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: J2LG9

Calculation Name: 5L0W-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5L0W

Chain ID: B

ChEMBL ID:

UniProt ID: G0SH41

Base Structure: X-ray

Registration Date: 2023-09-26

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2094476.674311
FMO2-HF: Nuclear repulsion 2012825.932986
FMO2-HF: Total energy -81650.741325
FMO2-MP2: Total energy -81889.795023


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:5:ASP)


Summations of interaction energy for fragment #1(B:5:ASP)
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.
-52.959-45.182.203-4.588-5.3940.022
Interaction energy analysis for fragmet #1(B:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.843 / q_NPA : -0.912
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].
3B7PHE0-0.054-0.0232.624-22.971-15.7412.190-4.317-5.1030.024
4B8THR00.004-0.0013.425-0.3730.0670.014-0.266-0.188-0.002
5B9PHE00.0220.0124.483-1.022-0.913-0.001-0.005-0.1030.000
6B10ILE00.0100.0025.980-2.848-2.8480.0000.0000.0000.000
7B11PRO0-0.0210.0069.7980.3780.3780.0000.0000.0000.000
8B12LEU00.0140.00112.019-1.331-1.3310.0000.0000.0000.000
9B13HIS0-0.034-0.02614.733-0.419-0.4190.0000.0000.0000.000
10B14ILE00.0100.00617.8790.0660.0660.0000.0000.0000.000
11B15ASP-1-0.805-0.87219.87711.35311.3530.0000.0000.0000.000
12B16PRO00.009-0.00823.716-0.112-0.1120.0000.0000.0000.000
13B17LYS10.9180.96625.363-11.128-11.1280.0000.0000.0000.000
14B18SER0-0.055-0.05626.666-0.061-0.0610.0000.0000.0000.000
15B19LYS10.8180.90923.299-11.558-11.5580.0000.0000.0000.000
16B20ALA00.0170.02922.1630.5210.5210.0000.0000.0000.000
17B21ILE00.0390.00816.3660.1730.1730.0000.0000.0000.000
18B22SER0-0.006-0.00318.948-0.883-0.8830.0000.0000.0000.000
19B23ALA00.0470.01916.9390.9720.9720.0000.0000.0000.000
20B24ALA00.0100.02415.444-0.637-0.6370.0000.0000.0000.000
21B25PRO0-0.002-0.01717.403-0.181-0.1810.0000.0000.0000.000
22B26ASN0-0.020-0.01118.2700.3600.3600.0000.0000.0000.000
23B27ALA00.0200.02513.9490.3570.3570.0000.0000.0000.000
24B28LEU00.0390.01312.5591.1061.1060.0000.0000.0000.000
25B29GLY0-0.026-0.00814.409-0.146-0.1460.0000.0000.0000.000
26B30THR00.0020.01116.992-0.915-0.9150.0000.0000.0000.000
27B31PRO00.0090.00219.2170.2750.2750.0000.0000.0000.000
28B32SER00.003-0.00221.5560.0590.0590.0000.0000.0000.000
29B33ALA00.0680.02716.3090.0290.0290.0000.0000.0000.000
30B34ASN00.014-0.00417.6381.0291.0290.0000.0000.0000.000
31B35LYS10.9490.98319.051-11.882-11.8820.0000.0000.0000.000
32B36ALA0-0.025-0.00919.044-0.327-0.3270.0000.0000.0000.000
33B37LEU00.0590.03814.907-0.043-0.0430.0000.0000.0000.000
