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: 6YKMZ

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2433838.535323
FMO2-HF: Nuclear repulsion 2353156.189834
FMO2-HF: Total energy -80682.34549
FMO2-MP2: Total energy -80915.98017


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.
-17.253-17.50829.759-12.926-16.576-0.088
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 : -0.057 / q_NPA : -0.042
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].
3A3ILE0-0.044-0.0202.417-2.0681.1440.929-1.512-2.6280.004
4A4GLY00.0070.0114.9360.2810.372-0.001-0.009-0.0820.000
5A5ASP-1-0.930-0.9608.459-0.828-0.8280.0000.0000.0000.000
6A6ASP-1-0.789-0.8598.884-1.592-1.5920.0000.0000.0000.000
7A7GLY00.0340.0059.7030.2870.2870.0000.0000.0000.000
8A8ARG10.6580.7766.6401.6141.6140.0000.0000.0000.000
9A9THR00.0130.00511.0480.1160.1160.0000.0000.0000.000
10A10LYS10.7930.88614.3120.1820.1820.0000.0000.0000.000
11A11VAL00.002-0.00315.5750.0120.0120.0000.0000.0000.000
12A12ALA00.0200.01118.0030.0340.0340.0000.0000.0000.000
13A13ASN00.024-0.00421.6900.0340.0340.0000.0000.0000.000
14A14THR0-0.026-0.01619.397-0.014-0.0140.0000.0000.0000.000
15A15ARG10.9630.98322.1480.0840.0840.0000.0000.0000.000
16A16VAL0-0.018-0.00123.8640.0110.0110.0000.0000.0000.000
17A17ALA00.0040.03823.166-0.009-0.0090.0000.0000.0000.000
18A18PRO0-0.001-0.01918.836-0.008-0.0080.0000.0000.0000.000
19A19TYR0-0.017-0.05016.8500.0320.0320.0000.0000.0000.000
20A20ASN00.0170.01019.6800.0060.0060.0000.0000.0000.000
21A21SER0-0.032-0.00520.8020.0200.0200.0000.0000.0000.000
22A22ILE0-0.032-0.00914.7620.0230.0230.0000.0000.0000.000
23A23ALA00.0170.00317.328-0.007-0.0070.0000.0000.0000.000
24A24TYR00.0290.02214.8730.0030.0030.0000.0000.0000.000
25A25ILE0-0.034-0.02615.790-0.013-0.0130.0000.0000.0000.000
26A26THR00.0330.00816.7050.0470.0470.0000.0000.0000.000
27A27PHE00.0270.00516.005-0.021-0.0210.0000.0000.0000.000
28A28GLY0-0.008-0.00620.417-0.006-0.0060.0000.0000.0000.000
29A29GLY00.0200.01219.840-0.018-0.0180.0000.0000.0000.000
30A30SER0-0.034-0.01014.8380.0410.0410.0000.0000.0000.000
31A31SER00.0340.01213.453-0.089-0.0890.0000.0000.0000.000
32A32CYS0-0.189-0.06111.9340.2410.2410.0000.0000.0000.000
33A33THR00.0430.02411.174-0.142-0.1420.0000.0000.0000.000
34A34GLY00.0450.02913.2320.0610.0610.0000.0000.0000.000
35A35THR0-0.033-0.00715.869-0.064-0.0640.0000.0000.0000.000
36A36LEU00.0030.01318.2250.0240.0240.0000.0000.0000.000
37A37ILE00.000-0.01120.834-0.020-0.0200.0000.0000.0000.000
38A38ALA0-0.014-0.01623.5760.0000.0000.0000.0000.0000.000
39A39PRO00.0280.01726.6560.0010.0010.0000.0000.0000.000
