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: JLLY9

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2076867.517954
FMO2-HF: Nuclear repulsion 1998046.574729
FMO2-HF: Total energy -78820.943225
FMO2-MP2: Total energy -79053.288435


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.
-24.243-5.8114.291-11.452-21.269-0.067
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 : -0.035 / q_NPA : -0.025
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].
3A3ILE0-0.028-0.0193.021-0.5711.2880.072-0.688-1.2420.003
4A4SER00.0130.0115.8430.1360.1360.0000.0000.0000.000
5A5GLU-1-0.841-0.8919.525-0.648-0.6480.0000.0000.0000.000
6A6GLY00.0170.01711.9870.0570.0570.0000.0000.0000.000
7A7ASN0-0.023-0.02114.4160.0250.0250.0000.0000.0000.000
8A8ARG10.9170.96613.8530.1710.1710.0000.0000.0000.000
9A9ASN00.0510.0198.397-0.069-0.0690.0000.0000.0000.000
10A10ARG10.8050.8698.0120.7960.7960.0000.0000.0000.000
11A11HIS0-0.001-0.0072.631-4.477-2.9880.560-0.671-1.3780.000
12A12ARG10.7560.8422.4770.6983.8830.621-1.252-2.555-0.001
13A13ALA00.0330.0232.217-7.569-6.1382.904-2.237-2.098-0.025
14A14TRP00.0290.0042.930-5.877-1.8862.622-1.617-4.995-0.020
15A15ALA00.0160.0203.9070.4540.4900.0010.009-0.0460.000
16A16LEU00.027-0.0036.6880.1400.1400.0000.0000.0000.000
17A17ARG10.8560.8999.5500.3040.3040.0000.0000.0000.000
18A18GLU-1-0.729-0.8324.339-1.341-1.1260.000-0.028-0.1870.000
19A19LEU00.0250.0175.9150.1860.1860.0000.0000.0000.000
20A20GLN0-0.010-0.0078.5770.1300.1300.0000.0000.0000.000
21A21ASP-1-0.800-0.86410.668-0.072-0.0720.0000.0000.0000.000
22A22ILE00.0500.0397.2370.0510.0510.0000.0000.0000.000
23A23LYS10.9170.96911.5800.0280.0280.0000.0000.0000.000
24A24LYS10.8840.92114.0070.0320.0320.0000.0000.0000.000
25A25GLU-1-0.920-0.95214.2900.1040.1040.0000.0000.0000.000
26A26ILE0-0.032-0.02514.2870.0100.0100.0000.0000.0000.000
27A27GLU-1-0.937-0.96816.7830.0070.0070.0000.0000.0000.000
28A28ASN0-0.033-0.01719.0080.0110.0110.0000.0000.0000.000
29A29LYS10.8070.91218.907-0.117-0.1170.0000.0000.0000.000
30A30ALA00.0330.02121.1900.0010.0010.0000.0000.0000.000
31A31PRO00.0820.03919.8300.0210.0210.0000.0000.0000.000
32A32GLY00.0290.01819.554-0.008-0.0080.0000.0000.0000.000
33A33SER0-0.015-0.01820.980-0.004-0.0040.0000.0000.0000.000
34A34GLN00.0290.00820.4250.0360.0360.0000.0000.0000.000
35A35VAL00.0570.02919.5650.0270.0270.0000.0000.0000.000
36A36TRP00.0290.03216.2510.0140.0140.0000.0000.0000.000
37A37ILE0-0.004-0.01416.0110.0400.0400.0000.0000.0000.000
38A38GLN0-0.059-0.04715.2730.0430.0430.0000.0000.0000.000
39A39THR0-0.021-0.02313.5650.0220.0220.0000.0000.0000.000
40A40LEU0-0.005-0.00210.8390.0390.0390.0000.0000.0000.000
41A41ARG10.9000.95310.405-0.381-0.3810.0000.0000.0000.000
42A42LEU00.0280.01511.4370.0870.0870.0000.0000.0000.000
43A43ALA00.0600.0247.9050.0400.0400.0000.0000.0000.000
44A44ILE0-0.061-0.0326.7000.2300.2300.0000.0000.0000.000
45A45LEU0-0.021-0.0096.5240.3190.3190.0000.0000.0000.000
46A46GLN0-0.061-0.0196.115-0.065-0.0650.0000.0000.0000.000
47A47ALA0-0.013-0.0062.299-1.044-1.0263.323-1.058-2.283-0.002
48A48ASP-1-0.755-0.8422.770-0.1561.5690.927-1.136-1.515-0.020
