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: YV4M2

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2590108.137758
FMO2-HF: Nuclear repulsion 2507097.640424
FMO2-HF: Total energy -83010.497334
FMO2-MP2: Total energy -83256.315076


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.
-144.884-146.20122.522-11.648-9.5550.127
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 : -0.833 / q_NPA : -0.909
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].
3A7PRO0-0.013-0.0083.5591.8254.0850.026-0.986-1.3000.003
4A8ALA0-0.014-0.0025.026-1.373-1.223-0.001-0.005-0.1430.000
5A9SER00.0340.0134.554-3.430-3.304-0.001-0.007-0.1170.000
6A10LYS10.8320.9081.646-124.627-128.50522.499-10.646-7.9750.124
7A11PRO00.0150.0364.979-2.148-2.123-0.001-0.004-0.0200.000
8A12THR0-0.023-0.0238.3892.7092.7090.0000.0000.0000.000
9A13PRO00.0050.00810.571-1.821-1.8210.0000.0000.0000.000
10A14VAL0-0.021-0.01913.4481.3991.3990.0000.0000.0000.000
11A15GLN0-0.055-0.02814.727-0.231-0.2310.0000.0000.0000.000
12A16ASP-1-0.751-0.86416.50313.49013.4900.0000.0000.0000.000
13A17VAL0-0.037-0.02218.579-0.013-0.0130.0000.0000.0000.000
14A18GLN0-0.054-0.02121.341-0.619-0.6190.0000.0000.0000.000
15A19GLY00.0290.00224.589-0.495-0.4950.0000.0000.0000.000
16A20ASP-1-0.837-0.89525.99211.92311.9230.0000.0000.0000.000
17A21GLY00.0420.03023.740-0.204-0.2040.0000.0000.0000.000
18A22LYS10.7920.86424.757-12.280-12.2800.0000.0000.0000.000
19A23TRP0-0.008-0.01016.2210.0560.0560.0000.0000.0000.000
20A24MET00.0240.00417.6450.1150.1150.0000.0000.0000.000
21A25SER0-0.0010.00422.119-0.317-0.3170.0000.0000.0000.000
22A26LEU0-0.057-0.02423.833-0.420-0.4200.0000.0000.0000.000
23A27HIS10.8180.91119.436-16.298-16.2980.0000.0000.0000.000
24A28HIS00.0380.00021.246-0.047-0.0470.0000.0000.0000.000
25A29ARG10.9240.97424.718-11.332-11.3320.0000.0000.0000.000
26A30PHE0-0.0030.00122.844-0.464-0.4640.0000.0000.0000.000
27A31VAL00.0010.00522.079-0.177-0.1770.0000.0000.0000.000
28A32ALA0-0.0170.00624.926-0.284-0.2840.0000.0000.0000.000
29A33ASP-1-0.901-0.97828.25310.19910.1990.0000.0000.0000.000
30A34SER0-0.045-0.04824.929-0.460-0.4600.0000.0000.0000.000
31A35LYS10.8030.89627.948-10.351-10.3510.0000.0000.0000.000
32A36ASP-1-0.870-0.91829.3719.5849.5840.0000.0000.0000.000
33A37LYS10.8300.93031.662-9.870-9.8700.0000.0000.0000.000
34A38GLU-1-0.846-0.93631.71910.12910.1290.0000.0000.0000.000
35A39PRO0-0.0590.00228.825-0.207-0.2070.0000.0000.0000.000
36A40GLU-1-0.829-0.92930.7879.0009.0000.0000.0000.0000.000
37A41VAL0-0.029-0.01828.1580.2300.2300.0000.0000.0000.000
38A42VAL00.0040.01423.946-0.097-0.0970.0000.0000.0000.000
