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: ZVKJN

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2440865.581316
FMO2-HF: Nuclear repulsion 2360183.340047
FMO2-HF: Total energy -80682.24127
FMO2-MP2: Total energy -80916.069542


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.
-19.265-12.25315.973-9.01-13.974-0.073
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 : -0.017 / 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].
3A3ILE0-0.061-0.0282.430-2.0630.9881.260-1.668-2.6430.001
4A4GLY00.0280.0164.9070.4240.527-0.001-0.009-0.0920.000
5A5ASP-1-0.936-0.9668.466-0.777-0.7770.0000.0000.0000.000
6A6ASP-1-0.796-0.8718.983-1.480-1.4800.0000.0000.0000.000
7A7GLY00.0430.0259.9030.2750.2750.0000.0000.0000.000
8A8ARG10.6600.7776.6431.6241.6240.0000.0000.0000.000
9A9THR00.0190.00111.2130.1440.1440.0000.0000.0000.000
10A10LYS10.8110.89814.5820.2000.2000.0000.0000.0000.000
11A11VAL00.006-0.00515.8530.0140.0140.0000.0000.0000.000
12A12ALA00.0240.01118.2220.0410.0410.0000.0000.0000.000
13A13ASN00.017-0.00421.8190.0380.0380.0000.0000.0000.000
14A14THR0-0.010-0.01019.462-0.014-0.0140.0000.0000.0000.000
15A15ARG10.9240.95722.2450.1090.1090.0000.0000.0000.000
16A16VAL0-0.023-0.00224.0620.0130.0130.0000.0000.0000.000
17A17ALA00.0170.03823.231-0.012-0.0120.0000.0000.0000.000
18A18PRO00.011-0.00218.878-0.006-0.0060.0000.0000.0000.000
19A19TYR0-0.011-0.02917.2160.0350.0350.0000.0000.0000.000
20A20ASN00.0450.02519.8170.0040.0040.0000.0000.0000.000
21A21SER0-0.034-0.00921.2690.0200.0200.0000.0000.0000.000
22A22ILE0-0.028-0.01015.0650.0120.0120.0000.0000.0000.000
23A23ALA00.0200.00517.602-0.002-0.0020.0000.0000.0000.000
24A24TYR00.0370.03514.4110.0200.0200.0000.0000.0000.000
25A25ILE0-0.030-0.02715.811-0.006-0.0060.0000.0000.0000.000
26A26THR00.021-0.00116.6840.0410.0410.0000.0000.0000.000
27A27PHE00.0420.00916.022-0.021-0.0210.0000.0000.0000.000
28A28GLY00.000-0.01020.4150.0060.0060.0000.0000.0000.000
29A29GLY00.0040.01019.957-0.012-0.0120.0000.0000.0000.000
30A30SER0-0.045-0.01514.8700.0450.0450.0000.0000.0000.000
31A31SER00.002-0.01014.396-0.048-0.0480.0000.0000.0000.000
32A32CYS0-0.149-0.04311.9370.2360.2360.0000.0000.0000.000
33A33THR00.0430.02811.127-0.130-0.1300.0000.0000.0000.000
34A34GLY00.0320.02113.2990.0670.0670.0000.0000.0000.000
35A35THR0-0.029-0.00915.740-0.061-0.0610.0000.0000.0000.000
36A36LEU00.0070.01018.2210.0270.0270.0000.0000.0000.000
37A37ILE00.0140.00220.903-0.022-0.0220.0000.0000.0000.000
38A38ALA0-0.008-0.01123.6700.0010.0010.0000.0000.0000.000
39A39PRO00.0200.01326.7510.0020.0020.0000.0000.0000.000
