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: LJ2J9

Calculation Name: 4P1N-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P1N

Chain ID: B

ChEMBL ID:

UniProt ID: W0TA43

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptH
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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2509727.14664
FMO2-HF: Nuclear repulsion 2421921.316175
FMO2-HF: Total energy -87805.830465
FMO2-MP2: Total energy -88056.932799


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:568:ASP)


Summations of interaction energy for fragment #1(B:568: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.
-56.975-59.02235.415-17.725-15.6410.132
Interaction energy analysis for fragmet #1(B:568:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.812 / q_NPA : -0.888
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].
3B570ASN00.005-0.0182.498-8.137-4.1911.300-2.379-2.8670.003
4B571ILE00.0720.0453.637-7.415-6.5770.012-0.284-0.5660.002
5B572THR00.0160.0045.482-5.740-5.646-0.001-0.004-0.0890.000
6B573PRO00.0210.0146.917-2.570-2.5700.0000.0000.0000.000
7B574PHE0-0.0030.0048.074-2.154-2.1540.0000.0000.0000.000
8B575VAL00.0210.0159.138-2.256-2.2560.0000.0000.0000.000
9B576GLU-1-0.897-0.96611.44619.30819.3080.0000.0000.0000.000
10B577SER0-0.033-0.00513.198-1.622-1.6220.0000.0000.0000.000
11B578LEU00.0300.01312.914-1.220-1.2200.0000.0000.0000.000
12B579SER00.003-0.00815.018-1.134-1.1340.0000.0000.0000.000
13B580ALA0-0.0110.00217.428-0.955-0.9550.0000.0000.0000.000
14B581LYS10.9590.98516.884-16.836-16.8360.0000.0000.0000.000
15B582ALA00.0000.00619.890-0.681-0.6810.0000.0000.0000.000
16B583PHE0-0.015-0.00121.328-0.662-0.6620.0000.0000.0000.000
17B584VAL0-0.0030.01023.283-0.644-0.6440.0000.0000.0000.000
18B585MET0-0.0100.00624.819-0.710-0.7100.0000.0000.0000.000
19B586TYR00.005-0.03925.421-0.379-0.3790.0000.0000.0000.000
20B587SER0-0.017-0.03327.024-0.442-0.4420.0000.0000.0000.000
21B588PHE0-0.073-0.03029.247-0.516-0.5160.0000.0000.0000.000
22B589ALA00.0600.01230.165-0.366-0.3660.0000.0000.0000.000
23B590GLU-1-0.769-0.85630.3309.4569.4560.0000.0000.0000.000
24B591MET0-0.071-0.01732.884-0.383-0.3830.0000.0000.0000.000
25B592LYS10.8560.90034.997-8.485-8.4850.0000.0000.0000.000
26B593PHE00.0290.01734.779-0.256-0.2560.0000.0000.0000.000
27B594SER00.028-0.00636.639-0.269-0.2690.0000.0000.0000.000
28B595GLN0-0.118-0.04538.557-0.324-0.3240.0000.0000.0000.000
29B596ILE0-0.037-0.00939.051-0.200-0.2000.0000.0000.0000.000
30B597LEU0-0.078-0.02338.253-0.191-0.1910.0000.0000.0000.000
31B654ILE0-0.026-0.02546.383-0.018-0.0180.0000.0000.0000.000