40A40ASN00.0000.00527.8290.0030.0030.0000.0000.0000.000
41A41LYS10.8320.92524.807-0.048-0.0480.0000.0000.0000.000
42A42ILE00.0110.01618.928-0.020-0.0200.0000.0000.0000.000
43A43LEU0-0.0100.00716.9520.0200.0200.0000.0000.0000.000
44A44THR00.036-0.01514.4290.0110.0110.0000.0000.0000.000
45A45ASN00.009-0.02110.7780.1220.1220.0000.0000.0000.000
46A46GLY00.0430.02514.430-0.015-0.0150.0000.0000.0000.000
47A47HIS10.8060.86710.004-1.136-1.1360.0000.0000.0000.000
48A49VAL00.0020.01815.420-0.038-0.0380.0000.0000.0000.000
49A50TYR00.0290.01118.341-0.044-0.0440.0000.0000.0000.000
50A51ASN00.0040.01317.3370.0610.0610.0000.0000.0000.000
51A52THR00.0510.00316.731-0.030-0.0300.0000.0000.0000.000
52A53ALA0-0.0010.01517.493-0.038-0.0380.0000.0000.0000.000
53A54SER0-0.001-0.01319.407-0.033-0.0330.0000.0000.0000.000
54A55ARG10.9260.96821.641-0.291-0.2910.0000.0000.0000.000
55A56SER00.0220.02622.198-0.041-0.0410.0000.0000.0000.000
56A57TYR0-0.023-0.01621.7430.0380.0380.0000.0000.0000.000
57A58SER0-0.053-0.03318.8350.0030.0030.0000.0000.0000.000
58A59ALA00.0140.00421.997-0.028-0.0280.0000.0000.0000.000
59A60LYS10.8270.88922.848-0.142-0.1420.0000.0000.0000.000
60A61GLY00.0630.02222.934-0.003-0.0030.0000.0000.0000.000
61A62SER0-0.022-0.00422.471-0.015-0.0150.0000.0000.0000.000
62A63VAL0-0.018-0.01020.9090.0180.0180.0000.0000.0000.000
63A64TYR00.0440.00320.594-0.011-0.0110.0000.0000.0000.000
64A65PRO00.0180.00520.304-0.011-0.0110.0000.0000.0000.000
65A66GLY00.0300.01919.884-0.003-0.0030.0000.0000.0000.000
66A67MET0-0.0460.00919.255-0.001-0.0010.0000.0000.0000.000
67A68ASN00.0580.01418.778-0.037-0.0370.0000.0000.0000.000
68A69ASP-1-0.787-0.86120.006-0.115-0.1150.0000.0000.0000.000
69A70SER00.0280.00520.5320.0100.0100.0000.0000.0000.000
70A71THR00.0000.01721.9900.0170.0170.0000.0000.0000.000
71A72ALA00.0050.00123.668-0.011-0.0110.0000.0000.0000.000
72A73VAL0-0.018-0.02024.5120.0030.0030.0000.0000.0000.000
73A74ASN0-0.060-0.03923.669-0.005-0.0050.0000.0000.0000.000
74A75GLY00.0210.02926.9050.0050.0050.0000.0000.0000.000
75A76SER00.000-0.02325.603-0.001-0.0010.0000.0000.0000.000
76A77ALA0-0.055-0.00825.650-0.005-0.0050.0000.0000.0000.000
77A78ASN00.002-0.01825.7010.0170.0170.0000.0000.0000.000
78A79MET0-0.0460.00619.858-0.003-0.0030.0000.0000.0000.000
79A80THR00.0130.00025.8400.0020.0020.0000.0000.0000.000
80A81GLU-1-0.878-0.92427.2790.1400.1400.0000.0000.0000.000
81A82PHE0-0.012-0.00822.4910.0040.0040.0000.0000.0000.000
82A83TYR00.0290.01223.967-0.012-0.0120.0000.0000.0000.000
83A84VAL00.010-0.00420.8310.0100.0100.0000.0000.0000.000
84A85PRO00.0260.02620.892-0.015-0.0150.0000.0000.0000.000
