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: 5J48Z

Calculation Name: 1ES9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ES9

Chain ID: A

ChEMBL ID:

UniProt ID: Q29460

Base Structure: X-ray

Registration Date: 2023-09-23

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2589400.576149
FMO2-HF: Nuclear repulsion 2506391.71352
FMO2-HF: Total energy -83008.862629
FMO2-MP2: Total energy -83254.720101


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:5:GLU)


Summations of interaction energy for fragment #1(A:5:GLU)
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.
-117.395-116.57415.111-7.879-8.0520.076
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.864 / q_NPA : -0.942
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].
3A7PRO0-0.025-0.0193.3322.3444.6530.076-1.050-1.3360.001
4A8ALA0-0.0020.0055.123-1.546-1.375-0.001-0.006-0.1630.000
5A9SER00.0400.0204.267-3.395-3.212-0.001-0.011-0.1700.000
6A10LYS10.8700.9431.581-95.247-97.12415.038-6.807-6.3540.075
7A11PRO00.0320.0424.929-2.229-2.194-0.001-0.005-0.0290.000
8A12THR0-0.020-0.0178.5262.3982.3980.0000.0000.0000.000
9A13PRO00.0180.01310.409-1.648-1.6480.0000.0000.0000.000
10A14VAL0-0.022-0.02113.4341.2831.2830.0000.0000.0000.000
11A15GLN0-0.054-0.03314.893-0.342-0.3420.0000.0000.0000.000
12A16ASP-1-0.751-0.86416.60713.19613.1960.0000.0000.0000.000
13A17VAL0-0.047-0.02418.8260.0030.0030.0000.0000.0000.000
14A18GLN0-0.080-0.04321.560-0.634-0.6340.0000.0000.0000.000
15A19GLY00.012-0.00524.720-0.467-0.4670.0000.0000.0000.000
16A20ASP-1-0.887-0.93926.13111.54711.5470.0000.0000.0000.000
17A21GLY00.0220.02423.749-0.187-0.1870.0000.0000.0000.000
18A22LYS10.9210.94824.162-12.357-12.3570.0000.0000.0000.000
19A23TRP0-0.042-0.03316.3840.0210.0210.0000.0000.0000.000
20A24MET00.0390.00917.5140.1160.1160.0000.0000.0000.000
21A25SER00.0060.01422.016-0.282-0.2820.0000.0000.0000.000
22A26LEU0-0.076-0.03923.903-0.433-0.4330.0000.0000.0000.000
23A27HIS10.8260.90219.692-15.799-15.7990.0000.0000.0000.000
24A28HIS00.0260.00121.837-0.056-0.0560.0000.0000.0000.000
25A29ARG10.9420.97924.959-11.076-11.0760.0000.0000.0000.000
26A30PHE0-0.0080.00222.540-0.392-0.3920.0000.0000.0000.000
27A31VAL0-0.023-0.01322.374-0.142-0.1420.0000.0000.0000.000
28A32ALA0-0.0160.00925.085-0.228-0.2280.0000.0000.0000.000
29A33ASP-1-0.889-0.96328.05610.25310.2530.0000.0000.0000.000
30A34SER0-0.063-0.05624.903-0.440-0.4400.0000.0000.0000.000
31A35LYS10.8940.95427.804-10.543-10.5430.0000.0000.0000.000
32A36ASP-1-0.910-0.94129.4239.5349.5340.0000.0000.0000.000
33A37LYS10.8330.91931.424-9.469-9.4690.0000.0000.0000.000
34A38GLU-1-0.884-0.95431.5169.9689.9680.0000.0000.0000.000
