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: 3Q6KL

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2711311.027455
FMO2-HF: Nuclear repulsion 2621864.565063
FMO2-HF: Total energy -89446.462392
FMO2-MP2: Total energy -89708.364911


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.
-50.801-48.631-0.031-1.139-10.003
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 : -0.989 / q_NPA : -1.002
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].
3A0LYS10.8310.9013.803-29.286-27.116-0.031-1.139-1.0000.003
4A1MET00.0320.0147.041-1.909-1.9090.0000.0000.0000.000
5A2ALA0-0.048-0.03210.060-0.323-0.3230.0000.0000.0000.000
6A3GLU-1-0.827-0.89313.28222.06022.0600.0000.0000.0000.000
7A4LEU0-0.019-0.01116.050-0.294-0.2940.0000.0000.0000.000
8A5SER00.0270.01218.275-0.099-0.0990.0000.0000.0000.000
9A6THR00.0140.00820.307-0.229-0.2290.0000.0000.0000.000
10A7ARG10.9330.95917.514-17.427-17.4270.0000.0000.0000.000
11A8TYR0-0.012-0.00821.2840.1450.1450.0000.0000.0000.000
12A9ASN00.0260.01925.123-0.284-0.2840.0000.0000.0000.000
13A10LEU0-0.021-0.00927.876-0.016-0.0160.0000.0000.0000.000
14A11PRO00.0120.01631.323-0.206-0.2060.0000.0000.0000.000
15A20ASN0-0.047-0.04352.9370.0020.0020.0000.0000.0000.000
16A21LEU0-0.027-0.00351.8640.0110.0110.0000.0000.0000.000
17A22ASP-1-0.802-0.91555.5695.5195.5190.0000.0000.0000.000
18A23LEU00.0590.02258.3490.0670.0670.0000.0000.0000.000
19A24ASN0-0.040-0.02259.9110.0870.0870.0000.0000.0000.000
20A25SER0-0.0020.00554.7250.0700.0700.0000.0000.0000.000
21A26THR0-0.022-0.00754.8710.0920.0920.0000.0000.0000.000
22A27ALA0-0.0050.01556.5420.0030.0030.0000.0000.0000.000
23A28ARG10.9580.96756.595-5.623-5.6230.0000.0000.0000.000
24A29TRP00.0140.00149.6930.0870.0870.0000.0000.0000.000
25A30ILE00.020-0.00653.897-0.064-0.0640.0000.0000.0000.000
26A31LYS10.9050.97349.462-6.174-6.1740.0000.0000.0000.000
27A32GLU-1-0.898-0.95448.7346.4356.4350.0000.0000.0000.000
28A33PRO0-0.035-0.00947.7300.1480.1480.0000.0000.0000.000
29A34SER00.0100.00143.2450.0700.0700.0000.0000.0000.000
30A35VAL00.0450.01039.073-0.038-0.0380.0000.0000.0000.000
31A36GLY00.0290.01839.0150.1450.1450.0000.0000.0000.000
32A37GLY0-0.018-0.01739.9140.0370.0370.0000.0000.0000.000
33A38TRP0-0.043-0.02643.054-0.152-0.1520.0000.0000.0000.000
34A39THR00.0160.01944.2770.1960.1960.0000.0000.0000.000
35A40VAL0-0.007-0.00346.124-0.172-0.1720.0000.0000.0000.000
36A41LYS10.9090.96547.844-6.549-6.5490.0000.0000.0000.000
37A42TRP00.0110.00949.755-0.101-0.1010.0000.0000.0000.000
38A43GLY00.0480.01250.3760.1080.1080.0000.0000.0000.000
39A44ASN0-0.036-0.03048.202-0.009-0.0090.0000.0000.0000.000