85A86SER00.0650.01223.2730.0230.0230.0000.0000.0000.000
86A87GLY00.0290.02523.0960.0100.0100.0000.0000.0000.000
87A88TYR00.0070.01114.6400.0170.0170.0000.0000.0000.000
88A89ILE0-0.0060.00220.3490.0330.0330.0000.0000.0000.000
89A90ASN0-0.031-0.02222.7290.0160.0160.0000.0000.0000.000
90A91THR0-0.028-0.03120.4450.0020.0020.0000.0000.0000.000
91A92GLY00.0070.01317.5410.0230.0230.0000.0000.0000.000
92A93ALA0-0.052-0.01215.5170.0780.0780.0000.0000.0000.000
93A94SER00.0770.00311.1200.0110.0110.0000.0000.0000.000
94A95GLN0-0.0180.00014.038-0.057-0.0570.0000.0000.0000.000
95A96TYR0-0.019-0.01316.816-0.043-0.0430.0000.0000.0000.000
96A97ASP-1-0.732-0.81712.4230.7570.7570.0000.0000.0000.000
97A98PHE0-0.057-0.03514.5920.0050.0050.0000.0000.0000.000
98A99ALA00.0110.00417.1270.0040.0040.0000.0000.0000.000
99A100VAL0-0.032-0.01019.290-0.019-0.0190.0000.0000.0000.000
100A101ILE0-0.008-0.00419.3180.0130.0130.0000.0000.0000.000
101A102LYS10.8960.94623.197-0.090-0.0900.0000.0000.0000.000
102A103THR0-0.005-0.01624.9360.0110.0110.0000.0000.0000.000
103A104ASP-1-0.805-0.89727.4490.0610.0610.0000.0000.0000.000
104A105THR00.0070.01229.983-0.009-0.0090.0000.0000.0000.000
105A106ASN0-0.003-0.01029.6930.0060.0060.0000.0000.0000.000
106A107ILE00.0650.03225.997-0.008-0.0080.0000.0000.0000.000
107A108GLY00.0210.00526.881-0.010-0.0100.0000.0000.0000.000
108A109ASN0-0.039-0.03627.706-0.010-0.0100.0000.0000.0000.000
109A110THR0-0.0320.00430.006-0.003-0.0030.0000.0000.0000.000
110A111VAL0-0.023-0.01124.712-0.007-0.0070.0000.0000.0000.000
111A112GLY00.0100.01826.540-0.015-0.0150.0000.0000.0000.000
112A113TYR0-0.059-0.05023.9350.0070.0070.0000.0000.0000.000
113A114ARG10.8720.94719.9180.1140.1140.0000.0000.0000.000
114A115SER00.003-0.00123.1240.0230.0230.0000.0000.0000.000
115A116ILE00.000-0.00621.005-0.013-0.0130.0000.0000.0000.000
116A117ARG10.8630.92821.5470.1710.1710.0000.0000.0000.000
117A118GLN00.0320.00922.1350.0000.0000.0000.0000.0000.000
118A119VAL0-0.048-0.02419.198-0.013-0.0130.0000.0000.0000.000
119A120THR0-0.011-0.00122.6670.0130.0130.0000.0000.0000.000
120A121ASN0-0.006-0.01820.1250.0160.0160.0000.0000.0000.000
121A122LEU00.002-0.01415.885-0.004-0.0040.0000.0000.0000.000
122A123THR0-0.047-0.04416.542-0.053-0.0530.0000.0000.0000.000
123A124GLY0-0.006-0.00216.9270.0330.0330.0000.0000.0000.000
124A125THR0-0.069-0.02817.5720.0160.0160.0000.0000.0000.000
125A126THR0-0.024-0.01616.405-0.068-0.0680.0000.0000.0000.000
126A127ILE0-0.029-0.01811.3740.0700.0700.0000.0000.0000.000
127A128LYS10.8270.90213.4480.3360.3360.0000.0000.0000.000
128A129ILE00.0140.0147.6600.1160.1160.0000.0000.0000.000
