Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 7GN9K

Calculation Name: 2I88-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I88

Chain ID: A

ChEMBL ID:

UniProt ID: P02978

Base Structure: X-ray

Registration Date: 2023-03-13

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1912045.576847
FMO2-HF: Nuclear repulsion 1844364.816206
FMO2-HF: Total energy -67680.760641
FMO2-MP2: Total energy -67882.988312


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:345:ILE)


Summations of interaction energy for fragment #1(A:345: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.
-10.001-10.14615.107-6.716-8.247-0.068
Interaction energy analysis for fragmet #1(A:345:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.025
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].
3A347ASP-1-0.638-0.8111.781-12.155-15.35713.055-5.503-4.351-0.066
4A348ALA0-0.033-0.0012.5160.5901.5860.799-0.645-1.150-0.002
5A349VAL0-0.0030.0043.2141.0281.6460.031-0.153-0.4950.000
6A350ASP-1-0.866-0.9365.833-0.300-0.3000.0000.0000.0000.000
7A351ALA0-0.025-0.0037.5200.3920.3920.0000.0000.0000.000
8A352THR0-0.001-0.0157.5270.3620.3620.0000.0000.0000.000
9A353VAL0-0.010-0.0109.9000.2240.2240.0000.0000.0000.000
10A354SER00.000-0.00411.7770.1910.1910.0000.0000.0000.000
11A355PHE0-0.0220.00012.7220.1140.1140.0000.0000.0000.000
12A356TYR00.0420.00111.6100.0900.0900.0000.0000.0000.000
13A357GLN0-0.0210.00615.9850.0710.0710.0000.0000.0000.000
14A358THR00.031-0.00116.9520.0520.0520.0000.0000.0000.000
15A359LEU0-0.082-0.04617.8690.0450.0450.0000.0000.0000.000
16A360THR0-0.053-0.03719.8960.0380.0380.0000.0000.0000.000
17A361GLU-1-0.909-0.93421.132-0.253-0.2530.0000.0000.0000.000
18A362LYS10.7970.90920.3130.3490.3490.0000.0000.0000.000
19A363TYR0-0.058-0.04622.9760.0140.0140.0000.0000.0000.000
20A364GLY00.0340.02525.5260.0020.0020.0000.0000.0000.000
21A365GLU-1-0.740-0.86022.817-0.243-0.2430.0000.0000.0000.000
22A366LYS10.8610.91622.9340.1390.1390.0000.0000.0000.000
23A367TYR0-0.021-0.02821.949-0.012-0.0120.0000.0000.0000.000
24A368SER00.0130.01018.433-0.031-0.0310.0000.0000.0000.000
25A369LYS10.8830.91318.5240.2000.2000.0000.0000.0000.000
26A370MET0-0.047-0.01419.641-0.006-0.0060.0000.0000.0000.000
27A371ALA00.0180.01117.722-0.002-0.0020.0000.0000.0000.000
28A372GLN00.0450.01814.1440.0070.0070.0000.0000.0000.000
29A373GLU-1-0.782-0.87215.959-0.228-0.2280.0000.0000.0000.000
30A374LEU0-0.054-0.01518.4620.0260.0260.0000.0000.0000.000
31A375ALA00.0600.02613.0850.0050.0050.0000.0000.0000.000
32A376ASP-1-0.798-0.87212.006-0.628-0.6280.0000.0000.0000.000
33A377LYS10.8290.90814.0730.2360.2360.0000.0000.0000.000
34A378SER0-0.027-0.04014.4050.0200.0200.0000.0000.0000.000
35A379LYS10.8170.9219.0790.8020.8020.0000.0000.0000.000
36A380GLY00.0270.02113.6910.0360.0360.0000.0000.0000.000