32B655PRO00.0250.01549.495-0.030-0.0300.0000.0000.0000.000
33B656ALA00.0940.04249.3090.1410.1410.0000.0000.0000.000
34B657PRO00.0340.01448.5090.1350.1350.0000.0000.0000.000
35B658GLU-1-0.938-0.97246.0706.7506.7500.0000.0000.0000.000
36B659LEU00.0020.00044.2760.2190.2190.0000.0000.0000.000
37B660LYS10.9090.93243.471-6.786-6.7860.0000.0000.0000.000
38B661LYS10.9320.98442.234-7.136-7.1360.0000.0000.0000.000
39B662LEU00.0110.00640.3920.2570.2570.0000.0000.0000.000
40B663CYS0-0.036-0.01938.8520.2580.2580.0000.0000.0000.000
41B664MET00.0240.00837.8040.3560.3560.0000.0000.0000.000
42B665GLU-1-0.827-0.90536.5438.1458.1450.0000.0000.0000.000
43B666SER00.000-0.00734.5830.3160.3160.0000.0000.0000.000
44B667LEU0-0.0040.00333.0830.3640.3640.0000.0000.0000.000
45B668LEU00.0400.01632.1090.3800.3800.0000.0000.0000.000
46B669LEU0-0.027-0.00230.1510.4020.4020.0000.0000.0000.000
47B670TYR0-0.025-0.05128.5520.4200.4200.0000.0000.0000.000
48B671LEU0-0.020-0.01127.5010.4840.4840.0000.0000.0000.000
49B672LYS10.8490.92425.124-11.153-11.1530.0000.0000.0000.000
50B673SER0-0.042-0.04624.1750.6670.6670.0000.0000.0000.000
51B674LEU0-0.002-0.01022.6840.7780.7780.0000.0000.0000.000
52B675THR0-0.026-0.03422.0360.7440.7440.0000.0000.0000.000
53B676ILE0-0.021-0.01718.8700.8930.8930.0000.0000.0000.000
54B677LEU0-0.014-0.00418.0281.1761.1760.0000.0000.0000.000
55B678ALA00.005-0.01117.4471.0961.0960.0000.0000.0000.000
56B679SER0-0.037-0.01416.4591.4211.4210.0000.0000.0000.000
57B680SER00.0580.02513.5691.9151.9150.0000.0000.0000.000
58B681MET0-0.018-0.00212.5352.2602.2600.0000.0000.0000.000
59B682LYS10.9560.98313.086-14.393-14.3930.0000.0000.0000.000
60B683LEU00.0150.0279.0381.3531.3530.0000.0000.0000.000
61B684THR0-0.003-0.0208.4333.7853.7850.0000.0000.0000.000
62B685SER0-0.053-0.0248.9092.9632.9630.0000.0000.0000.000
63B686LYS10.9420.9709.962-24.270-24.2700.0000.0000.0000.000
64B687TRP0-0.020-0.0161.726-13.964-11.6085.934-4.526-3.7640.007
65B688TRP0-0.034-0.0155.9815.7105.7100.0000.0000.0000.000
66B689TYR0-0.055-0.0357.9190.3260.3260.0000.0000.0000.000
67B690GLU-1-0.885-0.9417.50526.74526.7450.0000.0000.0000.000
68B691ASN0-0.113-0.0611.765-26.601-31.15813.969-5.108-4.3040.057
69B692GLU-1-0.830-0.8814.70339.75339.796-0.001-0.006-0.0350.000
70B693SER0-0.017-0.0296.0564.1974.1970.0000.0000.0000.000
71B694LYS10.8520.9146.304-39.657-39.6570.0000.0000.0000.000
72B695ASN0-0.038-0.0281.746-34.760-39.53414.203-5.417-4.0120.063
73B696CYS0-0.0190.0005.1442.1462.153-0.001-0.001-0.0040.000
74B697THR0-0.033-0.0087.505-3.301-3.3010.0000.0000.0000.000
75B698LEU00.0750.0249.309-1.345-1.3450.0000.0000.0000.000
76B699LYS10.9310.95611.837-20.921-20.9210.0000.0000.0000.000
