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

tag_button

FMODB ID: N99NQ

Calculation Name: 4I6L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I6L

Chain ID: A

ChEMBL ID:

UniProt ID: Q96FW1

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2852826.226346
FMO2-HF: Nuclear repulsion 2763410.775738
FMO2-HF: Total energy -89415.450609
FMO2-MP2: Total energy -89679.145535


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:43:GLY)


Summations of interaction energy for fragment #1(A:43:GLY)
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.
-0.5271.1720.003-0.749-0.9540.002
Interaction energy analysis for fragmet #1(A:43:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : -0.002
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].
3A45ASN00.0190.0113.479-0.4570.9400.003-0.676-0.7240.002
4A46PRO00.0250.0363.9800.5560.8430.001-0.071-0.2180.000
5A47LEU0-0.0070.0105.0430.2980.313-0.001-0.002-0.0120.000
6A48VAL00.0220.0098.3800.1540.1540.0000.0000.0000.000
7A49SER0-0.028-0.0117.994-0.187-0.1870.0000.0000.0000.000
8A50GLU-1-0.867-0.9438.253-0.695-0.6950.0000.0000.0000.000
9A51ARG10.9050.95810.4400.3530.3530.0000.0000.0000.000
10A52LEU00.0130.00210.7210.0060.0060.0000.0000.0000.000
11A53GLU-1-0.859-0.93914.805-0.260-0.2600.0000.0000.0000.000
12A54LEU00.013-0.01317.185-0.022-0.0220.0000.0000.0000.000
13A55SER00.0070.00718.7680.0070.0070.0000.0000.0000.000
14A56VAL00.003-0.02113.5310.0390.0390.0000.0000.0000.000
15A57LEU00.0210.01716.751-0.018-0.0180.0000.0000.0000.000
16A58TYR0-0.028-0.01219.3450.0170.0170.0000.0000.0000.000
17A59LYS10.9280.96917.3240.1410.1410.0000.0000.0000.000
18A60GLU-1-0.875-0.91315.851-0.381-0.3810.0000.0000.0000.000
19A61TYR0-0.122-0.07418.0230.0020.0020.0000.0000.0000.000
20A62ALA0-0.025-0.01520.8460.0080.0080.0000.0000.0000.000
21A63GLU-1-0.987-0.98222.874-0.014-0.0140.0000.0000.0000.000
22A64ASP-1-0.864-0.91626.497-0.049-0.0490.0000.0000.0000.000
23A65ASP-1-0.798-0.89224.884-0.089-0.0890.0000.0000.0000.000
24A66ASN0-0.070-0.07227.919-0.014-0.0140.0000.0000.0000.000
25A67ILE0-0.0110.00729.932-0.003-0.0030.0000.0000.0000.000
26A68TYR0-0.010-0.03225.402-0.006-0.0060.0000.0000.0000.000
27A69GLN00.0360.02224.168-0.018-0.0180.0000.0000.0000.000
28A70GLN0-0.031-0.02127.5830.0000.0000.0000.0000.0000.000
29A71LYS10.9670.98027.5850.1180.1180.0000.0000.0000.000
30A72ILE00.0820.05523.084-0.005-0.0050.0000.0000.0000.000
31A73LYS10.9190.97526.0300.0840.0840.0000.0000.0000.000
32A74ASP-1-0.887-0.93828.628-0.099-0.0990.0000.0000.0000.000
33A75LEU00.0510.02423.7520.0030.0030.0000.0000.0000.000
34A76HIS0-0.017-0.01024.519-0.007-0.0070.0000.0000.0000.000
35A77LYS10.8060.91126.6750.1070.1070.0000.0000.0000.000
36A78LYS10.8450.92028.4160.1390.1390.0000.0000.0000.000
