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: 2N9YR

Calculation Name: 1P3C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P3C

Chain ID: A

ChEMBL ID:

UniProt ID: Q9EXR9

Base Structure: X-ray

Registration Date: 2023-09-23

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2432379.46033
FMO2-HF: Nuclear repulsion 2351697.646502
FMO2-HF: Total energy -80681.813828
FMO2-MP2: Total energy -80915.43639


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:1:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-16.596-23.51940.596-15.608-18.067-0.102
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.049
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].
3A3ILE0-0.058-0.0232.225-1.9250.8181.904-1.634-3.0130.003
4A4GLY00.0040.0104.4890.2550.382-0.001-0.030-0.0970.000
5A5ASP-1-0.928-0.9598.221-0.796-0.7960.0000.0000.0000.000
6A6ASP-1-0.823-0.9048.790-1.644-1.6440.0000.0000.0000.000
7A7GLY00.0320.0099.5240.2830.2830.0000.0000.0000.000
8A8ARG10.6600.7976.7171.6041.6040.0000.0000.0000.000
9A9THR0-0.021-0.00811.0460.1470.1470.0000.0000.0000.000
10A10LYS10.8320.90014.3110.1780.1780.0000.0000.0000.000
11A11VAL00.0210.00515.5690.0130.0130.0000.0000.0000.000
12A12ALA00.0160.01118.0020.0340.0340.0000.0000.0000.000
13A13ASN00.027-0.00321.6890.0340.0340.0000.0000.0000.000
14A14THR0-0.028-0.01919.412-0.014-0.0140.0000.0000.0000.000
15A15ARG10.9880.99022.1460.0860.0860.0000.0000.0000.000
16A16VAL0-0.0090.00923.7540.0110.0110.0000.0000.0000.000
17A17ALA00.0030.03523.163-0.008-0.0080.0000.0000.0000.000
18A18PRO0-0.009-0.02018.870-0.009-0.0090.0000.0000.0000.000
19A19TYR00.010-0.03816.7750.0370.0370.0000.0000.0000.000
20A20ASN00.0240.01419.6770.0060.0060.0000.0000.0000.000
21A21SER0-0.037-0.00720.6840.0200.0200.0000.0000.0000.000
22A22ILE0-0.028-0.00714.8100.0220.0220.0000.0000.0000.000
23A23ALA00.0210.00617.339-0.006-0.0060.0000.0000.0000.000
24A24TYR00.0250.02315.0820.0050.0050.0000.0000.0000.000
25A25ILE0-0.031-0.02715.805-0.012-0.0120.0000.0000.0000.000
26A26THR00.0280.00516.7080.0480.0480.0000.0000.0000.000
27A27PHE00.0260.00616.216-0.019-0.0190.0000.0000.0000.000
28A28GLY0-0.011-0.00920.422-0.006-0.0060.0000.0000.0000.000
29A29GLY00.0230.01519.769-0.018-0.0180.0000.0000.0000.000
30A30SER0-0.029-0.00914.8900.0400.0400.0000.0000.0000.000
31A31SER0-0.010-0.00313.753-0.097-0.0970.0000.0000.0000.000
32A32CYS0-0.146-0.04811.9350.2400.2400.0000.0000.0000.000
33A33THR00.0440.02411.196-0.138-0.1380.0000.0000.0000.000
34A34GLY00.0400.02413.2320.0600.0600.0000.0000.0000.000
35A35THR0-0.031-0.00715.840-0.063-0.0630.0000.0000.0000.000
36A36LEU00.0030.00918.2220.0240.0240.0000.0000.0000.000