35A39PRO0-0.0570.00428.580-0.207-0.2070.0000.0000.0000.000
36A40GLU-1-0.894-0.97230.6348.8768.8760.0000.0000.0000.000
37A41VAL0-0.027-0.01828.0230.2410.2410.0000.0000.0000.000
38A42VAL00.0090.01023.422-0.091-0.0910.0000.0000.0000.000
39A43PHE00.0110.00824.4890.2180.2180.0000.0000.0000.000
40A44ILE0-0.002-0.00718.5240.0370.0370.0000.0000.0000.000
41A45GLY00.028-0.04619.0370.1510.1510.0000.0000.0000.000
42A46ASP-1-0.789-0.89219.25913.84413.8440.0000.0000.0000.000
43A47SER0-0.003-0.02220.977-0.594-0.5940.0000.0000.0000.000
44A48LEU0-0.0030.00923.304-0.528-0.5280.0000.0000.0000.000
45A49VAL00.0510.05622.678-0.504-0.5040.0000.0000.0000.000
46A50GLN00.0210.01425.056-0.360-0.3600.0000.0000.0000.000
47A51LEU0-0.032-0.01426.704-0.364-0.3640.0000.0000.0000.000
48A52MET00.0300.03128.345-0.471-0.4710.0000.0000.0000.000
49A53HIS0-0.015-0.02930.454-0.329-0.3290.0000.0000.0000.000
50A54GLN0-0.0420.00632.176-0.422-0.4220.0000.0000.0000.000
51A55CYS0-0.028-0.02433.110-0.335-0.3350.0000.0000.0000.000
52A56GLU-1-0.827-0.94933.4788.2208.2200.0000.0000.0000.000
53A57ILE0-0.205-0.03535.3710.0400.0400.0000.0000.0000.000
54A58TRP00.2250.05429.425-0.170-0.1700.0000.0000.0000.000
55A59ARG10.9490.96135.413-7.492-7.4920.0000.0000.0000.000
56A60GLU-1-0.968-0.97938.4557.0927.0920.0000.0000.0000.000
57A61LEU0-0.027-0.01435.731-0.087-0.0870.0000.0000.0000.000
58A62PHE00.016-0.01432.3690.0480.0480.0000.0000.0000.000
59A63SER0-0.071-0.02234.6280.0810.0810.0000.0000.0000.000
60A64PRO00.0200.00636.4270.0650.0650.0000.0000.0000.000
61A65LEU0-0.0140.00233.223-0.035-0.0350.0000.0000.0000.000
62A66HIS0-0.0080.01234.2020.2480.2480.0000.0000.0000.000
63A67ALA00.0200.00730.3900.2830.2830.0000.0000.0000.000
64A68LEU00.0000.00827.728-0.186-0.1860.0000.0000.0000.000
65A69ASN0-0.050-0.03926.6670.6100.6100.0000.0000.0000.000
66A70PHE00.0380.02922.473-0.038-0.0380.0000.0000.0000.000
67A71GLY00.011-0.01322.1020.7890.7890.0000.0000.0000.000
68A72ILE0-0.028-0.01920.147-0.532-0.5320.0000.0000.0000.000
69A73GLY0-0.034-0.02221.1170.4200.4200.0000.0000.0000.000
70A74GLY0-0.022-0.01520.3520.1730.1730.0000.0000.0000.000
71A75ASP-1-0.759-0.85216.67717.52217.5220.0000.0000.0000.000
72A76SER0-0.026-0.02412.578-0.637-0.6370.0000.0000.0000.000
73A77THR0-0.023-0.0369.754-0.096-0.0960.0000.0000.0000.000
74A78GLN00.0830.0398.156-1.292-1.2920.0000.0000.0000.000
75A79HIS00.0430.0299.929-0.125-0.1250.0000.0000.0000.000
76A80VAL00.0330.01013.287-0.630-0.6300.0000.0000.0000.000
77A81LEU0-0.0030.0038.414-0.645-0.6450.0000.0000.0000.000
78A82TRP00.0470.01211.358-1.378-1.3780.0000.0000.0000.000
79A83ARG10.7370.85813.023-16.508-16.5080.0000.0000.0000.000
