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: KGLZ3

Calculation Name: 2IMH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IMH

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LQD5

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2541316.630513
FMO2-HF: Nuclear repulsion 2455989.381752
FMO2-HF: Total energy -85327.24876
FMO2-MP2: Total energy -85576.746464


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-8.623-0.9652.735-3.696-6.6970.014
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.016
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].
3A2THR0-0.025-0.0203.3522.8965.5700.073-1.395-1.3520.005
4A3PHE00.0390.0095.513-0.395-0.318-0.001-0.010-0.0660.000
5A4SER0-0.045-0.0459.1690.2860.2860.0000.0000.0000.000
6A5ILE00.0070.00711.744-0.060-0.0600.0000.0000.0000.000
7A6LEU0-0.032-0.01115.5180.0480.0480.0000.0000.0000.000
8A7ALA00.032-0.00718.174-0.009-0.0090.0000.0000.0000.000
9A8HIS00.0350.01521.7520.0140.0140.0000.0000.0000.000
10A9ASP-1-0.826-0.91225.306-0.057-0.0570.0000.0000.0000.000
11A10PRO0-0.031-0.02427.7260.0070.0070.0000.0000.0000.000
12A11GLU-1-0.973-0.97131.024-0.035-0.0350.0000.0000.0000.000
13A12THR0-0.047-0.04729.8570.0040.0040.0000.0000.0000.000
14A13GLY00.0130.00230.6480.0030.0030.0000.0000.0000.000
15A14ALA0-0.058-0.01726.547-0.002-0.0020.0000.0000.0000.000
16A15ILE0-0.0090.00323.483-0.012-0.0120.0000.0000.0000.000
17A16GLY00.048-0.00920.8720.0210.0210.0000.0000.0000.000
18A17GLY00.0180.01216.871-0.038-0.0380.0000.0000.0000.000
19A18ALA0-0.024-0.01114.7000.0530.0530.0000.0000.0000.000
20A19ALA00.004-0.0029.463-0.115-0.1150.0000.0000.0000.000
21A20ALA00.0300.0188.3160.1110.1110.0000.0000.0000.000
22A21THR00.0100.0082.726-1.379-0.3340.474-0.544-0.9750.007
23A22GLY00.0450.0262.636-2.658-1.5840.698-0.702-1.0700.002
24A23SER0-0.032-0.0192.718-2.833-0.9891.218-0.736-2.3260.000
25A24LEU00.0230.0214.177-1.109-0.9890.005-0.045-0.0810.000
26A25CYS0-0.074-0.0377.161-0.131-0.1310.0000.0000.0000.000
27A26VAL00.0360.0416.923-0.269-0.2690.0000.0000.0000.000
28A27GLY00.028-0.0108.305-0.247-0.2470.0000.0000.0000.000
29A28GLY0-0.053-0.01611.595-0.077-0.0770.0000.0000.0000.000
30A29TRP0-0.037-0.0147.827-0.205-0.2050.0000.0000.0000.000
31A30VAL00.0100.0067.842-0.094-0.0940.0000.0000.0000.000
32A31LEU0-0.038-0.00610.775-0.042-0.0420.0000.0000.0000.000
33A32ARG10.8790.94913.1060.2750.2750.0000.0000.0000.000
34A33GLY00.0440.01017.508-0.024-0.0240.0000.0000.0000.000
35A34ASP-1-0.803-0.89820.974-0.054-0.0540.0000.0000.0000.000
36A35LEU00.0250.02024.689-0.010-0.0100.0000.0000.0000.000
37A36ASN0-0.0400.01227.692-0.009-0.0090.0000.0000.0000.000
