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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: 7GRGK

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2101782.667037
FMO2-HF: Nuclear repulsion 2022195.211816
FMO2-HF: Total energy -79587.455222
FMO2-MP2: Total energy -79815.159464


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.
-1.3872.8741.443-2.025-3.6780.002
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 : -0.035 / q_NPA : -0.031
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].
3A569SER0-0.035-0.0213.840-0.6680.566-0.017-0.631-0.5860.003
4A570ASN00.011-0.0066.3300.7680.7680.0000.0000.0000.000
5A571ILE00.0680.0522.447-0.615-0.4191.215-0.425-0.987-0.003
6A572THR0-0.026-0.0225.1480.4600.508-0.001-0.003-0.0430.000
7A573PRO00.0420.0118.1910.1170.1170.0000.0000.0000.000
8A574PHE00.0370.0264.585-0.0910.084-0.001-0.021-0.1530.000
9A575VAL00.0060.0036.9700.1160.1160.0000.0000.0000.000
10A576GLU-1-0.903-0.9479.372-0.109-0.1090.0000.0000.0000.000
11A577SER00.0080.00811.1370.0440.0440.0000.0000.0000.000
12A578LEU00.013-0.0018.7370.0190.0190.0000.0000.0000.000
13A579SER0-0.005-0.01512.7730.0060.0060.0000.0000.0000.000
14A580ALA00.0130.02215.198-0.001-0.0010.0000.0000.0000.000
15A581LYS10.9200.96913.328-0.216-0.2160.0000.0000.0000.000
16A582ALA00.011-0.00316.700-0.001-0.0010.0000.0000.0000.000
17A583PHE0-0.0160.00018.352-0.007-0.0070.0000.0000.0000.000
18A584VAL0-0.008-0.00320.844-0.004-0.0040.0000.0000.0000.000
19A585MET0-0.0240.00220.932-0.004-0.0040.0000.0000.0000.000
20A586TYR00.000-0.05722.399-0.005-0.0050.0000.0000.0000.000
21A587SER0-0.016-0.02024.134-0.008-0.0080.0000.0000.0000.000
22A588PHE0-0.027-0.01426.139-0.005-0.0050.0000.0000.0000.000
23A589ALA00.024-0.00726.415-0.003-0.0030.0000.0000.0000.000
24A590GLU-1-0.780-0.87027.9610.0460.0460.0000.0000.0000.000
25A591MET0-0.031-0.00930.127-0.005-0.0050.0000.0000.0000.000
26A592LYS10.8480.93531.673-0.062-0.0620.0000.0000.0000.000
27A593PHE00.0260.00931.811-0.003-0.0030.0000.0000.0000.000
28A594SER0-0.055-0.03933.821-0.004-0.0040.0000.0000.0000.000
29A595GLN0-0.022-0.01736.100-0.001-0.0010.0000.0000.0000.000
30A596ILE0-0.057-0.01435.896-0.001-0.0010.0000.0000.0000.000
31A597LEU0-0.050-0.00936.360-0.003-0.0030.0000.0000.0000.000
32A652ASN0-0.005-0.02146.9780.0000.0000.0000.0000.0000.000
33A653LEU0-0.016-0.00748.1560.0010.0010.0000.0000.0000.000
34A654ILE00.0370.02042.9770.0000.0000.0000.0000.0000.000
35A655PRO00.0230.01446.4820.0000.0000.0000.0000.0000.000
36A656ALA00.0790.03845.0700.0020.0020.0000.0000.0000.000
37A657PRO00.0490.01443.6340.0020.0020.0000.0000.0000.000
38A658GLU-1-0.945-0.96342.0040.0420.0420.0000.0000.0000.000
39A659LEU0-0.011-0.01440.0720.0030.0030.0000.0000.0000.000
40A660LYS10.9530.98239.335-0.050-0.0500.0000.0000.0000.000
41A661LYS10.9000.95436.471-0.056-0.0560.0000.0000.0000.000
42A662LEU0-0.0080.00135.9330.0040.0040.0000.0000.0000.000
43A663CYS0-0.045-0.02034.6580.0020.0020.0000.0000.0000.000
