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: M3M8Z

Calculation Name: 4P1N-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P1N

Chain ID: A

ChEMBL ID:

UniProt ID: W0TA43

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2127083.673783
FMO2-HF: Nuclear repulsion 2046983.340065
FMO2-HF: Total energy -80100.333718
FMO2-MP2: Total energy -80329.650801


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(A:566:ACE )


Summations of interaction energy for fragment #1(A:566:ACE )
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.
0.7951.592-0.005-0.327-0.4640
Interaction energy analysis for fragmet #1(A:566:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.004
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].
3A568ASP -1-0.871-0.9203.846-0.0540.743-0.005-0.327-0.4640.000
4A569SER 0-0.031-0.0206.5550.0410.0410.0000.0000.0000.000
5A570ASN 00.010-0.0059.7310.0420.0420.0000.0000.0000.000
6A571ILE 00.0680.0517.399-0.129-0.1290.0000.0000.0000.000
7A572THR 0-0.029-0.0239.9030.0750.0750.0000.0000.0000.000
8A573PRO 00.0420.01111.6880.0280.0280.0000.0000.0000.000
9A574PHE 00.0410.0286.930-0.036-0.0360.0000.0000.0000.000
10A575VAL 00.0100.00411.1880.0840.0840.0000.0000.0000.000
11A576GLU -1-0.907-0.94813.505-0.218-0.2180.0000.0000.0000.000
12A577SER 00.0060.00613.5740.0400.0400.0000.0000.0000.000
13A578LEU 00.0160.00111.2590.0520.0520.0000.0000.0000.000
14A579SER 0-0.008-0.01615.3920.0540.0540.0000.0000.0000.000
15A580ALA 00.0120.02118.5790.0340.0340.0000.0000.0000.000
16A581LYS 10.9210.96914.3790.3130.3130.0000.0000.0000.000
17A582ALA 00.012-0.00319.2820.0240.0240.0000.0000.0000.000
18A583PHE 0-0.0160.00020.9910.0200.0200.0000.0000.0000.000
19A584VAL 0-0.005-0.00222.7960.0170.0170.0000.0000.0000.000
20A585MET 0-0.0230.00322.9360.0180.0180.0000.0000.0000.000
21A586TYR 0-0.004-0.05924.9470.0100.0100.0000.0000.0000.000
22A587SER 0-0.015-0.01926.8040.0110.0110.0000.0000.0000.000
23A588PHE 0-0.028-0.01428.3430.0100.0100.0000.0000.0000.000
24A589ALA 00.027-0.00528.7060.0080.0080.0000.0000.0000.000
25A590GLU -1-0.788-0.87230.631-0.077-0.0770.0000.0000.0000.000
26A591MET 0-0.025-0.00732.8180.0060.0060.0000.0000.0000.000
27A592LYS 10.8520.93733.5430.0590.0590.0000.0000.0000.000
28A593PHE 00.0220.00934.4280.0050.0050.0000.0000.0000.000
29A594SER 0-0.048-0.03436.3780.0040.0040.0000.0000.0000.000
30A595GLN 0-0.002-0.01338.8150.0000.0000.0000.0000.0000.000
31A596ILE 0-0.050-0.01638.2280.0030.0030.0000.0000.0000.000
32A597LEU 0-0.096-0.03239.5350.0020.0020.0000.0000.0000.000
33A598NME 00.0020.01042.2060.0030.0030.0000.0000.0000.000
34A651ACE 00.0560.01948.3660.0000.0000.0000.0000.0000.000
35A652ASN 0-0.067-0.05649.3710.0020.0020.0000.0000.0000.000
36A653LEU 00.0070.01550.5570.0000.0000.0000.0000.0000.000
37A654ILE 00.0240.01744.905-0.001-0.0010.0000.0000.0000.000
38A655PRO 00.0230.01348.1160.0000.0000.0000.0000.0000.000
39A656ALA 00.0800.03946.864-0.002-0.0020.0000.0000.0000.000
40A657PRO 00.0480.01445.307-0.001-0.0010.0000.0000.0000.000
41A658GLU -1-0.945-0.96343.511-0.033-0.0330.0000.0000.0000.000
42A659LEU 0-0.011-0.01442.116-0.003-0.0030.0000.0000.0000.000
43A660LYS 10.9530.98241.2380.0260.0260.0000.0000.0000.000
