308-0.3080.0000.0000.0000.000
96A175LYS10.9080.95618.5610.2340.2340.0000.0000.0000.000
97A176VAL0-0.0010.01116.528-0.013-0.0130.0000.0000.0000.000
98A177LYS10.8780.92819.1650.3810.3810.0000.0000.0000.000
99A178GLY00.003-0.01121.378-0.023-0.0230.0000.0000.0000.000
100A179CYS0-0.144-0.03523.7340.0170.0170.0000.0000.0000.000
101A180ASP-1-0.693-0.82324.421-0.275-0.2750.0000.0000.0000.000
102A181PHE0-0.045-0.04325.8050.0180.0180.0000.0000.0000.000
103A182THR0-0.081-0.05826.3100.0150.0150.0000.0000.0000.000
104A183THR0-0.023-0.01227.6000.0080.0080.0000.0000.0000.000
105A184SER00.0070.00528.880-0.009-0.0090.0000.0000.0000.000
106A185GLU-1-0.958-0.97528.658-0.162-0.1620.0000.0000.0000.000
107A186SER0-0.0140.00923.399-0.014-0.0140.0000.0000.0000.000
108A187THR00.009-0.01020.234-0.007-0.0070.0000.0000.0000.000
109A188ILE0-0.0120.01217.675-0.017-0.0170.0000.0000.0000.000
110A189PHE0-0.006-0.01019.524-0.025-0.0250.0000.0000.0000.000
111A190SER0-0.021-0.02122.2440.0180.0180.0000.0000.0000.000
112A191LYS10.8660.93524.6030.2360.2360.0000.0000.0000.000
113A192GLY00.0380.02526.696-0.017-0.0170.0000.0000.0000.000
114A193TYR0-0.014-0.01028.8660.0130.0130.0000.0000.0000.000
115A194SER0-0.013-0.00631.590-0.001-0.0010.0000.0000.0000.000
116A195ILE00.0740.01233.9740.0000.0000.0000.0000.0000.000
117A196ASN00.020-0.00535.5960.0010.0010.0000.0000.0000.000
118A197GLU-1-0.885-0.93835.115-0.145-0.1450.0000.0000.0000.000
119A198ILE00.0410.02232.7320.0030.0030.0000.0000.0000.000
120A199SER0-0.0040.02036.3280.0040.0040.0000.0000.0000.000
121A200ASN00.032-0.01039.5010.0000.0000.0000.0000.0000.000
122A201LYS10.7800.91139.3890.1230.1230.0000.0000.0000.000
123A202SER0-0.017-0.00644.1120.0030.0030.0000.0000.0000.000
124A203SER00.0690.00547.044-0.002-0.0020.0000.0000.0000.000
125A204ASN0-0.0010.00348.5520.0010.0010.0000.0000.0000.000
126A205ASN00.0080.03343.616-0.005-0.0050.0000.0000.0000.000
127A206GLN00.0650.02043.250-0.004-0.0040.0000.0000.0000.000
128A207GLN0-0.056-0.02741.4530.0010.0010.0000.0000.0000.000
129A208ASP-1-0.865-0.92836.386-0.137-0.1370.0000.0000.0000.000
130A209ILE0-0.061-0.02033.5360.0030.0030.0000.0000.0000.000
131A210VAL00.0220.01533.148-0.008-0.0080.0000.0000.0000.000
132A212THR00.0230.00429.407-0.010-0.0100.0000.0000.0000.000
133A213VAL00.0000.01223.4860.0040.0040.0000.0000.0000.000
134A214LYS10.9020.95526.8090.2340.2340.0000.0000.0000.000
135A215ALA0-0.010-0.00821.580-0.009-0.0090.0000.0000.0000.000
136A216HIS10.8870.94120.8940.3710.3710.0000.0000.0000.000
137A217ALA00.0390.00819.291-0.034-0.0340.0000.0000.0000.000
138A218ASN0-0.001-0.02414.693-0.040-0.0400.0000.0000.0000.000
139A219ASP-1-0.815-0.87515.418-0.452-0.4520.0000.0000.0000.000
140A220LEU0-0.037-0.01012.914-0.037-0.0370.0000.0000.0000.000
141A221ILE0-0.020-0.02216.0360.0670.0670.0000.0000.0000.000
142A222GLY00.038-0.00717.884-0.052-0.0520.0000.0000.0000.000
143A223PHE0-0.039-0.02520.0150.0330.0330.0000.0000.0000.000
144A224LYS10.9981.01221.8860.2600.2600.0000.0000.0000.000
145A225CYS0-0.0610.00923.8230.0110.0110.0000.0000.0000.000
146A226PRO00.0730.03026.630-0.008-0.0080.0000.0000.0000.000
147A227SER00.0330.01227.2270.0020.0020.0000.0000.0000.000
148A228ASN0-0.047-0.03428.4280.0060.0060.0000.0000.0000.000
149A229TYR0-0.014-0.00330.2660.0100.0100.0000.0000.0000.000
150A230SER00.0380.03329.829-0.011-0.0110.0000.0000.0000.000
151A231VAL00.005-0.01125.4240.0010.0010.0000.0000.0000.000
152A232GLU-1-0.971-0.95428.626-0.152-0.1520.0000.0000.0000.000
153A233PRO00.027-0.01526.9180.0000.0000.0000.0000.0000.000
154A234HIS00.0460.00924.864-0.009-0.0090.0000.0000.0000.000
