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

tag_button

FMODB ID: 85NKY

Calculation Name: 4AEZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AEZ

Chain ID: B

ChEMBL ID:

UniProt ID: O14417

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptAll
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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2067153.168987
FMO2-HF: Nuclear repulsion 1993394.249478
FMO2-HF: Total energy -73758.919509
FMO2-MP2: Total energy -73973.497066


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(B:13:LYS)


Summations of interaction energy for fragment #1(B:13:LYS)
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.
-4.272-2.64813.3-6.923-8.001-0.01
Interaction energy analysis for fragmet #1(B:13:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.020 / q_NPA : 1.013
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].
3B15SER00.0220.0043.6634.1845.7890.005-0.655-0.9540.002
4B16SER00.0630.0271.740-2.139-5.44110.930-4.347-3.2810.004
5B17LYS10.8920.9573.92526.90627.2690.002-0.122-0.2430.000
6B18LEU0-0.044-0.0206.0072.8172.8170.0000.0000.0000.000
7B19VAL00.0400.0127.5501.9791.9790.0000.0000.0000.000
8B20SER00.0300.0016.8761.8591.8590.0000.0000.0000.000
9B21GLU-1-0.830-0.8839.473-19.206-19.2060.0000.0000.0000.000
10B22PHE00.0400.02011.6331.2341.2340.0000.0000.0000.000
11B23PHE00.0560.01510.4420.9170.9170.0000.0000.0000.000
12B24GLU-1-0.784-0.84913.659-15.046-15.0460.0000.0000.0000.000
13B25TYR00.003-0.01315.6031.0171.0170.0000.0000.0000.000
14B26ALA0-0.0050.01917.0390.7550.7550.0000.0000.0000.000
15B27VAL00.0250.01017.5070.6020.6020.0000.0000.0000.000
16B28ASN0-0.013-0.02119.0420.9540.9540.0000.0000.0000.000
17B29SER0-0.024-0.02021.3440.5060.5060.0000.0000.0000.000
18B30ILE00.0030.00921.2760.4210.4210.0000.0000.0000.000
19B31LEU0-0.011-0.00823.0940.3920.3920.0000.0000.0000.000
20B32PHE0-0.0110.00725.9600.3710.3710.0000.0000.0000.000
21B33GLN0-0.045-0.04526.1960.2590.2590.0000.0000.0000.000
22B34ARG10.7470.83727.6269.1519.1510.0000.0000.0000.000
23B35GLY00.0240.02530.1140.1830.1830.0000.0000.0000.000
24B36ILE0-0.065-0.03127.6150.1450.1450.0000.0000.0000.000
25B37TYR0-0.001-0.00126.702-0.070-0.0700.0000.0000.0000.000
26B38PRO00.0450.02530.889-0.021-0.0210.0000.0000.0000.000
27B39ALA0-0.001-0.01331.629-0.250-0.2500.0000.0000.0000.000
28B40GLU-1-0.953-0.97731.641-8.057-8.0570.0000.0000.0000.000
29B41ASP-1-0.823-0.90129.335-8.967-8.9670.0000.0000.0000.000
30B42PHE0-0.049-0.03324.994-0.590-0.5900.0000.0000.0000.000
31B43LYS10.9530.99325.26111.45111.4510.0000.0000.0000.000
32B44VAL00.0180.00626.354-0.336-0.3360.0000.0000.0000.000
33B45VAL0-0.049-0.02421.720-0.027-0.0270.0000.0000.0000.000
34B46ARG10.8470.92123.98211.49411.4940.0000.0000.0000.000
35B47LYS10.8650.93114.23917.64217.6420.0000.0000.0000.000
36B48TYR00.0650.01114.0770.7290.7290.0000.0000.0000.000