129A130SER0-0.004-0.02910.777-0.118-0.1180.0000.0000.0000.000
130A131GLY00.004-0.00410.8990.0920.0920.0000.0000.0000.000
131A132TYR0-0.041-0.03411.198-0.077-0.0770.0000.0000.0000.000
132A133PRO0-0.0280.0077.3140.1700.1700.0000.0000.0000.000
133A134GLY00.0680.0038.903-0.036-0.0360.0000.0000.0000.000
134A135ASP-1-0.823-0.8897.661-0.645-0.6450.0000.0000.0000.000
135A136LYS10.9000.9439.6550.7500.7500.0000.0000.0000.000
136A137MET0-0.0410.01012.2000.0370.0370.0000.0000.0000.000
137A138ARG10.9410.9819.468-0.124-0.1240.0000.0000.0000.000
138A139SER0-0.022-0.01713.571-0.019-0.0190.0000.0000.0000.000
139A140THR0-0.072-0.05215.318-0.008-0.0080.0000.0000.0000.000
140A141GLY00.0300.02617.4370.0020.0020.0000.0000.0000.000
141A142LYS10.8290.91018.1170.1100.1100.0000.0000.0000.000
142A143VAL00.0340.01716.155-0.015-0.0150.0000.0000.0000.000
143A144SER0-0.029-0.02315.785-0.005-0.0050.0000.0000.0000.000
144A145GLN00.0120.01814.271-0.039-0.0390.0000.0000.0000.000
145A146TRP0-0.002-0.00710.998-0.024-0.0240.0000.0000.0000.000
146A147GLU-1-0.753-0.84411.554-0.468-0.4680.0000.0000.0000.000
147A148MET00.0490.0619.286-0.154-0.1540.0000.0000.0000.000
148A149SER0-0.013-0.01211.6080.0620.0620.0000.0000.0000.000
149A150GLY00.0330.01812.271-0.098-0.0980.0000.0000.0000.000
150A151SER00.0060.00813.3320.0780.0780.0000.0000.0000.000
151A152VAL0-0.0200.00012.335-0.121-0.1210.0000.0000.0000.000
152A153THR00.003-0.00210.5760.0790.0790.0000.0000.0000.000
153A154ARG10.9410.9829.7820.3040.3040.0000.0000.0000.000
154A155GLU-1-0.708-0.81013.351-0.218-0.2180.0000.0000.0000.000
155A156ASP-1-0.781-0.85414.4560.0600.0600.0000.0000.0000.000
156A157THR00.014-0.01317.044-0.014-0.0140.0000.0000.0000.000
157A158ASN0-0.047-0.02117.336-0.015-0.0150.0000.0000.0000.000
158A159LEU0-0.0200.00111.6930.0180.0180.0000.0000.0000.000
159A160ALA00.0210.00712.668-0.034-0.0340.0000.0000.0000.000
160A161TYR0-0.054-0.0648.1080.0550.0550.0000.0000.0000.000
161A162TYR00.036-0.0246.2040.1870.1870.0000.0000.0000.000
162A163THR00.0380.0075.727-0.211-0.2110.0000.0000.0000.000
163A164ILE0-0.0180.0096.424-0.318-0.3180.0000.0000.0000.000
164A165ASP-1-0.734-0.8684.587-4.384-4.252-0.001-0.031-0.1000.000
165A166THR0-0.082-0.0542.2770.6092.0362.604-1.694-2.337-0.013
166A167PHE00.0350.0162.183-3.285-3.5693.971-1.451-2.236-0.025
167A168SER00.0280.0194.161-0.194-0.106-0.001-0.014-0.0720.000
168A169GLY00.0740.0406.926-0.475-0.4750.0000.0000.0000.000
169A170ASN00.0170.0055.572-0.499-0.4990.0000.0000.0000.000
170A171SER0-0.0240.0097.737-0.045-0.0450.0000.0000.0000.000
171A172GLY00.0620.0339.011-0.105-0.1050.0000.0000.0000.000