49A49PRO0-0.033-0.0162.299-2.1270.1871.928-1.962-2.2800.000
50A50THR0-0.011-0.0303.217-5.595-5.2630.0430.201-0.5770.002
51A51PRO00.012-0.0225.7910.0370.117-0.0010.000-0.0790.000
52A52ALA00.0180.0176.928-0.254-0.2540.0000.0000.0000.000
53A53ASP-1-0.811-0.8812.9054.9566.6371.292-1.006-1.966-0.004
54A54LEU00.023-0.0014.796-0.894-0.817-0.001-0.007-0.0680.000
55A55GLU-1-0.915-0.9587.2360.0570.0570.0000.0000.0000.000
56A56GLN00.0160.0085.271-0.573-0.5730.0000.0000.0000.000
57A57LEU00.0020.0035.998-0.194-0.1940.0000.0000.0000.000
58A58CYS0-0.068-0.0269.403-0.094-0.0940.0000.0000.0000.000
59A59GLN0-0.033-0.01112.157-0.120-0.1200.0000.0000.0000.000
60A60TYR0-0.032-0.01211.083-0.074-0.0740.0000.0000.0000.000
61A61ILE0-0.048-0.03211.805-0.021-0.0210.0000.0000.0000.000
62A62ALA0-0.0270.00214.627-0.002-0.0020.0000.0000.0000.000
63A63SER00.0150.00117.204-0.025-0.0250.0000.0000.0000.000
64A64PRO00.0930.01319.6910.0220.0220.0000.0000.0000.000
65A65VAL0-0.0050.00320.7120.0160.0160.0000.0000.0000.000
66A66ASP-1-0.827-0.90419.7540.1760.1760.0000.0000.0000.000
67A67GLN0-0.089-0.04616.1290.0380.0380.0000.0000.0000.000
68A68THR0-0.0040.00118.0730.0350.0350.0000.0000.0000.000
69A69ALA00.0060.00720.6740.0170.0170.0000.0000.0000.000
70A70HIS10.9060.96113.848-0.505-0.5050.0000.0000.0000.000
71A71MET00.0200.01115.7700.0460.0460.0000.0000.0000.000
72A72THR0-0.023-0.01718.270-0.001-0.0010.0000.0000.0000.000
73A73SER00.001-0.00920.818-0.009-0.0090.0000.0000.0000.000
74A74LEU0-0.018-0.00414.3070.0110.0110.0000.0000.0000.000
75A75THR0-0.042-0.03018.795-0.002-0.0020.0000.0000.0000.000
76A76ALA00.0070.01620.459-0.015-0.0150.0000.0000.0000.000
77A77ALA00.016-0.00220.363-0.013-0.0130.0000.0000.0000.000
78A78ILE0-0.023-0.00616.7940.0040.0040.0000.0000.0000.000
79A79ALA00.0570.03920.953-0.013-0.0130.0000.0000.0000.000
80A80ALA0-0.0050.00724.522-0.016-0.0160.0000.0000.0000.000
81A81ALA00.0070.00721.810-0.015-0.0150.0000.0000.0000.000
82A82GLU-1-0.918-0.97022.1310.2880.2880.0000.0000.0000.000
83A83ALA0-0.043-0.02424.881-0.018-0.0180.0000.0000.0000.000
84A84ALA0-0.063-0.03227.112-0.016-0.0160.0000.0000.0000.000
85A85ASN0-0.068-0.03726.260-0.007-0.0070.0000.0000.0000.000
86A86THR0-0.032-0.01723.9120.0000.0000.0000.0000.0000.000
87A87LEU0-0.039-0.01219.1150.0260.0260.0000.0000.0000.000
88A88GLN00.0120.01020.341-0.031-0.0310.0000.0000.0000.000
89A89GLY00.0570.01919.8730.0320.0320.0000.0000.0000.000
90A90PHE0-0.069-0.01918.9440.0100.0100.0000.0000.0000.000
91A91ASN00.0520.01221.069-0.028-0.0280.0000.0000.0000.000
92A92PRO00.0500.01621.7820.0110.0110.0000.0000.0000.000
93A93GLN0-0.0210.00623.056-0.001-0.0010.0000.0000.0000.000
94A94ASN0-0.076-0.01919.595-0.037-0.0370.0000.0000.0000.000
95A95GLY0-0.026-0.01018.9610.0200.0200.0000.0000.0000.000
96A96THR00.029-0.01118.1420.0320.0320.0000.0000.0000.000
97A97LEU00.0770.02315.0940.0370.0370.0000.0000.0000.000
98A98THR0-0.014-0.02613.0870.1100.1100.0000.0000.0000.000
99A99GLN00.0270.04012.5210.1160.1160.0000.0000.0000.000
100A100GLN00.0280.01613.086-0.018-0.0180.0000.0000.0000.000
101A101SER00.0100.00610.222-0.040-0.0400.0000.0000.0000.000
102A102ALA00.009-0.0028.2680.4090.4090.0000.0000.0000.000