34B38GLU-1-0.904-0.95518.24313.25613.2560.0000.0000.0000.000
35B39THR0-0.084-0.06621.434-0.524-0.5240.0000.0000.0000.000
36B40GLU-1-0.909-0.94317.01515.55915.5590.0000.0000.0000.000
37B41LEU00.0150.00216.3150.0770.0770.0000.0000.0000.000
38B42ALA0-0.029-0.01020.032-0.350-0.3500.0000.0000.0000.000
39B43ALA00.0070.00322.205-0.421-0.4210.0000.0000.0000.000
40B44LEU00.0370.02216.921-0.337-0.3370.0000.0000.0000.000
41B45ASN00.0360.00821.0760.0320.0320.0000.0000.0000.000
42B46ALA0-0.077-0.02323.344-0.532-0.5320.0000.0000.0000.000
43B47LEU00.0490.02821.513-0.434-0.4340.0000.0000.0000.000
44B48HIS00.0250.01221.483-0.023-0.0230.0000.0000.0000.000
45B49ARG10.8890.92024.301-11.647-11.6470.0000.0000.0000.000
46B50ALA00.0170.02827.727-0.400-0.4000.0000.0000.0000.000
47B51LEU00.012-0.00523.700-0.332-0.3320.0000.0000.0000.000
48B52HIS0-0.035-0.01427.691-0.069-0.0690.0000.0000.0000.000
49B53THR0-0.043-0.04429.292-0.385-0.3850.0000.0000.0000.000
50B54GLN0-0.049-0.02931.717-0.377-0.3770.0000.0000.0000.000
51B55ILE0-0.0250.01128.599-0.098-0.0980.0000.0000.0000.000
52B56GLU-1-0.900-0.93532.0868.3488.3480.0000.0000.0000.000
53B57GLY0-0.0060.00733.555-0.222-0.2220.0000.0000.0000.000
54B58PRO00.002-0.01432.3900.1960.1960.0000.0000.0000.000
55B59ILE00.0040.00426.9010.2560.2560.0000.0000.0000.000
56B60PRO0-0.0010.01324.929-0.136-0.1360.0000.0000.0000.000
57B61VAL0-0.013-0.02123.2510.5630.5630.0000.0000.0000.000
58B62PRO00.0170.00225.119-0.421-0.4210.0000.0000.0000.000
59B63PRO00.0040.02127.9150.1890.1890.0000.0000.0000.000
60B64PRO00.0120.00030.1180.1280.1280.0000.0000.0000.000
61B65PRO00.024-0.00329.878-0.330-0.3300.0000.0000.0000.000
62B66VAL00.0080.00332.921-0.262-0.2620.0000.0000.0000.000
63B67PRO0-0.038-0.00434.813-0.283-0.2830.0000.0000.0000.000
64B68VAL00.0130.00937.1770.0710.0710.0000.0000.0000.000
65B69ASN00.007-0.01238.115-0.466-0.4660.0000.0000.0000.000
66B70PRO00.0330.01340.121-0.028-0.0280.0000.0000.0000.000
67B71LYS10.9700.98342.821-7.565-7.5650.0000.0000.0000.000
68B72ARG10.8770.93437.966-8.396-8.3960.0000.0000.0000.000
69B73SER00.0610.00643.264-0.063-0.0630.0000.0000.0000.000
70B74ALA0-0.0130.01145.073-0.176-0.1760.0000.0000.0000.000
71B75ASN0-0.005-0.00246.365-0.291-0.2910.0000.0000.0000.000
72B76ILE00.0510.03842.927-0.150-0.1500.0000.0000.0000.000
73B77ASN0-0.004-0.01047.531-0.241-0.2410.0000.0000.0000.000
74B78LYS10.9040.95450.528-6.443-6.4430.0000.0000.0000.000
75B79LEU00.0190.00548.967-0.134-0.1340.0000.0000.0000.000
76B80ARG10.8670.93350.130-6.264-6.2640.0000.0000.0000.000
77B81GLU-1-0.787-0.86952.5975.4635.4630.0000.0000.0000.000
78B82SER00.0210.01555.345-0.130-0.1300.0000.0000.0000.000