44A661LYS 10.9010.95537.5060.0370.0370.0000.0000.0000.000
45A662LEU 0-0.0070.00237.423-0.003-0.0030.0000.0000.0000.000
46A663CYS 0-0.050-0.02336.529-0.004-0.0040.0000.0000.0000.000
47A664MET 00.0210.00633.398-0.005-0.0050.0000.0000.0000.000
48A665GLU -1-0.801-0.89732.965-0.050-0.0500.0000.0000.0000.000
49A666SER 0-0.015-0.00831.649-0.006-0.0060.0000.0000.0000.000
50A667LEU 00.0210.01030.477-0.007-0.0070.0000.0000.0000.000
51A668LEU 00.015-0.00228.726-0.007-0.0070.0000.0000.0000.000
52A669LEU 0-0.0040.01626.971-0.008-0.0080.0000.0000.0000.000
53A670TYR 00.016-0.01926.188-0.011-0.0110.0000.0000.0000.000
54A671LEU 0-0.0090.00625.499-0.012-0.0120.0000.0000.0000.000
55A672LYS 10.9060.95320.2320.1050.1050.0000.0000.0000.000
56A673SER 0-0.005-0.03321.382-0.019-0.0190.0000.0000.0000.000
57A674LEU 0-0.022-0.01721.219-0.022-0.0220.0000.0000.0000.000
58A675THR 0-0.0270.00217.875-0.014-0.0140.0000.0000.0000.000
59A676ILE 0-0.012-0.00116.634-0.030-0.0300.0000.0000.0000.000
60A677LEU 0-0.026-0.01616.451-0.046-0.0460.0000.0000.0000.000
61A678ALA 00.0230.00517.256-0.032-0.0320.0000.0000.0000.000
62A679SER 0-0.0010.00512.590-0.060-0.0600.0000.0000.0000.000
63A680SER 00.0670.03212.277-0.109-0.1090.0000.0000.0000.000
64A681MET 0-0.035-0.00413.253-0.081-0.0810.0000.0000.0000.000
65A682LYS 10.9270.97510.5400.2400.2400.0000.0000.0000.000
66A683LEU 00.0060.0046.436-0.022-0.0220.0000.0000.0000.000
67A684THR 00.006-0.0179.354-0.134-0.1340.0000.0000.0000.000
68A685SER 0-0.019-0.01211.8310.0290.0290.0000.0000.0000.000
69A686LYS 10.8780.9426.8300.1600.1600.0000.0000.0000.000
70A687TRP 0-0.016-0.0157.4860.1280.1280.0000.0000.0000.000
71A688TRP 0-0.018-0.0048.7160.1270.1270.0000.0000.0000.000
72A689TYR 0-0.033-0.03011.9760.0780.0780.0000.0000.0000.000
73A690GLU -1-0.875-0.9237.4360.0330.0330.0000.0000.0000.000
74A691ASN 0-0.026-0.0138.0980.1200.1200.0000.0000.0000.000
75A692GLU -1-0.904-0.95410.4870.0140.0140.0000.0000.0000.000
76A693SER 0-0.074-0.03113.7490.0200.0200.0000.0000.0000.000
77A694LYS 10.8760.93913.7780.2090.2090.0000.0000.0000.000
78A695ASN 00.0040.00515.4580.0250.0250.0000.0000.0000.000
79A696CYS 0-0.0100.00415.473-0.065-0.0650.0000.0000.0000.000
80A697THR 00.0010.00616.7400.0400.0400.0000.0000.0000.000
81A698LEU 00.0890.02718.978-0.007-0.0070.0000.0000.0000.000
82A699LYS 10.9030.94518.8310.2640.2640.0000.0000.0000.000
83A700LEU 00.0460.03813.9340.0040.0040.0000.0000.0000.000
84A701ASN 00.0360.00617.645-0.007-0.0070.0000.0000.0000.000
85A702ILE 00.0020.00620.3970.0090.0090.0000.0000.0000.000
86A703LEU 00.0160.00717.1640.0100.0100.0000.0000.0000.000
87A704VAL 00.0320.01016.6880.0050.0050.0000.0000.0000.000
88A705GLN 0-0.092-0.04619.4070.0240.0240.0000.0000.0000.000
89A706TRP 00.0670.03920.7640.0090.0090.0000.0000.0000.000
90A707ILE 00.0100.00217.1610.0120.0120.0000.0000.0000.000
91A708ARG 10.8920.95021.3310.1590.1590.0000.0000.0000.000
92A709ASP -1-0.902-0.94823.214-0.124-0.1240.0000.0000.0000.000
93A710ARG 10.8850.92823.8560.1430.1430.0000.0000.0000.000
94A711PHE 0-0.028-0.01220.9620.0080.0080.0000.0000.0000.000
95A712ASN 00.022-0.00924.4390.0090.0090.0000.0000.0000.000