37A37ILE00.001-0.00920.852-0.020-0.0200.0000.0000.0000.000
38A38ALA0-0.010-0.01623.572-0.001-0.0010.0000.0000.0000.000
39A39PRO00.0210.01226.6530.0010.0010.0000.0000.0000.000
40A40ASN00.0430.03227.842-0.002-0.0020.0000.0000.0000.000
41A41LYS10.8080.90424.879-0.045-0.0450.0000.0000.0000.000
42A42ILE00.0200.02518.966-0.019-0.0190.0000.0000.0000.000
43A43LEU0-0.0050.00916.9430.0200.0200.0000.0000.0000.000
44A44THR00.028-0.01714.4310.0120.0120.0000.0000.0000.000
45A45ASN00.003-0.01810.7900.1320.1320.0000.0000.0000.000
46A46GLY00.0420.02414.428-0.016-0.0160.0000.0000.0000.000
47A47HIS10.8000.86610.013-1.126-1.1260.0000.0000.0000.000
48A49VAL0-0.0050.01415.422-0.037-0.0370.0000.0000.0000.000
49A50TYR00.0270.00918.394-0.046-0.0460.0000.0000.0000.000
50A51ASN00.0120.01317.3310.0690.0690.0000.0000.0000.000
51A52THR00.044-0.00216.821-0.031-0.0310.0000.0000.0000.000
52A53ALA00.0060.01917.757-0.038-0.0380.0000.0000.0000.000
53A54SER00.000-0.00919.597-0.032-0.0320.0000.0000.0000.000
54A55ARG10.9240.96721.798-0.284-0.2840.0000.0000.0000.000
55A56SER00.0130.02522.356-0.040-0.0400.0000.0000.0000.000
56A57TYR0-0.011-0.01321.8920.0360.0360.0000.0000.0000.000
57A58SER0-0.049-0.03218.8620.0020.0020.0000.0000.0000.000
58A59ALA00.007-0.00122.001-0.029-0.0290.0000.0000.0000.000
59A60LYS10.9240.95422.852-0.158-0.1580.0000.0000.0000.000
60A61GLY00.0610.02422.938-0.003-0.0030.0000.0000.0000.000
61A62SER0-0.0100.00322.482-0.015-0.0150.0000.0000.0000.000
62A63VAL0-0.023-0.01320.9780.0180.0180.0000.0000.0000.000
63A64TYR00.032-0.00520.535-0.010-0.0100.0000.0000.0000.000
64A65PRO00.0250.00820.306-0.010-0.0100.0000.0000.0000.000
65A66GLY00.0350.02119.887-0.003-0.0030.0000.0000.0000.000
66A67MET0-0.0460.01319.2190.0000.0000.0000.0000.0000.000
67A68ASN00.0570.01718.740-0.035-0.0350.0000.0000.0000.000
68A69ASP-1-0.849-0.89820.028-0.109-0.1090.0000.0000.0000.000
69A70SER00.022-0.00220.5400.0110.0110.0000.0000.0000.000
70A71THR0-0.0100.01321.9940.0170.0170.0000.0000.0000.000
71A72ALA00.004-0.00123.671-0.011-0.0110.0000.0000.0000.000
72A73VAL0-0.034-0.02624.5070.0030.0030.0000.0000.0000.000
73A74ASN0-0.071-0.03723.706-0.004-0.0040.0000.0000.0000.000
74A75GLY00.0190.02526.9050.0050.0050.0000.0000.0000.000
75A76SER00.010-0.02225.608-0.001-0.0010.0000.0000.0000.000
76A77ALA0-0.064-0.01025.655-0.005-0.0050.0000.0000.0000.000
77A78ASN00.0180.00825.7030.0170.0170.0000.0000.0000.000
78A79MET0-0.056-0.00519.864-0.003-0.0030.0000.0000.0000.000
79A80THR0-0.022-0.01725.8420.0020.0020.0000.0000.0000.000
80A81GLU-1-0.941-0.96127.2970.1240.1240.0000.0000.0000.000
81A82PHE0-0.030-0.02022.6310.0050.0050.0000.0000.0000.000
82A83TYR00.0390.01523.968-0.011-0.0110.0000.0000.0000.000