37A79TYR0-0.063-0.02623.738-0.001-0.0010.0000.0000.0000.000
38A80SER0-0.0020.00223.5500.0070.0070.0000.0000.0000.000
39A81TYR0-0.034-0.02318.4470.0060.0060.0000.0000.0000.000
40A82ILE0-0.0080.01215.8010.0240.0240.0000.0000.0000.000
41A83ARG10.8650.93612.8910.5420.5420.0000.0000.0000.000
42A84LYS10.9100.96111.3180.6720.6720.0000.0000.0000.000
43A85THR00.0040.01511.380-0.094-0.0940.0000.0000.0000.000
44A86ARG10.8440.9085.9820.7750.7750.0000.0000.0000.000
45A87PRO0-0.0130.01010.7230.0870.0870.0000.0000.0000.000
46A88ASP-1-0.822-0.93912.823-0.346-0.3460.0000.0000.0000.000
47A89GLY00.0220.01714.7710.0420.0420.0000.0000.0000.000
48A90ASN0-0.0130.00015.5180.0570.0570.0000.0000.0000.000
49A91SER0-0.014-0.00415.687-0.008-0.0080.0000.0000.0000.000
50A92PHE00.0290.01916.688-0.018-0.0180.0000.0000.0000.000
51A93TYR00.016-0.00519.497-0.002-0.0020.0000.0000.0000.000
52A94ARG10.8030.88812.2790.4320.4320.0000.0000.0000.000
53A95ALA0-0.010-0.00516.408-0.028-0.0280.0000.0000.0000.000
54A96PHE0-0.001-0.01217.4690.0060.0060.0000.0000.0000.000
55A97GLY00.0140.00219.4390.0110.0110.0000.0000.0000.000
56A98PHE0-0.010-0.00714.894-0.002-0.0020.0000.0000.0000.000
57A99SER0-0.009-0.00617.8960.0220.0220.0000.0000.0000.000
58A100HIS00.0390.01220.3360.0110.0110.0000.0000.0000.000
59A101LEU0-0.005-0.01019.7120.0160.0160.0000.0000.0000.000
60A102GLU-1-0.746-0.82518.281-0.367-0.3670.0000.0000.0000.000
61A103ALA0-0.014-0.00621.1330.0140.0140.0000.0000.0000.000
62A104LEU0-0.057-0.03124.5390.0190.0190.0000.0000.0000.000
63A105LEU0-0.0290.00021.2620.0110.0110.0000.0000.0000.000
64A106ASP-1-0.935-0.95225.755-0.161-0.1610.0000.0000.0000.000
65A107ASP-1-0.920-0.97128.317-0.107-0.1070.0000.0000.0000.000
66A108SER00.0360.00630.637-0.003-0.0030.0000.0000.0000.000
67A109LYS10.9410.96132.1990.0860.0860.0000.0000.0000.000
68A110GLU-1-0.887-0.94030.573-0.115-0.1150.0000.0000.0000.000
69A111LEU00.0460.02927.2290.0000.0000.0000.0000.0000.000
70A112GLN0-0.080-0.05130.2760.0050.0050.0000.0000.0000.000
71A113ARG10.8640.94432.4380.1140.1140.0000.0000.0000.000
72A114PHE00.0330.02225.3230.0030.0030.0000.0000.0000.000
73A115LYS10.9300.96529.9250.0990.0990.0000.0000.0000.000
74A116ALA0-0.038-0.02230.8410.0040.0040.0000.0000.0000.000
75A117VAL0-0.048-0.02631.8900.0050.0050.0000.0000.0000.000
76A118SER00.0470.01228.4480.0000.0000.0000.0000.0000.000
77A119ALA0-0.0110.03730.4580.0020.0020.0000.0000.0000.000
78A120LYS10.9330.96432.4620.0800.0800.0000.0000.0000.000
79A121SER0-0.021-0.04630.7660.0020.0020.0000.0000.0000.000
80A122LYS11.0021.02131.0560.0770.0770.0000.0000.0000.000
81A123GLU-1-0.888-0.95932.795-0.055-0.0550.0000.0000.0000.000
82A124ASP-1-0.992-0.98835.133-0.073-0.0730.0000.0000.0000.000
83A125LEU00.0420.01930.1580.0020.0020.0000.0000.0000.000
