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: 94872

Calculation Name: 1ISE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ISE

Chain ID: A

ChEMBL ID:

UniProt ID: P0A805

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1718015.785795
FMO2-HF: Nuclear repulsion 1646369.265646
FMO2-HF: Total energy -71646.520149
FMO2-MP2: Total energy -71855.655892


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:2:ILE)


Summations of interaction energy for fragment #1(A:2:ILE)
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.
-15.501-16.60619.667-6.248-12.3140.002
Interaction energy analysis for fragmet #1(A:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.032
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].
3A4ASP-1-0.893-0.9412.882-0.9961.1830.112-0.609-1.6820.002
4A5ILE00.0100.0052.121-1.377-6.61614.214-3.894-5.0810.006
5A6ARG10.9610.9823.683-4.852-3.5410.010-0.548-0.7730.003
6A7LYS10.9680.9895.481-1.739-1.7390.0000.0000.0000.000
7A8ASP-1-0.962-0.9957.2971.0451.0450.0000.0000.0000.000
8A9ALA00.0450.0157.806-0.444-0.4440.0000.0000.0000.000
9A10GLU-1-0.938-0.9739.4820.4420.4420.0000.0000.0000.000
10A11VAL0-0.022-0.01611.577-0.219-0.2190.0000.0000.0000.000
11A12ARG10.8580.93910.977-1.278-1.2780.0000.0000.0000.000
12A13MET0-0.043-0.00512.012-0.151-0.1510.0000.0000.0000.000
13A14ASP-1-0.922-0.95315.3680.3570.3570.0000.0000.0000.000
14A15LYS10.9510.96817.115-0.545-0.5450.0000.0000.0000.000
15A16CYS0-0.023-0.00918.284-0.060-0.0600.0000.0000.0000.000
16A17VAL0-0.018-0.00318.829-0.051-0.0510.0000.0000.0000.000
17A18GLU-1-0.877-0.94821.5220.2470.2470.0000.0000.0000.000
18A19ALA0-0.035-0.00522.782-0.033-0.0330.0000.0000.0000.000
19A20PHE00.0170.00224.183-0.027-0.0270.0000.0000.0000.000
20A21LYS10.9400.95825.293-0.277-0.2770.0000.0000.0000.000
21A22THR00.0080.01627.180-0.023-0.0230.0000.0000.0000.000
22A23GLN0-0.061-0.02727.810-0.003-0.0030.0000.0000.0000.000
23A24ILE00.0150.01629.844-0.016-0.0160.0000.0000.0000.000
24A25SER0-0.070-0.05232.095-0.014-0.0140.0000.0000.0000.000
25A26LYS10.9520.97832.251-0.171-0.1710.0000.0000.0000.000
26A27ILE0-0.0220.01833.794-0.009-0.0090.0000.0000.0000.000
27A28ARG10.9000.93837.681-0.089-0.0890.0000.0000.0000.000
28A29THR0-0.065-0.06339.262-0.003-0.0030.0000.0000.0000.000
29A30GLY00.039-0.00142.174-0.003-0.0030.0000.0000.0000.000
30A31ARG10.8390.93238.349-0.113-0.1130.0000.0000.0000.000
31A32ALA0-0.042-0.02243.0590.0040.0040.0000.0000.0000.000
32A33SER00.0280.00339.1040.0030.0030.0000.0000.0000.000
33A34PRO00.010-0.01540.0160.0020.0020.0000.0000.0000.000
34A35SER0-0.033-0.01835.0130.0020.0020.0000.0000.0000.000
35A36LEU00.0070.01336.4990.0050.0050.0000.0000.0000.000
36A37LEU0-0.043-0.02738.6620.0000.0000.0000.0000.0000.000
37A38ASP-1-0.847-0.91234.9500.1360.1360.0000.0000.0000.000
38A39GLY0-0.082-0.04636.3990.0020.0020.0000.0000.0000.000
39A40ILE0-0.0130.01537.081-0.002-0.0020.0000.0000.0000.000
