FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

tag_button

FMODB ID: LZZ49

Calculation Name: 5DSS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DSS

Chain ID: B

ChEMBL ID:

UniProt ID: A0A158

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1908078.189887
FMO2-HF: Nuclear repulsion 1837061.037411
FMO2-HF: Total energy -71017.152476
FMO2-MP2: Total energy -71223.766662


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:1:LYS)


Summations of interaction energy for fragment #1(B:1:LYS)
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.
-74.314-66.4671.535-4.233-5.148-0.015
Interaction energy analysis for fragmet #1(B:1:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.912 / q_NPA : 0.926
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].
3B3ASP-1-0.862-0.9252.136-36.503-29.0211.517-4.299-4.700-0.016
4B4ALA0-0.056-0.0233.6430.6981.0630.0180.066-0.4480.001
5B5GLU-1-0.821-0.8986.037-18.419-18.4190.0000.0000.0000.000
6B6PRO0-0.080-0.0529.463-0.732-0.7320.0000.0000.0000.000
7B7VAL00.0170.00212.3560.3990.3990.0000.0000.0000.000
8B8ILE0-0.0100.02014.5311.0371.0370.0000.0000.0000.000
9B9ASP-1-0.804-0.91417.746-12.964-12.9640.0000.0000.0000.000
10B10THR0-0.048-0.03219.104-0.183-0.1830.0000.0000.0000.000
11B11ASP-1-0.927-0.95121.378-10.949-10.9490.0000.0000.0000.000
12B12GLY0-0.058-0.03922.0550.3660.3660.0000.0000.0000.000
13B13ASN0-0.092-0.05421.230-0.107-0.1070.0000.0000.0000.000
14B14PRO00.0050.00716.774-0.157-0.1570.0000.0000.0000.000
15B15LEU00.0140.01717.8540.8040.8040.0000.0000.0000.000
16B16LEU0-0.063-0.04518.225-0.471-0.4710.0000.0000.0000.000
17B17HIS00.0250.00116.772-0.233-0.2330.0000.0000.0000.000
18B18ARG10.8880.94821.54111.71511.7150.0000.0000.0000.000
19B19GLY0-0.064-0.03023.9720.6650.6650.0000.0000.0000.000
20B20LYS10.8830.94724.7349.4839.4830.0000.0000.0000.000
21B21TYR00.0840.05822.8240.2550.2550.0000.0000.0000.000
22B22TYR00.0200.02525.9390.2830.2830.0000.0000.0000.000
23B23ILE00.0260.00221.222-0.371-0.3710.0000.0000.0000.000
24B24MET00.0080.01924.6080.3970.3970.0000.0000.0000.000
25B25PRO0-0.0670.00024.657-0.569-0.5690.0000.0000.0000.000
26B26SER00.004-0.00922.4580.1060.1060.0000.0000.0000.000
27B27ASN0-0.019-0.01124.5100.1910.1910.0000.0000.0000.000
28B28TRP0-0.006-0.01826.916-0.066-0.0660.0000.0000.0000.000
29B29GLY00.0500.04826.9540.2130.2130.0000.0000.0000.000
30B30PRO00.0180.05627.010-0.283-0.2830.0000.0000.0000.000
31B31PRO00.004-0.02629.986-0.090-0.0900.0000.0000.0000.000
32B32GLY0-0.021-0.02929.446-0.065-0.0650.0000.0000.0000.000
33B33GLY00.0910.05529.3670.3420.3420.0000.0000.0000.000
34B34GLY00.0310.01028.695-0.442-0.4420.0000.0000.0000.000
35B35LEU00.006-0.01124.0760.0310.0310.0000.0000.0000.000
36B36ARG10.8670.94328.7869.4519.4510.0000.0000.0000.000
37B37LEU00.0190.03630.036-0.204-0.2040.0000.0000.0000.000
38B38GLY00.005-0.00432.2240.2480.2480.0000.0000.0000.000
