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: LJ1Q9

Calculation Name: 4OR8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OR8

Chain ID: A

ChEMBL ID:

UniProt ID: P35256

Base Structure: X-ray

Registration Date: 2023-06-20

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2711400.523292
FMO2-HF: Nuclear repulsion 2621952.955758
FMO2-HF: Total energy -89447.567534
FMO2-MP2: Total energy -89709.462687


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:-2:ASP)


Summations of interaction energy for fragment #1(A:-2:ASP)
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.
-51.312-48.285-0.036-1.639-1.3530.007
Interaction energy analysis for fragmet #1(A:-2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.982 / q_NPA : -0.979
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].
3A0LYS10.8290.9073.803-29.941-26.914-0.036-1.639-1.3530.007
4A1MET00.0250.0147.019-1.894-1.8940.0000.0000.0000.000
5A2ALA0-0.041-0.02310.039-0.380-0.3800.0000.0000.0000.000
6A3GLU-1-0.842-0.91212.96922.53122.5310.0000.0000.0000.000
7A4LEU0-0.005-0.00516.025-0.311-0.3110.0000.0000.0000.000
8A5SER00.0280.00718.1950.0050.0050.0000.0000.0000.000
9A6THR00.0220.01120.225-0.311-0.3110.0000.0000.0000.000
10A7ARG10.9290.95516.653-17.657-17.6570.0000.0000.0000.000
11A8TYR0-0.012-0.00121.0310.2280.2280.0000.0000.0000.000
12A9ASN00.0090.01325.057-0.301-0.3010.0000.0000.0000.000
13A10LEU0-0.014-0.00727.805-0.013-0.0130.0000.0000.0000.000
14A11PRO00.0170.01930.995-0.184-0.1840.0000.0000.0000.000
15A20ASN00.0410.02752.3520.0320.0320.0000.0000.0000.000
16A21LEU0-0.053-0.02851.8090.0140.0140.0000.0000.0000.000
17A22ASP-1-0.786-0.90755.5025.4185.4180.0000.0000.0000.000
18A23LEU00.0500.02858.2810.0660.0660.0000.0000.0000.000
19A24ASN00.0010.00760.1790.0820.0820.0000.0000.0000.000
20A25SER0-0.026-0.02154.6780.0730.0730.0000.0000.0000.000
21A26THR0-0.0030.00054.7690.0830.0830.0000.0000.0000.000
22A27ALA0-0.0210.01356.6940.0020.0020.0000.0000.0000.000
23A28ARG10.8990.93256.573-5.595-5.5950.0000.0000.0000.000
24A29TRP00.007-0.00649.7490.0890.0890.0000.0000.0000.000
25A30ILE00.009-0.00954.010-0.063-0.0630.0000.0000.0000.000
26A31LYS10.8290.91049.708-6.088-6.0880.0000.0000.0000.000
27A32GLU-1-0.804-0.87948.9036.4466.4460.0000.0000.0000.000
28A33PRO0-0.022-0.00447.9130.1430.1430.0000.0000.0000.000
29A34SER00.0470.01743.166-0.023-0.0230.0000.0000.0000.000
30A35VAL00.0150.00039.148-0.028-0.0280.0000.0000.0000.000
31A36GLY00.0220.01639.1220.1440.1440.0000.0000.0000.000
32A37GLY0-0.035-0.02840.0180.0420.0420.0000.0000.0000.000
33A38TRP0-0.033-0.01443.154-0.124-0.1240.0000.0000.0000.000
34A39THR00.0010.00544.5670.1960.1960.0000.0000.0000.000