172A173SER0-0.025-0.0409.326-0.120-0.1200.0000.0000.0000.000
173A174ALA0-0.017-0.00211.2640.0020.0020.0000.0000.0000.000
174A175MET0-0.0320.00110.616-0.116-0.1160.0000.0000.0000.000
175A176LEU0-0.043-0.01813.6540.0740.0740.0000.0000.0000.000
176A177ASP-1-0.700-0.84616.616-0.251-0.2510.0000.0000.0000.000
177A178GLN00.016-0.00219.116-0.002-0.0020.0000.0000.0000.000
178A179ASN0-0.054-0.02221.6140.0130.0130.0000.0000.0000.000
179A180GLN0-0.025-0.01620.4590.0330.0330.0000.0000.0000.000
180A181GLN00.0290.02021.5050.0370.0370.0000.0000.0000.000
181A182ILE0-0.015-0.01216.954-0.029-0.0290.0000.0000.0000.000
182A183VAL00.0130.00016.2480.0250.0250.0000.0000.0000.000
183A184GLY00.0820.02614.9310.0070.0070.0000.0000.0000.000
184A185VAL0-0.080-0.02312.117-0.033-0.0330.0000.0000.0000.000
185A186HIS00.0590.0604.106-0.644-0.500-0.001-0.015-0.1280.000
186A187ASN0-0.045-0.0448.1990.0530.0530.0000.0000.0000.000
187A188ALA0-0.0160.0055.8130.4150.4150.0000.0000.0000.000
188A189GLY00.0610.0382.803-1.154-0.4970.361-0.400-0.6180.002
189A190TYR0-0.028-0.0393.479-0.337-0.2540.0090.188-0.2800.000
190A191SER00.011-0.0095.059-0.290-0.228-0.0010.000-0.0610.000
191A192ASN0-0.019-0.0136.661-0.125-0.1250.0000.0000.0000.000
192A193GLY00.0300.0292.598-0.1580.1590.774-0.348-0.7420.002
193A194THR0-0.021-0.0132.461-2.552-2.1521.910-0.683-1.628-0.019
194A195ILE0-0.044-0.0093.774-0.459-0.1940.004-0.058-0.2100.000
195A196ASN0-0.0140.0071.804-1.018-8.00019.203-6.845-5.376-0.039
196A197GLY00.0660.0084.4770.0160.149-0.001-0.054-0.0780.000
197A198GLY00.0050.0117.6610.2990.2990.0000.0000.0000.000
198A199PRO0-0.0180.00110.442-0.100-0.1000.0000.0000.0000.000
199A200LYS10.8320.90214.2270.0480.0480.0000.0000.0000.000
200A201ALA0-0.016-0.00116.5110.0410.0410.0000.0000.0000.000
201A202THR00.0160.00219.550-0.010-0.0100.0000.0000.0000.000
202A203ALA00.0400.00321.9630.0060.0060.0000.0000.0000.000
203A204ALA00.0710.04423.1040.0040.0040.0000.0000.0000.000
204A205PHE0-0.026-0.00617.2390.0050.0050.0000.0000.0000.000
205A206VAL00.023-0.00722.0140.0050.0050.0000.0000.0000.000
206A207GLU-1-0.929-0.95224.5950.0450.0450.0000.0000.0000.000
207A208PHE00.0130.00222.7270.0050.0050.0000.0000.0000.000
208A209ILE00.000-0.01220.7690.0030.0030.0000.0000.0000.000
209A210ASN0-0.014-0.01324.855-0.005-0.0050.0000.0000.0000.000
210A211TYR00.0260.02827.6630.0010.0010.0000.0000.0000.000
211A212ALA00.0280.01225.569-0.001-0.0010.0000.0000.0000.000
212A213LYS10.9010.94925.2490.0000.0000.0000.0000.0000.000
213A214ALA0-0.0030.01328.717-0.004-0.0040.0000.0000.0000.000
214A215GLN0-0.0510.01030.1210.0030.0030.0000.0000.0000.000