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: NN39Q

Calculation Name: 3F5C-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5C

Chain ID: C

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2007322.571592
FMO2-HF: Nuclear repulsion 1931970.283608
FMO2-HF: Total energy -75352.287984
FMO2-MP2: Total energy -75564.419203


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(C:252:ASP)


Summations of interaction energy for fragment #1(C:252: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.
-12.736-5.3796.984-6.257-8.0850.067
Interaction energy analysis for fragmet #1(C:252:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.840 / q_NPA : -0.934
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].
3C254GLN00.0590.0103.831-3.790-1.9220.003-0.751-1.1200.004
4C255VAL0-0.0200.0022.596-6.449-5.4121.194-0.859-1.3720.001
5C256VAL00.0310.0083.090-6.958-6.0940.053-0.275-0.6420.000
6C257CYS0-0.020-0.0055.682-5.360-5.3600.0000.0000.0000.000
7C258GLU-1-0.917-0.9437.64321.36921.3690.0000.0000.0000.000
8C259ALA0-0.037-0.0298.793-2.967-2.9670.0000.0000.0000.000
9C260ALA0-0.014-0.0109.495-2.010-2.0100.0000.0000.0000.000
10C261SER00.0410.00911.235-2.344-2.3440.0000.0000.0000.000
11C262ALA0-0.033-0.00713.488-1.667-1.6670.0000.0000.0000.000
12C263GLY00.0530.03314.455-1.172-1.1720.0000.0000.0000.000
13C264LEU00.0230.02715.652-1.346-1.3460.0000.0000.0000.000
14C265LEU00.000-0.00917.575-1.248-1.2480.0000.0000.0000.000
15C266LYS10.7690.87017.603-16.755-16.7550.0000.0000.0000.000
16C267THR0-0.009-0.01818.928-0.706-0.7060.0000.0000.0000.000
17C268LEU00.004-0.01121.404-0.820-0.8200.0000.0000.0000.000
18C269ARG10.9210.97822.723-13.263-13.2630.0000.0000.0000.000
19C270PHE0-0.003-0.00124.068-0.617-0.6170.0000.0000.0000.000
20C271VAL0-0.0050.00025.312-0.452-0.4520.0000.0000.0000.000
21C272LYS10.8620.92727.514-10.425-10.4250.0000.0000.0000.000
22C273TYR0-0.077-0.04628.458-0.276-0.2760.0000.0000.0000.000
23C274LEU00.0400.02930.502-0.291-0.2910.0000.0000.0000.000
24C275PRO00.0560.02932.538-0.121-0.1210.0000.0000.0000.000
25C276CYS0-0.067-0.03035.366-0.079-0.0790.0000.0000.0000.000
26C277PHE00.0440.01130.030-0.050-0.0500.0000.0000.0000.000
27C278GLN00.0180.00233.644-0.003-0.0030.0000.0000.0000.000
28C279ILE0-0.079-0.01736.344-0.154-0.1540.0000.0000.0000.000
29C280LEU00.025-0.00434.475-0.029-0.0290.0000.0000.0000.000
30C281PRO00.0000.01737.5940.1160.1160.0000.0000.0000.000
31C282LEU0-0.0050.00132.4090.0100.0100.0000.0000.0000.000
32C283ASP-1-0.786-0.91233.8708.7058.7050.0000.0000.0000.000
33C284GLN0-0.021-0.02234.3070.2010.2010.0000.0000.0000.000
34C285GLN0-0.057-0.02731.9230.3180.3180.0000.0000.0000.000
35C286LEU00.0070.01728.1800.3780.3780.0000.0000.0000.000
36C287VAL00.0060.00729.3080.4240.4240.0000.0000.0000.000
37C288LEU0-0.0090.00629.6590.2550.2550.0000.0000.0000.000
38C289VAL00.0620.02024.8090.4130.4130.0000.0000.0000.000