37A381LYS10.7270.87815.8780.2540.2540.0000.0000.0000.000
38A382LYS10.8780.92816.6810.2020.2020.0000.0000.0000.000
39A383ILE0-0.013-0.01020.746-0.004-0.0040.0000.0000.0000.000
40A384GLY00.0340.02523.2520.0100.0100.0000.0000.0000.000
41A385ASN00.001-0.02426.7300.0000.0000.0000.0000.0000.000
42A386VAL00.0370.02127.806-0.003-0.0030.0000.0000.0000.000
43A387ASN0-0.007-0.01029.267-0.006-0.0060.0000.0000.0000.000
44A388GLU-1-0.871-0.91631.103-0.110-0.1100.0000.0000.0000.000
45A389ALA0-0.0020.00627.478-0.001-0.0010.0000.0000.0000.000
46A390LEU00.0140.00929.482-0.001-0.0010.0000.0000.0000.000
47A391ALA00.0120.00431.6870.0020.0020.0000.0000.0000.000
48A392ALA0-0.012-0.00430.7060.0030.0030.0000.0000.0000.000
49A393PHE0-0.003-0.00729.146-0.002-0.0020.0000.0000.0000.000
50A394GLU-1-0.845-0.92531.515-0.112-0.1120.0000.0000.0000.000
51A395LYS10.9410.97935.1930.1140.1140.0000.0000.0000.000
52A396TYR0-0.044-0.03730.6280.0000.0000.0000.0000.0000.000
53A397LYS10.8740.93933.6100.1140.1140.0000.0000.0000.000
54A398ASP-1-0.846-0.92534.723-0.094-0.0940.0000.0000.0000.000
55A399VAL0-0.049-0.01236.3210.0060.0060.0000.0000.0000.000
56A400LEU0-0.0060.00531.9570.0030.0030.0000.0000.0000.000
57A401ASN00.028-0.00935.969-0.002-0.0020.0000.0000.0000.000
58A402LYS10.7920.89038.4840.0950.0950.0000.0000.0000.000
59A403LYS10.9090.95937.1740.1060.1060.0000.0000.0000.000
60A404PHE00.0420.02934.527-0.003-0.0030.0000.0000.0000.000
61A405SER0-0.006-0.02039.2030.0020.0020.0000.0000.0000.000
62A406LYS10.8510.89539.6090.0910.0910.0000.0000.0000.000
63A407ALA00.0540.02939.791-0.003-0.0030.0000.0000.0000.000
64A408ASP-1-0.818-0.87237.272-0.105-0.1050.0000.0000.0000.000
65A409ARG10.8460.92235.1700.0970.0970.0000.0000.0000.000
66A410ASP-1-0.775-0.89334.869-0.107-0.1070.0000.0000.0000.000
67A411ALA0-0.0080.01135.794-0.002-0.0020.0000.0000.0000.000
68A412ILE0-0.043-0.01129.743-0.007-0.0070.0000.0000.0000.000
69A413PHE00.0320.00531.094-0.007-0.0070.0000.0000.0000.000
70A414ASN00.009-0.00432.504-0.001-0.0010.0000.0000.0000.000
71A415ALA00.0050.00929.9350.0000.0000.0000.0000.0000.000
72A416LEU0-0.003-0.01426.236-0.007-0.0070.0000.0000.0000.000
73A417ALA0-0.023-0.01128.572-0.005-0.0050.0000.0000.0000.000
74A418SER0-0.048-0.00930.1900.0100.0100.0000.0000.0000.000
75A419VAL0-0.068-0.01823.722-0.005-0.0050.0000.0000.0000.000
76A420LYS10.8400.90523.7890.1860.1860.0000.0000.0000.000
77A421TYR00.014-0.01917.843-0.020-0.0200.0000.0000.0000.000
78A422ASP-1-0.828-0.92119.382-0.229-0.2290.0000.0000.0000.000
79A423ASP-1-0.827-0.88619.039-0.231-0.2310.0000.0000.0000.000
80A424TRP0-0.034-0.03317.719-0.045-0.0450.0000.0000.0000.000
81A425ALA00.0410.02316.028-0.069-0.0690.0000.0000.0000.000
82A426LYS10.8400.91413.9330.3060.3060.0000.0000.0000.000
83A427HIS00.0030.00611.132-0.174-0.1740.0000.0000.0000.000
84A428LEU00.0160.01410.671-0.138-0.1380.0000.0000.0000.000