80A84LEU0-0.046-0.02615.434-0.965-0.9650.0000.0000.0000.000
81A85GLU-1-0.909-0.94710.90425.63025.6300.0000.0000.0000.000
82A86ASN0-0.110-0.04413.700-0.870-0.8700.0000.0000.0000.000
83A87GLY00.0610.00417.425-0.675-0.6750.0000.0000.0000.000
84A88GLU-1-0.759-0.86520.04514.26314.2630.0000.0000.0000.000
85A89LEU00.0230.02718.504-0.600-0.6000.0000.0000.0000.000
86A90GLU-1-0.857-0.92020.70414.15914.1590.0000.0000.0000.000
87A91HIS0-0.010-0.00723.931-0.411-0.4110.0000.0000.0000.000
88A92ILE00.0420.05424.481-0.348-0.3480.0000.0000.0000.000
89A93ARG10.9510.97826.858-9.819-9.8190.0000.0000.0000.000
90A94PRO0-0.0280.01225.286-0.383-0.3830.0000.0000.0000.000
91A95LYS10.9380.95527.813-8.841-8.8410.0000.0000.0000.000
92A96ILE0-0.053-0.02126.4720.1190.1190.0000.0000.0000.000
93A97VAL00.0240.02420.797-0.037-0.0370.0000.0000.0000.000
94A98VAL0-0.025-0.01023.2690.0790.0790.0000.0000.0000.000
95A99VAL00.0310.01417.1460.2350.2350.0000.0000.0000.000
96A100TRP0-0.054-0.04420.328-0.359-0.3590.0000.0000.0000.000
97A101VAL00.0500.06615.537-0.024-0.0240.0000.0000.0000.000
98A102GLY00.0720.03215.1480.2240.2240.0000.0000.0000.000
99A103THR00.0060.01416.1900.2620.2620.0000.0000.0000.000
100A104ASN0-0.007-0.00917.142-0.825-0.8250.0000.0000.0000.000
101A105ASN00.0090.01011.026-0.840-0.8400.0000.0000.0000.000
102A106HIS0-0.052-0.04614.1110.0700.0700.0000.0000.0000.000
103A107GLY00.0420.02113.0380.7230.7230.0000.0000.0000.000
104A108HIS0-0.0090.0249.3230.4440.4440.0000.0000.0000.000
105A109THR00.0680.01810.907-1.251-1.2510.0000.0000.0000.000
106A110ALA00.0510.00912.6460.6370.6370.0000.0000.0000.000
107A111GLU-1-0.866-0.93611.80817.43117.4310.0000.0000.0000.000
108A112GLN00.0130.0166.441-0.719-0.7190.0000.0000.0000.000
109A113VAL00.0160.0059.4560.9870.9870.0000.0000.0000.000
110A114THR00.0260.00611.864-0.443-0.4430.0000.0000.0000.000
111A115GLY0-0.031-0.0169.042-0.433-0.4330.0000.0000.0000.000
112A116GLY00.0030.0038.8520.9500.9500.0000.0000.0000.000
113A117ILE00.014-0.0029.686-0.422-0.4220.0000.0000.0000.000
114A118LYS10.9430.96911.751-19.705-19.7050.0000.0000.0000.000
115A119ALA00.0080.0078.673-0.571-0.5710.0000.0000.0000.000
116A120ILE0-0.0060.00010.764-0.538-0.5380.0000.0000.0000.000
117A121VAL0-0.015-0.00313.535-0.771-0.7710.0000.0000.0000.000
118A122GLN0-0.062-0.03712.834-1.332-1.3320.0000.0000.0000.000
119A123LEU00.0490.02912.872-0.698-0.6980.0000.0000.0000.000
120A124VAL0-0.025-0.01914.771-0.885-0.8850.0000.0000.0000.000
121A125ASN0-0.033-0.02717.960-1.253-1.2530.0000.0000.0000.000
122A126GLU-1-0.895-0.92814.33519.02219.0220.0000.0000.0000.000
123A127ARG10.8090.89218.115-14.549-14.5490.0000.0000.0000.000