40A45PHE0-0.041-0.00745.1550.1910.1910.0000.0000.0000.000
41A46VAL0-0.011-0.01443.936-0.139-0.1390.0000.0000.0000.000
42A47PHE0-0.0150.00543.3150.1930.1930.0000.0000.0000.000
43A48HIS00.0230.00939.995-0.181-0.1810.0000.0000.0000.000
44A49ILE0-0.027-0.01740.9480.1140.1140.0000.0000.0000.000
45A50PRO00.0310.03338.505-0.065-0.0650.0000.0000.0000.000
46A51ASN0-0.007-0.01440.591-0.011-0.0110.0000.0000.0000.000
47A52THR0-0.008-0.01437.5030.0200.0200.0000.0000.0000.000
48A53GLY00.0280.01739.7030.0050.0050.0000.0000.0000.000
49A54MET0-0.0160.00740.201-0.085-0.0850.0000.0000.0000.000
50A55THR00.0260.00341.531-0.206-0.2060.0000.0000.0000.000
51A56LEU00.0450.03339.073-0.115-0.1150.0000.0000.0000.000
52A57LEU00.0400.01842.740-0.109-0.1090.0000.0000.0000.000
53A58HIS00.0550.02245.624-0.174-0.1740.0000.0000.0000.000
54A59HIS0-0.033-0.01544.581-0.142-0.1420.0000.0000.0000.000
55A60LEU00.0130.00542.726-0.105-0.1050.0000.0000.0000.000
56A61LYS10.8580.96346.697-5.840-5.8400.0000.0000.0000.000
57A62SER0-0.033-0.02350.083-0.153-0.1530.0000.0000.0000.000
58A63ASN0-0.038-0.02148.7860.0340.0340.0000.0000.0000.000
59A64PHE00.0130.03147.096-0.003-0.0030.0000.0000.0000.000
60A65VAL0-0.027-0.02043.2990.1620.1620.0000.0000.0000.000
61A66VAL00.0570.03939.129-0.132-0.1320.0000.0000.0000.000
62A67PRO00.037-0.01541.890-0.018-0.0180.0000.0000.0000.000
63A68GLU-1-0.888-0.94036.4138.0848.0840.0000.0000.0000.000
64A69TRP00.0130.00037.517-0.036-0.0360.0000.0000.0000.000
65A70GLN0-0.011-0.02042.268-0.213-0.2130.0000.0000.0000.000
66A71GLN00.0420.02139.694-0.268-0.2680.0000.0000.0000.000
67A72THR00.0200.02041.117-0.041-0.0410.0000.0000.0000.000
68A73ARG10.8230.89844.124-6.346-6.3460.0000.0000.0000.000
69A74ASN0-0.021-0.02047.355-0.238-0.2380.0000.0000.0000.000
70A75LEU00.0120.02644.062-0.119-0.1190.0000.0000.0000.000
71A76PHE00.0160.00743.719-0.062-0.0620.0000.0000.0000.000
72A77SER00.0370.02348.964-0.073-0.0730.0000.0000.0000.000
73A78HIS0-0.016-0.00751.957-0.060-0.0600.0000.0000.0000.000
74A79LEU0-0.007-0.00848.900-0.065-0.0650.0000.0000.0000.000
75A80PHE0-0.012-0.00945.819-0.049-0.0490.0000.0000.0000.000
76A81LYS10.8610.94450.885-5.876-5.8760.0000.0000.0000.000
77A82ASN00.0800.02953.592-0.179-0.1790.0000.0000.0000.000
78A83PRO00.0140.01056.5320.0460.0460.0000.0000.0000.000
79A84LYS10.8350.92659.064-5.125-5.1250.0000.0000.0000.000
80A85SER0-0.021-0.01954.001-0.026-0.0260.0000.0000.0000.000
81A86THR0-0.042-0.03155.468-0.034-0.0340.0000.0000.0000.000
82A87ILE0-0.0070.00549.1510.0320.0320.0000.0000.0000.000
83A88ILE0-0.0080.00451.158-0.074-0.0740.0000.0000.0000.000