37B49GLY00.0120.01619.6810.3380.3380.0000.0000.0000.000
38B50LEU0-0.010-0.00122.4320.6650.6650.0000.0000.0000.000
39B51ASN00.0120.00124.408-0.509-0.5090.0000.0000.0000.000
40B52MET00.0080.02920.2240.2350.2350.0000.0000.0000.000
41B53LEU00.0420.02323.8670.1510.1510.0000.0000.0000.000
42B54VAL0-0.044-0.03020.650-0.433-0.4330.0000.0000.0000.000
43B55SER00.0280.01023.1930.3390.3390.0000.0000.0000.000
44B56VAL0-0.070-0.06424.247-0.424-0.4240.0000.0000.0000.000
45B57ASP-1-0.773-0.87626.884-9.625-9.6250.0000.0000.0000.000
46B58GLU-1-0.829-0.90325.202-11.391-11.3910.0000.0000.0000.000
47B59GLU-1-0.945-0.94224.859-9.705-9.7050.0000.0000.0000.000
48B60VAL00.0280.00923.599-0.463-0.4630.0000.0000.0000.000
49B61LYS10.7870.87421.39610.77010.7700.0000.0000.0000.000
50B62THR0-0.034-0.03220.100-0.805-0.8050.0000.0000.0000.000
51B63TYR0-0.0150.00020.097-0.556-0.5560.0000.0000.0000.000
52B64ILE00.0090.00017.236-0.515-0.5150.0000.0000.0000.000
53B65ARG10.8020.85915.87214.16214.1620.0000.0000.0000.000
54B66LYS10.8560.91815.17810.97110.9710.0000.0000.0000.000
55B67ILE00.0460.04015.330-0.790-0.7900.0000.0000.0000.000
56B68VAL00.0160.00411.663-0.959-0.9590.0000.0000.0000.000
57B69SER0-0.066-0.03410.755-1.578-1.5780.0000.0000.0000.000
58B70GLN00.0160.01010.390-1.568-1.5680.0000.0000.0000.000
59B71LEU00.0320.02110.430-0.859-0.8590.0000.0000.0000.000
60B72HIS00.0110.0033.888-1.131-0.904-0.001-0.028-0.1980.000
61B73LYS10.8580.9155.53016.34416.3440.0000.0000.0000.000
62B74TRP00.0170.0037.321-1.353-1.3530.0000.0000.0000.000
63B75MET0-0.039-0.0065.2660.0780.0780.0000.0000.0000.000
64B76PHE0-0.074-0.0392.350-7.816-5.4132.364-1.755-3.012-0.016
65B77ALA0-0.045-0.0263.788-1.952-1.8280.002-0.007-0.1190.000
66B78LYS10.8720.9285.79332.62932.6290.0000.0000.0000.000
67B79LYS10.8240.8988.11419.03219.0320.0000.0000.0000.000
68B80ILE0-0.023-0.0059.4131.1291.1290.0000.0000.0000.000
69B81GLN0-0.021-0.02111.656-0.177-0.1770.0000.0000.0000.000
70B82LYS10.8170.89914.49913.60413.6040.0000.0000.0000.000
71B83LEU0-0.0020.01114.249-0.134-0.1340.0000.0000.0000.000
72B84ILE0-0.034-0.01016.4710.2540.2540.0000.0000.0000.000
73B85LEU0-0.028-0.00920.121-0.213-0.2130.0000.0000.0000.000
74B86VAL0-0.0030.00422.0610.1660.1660.0000.0000.0000.000
75B87ILE00.005-0.00425.736-0.093-0.0930.0000.0000.0000.000
76B88THR0-0.005-0.02228.6730.0860.0860.0000.0000.0000.000
77B89SER00.021-0.02331.767-0.048-0.0480.0000.0000.0000.000
78B90LYS10.8890.92933.5978.0318.0310.0000.0000.0000.000
79B91CYS0-0.062-0.01036.3710.0930.0930.0000.0000.0000.000
80B92SER00.005-0.01838.7360.0780.0780.0000.0000.0000.000
81B93GLY0-0.028-0.00335.9360.0460.0460.0000.0000.0000.000
82B94GLU-1-0.788-0.85534.953-7.697-7.6970.0000.0000.0000.000
83B95ASP-1-0.808-0.87030.273-9.023-9.0230.0000.0000.0000.000
84B96LEU00.0760.03532.1420.0600.0600.0000.0000.0000.000
85B97GLU-1-0.740-0.85028.191-9.213-9.2130.0000.0000.0000.000
