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: ZY17N

Calculation Name: 1KUU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KUU

Chain ID: A

ChEMBL ID:

UniProt ID: O27099

Base Structure: X-ray

Registration Date: 2023-06-19

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280746.105598
FMO2-HF: Nuclear repulsion 2203870.30689
FMO2-HF: Total energy -76875.798709
FMO2-MP2: Total energy -77100.136185


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-11.836-4.4316.348-4.221-9.534-0.029
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.015
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].
3A3LEU00.0680.0343.588-1.1010.7120.002-0.687-1.1280.002
4A4GLY0-0.0190.0035.5560.5060.5060.0000.0000.0000.000
5A5ARG10.8560.9268.776-0.022-0.0220.0000.0000.0000.000
6A6ILE00.0110.0097.512-0.040-0.0400.0000.0000.0000.000
7A7LEU0-0.024-0.00911.1210.0600.0600.0000.0000.0000.000
8A8ALA00.0280.00913.368-0.032-0.0320.0000.0000.0000.000
9A9VAL0-0.014-0.00515.3040.0390.0390.0000.0000.0000.000
10A10GLY00.0370.01818.076-0.010-0.0100.0000.0000.0000.000
11A11ARG10.8470.90920.3310.1740.1740.0000.0000.0000.000
12A12ASN00.0070.00519.303-0.010-0.0100.0000.0000.0000.000
13A13SER0-0.041-0.04222.7780.0120.0120.0000.0000.0000.000
14A14ASN0-0.024-0.01423.2070.0270.0270.0000.0000.0000.000
15A15GLY00.0810.05025.9130.0060.0060.0000.0000.0000.000
16A16SER0-0.088-0.03223.844-0.007-0.0070.0000.0000.0000.000
17A17PHE00.0060.00116.6800.0040.0040.0000.0000.0000.000
18A18VAL00.0180.00219.6770.0040.0040.0000.0000.0000.000
19A19ALA00.0120.00715.9750.0010.0010.0000.0000.0000.000
20A20TYR00.022-0.01115.262-0.018-0.0180.0000.0000.0000.000
21A21ARG10.8310.9036.5871.7351.7350.0000.0000.0000.000
22A22VAL0-0.0090.00912.7870.0010.0010.0000.0000.0000.000
23A23SER00.0680.0258.661-0.163-0.1630.0000.0000.0000.000
24A24SER0-0.055-0.02410.6910.1450.1450.0000.0000.0000.000
25A25ARG10.9440.9685.761-2.042-2.0420.0000.0000.0000.000
26A26SER0-0.024-0.00512.5320.0390.0390.0000.0000.0000.000
27A27PHE00.0380.02615.962-0.005-0.0050.0000.0000.0000.000
28A28PRO00.0380.00715.072-0.043-0.0430.0000.0000.0000.000
29A29ASN0-0.0350.00616.802-0.041-0.0410.0000.0000.0000.000
30A30ARG10.8140.88916.0060.1540.1540.0000.0000.0000.000
31A31THR0-0.019-0.02119.592-0.017-0.0170.0000.0000.0000.000
32A32THR0-0.005-0.02719.3860.0090.0090.0000.0000.0000.000
33A33SER00.0180.01922.2230.0000.0000.0000.0000.0000.000
34A34ILE00.002-0.00226.0120.0010.0010.0000.0000.0000.000
35A35GLN0-0.041-0.03127.2820.0140.0140.0000.0000.0000.000
36A36GLU-1-0.825-0.90530.392-0.115-0.1150.0000.0000.0000.000
37A37GLU-1-0.908-0.94830.767-0.111-0.1110.0000.0000.0000.000
38A38ARG10.8040.87727.7310.1160.1160.0000.0000.0000.000
39A39VAL00.0200.00722.949-0.005-0.0050.0000.0000.0000.000
40A40ALA0-0.0040.00824.160-0.003-0.0030.0000.0000.0000.000
41A41VAL0-0.0020.00219.170-0.013-0.0130.0000.0000.0000.000
42A42VAL0-0.004-0.01522.1260.0250.0250.0000.0000.0000.000
43A43PRO0-0.023-0.02223.022-0.013-0.0130.0000.0000.0000.000
44A44VAL00.0150.02322.501-0.006-0.0060.0000.0000.0000.000
45A45GLU-1-0.926-0.96725.165-0.077-0.0770.0000.0000.0000.000