96A713GLU -1-0.752-0.79227.804-0.095-0.0950.0000.0000.0000.000
97A714CYS 0-0.037-0.02426.0910.0070.0070.0000.0000.0000.000
98A715LEU 0-0.0050.00826.4650.0070.0070.0000.0000.0000.000
99A716ASP -1-0.864-0.92828.700-0.072-0.0720.0000.0000.0000.000
100A717LYS 10.7550.85831.6160.0900.0900.0000.0000.0000.000
101A718ALA 00.015-0.00129.5890.0060.0060.0000.0000.0000.000
102A719GLU -1-0.936-0.95331.624-0.058-0.0580.0000.0000.0000.000
103A720PHE 0-0.029-0.01433.7540.0060.0060.0000.0000.0000.000
104A721LEU 0-0.014-0.01833.2850.0050.0050.0000.0000.0000.000
105A722ARG 10.9560.98132.9610.0540.0540.0000.0000.0000.000
106A723LEU 0-0.018-0.00435.9260.0040.0040.0000.0000.0000.000
107A724LYS 10.9620.98339.1300.0450.0450.0000.0000.0000.000
108A725LEU 00.0420.00636.1750.0030.0030.0000.0000.0000.000
109A726HIS 0-0.0280.02039.8760.0040.0040.0000.0000.0000.000
110A727THR 0-0.036-0.02941.4490.0020.0020.0000.0000.0000.000
111A728LEU 0-0.013-0.01843.5390.0010.0010.0000.0000.0000.000
112A729ASN 0-0.038-0.05340.9650.0030.0030.0000.0000.0000.000
113A730GLN 0-0.046-0.00244.8160.0030.0030.0000.0000.0000.000
114A731SER 0-0.075-0.03047.5870.0010.0010.0000.0000.0000.000
115A732GLU -1-0.954-0.98046.477-0.025-0.0250.0000.0000.0000.000
116A733ASP -1-0.942-0.98349.314-0.016-0.0160.0000.0000.0000.000
117A734PRO 0-0.0190.01845.8360.0010.0010.0000.0000.0000.000
118A735GLN 00.0330.00948.8170.0000.0000.0000.0000.0000.000
119A736VAL 0-0.018-0.01746.3460.0010.0010.0000.0000.0000.000
120A737LEU 0-0.041-0.02042.757-0.002-0.0020.0000.0000.0000.000
121A738ASP -1-0.969-0.97542.999-0.009-0.0090.0000.0000.0000.000
122A739ASP -1-0.871-0.92142.331-0.016-0.0160.0000.0000.0000.000
123A740GLU -1-0.883-0.91337.629-0.023-0.0230.0000.0000.0000.000
124A741PRO 0-0.156-0.07139.3900.0000.0000.0000.0000.0000.000
125A742THR 0-0.001-0.04932.797-0.003-0.0030.0000.0000.0000.000
126A743ILE 0-0.083-0.03632.564-0.001-0.0010.0000.0000.0000.000
127A744PHE 00.0520.01729.707-0.002-0.0020.0000.0000.0000.000
128A745VAL 00.005-0.00325.459-0.002-0.0020.0000.0000.0000.000
129A746GLU -1-0.833-0.93424.456-0.061-0.0610.0000.0000.0000.000
130A747LYS 10.9180.97126.8640.0360.0360.0000.0000.0000.000
131A748LEU 0-0.024-0.00630.0650.0000.0000.0000.0000.0000.000
132A749ILE 0-0.011-0.01423.959-0.001-0.0010.0000.0000.0000.000
133A750TYR 0-0.015-0.00527.7410.0000.0000.0000.0000.0000.000
134A751ASP -1-0.858-0.93928.790-0.042-0.0420.0000.0000.0000.000
135A752ARG 10.8910.96030.0300.0660.0660.0000.0000.0000.000
136A753ALA 00.0340.01827.6690.0000.0000.0000.0000.0000.000
137A754LEU 00.0510.02829.6450.0000.0000.0000.0000.0000.000
138A755ASP -1-0.945-0.95832.440-0.054-0.0540.0000.0000.0000.000
139A756ILE 00.0000.01429.9800.0020.0020.0000.0000.0000.000
140A757SER 0-0.0080.00231.6760.0020.0020.0000.0000.0000.000
141A758ARG 10.9240.92533.3450.0450.0450.0000.0000.0000.000
142A759ASN 0-0.020-0.00536.6670.0050.0050.0000.0000.0000.000
143A760ALA 00.0410.02034.9660.0020.0020.0000.0000.0000.000
144A761ALA 00.0390.02636.9200.0020.0020.0000.0000.0000.000
145A762ARG 10.8270.89338.3580.0420.0420.0000.0000.0000.000
146A763LEU 0-0.049-0.02039.0430.0010.0010.0000.0000.0000.000
147A764GLU -1-0.851-0.94637.627-0.042-0.0420.0000.0000.0000.000
