FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 4L3RN

Calculation Name: 2IF4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IF4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9LDC0

Base Structure: X-ray

Registration Date: 2023-09-26

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 258
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3321819.051519
FMO2-HF: Nuclear repulsion 3217352.818969
FMO2-HF: Total energy -104466.23255
FMO2-MP2: Total energy -104766.165289


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:35:ASN)


Summations of interaction energy for fragment #1(A:35:ASN)
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.
-8.477-5.9816.71-3.456-5.7470.005
Interaction energy analysis for fragmet #1(A:35:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.015
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].
3A37PRO0-0.0040.0183.664-1.8410.482-0.017-1.173-1.132-0.002
4A38PRO0-0.010-0.0084.499-0.489-0.351-0.001-0.004-0.1320.000
5A39LYS10.8730.9436.5933.3493.3490.0000.0000.0000.000
6A40VAL00.0260.02510.0290.0050.0050.0000.0000.0000.000
7A41ASP-1-0.916-0.96612.574-0.946-0.9460.0000.0000.0000.000
8A42SER0-0.080-0.05715.8170.0510.0510.0000.0000.0000.000
9A43GLU-1-0.838-0.92017.767-0.304-0.3040.0000.0000.0000.000
10A44ALA0-0.068-0.04718.7060.0140.0140.0000.0000.0000.000
11A45GLU-1-0.946-0.96819.9120.0220.0220.0000.0000.0000.000
12A46VAL00.007-0.02021.170-0.007-0.0070.0000.0000.0000.000
13A47LEU0-0.075-0.03420.0610.0140.0140.0000.0000.0000.000
14A48ASP-1-0.835-0.91923.8780.1020.1020.0000.0000.0000.000
15A49GLU-1-0.944-0.95424.270-0.027-0.0270.0000.0000.0000.000
16A50LYS10.8070.91222.830-0.019-0.0190.0000.0000.0000.000
17A51VAL00.022-0.00219.3570.0320.0320.0000.0000.0000.000
18A52SER0-0.0030.02118.333-0.031-0.0310.0000.0000.0000.000
19A53LYS10.8480.92415.978-0.086-0.0860.0000.0000.0000.000
20A54GLN0-0.0280.00814.203-0.020-0.0200.0000.0000.0000.000
21A55ILE00.0420.01014.043-0.024-0.0240.0000.0000.0000.000
22A56ILE0-0.0190.0209.596-0.081-0.0810.0000.0000.0000.000
23A57LYS10.9140.95013.592-0.358-0.3580.0000.0000.0000.000
24A58GLU-1-0.873-0.95415.3390.0890.0890.0000.0000.0000.000
25A59GLY0-0.0140.00818.8040.0540.0540.0000.0000.0000.000
26A60HIS0-0.0080.00120.326-0.033-0.0330.0000.0000.0000.000
27A61GLY00.011-0.00423.6680.0340.0340.0000.0000.0000.000
28A62SER00.013-0.00726.122-0.022-0.0220.0000.0000.0000.000
29A63LYS10.8680.93323.468-0.093-0.0930.0000.0000.0000.000
30A64PRO00.0330.02922.749-0.009-0.0090.0000.0000.0000.000
31A65SER00.0420.03325.900-0.026-0.0260.0000.0000.0000.000
32A66LYS10.8430.92128.565-0.149-0.1490.0000.0000.0000.000
33A67TYR00.016-0.02428.276-0.016-0.0160.0000.0000.0000.000
