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

tag_button

FMODB ID: LNLZ9

Calculation Name: 3F5C-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5C

Chain ID: B

ChEMBL ID:

UniProt ID: Q61066

Base Structure: X-ray

Registration Date: 2023-09-20

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 -2052117.536893
FMO2-HF: Nuclear repulsion 1975983.894642
FMO2-HF: Total energy -76133.642251
FMO2-MP2: Total energy -76348.257399


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:251:LYS)


Summations of interaction energy for fragment #1(B:251: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.
-54.506-50.9160.215-1.565-2.241-0.002
Interaction energy analysis for fragmet #1(B:251:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.950 / q_NPA : 0.965
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].
3B253PRO00.0120.0202.7242.9505.8840.210-1.446-1.699-0.002
4B254GLN00.0550.0164.016-0.395-0.1470.000-0.035-0.2130.000
5B255VAL00.0570.0224.8662.4802.4800.0000.0000.0000.000
6B256VAL00.0350.0216.1083.1223.1220.0000.0000.0000.000
7B257CYS0-0.0230.0018.4672.8072.8070.0000.0000.0000.000
8B258GLU-1-0.951-0.96610.033-18.755-18.7550.0000.0000.0000.000
9B259ALA00.010-0.00410.7671.7291.7290.0000.0000.0000.000
10B260ALA0-0.020-0.00912.4191.3511.3510.0000.0000.0000.000
11B261SER00.002-0.01514.1871.6601.6600.0000.0000.0000.000
12B262ALA0-0.032-0.01715.5031.1201.1200.0000.0000.0000.000
13B263GLY00.0170.00616.5380.8840.8840.0000.0000.0000.000
14B264LEU00.0480.02718.3370.8620.8620.0000.0000.0000.000
15B265LEU0-0.020-0.01320.1010.8870.8870.0000.0000.0000.000
16B266LYS10.8340.91517.73815.27115.2710.0000.0000.0000.000
17B267THR00.0320.01321.9730.4830.4830.0000.0000.0000.000
18B268LEU00.018-0.00424.4430.5230.5230.0000.0000.0000.000
19B269ARG10.9130.96823.30911.61611.6160.0000.0000.0000.000
20B270PHE0-0.0080.00127.0840.3850.3850.0000.0000.0000.000
21B271VAL00.0230.00528.6220.3310.3310.0000.0000.0000.000
22B272LYS10.8260.93730.4799.5819.5810.0000.0000.0000.000
23B273TYR0-0.017-0.02730.3920.1580.1580.0000.0000.0000.000
24B274LEU00.0020.02232.6540.2760.2760.0000.0000.0000.000
25B275PRO00.0370.02335.6320.0960.0960.0000.0000.0000.000
26B276CYS0-0.046-0.03038.4430.0360.0360.0000.0000.0000.000
27B277PHE00.0600.04433.5380.0650.0650.0000.0000.0000.000
28B278GLN0-0.020-0.00936.3970.2340.2340.0000.0000.0000.000
29B279ILE0-0.054-0.01938.3920.1220.1220.0000.0000.0000.000
30B280LEU0-0.046-0.01438.5190.1810.1810.0000.0000.0000.000
31B281PRO00.0410.02440.526-0.082-0.0820.0000.0000.0000.000
32B282LEU00.0460.02235.232-0.141-0.1410.0000.0000.0000.000
33B283ASP-1-0.810-0.90837.304-7.420-7.4200.0000.0000.0000.000
34B284GLN00.0410.01537.736-0.169-0.1690.0000.0000.0000.000
35B285GLN0-0.026-0.02635.181-0.382-0.3820.0000.0000.0000.000
36B286LEU0-0.016-0.01531.831-0.292-0.2920.0000.0000.0000.000
37B287VAL00.0130.01032.710-0.292-0.2920.0000.0000.0000.000
