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: 2212R

Calculation Name: 4P1N-A-Xray372

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: 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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2102377.64254
FMO2-HF: Nuclear repulsion 2022788.998724
FMO2-HF: Total energy -79588.643816
FMO2-MP2: Total energy -79816.328017


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:567:SER)


Summations of interaction energy for fragment #1(A:567:SER)
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.
-1.534.0212.128-3.114-4.5620.009
Interaction energy analysis for fragmet #1(A:567:SER)
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].
3A569SER0-0.017-0.0223.840-0.0972.047-0.019-1.220-0.9050.007
4A570ASN0-0.0040.0076.3941.1891.1890.0000.0000.0000.000
5A571ILE00.0880.0572.310-0.777-0.8441.766-0.560-1.138-0.003
6A572THR0-0.040-0.0385.1180.5420.593-0.001-0.004-0.0450.000
7A573PRO00.0360.0117.7000.1930.1930.0000.0000.0000.000
8A574PHE00.0470.0264.3290.0860.299-0.001-0.034-0.1780.000
9A575VAL00.0110.0076.9690.1510.1510.0000.0000.0000.000
10A576GLU-1-0.847-0.8979.314-0.103-0.1030.0000.0000.0000.000
11A577SER0-0.0090.00311.1730.0430.0430.0000.0000.0000.000
12A578LEU00.0290.0068.8300.0050.0050.0000.0000.0000.000
13A579SER0-0.023-0.02812.819-0.019-0.0190.0000.0000.0000.000
14A580ALA00.0060.01715.136-0.025-0.0250.0000.0000.0000.000
15A581LYS10.8210.91213.620-0.561-0.5610.0000.0000.0000.000
16A582ALA00.019-0.00116.752-0.018-0.0180.0000.0000.0000.000
17A583PHE0-0.024-0.00418.438-0.028-0.0280.0000.0000.0000.000
18A584VAL0-0.003-0.00120.780-0.020-0.0200.0000.0000.0000.000
19A585MET0-0.0190.00521.111-0.022-0.0220.0000.0000.0000.000
20A586TYR00.003-0.03122.495-0.017-0.0170.0000.0000.0000.000
21A587SER0-0.021-0.01624.192-0.024-0.0240.0000.0000.0000.000
22A588PHE0-0.032-0.01926.246-0.018-0.0180.0000.0000.0000.000
23A589ALA00.030-0.00226.502-0.012-0.0120.0000.0000.0000.000
24A590GLU-1-0.769-0.84527.7140.1640.1640.0000.0000.0000.000
25A591MET0-0.046-0.00730.153-0.013-0.0130.0000.0000.0000.000
26A592LYS10.8530.92031.949-0.158-0.1580.0000.0000.0000.000
27A593PHE00.0320.01431.888-0.009-0.0090.0000.0000.0000.000
28A594SER0-0.041-0.02933.909-0.010-0.0100.0000.0000.0000.000
29A595GLN0-0.0080.00536.100-0.003-0.0030.0000.0000.0000.000
30A596ILE0-0.051-0.01235.895-0.005-0.0050.0000.0000.0000.000
31A597LEU0-0.087-0.04536.098-0.012-0.0120.0000.0000.0000.000
32A652ASN0-0.007-0.02347.0510.0010.0010.0000.0000.0000.000
33A653LEU0-0.017-0.00848.2380.0030.0030.0000.0000.0000.000
34A654ILE00.0430.02343.1310.0000.0000.0000.0000.0000.000
35A655PRO00.0180.01346.5440.0010.0010.0000.0000.0000.000
36A656ALA00.0710.03445.1490.0040.0040.0000.0000.0000.000
37A657PRO00.0410.00843.7050.0060.0060.0000.0000.0000.000
38A658GLU-1-0.936-0.95942.1080.1050.1050.0000.0000.0000.000
39A659LEU0-0.010-0.01540.1930.0070.0070.0000.0000.0000.000
40A660LYS10.8420.90039.409-0.121-0.1210.0000.0000.0000.000
41A661LYS10.9100.95436.818-0.134-0.1340.0000.0000.0000.000