85A429ASP-1-0.788-0.8796.283-0.968-0.9680.0000.0000.0000.000
86A430GLN0-0.0080.0065.990-0.250-0.2500.0000.0000.0000.000
87A431PHE00.0580.0196.471-0.346-0.3460.0000.0000.0000.000
88A432ALA00.0250.0118.0820.0210.0210.0000.0000.0000.000
89A433LYS10.7990.8782.512-0.5850.6841.223-0.403-2.0890.000
90A434TYR0-0.030-0.0184.504-0.0980.076-0.001-0.012-0.1620.000
91A435LEU0-0.071-0.0485.9070.2880.2880.0000.0000.0000.000
92A436LYS10.8840.9525.5390.6350.6350.0000.0000.0000.000
93A437ILE0-0.015-0.0057.2630.1670.1670.0000.0000.0000.000
94A438THR0-0.054-0.0368.555-0.021-0.0210.0000.0000.0000.000
95A439GLY00.0230.02810.7910.0510.0510.0000.0000.0000.000
96A440HIS00.003-0.01012.683-0.027-0.0270.0000.0000.0000.000
97A441VAL0-0.006-0.00710.870-0.036-0.0360.0000.0000.0000.000
98A442SER0-0.022-0.00714.0810.0250.0250.0000.0000.0000.000
99A443PHE00.018-0.0019.775-0.004-0.0040.0000.0000.0000.000
100A444GLY0-0.0090.02915.983-0.008-0.0080.0000.0000.0000.000
101A445TYR0-0.071-0.08319.3980.0240.0240.0000.0000.0000.000
102A446ASP-1-0.736-0.86120.574-0.224-0.2240.0000.0000.0000.000
103A447VAL00.0110.00521.5610.0150.0150.0000.0000.0000.000
104A448VAL0-0.0050.00823.5970.0110.0110.0000.0000.0000.000
105A449SER0-0.007-0.03126.1250.0160.0160.0000.0000.0000.000
106A450ASP-1-0.808-0.87727.068-0.139-0.1390.0000.0000.0000.000
107A451ILE0-0.022-0.01525.1990.0080.0080.0000.0000.0000.000
108A452LEU0-0.014-0.00929.4120.0090.0090.0000.0000.0000.000
109A453LYS10.8750.93430.5220.1350.1350.0000.0000.0000.000
110A454ILE0-0.0110.01430.7540.0070.0070.0000.0000.0000.000
111A455LYS10.8630.95134.7960.1070.1070.0000.0000.0000.000
112A456ASP-1-0.923-0.96936.668-0.091-0.0910.0000.0000.0000.000
113A457THR0-0.061-0.04037.0600.0040.0040.0000.0000.0000.000
114A458GLY0-0.043-0.01637.5430.0030.0030.0000.0000.0000.000
115A459ASP-1-0.838-0.93136.273-0.107-0.1070.0000.0000.0000.000
116A460TRP00.0590.01229.681-0.010-0.0100.0000.0000.0000.000
117A461LYS10.9560.98231.3150.0820.0820.0000.0000.0000.000
118A462PRO0-0.012-0.00831.723-0.004-0.0040.0000.0000.0000.000
119A463LEU00.0410.02326.118-0.004-0.0040.0000.0000.0000.000
120A464PHE00.0380.00826.979-0.011-0.0110.0000.0000.0000.000
121A465LEU0-0.013-0.00426.991-0.004-0.0040.0000.0000.0000.000
122A466THR0-0.038-0.00825.9100.0010.0010.0000.0000.0000.000
123A467LEU00.0160.00021.732-0.009-0.0090.0000.0000.0000.000
124A468GLU-1-0.833-0.90922.165-0.147-0.1470.0000.0000.0000.000
125A469LYS10.8260.88522.9890.1220.1220.0000.0000.0000.000
126A470LYS10.8380.93520.8110.1680.1680.0000.0000.0000.000
127A471ALA00.0200.01918.401-0.015-0.0150.0000.0000.0000.000
128A472ALA0-0.0040.00418.395-0.008-0.0080.0000.0000.0000.000
129A473ASP-1-0.821-0.89717.025-0.174-0.1740.0000.0000.0000.000
130A474ALA00.0230.02914.435-0.004-0.0040.0000.0000.0000.000
131A475GLY0-0.018-0.00116.044-0.007-0.0070.0000.0000.0000.000