40A41VAL0-0.019-0.01438.7780.0010.0010.0000.0000.0000.000
41A42VAL0-0.017-0.02341.694-0.003-0.0030.0000.0000.0000.000
42A43GLU-1-0.957-0.96744.7880.0690.0690.0000.0000.0000.000
43A44TYR00.024-0.00946.064-0.003-0.0030.0000.0000.0000.000
44A45TYR0-0.020-0.01347.2400.0000.0000.0000.0000.0000.000
45A46GLY00.0280.02048.385-0.001-0.0010.0000.0000.0000.000
46A47THR0-0.0010.00042.3390.0020.0020.0000.0000.0000.000
47A48PRO0-0.031-0.00240.528-0.001-0.0010.0000.0000.0000.000
48A49THR00.017-0.00540.8720.0030.0030.0000.0000.0000.000
49A50PRO0-0.0080.00037.664-0.001-0.0010.0000.0000.0000.000
50A51LEU00.0880.04340.028-0.005-0.0050.0000.0000.0000.000
51A52ARG10.9410.96334.873-0.136-0.1360.0000.0000.0000.000
52A53GLN0-0.051-0.02639.3070.0020.0020.0000.0000.0000.000
53A54LEU00.0050.01342.507-0.004-0.0040.0000.0000.0000.000
54A55ALA00.0090.02144.868-0.005-0.0050.0000.0000.0000.000
55A56SER0-0.025-0.00244.2590.0050.0050.0000.0000.0000.000
56A57VAL00.0070.01542.279-0.004-0.0040.0000.0000.0000.000
57A58THR0-0.053-0.02743.2100.0020.0020.0000.0000.0000.000
58A59VAL0-0.001-0.01343.6750.0010.0010.0000.0000.0000.000
59A60GLU-1-0.951-0.97946.4360.0610.0610.0000.0000.0000.000
60A61ASP-1-0.843-0.91649.1480.0610.0610.0000.0000.0000.000
61A62SER0-0.032-0.02846.9300.0050.0050.0000.0000.0000.000
62A63ARG10.9440.97246.796-0.068-0.0680.0000.0000.0000.000
63A64THR00.0000.01848.735-0.001-0.0010.0000.0000.0000.000
64A65LEU00.0130.01443.6200.0010.0010.0000.0000.0000.000
65A66LYS10.9580.98547.375-0.069-0.0690.0000.0000.0000.000
66A67ILE00.0050.00246.1100.0040.0040.0000.0000.0000.000
67A68ASN0-0.008-0.00448.467-0.005-0.0050.0000.0000.0000.000
68A69VAL00.010-0.01548.8330.0030.0030.0000.0000.0000.000
69A70PHE0-0.061-0.04044.844-0.003-0.0030.0000.0000.0000.000
70A71ASP-1-0.798-0.88450.6110.0530.0530.0000.0000.0000.000
71A72ARG10.9660.98452.780-0.047-0.0470.0000.0000.0000.000
72A73SER0-0.053-0.03855.2170.0000.0000.0000.0000.0000.000
73A74MET0-0.022-0.01248.766-0.001-0.0010.0000.0000.0000.000
74A75SER0-0.025-0.01051.2540.0040.0040.0000.0000.0000.000
75A76PRO00.0470.01352.4820.0020.0020.0000.0000.0000.000
76A77ALA0-0.010-0.00150.1150.0010.0010.0000.0000.0000.000
77A78VAL00.0270.01847.3080.0030.0030.0000.0000.0000.000
78A79GLU-1-0.887-0.95648.3280.0640.0640.0000.0000.0000.000
79A80LYS10.9280.96350.592-0.064-0.0640.0000.0000.0000.000
80A81ALA0-0.025-0.01845.3780.0010.0010.0000.0000.0000.000
81A82ILE0-0.0020.00245.4140.0040.0040.0000.0000.0000.000
82A83MET0-0.0070.00546.5030.0020.0020.0000.0000.0000.000
83A84ALA0-0.053-0.02246.8890.0000.0000.0000.0000.0000.000
84A85SER0-0.079-0.02942.2890.0040.0040.0000.0000.0000.000
85A86ASP-1-0.768-0.88743.3400.0960.0960.0000.0000.0000.000
86A87LEU00.0100.01745.711-0.003-0.0030.0000.0000.0000.000
87A88GLY0-0.064-0.03147.750-0.003-0.0030.0000.0000.0000.000
88A89LEU0-0.055-0.02744.892-0.001-0.0010.0000.0000.0000.000