124A128GLN0-0.028-0.02219.723-1.144-1.1440.0000.0000.0000.000
125A129PRO00.0370.04122.174-0.333-0.3330.0000.0000.0000.000
126A130GLN0-0.103-0.08023.396-0.190-0.1900.0000.0000.0000.000
127A131ALA0-0.044-0.01223.926-0.417-0.4170.0000.0000.0000.000
128A132ARG10.8600.92124.517-9.787-9.7870.0000.0000.0000.000
129A133VAL00.0360.01919.4720.0500.0500.0000.0000.0000.000
130A134VAL0-0.008-0.00622.921-0.230-0.2300.0000.0000.0000.000
131A135VAL0-0.007-0.00618.6930.3900.3900.0000.0000.0000.000
132A136LEU00.0190.01321.528-0.417-0.4170.0000.0000.0000.000
133A137GLY0-0.050-0.03221.5050.6120.6120.0000.0000.0000.000
134A138LEU0-0.043-0.01217.537-0.157-0.1570.0000.0000.0000.000
135A139LEU00.0370.02222.076-0.250-0.2500.0000.0000.0000.000
136A140PRO0-0.0150.00324.5110.4980.4980.0000.0000.0000.000
137A141ARG10.9920.99321.466-12.830-12.8300.0000.0000.0000.000
138A142GLY0-0.023-0.01327.2450.0580.0580.0000.0000.0000.000
139A143GLN00.0570.04229.310-0.001-0.0010.0000.0000.0000.000
140A144HIS00.0780.04131.990-0.186-0.1860.0000.0000.0000.000
141A145PRO0-0.003-0.01230.3570.4210.4210.0000.0000.0000.000
142A146ASN0-0.026-0.02125.7420.5020.5020.0000.0000.0000.000
143A147PRO00.1030.02822.4030.1140.1140.0000.0000.0000.000
144A148LEU0-0.012-0.00120.0320.5950.5950.0000.0000.0000.000
145A149ARG10.7920.90922.529-9.484-9.4840.0000.0000.0000.000
146A150GLU-1-0.917-0.95423.56110.92910.9290.0000.0000.0000.000
147A151LYS10.8710.94914.805-17.189-17.1890.0000.0000.0000.000
148A152ASN0-0.028-0.03319.5111.0121.0120.0000.0000.0000.000
149A153ARG10.9310.96520.942-11.565-11.5650.0000.0000.0000.000
150A154ARG10.9190.96918.242-13.849-13.8490.0000.0000.0000.000
151A155VAL00.0090.00315.8220.3240.3240.0000.0000.0000.000
152A156ASN00.0230.01218.1090.5910.5910.0000.0000.0000.000
153A157GLU-1-0.915-0.94121.04011.74911.7490.0000.0000.0000.000
154A158LEU0-0.020-0.01015.438-0.106-0.1060.0000.0000.0000.000
155A159VAL00.004-0.00116.1800.2260.2260.0000.0000.0000.000
156A160ARG10.9470.98918.396-11.523-11.5230.0000.0000.0000.000
157A161ALA0-0.019-0.01420.317-0.266-0.2660.0000.0000.0000.000
158A162ALA0-0.063-0.03316.958-0.064-0.0640.0000.0000.0000.000
159A163LEU00.027-0.01018.4670.0570.0570.0000.0000.0000.000
160A164ALA0-0.0270.01121.088-0.412-0.4120.0000.0000.0000.000
161A165GLY0-0.012-0.00623.171-0.500-0.5000.0000.0000.0000.000
162A166HIS0-0.028-0.04017.9181.0111.0110.0000.0000.0000.000
163A167PRO00.0190.03223.610-0.161-0.1610.0000.0000.0000.000
164A168ARG10.8380.92524.581-11.807-11.8070.0000.0000.0000.000
165A169ALA00.0700.05821.2720.2850.2850.0000.0000.0000.000
166A170HIS00.001-0.00423.325-0.460-0.4600.0000.0000.0000.000
167A171PHE00.0500.02721.2980.2250.2250.0000.0000.0000.000