34A68SER0-0.0220.00225.8440.0080.0080.0000.0000.0000.000
35A69THR0-0.019-0.02723.8840.0110.0110.0000.0000.0000.000
36A70CYS0-0.049-0.02219.932-0.016-0.0160.0000.0000.0000.000
37A71PHE00.0420.04019.2710.0430.0430.0000.0000.0000.000
38A72LEU0-0.073-0.06113.802-0.037-0.0370.0000.0000.0000.000
39A73HIS00.1220.10310.3610.2940.2940.0000.0000.0000.000
40A74TYR0-0.001-0.0389.262-0.351-0.3510.0000.0000.0000.000
41A75ARG10.8410.9593.109-10.101-8.3690.285-0.611-1.407-0.002
42A76ALA00.0420.0247.054-0.797-0.7970.0000.0000.0000.000
43A77TRP0-0.007-0.0012.877-0.1240.6600.174-0.212-0.745-0.001
44A78THR00.0660.0489.276-0.147-0.1470.0000.0000.0000.000
45A79LYS10.9250.95411.7250.4070.4070.0000.0000.0000.000
46A80ASN0-0.049-0.04313.065-0.236-0.2360.0000.0000.0000.000
47A81SER00.0470.01712.499-0.099-0.0990.0000.0000.0000.000
48A82GLN0-0.054-0.0288.229-0.192-0.1920.0000.0000.0000.000
49A83HIS00.0160.0077.506-0.528-0.5280.0000.0000.0000.000
50A84LYS10.8800.9322.424-10.030-12.6066.270-1.455-2.2390.010
51A85PHE0-0.055-0.0256.508-0.067-0.0670.0000.0000.0000.000
52A86GLU-1-0.799-0.9078.4401.1661.1660.0000.0000.0000.000
53A87ASP-1-0.843-0.9645.34110.03810.0380.0000.0000.0000.000
54A88THR00.0770.0187.9350.0440.0440.0000.0000.0000.000
55A89TRP0-0.062-0.0286.5310.1640.1640.0000.0000.0000.000
56A90HIS0-0.065-0.0166.6090.1240.1240.0000.0000.0000.000
57A91GLU-1-0.925-0.9628.5341.4101.4100.0000.0000.0000.000
58A92GLN0-0.109-0.04310.906-0.339-0.3390.0000.0000.0000.000
59A93GLN0-0.023-0.01712.357-0.381-0.3810.0000.0000.0000.000
60A94PRO0-0.065-0.01914.0140.0810.0810.0000.0000.0000.000
61A95ILE00.0160.00814.799-0.123-0.1230.0000.0000.0000.000
62A96GLU-1-0.885-0.94017.1560.5960.5960.0000.0000.0000.000
63A97LEU0-0.051-0.03217.794-0.007-0.0070.0000.0000.0000.000
64A98VAL0-0.0120.00220.913-0.033-0.0330.0000.0000.0000.000
65A99LEU00.0310.01621.934-0.013-0.0130.0000.0000.0000.000
66A100GLY00.0330.01125.241-0.030-0.0300.0000.0000.0000.000
67A101LYS10.8710.93326.784-0.326-0.3260.0000.0000.0000.000
68A102GLU-1-0.877-0.93522.1000.3520.3520.0000.0000.0000.000
69A103LYS10.9600.98021.184-0.572-0.5720.0000.0000.0000.000
70A104LYS10.9400.96822.195-0.232-0.2320.0000.0000.0000.000
71A105GLU-1-0.878-0.94219.3510.5320.5320.0000.0000.0000.000
72A106LEU0-0.012-0.00115.945-0.006-0.0060.0000.0000.0000.000
73A107ALA00.0060.01819.3680.0000.0000.0000.0000.0000.000
74A108GLY00.043-0.01019.032-0.016-0.0160.0000.0000.0000.000
75A109LEU0-0.0050.00113.994-0.035-0.0350.0000.0000.0000.000
76A110ALA00.0290.02617.3080.0020.0020.0000.0000.0000.000
77A111ILE00.0080.01620.471-0.019-0.0190.0000.0000.0000.000
78A112GLY00.026-0.01018.072-0.036-0.0360.0000.0000.0000.000
