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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: 66Q6Z

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 OptAll
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 -2111864.943895
FMO2-HF: Nuclear repulsion 2032275.476573
FMO2-HF: Total energy -79589.467322
FMO2-MP2: Total energy -79817.123382


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.
-5.2040.1043.914-3.679-5.5390.003
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 : 0.015 / q_NPA : 0.009
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].
3A569SER0-0.040-0.0403.8470.1561.874-0.007-0.920-0.7910.005
4A570ASN0-0.0010.0045.7300.9160.9160.0000.0000.0000.000
5A571ILE00.0730.0482.256-0.750-0.9492.225-0.755-1.271-0.003
6A572THR0-0.021-0.0245.0560.3860.431-0.001-0.005-0.0390.000
7A573PRO00.0420.0158.1670.1600.1600.0000.0000.0000.000
8A574PHE00.0300.0224.6630.0440.182-0.001-0.013-0.1230.000
9A575VAL00.0310.0177.0860.1180.1180.0000.0000.0000.000
10A576GLU-1-0.809-0.8719.630-0.040-0.0400.0000.0000.0000.000
11A577SER0-0.0250.00111.4560.0260.0260.0000.0000.0000.000
12A578LEU00.0290.0058.8840.0080.0080.0000.0000.0000.000
13A579SER0-0.016-0.02912.8150.0030.0030.0000.0000.0000.000
14A580ALA0-0.0110.00215.375-0.017-0.0170.0000.0000.0000.000
15A581LYS10.8080.89113.240-0.283-0.2830.0000.0000.0000.000
16A582ALA00.0130.00116.700-0.010-0.0100.0000.0000.0000.000
17A583PHE0-0.006-0.00118.388-0.015-0.0150.0000.0000.0000.000
18A584VAL0-0.0010.00820.567-0.015-0.0150.0000.0000.0000.000
19A585MET0-0.0240.00421.098-0.018-0.0180.0000.0000.0000.000
20A586TYR0-0.001-0.03422.402-0.012-0.0120.0000.0000.0000.000
21A587SER0-0.009-0.01724.154-0.016-0.0160.0000.0000.0000.000
22A588PHE0-0.039-0.02326.263-0.015-0.0150.0000.0000.0000.000
23A589ALA00.0390.01026.206-0.009-0.0090.0000.0000.0000.000
24A590GLU-1-0.740-0.83527.5640.1490.1490.0000.0000.0000.000
25A591MET0-0.052-0.00430.035-0.011-0.0110.0000.0000.0000.000
26A592LYS10.8620.93131.548-0.110-0.1100.0000.0000.0000.000
27A593PHE00.0320.01131.614-0.006-0.0060.0000.0000.0000.000
28A594SER0-0.041-0.03533.614-0.007-0.0070.0000.0000.0000.000
29A595GLN00.0130.00836.081-0.002-0.0020.0000.0000.0000.000
30A596ILE0-0.036-0.00735.516-0.004-0.0040.0000.0000.0000.000
31A597LEU0-0.084-0.04436.042-0.006-0.0060.0000.0000.0000.000
32A652ASN00.008-0.01346.6410.0010.0010.0000.0000.0000.000
33A653LEU0-0.025-0.01048.4660.0010.0010.0000.0000.0000.000
34A654ILE00.0360.02042.8460.0000.0000.0000.0000.0000.000
35A655PRO00.0140.01046.1260.0010.0010.0000.0000.0000.000
36A656ALA00.0560.03245.1070.0030.0030.0000.0000.0000.000
37A657PRO00.0470.01143.7250.0040.0040.0000.0000.0000.000
38A658GLU-1-0.912-0.95241.9680.0760.0760.0000.0000.0000.000
39A659LEU00.005-0.00740.0930.0060.0060.0000.0000.0000.000
40A660LYS10.8470.89639.313-0.089-0.0890.0000.0000.0000.000
41A661LYS10.8980.94836.891-0.090-0.0900.0000.0000.0000.000
42A662LEU0-0.012-0.00636.0820.0080.0080.0000.0000.0000.000
43A663CYS0-0.041-0.02634.7680.0070.0070.0000.0000.0000.000