77B700LEU00.0300.0276.911-1.489-1.4890.0000.0000.0000.000
78B701ASN00.0380.00810.908-1.944-1.9440.0000.0000.0000.000
79B702ILE0-0.0110.00413.432-1.163-1.1630.0000.0000.0000.000
80B703LEU00.0090.00112.196-0.944-0.9440.0000.0000.0000.000
81B704VAL00.0330.01511.680-1.035-1.0350.0000.0000.0000.000
82B705GLN0-0.060-0.02714.816-1.503-1.5030.0000.0000.0000.000
83B706TRP00.0340.02518.075-0.745-0.7450.0000.0000.0000.000
84B707ILE0-0.003-0.00414.541-0.748-0.7480.0000.0000.0000.000
85B708ARG10.9330.96618.417-15.912-15.9120.0000.0000.0000.000
86B709ASP-1-0.926-0.96520.04513.23813.2380.0000.0000.0000.000
87B710ARG10.8760.92521.900-13.152-13.1520.0000.0000.0000.000
88B711PHE0-0.032-0.00221.247-0.483-0.4830.0000.0000.0000.000
89B712ASN00.036-0.00223.316-0.367-0.3670.0000.0000.0000.000
90B713GLU-1-0.723-0.78726.06510.61710.6170.0000.0000.0000.000
91B714CYS0-0.065-0.04025.914-0.418-0.4180.0000.0000.0000.000
92B715LEU00.003-0.00226.990-0.378-0.3780.0000.0000.0000.000
93B716ASP-1-0.910-0.94128.8499.9249.9240.0000.0000.0000.000
94B717LYS10.7770.86331.168-10.252-10.2520.0000.0000.0000.000
95B718ALA00.0120.00131.081-0.340-0.3400.0000.0000.0000.000
96B719GLU-1-0.837-0.91832.4779.0769.0760.0000.0000.0000.000
97B720PHE0-0.036-0.01034.724-0.385-0.3850.0000.0000.0000.000
98B721LEU0-0.018-0.01934.609-0.282-0.2820.0000.0000.0000.000
99B722ARG10.8560.93532.679-9.465-9.4650.0000.0000.0000.000
100B723LEU0-0.0190.00338.039-0.223-0.2230.0000.0000.0000.000
101B724LYS10.9590.97140.579-7.488-7.4880.0000.0000.0000.000
102B725LEU00.011-0.01339.434-0.202-0.2020.0000.0000.0000.000
103B726HIS0-0.0070.00340.724-0.286-0.2860.0000.0000.0000.000
104B727THR0-0.0220.00144.202-0.197-0.1970.0000.0000.0000.000
105B728LEU0-0.013-0.01644.390-0.146-0.1460.0000.0000.0000.000
106B729ASN00.0610.04543.915-0.178-0.1780.0000.0000.0000.000
107B730GLN0-0.047-0.01047.858-0.034-0.0340.0000.0000.0000.000
108B731SER0-0.089-0.04450.244-0.156-0.1560.0000.0000.0000.000
109B732GLU-1-0.969-0.98350.4646.0216.0210.0000.0000.0000.000
110B733ASP-1-0.971-1.05352.2735.8725.8720.0000.0000.0000.000
111B734PRO00.0830.13053.3660.0470.0470.0000.0000.0000.000
112B735GLN0-0.121-0.07654.740-0.067-0.0670.0000.0000.0000.000
113B736VAL0-0.0080.00252.1860.0610.0610.0000.0000.0000.000
114B737LEU0-0.014-0.01646.7890.1240.1240.0000.0000.0000.000
115B738ASP-1-0.987-0.99348.2256.4426.4420.0000.0000.0000.000
116B739ASP-1-0.876-0.94049.0446.0046.0040.0000.0000.0000.000
117B740GLU-1-0.961-0.96846.5006.8266.8260.0000.0000.0000.000
118B741PRO0-0.036-0.00944.8630.0810.0810.0000.0000.0000.000
119B742THR00.0290.00239.7880.1040.1040.0000.0000.0000.000