79A113VAL00.020-0.00516.969-0.024-0.0240.0000.0000.0000.000
80A114ALA0-0.0190.00218.868-0.029-0.0290.0000.0000.0000.000
81A115SER0-0.0140.00020.465-0.033-0.0330.0000.0000.0000.000
82A116MET0-0.166-0.08514.427-0.053-0.0530.0000.0000.0000.000
83A117LYS10.9300.97920.134-0.112-0.1120.0000.0000.0000.000
84A118SER0-0.010-0.01919.2530.0450.0450.0000.0000.0000.000
85A119GLY00.000-0.00217.501-0.067-0.0670.0000.0000.0000.000
86A120GLU-1-0.851-0.94616.4380.1570.1570.0000.0000.0000.000
87A121ARG10.8970.9496.433-0.878-0.8780.0000.0000.0000.000
88A122ALA0-0.011-0.01612.270-0.209-0.2090.0000.0000.0000.000
89A123LEU0-0.0080.0178.3580.1690.1690.0000.0000.0000.000
90A124VAL00.0100.00411.987-0.044-0.0440.0000.0000.0000.000
91A125HIS10.7910.89213.2170.3930.3930.0000.0000.0000.000
92A126VAL00.0410.03515.7020.0190.0190.0000.0000.0000.000
93A127GLY00.0400.03417.790-0.024-0.0240.0000.0000.0000.000
94A128TRP00.0220.02519.9170.0460.0460.0000.0000.0000.000
95A129GLU-1-0.901-0.96220.7880.0580.0580.0000.0000.0000.000
96A130LEU0-0.069-0.03421.4780.0170.0170.0000.0000.0000.000
97A131ALA00.0690.02517.7690.0520.0520.0000.0000.0000.000
98A132TYR0-0.049-0.02415.542-0.077-0.0770.0000.0000.0000.000
99A133GLY0-0.008-0.03019.912-0.028-0.0280.0000.0000.0000.000
100A134LYN0-0.031-0.02022.5140.0050.0050.0000.0000.0000.000
101A135GLU-1-0.885-0.94324.9170.0940.0940.0000.0000.0000.000
102A136GLY0-0.072-0.01520.708-0.004-0.0040.0000.0000.0000.000
103A137ASN00.0230.00718.099-0.004-0.0040.0000.0000.0000.000
104A138PHE00.0500.01819.385-0.018-0.0180.0000.0000.0000.000
105A139SER0-0.062-0.03218.901-0.016-0.0160.0000.0000.0000.000
106A140PHE00.0080.00017.0390.0110.0110.0000.0000.0000.000
107A141PRO0-0.0090.03614.1470.0770.0770.0000.0000.0000.000
108A142ASN00.007-0.01514.150-0.131-0.1310.0000.0000.0000.000
109A143VAL0-0.038-0.02214.0730.0080.0080.0000.0000.0000.000
110A144PRO0-0.020-0.00515.110-0.036-0.0360.0000.0000.0000.000
111A145PRO00.0360.00418.0840.0080.0080.0000.0000.0000.000
112A146MET0-0.044-0.03320.781-0.038-0.0380.0000.0000.0000.000
113A147ALA00.0220.03716.294-0.055-0.0550.0000.0000.0000.000
114A148ASP-1-0.857-0.92717.198-0.022-0.0220.0000.0000.0000.000
115A149LEU0-0.0100.00213.221-0.051-0.0510.0000.0000.0000.000
116A150LEU0-0.053-0.0299.442-0.140-0.1400.0000.0000.0000.000
117A151TYR00.0400.0099.6810.0740.0740.0000.0000.0000.000
118A152GLU-1-0.813-0.9054.9000.5210.616-0.001-0.001-0.0920.000
119A153VAL0-0.016-0.0228.6320.5580.5580.0000.0000.0000.000
120A154GLU-1-0.899-0.97110.8721.1341.1340.0000.0000.0000.000
121A155VAL00.0060.02312.6080.1370.1370.0000.0000.0000.000
122A156ILE00.0040.01515.352-0.051-0.0510.0000.0000.0000.000