39A43PHE00.0200.00524.6900.2060.2060.0000.0000.0000.000
40A44ILE00.001-0.00418.6520.0300.0300.0000.0000.0000.000
41A45GLY00.038-0.01419.2040.1180.1180.0000.0000.0000.000
42A46ASP-1-0.809-0.89919.38814.14414.1440.0000.0000.0000.000
43A47SER00.017-0.00921.149-0.600-0.6000.0000.0000.0000.000
44A48LEU0-0.0100.00223.974-0.546-0.5460.0000.0000.0000.000
45A49VAL00.0510.04922.875-0.522-0.5220.0000.0000.0000.000
46A50GLN00.0090.01625.177-0.425-0.4250.0000.0000.0000.000
47A51LEU0-0.019-0.00926.864-0.373-0.3730.0000.0000.0000.000
48A52MET0-0.0020.01328.426-0.487-0.4870.0000.0000.0000.000
49A53HIS00.019-0.01730.628-0.304-0.3040.0000.0000.0000.000
50A54GLN0-0.069-0.01032.345-0.393-0.3930.0000.0000.0000.000
51A55CYS0-0.045-0.02233.297-0.356-0.3560.0000.0000.0000.000
52A56GLU-1-0.752-0.85233.7288.2338.2330.0000.0000.0000.000
53A57ILE0-0.151-0.03435.5710.0810.0810.0000.0000.0000.000
54A58TRP00.1410.02929.687-0.132-0.1320.0000.0000.0000.000
55A59ARG10.8730.91935.607-7.461-7.4610.0000.0000.0000.000
56A60GLU-1-0.817-0.90938.6407.2777.2770.0000.0000.0000.000
57A61LEU0-0.059-0.02435.796-0.113-0.1130.0000.0000.0000.000
58A62PHE00.027-0.01732.6030.0370.0370.0000.0000.0000.000
59A63SER0-0.051-0.01634.8210.1010.1010.0000.0000.0000.000
60A64PRO00.0110.00236.6090.0530.0530.0000.0000.0000.000
61A65LEU0-0.027-0.00133.675-0.043-0.0430.0000.0000.0000.000
62A66HIS0-0.0070.00734.3900.2460.2460.0000.0000.0000.000
63A67ALA00.0240.01030.5500.2810.2810.0000.0000.0000.000
64A68LEU00.0040.01327.920-0.175-0.1750.0000.0000.0000.000
65A69ASN0-0.051-0.04026.8870.6110.6110.0000.0000.0000.000
66A70PHE00.0440.02322.627-0.079-0.0790.0000.0000.0000.000
67A71GLY00.015-0.00722.2370.8250.8250.0000.0000.0000.000
68A72ILE0-0.022-0.02220.375-0.541-0.5410.0000.0000.0000.000
69A73GLY0-0.020-0.02021.2490.4270.4270.0000.0000.0000.000
70A74GLY0-0.018-0.01120.3820.1900.1900.0000.0000.0000.000
71A75ASP-1-0.764-0.85116.87618.16718.1670.0000.0000.0000.000
72A76SER0-0.033-0.02212.786-0.678-0.6780.0000.0000.0000.000
73A77THR0-0.024-0.02810.019-0.178-0.1780.0000.0000.0000.000
74A78GLN00.0780.0408.265-1.276-1.2760.0000.0000.0000.000
75A79HIS00.0380.01910.0660.0940.0940.0000.0000.0000.000
76A80VAL00.0450.01713.377-0.629-0.6290.0000.0000.0000.000
77A81LEU0-0.0190.0028.574-0.720-0.7200.0000.0000.0000.000
78A82TRP00.0540.01511.102-1.586-1.5860.0000.0000.0000.000
79A83ARG10.7140.84213.069-16.988-16.9880.0000.0000.0000.000
80A84LEU0-0.026-0.01615.566-1.052-1.0520.0000.0000.0000.000
81A85GLU-1-0.886-0.94311.01127.38127.3810.0000.0000.0000.000
82A86ASN0-0.107-0.04813.111-0.749-0.7490.0000.0000.0000.000