44A664MET00.0190.01132.0850.0120.0120.0000.0000.0000.000
45A665GLU-1-0.803-0.89131.6540.1150.1150.0000.0000.0000.000
46A666SER0-0.007-0.00330.1440.0100.0100.0000.0000.0000.000
47A667LEU0-0.0030.00428.4940.0140.0140.0000.0000.0000.000
48A668LEU00.0280.00927.3360.0200.0200.0000.0000.0000.000
49A669LEU0-0.0050.01225.5030.0200.0200.0000.0000.0000.000
50A670TYR0-0.016-0.03024.1570.0180.0180.0000.0000.0000.000
51A671LEU00.0020.00623.1420.0290.0290.0000.0000.0000.000
52A672LYS10.8530.92819.944-0.241-0.2410.0000.0000.0000.000
53A673SER0-0.004-0.03119.5160.0300.0300.0000.0000.0000.000
54A674LEU0-0.022-0.01818.6300.0420.0420.0000.0000.0000.000
55A675THR0-0.009-0.00716.5460.0640.0640.0000.0000.0000.000
56A676ILE0-0.0080.00014.5360.0920.0920.0000.0000.0000.000
57A677LEU0-0.042-0.01313.6180.0950.0950.0000.0000.0000.000
58A678ALA00.0190.00813.8740.0920.0920.0000.0000.0000.000
59A679SER0-0.0030.00311.1100.2360.2360.0000.0000.0000.000
60A680SER00.0330.0149.4330.3270.3270.0000.0000.0000.000
61A681MET0-0.0130.0039.2180.2780.2780.0000.0000.0000.000
62A682LYS10.9540.9829.202-1.201-1.2010.0000.0000.0000.000
63A683LEU0-0.024-0.0072.9620.1070.4960.094-0.131-0.3520.000
64A684THR00.003-0.0225.4431.4301.456-0.0010.000-0.0240.000
65A685SER0-0.030-0.0117.1150.1770.1770.0000.0000.0000.000
66A686LYS10.8460.9154.733-2.059-2.002-0.001-0.004-0.0510.000
67A687TRP0-0.034-0.0322.270-3.299-0.6341.602-1.758-2.5090.000
68A688TRP0-0.0110.0034.004-1.826-1.7180.006-0.045-0.0690.001
69A689TYR0-0.011-0.0017.621-0.636-0.6360.0000.0000.0000.000
70A690GLU-1-0.829-0.9124.6320.6140.789-0.001-0.009-0.1650.000
71A691ASN00.0030.0164.532-1.276-1.090-0.001-0.039-0.1450.000
72A692GLU-1-0.919-0.9606.929-0.164-0.1640.0000.0000.0000.000
73A693SER0-0.033-0.0129.8170.0650.0650.0000.0000.0000.000
74A694LYS10.8170.9129.526-0.792-0.7920.0000.0000.0000.000
75A695ASN0-0.018-0.01211.5410.0890.0890.0000.0000.0000.000
76A696CYS00.0030.00110.0910.0650.0650.0000.0000.0000.000
77A697THR0-0.0030.01010.926-0.026-0.0260.0000.0000.0000.000
78A698LEU00.0740.03013.1420.0680.0680.0000.0000.0000.000
79A699LYS10.8440.89613.8980.0970.0970.0000.0000.0000.000
80A700LEU00.0320.0257.9010.0200.0200.0000.0000.0000.000
81A701ASN00.017-0.00212.1950.0480.0480.0000.0000.0000.000
82A702ILE0-0.003-0.00214.6230.0280.0280.0000.0000.0000.000
83A703LEU0-0.0010.00512.5940.0130.0130.0000.0000.0000.000
84A704VAL00.0290.01211.5420.0340.0340.0000.0000.0000.000
85A705GLN0-0.0090.00314.1100.0090.0090.0000.0000.0000.000
86A706TRP00.0360.01917.085-0.001-0.0010.0000.0000.0000.000
87A707ILE00.006-0.00512.614-0.006-0.0060.0000.0000.0000.000
88A708ARG10.7950.86016.826-0.294-0.2940.0000.0000.0000.000
89A709ASP-1-0.844-0.89418.5920.2400.2400.0000.0000.0000.000
90A710ARG10.8830.93320.258-0.239-0.2390.0000.0000.0000.000
91A711PHE0-0.031-0.00118.383-0.006-0.0060.0000.0000.0000.000
92A712ASN00.022-0.00720.7470.0030.0030.0000.0000.0000.000
93A713GLU-1-0.733-0.81323.9330.1690.1690.0000.0000.0000.000