35A40VAL0-0.003-0.00246.322-0.169-0.1690.0000.0000.0000.000
36A41LYS10.8070.88948.020-6.536-6.5360.0000.0000.0000.000
37A42TRP00.005-0.00149.909-0.110-0.1100.0000.0000.0000.000
38A43GLY00.0520.01150.5270.1070.1070.0000.0000.0000.000
39A44ASN0-0.047-0.03548.012-0.010-0.0100.0000.0000.0000.000
40A45PHE0-0.0180.00545.3270.1740.1740.0000.0000.0000.000
41A46VAL0-0.022-0.01844.013-0.138-0.1380.0000.0000.0000.000
42A47PHE0-0.0060.00443.4830.1910.1910.0000.0000.0000.000
43A48HIS00.0260.00540.180-0.169-0.1690.0000.0000.0000.000
44A49ILE0-0.023-0.01441.1360.1210.1210.0000.0000.0000.000
45A50PRO00.0280.03138.705-0.060-0.0600.0000.0000.0000.000
46A51ASN0-0.011-0.01740.799-0.004-0.0040.0000.0000.0000.000
47A52THR0-0.005-0.01137.5940.0200.0200.0000.0000.0000.000
48A53GLY00.0270.01739.9060.0070.0070.0000.0000.0000.000
49A54MET0-0.0090.00440.404-0.085-0.0850.0000.0000.0000.000
50A55THR00.0310.00341.623-0.205-0.2050.0000.0000.0000.000
51A56LEU00.0380.03139.193-0.113-0.1130.0000.0000.0000.000
52A57LEU00.0400.01542.943-0.100-0.1000.0000.0000.0000.000
53A58HIS00.0700.02545.817-0.159-0.1590.0000.0000.0000.000
54A59HIS0-0.040-0.00944.785-0.143-0.1430.0000.0000.0000.000
55A60LEU00.0110.00742.853-0.099-0.0990.0000.0000.0000.000
56A61LYS10.8330.94946.886-5.777-5.7770.0000.0000.0000.000
57A62SER0-0.035-0.02950.283-0.148-0.1480.0000.0000.0000.000
58A63ASN0-0.025-0.01348.9640.0310.0310.0000.0000.0000.000
59A64PHE00.0030.02247.3650.0010.0010.0000.0000.0000.000
60A65VAL0-0.026-0.02043.4600.1570.1570.0000.0000.0000.000
61A66VAL00.0780.04339.312-0.132-0.1320.0000.0000.0000.000
62A67PRO00.024-0.02042.299-0.012-0.0120.0000.0000.0000.000
63A68GLU-1-0.864-0.91436.7257.9577.9570.0000.0000.0000.000
64A69TRP0-0.019-0.02337.419-0.038-0.0380.0000.0000.0000.000
65A70GLN00.007-0.01042.435-0.203-0.2030.0000.0000.0000.000
66A71GLN00.0300.01939.527-0.226-0.2260.0000.0000.0000.000
67A72THR00.0220.01441.371-0.048-0.0480.0000.0000.0000.000
68A73ARG10.8230.89544.273-6.298-6.2980.0000.0000.0000.000
69A74ASN00.005-0.00347.489-0.231-0.2310.0000.0000.0000.000
70A75LEU00.0150.03344.096-0.121-0.1210.0000.0000.0000.000
71A76PHE00.0220.01143.838-0.060-0.0600.0000.0000.0000.000
72A77SER00.0380.01549.107-0.072-0.0720.0000.0000.0000.000
73A78HIS0-0.039-0.01752.104-0.040-0.0400.0000.0000.0000.000
74A79LEU0-0.0050.00449.043-0.067-0.0670.0000.0000.0000.000
75A80PHE0-0.012-0.00445.811-0.044-0.0440.0000.0000.0000.000
76A81LYS10.8510.93350.935-5.904-5.9040.0000.0000.0000.000
77A82ASN00.0470.00753.758-0.187-0.1870.0000.0000.0000.000
78A83PRO00.0230.00556.6990.0460.0460.0000.0000.0000.000
79A84LYS10.8290.92959.242-5.137-5.1370.0000.0000.0000.000