83A87GLY00.0620.01217.123-0.709-0.7090.0000.0000.0000.000
84A88GLU-1-0.769-0.88020.10714.67614.6760.0000.0000.0000.000
85A89LEU00.0210.03018.706-0.634-0.6340.0000.0000.0000.000
86A90GLU-1-0.839-0.89321.05214.17914.1790.0000.0000.0000.000
87A91HIS0-0.009-0.00724.093-0.438-0.4380.0000.0000.0000.000
88A92ILE00.0200.04324.634-0.361-0.3610.0000.0000.0000.000
89A93ARG10.9620.98927.291-9.973-9.9730.0000.0000.0000.000
90A94PRO0-0.0270.01525.563-0.355-0.3550.0000.0000.0000.000
91A95LYS10.8670.90727.988-8.852-8.8520.0000.0000.0000.000
92A96ILE0-0.069-0.02626.7270.1100.1100.0000.0000.0000.000
93A97VAL00.0290.02621.011-0.037-0.0370.0000.0000.0000.000
94A98VAL0-0.027-0.01223.4980.0650.0650.0000.0000.0000.000
95A99VAL00.0360.01717.3630.2430.2430.0000.0000.0000.000
96A100TRP0-0.049-0.04220.540-0.412-0.4120.0000.0000.0000.000
97A101VAL00.0940.06215.588-0.033-0.0330.0000.0000.0000.000
98A102GLY00.0450.00815.3830.1950.1950.0000.0000.0000.000
99A103THR00.0060.01316.4280.2610.2610.0000.0000.0000.000
100A104ASN0-0.023-0.02217.346-0.876-0.8760.0000.0000.0000.000
101A105ASN00.0120.01311.198-0.779-0.7790.0000.0000.0000.000
102A106HIS0-0.029-0.03814.115-0.013-0.0130.0000.0000.0000.000
103A107GLY00.0450.02413.0400.7710.7710.0000.0000.0000.000
104A108HIS00.0020.0209.1950.3630.3630.0000.0000.0000.000
105A109THR00.0670.03110.921-1.348-1.3480.0000.0000.0000.000
106A110ALA00.0500.00712.6460.7040.7040.0000.0000.0000.000
107A111GLU-1-0.794-0.90011.85017.21317.2130.0000.0000.0000.000
108A112GLN00.0200.0226.503-0.738-0.7380.0000.0000.0000.000
109A113VAL00.0110.0069.7480.9860.9860.0000.0000.0000.000
110A114THR00.0280.00512.142-0.389-0.3890.0000.0000.0000.000
111A115GLY0-0.021-0.0119.352-0.452-0.4520.0000.0000.0000.000
112A116GLY0-0.003-0.0029.1211.0021.0020.0000.0000.0000.000
113A117ILE00.012-0.0029.963-0.398-0.3980.0000.0000.0000.000
114A118LYS10.9470.97212.077-19.254-19.2540.0000.0000.0000.000
115A119ALA00.0040.0068.921-0.605-0.6050.0000.0000.0000.000
116A120ILE0-0.0050.00011.008-0.539-0.5390.0000.0000.0000.000
117A121VAL0-0.022-0.00713.757-0.799-0.7990.0000.0000.0000.000
118A122GLN0-0.040-0.03213.096-1.419-1.4190.0000.0000.0000.000
119A123LEU00.0580.03013.219-0.676-0.6760.0000.0000.0000.000
120A124VAL0-0.034-0.02315.062-0.919-0.9190.0000.0000.0000.000
121A125ASN0-0.042-0.02518.146-1.316-1.3160.0000.0000.0000.000
122A126GLU-1-0.893-0.92915.06319.22519.2250.0000.0000.0000.000
123A127ARG10.7950.86018.705-14.672-14.6720.0000.0000.0000.000
124A128GLN0-0.036-0.02420.348-1.138-1.1380.0000.0000.0000.000
125A129PRO00.0450.04522.901-0.327-0.3270.0000.0000.0000.000