44A664MET00.0200.00632.3180.0050.0050.0000.0000.0000.000
45A665GLU-1-0.802-0.89731.5030.0680.0680.0000.0000.0000.000
46A666SER0-0.009-0.00729.9660.0050.0050.0000.0000.0000.000
47A667LEU00.0170.01028.5310.0050.0050.0000.0000.0000.000
48A668LEU00.013-0.00327.1790.0090.0090.0000.0000.0000.000
49A669LEU0-0.0050.01725.3670.0110.0110.0000.0000.0000.000
50A670TYR00.010-0.02124.1100.0080.0080.0000.0000.0000.000
51A671LEU00.0010.00923.0960.0100.0100.0000.0000.0000.000
52A672LYS10.9030.95219.464-0.165-0.1650.0000.0000.0000.000
53A673SER0-0.004-0.03319.4390.0140.0140.0000.0000.0000.000
54A674LEU0-0.023-0.01718.6280.0130.0130.0000.0000.0000.000
55A675THR0-0.0240.00216.4440.0240.0240.0000.0000.0000.000
56A676ILE0-0.014-0.00214.4490.0410.0410.0000.0000.0000.000
57A677LEU0-0.023-0.01513.7250.0270.0270.0000.0000.0000.000
58A678ALA00.0230.00513.9100.0260.0260.0000.0000.0000.000
59A679SER0-0.0010.00510.5950.1020.1020.0000.0000.0000.000
60A680SER00.0640.0319.3350.1100.1100.0000.0000.0000.000
61A681MET0-0.032-0.0039.1510.0690.0690.0000.0000.0000.000
62A682LYS10.9290.9758.949-0.677-0.6770.0000.0000.0000.000
63A683LEU0-0.0010.0003.022-0.0730.3090.058-0.111-0.3290.000
64A684THR00.009-0.0155.2630.8210.8210.0000.0000.0000.000
65A685SER0-0.019-0.0117.001-0.036-0.0360.0000.0000.0000.000
66A686LYS10.8800.9434.521-1.803-1.712-0.001-0.008-0.0820.000
67A687TRP0-0.020-0.0162.924-0.4921.3600.191-0.777-1.2660.002
68A688TRP0-0.017-0.0034.383-1.453-1.3870.001-0.038-0.0290.000
69A689TYR0-0.035-0.0328.062-0.321-0.3210.0000.0000.0000.000
70A690GLU-1-0.874-0.9224.7320.1170.216-0.001-0.002-0.0950.000
71A691ASN0-0.025-0.0134.3830.1440.262-0.001-0.009-0.1080.000
72A692GLU-1-0.905-0.9546.621-0.210-0.2100.0000.0000.0000.000
73A693SER0-0.076-0.0319.8850.1770.1770.0000.0000.0000.000
74A694LYS10.8800.9409.8270.5090.5090.0000.0000.0000.000
75A695ASN00.0040.00511.0150.1790.1790.0000.0000.0000.000
76A696CYS0-0.0100.00510.572-0.138-0.1380.0000.0000.0000.000
77A697THR00.0000.00711.6390.0760.0760.0000.0000.0000.000
78A698LEU00.0890.02713.7440.0360.0360.0000.0000.0000.000
79A699LYS10.9030.94413.8280.2270.2270.0000.0000.0000.000
80A700LEU00.0480.0398.3790.0400.0400.0000.0000.0000.000
81A701ASN00.0340.00512.2650.0210.0210.0000.0000.0000.000
82A702ILE00.0010.00614.8730.0360.0360.0000.0000.0000.000
83A703LEU00.0170.00712.4620.0240.0240.0000.0000.0000.000
84A704VAL00.0310.00911.4480.0390.0390.0000.0000.0000.000
85A705GLN0-0.092-0.04614.2510.0270.0270.0000.0000.0000.000
86A706TRP00.0660.03916.8600.0140.0140.0000.0000.0000.000
87A707ILE00.0100.00212.6920.0150.0150.0000.0000.0000.000
88A708ARG10.8880.94816.854-0.025-0.0250.0000.0000.0000.000
89A709ASP-1-0.899-0.94718.6250.0270.0270.0000.0000.0000.000
90A710ARG10.9020.93320.030-0.044-0.0440.0000.0000.0000.000
91A711PHE0-0.047-0.01817.9500.0070.0070.0000.0000.0000.000
92A712ASN00.023-0.01020.8060.0100.0100.0000.0000.0000.000
93A713GLU-1-0.749-0.79123.9200.0470.0470.0000.0000.0000.000
94A714CYS0-0.035-0.02222.977-0.001-0.0010.0000.0000.0000.000