38A37ALA00.006-0.00624.938-0.002-0.0020.0000.0000.0000.000
39A38GLY00.0410.02524.148-0.008-0.0080.0000.0000.0000.000
40A39MET0-0.069-0.02118.4980.0210.0210.0000.0000.0000.000
41A40SER0-0.029-0.03417.126-0.020-0.0200.0000.0000.0000.000
42A41ALA00.0220.01712.2880.0380.0380.0000.0000.0000.000
43A42SER0-0.093-0.05212.212-0.110-0.1100.0000.0000.0000.000
44A43GLN00.0380.0087.1310.1480.1480.0000.0000.0000.000
45A44GLY00.015-0.0016.2030.4100.4100.0000.0000.0000.000
46A45ALA0-0.019-0.0094.793-0.642-0.600-0.001-0.003-0.0380.000
47A46ALA0-0.031-0.0135.8510.5930.5930.0000.0000.0000.000
48A47PRO00.0040.0306.6390.1530.1530.0000.0000.0000.000
49A48SER00.0500.0299.4500.2190.2190.0000.0000.0000.000
50A49THR00.0390.00313.227-0.032-0.0320.0000.0000.0000.000
51A50PHE00.0280.01414.7430.0110.0110.0000.0000.0000.000
52A51TRP00.0280.00813.399-0.017-0.0170.0000.0000.0000.000
53A52GLY00.0120.00715.8860.0050.0050.0000.0000.0000.000
54A53GLU-1-0.957-0.97316.621-0.088-0.0880.0000.0000.0000.000
55A54GLU-1-0.912-0.97019.910-0.171-0.1710.0000.0000.0000.000
56A55VAL0-0.034-0.01418.6090.0140.0140.0000.0000.0000.000
57A56LEU0-0.004-0.00320.1180.0130.0130.0000.0000.0000.000
58A57GLN0-0.018-0.01423.0030.0180.0180.0000.0000.0000.000
59A58HIS00.0220.00223.7600.0130.0130.0000.0000.0000.000
60A59LEU0-0.012-0.00323.0060.0050.0050.0000.0000.0000.000
61A60ARG10.7200.84124.4610.1120.1120.0000.0000.0000.000
62A61ASP-1-0.920-0.94629.173-0.092-0.0920.0000.0000.0000.000
63A62GLY0-0.042-0.01530.5990.0030.0030.0000.0000.0000.000
64A63SER0-0.058-0.02027.432-0.001-0.0010.0000.0000.0000.000
65A64HIS00.0710.03926.603-0.010-0.0100.0000.0000.0000.000
66A65PRO00.037-0.00223.076-0.010-0.0100.0000.0000.0000.000
67A66GLU-1-0.954-0.98723.020-0.252-0.2520.0000.0000.0000.000
68A67ASP-1-0.892-0.94223.717-0.199-0.1990.0000.0000.0000.000
69A68ALA0-0.015-0.00323.622-0.003-0.0030.0000.0000.0000.000
70A69VAL0-0.013-0.01318.251-0.015-0.0150.0000.0000.0000.000
71A70ASN00.0110.00420.425-0.047-0.0470.0000.0000.0000.000
72A71HIS0-0.039-0.02122.5720.0020.0020.0000.0000.0000.000
73A72VAL00.0300.02718.5370.0050.0050.0000.0000.0000.000
74A73THR0-0.046-0.02816.7300.0000.0000.0000.0000.0000.000
75A74SER0-0.053-0.02519.1450.0070.0070.0000.0000.0000.000
76A75GLN0-0.005-0.00322.2600.0040.0040.0000.0000.0000.000
77A76ASP-1-0.780-0.86216.808-0.322-0.3220.0000.0000.0000.000
78A77SER0-0.038-0.03619.158-0.031-0.0310.0000.0000.0000.000
79A78GLY0-0.009-0.00616.0590.0040.0040.0000.0000.0000.000
80A79ARG10.8810.93814.3570.2280.2280.0000.0000.0000.000
81A80ALA00.0030.00213.879-0.094-0.0940.0000.0000.0000.000
82A81TYR00.0030.0049.739-0.088-0.0880.0000.0000.0000.000