132A476VAL0-0.003-0.02217.406-0.020-0.0200.0000.0000.0000.000
133A477SER00.0440.02312.5220.0020.0020.0000.0000.0000.000
134A478TYR00.0360.00113.890-0.055-0.0550.0000.0000.0000.000
135A479VAL00.000-0.00315.237-0.011-0.0110.0000.0000.0000.000
136A480VAL00.006-0.00214.3610.0030.0030.0000.0000.0000.000
137A481ALA00.0170.01612.150-0.020-0.0200.0000.0000.0000.000
138A482LEU00.0020.01813.784-0.019-0.0190.0000.0000.0000.000
139A483LEU0-0.010-0.00616.9850.0040.0040.0000.0000.0000.000
140A484PHE0-0.011-0.01313.3770.0330.0330.0000.0000.0000.000
141A485SER00.008-0.00814.100-0.037-0.0370.0000.0000.0000.000
142A486LEU00.0100.01215.5990.0230.0230.0000.0000.0000.000
143A487LEU0-0.0210.00318.4430.0250.0250.0000.0000.0000.000
144A488ALA0-0.026-0.00715.1970.0170.0170.0000.0000.0000.000
145A489GLY0-0.033-0.02317.1950.0240.0240.0000.0000.0000.000
146A490THR0-0.045-0.02519.1100.0440.0440.0000.0000.0000.000
147A491THR00.0280.01022.205-0.028-0.0280.0000.0000.0000.000
148A492LEU00.0190.03124.9280.0230.0230.0000.0000.0000.000
149A493GLY00.0930.04027.202-0.002-0.0020.0000.0000.0000.000
150A494ILE00.035-0.00329.274-0.006-0.0060.0000.0000.0000.000
151A495TRP00.0270.02130.114-0.009-0.0090.0000.0000.0000.000
152A496GLY00.0580.02328.677-0.002-0.0020.0000.0000.0000.000
153A497ILE00.0050.02024.183-0.010-0.0100.0000.0000.0000.000
154A498ALA00.0120.02226.045-0.012-0.0120.0000.0000.0000.000
155A499ILE0-0.022-0.00428.165-0.002-0.0020.0000.0000.0000.000
156A500VAL00.0180.00622.308-0.002-0.0020.0000.0000.0000.000
157A501THR00.010-0.02023.338-0.020-0.0200.0000.0000.0000.000
158A502GLY00.0320.01424.465-0.001-0.0010.0000.0000.0000.000
159A503ILE0-0.0010.00423.8620.0040.0040.0000.0000.0000.000
160A504LEU00.0080.01819.0840.0010.0010.0000.0000.0000.000
161A505CYS0-0.053-0.03822.4730.0020.0020.0000.0000.0000.000
162A506SER0-0.077-0.02824.5340.0090.0090.0000.0000.0000.000
163A507TYR00.0500.02322.4200.0100.0100.0000.0000.0000.000
164A508ILE0-0.0020.00318.684-0.003-0.0030.0000.0000.0000.000
165A509ASP-1-0.754-0.84622.216-0.191-0.1910.0000.0000.0000.000
166A510LYS10.7920.87120.4680.2620.2620.0000.0000.0000.000
167A511ASN00.0460.01925.399-0.010-0.0100.0000.0000.0000.000
168A512LYS10.8250.90624.1840.2160.2160.0000.0000.0000.000
169A513LEU00.005-0.01028.354-0.004-0.0040.0000.0000.0000.000
170A514ASN0-0.018-0.02329.9150.0010.0010.0000.0000.0000.000
171A515THR00.004-0.00928.1110.0030.0030.0000.0000.0000.000
172A516ILE0-0.0130.00726.866-0.006-0.0060.0000.0000.0000.000
173A517ASN00.0060.00529.008-0.006-0.0060.0000.0000.0000.000
174A518GLU-1-0.838-0.89531.355-0.130-0.1300.0000.0000.0000.000
175A519VAL0-0.056-0.02425.5760.0020.0020.0000.0000.0000.000
176A520LEU0-0.002-0.01326.379-0.001-0.0010.0000.0000.0000.000
177A521GLY00.0110.02929.9610.0040.0040.0000.0000.0000.000
178A522ILE0-0.061-0.02732.5110.0130.0130.0000.0000.0000.000