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: N998Q

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2077029.269157
FMO2-HF: Nuclear repulsion 1998209.755121
FMO2-HF: Total energy -78819.514036
FMO2-MP2: Total energy -79052.041086


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.
-13.702-1.67524.087-12.572-23.538-0.069
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 : -0.012 / q_NPA : -0.013
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].
3A3ILE0-0.023-0.0153.536-0.2321.572-0.001-0.668-1.1350.002
4A4SER0-0.003-0.0216.0860.0390.0390.0000.0000.0000.000
5A5GLU-1-0.955-0.9579.526-0.609-0.6090.0000.0000.0000.000
6A6GLY00.0050.01212.2090.0650.0650.0000.0000.0000.000
7A7ASN0-0.039-0.03014.5670.0380.0380.0000.0000.0000.000
8A8ARG10.9090.96213.8200.2470.2470.0000.0000.0000.000
9A9ASN00.0860.0498.377-0.032-0.0320.0000.0000.0000.000
10A10ARG10.9310.9568.1670.8590.8590.0000.0000.0000.000
11A11HIS0-0.016-0.0062.515-2.541-1.2200.503-0.592-1.233-0.001
12A12ARG10.8350.9142.5691.1533.8500.901-1.050-2.548-0.002
13A13ALA00.0200.0192.410-6.290-5.1493.402-1.978-2.564-0.025
14A14TRP00.0410.0062.861-4.958-1.5343.322-1.325-5.420-0.015
15A15ALA00.0000.0054.0230.3280.3810.002-0.002-0.0520.000
16A16LEU00.011-0.0046.5680.1730.1730.0000.0000.0000.000
17A17ARG10.9260.9639.3610.1770.1770.0000.0000.0000.000
18A18GLU-1-0.747-0.8664.027-1.003-0.7280.001-0.083-0.1920.000
19A19LEU00.0200.0155.8200.1860.1860.0000.0000.0000.000
20A20GLN0-0.039-0.0348.8240.0860.0860.0000.0000.0000.000
21A21ASP-1-0.908-0.94310.7270.0700.0700.0000.0000.0000.000
22A22ILE00.0510.0297.3450.0250.0250.0000.0000.0000.000
23A23LYS10.9580.99011.662-0.056-0.0560.0000.0000.0000.000
24A24LYS10.9540.96814.104-0.078-0.0780.0000.0000.0000.000
25A25GLU-1-0.918-0.94914.2490.2150.2150.0000.0000.0000.000
26A26ILE0-0.058-0.06114.529-0.003-0.0030.0000.0000.0000.000
27A27GLU-1-0.971-0.98316.6930.0790.0790.0000.0000.0000.000
28A28ASN0-0.0030.00419.0140.0030.0030.0000.0000.0000.000
29A29LYS10.7840.91618.722-0.205-0.2050.0000.0000.0000.000
30A30ALA00.0270.01521.381-0.003-0.0030.0000.0000.0000.000
31A31PRO00.0870.04220.0710.0260.0260.0000.0000.0000.000
32A32GLY00.0310.01619.917-0.014-0.0140.0000.0000.0000.000
33A33SER0-0.034-0.02521.392-0.004-0.0040.0000.0000.0000.000
34A34GLN00.0510.01420.7110.0470.0470.0000.0000.0000.000
35A35VAL00.0850.04519.6140.0330.0330.0000.0000.0000.000
36A36TRP00.0340.07816.5610.0300.0300.0000.0000.0000.000
37A37ILE0-0.002-0.01116.1790.0510.0510.0000.0000.0000.000
38A38GLN0-0.084-0.06015.4710.0560.0560.0000.0000.0000.000
39A39THR0-0.036-0.07313.4100.0330.0330.0000.0000.0000.000
40A40LEU0-0.0040.00011.2720.0700.0700.0000.0000.0000.000
41A41ARG10.9330.97610.422-0.396-0.3960.0000.0000.0000.000
42A42LEU00.0360.01511.3200.1050.1050.0000.0000.0000.000
43A43ALA00.0630.0267.6510.0750.0750.0000.0000.0000.000
44A44ILE0-0.045-0.0256.5760.3770.3770.0000.0000.0000.000
45A45LEU0-0.034-0.0186.5150.3870.3870.0000.0000.0000.000
46A46GLN0-0.066-0.0175.788-0.067-0.0670.0000.0000.0000.000
47A47ALA0-0.0030.0002.126-0.076-1.6425.615-1.586-2.463-0.001
48A48ASP-1-0.743-0.8152.741-0.5721.4990.999-1.550-1.521-0.020