83A82ARG10.8060.9009.2540.3080.3080.0000.0000.0000.000
84A83GLN00.0010.0009.088-0.258-0.2580.0000.0000.0000.000
85A84LEU0-0.034-0.00411.279-0.030-0.0300.0000.0000.0000.000
86A85ALA00.0370.03214.0070.0180.0180.0000.0000.0000.000
87A86ALA00.0220.00416.1310.0200.0200.0000.0000.0000.000
88A87MET0-0.040-0.00719.416-0.004-0.0040.0000.0000.0000.000
89A88ASP-1-0.756-0.86822.192-0.137-0.1370.0000.0000.0000.000
90A89LEU0-0.005-0.02125.7130.0010.0010.0000.0000.0000.000
91A90LEU0-0.064-0.02727.9470.0110.0110.0000.0000.0000.000
92A91GLY0-0.017-0.01025.4370.0020.0020.0000.0000.0000.000
93A92ASN0-0.082-0.02425.383-0.016-0.0160.0000.0000.0000.000
94A93ALA00.017-0.00420.933-0.004-0.0040.0000.0000.0000.000
95A94ALA0-0.0080.01120.8910.0050.0050.0000.0000.0000.000
96A95ALA00.022-0.00815.592-0.021-0.0210.0000.0000.0000.000
97A96PHE0-0.0140.01614.4570.0370.0370.0000.0000.0000.000
98A97THR00.006-0.01511.118-0.164-0.1640.0000.0000.0000.000
99A98GLY0-0.0120.01312.4030.0850.0850.0000.0000.0000.000
100A99SER00.014-0.02111.747-0.140-0.1400.0000.0000.0000.000
101A100GLU-1-0.924-0.96611.099-0.468-0.4680.0000.0000.0000.000
102A101ASN0-0.095-0.0347.191-0.383-0.3830.0000.0000.0000.000
103A102GLN00.0340.0084.4500.3370.426-0.001-0.005-0.0830.000
104A103ASP-1-0.858-0.8916.662-1.176-1.1760.0000.0000.0000.000
105A104ILE0-0.002-0.0088.028-0.166-0.1660.0000.0000.0000.000
106A105LYS10.8650.8988.9370.6800.6800.0000.0000.0000.000
107A106GLY0-0.033-0.01110.6220.1340.1340.0000.0000.0000.000
108A107SER00.002-0.01212.915-0.066-0.0660.0000.0000.0000.000
109A108VAL0-0.0130.00515.6750.0330.0330.0000.0000.0000.000
110A109THR00.0140.01618.8280.0010.0010.0000.0000.0000.000
111A110PHE00.0100.00219.2730.0130.0130.0000.0000.0000.000
112A111ALA0-0.018-0.01824.0790.0030.0030.0000.0000.0000.000
113A112SER00.0210.01924.8720.0040.0040.0000.0000.0000.000
114A113GLY00.0700.01721.7430.0130.0130.0000.0000.0000.000
115A114ILE0-0.050-0.01017.200-0.011-0.0110.0000.0000.0000.000
116A115ALA00.0360.03715.5040.0070.0070.0000.0000.0000.000
117A116SER0-0.030-0.02712.471-0.047-0.0470.0000.0000.0000.000
118A117GLY00.0430.0088.9270.0670.0670.0000.0000.0000.000
119A118ASN0-0.077-0.0394.451-1.319-1.279-0.001-0.015-0.0240.000
120A119MET00.0050.0362.754-0.699-0.1380.272-0.235-0.5970.000
121A120LEU0-0.023-0.0065.4680.3950.3950.0000.0000.0000.000
122A121GLY00.0110.0018.6720.0900.0900.0000.0000.0000.000
123A122ASP-1-0.838-0.93010.820-0.282-0.2820.0000.0000.0000.000
124A123ASN0-0.011-0.01513.635-0.118-0.1180.0000.0000.0000.000
125A124SER0-0.033-0.01815.779-0.026-0.0260.0000.0000.0000.000
126A125VAL00.0510.04711.1370.0330.0330.0000.0000.0000.000