46A46GLY0-0.033-0.02128.3810.0030.0030.0000.0000.0000.000
47A47HIS0-0.017-0.00924.8530.0190.0190.0000.0000.0000.000
48A48GLU-1-0.814-0.91126.440-0.049-0.0490.0000.0000.0000.000
49A49ARG10.9160.93528.6040.0100.0100.0000.0000.0000.000
50A50ASP-1-0.794-0.87923.4390.0120.0120.0000.0000.0000.000
51A51VAL00.0170.00925.0340.0080.0080.0000.0000.0000.000
52A52PHE0-0.057-0.02526.0590.0040.0040.0000.0000.0000.000
53A53ARG10.7720.87424.046-0.017-0.0170.0000.0000.0000.000
54A54ASN00.0040.00018.6020.0080.0080.0000.0000.0000.000
55A55PRO00.0520.03323.084-0.014-0.0140.0000.0000.0000.000
56A56TYR0-0.031-0.00819.086-0.018-0.0180.0000.0000.0000.000
57A57ILE0-0.082-0.03718.962-0.021-0.0210.0000.0000.0000.000
58A58ALA00.0100.00220.605-0.022-0.0220.0000.0000.0000.000
59A59TYR0-0.0250.00117.6670.0040.0040.0000.0000.0000.000
60A60ASN00.0200.00823.584-0.019-0.0190.0000.0000.0000.000
61A61CYS0-0.0610.00219.391-0.003-0.0030.0000.0000.0000.000
62A62ILE00.0310.00820.289-0.016-0.0160.0000.0000.0000.000
63A63ARG10.7650.85823.4160.1230.1230.0000.0000.0000.000
64A64ILE0-0.026-0.00426.719-0.013-0.0130.0000.0000.0000.000
65A65VAL0-0.010-0.01929.3740.0100.0100.0000.0000.0000.000
66A66GLY00.0260.02832.4250.0040.0040.0000.0000.0000.000
67A67ASP-1-0.780-0.88633.156-0.120-0.1200.0000.0000.0000.000
68A68THR0-0.041-0.01328.474-0.009-0.0090.0000.0000.0000.000
69A69ALA0-0.0090.01625.3470.0020.0020.0000.0000.0000.000
70A70VAL0-0.014-0.02824.1770.0010.0010.0000.0000.0000.000
71A71VAL00.0040.00518.360-0.006-0.0060.0000.0000.0000.000
72A72SER0-0.011-0.03918.8200.0170.0170.0000.0000.0000.000
73A73ASN00.0540.03015.568-0.023-0.0230.0000.0000.0000.000
74A74GLY00.0260.00717.4360.0180.0180.0000.0000.0000.000
75A75SER00.0310.00520.805-0.007-0.0070.0000.0000.0000.000
76A76HIS0-0.0100.01119.3530.0210.0210.0000.0000.0000.000
77A77THR00.0200.01622.705-0.002-0.0020.0000.0000.0000.000
78A78ASP-1-0.781-0.85824.487-0.110-0.1100.0000.0000.0000.000
79A79THR0-0.049-0.02727.3620.0040.0040.0000.0000.0000.000
80A80ILE00.0010.00923.6190.0060.0060.0000.0000.0000.000
81A81ALA00.0140.00327.8440.0040.0040.0000.0000.0000.000
82A82ASP-1-0.788-0.89029.427-0.078-0.0780.0000.0000.0000.000
83A83LYS10.8870.94230.9880.0560.0560.0000.0000.0000.000
84A84VAL00.0180.01229.5660.0040.0040.0000.0000.0000.000
85A85ALA0-0.0150.00432.6900.0030.0030.0000.0000.0000.000
86A86LEU0-0.087-0.04035.3360.0050.0050.0000.0000.0000.000
87A87GLY00.0000.00736.2210.0050.0050.0000.0000.0000.000
88A88MET0-0.102-0.03332.3010.0020.0020.0000.0000.0000.000
89A89ASN00.016-0.01431.469-0.011-0.0110.0000.0000.0000.000
90A90LEU00.0830.02727.0850.0030.0030.0000.0000.0000.000
91A91ARG10.8640.92426.8830.0540.0540.0000.0000.0000.000
92A92ASP-1-0.783-0.86527.497-0.050-0.0500.0000.0000.0000.000
93A93ALA0-0.0040.00728.8880.0050.0050.0000.0000.0000.000
94A94ILE00.0290.02122.6630.0030.0030.0000.0000.0000.000
95A95GLY00.0090.00425.3870.0050.0050.0000.0000.0000.000
96A96LEU0-0.026-0.01826.6600.0080.0080.0000.0000.0000.000
97A97SER0-0.006-0.02226.0840.0080.0080.0000.0000.0000.000
98A98LEU0-0.022-0.00820.6830.0050.0050.0000.0000.0000.000
99A99LEU0-0.024-0.01124.0030.0100.0100.0000.0000.0000.000