39B39LYS10.9380.97034.1867.5717.5710.0000.0000.0000.000
40B40THR0-0.024-0.03432.633-0.099-0.0990.0000.0000.0000.000
41B41ARG10.7640.86135.0158.8398.8390.0000.0000.0000.000
42B42ASN0-0.032-0.05537.6460.2100.2100.0000.0000.0000.000
43B43LEU00.0170.01138.663-0.206-0.2060.0000.0000.0000.000
44B44ASN00.0240.05838.0840.0670.0670.0000.0000.0000.000
45B45CYS0-0.050-0.05336.025-0.047-0.0470.0000.0000.0000.000
46B46PRO00.0170.01434.263-0.224-0.2240.0000.0000.0000.000
47B47VAL00.0450.07528.786-0.102-0.1020.0000.0000.0000.000
48B48THR0-0.036-0.03028.943-0.406-0.4060.0000.0000.0000.000
49B49VAL00.0230.02925.7290.3560.3560.0000.0000.0000.000
50B50LEU0-0.050-0.03727.791-0.142-0.1420.0000.0000.0000.000
51B51GLN00.0350.02725.899-0.218-0.2180.0000.0000.0000.000
52B52ASP-1-0.863-0.92129.172-8.802-8.8020.0000.0000.0000.000
53B53TYR0-0.036-0.01731.922-0.201-0.2010.0000.0000.0000.000
54B54ASN0-0.037-0.03234.3000.2210.2210.0000.0000.0000.000
55B55GLU-1-0.820-0.93833.700-8.945-8.9450.0000.0000.0000.000
56B56ALA0-0.0090.02834.749-0.030-0.0300.0000.0000.0000.000
57B57ILE0-0.040-0.01134.1950.0600.0600.0000.0000.0000.000
58B58ASN00.009-0.00330.6370.0140.0140.0000.0000.0000.000
59B59GLY00.005-0.03630.255-0.343-0.3430.0000.0000.0000.000
60B60LEU0-0.054-0.03030.0840.2400.2400.0000.0000.0000.000
61B61PRO0-0.004-0.01528.519-0.374-0.3740.0000.0000.0000.000
62B62VAL0-0.029-0.01623.4200.0540.0540.0000.0000.0000.000
63B63LYS10.8450.92524.06410.79910.7990.0000.0000.0000.000
64B64PHE00.1090.05117.677-0.035-0.0350.0000.0000.0000.000
65B65ASN00.0180.03120.2280.0080.0080.0000.0000.0000.000
66B66ILE00.1630.08414.661-0.139-0.1390.0000.0000.0000.000
67B67ARG10.7040.81718.32313.53613.5360.0000.0000.0000.000
68B68GLU-1-0.839-0.88721.560-11.917-11.9170.0000.0000.0000.000
69B69ILE00.017-0.00918.7470.0880.0880.0000.0000.0000.000
70B70LEU0-0.013-0.00622.8540.4420.4420.0000.0000.0000.000
71B71PRO0-0.041-0.00617.9920.0910.0910.0000.0000.0000.000
72B72ARG10.9930.97518.55613.54813.5480.0000.0000.0000.000
73B73THR0-0.052-0.02914.0660.7060.7060.0000.0000.0000.000
74B74ILE00.0320.03414.104-0.498-0.4980.0000.0000.0000.000
75B75PHE00.0620.0249.3260.6430.6430.0000.0000.0000.000
76B76THR0-0.010-0.0047.487-0.357-0.3570.0000.0000.0000.000
77B77ASP-1-0.933-0.9755.303-49.697-49.6970.0000.0000.0000.000
78B78THR0-0.008-0.0057.899-0.623-0.6230.0000.0000.0000.000
79B79GLU-1-0.929-0.94310.617-20.564-20.5640.0000.0000.0000.000
80B80LEU0-0.004-0.02712.5571.4851.4850.0000.0000.0000.000
81B81ASN0-0.037-0.03016.124-0.135-0.1350.0000.0000.0000.000
82B82ILE00.0050.03719.2300.5520.5520.0000.0000.0000.000
83B83GLU-1-0.741-0.88321.105-11.499-11.4990.0000.0000.0000.000
84B84PHE00.0090.01424.855-0.031-0.0310.0000.0000.0000.000
85B85THR0-0.022-0.03827.8200.0010.0010.0000.0000.0000.000
86B86GLU-1-0.950-0.97030.433-8.351-8.3510.0000.0000.0000.000
87B87LYS10.8460.95132.1378.9078.9070.0000.0000.0000.000