84A89GLU-1-0.872-0.95549.1036.3576.3570.0000.0000.0000.000
85A90PRO00.0610.00344.891-0.080-0.0800.0000.0000.0000.000
86A91PHE0-0.010-0.00547.1880.0250.0250.0000.0000.0000.000
87A92LEU00.021-0.00149.326-0.057-0.0570.0000.0000.0000.000
88A93ALA00.0160.01148.103-0.069-0.0690.0000.0000.0000.000
89A94LEU00.0040.00545.861-0.004-0.0040.0000.0000.0000.000
90A95ARG10.8000.92248.713-5.597-5.5970.0000.0000.0000.000
91A96ILE00.0210.01052.202-0.058-0.0580.0000.0000.0000.000
92A97LEU0-0.010-0.00645.690-0.047-0.0470.0000.0000.0000.000
93A98LEU00.0130.00149.2920.0060.0060.0000.0000.0000.000
94A99GLY00.0420.00951.272-0.066-0.0660.0000.0000.0000.000
95A100VAL0-0.032-0.02052.050-0.107-0.1070.0000.0000.0000.000
96A101ALA00.0120.02050.198-0.033-0.0330.0000.0000.0000.000
97A102LEU0-0.026-0.01151.932-0.029-0.0290.0000.0000.0000.000
98A103LYS10.8660.93455.096-5.460-5.4600.0000.0000.0000.000
99A104ASP-1-0.825-0.88351.6806.1296.1290.0000.0000.0000.000
100A105GLN00.022-0.00854.328-0.022-0.0220.0000.0000.0000.000
101A106GLU-1-0.843-0.93050.1366.2916.2910.0000.0000.0000.000
102A107LEU0-0.0180.02152.9480.0040.0040.0000.0000.0000.000
103A108GLN0-0.0140.00854.639-0.153-0.1530.0000.0000.0000.000
104A109GLN0-0.036-0.02556.646-0.072-0.0720.0000.0000.0000.000
105A110SER0-0.056-0.03955.626-0.004-0.0040.0000.0000.0000.000
106A111LEU0-0.028-0.00757.158-0.007-0.0070.0000.0000.0000.000
107A112ILE00.0540.01960.332-0.064-0.0640.0000.0000.0000.000
108A113PRO00.0590.01264.0900.0260.0260.0000.0000.0000.000
109A114GLY00.0310.01666.651-0.023-0.0230.0000.0000.0000.000
110A115PHE00.022-0.00158.220-0.007-0.0070.0000.0000.0000.000
111A116ARG10.8690.94461.589-5.126-5.1260.0000.0000.0000.000
112A117SER00.0100.01163.1890.0380.0380.0000.0000.0000.000
113A118ILE00.0300.00362.3540.0020.0020.0000.0000.0000.000
114A119VAL00.0270.00758.0600.0370.0370.0000.0000.0000.000
115A120HIS0-0.0150.00260.2160.1200.1200.0000.0000.0000.000
116A121MET00.0010.00762.318-0.011-0.0110.0000.0000.0000.000
117A122LEU0-0.0150.00358.4160.0150.0150.0000.0000.0000.000
118A123SER0-0.036-0.01757.5150.0240.0240.0000.0000.0000.000
119A124GLU-1-0.911-0.97559.0174.9634.9630.0000.0000.0000.000
120A125TRP0-0.0190.00257.7490.0250.0250.0000.0000.0000.000
121A126LEU0-0.034-0.02054.5270.0300.0300.0000.0000.0000.000
122A127LEU0-0.058-0.03155.5120.0560.0560.0000.0000.0000.000
123A128LEU0-0.054-0.02658.2600.0120.0120.0000.0000.0000.000
124A129GLU-1-0.922-0.93760.5364.8904.8900.0000.0000.0000.000
125A130VAL0-0.033-0.02857.6300.1140.1140.0000.0000.0000.000
126A131THR00.0330.03059.4350.0640.0640.0000.0000.0000.000