42A662LEU00.0020.00736.0110.0100.0100.0000.0000.0000.000
43A663CYS0-0.044-0.02034.7380.0090.0090.0000.0000.0000.000
44A664MET00.004-0.00132.1790.0160.0160.0000.0000.0000.000
45A665GLU-1-0.779-0.87531.5730.1680.1680.0000.0000.0000.000
46A666SER0-0.006-0.00730.0470.0140.0140.0000.0000.0000.000
47A667LEU00.0070.00928.4560.0160.0160.0000.0000.0000.000
48A668LEU00.0250.00127.2560.0240.0240.0000.0000.0000.000
49A669LEU0-0.0030.01425.4390.0290.0290.0000.0000.0000.000
50A670TYR0-0.010-0.03824.1920.0250.0250.0000.0000.0000.000
51A671LEU00.0050.00823.1650.0320.0320.0000.0000.0000.000
52A672LYS10.9120.97219.877-0.391-0.3910.0000.0000.0000.000
53A673SER0-0.013-0.03719.5150.0420.0420.0000.0000.0000.000
54A674LEU0-0.029-0.01618.7050.0450.0450.0000.0000.0000.000
55A675THR0-0.019-0.00716.4440.0610.0610.0000.0000.0000.000
56A676ILE0-0.0080.00414.5880.1100.1100.0000.0000.0000.000
57A677LEU0-0.037-0.02413.8030.0950.0950.0000.0000.0000.000
58A678ALA00.0110.00413.9690.0750.0750.0000.0000.0000.000
59A679SER00.0450.0209.9250.1790.1790.0000.0000.0000.000
60A680SER00.0020.0069.3860.3570.3570.0000.0000.0000.000
61A681MET00.0040.0189.1160.1840.1840.0000.0000.0000.000
62A682LYS10.9310.9759.001-1.713-1.7130.0000.0000.0000.000
63A683LEU00.0010.0022.9570.0370.4500.101-0.138-0.3760.000
64A684THR00.002-0.0255.2581.0641.0640.0000.0000.0000.000
65A685SER0-0.028-0.0116.995-0.064-0.0640.0000.0000.0000.000
66A686LYS10.8640.9134.710-2.802-2.727-0.001-0.005-0.0680.000
67A687TRP0-0.028-0.0212.823-1.3421.0700.283-1.084-1.6100.005
68A688TRP0-0.022-0.0044.246-1.912-1.8170.002-0.052-0.0460.000
69A689TYR0-0.013-0.0197.906-0.521-0.5210.0000.0000.0000.000
70A690GLU-1-0.859-0.8984.6990.7120.816-0.001-0.003-0.1000.000
71A691ASN0-0.020-0.0093.910-0.143-0.032-0.001-0.014-0.0960.000
72A692GLU-1-0.905-0.9536.522-0.277-0.2770.0000.0000.0000.000
73A693SER0-0.071-0.0329.8550.2010.2010.0000.0000.0000.000
74A694LYS10.8600.9279.6170.2140.2140.0000.0000.0000.000
75A695ASN00.0050.00910.8900.1760.1760.0000.0000.0000.000
76A696CYS0-0.0120.00110.613-0.096-0.0960.0000.0000.0000.000
77A697THR00.0060.01211.6230.0450.0450.0000.0000.0000.000
78A698LEU00.0920.03113.7550.0730.0730.0000.0000.0000.000
79A699LYS10.8360.89613.8270.2220.2220.0000.0000.0000.000
80A700LEU00.0470.0358.1850.0480.0480.0000.0000.0000.000
81A701ASN00.0310.00712.2520.0580.0580.0000.0000.0000.000
82A702ILE0-0.0050.00014.8710.0500.0500.0000.0000.0000.000
83A703LEU00.0150.00612.7470.0280.0280.0000.0000.0000.000
84A704VAL00.0360.01411.4990.0590.0590.0000.0000.0000.000
85A705GLN0-0.046-0.02214.2310.0360.0360.0000.0000.0000.000
86A706TRP00.0610.03116.9150.0140.0140.0000.0000.0000.000
87A707ILE00.002-0.00212.5750.0130.0130.0000.0000.0000.000
88A708ARG10.8170.89116.818-0.209-0.2090.0000.0000.0000.000
89A709ASP-1-0.862-0.91218.6010.1940.1940.0000.0000.0000.000
90A710ARG10.8850.93020.010-0.225-0.2250.0000.0000.0000.000
91A711PHE0-0.034-0.00918.3450.0050.0050.0000.0000.0000.000
92A712ASN00.018-0.01320.7690.0120.0120.0000.0000.0000.000