94A714CYS0-0.047-0.03722.905-0.018-0.0180.0000.0000.0000.000
95A715LEU0-0.0040.01023.980-0.008-0.0080.0000.0000.0000.000
96A716ASP-1-0.904-0.94825.7980.1960.1960.0000.0000.0000.000
97A717LYS10.7630.86128.526-0.175-0.1750.0000.0000.0000.000
98A718ALA00.0160.00827.068-0.012-0.0120.0000.0000.0000.000
99A719GLU-1-0.786-0.85928.9250.1980.1980.0000.0000.0000.000
100A720PHE0-0.032-0.01231.255-0.014-0.0140.0000.0000.0000.000
101A721LEU0-0.018-0.01130.895-0.011-0.0110.0000.0000.0000.000
102A722ARG10.8270.87931.117-0.203-0.2030.0000.0000.0000.000
103A723LEU00.0040.00733.935-0.007-0.0070.0000.0000.0000.000
104A724LYS10.8960.97036.974-0.110-0.1100.0000.0000.0000.000
105A725LEU00.011-0.00134.699-0.007-0.0070.0000.0000.0000.000
106A726HIS00.0020.01037.839-0.004-0.0040.0000.0000.0000.000
107A727THR0-0.035-0.03939.509-0.006-0.0060.0000.0000.0000.000
108A728LEU0-0.025-0.01741.672-0.005-0.0050.0000.0000.0000.000
109A729ASN00.0220.01139.636-0.007-0.0070.0000.0000.0000.000
110A730GLN0-0.069-0.02142.926-0.005-0.0050.0000.0000.0000.000
111A731SER0-0.075-0.03245.589-0.004-0.0040.0000.0000.0000.000
112A732GLU-1-0.894-0.92844.6590.0850.0850.0000.0000.0000.000
113A733ASP-1-0.925-0.96348.3270.0760.0760.0000.0000.0000.000
114A734PRO0-0.021-0.00444.875-0.003-0.0030.0000.0000.0000.000
115A735GLN00.0100.00648.0240.0020.0020.0000.0000.0000.000
116A736VAL0-0.041-0.02046.579-0.002-0.0020.0000.0000.0000.000
117A737LEU0-0.003-0.01142.1450.0030.0030.0000.0000.0000.000
118A738ASP-1-0.958-0.97242.5640.0840.0840.0000.0000.0000.000
119A739ASP-1-0.953-0.98442.7480.0780.0780.0000.0000.0000.000
120A740GLU-1-0.866-0.89537.5080.1110.1110.0000.0000.0000.000
121A741PRO0-0.107-0.03338.779-0.004-0.0040.0000.0000.0000.000
122A742THR00.001-0.04032.6470.0080.0080.0000.0000.0000.000
123A743ILE0-0.066-0.03431.769-0.006-0.0060.0000.0000.0000.000
124A744PHE00.0530.01330.0860.0120.0120.0000.0000.0000.000
125A745VAL00.0150.00825.068-0.009-0.0090.0000.0000.0000.000
126A746GLU-1-0.788-0.90423.4710.2090.2090.0000.0000.0000.000
127A747LYS10.8330.90526.478-0.097-0.0970.0000.0000.0000.000
128A748LEU00.0040.00429.273-0.009-0.0090.0000.0000.0000.000
129A749ILE00.001-0.00423.226-0.009-0.0090.0000.0000.0000.000
130A750TYR00.0050.01227.061-0.011-0.0110.0000.0000.0000.000
131A751ASP-1-0.825-0.90728.5960.0760.0760.0000.0000.0000.000
132A752ARG10.8040.88328.571-0.096-0.0960.0000.0000.0000.000
133A753ALA00.0350.01926.750-0.008-0.0080.0000.0000.0000.000
134A754LEU00.0610.05128.686-0.012-0.0120.0000.0000.0000.000
135A755ASP-1-0.896-0.89031.9900.0640.0640.0000.0000.0000.000
136A756ILE00.0270.02528.788-0.006-0.0060.0000.0000.0000.000
137A757SER00.0190.00530.581-0.008-0.0080.0000.0000.0000.000
138A758ARG10.8720.89932.452-0.058-0.0580.0000.0000.0000.000
139A759ASN00.0080.00635.538-0.008-0.0080.0000.0000.0000.000
140A760ALA00.0300.02333.229-0.003-0.0030.0000.0000.0000.000
141A761ALA00.0640.03835.305-0.005-0.0050.0000.0000.0000.000
142A762ARG10.7800.84037.398-0.031-0.0310.0000.0000.0000.000
143A763LEU0-0.022-0.01336.645-0.002-0.0020.0000.0000.0000.000