79B83GLY0-0.005-0.00855.244-0.094-0.0940.0000.0000.0000.000
80B84ASN00.010-0.00155.741-0.053-0.0530.0000.0000.0000.000
81B85ALA0-0.085-0.01458.390-0.114-0.1140.0000.0000.0000.000
82B86GLU-1-0.760-0.88059.2155.1015.1010.0000.0000.0000.000
83B87TYR0-0.011-0.00259.003-0.043-0.0430.0000.0000.0000.000
84B88ARG10.8220.87459.891-5.408-5.4080.0000.0000.0000.000
85B89LYS10.7890.88063.602-5.156-5.1560.0000.0000.0000.000
86B90GLN0-0.0090.00564.640-0.075-0.0750.0000.0000.0000.000
87B91ARG10.8910.93760.875-5.203-5.2030.0000.0000.0000.000
88B92TYR00.049-0.00759.9380.1210.1210.0000.0000.0000.000
89B93GLY00.0290.01958.3120.1050.1050.0000.0000.0000.000
90B94ASP-1-0.808-0.87857.1645.4675.4670.0000.0000.0000.000
91B95ALA00.0150.01556.3210.1020.1020.0000.0000.0000.000
92B96ILE00.0300.02353.0180.1390.1390.0000.0000.0000.000
93B97LYS10.8710.94752.307-5.454-5.4540.0000.0000.0000.000
94B98LEU0-0.0050.00751.3490.1530.1530.0000.0000.0000.000
95B99TYR00.014-0.02850.9430.1120.1120.0000.0000.0000.000
96B100THR0-0.016-0.01247.3810.1700.1700.0000.0000.0000.000
97B101LEU00.0070.01046.7040.1680.1680.0000.0000.0000.000
98B102GLY00.0120.00546.2540.1500.1500.0000.0000.0000.000
99B103LEU00.001-0.00444.4850.1690.1690.0000.0000.0000.000
100B104GLN00.0050.00742.3250.1080.1080.0000.0000.0000.000
101B105MET0-0.0350.00441.3240.1890.1890.0000.0000.0000.000
102B106ALA00.0200.01741.6510.1260.1260.0000.0000.0000.000
103B107LEU00.003-0.01138.6410.2120.2120.0000.0000.0000.000
104B108THR0-0.057-0.03036.7240.2170.2170.0000.0000.0000.000
105B109ARG10.7360.82836.102-8.068-8.0680.0000.0000.0000.000
106B110PRO00.0220.01532.1210.1430.1430.0000.0000.0000.000
107B111ALA00.0120.00429.034-0.060-0.0600.0000.0000.0000.000
108B112TRP00.0190.01427.6880.3690.3690.0000.0000.0000.000
109B113GLU-1-0.860-0.92429.8648.6718.6710.0000.0000.0000.000
110B114PRO0-0.001-0.01433.2760.1050.1050.0000.0000.0000.000
111B115ALA00.0710.03533.120-0.276-0.2760.0000.0000.0000.000
112B116GLY0-0.007-0.00435.141-0.189-0.1890.0000.0000.0000.000
113B117LEU00.0100.01438.055-0.226-0.2260.0000.0000.0000.000
114B118VAL00.0170.01536.477-0.217-0.2170.0000.0000.0000.000
115B119ARG10.8130.88636.721-8.451-8.4510.0000.0000.0000.000
116B120ASP-1-0.795-0.89140.7606.9236.9230.0000.0000.0000.000
117B121GLU-1-0.785-0.86142.1137.3407.3400.0000.0000.0000.000
118B122ILE0-0.012-0.01640.513-0.195-0.1950.0000.0000.0000.000
119B123HIS0-0.020-0.00644.490-0.261-0.2610.0000.0000.0000.000
120B124GLN00.0530.04746.331-0.264-0.2640.0000.0000.0000.000
121B125LEU0-0.011-0.00546.325-0.170-0.1700.0000.0000.0000.000
122B126TYR00.0290.01243.161-0.072-0.0720.0000.0000.0000.000