84A126VAL0-0.031-0.00834.7680.0030.0030.0000.0000.0000.000
85A127SER0-0.058-0.02036.7870.0040.0040.0000.0000.0000.000
86A128GLN0-0.103-0.05236.1550.0010.0010.0000.0000.0000.000
87A129GLY0-0.037-0.02438.392-0.001-0.0010.0000.0000.0000.000
88A130PHE0-0.052-0.01331.1260.0010.0010.0000.0000.0000.000
89A131THR0-0.010-0.00633.8530.0040.0040.0000.0000.0000.000
90A132GLU-1-0.876-0.94932.975-0.062-0.0620.0000.0000.0000.000
91A133PHE00.019-0.00832.243-0.003-0.0030.0000.0000.0000.000
92A134THR0-0.055-0.02129.3190.0010.0010.0000.0000.0000.000
93A135ILE0-0.007-0.01828.089-0.005-0.0050.0000.0000.0000.000
94A136GLU-1-0.918-0.95727.985-0.067-0.0670.0000.0000.0000.000
95A137ASP-1-0.878-0.93924.751-0.079-0.0790.0000.0000.0000.000
96A138PHE0-0.061-0.02121.840-0.012-0.0120.0000.0000.0000.000
97A139HIS0-0.018-0.01823.949-0.011-0.0110.0000.0000.0000.000
98A140ASN00.000-0.00325.622-0.004-0.0040.0000.0000.0000.000
99A141THR00.0210.01719.453-0.004-0.0040.0000.0000.0000.000
100A142PHE0-0.028-0.01922.035-0.016-0.0160.0000.0000.0000.000
101A143MET0-0.050-0.03223.416-0.008-0.0080.0000.0000.0000.000
102A144ASP-1-0.879-0.92821.872-0.149-0.1490.0000.0000.0000.000
103A145LEU00.005-0.00117.857-0.010-0.0100.0000.0000.0000.000
104A146ILE0-0.022-0.01421.793-0.004-0.0040.0000.0000.0000.000
105A147GLU-1-0.915-0.95325.014-0.103-0.1030.0000.0000.0000.000
106A148GLN0-0.040-0.02619.365-0.017-0.0170.0000.0000.0000.000
107A149VAL00.007-0.00222.158-0.001-0.0010.0000.0000.0000.000
108A150GLU-1-0.853-0.91524.219-0.099-0.0990.0000.0000.0000.000
109A151LYS10.7880.90626.2450.1130.1130.0000.0000.0000.000
110A152GLN0-0.041-0.01725.473-0.004-0.0040.0000.0000.0000.000
111A153THR00.0110.02319.5290.0040.0040.0000.0000.0000.000
112A154SER0-0.0030.00718.286-0.016-0.0160.0000.0000.0000.000
113A155VAL00.0640.00616.180-0.015-0.0150.0000.0000.0000.000
114A156ALA0-0.031-0.01613.921-0.050-0.0500.0000.0000.0000.000
115A157ASP-1-0.866-0.94213.572-0.331-0.3310.0000.0000.0000.000
116A158LEU00.0010.01215.342-0.014-0.0140.0000.0000.0000.000
117A159LEU0-0.034-0.0289.857-0.004-0.0040.0000.0000.0000.000
118A160ALA00.0050.00310.555-0.106-0.1060.0000.0000.0000.000
119A161SER00.0300.01911.3690.0010.0010.0000.0000.0000.000
120A162PHE0-0.009-0.00112.4930.0230.0230.0000.0000.0000.000
121A163ASN0-0.075-0.0627.120-0.261-0.2610.0000.0000.0000.000
122A164ASP-1-0.837-0.8878.503-0.197-0.1970.0000.0000.0000.000
123A165GLN00.014-0.00110.186-0.035-0.0350.0000.0000.0000.000
124A166SER00.006-0.00211.7730.0120.0120.0000.0000.0000.000
125A167THR00.010-0.00214.8690.0160.0160.0000.0000.0000.000
126A168SER0-0.029-0.01712.4980.0220.0220.0000.0000.0000.000
127A169ASP-1-0.843-0.93014.039-0.288-0.2880.0000.0000.0000.000
128A170TYR0-0.022-0.00716.2350.0220.0220.0000.0000.0000.000
129A171LEU00.0060.01817.5910.0150.0150.0000.0000.0000.000