120B743ILE0-0.058-0.02737.5900.0600.0600.0000.0000.0000.000
121B744PHE00.0450.03235.4880.0950.0950.0000.0000.0000.000
122B745VAL00.0260.00030.529-0.060-0.0600.0000.0000.0000.000
123B746GLU-1-0.791-0.91630.6739.7019.7010.0000.0000.0000.000
124B747LYS10.9060.96632.256-7.741-7.7410.0000.0000.0000.000
125B748LEU0-0.0010.00133.690-0.065-0.0650.0000.0000.0000.000
126B749ILE00.0000.00028.0600.0000.0000.0000.0000.0000.000
127B750TYR00.0150.00731.4820.0790.0790.0000.0000.0000.000
128B751ASP-1-0.821-0.92632.9438.0558.0550.0000.0000.0000.000
129B752ARG10.9280.99132.489-9.063-9.0630.0000.0000.0000.000
130B753ALA00.018-0.00530.130-0.008-0.0080.0000.0000.0000.000
131B754LEU00.0320.03431.8250.0230.0230.0000.0000.0000.000
132B755ASP-1-0.867-0.90534.7247.8147.8140.0000.0000.0000.000
133B756ILE0-0.066-0.02531.181-0.151-0.1510.0000.0000.0000.000
134B757SER00.038-0.01031.6250.0090.0090.0000.0000.0000.000
135B758ARG10.8360.91334.111-7.759-7.7590.0000.0000.0000.000
136B759ASN0-0.009-0.02337.234-0.341-0.3410.0000.0000.0000.000
137B760ALA0-0.0040.00334.111-0.110-0.1100.0000.0000.0000.000
138B761ALA00.0360.02836.053-0.070-0.0700.0000.0000.0000.000
139B762ARG10.8130.88937.877-6.915-6.9150.0000.0000.0000.000
140B763LEU00.0400.00937.126-0.119-0.1190.0000.0000.0000.000
141B764GLU-1-0.798-0.90435.4558.3598.3590.0000.0000.0000.000
142B765MET0-0.093-0.04338.677-0.066-0.0660.0000.0000.0000.000
143B766GLU-1-0.858-0.90642.1286.7136.7130.0000.0000.0000.000
144B767GLY0-0.024-0.00141.794-0.086-0.0860.0000.0000.0000.000
145B768GLY0-0.0040.00939.9090.0320.0320.0000.0000.0000.000
146B769ASN00.010-0.01334.8620.3300.3300.0000.0000.0000.000
147B770TYR00.1100.02733.4070.1010.1010.0000.0000.0000.000
148B771ASN00.0700.03830.7630.1800.1800.0000.0000.0000.000
149B772THR0-0.045-0.01430.7170.2190.2190.0000.0000.0000.000
150B773CYS0-0.027-0.01232.2740.0630.0630.0000.0000.0000.000
151B774GLU-1-0.862-0.92925.85511.29511.2950.0000.0000.0000.000
152B775LEU00.0200.00826.5110.3080.3080.0000.0000.0000.000
153B776ALA00.0060.02528.0290.2290.2290.0000.0000.0000.000
154B777TYR0-0.008-0.02429.0280.0630.0630.0000.0000.0000.000
155B778ALA00.0190.00924.0210.1730.1730.0000.0000.0000.000
156B779THR0-0.035-0.03024.8840.4370.4370.0000.0000.0000.000
157B780SER0-0.016-0.04026.6140.1310.1310.0000.0000.0000.000
158B781LEU0-0.031-0.00824.188-0.066-0.0660.0000.0000.0000.000
159B782TRP00.0350.01317.5610.5340.5340.0000.0000.0000.000
160B783MET0-0.080-0.03523.2530.1000.1000.0000.0000.0000.000
161B784LEU00.014-0.00426.081-0.016-0.0160.0000.0000.0000.000
162B785GLU-1-0.930-0.97720.36513.70213.7020.0000.0000.0000.000
163B786ILE0-0.051-0.01522.2200.2940.2940.0000.0000.0000.000