127A126LEU00.0280.00912.1000.0550.0550.0000.0000.0000.000
128A127GLY0-0.018-0.00215.5230.0540.0540.0000.0000.0000.000
129A128ALA00.0520.02417.3450.0340.0340.0000.0000.0000.000
130A129MET0-0.059-0.01312.6980.0000.0000.0000.0000.0000.000
131A130THR0-0.026-0.02117.2580.0280.0280.0000.0000.0000.000
132A131GLU-1-0.967-0.98320.136-0.116-0.1160.0000.0000.0000.000
133A132ALA00.0070.00019.8860.0210.0210.0000.0000.0000.000
134A133PHE0-0.042-0.02620.1840.0190.0190.0000.0000.0000.000
135A134VAL0-0.057-0.04022.0820.0130.0130.0000.0000.0000.000
136A135ALA0-0.0090.00425.1350.0100.0100.0000.0000.0000.000
137A136SER0-0.064-0.00724.7500.0150.0150.0000.0000.0000.000
138A137ASP-1-0.883-0.94526.676-0.037-0.0370.0000.0000.0000.000
139A138LEU0-0.073-0.03625.3340.0100.0100.0000.0000.0000.000
140A139THR00.0490.00326.995-0.006-0.0060.0000.0000.0000.000
141A140PHE00.0330.01622.8970.0030.0030.0000.0000.0000.000
142A141GLU-1-0.850-0.94722.298-0.013-0.0130.0000.0000.0000.000
143A142ARG10.9500.96821.368-0.008-0.0080.0000.0000.0000.000
144A143ARG10.8920.98822.1830.0690.0690.0000.0000.0000.000
145A144LEU0-0.021-0.00518.171-0.012-0.0120.0000.0000.0000.000
146A145LEU0-0.018-0.02117.2240.0010.0010.0000.0000.0000.000
147A146ALA00.0200.01017.7290.0110.0110.0000.0000.0000.000
148A147ALA00.0060.00817.156-0.008-0.0080.0000.0000.0000.000
149A148LEU0-0.036-0.01811.902-0.029-0.0290.0000.0000.0000.000
150A149ILE00.0360.01513.9210.0050.0050.0000.0000.0000.000
151A150ALA0-0.0040.00415.972-0.004-0.0040.0000.0000.0000.000
152A151ALA0-0.034-0.02012.456-0.030-0.0300.0000.0000.0000.000
153A152GLU-1-0.934-0.98711.1430.2040.2040.0000.0000.0000.000
154A153GLY0-0.033-0.01312.498-0.014-0.0140.0000.0000.0000.000
155A154ALA0-0.037-0.00515.014-0.003-0.0030.0000.0000.0000.000
156A155GLY0-0.0310.00311.796-0.066-0.0660.0000.0000.0000.000
157A156SER0-0.050-0.0468.926-0.035-0.0350.0000.0000.0000.000
158A157ASP-1-0.808-0.9069.608-0.011-0.0110.0000.0000.0000.000
159A158PHE0-0.041-0.0139.8790.0660.0660.0000.0000.0000.000
160A159ARG10.7650.8444.6300.5880.680-0.001-0.006-0.0850.000
161A160GLY00.0610.0506.1120.2090.2090.0000.0000.0000.000
162A161LEU0-0.017-0.0125.4680.2800.2800.0000.0000.0000.000
163A162LEU0-0.018-0.0136.032-0.285-0.2850.0000.0000.0000.000
164A163SER0-0.061-0.0406.593-0.509-0.5090.0000.0000.0000.000
165A164ALA00.0440.0088.3620.0970.0970.0000.0000.0000.000
166A165ALA0-0.032-0.01610.862-0.030-0.0300.0000.0000.0000.000
167A166MET00.0170.01713.434-0.047-0.0470.0000.0000.0000.000
168A167LEU0-0.023-0.00416.6050.0200.0200.0000.0000.0000.000
169A168VAL0-0.003-0.00618.835-0.026-0.0260.0000.0000.0000.000