40A40ASN0-0.005-0.00827.9740.0040.0040.0000.0000.0000.000
41A41LYS10.8160.92124.826-0.016-0.0160.0000.0000.0000.000
42A42ILE00.0400.03018.805-0.023-0.0230.0000.0000.0000.000
43A43LEU0-0.0190.00417.1570.0190.0190.0000.0000.0000.000
44A44THR00.025-0.01614.330-0.006-0.0060.0000.0000.0000.000
45A45ASN0-0.008-0.03210.5010.0770.0770.0000.0000.0000.000
46A46GLY00.0520.02714.096-0.009-0.0090.0000.0000.0000.000
47A47HIS10.8150.8689.621-0.994-0.9940.0000.0000.0000.000
48A49VAL0-0.0090.01415.149-0.033-0.0330.0000.0000.0000.000
49A50TYR00.0040.00418.167-0.035-0.0350.0000.0000.0000.000
50A51ASN00.0150.01717.2800.0540.0540.0000.0000.0000.000
51A52THR00.0570.00717.090-0.027-0.0270.0000.0000.0000.000
52A53ALA0-0.0080.00917.886-0.037-0.0370.0000.0000.0000.000
53A54SER0-0.014-0.01819.813-0.031-0.0310.0000.0000.0000.000
54A55ARG10.9320.97221.844-0.294-0.2940.0000.0000.0000.000
55A56SER00.0130.02022.442-0.042-0.0420.0000.0000.0000.000
56A57TYR0-0.013-0.01721.9100.0350.0350.0000.0000.0000.000
57A58SER0-0.048-0.03618.3740.0140.0140.0000.0000.0000.000
58A59ALA00.0000.00021.464-0.030-0.0300.0000.0000.0000.000
59A60LYS10.8360.88722.798-0.119-0.1190.0000.0000.0000.000
60A61GLY00.0600.02223.0840.0010.0010.0000.0000.0000.000
61A62SER0-0.034-0.00922.463-0.013-0.0130.0000.0000.0000.000
62A63VAL0-0.016-0.00521.0000.0130.0130.0000.0000.0000.000
63A64TYR00.0380.00320.560-0.006-0.0060.0000.0000.0000.000
64A65PRO00.0150.00020.552-0.019-0.0190.0000.0000.0000.000
65A66GLY00.0440.02820.3060.0020.0020.0000.0000.0000.000
66A67MET0-0.0540.00619.5110.0020.0020.0000.0000.0000.000
67A68ASN00.0550.00618.991-0.044-0.0440.0000.0000.0000.000
68A69ASP-1-0.790-0.86420.368-0.128-0.1280.0000.0000.0000.000
69A70SER00.0290.00420.6560.0130.0130.0000.0000.0000.000
70A71THR00.0110.02322.0700.0200.0200.0000.0000.0000.000
71A72ALA00.0320.00923.641-0.014-0.0140.0000.0000.0000.000
72A73VAL0-0.046-0.02024.2520.0030.0030.0000.0000.0000.000
73A74ASN0-0.049-0.03524.030-0.001-0.0010.0000.0000.0000.000
74A75GLY00.0340.03427.1970.0040.0040.0000.0000.0000.000
75A76SER0-0.038-0.03925.568-0.003-0.0030.0000.0000.0000.000
76A77ALA0-0.0380.00125.544-0.002-0.0020.0000.0000.0000.000
77A78ASN00.012-0.01725.5690.0160.0160.0000.0000.0000.000
78A79MET0-0.0510.00719.752-0.003-0.0030.0000.0000.0000.000
79A80THR0-0.0040.00025.7400.0070.0070.0000.0000.0000.000
80A81GLU-1-0.851-0.91027.2760.1280.1280.0000.0000.0000.000
81A82PHE00.001-0.00522.178-0.001-0.0010.0000.0000.0000.000
82A83TYR00.0370.01023.648-0.009-0.0090.0000.0000.0000.000
83A84VAL00.0120.00220.2590.0020.0020.0000.0000.0000.000
84A85PRO00.0290.02820.568-0.009-0.0090.0000.0000.0000.000