38B288LEU00.0160.01832.894-0.252-0.2520.0000.0000.0000.000
39B289VAL00.0410.01428.340-0.311-0.3110.0000.0000.0000.000
40B290ARG10.8310.90228.5758.9068.9060.0000.0000.0000.000
41B291SER0-0.0090.01029.018-0.117-0.1170.0000.0000.0000.000
42B292CYS0-0.039-0.02027.770-0.317-0.3170.0000.0000.0000.000
43B293TRP00.0070.00420.309-0.598-0.5980.0000.0000.0000.000
44B294ALA00.0450.03422.612-0.478-0.4780.0000.0000.0000.000
45B295PRO0-0.013-0.01122.522-0.449-0.4490.0000.0000.0000.000
46B296LEU0-0.005-0.00823.769-0.286-0.2860.0000.0000.0000.000
47B297LEU00.0130.01318.293-0.198-0.1980.0000.0000.0000.000
48B298MET0-0.042-0.01017.305-0.805-0.8050.0000.0000.0000.000
49B299LEU0-0.007-0.00820.089-0.275-0.2750.0000.0000.0000.000
50B300GLU-1-0.877-0.93120.408-12.211-12.2110.0000.0000.0000.000
51B301LEU0-0.008-0.00214.759-0.318-0.3180.0000.0000.0000.000
52B302ALA00.0040.01516.631-0.603-0.6030.0000.0000.0000.000
53B303GLN00.0150.02618.6700.4200.4200.0000.0000.0000.000
54B304ASP-1-0.902-0.94216.516-14.092-14.0920.0000.0000.0000.000
55B305HIS0-0.053-0.02415.632-0.240-0.2400.0000.0000.0000.000
56B306LEU00.0070.01110.169-1.077-1.0770.0000.0000.0000.000
57B307HIS0-0.045-0.0289.7430.6510.6510.0000.0000.0000.000
58B308PHE0-0.022-0.0177.463-1.802-1.8020.0000.0000.0000.000
59B309GLU-1-1.000-1.0105.309-42.216-42.2160.0000.0000.0000.000
60B310MET0-0.0300.0015.725-3.973-3.9730.0000.0000.0000.000
61B311MET0-0.047-0.0023.769-0.1700.2380.005-0.084-0.3290.000
62B312GLU-1-0.868-0.9547.692-26.550-26.5500.0000.0000.0000.000
63B313ILE0-0.053-0.0226.3842.4242.4240.0000.0000.0000.000
64B353HIS0-0.086-0.05617.3590.2720.2720.0000.0000.0000.000
65B354LEU00.009-0.00911.0620.0440.0440.0000.0000.0000.000
66B355LEU00.0830.05312.901-1.014-1.0140.0000.0000.0000.000
67B356PRO0-0.0490.01015.2901.0801.0800.0000.0000.0000.000
68B357ALA00.044-0.00516.748-0.721-0.7210.0000.0000.0000.000
69B358ALA00.0140.00917.814-0.543-0.5430.0000.0000.0000.000
70B359ALA00.0320.01318.9880.0980.0980.0000.0000.0000.000
71B360VAL00.0770.03212.7280.3480.3480.0000.0000.0000.000
72B361GLN0-0.018-0.02115.487-1.553-1.5530.0000.0000.0000.000
73B362ALA00.0100.00817.6820.0380.0380.0000.0000.0000.000
74B363ILE00.0400.02315.5230.4120.4120.0000.0000.0000.000
75B364LYS10.9530.99712.54120.86120.8610.0000.0000.0000.000
76B365SER0-0.012-0.02216.5540.4260.4260.0000.0000.0000.000
77B366PHE00.0160.00720.1600.5060.5060.0000.0000.0000.000
78B367PHE00.0370.01813.9910.4780.4780.0000.0000.0000.000
79B368PHE00.0230.00414.7780.3870.3870.0000.0000.0000.000
80B369LYS10.9020.96519.72311.40311.4030.0000.0000.0000.000
81B370CYS0-0.011-0.00621.4040.6520.6520.0000.0000.0000.000
82B371TRP0-0.046-0.03014.0140.3560.3560.0000.0000.0000.000
83B372SER0-0.096-0.04621.5960.4670.4670.0000.0000.0000.000
84B373LEU0-0.021-0.01424.0660.4560.4560.0000.0000.0000.000
85B374ASN0-0.083-0.03325.0300.2010.2010.0000.0000.0000.000
86B375ILE0-0.0070.00825.0940.3840.3840.0000.0000.0000.000