89A90ASN0-0.006-0.00349.414-0.001-0.0010.0000.0000.0000.000
90A91PRO0-0.029-0.01950.956-0.001-0.0010.0000.0000.0000.000
91A92ASN0-0.0050.00052.922-0.003-0.0030.0000.0000.0000.000
92A93SER00.0550.04055.0950.0010.0010.0000.0000.0000.000
93A94ALA0-0.0220.00656.580-0.002-0.0020.0000.0000.0000.000
94A95GLY00.008-0.03057.690-0.002-0.0020.0000.0000.0000.000
95A96SER0-0.0040.00654.027-0.001-0.0010.0000.0000.0000.000
96A97ASP-1-0.932-0.94752.9220.0610.0610.0000.0000.0000.000
97A98ILE00.0250.00550.456-0.002-0.0020.0000.0000.0000.000
98A99ARG10.9540.97650.942-0.055-0.0550.0000.0000.0000.000
99A100VAL00.009-0.00547.401-0.001-0.0010.0000.0000.0000.000
100A101PRO00.0310.02348.9790.0030.0030.0000.0000.0000.000
101A102LEU0-0.014-0.01444.3900.0020.0020.0000.0000.0000.000
102A103PRO0-0.034-0.01547.700-0.002-0.0020.0000.0000.0000.000
103A104PRO0-0.0080.00148.3210.0030.0030.0000.0000.0000.000
104A105LEU00.0150.02043.284-0.001-0.0010.0000.0000.0000.000
105A106THR00.0590.03047.866-0.001-0.0010.0000.0000.0000.000
106A107GLU-1-0.852-0.94947.4960.0770.0770.0000.0000.0000.000
107A108GLU-1-0.999-1.01846.6320.0730.0730.0000.0000.0000.000
108A109ARG10.9901.00342.708-0.092-0.0920.0000.0000.0000.000
109A110ARG10.9320.97043.097-0.075-0.0750.0000.0000.0000.000
110A111LYS10.9220.99741.603-0.070-0.0700.0000.0000.0000.000
111A112ASP-1-0.929-0.96440.8950.0950.0950.0000.0000.0000.000
112A113LEU0-0.015-0.02839.5190.0060.0060.0000.0000.0000.000
113A114THR00.006-0.00936.9780.0080.0080.0000.0000.0000.000
114A115LYS10.8960.94636.056-0.089-0.0890.0000.0000.0000.000
115A116ILE00.0000.00434.9250.0070.0070.0000.0000.0000.000
116A117VAL00.0410.03832.0330.0090.0090.0000.0000.0000.000
117A118ARG10.7990.86031.332-0.115-0.1150.0000.0000.0000.000
118A119GLY0-0.021-0.00230.6220.0090.0090.0000.0000.0000.000
119A120GLU-1-0.873-0.95829.1640.1860.1860.0000.0000.0000.000
120A121ALA00.0340.02526.9650.0210.0210.0000.0000.0000.000
121A122GLU-1-0.834-0.89525.2370.2560.2560.0000.0000.0000.000
122A123GLN0-0.018-0.00824.6530.0300.0300.0000.0000.0000.000
123A124ALA00.0340.01422.9920.0290.0290.0000.0000.0000.000
124A125ARG10.7890.86821.179-0.183-0.1830.0000.0000.0000.000
125A126VAL0-0.054-0.02820.0380.0400.0400.0000.0000.0000.000
126A127ALA0-0.0040.00419.1210.0350.0350.0000.0000.0000.000
127A128VAL00.0340.01215.9520.0700.0700.0000.0000.0000.000
128A129ARG10.9320.96715.054-0.229-0.2290.0000.0000.0000.000
129A130ASN0-0.046-0.02314.4920.0560.0560.0000.0000.0000.000
130A131VAL0-0.0060.00611.7830.0400.0400.0000.0000.0000.000
131A132GLY00.0550.02410.5590.2310.2310.0000.0000.0000.000
132A133ARG10.8800.9309.976-0.277-0.2770.0000.0000.0000.000
133A134ASP-1-0.837-0.91810.1711.2771.2770.0000.0000.0000.000
134A135ALA00.0190.0106.4420.1290.1290.0000.0000.0000.000
135A136ASN00.034-0.0025.5780.6100.6100.0000.0000.0000.000
136A137ASP-1-0.937-0.9687.5940.2410.2410.0000.0000.0000.000
137A138LYS10.8900.9425.423-2.194-2.1940.0000.0000.0000.000