85A86SER00.0590.00922.8640.0250.0250.0000.0000.0000.000
86A87GLY00.0250.02722.9240.0100.0100.0000.0000.0000.000
87A88TYR00.0000.01214.5180.0130.0130.0000.0000.0000.000
88A89ILE0-0.001-0.00220.3590.0360.0360.0000.0000.0000.000
89A90ASN0-0.005-0.00922.8180.0200.0200.0000.0000.0000.000
90A91THR0-0.037-0.03720.5080.0010.0010.0000.0000.0000.000
91A92GLY0-0.0110.00317.2190.0290.0290.0000.0000.0000.000
92A93ALA0-0.0120.00415.4340.0740.0740.0000.0000.0000.000
93A94SER00.063-0.00411.1590.0000.0000.0000.0000.0000.000
94A95GLN0-0.0040.00814.035-0.069-0.0690.0000.0000.0000.000
95A96TYR0-0.006-0.00516.891-0.042-0.0420.0000.0000.0000.000
96A97ASP-1-0.746-0.81512.2880.6640.6640.0000.0000.0000.000
97A98PHE0-0.068-0.03414.233-0.001-0.0010.0000.0000.0000.000
98A99ALA00.008-0.00116.7800.0110.0110.0000.0000.0000.000
99A100VAL0-0.030-0.01418.979-0.025-0.0250.0000.0000.0000.000
100A101ILE00.000-0.00219.0360.0190.0190.0000.0000.0000.000
101A102LYS10.8700.94022.976-0.065-0.0650.0000.0000.0000.000
102A103THR0-0.006-0.01425.0900.0110.0110.0000.0000.0000.000
103A104ASP-1-0.781-0.88227.4390.0390.0390.0000.0000.0000.000
104A105THR00.006-0.00129.807-0.008-0.0080.0000.0000.0000.000
105A106ASN0-0.0040.00829.5830.0010.0010.0000.0000.0000.000
106A107ILE00.0720.03526.075-0.008-0.0080.0000.0000.0000.000
107A108GLY00.0280.01726.785-0.011-0.0110.0000.0000.0000.000
108A109ASN0-0.035-0.03927.649-0.012-0.0120.0000.0000.0000.000
109A110THR0-0.046-0.00829.7260.0000.0000.0000.0000.0000.000
110A111VAL0-0.034-0.01724.581-0.006-0.0060.0000.0000.0000.000
111A112GLY00.0110.02326.328-0.016-0.0160.0000.0000.0000.000
112A113TYR0-0.044-0.04124.1350.0050.0050.0000.0000.0000.000
113A114ARG10.8440.91920.0060.1670.1670.0000.0000.0000.000
114A115SER00.001-0.00823.1980.0240.0240.0000.0000.0000.000
115A116ILE0-0.002-0.01521.174-0.017-0.0170.0000.0000.0000.000
116A117ARG10.8580.93721.6460.2370.2370.0000.0000.0000.000
117A118GLN00.0330.00722.326-0.007-0.0070.0000.0000.0000.000
118A119VAL0-0.047-0.02519.468-0.012-0.0120.0000.0000.0000.000
119A120THR0-0.0100.00322.5840.0110.0110.0000.0000.0000.000
120A121ASN0-0.005-0.01420.0780.0130.0130.0000.0000.0000.000
121A122LEU00.002-0.01316.032-0.004-0.0040.0000.0000.0000.000
122A123THR0-0.052-0.03916.544-0.051-0.0510.0000.0000.0000.000
123A124GLY00.0070.01216.9610.0400.0400.0000.0000.0000.000
124A125THR0-0.073-0.04817.8950.0100.0100.0000.0000.0000.000
125A126THR0-0.007-0.00716.720-0.078-0.0780.0000.0000.0000.000
126A127ILE0-0.045-0.02211.9410.0780.0780.0000.0000.0000.000
127A128LYS10.8010.87914.0470.4270.4270.0000.0000.0000.000
128A129ILE00.0150.0207.9670.0970.0970.0000.0000.0000.000
