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: 399ZL

Calculation Name: 4PH0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PH0

Chain ID: A

ChEMBL ID:

UniProt ID: A7KWZ1

Base Structure: X-ray

Registration Date: 2023-06-21

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2087933.84379
FMO2-HF: Nuclear repulsion 2009112.067776
FMO2-HF: Total energy -78821.776014
FMO2-MP2: Total energy -79054.051929


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:PRO)


Summations of interaction energy for fragment #1(A:1:PRO)
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.
-26.144-9.08418.443-12.206-23.297-0.071
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.026
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].
3A3ILE0-0.0100.0003.477-0.5161.1290.011-0.676-0.9800.002
4A4SER00.0170.0116.1150.1430.1430.0000.0000.0000.000
5A5GLU-1-0.847-0.8819.925-0.617-0.6170.0000.0000.0000.000
6A6GLY00.0310.00312.1490.0460.0460.0000.0000.0000.000
7A7ASN0-0.056-0.01714.8990.0080.0080.0000.0000.0000.000
8A8ARG10.9310.95813.9630.1790.1790.0000.0000.0000.000
9A9ASN00.0490.0228.507-0.063-0.0630.0000.0000.0000.000
10A10ARG10.7870.8567.9370.8060.8060.0000.0000.0000.000
11A11HIS0-0.030-0.0322.831-4.334-3.1000.292-0.504-1.0220.000
12A12ARG10.7860.8552.3350.5223.3521.225-1.115-2.941-0.002
13A13ALA00.0500.0272.203-7.165-6.2664.555-2.595-2.859-0.031
14A14TRP0-0.004-0.0112.872-5.925-1.7963.466-1.619-5.976-0.018
15A15ALA00.0210.0143.5860.5870.5730.0110.089-0.0870.000
16A16LEU00.007-0.0086.4800.1500.1500.0000.0000.0000.000
17A17ARG10.8650.9089.3030.2850.2850.0000.0000.0000.000
18A18GLU-1-0.724-0.8234.249-1.406-1.0920.002-0.065-0.2500.000
19A19LEU00.0230.0205.8800.1470.1470.0000.0000.0000.000
20A20GLN00.0110.0068.7020.1060.1060.0000.0000.0000.000
21A21ASP-1-0.797-0.88410.919-0.074-0.0740.0000.0000.0000.000
22A22ILE00.0290.0166.7410.0500.0500.0000.0000.0000.000
23A23LYS10.8710.92211.1360.0100.0100.0000.0000.0000.000
24A24LYS10.8420.92213.7620.0300.0300.0000.0000.0000.000
25A25GLU-1-0.902-0.93914.2790.0550.0550.0000.0000.0000.000
26A26ILE00.006-0.00613.8210.0060.0060.0000.0000.0000.000
27A27GLU-1-0.905-0.93116.5500.0230.0230.0000.0000.0000.000
28A28ASN0-0.014-0.00519.0460.0030.0030.0000.0000.0000.000
29A29LYS10.7930.90118.597-0.092-0.0920.0000.0000.0000.000
30A30ALA00.0500.02820.6730.0050.0050.0000.0000.0000.000
31A31PRO00.0750.02919.3570.0160.0160.0000.0000.0000.000
32A32GLY0-0.0060.00318.984-0.011-0.0110.0000.0000.0000.000
33A33SER0-0.005-0.01320.415-0.005-0.0050.0000.0000.0000.000
34A34GLN00.0220.00720.1040.0310.0310.0000.0000.0000.000