95A715LEU0-0.0070.00723.3710.0010.0010.0000.0000.0000.000
96A716ASP-1-0.866-0.92825.6430.0620.0620.0000.0000.0000.000
97A717LYS10.7560.85928.483-0.054-0.0540.0000.0000.0000.000
98A718ALA00.015-0.00127.059-0.002-0.0020.0000.0000.0000.000
99A719GLU-1-0.937-0.95428.8740.0860.0860.0000.0000.0000.000
100A720PHE0-0.027-0.01431.064-0.005-0.0050.0000.0000.0000.000
101A721LEU0-0.013-0.01730.831-0.003-0.0030.0000.0000.0000.000
102A722ARG10.9530.98030.671-0.088-0.0880.0000.0000.0000.000
103A723LEU0-0.018-0.00433.750-0.002-0.0020.0000.0000.0000.000
104A724LYS10.9640.98336.740-0.045-0.0450.0000.0000.0000.000
105A725LEU00.0350.00334.405-0.003-0.0030.0000.0000.0000.000
106A726HIS0-0.0180.02537.9150.0000.0000.0000.0000.0000.000
107A727THR0-0.035-0.03039.529-0.003-0.0030.0000.0000.0000.000
108A728LEU0-0.022-0.02141.579-0.002-0.0020.0000.0000.0000.000
109A729ASN0-0.033-0.05139.492-0.002-0.0020.0000.0000.0000.000
110A730GLN0-0.045-0.00243.108-0.002-0.0020.0000.0000.0000.000
111A731SER0-0.075-0.03045.844-0.003-0.0030.0000.0000.0000.000
112A732GLU-1-0.953-0.97945.1590.0440.0440.0000.0000.0000.000
113A733ASP-1-0.943-0.98448.1670.0400.0400.0000.0000.0000.000
114A734PRO0-0.0200.02044.964-0.001-0.0010.0000.0000.0000.000
115A735GLN00.0330.01048.0270.0000.0000.0000.0000.0000.000
116A736VAL0-0.016-0.01546.0150.0000.0000.0000.0000.0000.000
117A737LEU0-0.043-0.02142.1080.0020.0020.0000.0000.0000.000
118A738ASP-1-0.968-0.97542.8090.0560.0560.0000.0000.0000.000
119A739ASP-1-0.872-0.92142.4090.0540.0540.0000.0000.0000.000
120A740GLU-1-0.882-0.91337.6790.0750.0750.0000.0000.0000.000
121A741PRO0-0.157-0.07039.116-0.002-0.0020.0000.0000.0000.000
122A742THR00.000-0.04932.6730.0030.0030.0000.0000.0000.000
123A743ILE0-0.083-0.03631.698-0.003-0.0030.0000.0000.0000.000
124A744PHE00.0500.01729.6370.0050.0050.0000.0000.0000.000
125A745VAL00.007-0.00224.695-0.004-0.0040.0000.0000.0000.000
126A746GLU-1-0.831-0.93424.3200.1280.1280.0000.0000.0000.000
127A747LYS10.9150.97026.600-0.071-0.0710.0000.0000.0000.000
128A748LEU0-0.024-0.00628.983-0.005-0.0050.0000.0000.0000.000
129A749ILE0-0.012-0.01423.040-0.005-0.0050.0000.0000.0000.000
130A750TYR0-0.015-0.00527.017-0.006-0.0060.0000.0000.0000.000
131A751ASP-1-0.858-0.93928.4870.0660.0660.0000.0000.0000.000
132A752ARG10.8920.96128.729-0.058-0.0580.0000.0000.0000.000
133A753ALA00.0360.01826.895-0.005-0.0050.0000.0000.0000.000
134A754LEU00.0520.03028.800-0.006-0.0060.0000.0000.0000.000
135A755ASP-1-0.950-0.96031.9020.0450.0450.0000.0000.0000.000
136A756ILE0-0.0010.01428.481-0.004-0.0040.0000.0000.0000.000
137A757SER0-0.0020.00530.704-0.005-0.0050.0000.0000.0000.000
138A758ARG10.9180.92132.264-0.055-0.0550.0000.0000.0000.000
139A759ASN0-0.021-0.00535.534-0.005-0.0050.0000.0000.0000.000
140A760ALA00.0430.02133.346-0.003-0.0030.0000.0000.0000.000
141A761ALA00.0410.02735.356-0.003-0.0030.0000.0000.0000.000
142A762ARG10.8240.89137.054-0.025-0.0250.0000.0000.0000.000
143A763LEU0-0.049-0.01936.942-0.002-0.0020.0000.0000.0000.000