129A130SER00.006-0.03011.382-0.069-0.0690.0000.0000.0000.000
130A131GLY00.012-0.00111.2350.0760.0760.0000.0000.0000.000
131A132TYR0-0.037-0.02911.289-0.052-0.0520.0000.0000.0000.000
132A133PRO0-0.0130.0137.4530.1650.1650.0000.0000.0000.000
133A134GLY00.0640.0099.075-0.002-0.0020.0000.0000.0000.000
134A135ASP-1-0.802-0.8797.861-0.580-0.5800.0000.0000.0000.000
135A136LYS10.8930.9519.8430.8320.8320.0000.0000.0000.000
136A137MET0-0.0430.01912.1300.0450.0450.0000.0000.0000.000
137A138ARG10.9300.9629.454-0.132-0.1320.0000.0000.0000.000
138A139SER0-0.017-0.01113.565-0.010-0.0100.0000.0000.0000.000
139A140THR0-0.075-0.05315.292-0.023-0.0230.0000.0000.0000.000
140A141GLY00.0130.01817.8510.0000.0000.0000.0000.0000.000
141A142LYS10.8330.90918.3180.1210.1210.0000.0000.0000.000
142A143VAL00.0510.02816.247-0.020-0.0200.0000.0000.0000.000
143A144SER0-0.049-0.03815.776-0.010-0.0100.0000.0000.0000.000
144A145GLN00.0170.02214.639-0.052-0.0520.0000.0000.0000.000
145A146TRP0-0.016-0.02111.411-0.014-0.0140.0000.0000.0000.000
146A147GLU-1-0.784-0.85311.879-0.573-0.5730.0000.0000.0000.000
147A148MET00.0370.0519.492-0.190-0.1900.0000.0000.0000.000
148A149SER00.004-0.00711.9900.0690.0690.0000.0000.0000.000
149A150GLY00.0400.02212.803-0.065-0.0650.0000.0000.0000.000
150A151SER0-0.0100.00213.7770.0440.0440.0000.0000.0000.000
151A152VAL0-0.0170.00212.609-0.128-0.1280.0000.0000.0000.000
152A153THR00.010-0.00310.4850.0880.0880.0000.0000.0000.000
153A154ARG10.9290.97910.0700.3600.3600.0000.0000.0000.000
154A155GLU-1-0.707-0.81713.321-0.299-0.2990.0000.0000.0000.000
155A156ASP-1-0.770-0.84714.4160.0120.0120.0000.0000.0000.000
156A157THR00.0230.00317.043-0.018-0.0180.0000.0000.0000.000
157A158ASN0-0.062-0.02917.690-0.020-0.0200.0000.0000.0000.000
158A159LEU0-0.033-0.01111.6550.0070.0070.0000.0000.0000.000
159A160ALA00.0160.00112.738-0.014-0.0140.0000.0000.0000.000
160A161TYR0-0.038-0.0568.0650.0250.0250.0000.0000.0000.000
161A162TYR00.033-0.0206.4900.3060.3060.0000.0000.0000.000
162A163THR00.0350.0095.985-0.300-0.3000.0000.0000.0000.000
163A164ILE0-0.0070.0156.773-0.228-0.2280.0000.0000.0000.000
164A165ASP-1-0.739-0.8724.969-4.206-4.2060.0000.0000.0000.000
165A166THR0-0.083-0.0572.474-0.7321.2131.358-1.417-1.886-0.012
166A167PHE00.0240.0122.527-3.377-2.0001.032-1.090-1.320-0.017
167A168SER00.0370.0184.114-0.0310.046-0.001-0.003-0.0730.000
168A169GLY00.0730.0386.930-0.452-0.4520.0000.0000.0000.000
169A170ASN0-0.007-0.0075.654-0.407-0.4070.0000.0000.0000.000
170A171SER00.0060.0267.6540.0140.0140.0000.0000.0000.000
171A172GLY00.0600.0349.007-0.059-0.0590.0000.0000.0000.000