164B787LEU0-0.027-0.02323.3130.0370.0370.0000.0000.0000.000
165B788LEU0-0.048-0.01723.794-0.270-0.2700.0000.0000.0000.000
166B789ASP-1-0.850-0.90518.16716.04116.0410.0000.0000.0000.000
167B790GLU-1-0.895-0.93820.69011.85711.8570.0000.0000.0000.000
168B791HIS0-0.091-0.05315.9410.2330.2330.0000.0000.0000.000
169B792LEU0-0.098-0.05718.6710.1650.1650.0000.0000.0000.000
170B793SER0-0.042-0.00922.087-0.582-0.5820.0000.0000.0000.000
171B794SER00.0070.00524.902-0.508-0.5080.0000.0000.0000.000
172B795ASN0-0.022-0.03326.8390.1770.1770.0000.0000.0000.000
173B796GLU-1-0.786-0.85026.41911.34811.3480.0000.0000.0000.000
174B797VAL0-0.050-0.01529.602-0.086-0.0860.0000.0000.0000.000
175B798TYR0-0.069-0.02232.327-0.374-0.3740.0000.0000.0000.000
176B799ASP-1-0.830-0.91531.07810.25010.2500.0000.0000.0000.000
177B800ASP-1-0.883-0.96030.5919.6819.6810.0000.0000.0000.000
178B801GLY0-0.064-0.01932.754-0.306-0.3060.0000.0000.0000.000
179B802TYR0-0.111-0.06630.333-0.103-0.1030.0000.0000.0000.000
180B803SER0-0.055-0.05226.9290.4960.4960.0000.0000.0000.000
181B804SER0-0.0290.02526.9400.7260.7260.0000.0000.0000.000
182B805ASN00.0140.00626.194-0.754-0.7540.0000.0000.0000.000
183B806ILE00.0480.03527.7520.2600.2600.0000.0000.0000.000
184B807THR0-0.029-0.02127.157-0.009-0.0090.0000.0000.0000.000
185B808SER00.0170.00529.824-0.288-0.2880.0000.0000.0000.000
186B809LEU0-0.054-0.01129.125-0.225-0.2250.0000.0000.0000.000
187B810ASP-1-0.782-0.85332.6918.4418.4410.0000.0000.0000.000
188B811GLU-1-0.900-0.98230.7689.9619.9610.0000.0000.0000.000
189B812SER0-0.096-0.07133.3030.0520.0520.0000.0000.0000.000
190B813ASP-1-0.800-0.90533.5158.5348.5340.0000.0000.0000.000
191B814LYS10.9220.96228.179-10.032-10.0320.0000.0000.0000.000
192B815GLU-1-0.904-0.95930.2449.5259.5250.0000.0000.0000.000
193B816MET0-0.010-0.00332.352-0.006-0.0060.0000.0000.0000.000
194B817ILE00.001-0.00928.2870.0290.0290.0000.0000.0000.000
195B818ARG10.9530.98126.406-10.283-10.2830.0000.0000.0000.000
196B819LYS10.8820.95829.236-8.372-8.3720.0000.0000.0000.000
197B820TYR00.0210.00131.758-0.012-0.0120.0000.0000.0000.000
198B821VAL00.0570.03325.0790.0120.0120.0000.0000.0000.000
199B822SER0-0.024-0.00727.9470.1730.1730.0000.0000.0000.000
200B823SER0-0.085-0.03929.097-0.069-0.0690.0000.0000.0000.000
201B824ILE00.0350.01828.819-0.101-0.1010.0000.0000.0000.000
202B825ALA00.0450.02425.7860.0490.0490.0000.0000.0000.000
203B826ASN0-0.063-0.04427.4710.2010.2010.0000.0000.0000.000
204B827ARG10.8510.93830.108-8.600-8.6000.0000.0000.0000.000
205B828LEU00.0320.01825.112-0.111-0.1110.0000.0000.0000.000
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