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: K9Z73

Calculation Name: 4FCZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FCZ

Chain ID: B

ChEMBL ID:

UniProt ID: Q88P91

Base Structure: X-ray

Registration Date: 2023-06-26

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1881265.012775
FMO2-HF: Nuclear repulsion 1809830.813205
FMO2-HF: Total energy -71434.19957
FMO2-MP2: Total energy -71642.958145


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(B:22:ALA)


Summations of interaction energy for fragment #1(B:22:ALA)
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.
-5.787-8.59217.047-6.929-7.312-0.023
Interaction energy analysis for fragmet #1(B:22:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / 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].
3B24GLN0-0.0330.0073.268-2.1070.873-0.011-1.514-1.4540.005
4B25THR0-0.007-0.0245.271-0.624-0.6240.0000.0000.0000.000
5B26PRO00.041-0.0018.0470.1540.1540.0000.0000.0000.000
6B27HIS00.0210.0039.8290.1460.1460.0000.0000.0000.000
7B28GLU-1-0.835-0.9178.433-1.279-1.2790.0000.0000.0000.000
8B29VAL00.0140.0346.3350.1080.1080.0000.0000.0000.000
9B30VAL0-0.0080.0189.4760.1870.1870.0000.0000.0000.000
10B31GLN00.0270.03213.0870.0880.0880.0000.0000.0000.000
11B32SER00.0230.00510.5010.0220.0220.0000.0000.0000.000
12B33THR00.0550.01811.2720.0830.0830.0000.0000.0000.000
13B34THR0-0.040-0.04513.4890.0750.0750.0000.0000.0000.000
14B35ASN0-0.055-0.03716.0610.0420.0420.0000.0000.0000.000
15B36GLU-1-0.923-0.95612.447-0.138-0.1380.0000.0000.0000.000
16B37LEU0-0.0010.00716.3110.0360.0360.0000.0000.0000.000
17B38LEU00.022-0.01118.2830.0260.0260.0000.0000.0000.000
18B39GLY0-0.068-0.02420.2050.0160.0160.0000.0000.0000.000
19B40ASP-1-0.776-0.85219.984-0.026-0.0260.0000.0000.0000.000
20B41LEU00.0180.00121.8320.0140.0140.0000.0000.0000.000
21B42LYS10.9460.96924.5090.0860.0860.0000.0000.0000.000
22B43ALA0-0.043-0.01924.8810.0060.0060.0000.0000.0000.000
23B44ASN0-0.0040.00623.8940.0120.0120.0000.0000.0000.000
24B45LYS10.8580.94327.4880.0580.0580.0000.0000.0000.000
25B46GLU-1-0.850-0.96129.372-0.029-0.0290.0000.0000.0000.000
26B47GLN0-0.0020.00027.9210.0010.0010.0000.0000.0000.000
27B48TYR0-0.042-0.03822.8940.0090.0090.0000.0000.0000.000
28B49LYS10.7830.89129.3810.0410.0410.0000.0000.0000.000
29B50SER0-0.0240.00032.6390.0020.0020.0000.0000.0000.000
30B51ASN0-0.032-0.01830.5620.0050.0050.0000.0000.0000.000
31B52PRO00.0730.02229.3280.0000.0000.0000.0000.0000.000
32B53ASN00.0190.01227.681-0.003-0.0030.0000.0000.0000.000
33B54ALA00.0850.05225.8130.0020.0020.0000.0000.0000.000
34B55PHE0-0.0020.00524.320-0.004-0.0040.0000.0000.0000.000
35B56TYR0-0.009-0.07123.467-0.012-0.0120.0000.0000.0000.000
36B57ASP-1-0.919-0.94721.7660.0490.0490.0000.0000.0000.000
37B58SER0-0.013-0.01019.8620.0100.0100.0000.0000.0000.000
38B59LEU0-0.0020.00318.520-0.012-0.0120.0000.0000.0000.000