170A169LEU0-0.0130.00022.3500.0140.0140.0000.0000.0000.000
171A170HIS00.0450.00325.208-0.005-0.0050.0000.0000.0000.000
172A171PRO00.0320.01828.8990.0050.0050.0000.0000.0000.000
173A172ASP-1-0.815-0.90031.943-0.018-0.0180.0000.0000.0000.000
174A173ARG10.8760.93827.8420.0240.0240.0000.0000.0000.000
175A174PRO00.0230.02928.420-0.005-0.0050.0000.0000.0000.000
176A175PRO0-0.017-0.01723.771-0.001-0.0010.0000.0000.0000.000
177A176VAL00.0310.02721.9450.0140.0140.0000.0000.0000.000
178A177THR0-0.018-0.00918.996-0.010-0.0100.0000.0000.0000.000
179A178LEU0-0.042-0.01818.3560.0160.0160.0000.0000.0000.000
180A179ARG10.8490.89113.901-0.242-0.2420.0000.0000.0000.000
181A180ILE0-0.0180.01912.902-0.022-0.0220.0000.0000.0000.000
182A181ASP-1-0.764-0.88611.2580.5280.5280.0000.0000.0000.000
183A182TYR00.039-0.01010.0860.1820.1820.0000.0000.0000.000
184A183HIS0-0.0200.00711.072-0.120-0.1200.0000.0000.0000.000
185A184PRO0-0.057-0.01811.1060.1160.1160.0000.0000.0000.000
186A185ASP-1-0.915-0.96911.7430.4000.4000.0000.0000.0000.000
187A186ASN00.0670.03012.875-0.013-0.0130.0000.0000.0000.000
188A187PRO00.0250.0189.486-0.084-0.0840.0000.0000.0000.000
189A188ILE00.0440.02411.789-0.051-0.0510.0000.0000.0000.000
190A189GLY00.0350.02014.281-0.054-0.0540.0000.0000.0000.000
191A190ALA0-0.024-0.01715.851-0.035-0.0350.0000.0000.0000.000
192A191LEU0-0.010-0.00814.305-0.030-0.0300.0000.0000.0000.000
193A192GLU-1-0.927-0.95317.1420.0550.0550.0000.0000.0000.000
194A193GLN0-0.044-0.03420.084-0.007-0.0070.0000.0000.0000.000
195A194LEU0-0.041-0.01518.407-0.018-0.0180.0000.0000.0000.000
196A195TYR00.0520.01220.933-0.018-0.0180.0000.0000.0000.000
197A196GLN00.0230.01922.488-0.019-0.0190.0000.0000.0000.000
198A197LYS10.8870.95524.657-0.140-0.1400.0000.0000.0000.000
199A198ALA0-0.0100.00624.147-0.007-0.0070.0000.0000.0000.000
200A199THR0-0.041-0.03425.429-0.012-0.0120.0000.0000.0000.000
201A200THR0-0.026-0.01828.163-0.008-0.0080.0000.0000.0000.000
202A201GLY0-0.002-0.01031.1260.0040.0040.0000.0000.0000.000
203A202ASP-1-0.810-0.89334.0890.0540.0540.0000.0000.0000.000
204A203TYR0-0.0180.00626.847-0.002-0.0020.0000.0000.0000.000
205A204ALA00.0450.01930.813-0.003-0.0030.0000.0000.0000.000
206A205ASP-1-0.881-0.94331.9200.0240.0240.0000.0000.0000.000
207A206TRP00.0000.00029.522-0.002-0.0020.0000.0000.0000.000
208A207ALA00.008-0.00230.209-0.003-0.0030.0000.0000.0000.000
209A208ARG10.7590.86932.188-0.025-0.0250.0000.0000.0000.000
210A209GLN0-0.024-0.01234.745-0.005-0.0050.0000.0000.0000.000
211A210VAL0-0.0110.00131.7030.0010.0010.0000.0000.0000.000
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