87B376ASP-1-0.769-0.87025.703-9.725-9.7250.0000.0000.0000.000
88B377THR00.034-0.01325.4720.0760.0760.0000.0000.0000.000
89B378LYS10.8330.91427.6638.3048.3040.0000.0000.0000.000
90B379GLU-1-0.801-0.90829.668-9.342-9.3420.0000.0000.0000.000
91B380TYR00.0680.02921.9620.0240.0240.0000.0000.0000.000
92B381ALA0-0.026-0.00427.633-0.004-0.0040.0000.0000.0000.000
93B382TYR00.0380.01629.8200.1840.1840.0000.0000.0000.000
94B383LEU0-0.0140.00427.5290.1420.1420.0000.0000.0000.000
95B384LYS10.8340.88624.54711.40811.4080.0000.0000.0000.000
96B385GLY0-0.0010.00429.0920.1080.1080.0000.0000.0000.000
97B386THR0-0.045-0.04532.4230.2910.2910.0000.0000.0000.000
98B387VAL0-0.052-0.01628.1510.1140.1140.0000.0000.0000.000
99B388LEU0-0.026-0.01231.2730.0820.0820.0000.0000.0000.000
100B389PHE0-0.014-0.03132.4890.1660.1660.0000.0000.0000.000
101B390ASN0-0.002-0.01634.5840.0650.0650.0000.0000.0000.000
102B391PRO0-0.008-0.02236.500-0.021-0.0210.0000.0000.0000.000
103B392ASP-1-0.883-0.92537.636-7.707-7.7070.0000.0000.0000.000
104B393LEU0-0.039-0.01232.977-0.024-0.0240.0000.0000.0000.000
105B394PRO00.0360.01035.7020.2200.2200.0000.0000.0000.000
106B395GLY00.0040.00137.412-0.151-0.1510.0000.0000.0000.000
107B396LEU0-0.041-0.00837.8780.1030.1030.0000.0000.0000.000
108B397GLN0-0.023-0.01840.8440.2710.2710.0000.0000.0000.000
109B398CYS0-0.110-0.05541.7050.1340.1340.0000.0000.0000.000
110B399VAL00.0870.03843.025-0.034-0.0340.0000.0000.0000.000
111B400LYS10.9950.98943.9765.9945.9940.0000.0000.0000.000
112B401TYR0-0.088-0.04841.4100.0740.0740.0000.0000.0000.000
113B402ILE00.0560.01838.523-0.049-0.0490.0000.0000.0000.000
114B403GLU-1-0.871-0.92641.376-6.760-6.7600.0000.0000.0000.000
115B404GLY00.0110.00842.968-0.060-0.0600.0000.0000.0000.000
116B405LEU0-0.049-0.01639.3170.0060.0060.0000.0000.0000.000
117B406GLN00.0810.05337.797-0.027-0.0270.0000.0000.0000.000
118B407TRP0-0.033-0.01239.580-0.073-0.0730.0000.0000.0000.000
119B408ARG10.9350.94941.9196.9826.9820.0000.0000.0000.000
120B409THR0-0.047-0.02535.322-0.090-0.0900.0000.0000.0000.000
121B410GLN00.022-0.00135.901-0.045-0.0450.0000.0000.0000.000
122B411GLN0-0.0420.00339.2440.1360.1360.0000.0000.0000.000
123B412ILE0-0.013-0.02137.5770.0500.0500.0000.0000.0000.000
124B413LEU00.0120.01834.128-0.096-0.0960.0000.0000.0000.000
125B414THR0-0.004-0.01937.613-0.099-0.0990.0000.0000.0000.000
126B415GLU-1-0.828-0.87240.261-6.806-6.8060.0000.0000.0000.000
127B416HIS00.0180.01233.2870.2680.2680.0000.0000.0000.000
128B417ILE00.003-0.00935.530-0.032-0.0320.0000.0000.0000.000
129B418ARG10.8060.87537.9536.8686.8680.0000.0000.0000.000
130B419MET0-0.095-0.04339.8320.1770.1770.0000.0000.0000.000
131B420MET0-0.0480.00733.6570.1120.1120.0000.0000.0000.000
132B421GLN00.0090.00334.4630.0620.0620.0000.0000.0000.000
133B422ARG10.9620.96638.6066.9086.9080.0000.0000.0000.000
134B423GLU-1-0.893-0.95439.653-7.579-7.5790.0000.0000.0000.000
135B424TYR0-0.004-0.00938.6610.1820.1820.0000.0000.0000.000