39B60ASN0-0.052-0.04817.665-0.002-0.0020.0000.0000.0000.000
40B61ARG10.8230.89415.9570.0200.0200.0000.0000.0000.000
41B62ILE0-0.032-0.00914.1730.0060.0060.0000.0000.0000.000
42B63LEU0-0.007-0.01413.134-0.045-0.0450.0000.0000.0000.000
43B64GLY0-0.0130.00813.099-0.028-0.0280.0000.0000.0000.000
44B65PRO00.0260.0129.1840.0310.0310.0000.0000.0000.000
45B66VAL00.0230.0218.045-0.016-0.0160.0000.0000.0000.000
46B67VAL0-0.0020.0059.813-0.087-0.0870.0000.0000.0000.000
47B68ASP-1-0.828-0.91611.7260.1200.1200.0000.0000.0000.000
48B69ALA00.0440.01513.013-0.013-0.0130.0000.0000.0000.000
49B70ASP-1-0.821-0.91015.8070.1470.1470.0000.0000.0000.000
50B71GLY0-0.043-0.03415.832-0.009-0.0090.0000.0000.0000.000
51B72ILE0-0.059-0.02415.943-0.018-0.0180.0000.0000.0000.000
52B73SER00.011-0.01218.792-0.007-0.0070.0000.0000.0000.000
53B74ARG10.8690.94515.920-0.093-0.0930.0000.0000.0000.000
54B75SER0-0.063-0.01220.982-0.006-0.0060.0000.0000.0000.000
55B76ILE0-0.044-0.00622.784-0.006-0.0060.0000.0000.0000.000
56B77MET00.0290.02725.1320.0030.0030.0000.0000.0000.000
57B78THR00.001-0.00125.593-0.001-0.0010.0000.0000.0000.000
58B79VAL00.1110.04823.4950.0080.0080.0000.0000.0000.000
59B80LYS10.8910.94525.7550.0050.0050.0000.0000.0000.000
60B81TYR00.033-0.02529.0820.0050.0050.0000.0000.0000.000
61B82SER00.0890.04124.3670.0020.0020.0000.0000.0000.000
62B83ARG10.8760.94625.927-0.049-0.0490.0000.0000.0000.000
63B84LYS10.8200.91527.688-0.029-0.0290.0000.0000.0000.000
64B85ALA00.0240.02926.970-0.004-0.0040.0000.0000.0000.000
65B86THR00.0270.01427.3280.0090.0090.0000.0000.0000.000
66B87PRO00.0670.01724.481-0.005-0.0050.0000.0000.0000.000
67B88GLU-1-0.902-0.93925.7290.0790.0790.0000.0000.0000.000
68B89GLN0-0.017-0.01527.877-0.001-0.0010.0000.0000.0000.000
69B90MET0-0.019-0.01122.498-0.013-0.0130.0000.0000.0000.000
70B91GLN0-0.015-0.01822.6810.0020.0020.0000.0000.0000.000
71B92ARG10.7840.85924.518-0.048-0.0480.0000.0000.0000.000
72B93PHE00.0100.00623.449-0.009-0.0090.0000.0000.0000.000
73B94GLN0-0.006-0.02119.319-0.012-0.0120.0000.0000.0000.000
74B95GLU-1-0.787-0.85723.4570.0390.0390.0000.0000.0000.000
75B96ASN00.001-0.01625.210-0.007-0.0070.0000.0000.0000.000
76B97PHE0-0.022-0.01022.147-0.010-0.0100.0000.0000.0000.000
77B98LYS10.8950.95719.827-0.065-0.0650.0000.0000.0000.000
78B99ARG10.8850.94723.938-0.036-0.0360.0000.0000.0000.000
79B100SER00.0320.01227.129-0.005-0.0050.0000.0000.0000.000
80B101LEU0-0.048-0.00422.742-0.007-0.0070.0000.0000.0000.000
81B102MET00.0020.01824.954-0.008-0.0080.0000.0000.0000.000
82B103GLN0-0.0300.00326.6720.0000.0000.0000.0000.0000.000
83B104PHE0-0.019-0.02729.863-0.002-0.0020.0000.0000.0000.000
84B105TYR0-0.010-0.01626.610-0.006-0.0060.0000.0000.0000.000
85B106GLY00.0390.02826.689-0.008-0.0080.0000.0000.0000.000
86B107ASN0-0.024-0.02027.6950.0000.0000.0000.0000.0000.000
87B108ALA0-0.004-0.00228.989-0.002-0.0020.0000.0000.0000.000