80A85SER0-0.011-0.00554.058-0.020-0.0200.0000.0000.0000.000
81A86THR0-0.036-0.03755.657-0.035-0.0350.0000.0000.0000.000
82A87ILE0-0.0060.00849.4370.0330.0330.0000.0000.0000.000
83A88ILE0-0.0030.00551.459-0.072-0.0720.0000.0000.0000.000
84A89GLU-1-0.800-0.89549.2996.3316.3310.0000.0000.0000.000
85A90PRO00.0700.01345.082-0.080-0.0800.0000.0000.0000.000
86A91PHE0-0.001-0.00447.3760.0170.0170.0000.0000.0000.000
87A92LEU00.017-0.00149.516-0.052-0.0520.0000.0000.0000.000
88A93ALA00.0090.01048.277-0.067-0.0670.0000.0000.0000.000
89A94LEU00.0100.00345.813-0.002-0.0020.0000.0000.0000.000
90A95ARG10.7990.91748.879-5.555-5.5550.0000.0000.0000.000
91A96ILE00.0200.01152.464-0.054-0.0540.0000.0000.0000.000
92A97LEU0-0.009-0.00545.840-0.044-0.0440.0000.0000.0000.000
93A98LEU00.0060.00149.7990.0080.0080.0000.0000.0000.000
94A99GLY00.0420.00951.413-0.064-0.0640.0000.0000.0000.000
95A100VAL0-0.025-0.01752.243-0.102-0.1020.0000.0000.0000.000
96A101ALA00.0060.01750.266-0.032-0.0320.0000.0000.0000.000
97A102LEU0-0.025-0.00952.050-0.028-0.0280.0000.0000.0000.000
98A103LYS10.8290.91455.213-5.393-5.3930.0000.0000.0000.000
99A104ASP-1-0.813-0.87851.2236.1216.1210.0000.0000.0000.000
100A105GLN00.0280.00054.421-0.049-0.0490.0000.0000.0000.000
101A106GLU-1-0.813-0.90050.0776.2956.2950.0000.0000.0000.000
102A107LEU0-0.0270.01053.0550.0050.0050.0000.0000.0000.000
103A108GLN0-0.001-0.00554.722-0.145-0.1450.0000.0000.0000.000
104A109GLN0-0.053-0.02756.723-0.070-0.0700.0000.0000.0000.000
105A110SER0-0.059-0.02755.678-0.009-0.0090.0000.0000.0000.000
106A111LEU0-0.0080.00657.252-0.011-0.0110.0000.0000.0000.000
107A112ILE00.0430.01560.414-0.064-0.0640.0000.0000.0000.000
108A113PRO00.0670.01864.1730.0260.0260.0000.0000.0000.000
109A114GLY00.0170.01766.742-0.023-0.0230.0000.0000.0000.000
110A115PHE00.0300.00058.283-0.005-0.0050.0000.0000.0000.000
111A116ARG10.8790.94461.810-5.112-5.1120.0000.0000.0000.000
112A117SER00.0170.01063.2910.0540.0540.0000.0000.0000.000
113A118ILE00.0240.00662.2950.0020.0020.0000.0000.0000.000
114A119VAL00.0230.00758.1280.0360.0360.0000.0000.0000.000
115A120HIS0-0.014-0.00260.3420.1290.1290.0000.0000.0000.000
116A121MET00.0000.00162.439-0.018-0.0180.0000.0000.0000.000
117A122LEU0-0.0090.00458.6000.0130.0130.0000.0000.0000.000
118A123SER0-0.027-0.00757.6940.0190.0190.0000.0000.0000.000
119A124GLU-1-0.859-0.95359.1524.9724.9720.0000.0000.0000.000
120A125TRP0-0.0120.00857.7940.0250.0250.0000.0000.0000.000
121A126LEU0-0.029-0.01254.5260.0250.0250.0000.0000.0000.000
122A127LEU0-0.061-0.03255.8380.0590.0590.0000.0000.0000.000
123A128LEU0-0.061-0.03258.4120.0090.0090.0000.0000.0000.000
124A129GLU-1-0.920-0.93960.6924.8744.8740.0000.0000.0000.000