35A35VAL00.0590.02819.5830.0190.0190.0000.0000.0000.000
36A36TRP00.0130.02515.7970.0040.0040.0000.0000.0000.000
37A37ILE00.008-0.00515.5290.0360.0360.0000.0000.0000.000
38A38GLN0-0.031-0.02715.0030.0390.0390.0000.0000.0000.000
39A39THR0-0.003-0.00613.2820.0030.0030.0000.0000.0000.000
40A40LEU0-0.003-0.00210.4190.0240.0240.0000.0000.0000.000
41A41ARG10.8400.91210.297-0.296-0.2960.0000.0000.0000.000
42A42LEU0-0.0010.00411.7590.0370.0370.0000.0000.0000.000
43A43ALA00.0290.0097.9760.0040.0040.0000.0000.0000.000
44A44ILE0-0.034-0.0166.5460.0910.0910.0000.0000.0000.000
45A45LEU0-0.013-0.0106.3930.1580.1580.0000.0000.0000.000
46A46GLN0-0.050-0.0176.258-0.071-0.0710.0000.0000.0000.000
47A47ALA0-0.012-0.0092.334-1.125-0.6891.550-0.497-1.489-0.002
48A48ASP-1-0.763-0.8392.429-0.8920.5523.113-2.250-2.307-0.028
49A49PRO0-0.0020.0092.175-1.9570.0642.749-2.350-2.4190.006
50A50THR00.021-0.0283.080-5.219-5.1420.0580.536-0.6710.003
51A51PRO00.010-0.0125.747-0.0150.071-0.001-0.001-0.0840.000
52A52ALA00.0500.0327.225-0.256-0.2560.0000.0000.0000.000
53A53ASP-1-0.817-0.8602.6823.8385.6761.413-1.149-2.102-0.001
54A54LEU00.0380.0044.686-1.200-1.079-0.001-0.010-0.1100.000
55A55GLU-1-0.907-0.9446.9300.1020.1020.0000.0000.0000.000
56A56GLN00.001-0.0134.857-0.738-0.7380.0000.0000.0000.000
57A57LEU0-0.023-0.0015.908-0.253-0.2530.0000.0000.0000.000
58A58CYS0-0.078-0.0308.794-0.152-0.1520.0000.0000.0000.000
59A59GLN0-0.047-0.03711.642-0.149-0.1490.0000.0000.0000.000
60A60TYR0-0.036-0.01210.899-0.093-0.0930.0000.0000.0000.000
61A61ILE0-0.047-0.02011.382-0.039-0.0390.0000.0000.0000.000
62A62ALA0-0.0030.00914.334-0.010-0.0100.0000.0000.0000.000
63A63SER00.008-0.01116.994-0.013-0.0130.0000.0000.0000.000
64A64PRO00.0820.01919.4580.0240.0240.0000.0000.0000.000
65A65VAL00.0110.02620.5510.0150.0150.0000.0000.0000.000
66A66ASP-1-0.795-0.86919.4720.1910.1910.0000.0000.0000.000
67A67GLN0-0.053-0.03415.6030.0390.0390.0000.0000.0000.000
68A68THR00.0110.00217.7260.0370.0370.0000.0000.0000.000
69A69ALA00.0000.01020.5010.0120.0120.0000.0000.0000.000
70A70HIS10.8580.93013.238-0.527-0.5270.0000.0000.0000.000
71A71MET00.0210.01315.2040.0460.0460.0000.0000.0000.000
72A72THR0-0.015-0.01517.833-0.001-0.0010.0000.0000.0000.000
73A73SER0-0.036-0.01620.212-0.009-0.0090.0000.0000.0000.000
74A74LEU00.0030.00213.8520.0030.0030.0000.0000.0000.000
75A75THR0-0.027-0.03118.339-0.006-0.0060.0000.0000.0000.000
76A76ALA00.0090.01320.067-0.015-0.0150.0000.0000.0000.000
77A77ALA00.000-0.00519.869-0.015-0.0150.0000.0000.0000.000
78A78ILE0-0.032-0.01416.198-0.001-0.0010.0000.0000.0000.000