49A49PRO0-0.022-0.0072.336-2.4200.0721.470-1.972-1.9890.001
50A50THR0-0.025-0.0123.249-5.622-5.0900.0360.036-0.6040.003
51A51PRO00.014-0.0195.7910.1660.241-0.0010.000-0.0740.000
52A52ALA00.0150.0146.607-0.140-0.1400.0000.0000.0000.000
53A53ASP-1-0.798-0.9022.5968.9556.5827.839-1.793-3.672-0.011
54A54LEU00.009-0.0104.597-0.691-0.610-0.001-0.009-0.0710.000
55A55GLU-1-0.946-0.9677.2110.0330.0330.0000.0000.0000.000
56A56GLN00.001-0.0076.016-0.366-0.3660.0000.0000.0000.000
57A57LEU00.0170.0106.041-0.136-0.1360.0000.0000.0000.000
58A58CYS0-0.052-0.0209.113-0.082-0.0820.0000.0000.0000.000
59A59GLN00.0090.00711.966-0.096-0.0960.0000.0000.0000.000
60A60TYR0-0.030-0.00811.008-0.051-0.0510.0000.0000.0000.000
61A61ILE0-0.053-0.04011.694-0.018-0.0180.0000.0000.0000.000
62A62ALA00.0010.01714.434-0.002-0.0020.0000.0000.0000.000
63A63SER00.0260.04017.003-0.030-0.0300.0000.0000.0000.000
64A64PRO00.0690.00419.4980.0200.0200.0000.0000.0000.000
65A65VAL00.0040.00420.5020.0100.0100.0000.0000.0000.000
66A66ASP-1-0.845-0.93019.5570.1870.1870.0000.0000.0000.000
67A67GLN0-0.147-0.08716.0430.0290.0290.0000.0000.0000.000
68A68THR00.0120.01217.8520.0250.0250.0000.0000.0000.000
69A69ALA00.0100.00420.4190.0130.0130.0000.0000.0000.000
70A70HIS10.9020.96314.637-0.482-0.4820.0000.0000.0000.000
71A71MET00.0190.01315.6080.0420.0420.0000.0000.0000.000
72A72THR0-0.017-0.01118.193-0.006-0.0060.0000.0000.0000.000
73A73SER0-0.026-0.01721.061-0.007-0.0070.0000.0000.0000.000
74A74LEU0-0.0040.00114.4060.0100.0100.0000.0000.0000.000
75A75THR0-0.039-0.02618.972-0.004-0.0040.0000.0000.0000.000
76A76ALA00.0120.01620.529-0.015-0.0150.0000.0000.0000.000
77A77ALA00.021-0.00320.758-0.012-0.0120.0000.0000.0000.000
78A78ILE0-0.0140.00217.3530.0020.0020.0000.0000.0000.000
79A79ALA00.0550.03421.107-0.012-0.0120.0000.0000.0000.000
80A80ALA0-0.0040.00724.648-0.013-0.0130.0000.0000.0000.000
81A81ALA00.0000.00521.881-0.012-0.0120.0000.0000.0000.000
82A82GLU-1-0.932-0.97622.1490.2180.2180.0000.0000.0000.000
83A83ALA0-0.038-0.01724.914-0.015-0.0150.0000.0000.0000.000
84A84ALA0-0.067-0.03227.186-0.013-0.0130.0000.0000.0000.000
85A85ASN0-0.042-0.02126.326-0.002-0.0020.0000.0000.0000.000
86A86THR0-0.043-0.02723.8000.0010.0010.0000.0000.0000.000
87A87LEU0-0.041-0.01219.4430.0270.0270.0000.0000.0000.000
88A88GLN0-0.0040.00020.313-0.039-0.0390.0000.0000.0000.000
89A89GLY00.0580.01919.8930.0260.0260.0000.0000.0000.000
90A90PHE0-0.064-0.01219.1680.0000.0000.0000.0000.0000.000
91A91ASN00.029-0.00821.088-0.020-0.0200.0000.0000.0000.000
92A92PRO00.0550.01321.7340.0030.0030.0000.0000.0000.000
93A93GLN0-0.0130.01322.767-0.005-0.0050.0000.0000.0000.000
94A94ASN0-0.078-0.01919.467-0.035-0.0350.0000.0000.0000.000
95A95GLY0-0.0040.00318.5670.0000.0000.0000.0000.0000.000
96A96THR00.0400.01317.9740.0360.0360.0000.0000.0000.000
97A97LEU00.0870.03215.0360.0140.0140.0000.0000.0000.000
98A98THR0-0.035-0.03513.0500.0890.0890.0000.0000.0000.000
99A99GLN0-0.0030.00312.2950.0650.0650.0000.0000.0000.000
100A100GLN00.0540.03512.680-0.033-0.0330.0000.0000.0000.000
101A101SER00.008-0.00210.182-0.033-0.0330.0000.0000.0000.000
102A102ALA00.002-0.0087.9560.3410.3410.0000.0000.0000.000