100A100ALA0-0.048-0.01826.4420.0080.0080.0000.0000.0000.000
101A101MET0-0.058-0.02824.3840.0010.0010.0000.0000.0000.000
102A102ASP-1-0.807-0.87122.7630.0290.0290.0000.0000.0000.000
103A103TYR0-0.002-0.00418.007-0.008-0.0080.0000.0000.0000.000
104A104GLU-1-0.861-0.93917.892-0.063-0.0630.0000.0000.0000.000
105A105LYS10.7930.89618.780-0.018-0.0180.0000.0000.0000.000
106A106ASP-1-0.798-0.87816.0220.0980.0980.0000.0000.0000.000
107A107GLU-1-0.945-0.97416.1420.2380.2380.0000.0000.0000.000
108A108LEU0-0.080-0.03410.7100.0560.0560.0000.0000.0000.000
109A109ASN0-0.057-0.02114.121-0.023-0.0230.0000.0000.0000.000
110A110THR0-0.001-0.02813.411-0.015-0.0150.0000.0000.0000.000
111A111PRO00.0280.01912.629-0.021-0.0210.0000.0000.0000.000
112A112ARG10.7510.88415.3930.0190.0190.0000.0000.0000.000
113A113ILE00.0010.00312.8540.0120.0120.0000.0000.0000.000
114A114ALA00.001-0.02316.978-0.002-0.0020.0000.0000.0000.000
115A115ALA00.0060.00518.913-0.001-0.0010.0000.0000.0000.000
116A116ALA0-0.0090.00120.8080.0040.0040.0000.0000.0000.000
117A117ILE0-0.001-0.00122.266-0.001-0.0010.0000.0000.0000.000
118A118ASN00.0020.00626.0780.0010.0010.0000.0000.0000.000
119A119GLY00.0320.01729.114-0.008-0.0080.0000.0000.0000.000
120A120SER00.0070.01031.4180.0000.0000.0000.0000.0000.000
121A121GLU-1-0.920-0.93328.470-0.095-0.0950.0000.0000.0000.000
122A122ALA00.0660.02323.425-0.008-0.0080.0000.0000.0000.000
123A123PHE0-0.053-0.02423.4300.0140.0140.0000.0000.0000.000
124A124ILE00.0520.02315.717-0.015-0.0150.0000.0000.0000.000
125A125GLY0-0.016-0.01419.3130.0240.0240.0000.0000.0000.000
126A126ILE00.0070.00513.738-0.029-0.0290.0000.0000.0000.000
127A127VAL0-0.035-0.00718.0120.0170.0170.0000.0000.0000.000
128A128THR00.005-0.04514.946-0.018-0.0180.0000.0000.0000.000
129A129ALA00.004-0.00317.536-0.004-0.0040.0000.0000.0000.000
130A130ASP-1-0.890-0.91116.5940.1330.1330.0000.0000.0000.000
131A131GLY0-0.024-0.01019.679-0.001-0.0010.0000.0000.0000.000
132A132LEU0-0.027-0.00520.183-0.008-0.0080.0000.0000.0000.000
133A133MET0-0.0300.00018.4450.0080.0080.0000.0000.0000.000
134A134VAL0-0.010-0.01420.831-0.017-0.0170.0000.0000.0000.000
135A135SER0-0.045-0.01620.4420.0100.0100.0000.0000.0000.000
136A136ARG10.8460.89022.7380.0880.0880.0000.0000.0000.000
137A137VAL00.003-0.00219.918-0.001-0.0010.0000.0000.0000.000
138A138PRO0-0.024-0.00419.3980.0140.0140.0000.0000.0000.000
139A139GLU-1-0.956-0.99122.003-0.139-0.1390.0000.0000.0000.000
140A140GLU-1-0.986-0.98520.562-0.145-0.1450.0000.0000.0000.000
141A141THR0-0.029-0.03416.479-0.020-0.0200.0000.0000.0000.000
142A142PRO0-0.0230.00616.0820.0120.0120.0000.0000.0000.000
143A143VAL0-0.0060.00214.455-0.004-0.0040.0000.0000.0000.000
144A144TYR0-0.029-0.0197.231-0.084-0.0840.0000.0000.0000.000
145A145ILE00.0130.01711.3780.0630.0630.0000.0000.0000.000
146A146SER0-0.017-0.0387.698-0.111-0.1110.0000.0000.0000.000
147A147THR00.0020.0109.8600.0760.0760.0000.0000.0000.000
148A148TYR0-0.025-0.0246.2730.1920.1920.0000.0000.0000.000
149A149GLU-1-0.875-0.9492.384-1.103-0.2050.383-0.450-0.832-0.004
150A150GLN0-0.043-0.0015.8290.3320.3320.0000.0000.0000.000
151A151THR0-0.004-0.0088.192-0.046-0.0460.0000.0000.0000.000