126A130GLN0-0.112-0.07723.851-0.217-0.2170.0000.0000.0000.000
127A131ALA0-0.0170.00424.113-0.413-0.4130.0000.0000.0000.000
128A132ARG10.8650.92624.729-9.672-9.6720.0000.0000.0000.000
129A133VAL00.0330.02519.7190.0610.0610.0000.0000.0000.000
130A134VAL0-0.018-0.00923.164-0.258-0.2580.0000.0000.0000.000
131A135VAL0-0.001-0.00518.9100.3990.3990.0000.0000.0000.000
132A136LEU00.0110.01021.801-0.444-0.4440.0000.0000.0000.000
133A137GLY0-0.032-0.02321.7800.6260.6260.0000.0000.0000.000
134A138LEU0-0.045-0.01517.810-0.137-0.1370.0000.0000.0000.000
135A139LEU00.0190.01622.344-0.290-0.2900.0000.0000.0000.000
136A140PRO0-0.024-0.00524.7610.4980.4980.0000.0000.0000.000
137A141ARG10.9680.98821.076-13.248-13.2480.0000.0000.0000.000
138A142GLY0-0.014-0.00727.4690.0470.0470.0000.0000.0000.000
139A143GLN00.0620.04229.422-0.076-0.0760.0000.0000.0000.000
140A144HIS00.0620.03331.995-0.201-0.2010.0000.0000.0000.000
141A145PRO00.0160.00230.3680.4280.4280.0000.0000.0000.000
142A146ASN0-0.034-0.03025.8140.4520.4520.0000.0000.0000.000
143A147PRO00.0760.01522.3980.0910.0910.0000.0000.0000.000
144A148LEU0-0.0050.00320.2530.5630.5630.0000.0000.0000.000
145A149ARG10.7710.89522.680-9.588-9.5880.0000.0000.0000.000
146A150GLU-1-0.852-0.92223.52411.12611.1260.0000.0000.0000.000
147A151LYS10.8420.92814.981-17.681-17.6810.0000.0000.0000.000
148A152ASN0-0.037-0.03819.6281.0361.0360.0000.0000.0000.000
149A153ARG10.8780.92921.209-11.555-11.5550.0000.0000.0000.000
150A154ARG10.8650.94717.898-14.144-14.1440.0000.0000.0000.000
151A155VAL0-0.004-0.00416.0780.3410.3410.0000.0000.0000.000
152A156ASN00.0260.01318.4040.6740.6740.0000.0000.0000.000
153A157GLU-1-0.857-0.90721.34112.11912.1190.0000.0000.0000.000
154A158LEU0-0.039-0.01915.403-0.102-0.1020.0000.0000.0000.000
155A159VAL0-0.010-0.01316.5110.2480.2480.0000.0000.0000.000
156A160ARG10.8670.93718.705-11.443-11.4430.0000.0000.0000.000
157A161ALA0-0.012-0.00720.309-0.273-0.2730.0000.0000.0000.000
158A162ALA0-0.076-0.04317.116-0.057-0.0570.0000.0000.0000.000
159A163LEU00.008-0.01218.4320.0900.0900.0000.0000.0000.000
160A164ALA0-0.0200.01721.383-0.413-0.4130.0000.0000.0000.000
161A165GLY0-0.013-0.00823.235-0.498-0.4980.0000.0000.0000.000
162A166HIS00.000-0.03018.2671.0301.0300.0000.0000.0000.000
163A167PRO0-0.0050.02323.880-0.139-0.1390.0000.0000.0000.000
164A168ARG10.8230.89624.697-11.981-11.9810.0000.0000.0000.000
165A169ALA00.0670.05421.5140.2970.2970.0000.0000.0000.000
166A170HIS0-0.022-0.01423.593-0.599-0.5990.0000.0000.0000.000
167A171PHE00.0450.03221.1840.2660.2660.0000.0000.0000.000
168A172LEU0-0.0050.00124.550-0.515-0.5150.0000.0000.0000.000