144A764GLU-1-0.843-0.94236.0640.0200.0200.0000.0000.0000.000
145A765MET0-0.078-0.04638.948-0.001-0.0010.0000.0000.0000.000
146A766GLU-1-0.894-0.92042.1240.0170.0170.0000.0000.0000.000
147A767GLY00.000-0.01142.238-0.002-0.0020.0000.0000.0000.000
148A768GLY0-0.0220.01140.6180.0010.0010.0000.0000.0000.000
149A769ASN0-0.0160.00237.620-0.003-0.0030.0000.0000.0000.000
150A770TYR00.0460.00135.5390.0010.0010.0000.0000.0000.000
151A771ASN00.0680.01930.6740.0020.0020.0000.0000.0000.000
152A772THR0-0.020-0.01131.2640.0000.0000.0000.0000.0000.000
153A773CYS0-0.023-0.00331.9810.0040.0040.0000.0000.0000.000
154A774GLU-1-0.903-0.93927.3620.0050.0050.0000.0000.0000.000
155A775LEU00.0300.01626.3180.0050.0050.0000.0000.0000.000
156A776ALA0-0.0120.00027.0640.0060.0060.0000.0000.0000.000
157A777TYR0-0.013-0.01428.1520.0080.0080.0000.0000.0000.000
158A778ALA00.039-0.01023.3490.0070.0070.0000.0000.0000.000
159A779THR0-0.061-0.03223.2800.0090.0090.0000.0000.0000.000
160A780SER0-0.027-0.02824.2600.0070.0070.0000.0000.0000.000
161A781LEU0-0.0090.00122.2100.0080.0080.0000.0000.0000.000
162A782TRP00.0630.02915.3330.0170.0170.0000.0000.0000.000
163A783MET0-0.058-0.02419.8280.0150.0150.0000.0000.0000.000
164A784LEU00.007-0.01022.0020.0100.0100.0000.0000.0000.000
165A785GLU-1-0.942-0.97017.1720.1560.1560.0000.0000.0000.000
166A786ILE0-0.055-0.02617.4860.0210.0210.0000.0000.0000.000
167A787LEU0-0.089-0.03218.5630.0120.0120.0000.0000.0000.000
168A788LEU0-0.047-0.02419.1060.0040.0040.0000.0000.0000.000
169A789ASP-1-0.861-0.92513.2520.3380.3380.0000.0000.0000.000
170A790GLU-1-0.881-0.94412.1480.3950.3950.0000.0000.0000.000
171A791HIS0-0.067-0.0309.621-0.004-0.0040.0000.0000.0000.000
172A792LEU0-0.049-0.02212.990-0.001-0.0010.0000.0000.0000.000
173A793SER0-0.0040.02315.952-0.031-0.0310.0000.0000.0000.000
174A810ASP-1-0.763-0.88024.8280.1470.1470.0000.0000.0000.000
175A811GLU-1-0.801-0.90824.7400.1490.1490.0000.0000.0000.000
176A812SER00.0250.01427.469-0.002-0.0020.0000.0000.0000.000
177A813ASP-1-0.885-0.94128.1630.0960.0960.0000.0000.0000.000
178A814LYS10.8550.91322.139-0.163-0.1630.0000.0000.0000.000
179A815GLU-1-0.974-0.99125.2490.1010.1010.0000.0000.0000.000
180A816MET0-0.021-0.01727.290-0.004-0.0040.0000.0000.0000.000
181A817ILE0-0.005-0.00823.747-0.005-0.0050.0000.0000.0000.000
182A818ARG10.8170.89921.931-0.149-0.1490.0000.0000.0000.000
183A819LYS10.8980.96224.489-0.094-0.0940.0000.0000.0000.000
184A820TYR0-0.025-0.01027.247-0.009-0.0090.0000.0000.0000.000
185A821VAL00.0230.01421.886-0.008-0.0080.0000.0000.0000.000
186A822SER00.0480.02225.019-0.006-0.0060.0000.0000.0000.000
187A823SER0-0.0020.00826.686-0.008-0.0080.0000.0000.0000.000
188A824ILE00.0140.00226.799-0.006-0.0060.0000.0000.0000.000
189A825ALA00.0220.00924.368-0.005-0.0050.0000.0000.0000.000
190A826ASN0-0.124-0.06026.238-0.005-0.0050.0000.0000.0000.000
191A827ARG10.7860.90729.400-0.033-0.0330.0000.0000.0000.000
192A828LEU0-0.0060.01625.228-0.006-0.0060.0000.0000.0000.000