144A764GLU-1-0.790-0.86835.993-0.006-0.0060.0000.0000.0000.000
145A765MET0-0.094-0.04739.256-0.003-0.0030.0000.0000.0000.000
146A766GLU-1-0.843-0.87742.5670.0200.0200.0000.0000.0000.000
147A767GLY0-0.0040.00442.5350.0000.0000.0000.0000.0000.000
148A768GLY00.0090.00640.8240.0000.0000.0000.0000.0000.000
149A769ASN0-0.061-0.03138.1640.0000.0000.0000.0000.0000.000
150A770TYR00.0400.01035.5880.0020.0020.0000.0000.0000.000
151A771ASN0-0.001-0.02230.6590.0000.0000.0000.0000.0000.000
152A772THR0-0.0080.00031.6590.0030.0030.0000.0000.0000.000
153A773CYS0-0.044-0.01432.3900.0060.0060.0000.0000.0000.000
154A774GLU-1-0.866-0.91328.049-0.014-0.0140.0000.0000.0000.000
155A775LEU00.0370.01126.6660.0040.0040.0000.0000.0000.000
156A776ALA0-0.0190.01127.3650.0120.0120.0000.0000.0000.000
157A777TYR0-0.014-0.04928.2770.0110.0110.0000.0000.0000.000
158A778ALA00.017-0.00223.8370.0040.0040.0000.0000.0000.000
159A779THR0-0.058-0.03723.4110.0150.0150.0000.0000.0000.000
160A780SER0-0.023-0.04324.2560.0140.0140.0000.0000.0000.000
161A781LEU0-0.032-0.00622.2910.0100.0100.0000.0000.0000.000
162A782TRP00.0540.02115.5940.0180.0180.0000.0000.0000.000
163A783MET0-0.045-0.01920.1370.0220.0220.0000.0000.0000.000
164A784LEU00.014-0.00222.4790.0140.0140.0000.0000.0000.000
165A785GLU-1-0.843-0.91815.5940.1240.1240.0000.0000.0000.000
166A786ILE0-0.032-0.01917.6450.0300.0300.0000.0000.0000.000
167A787LEU0-0.070-0.02518.9500.0210.0210.0000.0000.0000.000
168A788LEU0-0.066-0.03519.136-0.012-0.0120.0000.0000.0000.000
169A789ASP-1-0.821-0.90213.5770.4580.4580.0000.0000.0000.000
170A790GLU-1-0.809-0.90813.2440.4270.4270.0000.0000.0000.000
171A791HIS0-0.128-0.06010.5950.1620.1620.0000.0000.0000.000
172A792LEU0-0.066-0.02313.5360.0430.0430.0000.0000.0000.000
173A793SER0-0.0360.00316.260-0.048-0.0480.0000.0000.0000.000
174A810ASP-1-0.774-0.89025.0610.1380.1380.0000.0000.0000.000
175A811GLU-1-0.788-0.89024.7090.0870.0870.0000.0000.0000.000
176A812SER00.0370.02027.818-0.010-0.0100.0000.0000.0000.000
177A813ASP-1-0.889-0.94728.4080.0810.0810.0000.0000.0000.000
178A814LYS10.8870.93722.381-0.145-0.1450.0000.0000.0000.000
179A815GLU-1-0.911-0.92125.6990.0170.0170.0000.0000.0000.000
180A816MET0-0.0210.00128.110-0.013-0.0130.0000.0000.0000.000
181A817ILE00.0120.00523.752-0.010-0.0100.0000.0000.0000.000
182A818ARG10.7850.84322.731-0.072-0.0720.0000.0000.0000.000
183A819LYS10.8000.89424.991-0.036-0.0360.0000.0000.0000.000
184A820TYR0-0.002-0.01628.002-0.008-0.0080.0000.0000.0000.000
185A821VAL00.0180.01122.493-0.004-0.0040.0000.0000.0000.000
186A822SER00.0370.01225.485-0.008-0.0080.0000.0000.0000.000
187A823SER0-0.0240.00226.857-0.009-0.0090.0000.0000.0000.000
188A824ILE00.0090.00127.443-0.003-0.0030.0000.0000.0000.000
189A825ALA00.0290.01824.809-0.004-0.0040.0000.0000.0000.000
190A826ASN0-0.089-0.03526.702-0.009-0.0090.0000.0000.0000.000
191A827ARG10.7950.89929.8510.0030.0030.0000.0000.0000.000
192A828LEU0-0.049-0.02525.322-0.007-0.0070.0000.0000.0000.000