138A139VAL00.0180.0212.547-1.471-0.5730.213-0.253-0.857-0.002
139A140LYS10.9750.9814.654-0.495-0.432-0.001-0.005-0.0570.000
140A141ALA0-0.057-0.0347.978-0.099-0.0990.0000.0000.0000.000
141A142LEU00.0770.0412.415-1.177-0.5421.449-0.353-1.732-0.004
142A143LEU0-0.059-0.0176.646-0.002-0.0020.0000.0000.0000.000
143A144LYS10.8360.9248.2840.2150.2150.0000.0000.0000.000
144A145ASP-1-0.937-0.9449.211-0.627-0.6270.0000.0000.0000.000
145A146LYS10.9230.9239.3310.7150.7150.0000.0000.0000.000
146A147GLU-1-0.992-0.9795.045-2.703-2.7030.0000.0000.0000.000
147A148ILE00.0010.0252.116-0.026-1.2503.671-0.533-1.914-0.003
148A149SER00.0310.0135.9990.4240.4240.0000.0000.0000.000
149A150GLU-1-0.921-0.9847.829-0.310-0.3100.0000.0000.0000.000
150A151ASP-1-0.947-1.0009.722-0.304-0.3040.0000.0000.0000.000
151A152ASP-1-0.820-0.9154.073-1.349-1.291-0.001-0.010-0.0470.000
152A153ASP-1-0.888-0.9565.496-0.065-0.0650.0000.0000.0000.000
153A154ARG10.9250.9756.5400.5100.5100.0000.0000.0000.000
154A155ARG10.9280.9717.2190.3500.3500.0000.0000.0000.000
155A156SER0-0.009-0.0014.1140.2680.4820.000-0.043-0.1710.000
156A157GLN0-0.045-0.0205.6280.2870.2870.0000.0000.0000.000
157A158ASP-1-0.900-0.9408.8820.2430.2430.0000.0000.0000.000
158A159ASP-1-0.952-0.9966.7100.7350.7350.0000.0000.0000.000
159A160VAL00.0090.0096.3910.0780.0780.0000.0000.0000.000
160A161GLN0-0.0180.0048.959-0.086-0.0860.0000.0000.0000.000
161A162LYS10.9340.96111.807-0.344-0.3440.0000.0000.0000.000
162A163LEU0-0.0040.0048.711-0.057-0.0570.0000.0000.0000.000
163A164THR0-0.019-0.01912.662-0.043-0.0430.0000.0000.0000.000
164A165ASP-1-0.893-0.95114.8910.2900.2900.0000.0000.0000.000
165A166ALA0-0.051-0.02815.801-0.051-0.0510.0000.0000.0000.000
166A167ALA00.013-0.00216.655-0.044-0.0440.0000.0000.0000.000
167A168ILE00.004-0.01018.289-0.044-0.0440.0000.0000.0000.000
168A169LYS10.9380.97120.419-0.261-0.2610.0000.0000.0000.000
169A170LYS10.9370.97119.280-0.368-0.3680.0000.0000.0000.000
170A171ILE0-0.0070.01021.175-0.018-0.0180.0000.0000.0000.000
171A172GLU-1-0.833-0.93324.6290.2030.2030.0000.0000.0000.000
172A173ALA0-0.0290.00026.212-0.019-0.0190.0000.0000.0000.000
173A174ALA00.0140.01527.252-0.013-0.0130.0000.0000.0000.000
174A175LEU0-0.005-0.00128.623-0.012-0.0120.0000.0000.0000.000
175A176ALA0-0.013-0.01030.441-0.013-0.0130.0000.0000.0000.000
176A177ASP-1-0.890-0.94131.7600.1420.1420.0000.0000.0000.000
177A178LYS10.8140.91333.106-0.148-0.1480.0000.0000.0000.000
178A179GLU-1-0.809-0.89333.9640.1250.1250.0000.0000.0000.000
179A180ALA0-0.0030.00136.418-0.009-0.0090.0000.0000.0000.000
180A181GLU-1-0.825-0.90537.9050.1100.1100.0000.0000.0000.000
181A182LEU0-0.026-0.01337.736-0.007-0.0070.0000.0000.0000.000
182A183MET00.002-0.01740.990-0.007-0.0070.0000.0000.0000.000
183A184GLN0-0.0330.00541.810-0.004-0.0040.0000.0000.0000.000
184A185PHE0-0.072-0.01242.048-0.005-0.0050.0000.0000.0000.000