88B109LEU00.0120.00922.764-0.005-0.0050.0000.0000.0000.000
89B110LEU00.0780.04626.994-0.003-0.0030.0000.0000.0000.000
90B111GLU-1-0.865-0.89828.759-0.047-0.0470.0000.0000.0000.000
91B112TYR0-0.012-0.01926.049-0.002-0.0020.0000.0000.0000.000
92B113ASN0-0.039-0.00828.442-0.001-0.0010.0000.0000.0000.000
93B114ASN0-0.0180.00029.2540.0030.0030.0000.0000.0000.000
94B115GLN00.0560.01627.078-0.007-0.0070.0000.0000.0000.000
95B116GLY00.0120.01026.8340.0030.0030.0000.0000.0000.000
96B117ILE00.0010.01520.644-0.002-0.0020.0000.0000.0000.000
97B118THR00.0070.00722.430-0.005-0.0050.0000.0000.0000.000
98B119VAL00.0350.02115.8090.0080.0080.0000.0000.0000.000
99B120ASP-1-0.872-0.91719.294-0.260-0.2600.0000.0000.0000.000
100B121PRO00.0270.00618.305-0.037-0.0370.0000.0000.0000.000
101B122ALA00.0330.03514.7330.0380.0380.0000.0000.0000.000
102B123LYS10.8020.89416.7240.3990.3990.0000.0000.0000.000
103B124ALA00.0580.03415.190-0.060-0.0600.0000.0000.0000.000
104B125ASP-1-0.901-0.95810.728-0.987-0.9870.0000.0000.0000.000
105B126ASP-1-0.831-0.91913.454-0.396-0.3960.0000.0000.0000.000
106B127GLY00.0080.0189.6180.0670.0670.0000.0000.0000.000
107B128LYS10.7590.8739.3100.1990.1990.0000.0000.0000.000
108B129ARG10.9080.94310.9720.2970.2970.0000.0000.0000.000
109B130ALA00.0610.02711.483-0.047-0.0470.0000.0000.0000.000
110B131SER0-0.065-0.06813.3560.0700.0700.0000.0000.0000.000
111B132VAL0-0.0070.01113.162-0.015-0.0150.0000.0000.0000.000
112B133GLY00.0010.01216.4160.0380.0380.0000.0000.0000.000
113B134MET00.0090.00218.314-0.018-0.0180.0000.0000.0000.000
114B135LYS10.8290.89721.2540.2410.2410.0000.0000.0000.000
115B136VAL00.0420.02023.862-0.005-0.0050.0000.0000.0000.000
116B137THR0-0.069-0.05326.0350.0120.0120.0000.0000.0000.000
117B138GLY00.0230.00429.2330.0030.0030.0000.0000.0000.000
118B139ASN0-0.032-0.02731.3300.0000.0000.0000.0000.0000.000
119B140ASN00.0100.00534.012-0.002-0.0020.0000.0000.0000.000
120B141GLY00.0670.03434.6760.0020.0020.0000.0000.0000.000
121B142ALA0-0.077-0.01834.261-0.003-0.0030.0000.0000.0000.000
122B143VAL00.0040.00328.733-0.005-0.0050.0000.0000.0000.000
123B144TYR00.0010.00627.8960.0060.0060.0000.0000.0000.000
124B145PRO0-0.042-0.01425.766-0.014-0.0140.0000.0000.0000.000
125B146VAL0-0.004-0.01020.3180.0120.0120.0000.0000.0000.000
126B147GLN00.0190.03019.331-0.052-0.0520.0000.0000.0000.000
127B148TYR00.0340.00215.0850.0340.0340.0000.0000.0000.000
128B149THR0-0.058-0.02415.556-0.011-0.0110.0000.0000.0000.000
129B150LEU00.0090.00110.0790.0370.0370.0000.0000.0000.000
130B151GLU-1-0.838-0.91010.614-0.112-0.1120.0000.0000.0000.000
131B152ASN0-0.0170.0094.0010.7450.836-0.001-0.026-0.0640.000
132B153ILE0-0.017-0.0216.7310.2150.2150.0000.0000.0000.000
133B154GLY00.0180.0076.2590.4480.4480.0000.0000.0000.000
134B155GLY00.0410.0193.3921.1111.6480.029-0.262-0.3040.000
135B156GLU-1-0.844-0.9071.833-6.115-12.20016.967-5.659-5.223-0.028