172A173SER0-0.043-0.0419.156-0.079-0.0790.0000.0000.0000.000
173A174ALA0-0.013-0.00211.235-0.037-0.0370.0000.0000.0000.000
174A175MET0-0.0360.00310.634-0.104-0.1040.0000.0000.0000.000
175A176LEU0-0.027-0.00813.9680.0940.0940.0000.0000.0000.000
176A177ASP-1-0.696-0.84016.961-0.311-0.3110.0000.0000.0000.000
177A178GLN00.010-0.00419.386-0.006-0.0060.0000.0000.0000.000
178A179ASN0-0.068-0.03421.9050.0240.0240.0000.0000.0000.000
179A180GLN0-0.032-0.02020.8640.0350.0350.0000.0000.0000.000
180A181GLN00.0330.02621.8860.0390.0390.0000.0000.0000.000
181A182ILE0-0.025-0.01217.079-0.034-0.0340.0000.0000.0000.000
182A183VAL00.0170.00316.5650.0310.0310.0000.0000.0000.000
183A184GLY00.0850.02915.0900.0130.0130.0000.0000.0000.000
184A185VAL0-0.072-0.02512.062-0.029-0.0290.0000.0000.0000.000
185A186HIS00.0560.0604.088-0.289-0.151-0.001-0.012-0.1240.000
186A187ASN0-0.061-0.0468.1140.0650.0650.0000.0000.0000.000
187A188ALA0-0.0040.0075.5930.5020.5020.0000.0000.0000.000
188A189GLY00.0690.0412.458-2.042-1.3691.007-0.801-0.8790.004
189A190TYR0-0.032-0.0403.1710.5590.2210.0060.697-0.365-0.001
190A191SER00.013-0.0074.926-0.244-0.173-0.0010.000-0.0700.000
191A192ASN0-0.011-0.0036.676-0.142-0.1420.0000.0000.0000.000
192A193GLY00.0210.0262.5300.0790.3480.986-0.463-0.7920.001
193A194THR0-0.026-0.0242.683-2.218-1.6750.946-0.263-1.226-0.014
194A195ILE0-0.051-0.0133.811-0.336-0.1320.001-0.039-0.1670.000
195A196ASN0-0.030-0.0221.948-4.481-5.6649.382-3.922-4.277-0.035
196A197GLY00.0670.0174.6520.3040.386-0.001-0.020-0.0600.000
197A198GLY00.0120.0227.6910.2360.2360.0000.0000.0000.000
198A199PRO0-0.018-0.00210.518-0.072-0.0720.0000.0000.0000.000
199A200LYS10.8140.88414.3710.0980.0980.0000.0000.0000.000
200A201ALA0-0.009-0.00216.7520.0450.0450.0000.0000.0000.000
201A202THR00.0170.00219.737-0.003-0.0030.0000.0000.0000.000
202A203ALA00.0230.00522.1460.0040.0040.0000.0000.0000.000
203A204ALA00.0910.04723.4000.0030.0030.0000.0000.0000.000
204A205PHE0-0.037-0.00617.0270.0070.0070.0000.0000.0000.000
205A206VAL00.028-0.00222.1150.0050.0050.0000.0000.0000.000
206A207GLU-1-0.925-0.95924.7570.0150.0150.0000.0000.0000.000
207A208PHE00.0180.00522.9000.0050.0050.0000.0000.0000.000
208A209ILE00.014-0.00320.5270.0050.0050.0000.0000.0000.000
209A210ASN0-0.001-0.00624.627-0.004-0.0040.0000.0000.0000.000
210A211TYR00.0180.01927.4810.0030.0030.0000.0000.0000.000
211A212ALA00.0400.01625.2520.0020.0020.0000.0000.0000.000
212A213LYS10.8500.92825.2530.0470.0470.0000.0000.0000.000
213A214ALA00.0220.02528.403-0.001-0.0010.0000.0000.0000.000
214A215GLN0-0.073-0.01429.7110.0060.0060.0000.0000.0000.000