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: M385Z

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1904020.417675
FMO2-HF: Nuclear repulsion 1836340.479615
FMO2-HF: Total energy -67679.938061
FMO2-MP2: Total energy -67882.230215


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.
-8.162-0.4762.827-3.392-7.119-0.021
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 : 0.011 / q_NPA : 0.001
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-1-0.758-0.8912.811-9.037-4.8170.218-2.002-2.436-0.016
4A348ALA0-0.039-0.0012.551-0.1080.9371.073-0.721-1.398-0.003
5A349VAL00.0080.0112.6300.7901.5020.404-0.233-0.883-0.001
6A350ASP-1-0.856-0.9195.185-0.485-0.403-0.001-0.007-0.0730.000
7A351ALA0-0.050-0.0367.1040.4190.4190.0000.0000.0000.000
8A352THR0-0.015-0.0347.0640.3780.3780.0000.0000.0000.000
9A353VAL00.0020.0029.4410.2460.2460.0000.0000.0000.000
10A354SER0-0.015-0.00111.4440.2050.2050.0000.0000.0000.000
11A355PHE0-0.005-0.00512.4970.1220.1220.0000.0000.0000.000
12A356TYR00.0320.00211.1260.1070.1070.0000.0000.0000.000
13A357GLN00.0380.01915.4760.0730.0730.0000.0000.0000.000
14A358THR00.0300.01617.2690.0560.0560.0000.0000.0000.000
15A359LEU0-0.076-0.03317.2420.0510.0510.0000.0000.0000.000
16A360THR0-0.039-0.03219.8180.0300.0300.0000.0000.0000.000
17A361GLU-1-0.971-0.96521.535-0.267-0.2670.0000.0000.0000.000
18A362LYS10.8200.92220.6480.3730.3730.0000.0000.0000.000
19A363TYR0-0.044-0.03922.7410.0140.0140.0000.0000.0000.000
20A364GLY00.0380.02425.2350.0040.0040.0000.0000.0000.000
21A365GLU-1-0.764-0.87322.392-0.275-0.2750.0000.0000.0000.000
22A366LYS10.8850.93122.5030.1530.1530.0000.0000.0000.000
23A367TYR0-0.014-0.02821.046-0.013-0.0130.0000.0000.0000.000
24A368SER00.0290.01618.378-0.028-0.0280.0000.0000.0000.000
25A369LYS10.8870.92218.1340.2270.2270.0000.0000.0000.000
26A370MET0-0.0430.00319.101-0.007-0.0070.0000.0000.0000.000
27A371ALA00.0320.01217.339-0.005-0.0050.0000.0000.0000.000
28A372GLN00.0510.02713.8860.0050.0050.0000.0000.0000.000
29A373GLU-1-0.792-0.87215.329-0.259-0.2590.0000.0000.0000.000
30A374LEU0-0.073-0.04117.4570.0090.0090.0000.0000.0000.000
31A375ALA00.0390.01812.3670.0010.0010.0000.0000.0000.000
32A376ASP-1-0.866-0.92712.201-0.620-0.6200.0000.0000.0000.000
33A377LYS10.8200.89314.1100.2460.2460.0000.0000.0000.000
34A378SER0-0.020-0.02614.4850.0230.0230.0000.0000.0000.000
35A379LYS10.8820.9479.1660.8240.8240.0000.0000.0000.000
36A380GLY0-0.0090.00813.7010.0450.0450.0000.0000.0000.000
37A381LYS10.7850.91515.6640.2790.2790.0000.0000.0000.000
38A382LYS10.9170.94716.8400.2000.2000.0000.0000.0000.000
39A383ILE0-0.011-0.01620.545-0.004-0.0040.0000.0000.0000.000
40A384GLY00.0150.01422.8190.0120.0120.0000.0000.0000.000
41A385ASN00.011-0.00126.3100.0020.0020.0000.0000.0000.000