79A79ALA00.0470.02920.529-0.019-0.0190.0000.0000.0000.000
80A80ALA0-0.012-0.00524.091-0.022-0.0220.0000.0000.0000.000
81A81ALA0-0.0030.00021.483-0.018-0.0180.0000.0000.0000.000
82A82GLU-1-0.925-0.97822.1010.2780.2780.0000.0000.0000.000
83A83ALA0-0.026-0.00724.637-0.019-0.0190.0000.0000.0000.000
84A84ALA0-0.050-0.02926.529-0.015-0.0150.0000.0000.0000.000
85A85ASN0-0.070-0.03726.205-0.010-0.0100.0000.0000.0000.000
86A86THR0-0.014-0.00523.7580.0000.0000.0000.0000.0000.000
87A87LEU0-0.038-0.00918.6950.0190.0190.0000.0000.0000.000
88A88GLN00.0400.02120.326-0.022-0.0220.0000.0000.0000.000
89A89GLY00.0380.01519.6960.0290.0290.0000.0000.0000.000
90A90PHE0-0.057-0.02118.6700.0130.0130.0000.0000.0000.000
91A91ASN00.031-0.00320.806-0.027-0.0270.0000.0000.0000.000
92A92PRO00.0450.02221.7240.0110.0110.0000.0000.0000.000
93A93GLN0-0.0240.00823.0670.0000.0000.0000.0000.0000.000
94A94ASN0-0.070-0.03019.161-0.030-0.0300.0000.0000.0000.000
95A95GLY0-0.026-0.00118.8120.0260.0260.0000.0000.0000.000
96A96THR00.041-0.01817.7400.0310.0310.0000.0000.0000.000
97A97LEU00.0600.03215.0480.0410.0410.0000.0000.0000.000
98A98THR00.0150.00112.9020.1070.1070.0000.0000.0000.000
99A99GLN00.0320.04812.3790.1250.1250.0000.0000.0000.000
100A100GLN00.0300.01912.9640.0040.0040.0000.0000.0000.000
101A101SER00.011-0.00610.452-0.049-0.0490.0000.0000.0000.000
102A102ALA00.0070.0038.3620.3130.3130.0000.0000.0000.000
103A103GLN00.0120.0218.453-0.136-0.1360.0000.0000.0000.000
104A104PRO00.0680.0277.8420.1210.1210.0000.0000.0000.000
105A105ASN00.004-0.0078.879-0.058-0.0580.0000.0000.0000.000
106A106ALA0-0.0140.01611.333-0.018-0.0180.0000.0000.0000.000
107A107GLY00.0650.0279.9500.1090.1090.0000.0000.0000.000
108A108ASP-1-0.857-0.91711.0120.3850.3850.0000.0000.0000.000
109A109LEU0-0.027-0.01313.8530.0220.0220.0000.0000.0000.000
110A110ARG10.7720.8455.918-1.137-1.1370.0000.0000.0000.000
111A111SER00.0060.00310.4620.1000.1000.0000.0000.0000.000
112A112GLN0-0.062-0.03311.766-0.039-0.0390.0000.0000.0000.000
113A113TYR00.003-0.00710.9270.0230.0230.0000.0000.0000.000
114A114GLN0-0.012-0.0266.318-0.367-0.3670.0000.0000.0000.000
115A115ASN0-0.013-0.01011.072-0.137-0.1370.0000.0000.0000.000
116A116LEU00.0190.01314.616-0.057-0.0570.0000.0000.0000.000
117A117TRP00.0270.00810.191-0.050-0.0500.0000.0000.0000.000
118A118LEU0-0.032-0.00712.045-0.066-0.0660.0000.0000.0000.000
119A119GLN00.0180.00114.692-0.039-0.0390.0000.0000.0000.000
120A120ALA00.0270.02416.897-0.041-0.0410.0000.0000.0000.000
121A121TRP0-0.041-0.03012.789-0.065-0.0650.0000.0000.0000.000