103A103GLN0-0.0100.0108.175-0.137-0.1370.0000.0000.0000.000
104A104PRO00.0910.0357.6700.2050.2050.0000.0000.0000.000
105A105ASN0-0.014-0.0248.711-0.012-0.0120.0000.0000.0000.000
106A106ALA0-0.0210.00911.044-0.022-0.0220.0000.0000.0000.000
107A107GLY00.0910.0349.5970.1490.1490.0000.0000.0000.000
108A108ASP-1-0.852-0.89910.6070.5280.5280.0000.0000.0000.000
109A109LEU0-0.003-0.01013.6130.0210.0210.0000.0000.0000.000
110A110ARG10.7970.8795.834-1.623-1.6230.0000.0000.0000.000
111A111SER0-0.013-0.01110.4760.0760.0760.0000.0000.0000.000
112A112GLN0-0.057-0.02811.734-0.052-0.0520.0000.0000.0000.000
113A113TYR0-0.025-0.02510.709-0.001-0.0010.0000.0000.0000.000
114A114GLN0-0.020-0.0406.538-0.381-0.3810.0000.0000.0000.000
115A115ASN0-0.047-0.02911.253-0.144-0.1440.0000.0000.0000.000
116A116LEU00.0290.01914.768-0.058-0.0580.0000.0000.0000.000
117A117TRP00.0520.02110.806-0.049-0.0490.0000.0000.0000.000
118A118LEU0-0.033-0.01012.160-0.077-0.0770.0000.0000.0000.000
119A119GLN00.0310.00614.976-0.041-0.0410.0000.0000.0000.000
120A120ALA00.0280.02917.051-0.048-0.0480.0000.0000.0000.000
121A121TRP0-0.062-0.04213.457-0.074-0.0740.0000.0000.0000.000
122A122LYS10.8560.92519.148-0.273-0.2730.0000.0000.0000.000
123A123ASN0-0.043-0.01422.083-0.001-0.0010.0000.0000.0000.000
124A124LEU0-0.0070.01019.930-0.011-0.0110.0000.0000.0000.000
125A125PRO00.018-0.00123.979-0.008-0.0080.0000.0000.0000.000
126A126THR00.0340.03123.533-0.008-0.0080.0000.0000.0000.000
127A127ARG10.8410.91623.478-0.196-0.1960.0000.0000.0000.000
128A128PRO0-0.021-0.00925.243-0.006-0.0060.0000.0000.0000.000
129A129SER00.0060.00228.292-0.013-0.0130.0000.0000.0000.000
130A130VAL0-0.073-0.01928.412-0.010-0.0100.0000.0000.0000.000
131A131GLN0-0.003-0.00830.7520.0000.0000.0000.0000.0000.000
132A132PRO0-0.031-0.01333.4540.0050.0050.0000.0000.0000.000
133A133TRP00.0970.02532.362-0.005-0.0050.0000.0000.0000.000
134A134SER0-0.036-0.01234.319-0.002-0.0020.0000.0000.0000.000
135A135THR0-0.059-0.03437.458-0.005-0.0050.0000.0000.0000.000
136A136ILE0-0.0350.01135.030-0.006-0.0060.0000.0000.0000.000
137A137VAL00.0290.01039.1560.0010.0010.0000.0000.0000.000
138A138GLN0-0.014-0.01841.7340.0010.0010.0000.0000.0000.000
139A139GLY00.0130.00043.112-0.002-0.0020.0000.0000.0000.000
140A140PRO0-0.016-0.03145.2290.0000.0000.0000.0000.0000.000
141A141ALA00.0140.00046.897-0.001-0.0010.0000.0000.0000.000
142A142GLU-1-0.761-0.83339.4250.0640.0640.0000.0000.0000.000
143A143SER00.0310.01140.7360.0010.0010.0000.0000.0000.000
144A144TYR00.039-0.00940.7100.0040.0040.0000.0000.0000.000
145A145VAL00.0440.01536.1460.0040.0040.0000.0000.0000.000
146A146GLU-1-0.871-0.91836.4580.0580.0580.0000.0000.0000.000
147A147PHE0-0.019-0.01536.6580.0050.0050.0000.0000.0000.000
148A148VAL0-0.033-0.03234.7740.0050.0050.0000.0000.0000.000
149A149ASN0-0.030-0.00731.3380.0120.0120.0000.0000.0000.000
150A150ARG10.8180.88132.263-0.063-0.0630.0000.0000.0000.000
151A151LEU0-0.0030.00333.0320.0070.0070.0000.0000.0000.000
152A152GLN0-0.004-0.01930.2030.0050.0050.0000.0000.0000.000
153A153ILE0-0.029-0.00527.4970.0130.0130.0000.0000.0000.000
154A154SER00.0640.03028.1820.0100.0100.0000.0000.0000.000