148A765MET 0-0.075-0.04440.7370.0020.0020.0000.0000.0000.000
149A766GLU -1-0.890-0.91643.880-0.035-0.0350.0000.0000.0000.000
150A767GLY 0-0.0010.00244.1990.0010.0010.0000.0000.0000.000
151A768GLY 00.002-0.00342.261-0.002-0.0020.0000.0000.0000.000
152A769ASN 0-0.038-0.01740.043-0.002-0.0020.0000.0000.0000.000
153A770TYR 00.0370.01238.024-0.002-0.0020.0000.0000.0000.000
154A771ASN 00.0720.02433.7660.0010.0010.0000.0000.0000.000
155A772THR 0-0.017-0.00933.852-0.005-0.0050.0000.0000.0000.000
156A773CYS 0-0.028-0.00434.211-0.002-0.0020.0000.0000.0000.000
157A774GLU -1-0.899-0.93829.766-0.090-0.0900.0000.0000.0000.000
158A775LEU 00.0290.01629.128-0.006-0.0060.0000.0000.0000.000
159A776ALA 0-0.0080.00229.160-0.005-0.0050.0000.0000.0000.000
160A777TYR 0-0.011-0.01329.782-0.002-0.0020.0000.0000.0000.000
161A778ALA 00.035-0.01225.512-0.003-0.0030.0000.0000.0000.000
162A779THR 0-0.064-0.03224.937-0.012-0.0120.0000.0000.0000.000
163A780SER 0-0.031-0.02925.611-0.005-0.0050.0000.0000.0000.000
164A781LEU 0-0.0060.00123.1050.0020.0020.0000.0000.0000.000
165A782TRP 00.0640.03017.048-0.016-0.0160.0000.0000.0000.000
166A783MET 0-0.062-0.02520.783-0.004-0.0040.0000.0000.0000.000
167A784LEU 00.011-0.00922.6080.0020.0020.0000.0000.0000.000
168A785GLU -1-0.945-0.97117.703-0.170-0.1700.0000.0000.0000.000
169A786ILE 0-0.054-0.02617.984-0.008-0.0080.0000.0000.0000.000
170A787LEU 0-0.088-0.03118.8480.0040.0040.0000.0000.0000.000
171A788LEU 0-0.049-0.02518.2200.0110.0110.0000.0000.0000.000
172A789ASP -1-0.862-0.92613.005-0.271-0.2710.0000.0000.0000.000
173A790GLU -1-0.882-0.94510.609-0.107-0.1070.0000.0000.0000.000
174A791HIS 0-0.067-0.0298.3320.0150.0150.0000.0000.0000.000
175A792LEU 0-0.046-0.02413.207-0.010-0.0100.0000.0000.0000.000
176A793SER 0-0.0180.00816.5030.0170.0170.0000.0000.0000.000
177A794NME 00.0140.01719.259-0.005-0.0050.0000.0000.0000.000
178A809ACE 0-0.015-0.02127.9200.0010.0010.0000.0000.0000.000
179A810ASP -1-0.749-0.87223.222-0.010-0.0100.0000.0000.0000.000
180A811GLU -1-0.807-0.90422.8630.0070.0070.0000.0000.0000.000
181A812SER 00.0210.01425.694-0.001-0.0010.0000.0000.0000.000
182A813ASP -1-0.877-0.93626.849-0.022-0.0220.0000.0000.0000.000
183A814LYS 10.8570.91420.398-0.001-0.0010.0000.0000.0000.000
184A815GLU -1-0.976-0.99123.8660.0000.0000.0000.0000.0000.000
185A816MET 0-0.020-0.01625.747-0.004-0.0040.0000.0000.0000.000
186A817ILE 0-0.004-0.00823.019-0.004-0.0040.0000.0000.0000.000
187A818ARG 10.8210.90320.313-0.005-0.0050.0000.0000.0000.000
188A819LYS 10.8960.96223.3090.0080.0080.0000.0000.0000.000
189A820TYR 0-0.022-0.00926.479-0.001-0.0010.0000.0000.0000.000
190A821VAL 00.0200.01221.871-0.002-0.0020.0000.0000.0000.000
191A822SER 00.0490.02225.090-0.005-0.0050.0000.0000.0000.000
192A823SER 0-0.0040.00826.7530.0000.0000.0000.0000.0000.000
193A824ILE 00.0160.00327.4180.0010.0010.0000.0000.0000.000
194A825ALA 00.0130.00225.133-0.003-0.0030.0000.0000.0000.000
195A826ASN 0-0.110-0.05627.1640.0040.0040.0000.0000.0000.000
196A827ARG 10.7920.90430.2220.0420.0420.0000.0000.0000.000
197A828LEU 0-0.030-0.00127.0260.0000.0000.0000.0000.0000.000
198A829NME 00.0110.02026.9410.0020.0020.0000.0000.0000.000