39C290ARG10.7780.86924.881-11.285-11.2850.0000.0000.0000.000
40C291SER0-0.011-0.01324.8560.2500.2500.0000.0000.0000.000
41C292CYS0-0.051-0.02323.6030.4160.4160.0000.0000.0000.000
42C293TRP00.0180.01716.6140.5820.5820.0000.0000.0000.000
43C294ALA00.0580.03518.2590.6250.6250.0000.0000.0000.000
44C295PRO00.002-0.01018.2350.7000.7000.0000.0000.0000.000
45C296LEU0-0.012-0.01119.4400.4060.4060.0000.0000.0000.000
46C297LEU0-0.0020.01914.4540.1030.1030.0000.0000.0000.000
47C298MET0-0.015-0.00313.4001.0421.0420.0000.0000.0000.000
48C299LEU0-0.014-0.01216.3140.1870.1870.0000.0000.0000.000
49C300GLU-1-0.834-0.88817.01814.40014.4000.0000.0000.0000.000
50C301LEU00.0050.00411.0910.2090.2090.0000.0000.0000.000
51C302ALA00.0060.00613.7570.5600.5600.0000.0000.0000.000
52C303GLN0-0.0050.00715.632-0.548-0.5480.0000.0000.0000.000
53C304ASP-1-0.864-0.91414.29216.43616.4360.0000.0000.0000.000
54C305HIS0-0.090-0.03913.7160.1400.1400.0000.0000.0000.000
55C306LEU00.0240.0067.5040.8110.8110.0000.0000.0000.000
56C307HIS0-0.050-0.0347.045-1.234-1.2340.0000.0000.0000.000
57C308PHE0-0.039-0.0244.2461.9052.006-0.001-0.018-0.0820.000
58C309GLU-1-0.905-0.9314.07230.01930.166-0.001-0.023-0.1230.000
59C310MET0-0.059-0.0494.1296.4656.7180.001-0.038-0.2170.000
60C311MET00.0260.0253.738-2.882-2.5090.005-0.115-0.2630.001
61C312GLU-1-0.952-0.9597.05127.33727.3370.0000.0000.0000.000
62C353HIS0-0.018-0.0292.037-36.702-33.9885.730-4.178-4.2660.061
63C354LEU0-0.038-0.0287.532-4.047-4.0470.0000.0000.0000.000
64C355LEU00.0140.01211.0530.0650.0650.0000.0000.0000.000
65C356PRO00.004-0.00513.688-0.686-0.6860.0000.0000.0000.000
66C357ALA00.0710.04413.7501.1601.1600.0000.0000.0000.000
67C358ALA0-0.011-0.01115.3190.4260.4260.0000.0000.0000.000
68C359ALA00.0100.00414.994-0.110-0.1100.0000.0000.0000.000
69C360VAL00.0790.03810.4340.0580.0580.0000.0000.0000.000
70C361GLN0-0.004-0.01512.8171.4361.4360.0000.0000.0000.000
71C362ALA00.0010.02315.141-0.617-0.6170.0000.0000.0000.000
72C363ILE00.0480.01711.725-0.681-0.6810.0000.0000.0000.000
73C364LYS10.9710.99710.576-27.596-27.5960.0000.0000.0000.000
74C365SER0-0.035-0.04613.669-0.886-0.8860.0000.0000.0000.000
75C366PHE0-0.026-0.00816.350-1.018-1.0180.0000.0000.0000.000
76C367PHE00.0630.02212.035-0.795-0.7950.0000.0000.0000.000
77C368PHE00.0080.01013.075-0.518-0.5180.0000.0000.0000.000
78C369LYS10.9200.97517.173-13.372-13.3720.0000.0000.0000.000
79C370CYS0-0.013-0.01418.290-0.920-0.9200.0000.0000.0000.000
80C371TRP0-0.030-0.01811.429-0.645-0.6450.0000.0000.0000.000
81C372SER0-0.057-0.02319.236-0.604-0.6040.0000.0000.0000.000
82C373LEU0-0.080-0.02921.893-0.601-0.6010.0000.0000.0000.000
83C374ASN0-0.030-0.00823.052-0.099-0.0990.0000.0000.0000.000
84C375ILE0-0.0120.01222.038-0.478-0.4780.0000.0000.0000.000
85C376ASP-1-0.740-0.85723.44710.84910.8490.0000.0000.0000.000
86C377THR00.026-0.01524.6220.3270.3270.0000.0000.0000.000