123A157GLY00.007-0.00117.841-0.088-0.0880.0000.0000.0000.000
124A158PHE0-0.044-0.01521.0370.0540.0540.0000.0000.0000.000
125A159ASP-1-0.865-0.93723.6140.3360.3360.0000.0000.0000.000
126A160GLU-1-0.896-0.93526.9560.2400.2400.0000.0000.0000.000
127A161THR00.0290.01529.6160.0020.0020.0000.0000.0000.000
128A162LYS10.8810.93931.370-0.311-0.3110.0000.0000.0000.000
129A163GLU-1-0.821-0.91435.8580.1650.1650.0000.0000.0000.000
130A164GLY00.0540.03139.4110.0000.0000.0000.0000.0000.000
131A165LYS10.9320.95043.144-0.116-0.1160.0000.0000.0000.000
132A166ALA00.0060.00244.8480.0020.0020.0000.0000.0000.000
133A167ARG10.9560.95644.491-0.099-0.0990.0000.0000.0000.000
134A168SER0-0.036-0.01445.8600.0010.0010.0000.0000.0000.000
135A169ASP-1-0.913-0.94043.7070.1560.1560.0000.0000.0000.000
136A170MET0-0.047-0.01240.0260.0060.0060.0000.0000.0000.000
137A171THR00.0180.00137.005-0.009-0.0090.0000.0000.0000.000
138A172VAL0-0.006-0.01036.645-0.003-0.0030.0000.0000.0000.000
139A173GLU-1-0.803-0.90633.1090.2280.2280.0000.0000.0000.000
140A174GLU-1-0.852-0.90634.8260.2150.2150.0000.0000.0000.000
141A175ARG10.9180.97436.435-0.142-0.1420.0000.0000.0000.000
142A176ILE00.006-0.00733.911-0.009-0.0090.0000.0000.0000.000
143A177GLY00.0490.03632.958-0.006-0.0060.0000.0000.0000.000
144A178ALA00.0500.04033.736-0.003-0.0030.0000.0000.0000.000
145A179ALA0-0.040-0.01536.650-0.010-0.0100.0000.0000.0000.000
146A180ASP-1-0.837-0.95030.9110.1580.1580.0000.0000.0000.000
147A181ARG10.8820.93032.440-0.216-0.2160.0000.0000.0000.000
148A182ARG10.8920.93934.472-0.144-0.1440.0000.0000.0000.000
149A183LYS10.9410.99033.957-0.101-0.1010.0000.0000.0000.000
150A184MET0-0.089-0.05528.644-0.010-0.0100.0000.0000.0000.000
151A185ASP-1-0.918-0.96334.6490.1060.1060.0000.0000.0000.000
152A186GLY00.0380.00937.162-0.009-0.0090.0000.0000.0000.000
153A187ASN0-0.040-0.01133.794-0.016-0.0160.0000.0000.0000.000
154A188SER0-0.055-0.01035.449-0.015-0.0150.0000.0000.0000.000
155A189LEU0-0.0140.02036.845-0.009-0.0090.0000.0000.0000.000
156A190PHE00.036-0.00739.141-0.008-0.0080.0000.0000.0000.000
157A191LYS10.8700.93635.146-0.030-0.0300.0000.0000.0000.000
158A192GLU-1-0.952-0.96039.096-0.026-0.0260.0000.0000.0000.000
159A193GLU-1-0.904-0.95041.6190.0240.0240.0000.0000.0000.000
160A194LYS10.8060.86743.346-0.006-0.0060.0000.0000.0000.000
161A195LEU00.0300.04743.6020.0010.0010.0000.0000.0000.000
162A196GLU-1-0.892-0.96545.7040.0440.0440.0000.0000.0000.000
163A197GLU-1-0.830-0.92045.4220.0560.0560.0000.0000.0000.000
164A198ALA00.0600.02341.7360.0060.0060.0000.0000.0000.000
165A199MET0-0.021-0.03543.1840.0040.0040.0000.0000.0000.000
166A200GLN0-0.038-0.00945.3030.0080.0080.0000.0000.0000.000