103A103GLN0-0.037-0.0017.785-0.265-0.2650.0000.0000.0000.000
104A104PRO00.0700.0157.5590.2210.2210.0000.0000.0000.000
105A105ASN00.029-0.0158.7110.0750.0750.0000.0000.0000.000
106A106ALA0-0.0310.00411.0620.0190.0190.0000.0000.0000.000
107A107GLY00.0990.0299.6320.1310.1310.0000.0000.0000.000
108A108ASP-1-0.853-0.89010.6160.5140.5140.0000.0000.0000.000
109A109LEU0-0.018-0.01513.5930.0270.0270.0000.0000.0000.000
110A110ARG10.7620.8515.873-1.413-1.4130.0000.0000.0000.000
111A111SER0-0.014-0.02610.5000.1120.1120.0000.0000.0000.000
112A112GLN0-0.082-0.04711.748-0.030-0.0300.0000.0000.0000.000
113A113TYR0-0.014-0.02110.8560.0040.0040.0000.0000.0000.000
114A114GLN0-0.016-0.0276.601-0.377-0.3770.0000.0000.0000.000
115A115ASN0-0.011-0.00411.275-0.050-0.0500.0000.0000.0000.000
116A116LEU00.0150.00714.786-0.052-0.0520.0000.0000.0000.000
117A117TRP00.0500.02611.145-0.047-0.0470.0000.0000.0000.000
118A118LEU0-0.016-0.01012.769-0.073-0.0730.0000.0000.0000.000
119A119GLN00.0190.00015.579-0.033-0.0330.0000.0000.0000.000
120A120ALA00.0370.02917.363-0.046-0.0460.0000.0000.0000.000
121A121TRP0-0.069-0.04113.801-0.083-0.0830.0000.0000.0000.000
122A122LYS10.9110.95519.510-0.302-0.3020.0000.0000.0000.000
123A123ASN0-0.038-0.01522.450-0.002-0.0020.0000.0000.0000.000
124A124LEU0-0.0170.00219.924-0.014-0.0140.0000.0000.0000.000
125A125PRO00.0270.00524.180-0.006-0.0060.0000.0000.0000.000
126A126THR00.0310.02923.654-0.006-0.0060.0000.0000.0000.000
127A127ARG10.8210.90823.792-0.211-0.2110.0000.0000.0000.000
128A128PRO0-0.0180.01025.510-0.002-0.0020.0000.0000.0000.000
129A129SER0-0.030-0.02628.623-0.015-0.0150.0000.0000.0000.000
130A130VAL0-0.016-0.00429.364-0.011-0.0110.0000.0000.0000.000
131A131GLN00.0170.00631.4310.0000.0000.0000.0000.0000.000
132A132PRO0-0.040-0.01133.8470.0060.0060.0000.0000.0000.000
133A133TRP00.0790.01732.818-0.006-0.0060.0000.0000.0000.000
134A134SER0-0.019-0.02234.746-0.002-0.0020.0000.0000.0000.000
135A135THR0-0.042-0.02137.852-0.005-0.0050.0000.0000.0000.000
136A136ILE0-0.0270.01235.305-0.006-0.0060.0000.0000.0000.000
137A137VAL00.0220.00339.3930.0010.0010.0000.0000.0000.000
138A138GLN0-0.016-0.00141.8180.0010.0010.0000.0000.0000.000
139A139GLY00.0070.01043.113-0.003-0.0030.0000.0000.0000.000
140A140PRO0-0.015-0.02845.2220.0000.0000.0000.0000.0000.000
141A141ALA00.0220.00446.811-0.002-0.0020.0000.0000.0000.000
142A142GLU-1-0.781-0.88039.0790.0840.0840.0000.0000.0000.000
143A143SER00.0430.03440.1860.0010.0010.0000.0000.0000.000
144A144TYR00.0770.01640.3880.0050.0050.0000.0000.0000.000
145A145VAL00.0420.01635.9920.0050.0050.0000.0000.0000.000
146A146GLU-1-0.912-0.94836.1780.0820.0820.0000.0000.0000.000
147A147PHE0-0.020-0.01236.5080.0050.0050.0000.0000.0000.000
148A148VAL0-0.042-0.03734.4850.0050.0050.0000.0000.0000.000
149A149ASN0-0.024-0.00731.0650.0130.0130.0000.0000.0000.000
150A150ARG10.8350.91132.199-0.081-0.0810.0000.0000.0000.000
151A151LEU0-0.004-0.00933.1300.0070.0070.0000.0000.0000.000
152A152GLN00.009-0.01330.0280.0060.0060.0000.0000.0000.000
153A153ILE0-0.030-0.00527.6620.0140.0140.0000.0000.0000.000
154A154SER00.0470.03628.3730.0150.0150.0000.0000.0000.000