123B127SER00.0060.01348.882-0.186-0.1860.0000.0000.0000.000
124B128ASN0-0.042-0.02351.726-0.173-0.1730.0000.0000.0000.000
125B129ARG10.7730.84447.940-6.639-6.6390.0000.0000.0000.000
126B130ALA00.0380.01952.093-0.095-0.0950.0000.0000.0000.000
127B131GLN00.0220.01653.793-0.077-0.0770.0000.0000.0000.000
128B132ALA00.000-0.01256.176-0.117-0.1170.0000.0000.0000.000
129B133TYR0-0.001-0.00651.759-0.051-0.0510.0000.0000.0000.000
130B134MET0-0.0170.00056.643-0.101-0.1010.0000.0000.0000.000
131B135GLN0-0.044-0.00459.359-0.158-0.1580.0000.0000.0000.000
132B136LEU0-0.044-0.01358.754-0.097-0.0970.0000.0000.0000.000
133B137GLY00.0190.02061.845-0.026-0.0260.0000.0000.0000.000
134B138GLN0-0.075-0.04356.215-0.039-0.0390.0000.0000.0000.000
135B139TRP00.073-0.00156.3410.1400.1400.0000.0000.0000.000
136B140PRO00.0150.00253.6690.0800.0800.0000.0000.0000.000
137B141GLU-1-0.808-0.89951.4815.9385.9380.0000.0000.0000.000
138B142ALA0-0.013-0.00351.5010.1170.1170.0000.0000.0000.000
139B143ALA00.0160.00452.5540.0680.0680.0000.0000.0000.000
140B144ALA00.0400.03447.6990.1150.1150.0000.0000.0000.000
141B145ASP-1-0.752-0.84347.5996.6566.6560.0000.0000.0000.000
142B146ALA0-0.020-0.02048.5230.0960.0960.0000.0000.0000.000
143B147GLU-1-0.827-0.89445.4706.8496.8490.0000.0000.0000.000
144B148CYS0-0.049-0.02244.2410.1880.1880.0000.0000.0000.000
145B149SER0-0.067-0.05644.4870.1130.1130.0000.0000.0000.000
146B150VAL00.0130.00846.2310.0830.0830.0000.0000.0000.000
147B151GLU-1-0.806-0.87039.5408.0808.0800.0000.0000.0000.000
148B152ALA0-0.058-0.01141.3530.1690.1690.0000.0000.0000.000
149B153LYS10.8330.90141.961-6.804-6.8040.0000.0000.0000.000
150B154ARG10.9250.94639.913-7.848-7.8480.0000.0000.0000.000
151B155GLN00.0360.02645.105-0.191-0.1910.0000.0000.0000.000
152B156GLY00.0140.00747.9060.0650.0650.0000.0000.0000.000
153B157ASN0-0.054-0.04047.910-0.191-0.1910.0000.0000.0000.000
154B158ALA00.0740.04051.0610.0090.0090.0000.0000.0000.000
155B159LYS10.8420.90954.112-5.443-5.4430.0000.0000.0000.000
156B160ALA0-0.018-0.00250.525-0.063-0.0630.0000.0000.0000.000
157B161TRP00.0450.02047.791-0.017-0.0170.0000.0000.0000.000
158B162TYR00.0500.02353.165-0.044-0.0440.0000.0000.0000.000
159B163ARG10.8370.90254.010-5.878-5.8780.0000.0000.0000.000
160B164ARG10.8310.89948.257-6.569-6.5690.0000.0000.0000.000
161B165GLY00.0480.02354.341-0.035-0.0350.0000.0000.0000.000
162B166LYS10.8870.92956.716-5.107-5.1070.0000.0000.0000.000
163B167CYS0-0.052-0.02555.758-0.066-0.0660.0000.0000.0000.000
164B168LEU0-0.013-0.00552.971-0.040-0.0400.0000.0000.0000.000
165B169MET00.0000.01957.028-0.073-0.0730.0000.0000.0000.000
166B170GLU-1-0.820-0.88060.5264.8644.8640.0000.0000.0000.000