122A122LYS10.8710.93418.528-0.246-0.2460.0000.0000.0000.000
123A123ASN0-0.032-0.01221.809-0.003-0.0030.0000.0000.0000.000
124A124LEU0-0.0200.01319.312-0.010-0.0100.0000.0000.0000.000
125A125PRO00.012-0.00223.390-0.010-0.0100.0000.0000.0000.000
126A126THR0-0.007-0.02122.923-0.009-0.0090.0000.0000.0000.000
127A127ARG10.8720.92723.144-0.188-0.1880.0000.0000.0000.000
128A128PRO0-0.025-0.01325.027-0.008-0.0080.0000.0000.0000.000
129A129SER00.0110.00928.099-0.012-0.0120.0000.0000.0000.000
130A130VAL0-0.086-0.02227.747-0.009-0.0090.0000.0000.0000.000
131A131GLN0-0.009-0.00930.3210.0000.0000.0000.0000.0000.000
132A132PRO00.001-0.00533.3130.0040.0040.0000.0000.0000.000
133A133TRP00.0880.03132.292-0.007-0.0070.0000.0000.0000.000
134A134SER0-0.024-0.00534.341-0.003-0.0030.0000.0000.0000.000
135A135THR0-0.053-0.03937.675-0.005-0.0050.0000.0000.0000.000
136A136ILE0-0.0290.00234.765-0.005-0.0050.0000.0000.0000.000
137A137VAL00.0240.01738.8920.0000.0000.0000.0000.0000.000
138A138GLN0-0.018-0.01241.6600.0020.0020.0000.0000.0000.000
139A139GLY00.0280.00443.019-0.002-0.0020.0000.0000.0000.000
140A140PRO0-0.024-0.03645.2230.0000.0000.0000.0000.0000.000
141A141ALA0-0.002-0.00346.943-0.002-0.0020.0000.0000.0000.000
142A142GLU-1-0.737-0.82539.6070.0510.0510.0000.0000.0000.000
143A143SER00.018-0.00740.6940.0000.0000.0000.0000.0000.000
144A144TYR00.015-0.04140.5750.0030.0030.0000.0000.0000.000
145A145VAL00.018-0.00135.9490.0030.0030.0000.0000.0000.000
146A146GLU-1-0.869-0.89836.3530.0460.0460.0000.0000.0000.000
147A147PHE00.0130.00836.4200.0040.0040.0000.0000.0000.000
148A148VAL0-0.024-0.01034.9650.0050.0050.0000.0000.0000.000
149A149ASN00.0130.00731.1940.0090.0090.0000.0000.0000.000
150A150ARG10.7830.86832.002-0.052-0.0520.0000.0000.0000.000
151A151LEU00.0020.00332.8100.0070.0070.0000.0000.0000.000
152A152GLN0-0.006-0.01830.3540.0050.0050.0000.0000.0000.000
153A153ILE0-0.0150.00227.4880.0110.0110.0000.0000.0000.000
154A154SER00.0240.00228.1760.0090.0090.0000.0000.0000.000
155A155LEU0-0.030-0.01429.9310.0070.0070.0000.0000.0000.000
156A156ALA0-0.0020.00225.4080.0100.0100.0000.0000.0000.000
157A157ASP-1-0.880-0.93924.8780.1780.1780.0000.0000.0000.000
158A158ASN00.0330.01125.6970.0070.0070.0000.0000.0000.000
159A159LEU0-0.0210.01928.5290.0010.0010.0000.0000.0000.000
160A160PRO00.020-0.00328.3440.0090.0090.0000.0000.0000.000
161A161ASP-1-0.882-0.94423.9980.2110.2110.0000.0000.0000.000
162A162GLY0-0.020-0.00826.969-0.002-0.0020.0000.0000.0000.000
163A163VAL0-0.036-0.00829.667-0.011-0.0110.0000.0000.0000.000
164A164PRO00.0160.01530.7020.0060.0060.0000.0000.0000.000