168A172LEU0-0.009-0.00524.257-0.486-0.4860.0000.0000.0000.000
169A173ASP-1-0.883-0.94225.78210.65210.6520.0000.0000.0000.000
170A174ALA0-0.055-0.05027.537-0.336-0.3360.0000.0000.0000.000
171A175ASP-1-0.810-0.89428.7199.4739.4730.0000.0000.0000.000
172A176PRO0-0.040-0.00330.527-0.114-0.1140.0000.0000.0000.000
173A177GLY00.001-0.01333.109-0.268-0.2680.0000.0000.0000.000
174A178PHE0-0.048-0.03430.480-0.133-0.1330.0000.0000.0000.000
175A179VAL0-0.085-0.04330.638-0.056-0.0560.0000.0000.0000.000
176A180HIS0-0.001-0.00533.700-0.185-0.1850.0000.0000.0000.000
177A181SER00.0230.00936.8440.1080.1080.0000.0000.0000.000
178A182ASP-1-0.862-0.91639.1337.7277.7270.0000.0000.0000.000
179A183GLY00.0200.02835.1100.0630.0630.0000.0000.0000.000
180A184THR0-0.052-0.06734.2770.3670.3670.0000.0000.0000.000
181A185ILE00.0020.01530.1530.0450.0450.0000.0000.0000.000
182A186SER00.0430.02134.604-0.064-0.0640.0000.0000.0000.000
183A187HIS00.025-0.00235.9130.2440.2440.0000.0000.0000.000
184A188HIS0-0.013-0.01336.9780.0880.0880.0000.0000.0000.000
185A189ASP-1-0.851-0.89434.6028.2168.2160.0000.0000.0000.000
186A190MET0-0.038-0.02329.1140.2910.2910.0000.0000.0000.000
187A191TYR0-0.0140.00831.346-0.015-0.0150.0000.0000.0000.000
188A192ASP-1-0.758-0.85029.95310.07710.0770.0000.0000.0000.000
189A193TYR0-0.024-0.01530.5900.2760.2760.0000.0000.0000.000
190A194LEU0-0.021-0.01623.7420.4040.4040.0000.0000.0000.000
191A195HIS10.7970.86525.275-10.891-10.8910.0000.0000.0000.000
192A196LEU00.0010.01929.056-0.245-0.2450.0000.0000.0000.000
193A197SER00.007-0.01831.561-0.007-0.0070.0000.0000.0000.000
194A198ARG10.9550.98134.826-7.795-7.7950.0000.0000.0000.000
195A199LEU00.000-0.01337.042-0.023-0.0230.0000.0000.0000.000
196A200GLY00.0710.02934.1830.0000.0000.0000.0000.0000.000
197A201TYR0-0.020-0.05328.3590.1370.1370.0000.0000.0000.000
198A202THR0-0.0270.01733.773-0.036-0.0360.0000.0000.0000.000
199A203PRO0-0.017-0.02834.874-0.020-0.0200.0000.0000.0000.000
200A204VAL00.0200.03129.2740.0900.0900.0000.0000.0000.000
201A205CYS0-0.036-0.01431.8050.2100.2100.0000.0000.0000.000
202A206ARG10.9841.00133.217-7.632-7.6320.0000.0000.0000.000
203A207ALA0-0.0020.00532.122-0.069-0.0690.0000.0000.0000.000
204A208LEU00.0120.00427.9310.0670.0670.0000.0000.0000.000
205A209HIS0-0.010-0.00931.1400.0640.0640.0000.0000.0000.000
206A210SER00.0090.00934.149-0.067-0.0670.0000.0000.0000.000
207A211LEU0-0.027-0.00428.192-0.052-0.0520.0000.0000.0000.000
208A212LEU00.011-0.02528.6450.0330.0330.0000.0000.0000.000
209A213LEU00.0160.01832.281-0.050-0.0500.0000.0000.0000.000
210A214ARG10.9090.95932.121-9.038-9.0380.0000.0000.0000.000
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