167B171MET0-0.115-0.03154.678-0.002-0.0020.0000.0000.0000.000
168B172ARG10.8550.90759.352-4.933-4.9330.0000.0000.0000.000
169B173ARG10.8280.88950.994-6.061-6.0610.0000.0000.0000.000
170B174LEU00.029-0.00157.6330.0780.0780.0000.0000.0000.000
171B175GLN0-0.006-0.01456.984-0.088-0.0880.0000.0000.0000.000
172B176GLU-1-0.749-0.83252.0906.1116.1110.0000.0000.0000.000
173B177ALA0-0.009-0.00654.5480.0800.0800.0000.0000.0000.000
174B178ARG10.9090.94456.894-5.341-5.3410.0000.0000.0000.000
175B179GLU-1-0.906-0.95353.1445.9585.9580.0000.0000.0000.000
176B180TRP0-0.059-0.02848.0390.1390.1390.0000.0000.0000.000
177B181VAL0-0.006-0.01653.1080.0690.0690.0000.0000.0000.000
178B182ALA0-0.0230.00155.422-0.006-0.0060.0000.0000.0000.000
179B183ARG10.8320.88847.483-6.448-6.4480.0000.0000.0000.000
180B184GLY0-0.024-0.03951.2010.0940.0940.0000.0000.0000.000
181B185LEU0-0.043-0.02152.726-0.038-0.0380.0000.0000.0000.000
182B186GLU-1-0.832-0.87049.7596.3926.3920.0000.0000.0000.000
183B187PHE0-0.081-0.04345.0040.1480.1480.0000.0000.0000.000
184B188GLU-1-0.893-0.93150.0325.8915.8910.0000.0000.0000.000
185B189GLY0-0.017-0.03851.5210.1420.1420.0000.0000.0000.000
186B190GLU-1-0.866-0.92254.2335.1965.1960.0000.0000.0000.000
187B191GLU-1-0.851-0.91757.8295.4425.4420.0000.0000.0000.000
188B192LYS10.8790.92159.172-5.111-5.1110.0000.0000.0000.000
189B193GLU-1-0.802-0.89259.9945.2985.2980.0000.0000.0000.000
190B194LEU00.0120.00455.146-0.029-0.0290.0000.0000.0000.000
191B195ALA00.0390.02159.655-0.016-0.0160.0000.0000.0000.000
192B196GLU-1-0.938-0.96362.3054.6794.6790.0000.0000.0000.000
193B197LEU0-0.036-0.01758.799-0.042-0.0420.0000.0000.0000.000
194B198LEU0-0.015-0.00559.218-0.012-0.0120.0000.0000.0000.000
195B199LYS10.9250.96961.982-4.749-4.7490.0000.0000.0000.000
196B200GLU-1-0.877-0.90165.1074.8274.8270.0000.0000.0000.000
197B201ILE0-0.038-0.02559.663-0.021-0.0210.0000.0000.0000.000
198B202ASP-1-0.802-0.91063.0155.0505.0500.0000.0000.0000.000
199B203SER0-0.030-0.03064.719-0.071-0.0710.0000.0000.0000.000
200B204LYS10.8320.90465.591-4.937-4.9370.0000.0000.0000.000
201B205LEU0-0.005-0.01161.433-0.035-0.0350.0000.0000.0000.000
202B206ALA0-0.0090.00366.113-0.034-0.0340.0000.0000.0000.000
203B207ALA00.0180.00868.940-0.055-0.0550.0000.0000.0000.000
204B208GLU-1-0.877-0.91466.0914.8244.8240.0000.0000.0000.000
205B209LYS10.8110.87565.029-4.885-4.8850.0000.0000.0000.000
206B210ALA00.0280.01769.364-0.033-0.0330.0000.0000.0000.000
207B211SER0-0.064-0.03572.517-0.086-0.0860.0000.0000.0000.000
208B212ARG10.7370.85766.153-4.711-4.7110.0000.0000.0000.000
209B213ASP-1-0.832-0.88170.9684.5054.5050.0000.0000.0000.000