88B88PRO00.0530.02932.9690.2530.2530.0000.0000.0000.000
89B89ASN00.002-0.03335.809-0.160-0.1600.0000.0000.0000.000
90B91ALA00.0480.06532.5230.0130.0130.0000.0000.0000.000
91B92GLU-1-0.855-0.93832.097-9.359-9.3590.0000.0000.0000.000
92B93ASN00.0230.00227.1070.1340.1340.0000.0000.0000.000
93B94ARG10.8700.91228.20410.78510.7850.0000.0000.0000.000
94B95ALA0-0.023-0.01323.903-0.213-0.2130.0000.0000.0000.000
95B96TRP0-0.032-0.00520.7280.1660.1660.0000.0000.0000.000
96B97SER00.0310.00921.514-0.714-0.7140.0000.0000.0000.000
97B98LEU00.0040.00118.4550.3150.3150.0000.0000.0000.000
98B99PHE00.0230.03922.415-0.137-0.1370.0000.0000.0000.000
99B100LYS10.8920.93523.07111.60111.6010.0000.0000.0000.000
100B101GLY0-0.043-0.02825.1380.3490.3490.0000.0000.0000.000
101B102ASP-1-0.786-0.87426.057-10.726-10.7260.0000.0000.0000.000
102B103ASP-1-0.878-0.95529.708-9.262-9.2620.0000.0000.0000.000
103B104ARG10.9480.98832.2308.6178.6170.0000.0000.0000.000
104B105GLY0-0.074-0.05529.5550.1310.1310.0000.0000.0000.000
105B106HIS0-0.038-0.02928.289-0.112-0.1120.0000.0000.0000.000
106B107LYS10.9390.98321.51113.48213.4820.0000.0000.0000.000
107B108ALA0-0.037-0.01820.8180.4440.4440.0000.0000.0000.000
108B109ARG10.8120.93122.42511.10311.1030.0000.0000.0000.000
109B110VAL00.0140.02022.868-0.178-0.1780.0000.0000.0000.000
110B111GLY00.004-0.03324.2820.5600.5600.0000.0000.0000.000
111B112ILE0-0.0110.03125.609-0.350-0.3500.0000.0000.0000.000
112B113GLY0-0.001-0.01728.0770.3350.3350.0000.0000.0000.000
113B114GLY0-0.012-0.00628.701-0.373-0.3730.0000.0000.0000.000
114B115SER00.0460.02630.270-0.006-0.0060.0000.0000.0000.000
115B116ASN0-0.064-0.04531.552-0.235-0.2350.0000.0000.0000.000
116B117GLY00.0300.02133.2130.2750.2750.0000.0000.0000.000
117B118HIS0-0.020-0.03935.000-0.287-0.2870.0000.0000.0000.000
118B119PRO00.0230.04132.6570.0040.0040.0000.0000.0000.000
119B120GLY0-0.033-0.05330.295-0.268-0.2680.0000.0000.0000.000
120B121GLY00.0180.01229.7010.2620.2620.0000.0000.0000.000
121B122GLU-1-0.791-0.87427.167-11.463-11.4630.0000.0000.0000.000
122B123MET0-0.008-0.00224.946-0.319-0.3190.0000.0000.0000.000
123B124LEU0-0.051-0.03519.838-0.093-0.0930.0000.0000.0000.000
124B125ARG10.8010.88920.15013.03313.0330.0000.0000.0000.000
125B126GLY00.0860.02116.560-0.502-0.5020.0000.0000.0000.000
126B127GLY0-0.0090.02514.8811.2501.2500.0000.0000.0000.000
127B128PHE0-0.087-0.06613.564-0.875-0.8750.0000.0000.0000.000
128B129TYR00.0220.0117.3430.2460.2460.0000.0000.0000.000
129B130GLY0-0.100-0.06110.6032.3032.3030.0000.0000.0000.000
130B131GLU-1-0.737-0.85010.691-21.319-21.3190.0000.0000.0000.000
131B132GLN0-0.114-0.07111.119-1.738-1.7380.0000.0000.0000.000
132B133HIS00.0030.0257.1850.4480.4480.0000.0000.0000.000
133B134GLY0-0.041-0.02411.5331.0671.0670.0000.0000.0000.000
134B135LEU0-0.006-0.01614.031-0.016-0.0160.0000.0000.0000.000
135B136ARG10.9650.97916.65313.18313.1830.0000.0000.0000.000