83A84VAL00.004-0.00520.7660.0100.0100.0000.0000.0000.000
84A85PRO00.0220.02520.777-0.016-0.0160.0000.0000.0000.000
85A86SER00.0540.00823.1210.0230.0230.0000.0000.0000.000
86A87GLY00.0210.02022.8710.0100.0100.0000.0000.0000.000
87A88TYR00.0070.00814.6340.0160.0160.0000.0000.0000.000
88A89ILE0-0.0020.00420.2620.0320.0320.0000.0000.0000.000
89A90ASN0-0.023-0.01822.6650.0150.0150.0000.0000.0000.000
90A91THR0-0.030-0.02920.2340.0020.0020.0000.0000.0000.000
91A92GLY00.0000.01017.4870.0230.0230.0000.0000.0000.000
92A93ALA0-0.049-0.01115.4070.0770.0770.0000.0000.0000.000
93A94SER00.0830.00810.8000.0200.0200.0000.0000.0000.000
94A95GLN0-0.0260.00013.757-0.057-0.0570.0000.0000.0000.000
95A96TYR0-0.004-0.00616.798-0.044-0.0440.0000.0000.0000.000
96A97ASP-1-0.723-0.82012.3350.7400.7400.0000.0000.0000.000
97A98PHE0-0.055-0.03514.6100.0050.0050.0000.0000.0000.000
98A99ALA00.0110.00117.1230.0050.0050.0000.0000.0000.000
99A100VAL0-0.025-0.00619.287-0.019-0.0190.0000.0000.0000.000
100A101ILE0-0.007-0.00519.3150.0140.0140.0000.0000.0000.000
101A102LYS10.9310.97423.196-0.089-0.0890.0000.0000.0000.000
102A103THR0-0.023-0.02524.9790.0110.0110.0000.0000.0000.000
103A104ASP-1-0.813-0.92127.4500.0600.0600.0000.0000.0000.000
104A105THR00.0140.02029.984-0.009-0.0090.0000.0000.0000.000
105A106ASN0-0.020-0.01929.6920.0060.0060.0000.0000.0000.000
106A107ILE00.0590.02725.999-0.008-0.0080.0000.0000.0000.000
107A108GLY00.0250.00826.878-0.010-0.0100.0000.0000.0000.000
108A109ASN0-0.038-0.03527.703-0.011-0.0110.0000.0000.0000.000
109A110THR0-0.046-0.00229.746-0.005-0.0050.0000.0000.0000.000
110A111VAL0-0.021-0.00924.906-0.007-0.0070.0000.0000.0000.000
111A112GLY0-0.0020.01426.537-0.014-0.0140.0000.0000.0000.000
112A113TYR0-0.067-0.05023.9320.0070.0070.0000.0000.0000.000
113A114ARG10.8860.95319.9880.1090.1090.0000.0000.0000.000
114A115SER0-0.0010.00223.1180.0220.0220.0000.0000.0000.000
115A116ILE00.009-0.00121.151-0.013-0.0130.0000.0000.0000.000
116A117ARG10.8830.95021.6710.1710.1710.0000.0000.0000.000
117A118GLN00.0290.00822.1510.0000.0000.0000.0000.0000.000
118A119VAL0-0.049-0.02319.210-0.013-0.0130.0000.0000.0000.000
119A120THR0-0.022-0.00622.6820.0130.0130.0000.0000.0000.000
120A121ASN00.002-0.01020.1440.0140.0140.0000.0000.0000.000
121A122LEU0-0.007-0.01715.805-0.003-0.0030.0000.0000.0000.000
122A123THR0-0.040-0.04016.656-0.055-0.0550.0000.0000.0000.000
123A124GLY0-0.007-0.00317.0310.0340.0340.0000.0000.0000.000
124A125THR0-0.063-0.01717.6540.0160.0160.0000.0000.0000.000
125A126THR0-0.024-0.01616.413-0.067-0.0670.0000.0000.0000.000
126A127ILE0-0.025-0.01611.2180.0700.0700.0000.0000.0000.000