155A155LEU0-0.017-0.00430.0390.0070.0070.0000.0000.0000.000
156A156ALA0-0.0030.00625.1160.0110.0110.0000.0000.0000.000
157A157ASP-1-0.871-0.93824.9230.1950.1950.0000.0000.0000.000
158A158ASN00.012-0.00126.1020.0050.0050.0000.0000.0000.000
159A159LEU0-0.0370.00328.7480.0030.0030.0000.0000.0000.000
160A160PRO00.011-0.00528.3030.0120.0120.0000.0000.0000.000
161A161ASP-1-0.862-0.93424.7950.2330.2330.0000.0000.0000.000
162A162GLY0-0.061-0.01527.6170.0000.0000.0000.0000.0000.000
163A163VAL0-0.040-0.02930.131-0.012-0.0120.0000.0000.0000.000
164A164PRO00.0140.02430.5430.0070.0070.0000.0000.0000.000
165A165LYS10.9400.95727.006-0.191-0.1910.0000.0000.0000.000
166A166GLU-1-0.829-0.91930.8470.1380.1380.0000.0000.0000.000
167A167PRO00.0120.00433.875-0.007-0.0070.0000.0000.0000.000
168A168ILE00.0050.00034.534-0.007-0.0070.0000.0000.0000.000
169A169ILE0-0.0080.00432.319-0.006-0.0060.0000.0000.0000.000
170A170ASP-1-0.788-0.88336.0180.0880.0880.0000.0000.0000.000
171A171SER0-0.0320.00938.906-0.007-0.0070.0000.0000.0000.000
172A172LEU00.031-0.01137.267-0.004-0.0040.0000.0000.0000.000
173A173SER0-0.022-0.02038.579-0.005-0.0050.0000.0000.0000.000
174A174TYR00.0280.03640.294-0.005-0.0050.0000.0000.0000.000
175A175ALA0-0.006-0.00343.436-0.003-0.0030.0000.0000.0000.000
176A176ASN0-0.042-0.02840.749-0.003-0.0030.0000.0000.0000.000
177A177ALA00.0160.01743.4530.0000.0000.0000.0000.0000.000
178A178ASN00.0070.01444.930-0.002-0.0020.0000.0000.0000.000
179A179LYS11.0120.96947.947-0.040-0.0400.0000.0000.0000.000
180A180GLU-1-0.864-0.90949.6550.0370.0370.0000.0000.0000.000
181A181CYS0-0.0090.01046.146-0.001-0.0010.0000.0000.0000.000
182A182GLN0-0.065-0.02647.062-0.002-0.0020.0000.0000.0000.000
183A183GLN00.017-0.00649.4300.0000.0000.0000.0000.0000.000
184A184ILE00.0280.02949.269-0.001-0.0010.0000.0000.0000.000
185A185LEU0-0.019-0.00544.9490.0000.0000.0000.0000.0000.000
186A186GLN0-0.005-0.00449.193-0.001-0.0010.0000.0000.0000.000
187A187GLY00.0000.00852.479-0.001-0.0010.0000.0000.0000.000
188A188ARG10.8950.94147.284-0.045-0.0450.0000.0000.0000.000
189A189GLY00.0370.03251.2580.0000.0000.0000.0000.0000.000
190A190LEU0-0.078-0.05445.8880.0010.0010.0000.0000.0000.000
191A191VAL00.001-0.00845.5610.0030.0030.0000.0000.0000.000
192A192ALA00.0150.00344.8270.0030.0030.0000.0000.0000.000
193A193ALA0-0.0210.02043.2590.0030.0030.0000.0000.0000.000
194A194PRO00.0810.03737.6200.0010.0010.0000.0000.0000.000
195A195VAL00.0450.02035.741-0.004-0.0040.0000.0000.0000.000
196A196GLY00.0040.01437.243-0.003-0.0030.0000.0000.0000.000
197A197GLN00.004-0.02337.891-0.004-0.0040.0000.0000.0000.000
198A198LYS10.8080.88841.119-0.076-0.0760.0000.0000.0000.000
199A199LEU0-0.035-0.02736.027-0.003-0.0030.0000.0000.0000.000
200A200GLN0-0.059-0.02240.508-0.001-0.0010.0000.0000.0000.000
201A201ALA0-0.074-0.03042.062-0.003-0.0030.0000.0000.0000.000
202A202CYS0-0.036-0.02443.575-0.003-0.0030.0000.0000.0000.000
203A203ALA0-0.019-0.00841.6140.0000.0000.0000.0000.0000.000
204A204HIS0-0.003-0.00643.033-0.002-0.0020.0000.0000.0000.000
205A205TRP0-0.096-0.04145.728-0.001-0.0010.0000.0000.0000.000
206A206ALA00.0310.03146.6320.0000.0000.0000.0000.0000.000