169A173ASP-1-0.786-0.89726.06711.46811.4680.0000.0000.0000.000
170A174ALA0-0.062-0.04627.805-0.358-0.3580.0000.0000.0000.000
171A175ASP-1-0.805-0.89728.9709.6159.6150.0000.0000.0000.000
172A176PRO0-0.0190.00630.804-0.094-0.0940.0000.0000.0000.000
173A177GLY0-0.005-0.01533.394-0.267-0.2670.0000.0000.0000.000
174A178PHE0-0.034-0.03030.783-0.139-0.1390.0000.0000.0000.000
175A179VAL0-0.088-0.04230.871-0.058-0.0580.0000.0000.0000.000
176A180HIS00.0170.00333.959-0.181-0.1810.0000.0000.0000.000
177A181SER00.0430.01637.0570.0750.0750.0000.0000.0000.000
178A182ASP-1-0.894-0.92839.1927.8087.8080.0000.0000.0000.000
179A183GLY00.0260.03335.1940.0620.0620.0000.0000.0000.000
180A184THR0-0.051-0.06134.4080.3850.3850.0000.0000.0000.000
181A185ILE0-0.0090.00930.3910.0430.0430.0000.0000.0000.000
182A186SER00.0490.02934.836-0.067-0.0670.0000.0000.0000.000
183A187HIS00.020-0.00436.1180.2490.2490.0000.0000.0000.000
184A188HIS0-0.014-0.01537.1830.0790.0790.0000.0000.0000.000
185A189ASP-1-0.856-0.90234.8588.2718.2710.0000.0000.0000.000
186A190MET0-0.025-0.01629.2760.2860.2860.0000.0000.0000.000
187A191TYR0-0.0050.01331.294-0.052-0.0520.0000.0000.0000.000
188A192ASP-1-0.776-0.86730.11710.28610.2860.0000.0000.0000.000
189A193TYR0-0.025-0.01930.6210.2520.2520.0000.0000.0000.000
190A194LEU0-0.010-0.00423.9410.3930.3930.0000.0000.0000.000
191A195HIS10.8050.87325.489-11.104-11.1040.0000.0000.0000.000
192A196LEU0-0.0040.01829.247-0.260-0.2600.0000.0000.0000.000
193A197SER0-0.007-0.02331.770-0.021-0.0210.0000.0000.0000.000
194A198ARG10.8770.90935.038-7.999-7.9990.0000.0000.0000.000
195A199LEU0-0.004-0.01237.249-0.020-0.0200.0000.0000.0000.000
196A200GLY00.0770.03434.413-0.001-0.0010.0000.0000.0000.000
197A201TYR0-0.026-0.05428.6130.1190.1190.0000.0000.0000.000
198A202THR0-0.0320.01034.002-0.035-0.0350.0000.0000.0000.000
199A203PRO0-0.022-0.02435.002-0.020-0.0200.0000.0000.0000.000
200A204VAL00.0230.03229.5340.0900.0900.0000.0000.0000.000
201A205CYS0-0.009-0.00632.0620.2720.2720.0000.0000.0000.000
202A206ARG10.9911.00633.460-7.716-7.7160.0000.0000.0000.000
203A207ALA00.0000.00532.434-0.072-0.0720.0000.0000.0000.000
204A208LEU00.0170.00428.1150.0550.0550.0000.0000.0000.000
205A209HIS0-0.017-0.01331.3990.0280.0280.0000.0000.0000.000
206A210SER00.0060.00734.397-0.080-0.0800.0000.0000.0000.000
207A211LEU0-0.040-0.00728.546-0.054-0.0540.0000.0000.0000.000
208A212LEU00.007-0.02328.8220.0340.0340.0000.0000.0000.000
209A213LEU00.0140.01832.529-0.049-0.0490.0000.0000.0000.000
210A214ARG10.9080.95431.747-9.219-9.2190.0000.0000.0000.000
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