136B137ASN0-0.019-0.02319.5950.5840.5840.0000.0000.0000.000
137B138GLY00.0120.01819.693-0.088-0.0880.0000.0000.0000.000
138B139THR00.0220.02216.422-0.336-0.3360.0000.0000.0000.000
139B140TYR0-0.064-0.03515.0520.2930.2930.0000.0000.0000.000
140B141LYS10.8940.94811.22124.25424.2540.0000.0000.0000.000
141B142LEU00.0680.04313.651-0.956-0.9560.0000.0000.0000.000
142B143VAL0-0.037-0.0189.6200.6000.6000.0000.0000.0000.000
143B144PHE00.0150.01112.8100.4560.4560.0000.0000.0000.000
144B145CYS0-0.042-0.0728.581-1.256-1.2560.0000.0000.0000.000
145B146ARG10.8820.94512.23118.37118.3710.0000.0000.0000.000
146B147ASP-1-0.792-0.90614.130-17.844-17.8440.0000.0000.0000.000
147B148GLY0-0.077-0.02916.6770.0030.0030.0000.0000.0000.000
148B149SER0-0.014-0.03415.6980.3920.3920.0000.0000.0000.000
149B150SER0-0.104-0.04213.6030.0620.0620.0000.0000.0000.000
150B151THR00.1070.0978.611-1.780-1.7800.0000.0000.0000.000
151B153LEU00.0000.01910.504-0.971-0.9710.0000.0000.0000.000
152B154ASP-1-0.783-0.88712.601-22.874-22.8740.0000.0000.0000.000
153B155VAL00.000-0.01314.4430.9290.9290.0000.0000.0000.000
154B156GLY0-0.011-0.00817.7570.0440.0440.0000.0000.0000.000
155B157ARG10.7300.81620.51612.79612.7960.0000.0000.0000.000
156B158TYR00.0040.01024.2100.1000.1000.0000.0000.0000.000
157B159GLY00.0440.01727.1630.0830.0830.0000.0000.0000.000
158B160ASN0-0.047-0.03730.657-0.068-0.0680.0000.0000.0000.000
159B161ARG10.9500.97533.5718.2728.2720.0000.0000.0000.000
160B162GLU-1-0.768-0.85034.862-8.644-8.6440.0000.0000.0000.000
161B163GLY00.0820.03033.4110.1360.1360.0000.0000.0000.000
162B164ARG10.8340.92028.27610.61910.6190.0000.0000.0000.000
163B165ARG10.9270.99028.0379.9649.9640.0000.0000.0000.000
164B166LEU00.0850.03522.131-0.123-0.1230.0000.0000.0000.000
165B167GLY0-0.004-0.01122.1140.4510.4510.0000.0000.0000.000
166B168LEU0-0.0080.02216.831-0.177-0.1770.0000.0000.0000.000
167B169SER0-0.012-0.02118.6040.7410.7410.0000.0000.0000.000
168B170GLU-1-0.863-0.93017.367-14.926-14.9260.0000.0000.0000.000
169B171ALA0-0.027-0.00816.687-0.760-0.7600.0000.0000.0000.000
170B172GLY00.0530.02215.634-1.250-1.2500.0000.0000.0000.000
171B173GLU-1-0.906-0.92216.671-12.246-12.2460.0000.0000.0000.000
172B174LEU0-0.049-0.02118.395-0.437-0.4370.0000.0000.0000.000
173B175GLY00.0550.03618.839-0.817-0.8170.0000.0000.0000.000
174B176VAL0-0.058-0.04718.0950.7880.7880.0000.0000.0000.000
175B177GLY00.0390.03419.688-0.431-0.4310.0000.0000.0000.000
176B178PHE0-0.025-0.01817.3940.3520.3520.0000.0000.0000.000
177B179GLU-1-0.753-0.86722.652-10.161-10.1610.0000.0000.0000.000
178B180LYS10.9300.96425.31811.46611.4660.0000.0000.0000.000
179B181ALA0-0.023-0.03026.4250.3030.3030.0000.0000.0000.000
180B182GLY00.0250.02029.4580.3890.3890.0000.0000.0000.000
181B183GLY0-0.068-0.05730.365-0.279-0.2790.0000.0000.0000.000
182B184GLY00.0680.04231.4530.0310.0310.0000.0000.0000.000
183B185ASN0-0.023-0.00228.709-0.352-0.3520.0000.0000.0000.000