136B157TRP0-0.049-0.0123.2031.3140.9860.0630.532-0.2670.000
137B158LYS10.8360.9156.074-0.238-0.2380.0000.0000.0000.000
138B159VAL00.011-0.0108.9040.0040.0040.0000.0000.0000.000
139B160ARG10.8170.90112.5320.1620.1620.0000.0000.0000.000
140B161ASN0-0.046-0.04814.9930.0540.0540.0000.0000.0000.000
141B162VAL00.0380.02417.448-0.040-0.0400.0000.0000.0000.000
142B163ILE0-0.040-0.01019.9460.0300.0300.0000.0000.0000.000
143B164VAL00.0630.01923.144-0.015-0.0150.0000.0000.0000.000
144B165ASN00.0350.01225.3600.0070.0070.0000.0000.0000.000
145B166GLY00.0120.00927.5360.0090.0090.0000.0000.0000.000
146B167ILE00.0190.02027.7680.0070.0070.0000.0000.0000.000
147B168ASN0-0.021-0.01723.219-0.003-0.0030.0000.0000.0000.000
148B169ILE00.0790.04022.7010.0140.0140.0000.0000.0000.000
149B170GLY00.0290.00622.4630.0150.0150.0000.0000.0000.000
150B171LYS10.8700.93123.2900.1060.1060.0000.0000.0000.000
151B172LEU00.0270.03326.6000.0080.0080.0000.0000.0000.000
152B173PHE00.042-0.00224.8930.0090.0090.0000.0000.0000.000
153B174ARG10.8310.90026.1790.0620.0620.0000.0000.0000.000
154B175ASP-1-0.810-0.87727.978-0.047-0.0470.0000.0000.0000.000
155B176GLN00.0470.02930.7080.0090.0090.0000.0000.0000.000
156B177PHE00.022-0.00429.1680.0060.0060.0000.0000.0000.000
157B178ALA00.0080.00431.2770.0060.0060.0000.0000.0000.000
158B179ASP-1-0.885-0.93833.416-0.025-0.0250.0000.0000.0000.000
159B180ALA0-0.027-0.00234.2840.0030.0030.0000.0000.0000.000
160B181MET0-0.061-0.00632.9320.0050.0050.0000.0000.0000.000
161B182GLN0-0.042-0.01836.0180.0030.0030.0000.0000.0000.000
162B183ARG10.8420.91036.4280.0170.0170.0000.0000.0000.000
163B184ASN0-0.047-0.02637.0230.0020.0020.0000.0000.0000.000
164B185GLY00.0550.02540.0570.0030.0030.0000.0000.0000.000
165B186ASN0-0.067-0.03536.7820.0010.0010.0000.0000.0000.000
166B187ASP-1-0.822-0.89136.8790.0250.0250.0000.0000.0000.000
167B188LEU00.029-0.00630.766-0.003-0.0030.0000.0000.0000.000
168B189ASP-1-0.762-0.85033.3010.0420.0420.0000.0000.0000.000
169B190LYS10.9040.94234.817-0.012-0.0120.0000.0000.0000.000
170B191THR0-0.077-0.04832.414-0.004-0.0040.0000.0000.0000.000
171B192ILE0-0.048-0.02729.348-0.004-0.0040.0000.0000.0000.000
172B193ASP-1-0.814-0.88331.7450.0300.0300.0000.0000.0000.000
173B194GLY0-0.0280.00434.339-0.001-0.0010.0000.0000.0000.000
174B195TRP0-0.007-0.01326.698-0.006-0.0060.0000.0000.0000.000
175B196ALA00.0750.04031.350-0.005-0.0050.0000.0000.0000.000
176B197GLY00.0430.00832.368-0.005-0.0050.0000.0000.0000.000
177B198GLU-1-0.791-0.86932.371-0.015-0.0150.0000.0000.0000.000
178B199VAL0-0.052-0.02428.293-0.006-0.0060.0000.0000.0000.000
179B200ALA0-0.034-0.02131.025-0.006-0.0060.0000.0000.0000.000
180B201LYS10.8610.90633.7660.0140.0140.0000.0000.0000.000
181B202ALA0-0.051-0.02330.812-0.003-0.0030.0000.0000.0000.000
182B203LYS10.8130.92130.8540.0480.0480.0000.0000.0000.000
183B204GLN00.0000.01332.708-0.004-0.0040.0000.0000.0000.000