127A132SER00.0290.00758.1790.0330.0330.0000.0000.0000.000
128A133ALA0-0.007-0.00558.6680.0930.0930.0000.0000.0000.000
129A134ILE00.0130.02461.042-0.077-0.0770.0000.0000.0000.000
130A135HIS00.002-0.00763.4750.0850.0850.0000.0000.0000.000
131A136ILE00.0240.01364.156-0.057-0.0570.0000.0000.0000.000
132A137SER0-0.016-0.01567.8430.0100.0100.0000.0000.0000.000
133A138PRO00.0510.00870.7140.0110.0110.0000.0000.0000.000
134A139ASN00.0010.00271.720-0.024-0.0240.0000.0000.0000.000
135A140LEU0-0.002-0.00569.789-0.015-0.0150.0000.0000.0000.000
136A141LEU0-0.057-0.01366.4290.0470.0470.0000.0000.0000.000
137A142GLY00.0240.03169.837-0.046-0.0460.0000.0000.0000.000
138A143ILE0-0.037-0.01865.665-0.036-0.0360.0000.0000.0000.000
139A144TYR00.0230.00966.6900.0380.0380.0000.0000.0000.000
140A145LEU0-0.005-0.00562.3000.0410.0410.0000.0000.0000.000
141A146THR00.0470.01760.6970.0420.0420.0000.0000.0000.000
142A147SER00.0410.00355.8010.1050.1050.0000.0000.0000.000
143A148ASP-1-0.891-0.95355.5455.8995.8990.0000.0000.0000.000
144A149MET0-0.0150.00355.7960.0650.0650.0000.0000.0000.000
145A150PHE00.0730.03055.5610.0420.0420.0000.0000.0000.000
146A151LYS10.9280.97351.205-6.034-6.0340.0000.0000.0000.000
147A152ILE00.0010.00351.5450.1460.1460.0000.0000.0000.000
148A153LEU00.0140.01652.7980.0300.0300.0000.0000.0000.000
149A154MET0-0.060-0.02349.2740.0820.0820.0000.0000.0000.000
150A155ALA00.0050.00047.9940.1430.1430.0000.0000.0000.000
151A156GLY00.0380.01448.2360.0970.0970.0000.0000.0000.000
152A157VAL0-0.0040.00247.5350.0390.0390.0000.0000.0000.000
153A158LYS10.9160.96442.408-7.408-7.4080.0000.0000.0000.000
154A159ASN00.0200.01944.3650.3120.3120.0000.0000.0000.000
155A160PHE00.0090.00345.8280.0550.0550.0000.0000.0000.000
156A161PHE0-0.025-0.03542.7400.0380.0380.0000.0000.0000.000
157A162ASN0-0.037-0.02139.6570.0700.0700.0000.0000.0000.000
158A163LYS10.8800.93241.671-6.301-6.3010.0000.0000.0000.000
159A164MET0-0.0080.04243.266-0.016-0.0160.0000.0000.0000.000
160A165PHE0-0.089-0.04236.5870.1190.1190.0000.0000.0000.000
161A166THR0-0.068-0.05038.4640.1650.1650.0000.0000.0000.000
162A167LEU0-0.0340.00540.628-0.029-0.0290.0000.0000.0000.000
163A168HIS0-0.0030.00337.3200.3790.3790.0000.0000.0000.000
164A169VAL00.0090.00135.709-0.177-0.1770.0000.0000.0000.000
165A170VAL0-0.004-0.00338.830-0.054-0.0540.0000.0000.0000.000
166A171ASN0-0.038-0.02538.9190.1150.1150.0000.0000.0000.000
167A172ASP-1-0.900-0.94639.6557.3777.3770.0000.0000.0000.000
168A173HIS0-0.024-0.02436.3100.0120.0120.0000.0000.0000.000
169A174GLY0-0.0050.00041.928-0.048-0.0480.0000.0000.0000.000
170A175LYS10.9070.97037.048-8.064-8.0640.0000.0000.0000.000