165A165LYS10.8780.93126.933-0.154-0.1540.0000.0000.0000.000
166A166GLU-1-0.813-0.91330.8820.1040.1040.0000.0000.0000.000
167A167PRO00.0090.00133.794-0.006-0.0060.0000.0000.0000.000
168A168ILE0-0.0110.00034.806-0.005-0.0050.0000.0000.0000.000
169A169ILE0-0.002-0.00331.967-0.004-0.0040.0000.0000.0000.000
170A170ASP-1-0.790-0.87835.7840.0640.0640.0000.0000.0000.000
171A171SER0-0.0160.01838.769-0.006-0.0060.0000.0000.0000.000
172A172LEU00.027-0.00137.038-0.004-0.0040.0000.0000.0000.000
173A173SER0-0.001-0.01438.430-0.004-0.0040.0000.0000.0000.000
174A174TYR00.0120.03340.287-0.004-0.0040.0000.0000.0000.000
175A175ALA0-0.020-0.01243.165-0.002-0.0020.0000.0000.0000.000
176A176ASN0-0.040-0.02340.154-0.002-0.0020.0000.0000.0000.000
177A177ALA00.0100.01543.158-0.001-0.0010.0000.0000.0000.000
178A178ASN00.0060.00744.470-0.001-0.0010.0000.0000.0000.000
179A179LYS11.0010.97847.514-0.034-0.0340.0000.0000.0000.000
180A180GLU-1-0.839-0.89049.8510.0280.0280.0000.0000.0000.000
181A181CYS0-0.0050.01345.876-0.001-0.0010.0000.0000.0000.000
182A182GLN0-0.062-0.03446.836-0.002-0.0020.0000.0000.0000.000
183A183GLN00.013-0.00649.1810.0000.0000.0000.0000.0000.000
184A184ILE00.0060.01148.746-0.001-0.0010.0000.0000.0000.000
185A185LEU0-0.041-0.02344.5900.0000.0000.0000.0000.0000.000
186A186GLN0-0.034-0.03948.930-0.001-0.0010.0000.0000.0000.000
187A187GLY00.0020.01252.193-0.001-0.0010.0000.0000.0000.000
188A188ARG10.9130.95447.435-0.031-0.0310.0000.0000.0000.000
189A189GLY00.0280.01850.8820.0000.0000.0000.0000.0000.000
190A190LEU0-0.045-0.02345.7920.0020.0020.0000.0000.0000.000
191A191VAL00.0180.00945.5340.0020.0020.0000.0000.0000.000
192A192ALA00.0090.01044.9720.0030.0030.0000.0000.0000.000
193A193ALA0-0.0100.02143.5540.0010.0010.0000.0000.0000.000
194A194PRO00.0520.02637.8330.0010.0010.0000.0000.0000.000
195A195VAL00.0280.00635.316-0.004-0.0040.0000.0000.0000.000
196A196GLY0-0.0090.00237.240-0.002-0.0020.0000.0000.0000.000
197A197GLN00.016-0.01037.787-0.002-0.0020.0000.0000.0000.000
198A198LYS10.7930.88241.069-0.056-0.0560.0000.0000.0000.000
199A199LEU00.021-0.00235.926-0.003-0.0030.0000.0000.0000.000
200A200GLN0-0.047-0.01840.398-0.001-0.0010.0000.0000.0000.000
201A201ALA0-0.073-0.03042.026-0.003-0.0030.0000.0000.0000.000
202A202CYS0-0.024-0.01643.518-0.002-0.0020.0000.0000.0000.000
203A203ALA0-0.029-0.01841.0380.0000.0000.0000.0000.0000.000
204A204HIS0-0.018-0.00642.606-0.001-0.0010.0000.0000.0000.000
205A205TRP0-0.088-0.04545.776-0.001-0.0010.0000.0000.0000.000
206A206ALA00.0080.01546.1950.0000.0000.0000.0000.0000.000