127A128LYS10.8880.94813.4720.3050.3050.0000.0000.0000.000
128A129ILE00.0030.0107.6050.1100.1100.0000.0000.0000.000
129A130SER00.002-0.03210.771-0.114-0.1140.0000.0000.0000.000
130A131GLY00.000-0.00110.8980.0890.0890.0000.0000.0000.000
131A132TYR0-0.045-0.04411.229-0.077-0.0770.0000.0000.0000.000
132A133PRO0-0.0370.0037.3260.1630.1630.0000.0000.0000.000
133A134GLY00.0620.0028.918-0.037-0.0370.0000.0000.0000.000
134A135ASP-1-0.818-0.8997.218-0.610-0.6100.0000.0000.0000.000
135A136LYS10.9330.9759.6740.6710.6710.0000.0000.0000.000
136A137MET0-0.0330.01412.2250.0300.0300.0000.0000.0000.000
137A138ARG10.9530.9879.274-0.198-0.1980.0000.0000.0000.000
138A139SER0-0.024-0.02113.570-0.023-0.0230.0000.0000.0000.000
139A140THR0-0.082-0.05915.331-0.010-0.0100.0000.0000.0000.000
140A141GLY00.0320.02617.4530.0010.0010.0000.0000.0000.000
141A142LYS10.8840.95518.1330.1060.1060.0000.0000.0000.000
142A143VAL00.0360.01616.130-0.014-0.0140.0000.0000.0000.000
143A144SER0-0.028-0.02415.785-0.006-0.0060.0000.0000.0000.000
144A145GLN00.0070.02314.274-0.037-0.0370.0000.0000.0000.000
145A146TRP0-0.003-0.00710.917-0.024-0.0240.0000.0000.0000.000
146A147GLU-1-0.811-0.88911.552-0.466-0.4660.0000.0000.0000.000
147A148MET00.0360.0429.250-0.134-0.1340.0000.0000.0000.000
148A149SER0-0.022-0.01411.6010.0600.0600.0000.0000.0000.000
149A150GLY00.0280.01512.212-0.096-0.0960.0000.0000.0000.000
150A151SER00.0040.01013.2780.0800.0800.0000.0000.0000.000
151A152VAL0-0.019-0.00212.424-0.123-0.1230.0000.0000.0000.000
152A153THR0-0.001-0.00610.7210.0790.0790.0000.0000.0000.000
153A154ARG10.9540.9869.5510.3430.3430.0000.0000.0000.000
154A155GLU-1-0.711-0.82413.252-0.227-0.2270.0000.0000.0000.000
155A156ASP-1-0.791-0.86614.8020.0540.0540.0000.0000.0000.000
156A157THR00.012-0.01417.107-0.013-0.0130.0000.0000.0000.000
157A158ASN0-0.047-0.01717.289-0.016-0.0160.0000.0000.0000.000
158A159LEU0-0.022-0.00111.7810.0190.0190.0000.0000.0000.000
159A160ALA00.0240.01112.667-0.031-0.0310.0000.0000.0000.000
160A161TYR0-0.069-0.0648.2240.0460.0460.0000.0000.0000.000
161A162TYR00.028-0.0246.1240.2120.2120.0000.0000.0000.000
162A163THR00.0330.0005.743-0.210-0.2100.0000.0000.0000.000
163A164ILE0-0.0180.0136.256-0.291-0.2910.0000.0000.0000.000
164A165ASP-1-0.725-0.8674.568-4.319-4.163-0.001-0.032-0.1230.000
165A166THR0-0.078-0.0412.0191.7330.2907.210-2.754-3.013-0.019
166A167PHE00.0370.0132.188-2.970-3.3143.925-1.375-2.206-0.025
167A168SER00.0130.0124.169-0.218-0.137-0.001-0.014-0.0660.000
168A169GLY00.0880.0466.934-0.454-0.4540.0000.0000.0000.000
169A170ASN00.0230.0095.568-0.493-0.4930.0000.0000.0000.000
170A171SER0-0.0260.0027.738-0.037-0.0370.0000.0000.0000.000