136B425GLN00.0170.01040.377-0.103-0.1030.0000.0000.0000.000
137B426ILE00.0110.01336.302-0.127-0.1270.0000.0000.0000.000
138B427ARG10.8700.90929.5659.3999.3990.0000.0000.0000.000
139B428SER00.0160.01734.218-0.308-0.3080.0000.0000.0000.000
140B429ALA00.0120.00634.897-0.190-0.1900.0000.0000.0000.000
141B430GLU-1-0.885-0.95531.365-9.590-9.5900.0000.0000.0000.000
142B431LEU00.0020.00429.844-0.382-0.3820.0000.0000.0000.000
143B432ASN0-0.004-0.01330.404-0.341-0.3410.0000.0000.0000.000
144B433SER0-0.052-0.00630.081-0.266-0.2660.0000.0000.0000.000
145B434ALA00.0350.00925.860-0.242-0.2420.0000.0000.0000.000
146B435LEU00.0250.01026.781-0.297-0.2970.0000.0000.0000.000
147B436PHE0-0.051-0.03228.692-0.091-0.0910.0000.0000.0000.000
148B437LEU0-0.026-0.01023.634-0.065-0.0650.0000.0000.0000.000
149B438LEU0-0.0100.00723.191-0.430-0.4300.0000.0000.0000.000
150B439ARG10.9040.96025.2889.2369.2360.0000.0000.0000.000
151B440PHE0-0.045-0.02425.5710.2230.2230.0000.0000.0000.000
152B441ILE0-0.0040.00220.093-0.436-0.4360.0000.0000.0000.000
153B442ASN0-0.029-0.02722.015-0.181-0.1810.0000.0000.0000.000
154B443SER00.0090.00722.4580.1830.1830.0000.0000.0000.000
155B444ASP-1-0.845-0.90421.963-11.756-11.7560.0000.0000.0000.000
156B445VAL0-0.003-0.01217.486-0.523-0.5230.0000.0000.0000.000
157B446VAL00.0120.01217.037-0.855-0.8550.0000.0000.0000.000
158B447THR00.0220.00116.398-0.895-0.8950.0000.0000.0000.000
159B448GLU-1-0.817-0.92316.183-15.317-15.3170.0000.0000.0000.000
160B449LEU0-0.040-0.01611.263-0.776-0.7760.0000.0000.0000.000
161B450PHE0-0.026-0.02711.357-1.235-1.2350.0000.0000.0000.000
162B451PHE00.0260.00412.773-0.280-0.2800.0000.0000.0000.000
163B452ARG10.8470.94715.08113.91613.9160.0000.0000.0000.000
164B453PRO0-0.010-0.00610.4790.4880.4880.0000.0000.0000.000
165B454ILE0-0.037-0.00912.0540.2620.2620.0000.0000.0000.000
166B455ILE0-0.064-0.02414.5070.6590.6590.0000.0000.0000.000
167B456GLY00.0510.02916.6640.7240.7240.0000.0000.0000.000
168B457ALA0-0.044-0.02518.0350.0170.0170.0000.0000.0000.000
169B458VAL00.0200.00621.5000.5410.5410.0000.0000.0000.000
170B459SER00.014-0.01222.769-0.460-0.4600.0000.0000.0000.000
171B460MET00.0160.01420.824-0.091-0.0910.0000.0000.0000.000
172B461ASP-1-0.850-0.94023.957-10.266-10.2660.0000.0000.0000.000
173B462ASP-1-0.874-0.91927.230-9.437-9.4370.0000.0000.0000.000
174B463MET0-0.0120.00221.6110.2260.2260.0000.0000.0000.000
175B464MET0-0.011-0.00725.0600.0480.0480.0000.0000.0000.000
176B465LEU00.0390.02427.5790.1780.1780.0000.0000.0000.000
177B466GLU-1-0.825-0.91027.724-9.199-9.1990.0000.0000.0000.000
178B467MET0-0.070-0.01322.5350.0000.0000.0000.0000.0000.000
179B468LEU0-0.034-0.01627.9750.0320.0320.0000.0000.0000.000
180B469CYS0-0.065-0.03631.0400.3800.3800.0000.0000.0000.000
181B470ALA00.0110.00228.1830.0860.0860.0000.0000.0000.000
182B471LYS10.8430.91525.64110.63510.6350.0000.0000.0000.000
183B472LEU00.0220.02729.3270.2300.2300.0000.0000.0000.000