130A172VAL0-0.036-0.02116.4760.0140.0140.0000.0000.0000.000
131A173VAL00.0330.01319.5350.0150.0150.0000.0000.0000.000
132A174TYR00.0280.00221.9970.0150.0150.0000.0000.0000.000
133A175LEU0-0.006-0.00120.7460.0090.0090.0000.0000.0000.000
134A176ARG10.7950.89119.6060.1870.1870.0000.0000.0000.000
135A177LEU00.0110.00425.1110.0110.0110.0000.0000.0000.000
136A178LEU0-0.0220.00426.5860.0080.0080.0000.0000.0000.000
137A179THR0-0.036-0.02626.5810.0050.0050.0000.0000.0000.000
138A180SER0-0.032-0.04729.1150.0090.0090.0000.0000.0000.000
139A181GLY00.0590.02330.9910.0070.0070.0000.0000.0000.000
140A182TYR00.0190.00932.6390.0060.0060.0000.0000.0000.000
141A183LEU00.0030.00031.1490.0050.0050.0000.0000.0000.000
142A184GLN00.002-0.02033.6290.0100.0100.0000.0000.0000.000
143A185ARG10.9030.97136.6660.0820.0820.0000.0000.0000.000
144A186GLU-1-0.959-0.97838.012-0.064-0.0640.0000.0000.0000.000
145A187SER00.010-0.00539.4140.0000.0000.0000.0000.0000.000
146A188LYS10.8940.92940.3650.0490.0490.0000.0000.0000.000
147A189PHE0-0.0380.00037.8090.0020.0020.0000.0000.0000.000
148A190PHE00.036-0.01635.223-0.001-0.0010.0000.0000.0000.000
149A191GLU-1-0.843-0.92338.629-0.053-0.0530.0000.0000.0000.000
150A192HIS0-0.071-0.01640.9930.0020.0020.0000.0000.0000.000
151A193PHE0-0.066-0.02937.2600.0000.0000.0000.0000.0000.000
152A194ILE0-0.052-0.01235.556-0.003-0.0030.0000.0000.0000.000
153A195GLU-1-0.951-0.96438.259-0.053-0.0530.0000.0000.0000.000
154A196GLY00.000-0.00440.1470.0000.0000.0000.0000.0000.000
155A197GLY0-0.017-0.02041.4190.0000.0000.0000.0000.0000.000
156A198ARG10.8520.92832.7230.0660.0660.0000.0000.0000.000
157A199THR0-0.0010.02639.5910.0000.0000.0000.0000.0000.000
158A200VAL00.0650.03136.032-0.002-0.0020.0000.0000.0000.000
159A201LYS10.9400.97835.3280.0520.0520.0000.0000.0000.000
160A202GLU-1-0.892-0.96134.567-0.050-0.0500.0000.0000.0000.000
161A203PHE00.0230.00931.415-0.001-0.0010.0000.0000.0000.000
162A204CYS00.0080.00831.109-0.007-0.0070.0000.0000.0000.000
163A205GLN00.001-0.00129.738-0.005-0.0050.0000.0000.0000.000
164A206GLN0-0.056-0.02329.7980.0040.0040.0000.0000.0000.000
165A207GLU-1-0.871-0.94327.732-0.090-0.0900.0000.0000.0000.000
166A208VAL0-0.063-0.02126.561-0.011-0.0110.0000.0000.0000.000
167A209GLU-1-0.839-0.92525.360-0.093-0.0930.0000.0000.0000.000
168A210PRO0-0.053-0.00524.679-0.005-0.0050.0000.0000.0000.000
169A211MET00.0570.02617.556-0.009-0.0090.0000.0000.0000.000
170A212CYS0-0.087-0.04818.5580.0150.0150.0000.0000.0000.000
171A213LYS10.8730.96819.5260.0970.0970.0000.0000.0000.000
172A214GLU-1-0.749-0.85618.990-0.266-0.2660.0000.0000.0000.000
173A215SER0-0.033-0.01222.0880.0110.0110.0000.0000.0000.000
174A216ASP-1-0.811-0.92724.381-0.121-0.1210.0000.0000.0000.000