86B98ARG10.7870.87923.74310.38210.3820.0000.0000.0000.000
87B99TRP00.023-0.00622.265-0.243-0.2430.0000.0000.0000.000
88B100GLN00.005-0.00120.3180.0250.0250.0000.0000.0000.000
89B101PHE0-0.017-0.01815.940-0.075-0.0750.0000.0000.0000.000
90B102ASN0-0.022-0.00916.572-0.105-0.1050.0000.0000.0000.000
91B103VAL0-0.012-0.03010.302-0.680-0.6800.0000.0000.0000.000
92B104GLU-1-0.837-0.91813.011-15.105-15.1050.0000.0000.0000.000
93B105MET0-0.029-0.0219.363-1.988-1.9880.0000.0000.0000.000
94B106VAL0-0.058-0.02211.7751.0711.0710.0000.0000.0000.000
95B107ASP-1-0.951-0.96313.521-17.312-17.3120.0000.0000.0000.000
96B117ASN00.032-0.01310.273-0.178-0.1780.0000.0000.0000.000
97B118LYS10.7720.86411.27723.67023.6700.0000.0000.0000.000
98B119GLU-1-0.894-0.94613.003-15.577-15.5770.0000.0000.0000.000
99B120ASP-1-0.771-0.86011.793-21.413-21.4130.0000.0000.0000.000
100B121GLU-1-0.837-0.89810.266-26.272-26.2720.0000.0000.0000.000
101B122LEU00.003-0.00312.7400.9100.9100.0000.0000.0000.000
102B123ARG10.7700.85613.39020.55320.5530.0000.0000.0000.000
103B124VAL00.0320.01411.8100.6990.6990.0000.0000.0000.000
104B125GLN0-0.039-0.02113.9181.4651.4650.0000.0000.0000.000
105B126LYS10.8870.93417.05513.57613.5760.0000.0000.0000.000
106B127GLU-1-0.800-0.88516.445-16.567-16.5670.0000.0000.0000.000
107B128ILE00.0010.00813.3440.5870.5870.0000.0000.0000.000
108B129GLN0-0.031-0.01117.9301.0141.0140.0000.0000.0000.000
109B130ALA0-0.015-0.01421.3480.6150.6150.0000.0000.0000.000
110B131LEU0-0.0210.00217.6120.4960.4960.0000.0000.0000.000
111B132ILE00.0410.00418.5170.4170.4170.0000.0000.0000.000
112B133ALA0-0.0170.00421.9870.4910.4910.0000.0000.0000.000
113B134GLN00.016-0.00524.5770.1040.1040.0000.0000.0000.000
114B135ILE00.0180.01020.2930.2620.2620.0000.0000.0000.000
115B136THR0-0.0060.00724.7860.3310.3310.0000.0000.0000.000
116B137ALA0-0.021-0.01027.3180.3330.3330.0000.0000.0000.000
117B138THR0-0.009-0.00427.1370.3660.3660.0000.0000.0000.000
118B139VAL00.0040.01129.9910.2520.2520.0000.0000.0000.000
119B140THR0-0.091-0.05932.5150.2710.2710.0000.0000.0000.000
120B141PHE0-0.018-0.01229.5690.1260.1260.0000.0000.0000.000
121B142LEU0-0.0380.00028.8540.1000.1000.0000.0000.0000.000
122B143PRO00.0200.02433.5920.1010.1010.0000.0000.0000.000
123B144GLN0-0.011-0.01335.018-0.130-0.1300.0000.0000.0000.000
124B145LEU0-0.019-0.01431.5390.1130.1130.0000.0000.0000.000
125B146GLU-1-0.932-0.96136.161-6.767-6.7670.0000.0000.0000.000
126B147GLU-1-0.811-0.85338.041-6.948-6.9480.0000.0000.0000.000
127B148GLN0-0.018-0.01333.407-0.058-0.0580.0000.0000.0000.000
128B149CYS0-0.0200.00531.8180.0260.0260.0000.0000.0000.000
129B150THR0-0.018-0.01129.558-0.030-0.0300.0000.0000.0000.000
130B151PHE00.0270.00721.819-0.098-0.0980.0000.0000.0000.000
131B152ASN0-0.0190.00224.5070.2160.2160.0000.0000.0000.000
132B153VAL00.005-0.00318.855-0.130-0.1300.0000.0000.0000.000
133B154LEU00.0200.01920.2310.1480.1480.0000.0000.0000.000