42A386VAL00.0320.01027.758-0.005-0.0050.0000.0000.0000.000
43A387ASN0-0.015-0.01729.041-0.006-0.0060.0000.0000.0000.000
44A388GLU-1-0.867-0.90930.954-0.119-0.1190.0000.0000.0000.000
45A389ALA00.0250.01627.4960.0000.0000.0000.0000.0000.000
46A390LEU0-0.001-0.00229.448-0.002-0.0020.0000.0000.0000.000
47A391ALA0-0.0060.00431.6630.0010.0010.0000.0000.0000.000
48A392ALA0-0.0040.00230.5740.0040.0040.0000.0000.0000.000
49A393PHE0-0.005-0.00328.762-0.001-0.0010.0000.0000.0000.000
50A394GLU-1-0.839-0.93831.328-0.125-0.1250.0000.0000.0000.000
51A395LYS10.9440.98734.8110.1220.1220.0000.0000.0000.000
52A396TYR0-0.037-0.04130.1600.0010.0010.0000.0000.0000.000
53A397LYS10.8870.94833.3250.1260.1260.0000.0000.0000.000
54A398ASP-1-0.862-0.93134.477-0.103-0.1030.0000.0000.0000.000
55A399VAL0-0.058-0.01936.0970.0050.0050.0000.0000.0000.000
56A400LEU00.0190.01631.4910.0040.0040.0000.0000.0000.000
57A401ASN00.026-0.01335.557-0.002-0.0020.0000.0000.0000.000
58A402LYS10.8190.91337.9230.1050.1050.0000.0000.0000.000
59A403LYS10.8900.94837.1060.1160.1160.0000.0000.0000.000
60A404PHE00.0360.02634.060-0.003-0.0030.0000.0000.0000.000
61A405SER0-0.011-0.02338.9740.0030.0030.0000.0000.0000.000
62A406LYS10.8770.90239.6970.1000.1000.0000.0000.0000.000
63A407ALA00.0420.02339.840-0.004-0.0040.0000.0000.0000.000
64A408ASP-1-0.802-0.87137.349-0.118-0.1180.0000.0000.0000.000
65A409ARG10.8570.92835.3220.1080.1080.0000.0000.0000.000
66A410ASP-1-0.799-0.89435.112-0.119-0.1190.0000.0000.0000.000
67A411ALA00.0010.01135.951-0.003-0.0030.0000.0000.0000.000
68A412ILE0-0.020-0.01129.956-0.008-0.0080.0000.0000.0000.000
69A413PHE00.004-0.00531.328-0.008-0.0080.0000.0000.0000.000
70A414ASN00.0260.00432.5250.0000.0000.0000.0000.0000.000
71A415ALA0-0.0050.00830.0430.0000.0000.0000.0000.0000.000
72A416LEU0-0.001-0.02026.377-0.007-0.0070.0000.0000.0000.000
73A417ALA0-0.0220.00228.748-0.005-0.0050.0000.0000.0000.000
74A418SER0-0.048-0.01830.1210.0090.0090.0000.0000.0000.000
75A419VAL0-0.050-0.00823.686-0.006-0.0060.0000.0000.0000.000
76A420LYS10.9060.96523.9190.2010.2010.0000.0000.0000.000
77A421TYR00.010-0.01618.232-0.020-0.0200.0000.0000.0000.000
78A422ASP-1-0.871-0.94319.817-0.257-0.2570.0000.0000.0000.000
79A423ASP-1-0.898-0.95318.693-0.282-0.2820.0000.0000.0000.000
80A424TRP0-0.043-0.03417.622-0.050-0.0500.0000.0000.0000.000
81A425ALA00.0280.02016.015-0.076-0.0760.0000.0000.0000.000
82A426LYS10.9290.97114.4880.3860.3860.0000.0000.0000.000
83A427HIS0-0.020-0.01511.394-0.169-0.1690.0000.0000.0000.000
84A428LEU00.0230.01910.646-0.160-0.1600.0000.0000.0000.000
85A429ASP-1-0.799-0.8836.494-1.160-1.1600.0000.0000.0000.000
86A430GLN00.0100.0175.907-0.259-0.2590.0000.0000.0000.000
87A431PHE00.0510.0226.235-0.415-0.4150.0000.0000.0000.000