171A176PRO00.0430.01343.252-0.011-0.0110.0000.0000.0000.000
172A177SER00.0390.02342.7600.1210.1210.0000.0000.0000.000
173A178SER00.0080.00743.9780.0180.0180.0000.0000.0000.000
174A179ILE0-0.0050.02047.001-0.045-0.0450.0000.0000.0000.000
175A180GLU-1-0.928-0.96349.4235.7695.7690.0000.0000.0000.000
176A181ILE00.0130.00653.032-0.039-0.0390.0000.0000.0000.000
177A182LYS10.8890.95355.961-5.091-5.0910.0000.0000.0000.000
178A183LEU00.0200.00758.509-0.035-0.0350.0000.0000.0000.000
179A184THR00.033-0.00461.957-0.035-0.0350.0000.0000.0000.000
180A185GLY0-0.0200.00464.9810.0050.0050.0000.0000.0000.000
181A186GLN00.006-0.01359.606-0.012-0.0120.0000.0000.0000.000
182A187GLN0-0.033-0.00856.644-0.039-0.0390.0000.0000.0000.000
183A188ILE00.0030.01052.7990.0150.0150.0000.0000.0000.000
184A189ILE00.0250.01849.829-0.003-0.0030.0000.0000.0000.000
185A190ILE0-0.007-0.00245.8670.0540.0540.0000.0000.0000.000
186A191THR00.011-0.02644.1110.0050.0050.0000.0000.0000.000
187A192ARG10.8320.93735.540-8.180-8.1800.0000.0000.0000.000
188A193VAL0-0.014-0.01839.7790.0330.0330.0000.0000.0000.000
189A194ASN00.044-0.00334.5050.1300.1300.0000.0000.0000.000
190A195MET0-0.016-0.00535.2430.0990.0990.0000.0000.0000.000
191A196GLY00.0110.00737.1390.0210.0210.0000.0000.0000.000
192A197PHE00.0020.00939.364-0.043-0.0430.0000.0000.0000.000
193A198LEU0-0.008-0.01442.933-0.058-0.0580.0000.0000.0000.000
194A199VAL0-0.0020.01645.704-0.069-0.0690.0000.0000.0000.000
195A200GLU-1-0.824-0.93448.9945.9425.9420.0000.0000.0000.000
196A201VAL00.013-0.00252.133-0.036-0.0360.0000.0000.0000.000
197A202ARG10.8740.93853.510-5.707-5.7070.0000.0000.0000.000
198A203ARG10.9600.97558.571-5.157-5.1570.0000.0000.0000.000
199A204ILE00.0280.01862.280-0.003-0.0030.0000.0000.0000.000
200A216SER00.019-0.01066.829-0.002-0.0020.0000.0000.0000.000
201A217GLU-1-0.874-0.93661.0025.1585.1580.0000.0000.0000.000
202A218SER0-0.0380.00860.9280.0590.0590.0000.0000.0000.000
203A219VAL0-0.0020.00054.7790.0070.0070.0000.0000.0000.000
204A220VAL00.0150.01354.5130.0040.0040.0000.0000.0000.000
205A221PHE00.0120.00048.2400.0370.0370.0000.0000.0000.000
206A222GLY00.0460.02548.513-0.031-0.0310.0000.0000.0000.000
207A223LEU0-0.025-0.00840.5870.0140.0140.0000.0000.0000.000
208A224VAL0-0.0040.00642.726-0.001-0.0010.0000.0000.0000.000
209A225ALA00.0270.00838.3200.0970.0970.0000.0000.0000.000
210A226GLU-1-0.744-0.88634.8418.8038.8030.0000.0000.0000.000
211A227ALA0-0.003-0.01035.2930.0190.0190.0000.0000.0000.000
212A228VAL0-0.0040.00636.803-0.009-0.0090.0000.0000.0000.000
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