134B155VAL0-0.006-0.01314.694-0.430-0.4300.0000.0000.0000.000
135B156TYR0-0.0030.01317.0700.6440.6440.0000.0000.0000.000
136B157ALA00.0420.00614.789-0.794-0.7940.0000.0000.0000.000
137B158ASP-1-0.786-0.84913.998-15.807-15.8070.0000.0000.0000.000
138B159LYS10.9290.95716.82211.41911.4190.0000.0000.0000.000
139B160ASP-1-0.827-0.88515.115-15.987-15.9870.0000.0000.0000.000
140B161SER0-0.042-0.04614.466-1.034-1.0340.0000.0000.0000.000
141B162GLU-1-0.899-0.94413.837-14.389-14.3890.0000.0000.0000.000
142B163VAL0-0.012-0.00815.095-0.518-0.5180.0000.0000.0000.000
143B164PRO0-0.046-0.02215.6620.4220.4220.0000.0000.0000.000
144B165THR00.031-0.00318.5270.1660.1660.0000.0000.0000.000
145B166ASP-1-0.885-0.91219.558-11.564-11.5640.0000.0000.0000.000
146B167TRP0-0.021-0.01815.822-0.158-0.1580.0000.0000.0000.000
147B168VAL00.0040.00620.7220.0960.0960.0000.0000.0000.000
148B169ASP-1-0.929-0.95623.119-10.813-10.8130.0000.0000.0000.000
149B170SER0-0.023-0.03024.5350.3590.3590.0000.0000.0000.000
150B171ASP-1-0.861-0.91825.740-9.260-9.2600.0000.0000.0000.000
151B172PRO0-0.012-0.00524.783-0.190-0.1900.0000.0000.0000.000
152B173ARG10.8470.88425.7539.0629.0620.0000.0000.0000.000
153B174ILE0-0.026-0.01127.320-0.105-0.1050.0000.0000.0000.000
154B175LEU0-0.061-0.01729.1530.2150.2150.0000.0000.0000.000
155B176ARG10.8390.91431.7528.0968.0960.0000.0000.0000.000
156B177ASP-1-0.906-0.97535.292-7.273-7.2730.0000.0000.0000.000
157B178ALA0-0.025-0.01632.9320.0610.0610.0000.0000.0000.000
158B179GLU-1-0.892-0.92134.140-7.822-7.8220.0000.0000.0000.000
159B180GLN0-0.033-0.03928.965-0.402-0.4020.0000.0000.0000.000
160B181VAL0-0.0170.00428.0420.1020.1020.0000.0000.0000.000
161B182GLN0-0.035-0.01621.896-0.105-0.1050.0000.0000.0000.000
162B183LEU0-0.020-0.00722.8980.2180.2180.0000.0000.0000.000
163B184ARG10.9370.95921.99711.27911.2790.0000.0000.0000.000
164B185SER00.0290.00917.9420.0280.0280.0000.0000.0000.000
165B186PHE0-0.052-0.03111.3990.0720.0720.0000.0000.0000.000
166B187SER00.0280.01913.401-0.221-0.2210.0000.0000.0000.000
167B188THR0-0.008-0.0187.919-0.260-0.2600.0000.0000.0000.000
168B189SER00.000-0.0077.2690.9630.9630.0000.0000.0000.000
169B190MET0-0.058-0.0244.728-1.283-1.143-0.001-0.004-0.1350.000
170B191HIS00.0750.0474.9570.1890.253-0.001-0.005-0.0590.000
171B192LYS10.9030.94310.08415.22815.2280.0000.0000.0000.000
172B193ILE0-0.0040.01610.4310.6550.6550.0000.0000.0000.000
173B194ASP-1-0.794-0.87514.319-13.350-13.3500.0000.0000.0000.000
174B195CYS0-0.050-0.00317.783-0.084-0.0840.0000.0000.0000.000
175B196GLN00.0340.01620.2890.1900.1900.0000.0000.0000.000
176B197VAL00.0280.01523.366-0.210-0.2100.0000.0000.0000.000
177B198ALA00.0140.01426.1330.1910.1910.0000.0000.0000.000
178B199TYR00.032-0.01029.148-0.170-0.1700.0000.0000.0000.000
179B200ARG10.8080.89532.1377.6297.6290.0000.0000.0000.000
180B201VAL00.0020.01535.6090.1390.1390.0000.0000.0000.000