171A172GLY00.0530.0309.011-0.100-0.1000.0000.0000.0000.000
172A173SER0-0.012-0.0269.272-0.116-0.1160.0000.0000.0000.000
173A174ALA0-0.0120.00111.2610.0000.0000.0000.0000.0000.000
174A175MET0-0.025-0.00310.677-0.114-0.1140.0000.0000.0000.000
175A176LEU0-0.047-0.01713.6460.0730.0730.0000.0000.0000.000
176A177ASP-1-0.712-0.86116.608-0.253-0.2530.0000.0000.0000.000
177A178GLN00.013-0.00619.1070.0070.0070.0000.0000.0000.000
178A179ASN0-0.044-0.01721.6060.0100.0100.0000.0000.0000.000
179A180GLN0-0.031-0.02120.4560.0300.0300.0000.0000.0000.000
180A181GLN00.0140.01121.4940.0400.0400.0000.0000.0000.000
181A182ILE0-0.016-0.01217.051-0.030-0.0300.0000.0000.0000.000
182A183VAL00.0140.00116.2510.0250.0250.0000.0000.0000.000
183A184GLY00.0770.02614.9470.0070.0070.0000.0000.0000.000
184A185VAL0-0.065-0.01712.092-0.032-0.0320.0000.0000.0000.000
185A186HIS00.0620.0634.111-0.732-0.599-0.001-0.012-0.1200.000
186A187ASN0-0.054-0.0548.2180.0510.0510.0000.0000.0000.000
187A188ALA0-0.0230.0005.6280.4290.4290.0000.0000.0000.000
188A189GLY00.0670.0432.441-1.252-0.6110.686-0.624-0.7030.004
189A190TYR0-0.027-0.0333.335-0.127-0.1890.0170.331-0.2860.000
190A191SER0-0.009-0.0205.359-0.269-0.2690.0000.0000.0000.000
191A192ASN0-0.007-0.0116.586-0.099-0.0990.0000.0000.0000.000
192A193GLY00.0330.0302.554-0.2860.1770.695-0.457-0.7010.002
193A194THR0-0.020-0.0062.400-3.206-2.5842.100-0.923-1.799-0.021
194A195ILE0-0.034-0.0093.917-0.392-0.1430.003-0.049-0.2030.000
195A196ASN0-0.0070.0101.726-1.316-11.75324.061-7.974-5.650-0.046
196A197GLY00.0740.0124.4510.0480.196-0.001-0.061-0.0870.000
197A198GLY00.0050.0137.6770.2970.2970.0000.0000.0000.000
198A199PRO0-0.0160.00210.458-0.100-0.1000.0000.0000.0000.000
199A200LYS10.8350.90514.2440.0540.0540.0000.0000.0000.000
200A201ALA0-0.0110.00116.5270.0410.0410.0000.0000.0000.000
201A202THR00.0210.00419.567-0.009-0.0090.0000.0000.0000.000
202A203ALA00.0430.00321.9790.0060.0060.0000.0000.0000.000
203A204ALA00.0720.04123.0850.0040.0040.0000.0000.0000.000
204A205PHE0-0.0200.00017.0710.0060.0060.0000.0000.0000.000
205A206VAL00.027-0.00222.0320.0060.0060.0000.0000.0000.000
206A207GLU-1-0.922-0.95624.6130.0390.0390.0000.0000.0000.000
207A208PHE0-0.003-0.00222.5940.0050.0050.0000.0000.0000.000
208A209ILE0-0.012-0.01220.8590.0030.0030.0000.0000.0000.000
209A210ASN0-0.012-0.01524.850-0.005-0.0050.0000.0000.0000.000
210A211TYR00.0230.02527.7430.0010.0010.0000.0000.0000.000
211A212ALA00.0290.01225.5530.0000.0000.0000.0000.0000.000
212A213LYS10.9190.95925.4870.0010.0010.0000.0000.0000.000
213A214ALA0-0.0030.01128.714-0.004-0.0040.0000.0000.0000.000
214A215GLN0-0.071-0.00930.1530.0030.0030.0000.0000.0000.000