167A201GLN00.0130.00541.0190.0050.0050.0000.0000.0000.000
168A202TYR0-0.111-0.08438.2300.0040.0040.0000.0000.0000.000
169A203GLU-1-0.899-0.97842.4560.0630.0630.0000.0000.0000.000
170A204MET0-0.017-0.00243.3100.0050.0050.0000.0000.0000.000
171A205ALA00.0030.01639.4030.0080.0080.0000.0000.0000.000
172A206ILE0-0.057-0.05341.0750.0050.0050.0000.0000.0000.000
173A207ALA0-0.012-0.01143.5460.0030.0030.0000.0000.0000.000
174A208TYR0-0.074-0.01640.4830.0010.0010.0000.0000.0000.000
175A209MET0-0.108-0.03737.4550.0020.0020.0000.0000.0000.000
176A210GLY00.0590.02342.868-0.005-0.0050.0000.0000.0000.000
177A211ASP-1-0.889-0.95446.1360.0850.0850.0000.0000.0000.000
178A212ASP-1-0.903-0.93948.1100.0900.0900.0000.0000.0000.000
179A213PHE0-0.059-0.04839.0710.0040.0040.0000.0000.0000.000
180A214MET0-0.053-0.04240.4710.0060.0060.0000.0000.0000.000
181A215PHE0-0.0040.02843.8990.0010.0010.0000.0000.0000.000
182A216GLN0-0.073-0.02344.979-0.002-0.0020.0000.0000.0000.000
183A217LEU00.0120.00738.7290.0100.0100.0000.0000.0000.000
184A218TYR00.001-0.00537.590-0.009-0.0090.0000.0000.0000.000
185A219GLY00.0660.02336.3710.0110.0110.0000.0000.0000.000
186A220LYS10.9400.98127.366-0.251-0.2510.0000.0000.0000.000
187A221TYR0-0.055-0.04633.3810.0050.0050.0000.0000.0000.000
188A222GLN00.010-0.00735.555-0.007-0.0070.0000.0000.0000.000
189A223ASP-1-0.890-0.94433.2380.1300.1300.0000.0000.0000.000
190A224MET0-0.067-0.03729.326-0.008-0.0080.0000.0000.0000.000
191A225ALA00.0380.02733.502-0.004-0.0040.0000.0000.0000.000
192A226LEU00.0560.04536.832-0.008-0.0080.0000.0000.0000.000
193A227ALA00.0010.00432.354-0.011-0.0110.0000.0000.0000.000
194A228VAL0-0.036-0.03433.703-0.006-0.0060.0000.0000.0000.000
195A229LYS10.9700.96635.802-0.089-0.0890.0000.0000.0000.000
196A230ASN00.0310.01638.508-0.008-0.0080.0000.0000.0000.000
197A231PRO0-0.088-0.03535.213-0.011-0.0110.0000.0000.0000.000
198A232CYS0-0.0050.02638.243-0.007-0.0070.0000.0000.0000.000
199A233HIS00.0750.04439.809-0.002-0.0020.0000.0000.0000.000
200A234LEU0-0.020-0.02040.011-0.007-0.0070.0000.0000.0000.000
201A235ASN0-0.016-0.03738.177-0.004-0.0040.0000.0000.0000.000
202A236ILE00.1210.06741.622-0.002-0.0020.0000.0000.0000.000
203A237ALA0-0.046-0.01344.791-0.005-0.0050.0000.0000.0000.000
204A238ALA0-0.022-0.00843.232-0.003-0.0030.0000.0000.0000.000
205A239CYS0-0.0420.02044.254-0.003-0.0030.0000.0000.0000.000
206A240LEU00.0180.01745.8340.0000.0000.0000.0000.0000.000
207A241ILE0-0.071-0.03847.292-0.004-0.0040.0000.0000.0000.000
208A242LYS10.8340.90647.4140.0030.0030.0000.0000.0000.000
209A243LEU00.0630.04549.427-0.001-0.0010.0000.0000.0000.000
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