93A713GLU-1-0.730-0.80023.8910.1780.1780.0000.0000.0000.000
94A714CYS0-0.041-0.03023.023-0.011-0.0110.0000.0000.0000.000
95A715LEU0-0.0010.01123.669-0.005-0.0050.0000.0000.0000.000
96A716ASP-1-0.892-0.94125.6910.2000.2000.0000.0000.0000.000
97A717LYS10.7490.84628.492-0.188-0.1880.0000.0000.0000.000
98A718ALA00.0150.00327.059-0.011-0.0110.0000.0000.0000.000
99A719GLU-1-0.826-0.87628.8670.2320.2320.0000.0000.0000.000
100A720PHE0-0.026-0.01031.107-0.015-0.0150.0000.0000.0000.000
101A721LEU0-0.027-0.02330.893-0.012-0.0120.0000.0000.0000.000
102A722ARG10.8450.89530.831-0.241-0.2410.0000.0000.0000.000
103A723LEU0-0.0020.00433.796-0.008-0.0080.0000.0000.0000.000
104A724LYS10.9530.98236.783-0.132-0.1320.0000.0000.0000.000
105A725LEU00.0270.00534.811-0.008-0.0080.0000.0000.0000.000
106A726HIS00.0000.02037.986-0.002-0.0020.0000.0000.0000.000
107A727THR0-0.051-0.04639.569-0.008-0.0080.0000.0000.0000.000
108A728LEU0-0.018-0.01641.630-0.006-0.0060.0000.0000.0000.000
109A729ASN00.010-0.00839.566-0.008-0.0080.0000.0000.0000.000
110A730GLN0-0.055-0.00642.960-0.007-0.0070.0000.0000.0000.000
111A731SER0-0.073-0.02845.883-0.006-0.0060.0000.0000.0000.000
112A732GLU-1-0.884-0.92344.9210.1140.1140.0000.0000.0000.000
113A733ASP-1-0.949-0.98848.2520.1020.1020.0000.0000.0000.000
114A734PRO0-0.0140.01444.930-0.003-0.0030.0000.0000.0000.000
115A735GLN00.0340.01648.0670.0020.0020.0000.0000.0000.000
116A736VAL0-0.019-0.01746.269-0.001-0.0010.0000.0000.0000.000
117A737LEU0-0.029-0.01241.8720.0040.0040.0000.0000.0000.000
118A738ASP-1-0.955-0.97142.8410.1260.1260.0000.0000.0000.000
119A739ASP-1-0.903-0.93542.4490.1230.1230.0000.0000.0000.000
120A740GLU-1-0.892-0.91637.6860.1700.1700.0000.0000.0000.000
121A741PRO0-0.126-0.05539.146-0.006-0.0060.0000.0000.0000.000
122A742THR0-0.006-0.05032.8250.0090.0090.0000.0000.0000.000
123A743ILE0-0.080-0.03631.756-0.008-0.0080.0000.0000.0000.000
124A744PHE00.0530.01829.7340.0130.0130.0000.0000.0000.000
125A745VAL00.0140.00424.751-0.011-0.0110.0000.0000.0000.000
126A746GLU-1-0.786-0.91323.6040.3280.3280.0000.0000.0000.000
127A747LYS10.8340.90626.685-0.162-0.1620.0000.0000.0000.000
128A748LEU0-0.0060.00329.190-0.013-0.0130.0000.0000.0000.000
129A749ILE0-0.013-0.01523.133-0.012-0.0120.0000.0000.0000.000
130A750TYR0-0.0100.00127.119-0.015-0.0150.0000.0000.0000.000
131A751ASP-1-0.818-0.89628.5910.1380.1380.0000.0000.0000.000
132A752ARG10.8400.90328.659-0.147-0.1470.0000.0000.0000.000
133A753ALA00.0370.01527.003-0.012-0.0120.0000.0000.0000.000
134A754LEU00.0440.04028.917-0.015-0.0150.0000.0000.0000.000
135A755ASP-1-0.921-0.90531.9550.1070.1070.0000.0000.0000.000
136A756ILE00.0290.02428.828-0.009-0.0090.0000.0000.0000.000
137A757SER00.0340.01730.437-0.010-0.0100.0000.0000.0000.000
138A758ARG10.8960.90932.259-0.112-0.1120.0000.0000.0000.000
139A759ASN0-0.0090.00235.492-0.013-0.0130.0000.0000.0000.000
140A760ALA00.0530.02833.364-0.006-0.0060.0000.0000.0000.000
141A761ALA00.0390.02835.355-0.007-0.0070.0000.0000.0000.000
142A762ARG10.8130.87037.051-0.057-0.0570.0000.0000.0000.000