175A217HIS0-0.009-0.03027.4130.0020.0020.0000.0000.0000.000
176A218ILE0-0.0180.00430.1530.0010.0010.0000.0000.0000.000
177A219HIS00.0420.02326.204-0.005-0.0050.0000.0000.0000.000
178A220ILE0-0.009-0.00425.908-0.001-0.0010.0000.0000.0000.000
179A221ILE0-0.021-0.00328.1510.0010.0010.0000.0000.0000.000
180A222ALA00.0120.01130.6130.0040.0040.0000.0000.0000.000
181A223LEU00.0060.00824.4290.0030.0030.0000.0000.0000.000
182A224ALA0-0.011-0.00628.9090.0000.0000.0000.0000.0000.000
183A225GLN0-0.025-0.01630.3830.0030.0030.0000.0000.0000.000
184A226ALA0-0.052-0.01730.6630.0050.0050.0000.0000.0000.000
185A227LEU0-0.016-0.00726.6000.0030.0030.0000.0000.0000.000
186A228SER0-0.103-0.03830.8750.0020.0020.0000.0000.0000.000
187A229VAL0-0.017-0.00827.3260.0010.0010.0000.0000.0000.000
188A230SER0-0.011-0.00430.297-0.005-0.0050.0000.0000.0000.000
189A231ILE00.0310.00225.758-0.012-0.0120.0000.0000.0000.000
190A232GLN0-0.015-0.00827.6110.0150.0150.0000.0000.0000.000
191A233VAL0-0.013-0.00124.997-0.017-0.0170.0000.0000.0000.000
192A234GLU-1-0.816-0.91225.419-0.132-0.1320.0000.0000.0000.000
193A235TYR00.0320.03125.162-0.016-0.0160.0000.0000.0000.000
194A236MET0-0.053-0.01622.8360.0050.0050.0000.0000.0000.000
195A246PRO0-0.089-0.04730.9210.0020.0020.0000.0000.0000.000
196A247HIS00.0600.03730.9270.0030.0030.0000.0000.0000.000
197A248ILE00.015-0.00330.960-0.011-0.0110.0000.0000.0000.000
198A249PHE0-0.0410.02129.5410.0080.0080.0000.0000.0000.000
199A250PRO00.0530.00031.767-0.007-0.0070.0000.0000.0000.000
200A251GLU-1-0.869-0.93335.123-0.089-0.0890.0000.0000.0000.000
201A252GLY0-0.037-0.00637.6160.0030.0030.0000.0000.0000.000
202A253SER0-0.051-0.04135.0650.0000.0000.0000.0000.0000.000
203A254GLU-1-0.924-0.97834.900-0.100-0.1000.0000.0000.0000.000
204A255PRO0-0.018-0.00329.750-0.003-0.0030.0000.0000.0000.000
205A256LYS10.9060.95628.3990.1270.1270.0000.0000.0000.000
206A257VAL00.0100.02023.054-0.011-0.0110.0000.0000.0000.000
207A258TYR0-0.009-0.00624.1660.0170.0170.0000.0000.0000.000
208A259LEU00.0240.01220.246-0.026-0.0260.0000.0000.0000.000
209A260LEU0-0.018-0.01119.8200.0260.0260.0000.0000.0000.000
210A261TYR00.0120.01420.755-0.019-0.0190.0000.0000.0000.000
211A262ARG10.7650.85616.5980.3530.3530.0000.0000.0000.000
212A263PRO0-0.013-0.02221.429-0.007-0.0070.0000.0000.0000.000
213A264GLY00.0210.00521.206-0.006-0.0060.0000.0000.0000.000
214A265HIS0-0.054-0.02514.1130.0200.0200.0000.0000.0000.000
215A266TYR0-0.003-0.01217.9870.0290.0290.0000.0000.0000.000
216A267ASP-1-0.783-0.89515.125-0.554-0.5540.0000.0000.0000.000
217A268ILE00.0160.00916.1090.0490.0490.0000.0000.0000.000
218A269LEU0-0.042-0.01518.479-0.019-0.0190.0000.0000.0000.000
219A270TYR0-0.043-0.06617.348-0.007-0.0070.0000.0000.0000.000
220A271LYS10.9050.96122.4860.1640.1640.0000.0000.0000.000