125A130VAL0-0.037-0.03057.9250.1150.1150.0000.0000.0000.000
126A131THR00.0320.02859.6250.0630.0630.0000.0000.0000.000
127A132SER00.0280.01158.3560.0350.0350.0000.0000.0000.000
128A133ALA0-0.008-0.00658.8510.0930.0930.0000.0000.0000.000
129A134ILE00.0140.02661.140-0.078-0.0780.0000.0000.0000.000
130A135HIS00.003-0.00663.6430.0870.0870.0000.0000.0000.000
131A136ILE00.0100.00564.090-0.060-0.0600.0000.0000.0000.000
132A137SER00.003-0.00767.9960.0100.0100.0000.0000.0000.000
133A138PRO00.0490.00670.7780.0110.0110.0000.0000.0000.000
134A139ASN00.0000.00471.806-0.001-0.0010.0000.0000.0000.000
135A140LEU0-0.007-0.00670.127-0.014-0.0140.0000.0000.0000.000
136A141LEU0-0.060-0.01466.5870.0470.0470.0000.0000.0000.000
137A142GLY00.0240.03069.962-0.046-0.0460.0000.0000.0000.000
138A143ILE0-0.040-0.02165.665-0.035-0.0350.0000.0000.0000.000
139A144TYR00.0240.01166.6970.0380.0380.0000.0000.0000.000
140A145LEU0-0.006-0.01062.2810.0400.0400.0000.0000.0000.000
141A146THR00.0380.00560.4530.0410.0410.0000.0000.0000.000
142A147SER00.054-0.00355.8730.0960.0960.0000.0000.0000.000
143A148ASP-1-0.863-0.93055.4655.8915.8910.0000.0000.0000.000
144A149MET0-0.0010.02655.7200.0640.0640.0000.0000.0000.000
145A150PHE00.0710.02855.5080.0390.0390.0000.0000.0000.000
146A151LYS10.8690.93251.366-5.930-5.9300.0000.0000.0000.000
147A152ILE0-0.005-0.00251.4690.1370.1370.0000.0000.0000.000
148A153LEU00.0160.01852.8890.0300.0300.0000.0000.0000.000
149A154MET0-0.051-0.01849.2970.0700.0700.0000.0000.0000.000
150A155ALA0-0.002-0.00248.0890.1400.1400.0000.0000.0000.000
151A156GLY00.0340.01648.3260.0960.0960.0000.0000.0000.000
152A157VAL0-0.008-0.00347.8590.0410.0410.0000.0000.0000.000
153A158LYS10.8960.94942.032-7.479-7.4790.0000.0000.0000.000
154A159ASN0-0.010-0.00144.4630.2720.2720.0000.0000.0000.000
155A160PHE00.0190.00745.9120.0560.0560.0000.0000.0000.000
156A161PHE0-0.030-0.03542.9720.0370.0370.0000.0000.0000.000
157A162ASN0-0.043-0.02939.6810.0860.0860.0000.0000.0000.000
158A163LYS10.8350.90041.751-6.297-6.2970.0000.0000.0000.000
159A164MET0-0.0190.01843.601-0.023-0.0230.0000.0000.0000.000
160A165PHE0-0.069-0.02936.7450.1190.1190.0000.0000.0000.000
161A166THR0-0.059-0.03338.5460.1720.1720.0000.0000.0000.000
162A167LEU0-0.0370.00540.698-0.024-0.0240.0000.0000.0000.000
163A168HIS0-0.024-0.00537.5630.3680.3680.0000.0000.0000.000
164A169VAL0-0.004-0.00435.939-0.174-0.1740.0000.0000.0000.000
165A170VAL0-0.002-0.00638.931-0.051-0.0510.0000.0000.0000.000
166A171ASN0-0.061-0.03539.0710.1150.1150.0000.0000.0000.000
167A172ASP-1-0.869-0.93539.4477.3697.3690.0000.0000.0000.000
168A173HIS00.0270.00836.2680.0320.0320.0000.0000.0000.000
169A174GLY00.0060.00741.970-0.043-0.0430.0000.0000.0000.000