143A763LEU0-0.040-0.01636.697-0.004-0.0040.0000.0000.0000.000
144A764GLU-1-0.786-0.87735.7870.0240.0240.0000.0000.0000.000
145A765MET0-0.098-0.04938.949-0.004-0.0040.0000.0000.0000.000
146A766GLU-1-0.871-0.89742.1340.0390.0390.0000.0000.0000.000
147A767GLY00.001-0.01042.242-0.002-0.0020.0000.0000.0000.000
148A768GLY0-0.0170.00540.6210.0010.0010.0000.0000.0000.000
149A769ASN0-0.0330.00037.713-0.004-0.0040.0000.0000.0000.000
150A770TYR00.0440.00135.5490.0030.0030.0000.0000.0000.000
151A771ASN00.0130.00330.255-0.002-0.0020.0000.0000.0000.000
152A772THR0-0.003-0.00531.2680.0030.0030.0000.0000.0000.000
153A773CYS0-0.0140.00031.9830.0090.0090.0000.0000.0000.000
154A774GLU-1-0.882-0.93527.3520.0100.0100.0000.0000.0000.000
155A775LEU00.0300.01926.3100.0110.0110.0000.0000.0000.000
156A776ALA00.0000.00727.0650.0160.0160.0000.0000.0000.000
157A777TYR0-0.044-0.04928.1500.0170.0170.0000.0000.0000.000
158A778ALA00.024-0.00923.3590.0130.0130.0000.0000.0000.000
159A779THR0-0.068-0.03923.2780.0240.0240.0000.0000.0000.000
160A780SER0-0.007-0.02824.2730.0200.0200.0000.0000.0000.000
161A781LEU0-0.034-0.00921.9590.0180.0180.0000.0000.0000.000
162A782TRP00.0650.02315.2920.0340.0340.0000.0000.0000.000
163A783MET0-0.046-0.01319.9470.0370.0370.0000.0000.0000.000
164A784LEU00.007-0.00922.1110.0240.0240.0000.0000.0000.000
165A785GLU-1-0.868-0.93715.6620.3470.3470.0000.0000.0000.000
166A786ILE0-0.032-0.01817.5870.0530.0530.0000.0000.0000.000
167A787LEU0-0.079-0.02318.6660.0320.0320.0000.0000.0000.000
168A788LEU0-0.055-0.03019.2200.0060.0060.0000.0000.0000.000
169A789ASP-1-0.831-0.90413.3800.8590.8590.0000.0000.0000.000
170A790GLU-1-0.840-0.92912.8160.9180.9180.0000.0000.0000.000
171A791HIS0-0.125-0.05710.5000.1500.1500.0000.0000.0000.000
172A792LEU0-0.066-0.02713.112-0.004-0.0040.0000.0000.0000.000
173A793SER0-0.030-0.00116.017-0.083-0.0830.0000.0000.0000.000
174A810ASP-1-0.773-0.88425.0040.2900.2900.0000.0000.0000.000
175A811GLU-1-0.785-0.88624.8970.2530.2530.0000.0000.0000.000
176A812SER00.0360.01227.880-0.010-0.0100.0000.0000.0000.000
177A813ASP-1-0.871-0.93628.1830.1820.1820.0000.0000.0000.000
178A814LYS10.8800.92822.241-0.320-0.3200.0000.0000.0000.000
179A815GLU-1-0.914-0.93825.4170.1310.1310.0000.0000.0000.000
180A816MET0-0.031-0.01627.551-0.014-0.0140.0000.0000.0000.000
181A817ILE00.000-0.01023.784-0.013-0.0130.0000.0000.0000.000
182A818ARG10.7690.85822.256-0.233-0.2330.0000.0000.0000.000
183A819LYS10.8360.91624.474-0.137-0.1370.0000.0000.0000.000
184A820TYR0-0.018-0.01227.223-0.018-0.0180.0000.0000.0000.000
185A821VAL00.0220.01221.867-0.011-0.0110.0000.0000.0000.000
186A822SER00.0470.02225.009-0.012-0.0120.0000.0000.0000.000
187A823SER0-0.0040.00626.677-0.016-0.0160.0000.0000.0000.000
188A824ILE00.0150.00126.945-0.009-0.0090.0000.0000.0000.000
189A825ALA00.0140.01024.356-0.007-0.0070.0000.0000.0000.000
190A826ASN0-0.118-0.06126.233-0.013-0.0130.0000.0000.0000.000
191A827ARG10.7580.87429.395-0.038-0.0380.0000.0000.0000.000
192A828LEU0-0.0030.01725.199-0.010-0.0100.0000.0000.0000.000