87C378LYS10.9350.97725.665-8.972-8.9720.0000.0000.0000.000
88C379GLU-1-0.803-0.89226.87610.68810.6880.0000.0000.0000.000
89C380TYR00.0530.00818.692-0.052-0.0520.0000.0000.0000.000
90C381ALA0-0.056-0.01424.5830.1610.1610.0000.0000.0000.000
91C382TYR00.006-0.02226.670-0.059-0.0590.0000.0000.0000.000
92C383LEU00.0080.02024.160-0.166-0.1660.0000.0000.0000.000
93C384LYS10.8590.91921.035-13.773-13.7730.0000.0000.0000.000
94C385GLY0-0.0060.00325.558-0.059-0.0590.0000.0000.0000.000
95C386THR0-0.036-0.02828.747-0.275-0.2750.0000.0000.0000.000
96C387VAL0-0.026-0.00824.306-0.104-0.1040.0000.0000.0000.000
97C388LEU0-0.029-0.01327.339-0.047-0.0470.0000.0000.0000.000
98C389PHE0-0.005-0.01528.480-0.190-0.1900.0000.0000.0000.000
99C390ASN00.0230.01129.463-0.263-0.2630.0000.0000.0000.000
100C391PRO00.006-0.01333.0160.0670.0670.0000.0000.0000.000
101C392ASP-1-0.896-0.94833.3058.9548.9540.0000.0000.0000.000
102C393LEU0-0.042-0.00629.231-0.038-0.0380.0000.0000.0000.000
103C394PRO00.0430.00632.428-0.283-0.2830.0000.0000.0000.000
104C395GLY00.0080.00534.2240.2020.2020.0000.0000.0000.000
105C396LEU0-0.0190.00334.290-0.115-0.1150.0000.0000.0000.000
106C397GLN0-0.027-0.01337.488-0.352-0.3520.0000.0000.0000.000
107C398CYS0-0.050-0.02838.497-0.168-0.1680.0000.0000.0000.000
108C399VAL00.0790.04739.1630.0730.0730.0000.0000.0000.000
109C400LYS10.9910.98140.032-6.651-6.6510.0000.0000.0000.000
110C401TYR0-0.093-0.03937.899-0.132-0.1320.0000.0000.0000.000
111C402ILE00.0490.01334.9470.0380.0380.0000.0000.0000.000
112C403GLU-1-0.849-0.92037.0737.7667.7660.0000.0000.0000.000
113C404GLY00.0050.01039.065-0.002-0.0020.0000.0000.0000.000
114C405LEU0-0.051-0.01635.698-0.009-0.0090.0000.0000.0000.000
115C406GLN00.0160.00732.0110.0450.0450.0000.0000.0000.000
116C407TRP00.0140.00735.6650.0650.0650.0000.0000.0000.000
117C408ARG10.9280.93237.942-7.516-7.5160.0000.0000.0000.000
118C409THR0-0.042-0.01131.5920.0690.0690.0000.0000.0000.000
119C410GLN00.034-0.00733.6180.0170.0170.0000.0000.0000.000
120C411GLN0-0.0390.01135.354-0.062-0.0620.0000.0000.0000.000
121C412ILE0-0.054-0.03934.528-0.086-0.0860.0000.0000.0000.000
122C413LEU00.0060.01830.9900.0540.0540.0000.0000.0000.000
123C414THR0-0.029-0.03134.4680.0420.0420.0000.0000.0000.000
124C415GLU-1-0.927-0.95837.1547.4017.4010.0000.0000.0000.000
125C416HIS0-0.080-0.05930.862-0.341-0.3410.0000.0000.0000.000
126C417ILE00.0180.00532.836-0.022-0.0220.0000.0000.0000.000
127C418ARG10.9290.96835.742-7.589-7.5890.0000.0000.0000.000
128C419MET0-0.077-0.03437.515-0.200-0.2000.0000.0000.0000.000
129C420MET0-0.061-0.01933.6250.0720.0720.0000.0000.0000.000
130C421GLN0-0.0090.00930.362-0.084-0.0840.0000.0000.0000.000
131C422ARG10.9740.97635.844-7.401-7.4010.0000.0000.0000.000
132C423GLU-1-0.904-0.95537.1797.8667.8660.0000.0000.0000.000
133C424TYR00.011-0.00736.5000.2170.2170.0000.0000.0000.000
134C425GLN00.028-0.00636.2340.2290.2290.0000.0000.0000.000