170A175LYS10.8400.93237.210-7.985-7.9850.0000.0000.0000.000
171A176PRO00.0500.01743.303-0.009-0.0090.0000.0000.0000.000
172A177SER00.0560.02842.9060.1370.1370.0000.0000.0000.000
173A178SER0-0.005-0.01444.0670.0870.0870.0000.0000.0000.000
174A179ILE00.0060.02347.164-0.047-0.0470.0000.0000.0000.000
175A180GLU-1-0.869-0.93149.5215.7135.7130.0000.0000.0000.000
176A181ILE00.000-0.00353.134-0.036-0.0360.0000.0000.0000.000
177A182LYS10.8940.96056.066-5.051-5.0510.0000.0000.0000.000
178A183LEU00.0340.01358.532-0.035-0.0350.0000.0000.0000.000
179A184THR00.024-0.01062.074-0.035-0.0350.0000.0000.0000.000
180A185GLY0-0.0210.00265.1140.0040.0040.0000.0000.0000.000
181A186GLN00.009-0.00959.253-0.036-0.0360.0000.0000.0000.000
182A187GLN0-0.070-0.03056.581-0.072-0.0720.0000.0000.0000.000
183A188ILE0-0.0060.00452.9440.0140.0140.0000.0000.0000.000
184A189ILE00.0100.01049.9670.0100.0100.0000.0000.0000.000
185A190ILE0-0.012-0.00446.0370.0550.0550.0000.0000.0000.000
186A191THR0-0.004-0.01544.289-0.001-0.0010.0000.0000.0000.000
187A192ARG10.8250.92635.822-8.133-8.1330.0000.0000.0000.000
188A193VAL0-0.006-0.01639.9580.0350.0350.0000.0000.0000.000
189A194ASN00.0510.00334.7310.1430.1430.0000.0000.0000.000
190A195MET0-0.024-0.01035.3920.0970.0970.0000.0000.0000.000
191A196GLY00.0010.00137.3020.0260.0260.0000.0000.0000.000
192A197PHE00.0060.01039.515-0.035-0.0350.0000.0000.0000.000
193A198LEU0-0.013-0.01543.077-0.063-0.0630.0000.0000.0000.000
194A199VAL00.0020.01545.854-0.066-0.0660.0000.0000.0000.000
195A200GLU-1-0.784-0.87949.1435.8515.8510.0000.0000.0000.000
196A201VAL00.013-0.00252.282-0.032-0.0320.0000.0000.0000.000
197A202ARG10.8390.88953.343-5.710-5.7100.0000.0000.0000.000
198A203ARG10.9600.97058.716-5.147-5.1470.0000.0000.0000.000
199A204ILE00.0250.01962.427-0.002-0.0020.0000.0000.0000.000
200A216SER0-0.004-0.02366.9790.0070.0070.0000.0000.0000.000
201A217GLU-1-0.818-0.91160.0345.2095.2090.0000.0000.0000.000
202A218SER0-0.0400.01061.0170.0530.0530.0000.0000.0000.000
203A219VAL00.0180.00954.9170.0120.0120.0000.0000.0000.000
204A220VAL00.0010.00554.6230.0050.0050.0000.0000.0000.000
205A221PHE00.015-0.00148.4130.0430.0430.0000.0000.0000.000
206A222GLY00.0490.02748.692-0.031-0.0310.0000.0000.0000.000
207A223LEU0-0.045-0.01240.8220.0170.0170.0000.0000.0000.000
208A224VAL00.0020.00842.9940.0000.0000.0000.0000.0000.000
209A225ALA00.0290.01038.5260.1000.1000.0000.0000.0000.000
210A226GLU-1-0.721-0.85634.8028.7928.7920.0000.0000.0000.000
211A227ALA00.0100.00135.4790.0200.0200.0000.0000.0000.000
212A228VAL0-0.021-0.00636.967-0.004-0.0040.0000.0000.0000.000
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