155A155LEU00.0400.02330.3910.0070.0070.0000.0000.0000.000
156A156ALA0-0.102-0.05425.2190.0120.0120.0000.0000.0000.000
157A157ASP-1-0.851-0.93125.2690.2170.2170.0000.0000.0000.000
158A158ASN0-0.073-0.04026.622-0.002-0.0020.0000.0000.0000.000
159A159LEU0-0.0300.00529.2700.0010.0010.0000.0000.0000.000
160A160PRO0-0.008-0.01428.8410.0130.0130.0000.0000.0000.000
161A161ASP-1-0.827-0.90225.8460.2330.2330.0000.0000.0000.000
162A162GLY0-0.089-0.03427.7920.0010.0010.0000.0000.0000.000
163A163VAL0-0.047-0.03230.144-0.013-0.0130.0000.0000.0000.000
164A164PRO00.0190.03130.5990.0090.0090.0000.0000.0000.000
165A165LYS10.9830.96926.297-0.225-0.2250.0000.0000.0000.000
166A166GLU-1-0.835-0.92030.7890.1600.1600.0000.0000.0000.000
167A167PRO00.0160.01233.874-0.007-0.0070.0000.0000.0000.000
168A168ILE00.0020.00034.257-0.008-0.0080.0000.0000.0000.000
169A169ILE0-0.0070.00332.689-0.006-0.0060.0000.0000.0000.000
170A170ASP-1-0.833-0.90936.0810.1090.1090.0000.0000.0000.000
171A171SER0-0.041-0.00538.889-0.008-0.0080.0000.0000.0000.000
172A172LEU00.043-0.01037.880-0.005-0.0050.0000.0000.0000.000
173A173SER0-0.045-0.03138.620-0.005-0.0050.0000.0000.0000.000
174A174TYR0-0.0030.00640.274-0.005-0.0050.0000.0000.0000.000
175A175ALA0-0.004-0.00243.576-0.003-0.0030.0000.0000.0000.000
176A176ASN0-0.025-0.01240.509-0.005-0.0050.0000.0000.0000.000
177A177ALA00.0170.01943.5270.0000.0000.0000.0000.0000.000
178A178ASN00.0230.02044.925-0.002-0.0020.0000.0000.0000.000
179A179LYS11.0030.96447.927-0.050-0.0500.0000.0000.0000.000
180A180GLU-1-0.902-0.93449.4930.0490.0490.0000.0000.0000.000
181A181CYS0-0.0040.00045.9790.0000.0000.0000.0000.0000.000
182A182GLN0-0.058-0.02747.137-0.002-0.0020.0000.0000.0000.000
183A183GLN00.029-0.01149.3240.0000.0000.0000.0000.0000.000
184A184ILE00.0060.02548.526-0.001-0.0010.0000.0000.0000.000
185A185LEU0-0.021-0.01044.9090.0000.0000.0000.0000.0000.000
186A186GLN00.0080.01748.975-0.001-0.0010.0000.0000.0000.000
187A187GLY0-0.0030.00552.310-0.001-0.0010.0000.0000.0000.000
188A188ARG10.8920.94147.503-0.060-0.0600.0000.0000.0000.000
189A189GLY00.0390.03351.0400.0000.0000.0000.0000.0000.000
190A190LEU0-0.075-0.05245.4080.0020.0020.0000.0000.0000.000
191A191VAL0-0.001-0.01245.3790.0040.0040.0000.0000.0000.000
192A192ALA00.016-0.00244.7810.0030.0030.0000.0000.0000.000
193A193ALA0-0.0150.02343.0020.0030.0030.0000.0000.0000.000
194A194PRO00.0860.04637.5790.0010.0010.0000.0000.0000.000
195A195VAL00.0630.03035.625-0.004-0.0040.0000.0000.0000.000
196A196GLY00.0100.01836.944-0.003-0.0030.0000.0000.0000.000
197A197GLN0-0.001-0.02537.539-0.005-0.0050.0000.0000.0000.000
198A198LYS10.8220.91040.800-0.093-0.0930.0000.0000.0000.000
199A199LEU0-0.035-0.02635.511-0.004-0.0040.0000.0000.0000.000
200A200GLN0-0.053-0.01540.173-0.001-0.0010.0000.0000.0000.000
201A201ALA0-0.072-0.03241.765-0.004-0.0040.0000.0000.0000.000
202A202CYS0-0.038-0.02543.206-0.004-0.0040.0000.0000.0000.000
203A203ALA0-0.020-0.00841.375-0.001-0.0010.0000.0000.0000.000
204A204HIS00.002-0.00642.793-0.001-0.0010.0000.0000.0000.000
205A205TRP0-0.056-0.01045.688-0.002-0.0020.0000.0000.0000.000
206A206ALA00.0190.02446.4250.0010.0010.0000.0000.0000.000