88A432ALA00.0360.0187.8580.0060.0060.0000.0000.0000.000
89A433LYS10.7820.8632.565-0.4820.8091.134-0.396-2.029-0.001
90A434TYR0-0.020-0.0014.224-0.2350.0690.000-0.033-0.2700.000
91A435LEU0-0.047-0.0265.1420.2680.300-0.0010.000-0.0300.000
92A436LYS10.8740.9435.3320.7470.7470.0000.0000.0000.000
93A437ILE0-0.0010.0077.3250.1950.1950.0000.0000.0000.000
94A438THR0-0.053-0.0328.651-0.036-0.0360.0000.0000.0000.000
95A439GLY0-0.0110.00710.3260.0510.0510.0000.0000.0000.000
96A440HIS00.0190.00812.249-0.035-0.0350.0000.0000.0000.000
97A441VAL00.010-0.00510.966-0.037-0.0370.0000.0000.0000.000
98A442SER0-0.044-0.01714.1500.0340.0340.0000.0000.0000.000
99A443PHE00.016-0.00610.002-0.013-0.0130.0000.0000.0000.000
100A444GLY00.0030.01316.121-0.015-0.0150.0000.0000.0000.000
101A445TYR0-0.080-0.05719.4160.0230.0230.0000.0000.0000.000
102A446ASP-1-0.765-0.90920.543-0.256-0.2560.0000.0000.0000.000
103A447VAL00.004-0.00321.1070.0180.0180.0000.0000.0000.000
104A448VAL00.0360.01623.4370.0150.0150.0000.0000.0000.000
105A449SER00.0060.01725.9220.0190.0190.0000.0000.0000.000
106A450ASP-1-0.797-0.88326.992-0.156-0.1560.0000.0000.0000.000
107A451ILE0-0.037-0.02224.9700.0090.0090.0000.0000.0000.000
108A452LEU0-0.0050.00429.2800.0100.0100.0000.0000.0000.000
109A453LYS10.8750.93230.3840.1520.1520.0000.0000.0000.000
110A454ILE0-0.042-0.01530.4700.0070.0070.0000.0000.0000.000
111A455LYS10.8490.94534.3770.1210.1210.0000.0000.0000.000
112A456ASP-1-0.942-0.97036.312-0.100-0.1000.0000.0000.0000.000
113A457THR0-0.010-0.00336.4690.0030.0030.0000.0000.0000.000
114A458GLY0-0.021-0.00237.1550.0040.0040.0000.0000.0000.000
115A459ASP-1-0.903-0.97036.168-0.116-0.1160.0000.0000.0000.000
116A460TRP00.0560.00928.970-0.010-0.0100.0000.0000.0000.000
117A461LYS10.9720.99031.1890.0920.0920.0000.0000.0000.000
118A462PRO0-0.015-0.00731.329-0.006-0.0060.0000.0000.0000.000
119A463LEU00.0470.02725.588-0.005-0.0050.0000.0000.0000.000
120A464PHE00.0580.02826.783-0.012-0.0120.0000.0000.0000.000
121A465LEU0-0.012-0.00426.817-0.004-0.0040.0000.0000.0000.000
122A466THR0-0.050-0.02625.7100.0000.0000.0000.0000.0000.000
123A467LEU00.0090.00021.440-0.011-0.0110.0000.0000.0000.000
124A468GLU-1-0.853-0.91422.226-0.159-0.1590.0000.0000.0000.000
125A469LYS10.8280.87523.0560.1350.1350.0000.0000.0000.000
126A470LYS10.8700.95120.6820.1850.1850.0000.0000.0000.000
127A471ALA00.0120.02718.408-0.016-0.0160.0000.0000.0000.000
128A472ALA00.0250.02118.382-0.007-0.0070.0000.0000.0000.000
129A473ASP-1-0.863-0.93216.808-0.194-0.1940.0000.0000.0000.000
130A474ALA00.0480.02114.609-0.003-0.0030.0000.0000.0000.000
131A475GLY0-0.097-0.03215.520-0.030-0.0300.0000.0000.0000.000
132A476VAL00.018-0.01917.930-0.009-0.0090.0000.0000.0000.000