155A235ASP-1-0.877-0.94222.423-0.273-0.2730.0000.0000.0000.000
156A236CYS00.0010.02722.773-0.024-0.0240.0000.0000.0000.000
157A237PHE0-0.005-0.02318.721-0.033-0.0330.0000.0000.0000.000
158A238VAL0-0.0110.01519.003-0.026-0.0260.0000.0000.0000.000
159A239SER0-0.032-0.02421.2170.0250.0250.0000.0000.0000.000
160A240ALA00.0110.00024.661-0.016-0.0160.0000.0000.0000.000
161A241PHE00.0020.00226.7160.0130.0130.0000.0000.0000.000
162A242ASN0-0.029-0.04129.905-0.015-0.0150.0000.0000.0000.000
163A243LEU00.000-0.01331.9260.0070.0070.0000.0000.0000.000
164A244SER0-0.022-0.00533.9680.0090.0090.0000.0000.0000.000
165A245GLY00.0170.01534.9640.0050.0050.0000.0000.0000.000
166A246LYS10.9690.98932.9320.1410.1410.0000.0000.0000.000
167A247ASN00.0340.01928.756-0.013-0.0130.0000.0000.0000.000
168A248GLU-1-0.850-0.91928.002-0.169-0.1690.0000.0000.0000.000
169A249ASN00.0250.02022.819-0.031-0.0310.0000.0000.0000.000
170A250LEU00.0700.06021.9970.0120.0120.0000.0000.0000.000
171A251GLU-1-0.857-0.96618.818-0.338-0.3380.0000.0000.0000.000
172A252ASN0-0.067-0.03621.3640.0050.0050.0000.0000.0000.000
173A253LYS10.7340.87224.3900.1950.1950.0000.0000.0000.000
174A254LEU00.005-0.02621.1030.0010.0010.0000.0000.0000.000
175A255LYS10.9411.01917.4110.2640.2640.0000.0000.0000.000
176A256LEU0-0.049-0.02216.709-0.049-0.0490.0000.0000.0000.000
177A257THR0-0.0130.00011.559-0.063-0.0630.0000.0000.0000.000
178A258ASN0-0.003-0.0237.689-0.075-0.0750.0000.0000.0000.000
179A259ILE00.0040.00411.0630.0210.0210.0000.0000.0000.000
180A260ILE0-0.064-0.02311.290-0.045-0.0450.0000.0000.0000.000
181A261MET0-0.035-0.01015.1410.0430.0430.0000.0000.0000.000
182A262ASP-1-0.768-0.88717.188-0.375-0.3750.0000.0000.0000.000
183A263HIS00.010-0.02219.0060.0150.0150.0000.0000.0000.000
184A264TYR0-0.0520.00519.3600.0400.0400.0000.0000.0000.000
185A265ASN0-0.085-0.04718.6410.0340.0340.0000.0000.0000.000
186A266ASN0-0.031-0.01422.718-0.008-0.0080.0000.0000.0000.000
187A267THR0-0.066-0.03418.5180.0100.0100.0000.0000.0000.000
188A268PHE00.0200.02018.915-0.028-0.0280.0000.0000.0000.000
189A269TYR00.021-0.01914.858-0.002-0.0020.0000.0000.0000.000
190A270SER00.0140.01314.542-0.003-0.0030.0000.0000.0000.000
191A271ARG10.9250.9819.9981.0781.0780.0000.0000.0000.000
192A272LEU0-0.006-0.00414.7810.0280.0280.0000.0000.0000.000
193A273PRO00.0590.03115.866-0.062-0.0620.0000.0000.0000.000
194A274SER00.0240.01515.2220.0250.0250.0000.0000.0000.000
195A275LEU0-0.015-0.00117.2050.0430.0430.0000.0000.0000.000
196A276ILE0-0.035-0.00520.665-0.010-0.0100.0000.0000.0000.000
197A277SER00.031-0.00523.1600.0190.0190.0000.0000.0000.000
198A278ASP-1-0.876-0.92726.416-0.160-0.1600.0000.0000.0000.000
199A279ASN0-0.040-0.02527.271-0.025-0.0250.0000.0000.0000.000
200A280TRP00.0180.00925.7850.0150.0150.0000.0000.0000.000
201A281LYS10.9320.96327.7350.1580.1580.0000.0000.0000.000
202A282PHE0-0.0140.00322.5640.0060.0060.0000.0000.0000.000
203A283PHE00.0380.00027.999-0.007-0.0070.0000.0000.0000.000
204A285VAL00.0280.00228.2190.0040.0040.0000.0000.0000.000
205A287SER0-0.054-0.03430.8950.0130.0130.0000.0000.0000.000
206A288LYS11.0251.01233.8690.1240.1240.0000.0000.0000.000
207A289ASP-1-0.918-0.96136.358-0.107-0.1070.0000.0000.0000.000
208A290ASN0-0.063-0.04940.0680.0020.0020.0000.0000.0000.000
209A291GLU-1-0.926-0.93137.500-0.114-0.1140.0000.0000.0000.000
210A292LYS10.8260.91737.9660.1180.1180.0000.0000.0000.000
211A293LYS10.9360.97735.3820.1230.1230.0000.0000.0000.000
212A294LEU0-0.006-0.00531.2000.0010.0010.0000.0000.0000.000
213A295VAL00.0230.01331.299-0.009-0.0090.0000.0000.0000.000
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