135C426ILE00.0040.01433.7170.1990.1990.0000.0000.0000.000
136C427ARG10.8180.87627.262-10.403-10.4030.0000.0000.0000.000
137C428SER0-0.0040.00431.2630.3880.3880.0000.0000.0000.000
138C429ALA00.0070.00131.7380.2880.2880.0000.0000.0000.000
139C430GLU-1-0.847-0.90228.21410.73410.7340.0000.0000.0000.000
140C431LEU00.0310.01026.4660.4940.4940.0000.0000.0000.000
141C432ASN0-0.070-0.04827.0380.3840.3840.0000.0000.0000.000
142C433SER0-0.053-0.02126.8520.1610.1610.0000.0000.0000.000
143C434ALA00.0380.01322.7500.3820.3820.0000.0000.0000.000
144C435LEU00.0320.00423.1960.5260.5260.0000.0000.0000.000
145C436PHE0-0.062-0.02625.1480.0910.0910.0000.0000.0000.000
146C437LEU0-0.019-0.01620.5660.0580.0580.0000.0000.0000.000
147C438LEU00.0120.01419.7790.3710.3710.0000.0000.0000.000
148C439ARG10.9080.95321.666-10.721-10.7210.0000.0000.0000.000
149C440PHE0-0.071-0.01220.997-0.328-0.3280.0000.0000.0000.000
150C441ILE00.0910.03616.7870.8030.8030.0000.0000.0000.000
151C442ASN0-0.066-0.01717.8790.8630.8630.0000.0000.0000.000
152C443SER0-0.013-0.02317.817-0.519-0.5190.0000.0000.0000.000
153C444ASP-1-0.851-0.91918.19015.18515.1850.0000.0000.0000.000
154C445VAL00.014-0.00913.0730.8140.8140.0000.0000.0000.000
155C446VAL00.0300.01412.9761.6161.6160.0000.0000.0000.000
156C447THR00.0140.00512.4901.5011.5010.0000.0000.0000.000
157C448GLU-1-0.823-0.90612.67321.01721.0170.0000.0000.0000.000
158C449LEU0-0.052-0.0167.7251.6601.6600.0000.0000.0000.000
159C450PHE0-0.010-0.0037.4533.8093.8090.0000.0000.0000.000
160C451PHE00.0300.0009.589-0.559-0.5590.0000.0000.0000.000
161C452ARG10.8280.91912.102-19.218-19.2180.0000.0000.0000.000
162C453PRO00.001-0.0107.928-1.581-1.5810.0000.0000.0000.000
163C454ILE0-0.022-0.0139.302-0.171-0.1710.0000.0000.0000.000
164C455ILE0-0.055-0.02312.970-1.496-1.4960.0000.0000.0000.000
165C456GLY0-0.002-0.00115.238-1.041-1.0410.0000.0000.0000.000
166C457ALA0-0.062-0.04917.011-0.897-0.8970.0000.0000.0000.000
167C458VAL00.0140.02219.661-0.644-0.6440.0000.0000.0000.000
168C459SER00.0060.00920.242-0.451-0.4510.0000.0000.0000.000
169C460MET0-0.061-0.02716.6950.5250.5250.0000.0000.0000.000
170C461ASP-1-0.828-0.89420.54012.87612.8760.0000.0000.0000.000
171C462ASP-1-0.834-0.94024.08712.08612.0860.0000.0000.0000.000
172C463MET0-0.037-0.00618.188-0.301-0.3010.0000.0000.0000.000
173C464MET00.005-0.00120.001-0.445-0.4450.0000.0000.0000.000
174C465LEU00.0120.00024.466-0.299-0.2990.0000.0000.0000.000
175C466GLU-1-0.858-0.91025.34910.96710.9670.0000.0000.0000.000
176C467MET0-0.022-0.01620.406-0.407-0.4070.0000.0000.0000.000
177C468LEU0-0.030-0.02225.897-0.253-0.2530.0000.0000.0000.000
178C469CYS0-0.008-0.00628.875-0.457-0.4570.0000.0000.0000.000
179C470ALA00.0330.02927.244-0.243-0.2430.0000.0000.0000.000
180C471LYS10.8360.93424.868-12.406-12.4060.0000.0000.0000.000
181C472LEU00.0070.01829.462-0.136-0.1360.0000.0000.0000.000