133A477SER00.0480.02512.4470.0000.0000.0000.0000.0000.000
134A478TYR00.008-0.00613.602-0.056-0.0560.0000.0000.0000.000
135A479VAL00.0200.00415.038-0.020-0.0200.0000.0000.0000.000
136A480VAL0-0.017-0.00313.7040.0040.0040.0000.0000.0000.000
137A481ALA00.0390.02311.621-0.030-0.0300.0000.0000.0000.000
138A482LEU00.0150.01813.230-0.013-0.0130.0000.0000.0000.000
139A483LEU0-0.006-0.01116.3880.0010.0010.0000.0000.0000.000
140A484PHE0-0.022-0.00912.8780.0390.0390.0000.0000.0000.000
141A485SER00.019-0.00313.939-0.047-0.0470.0000.0000.0000.000
142A486LEU0-0.0130.00115.5990.0260.0260.0000.0000.0000.000
143A487LEU0-0.029-0.01018.2860.0240.0240.0000.0000.0000.000
144A488ALA0-0.042-0.01815.0960.0180.0180.0000.0000.0000.000
145A489GLY0-0.039-0.00817.0470.0100.0100.0000.0000.0000.000
146A490THR0-0.051-0.02419.2930.0450.0450.0000.0000.0000.000
147A491THR00.0400.01422.373-0.028-0.0280.0000.0000.0000.000
148A492LEU0-0.0090.01824.9750.0230.0230.0000.0000.0000.000
149A493GLY00.0790.03027.3300.0000.0000.0000.0000.0000.000
150A494ILE00.0610.00829.078-0.008-0.0080.0000.0000.0000.000
151A495TRP00.0110.01329.446-0.010-0.0100.0000.0000.0000.000
152A496GLY00.0620.02028.560-0.001-0.0010.0000.0000.0000.000
153A497ILE00.0070.02523.696-0.012-0.0120.0000.0000.0000.000
154A498ALA00.0000.01125.477-0.013-0.0130.0000.0000.0000.000
155A499ILE0-0.0150.00127.697-0.001-0.0010.0000.0000.0000.000
156A500VAL00.0190.00321.935-0.002-0.0020.0000.0000.0000.000
157A501THR0-0.003-0.02322.768-0.022-0.0220.0000.0000.0000.000
158A502GLY00.0180.00923.919-0.001-0.0010.0000.0000.0000.000
159A503ILE00.0030.00323.5800.0060.0060.0000.0000.0000.000
160A504LEU00.0120.02018.7680.0000.0000.0000.0000.0000.000
161A505CYS0-0.062-0.03822.1000.0030.0030.0000.0000.0000.000
162A506SER0-0.075-0.03024.2870.0100.0100.0000.0000.0000.000
163A507TYR00.0400.02322.4000.0110.0110.0000.0000.0000.000
164A508ILE0-0.067-0.03518.2400.0060.0060.0000.0000.0000.000
165A509ASP-1-0.712-0.85421.988-0.205-0.2050.0000.0000.0000.000
166A510LYS10.8120.91820.6500.2700.2700.0000.0000.0000.000
167A511ASN00.0600.03125.164-0.011-0.0110.0000.0000.0000.000
168A512LYS10.8310.90923.1360.2430.2430.0000.0000.0000.000
169A513LEU00.0470.00927.674-0.004-0.0040.0000.0000.0000.000
170A514ASN0-0.048-0.03829.344-0.003-0.0030.0000.0000.0000.000
171A515THR00.0020.00927.6330.0040.0040.0000.0000.0000.000
172A516ILE00.0050.01726.392-0.004-0.0040.0000.0000.0000.000
173A517ASN00.0190.00528.550-0.008-0.0080.0000.0000.0000.000
174A518GLU-1-0.852-0.91230.857-0.143-0.1430.0000.0000.0000.000
175A519VAL0-0.073-0.03525.0120.0010.0010.0000.0000.0000.000
176A520LEU0-0.034-0.03226.103-0.006-0.0060.0000.0000.0000.000
177A521GLY0-0.0160.02329.4730.0030.0030.0000.0000.0000.000
178A522ILE0-0.029-0.01831.9480.0070.0070.0000.0000.0000.000