152A152GLU-1-0.921-0.96711.2020.0790.0790.0000.0000.0000.000
153A153PRO0-0.034-0.01712.358-0.055-0.0550.0000.0000.0000.000
154A154ALA00.0160.02510.6370.0490.0490.0000.0000.0000.000
155A155ALA0-0.004-0.00812.600-0.053-0.0530.0000.0000.0000.000
156A156THR0-0.027-0.04110.138-0.049-0.0490.0000.0000.0000.000
157A157GLU-1-0.826-0.88812.592-0.325-0.3250.0000.0000.0000.000
158A158PHE0-0.018-0.01613.491-0.040-0.0400.0000.0000.0000.000
159A159LYS10.7960.88315.3300.4590.4590.0000.0000.0000.000
160A160ALA00.0250.00917.424-0.028-0.0280.0000.0000.0000.000
161A161GLY0-0.032-0.01120.0890.0220.0220.0000.0000.0000.000
162A162SER00.010-0.00922.9160.0190.0190.0000.0000.0000.000
163A163PRO00.0140.01122.159-0.031-0.0310.0000.0000.0000.000
164A164GLU-1-0.870-0.95920.921-0.289-0.2890.0000.0000.0000.000
165A165GLU-1-0.842-0.88319.571-0.358-0.3580.0000.0000.0000.000
166A166ALA00.0030.00517.604-0.064-0.0640.0000.0000.0000.000
167A167ALA0-0.005-0.00616.228-0.067-0.0670.0000.0000.0000.000
168A168GLU-1-0.770-0.89015.607-0.580-0.5800.0000.0000.0000.000
169A169PHE0-0.028-0.00711.729-0.121-0.1210.0000.0000.0000.000
170A170ILE0-0.0170.00011.335-0.153-0.1530.0000.0000.0000.000
171A171LEU0-0.044-0.02810.518-0.195-0.1950.0000.0000.0000.000
172A172LYS10.7940.87910.6070.4440.4440.0000.0000.0000.000
173A173GLY00.0000.02010.998-0.016-0.0160.0000.0000.0000.000
174A174GLY00.002-0.0099.428-0.192-0.1920.0000.0000.0000.000
175A175GLU-1-0.821-0.8995.300-1.216-1.2160.0000.0000.0000.000
176A176PHE00.010-0.0024.836-1.146-1.058-0.001-0.001-0.0860.000
177A177ALA0-0.0270.0086.446-0.210-0.2100.0000.0000.0000.000
178A178ALA0-0.028-0.0102.403-0.1840.0281.266-0.417-1.061-0.001
179A179PHE00.0080.0172.310-7.475-3.8913.709-2.360-4.934-0.025
180A180THR00.006-0.0132.4111.4092.1400.990-0.297-1.424-0.001
181A181HIS0-0.019-0.0094.8000.0880.167-0.001-0.009-0.0690.000
182A182PRO00.0750.0437.8360.1060.1060.0000.0000.0000.000
183A183VAL0-0.071-0.02510.2710.1300.1300.0000.0000.0000.000
184A184THR0-0.016-0.02714.0170.0180.0180.0000.0000.0000.000
185A185ALA0-0.013-0.00514.747-0.054-0.0540.0000.0000.0000.000
186A186ALA00.0260.01216.7560.0490.0490.0000.0000.0000.000
187A187ALA0-0.027-0.01818.443-0.043-0.0430.0000.0000.0000.000
188A188ALA00.0160.01520.6170.0300.0300.0000.0000.0000.000
189A189PHE0-0.008-0.02022.085-0.025-0.0250.0000.0000.0000.000
190A190ASN00.0220.00624.9100.0180.0180.0000.0000.0000.000
191A191ASP-1-0.809-0.92027.882-0.174-0.1740.0000.0000.0000.000
192A192GLY0-0.0230.00029.2190.0050.0050.0000.0000.0000.000
193A193GLU-1-1.022-0.99632.230-0.110-0.1100.0000.0000.0000.000
194A194GLY0-0.015-0.01432.3440.0090.0090.0000.0000.0000.000
195A195TRP0-0.081-0.04724.736-0.017-0.0170.0000.0000.0000.000
196A196ASN0-0.0060.01528.0120.0110.0110.0000.0000.0000.000
197A197LEU0-0.011-0.02325.350-0.016-0.0160.0000.0000.0000.000
198A198ALA0-0.007-0.00223.2400.0100.0100.0000.0000.0000.000
199A199THR0-0.033-0.01620.946-0.016-0.0160.0000.0000.0000.000
200A200ARG10.8600.91217.8940.3640.3640.0000.0000.0000.000
201A201GLU-1-0.698-0.78718.229-0.303-0.3030.0000.0000.0000.000
202A202MET0-0.0250.00011.598-0.015-0.0150.0000.0000.0000.000