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: YZQL2

Calculation Name: 2A6T-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A6T

Chain ID: B

ChEMBL ID:

UniProt ID: O13828

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2129231.238622
FMO2-HF: Nuclear repulsion 2050146.519432
FMO2-HF: Total energy -79084.71919
FMO2-MP2: Total energy -79311.457664


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:35:CYS)


Summations of interaction energy for fragment #1(B:35:CYS)
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.
-7.68-10.88224.104-8.295-12.608-0.029
Interaction energy analysis for fragmet #1(B:35:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.009
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].
3B37GLN00.034-0.0013.010-4.472-1.9230.135-1.191-1.4940.006
4B38ILE00.0000.0191.6650.917-2.5399.380-2.861-3.063-0.009
5B39GLU-1-0.865-0.9574.149-2.868-2.451-0.001-0.096-0.3200.000
6B40GLN0-0.0070.0136.1320.4640.4640.0000.0000.0000.000
7B41ALA00.0110.0037.5860.1920.1920.0000.0000.0000.000
8B42HIS0-0.047-0.0228.3440.0010.0010.0000.0000.0000.000
9B43TRP00.0220.0049.7760.2580.2580.0000.0000.0000.000
10B44PHE00.0070.01411.8640.1390.1390.0000.0000.0000.000
11B45TYR0-0.025-0.02112.9600.1090.1090.0000.0000.0000.000
12B46GLU-1-0.809-0.91213.770-0.510-0.5100.0000.0000.0000.000
13B47ASP-1-0.920-0.96315.600-0.481-0.4810.0000.0000.0000.000
14B48PHE0-0.040-0.01017.0980.0570.0570.0000.0000.0000.000
15B49ILE0-0.002-0.01015.8500.0330.0330.0000.0000.0000.000
16B50ARG10.8510.93118.3370.3730.3730.0000.0000.0000.000
17B51ALA0-0.0300.00420.7780.0210.0210.0000.0000.0000.000
18B52GLN0-0.069-0.03022.8320.0270.0270.0000.0000.0000.000
19B53ASN00.0180.00823.2990.0090.0090.0000.0000.0000.000
20B54ASP-1-0.876-0.92123.483-0.216-0.2160.0000.0000.0000.000
21B55GLN0-0.041-0.03924.626-0.010-0.0100.0000.0000.0000.000
22B56LEU0-0.009-0.00722.751-0.020-0.0200.0000.0000.0000.000
23B57PRO0-0.066-0.02319.921-0.022-0.0220.0000.0000.0000.000
24B58SER0-0.073-0.03417.5450.0080.0080.0000.0000.0000.000
25B59LEU0-0.048-0.05814.7260.0420.0420.0000.0000.0000.000
26B60GLY00.0580.03613.834-0.066-0.0660.0000.0000.0000.000
27B61LEU00.0180.0136.1370.0910.0910.0000.0000.0000.000
28B62ARG10.9850.9819.3950.6340.6340.0000.0000.0000.000
29B63VAL0-0.012-0.00710.5910.0700.0700.0000.0000.0000.000
30B64PHE00.0020.0138.2240.0850.0850.0000.0000.0000.000
31B65SER00.008-0.0157.0850.0860.0860.0000.0000.0000.000
32B66ALA00.0080.0178.9460.1170.1170.0000.0000.0000.000
33B67LYS10.8600.93612.0170.4690.4690.0000.0000.0000.000
34B68LEU00.0000.0228.4650.0850.0850.0000.0000.0000.000
35B83GLU-1-0.947-0.9897.9100.3520.3520.0000.0000.0000.000
36B84GLU-1-0.912-0.9509.5940.1380.1380.0000.0000.0000.000
37B85ALA00.011-0.0036.060-0.081-0.0810.0000.0000.0000.000
38B86PHE0-0.014-0.0183.755-1.022-0.0940.193-0.305-0.8160.000
39B87ASP-1-0.843-0.9284.794-1.568-1.562-0.0010.004-0.0090.000
40B88ASP-1-0.850-0.9357.257-0.296-0.2960.0000.0000.0000.000
41B89PHE0-0.056-0.0252.204-4.712-8.46614.399-3.817-6.828-0.026
42B90LEU0-0.0050.0074.377-0.408-0.300-0.001-0.029-0.0780.000
43B91ARG10.8450.9216.0320.4970.4970.0000.0000.0000.000
44B92TYR00.0010.0087.9930.0150.0150.0000.0000.0000.000
45B93LYS10.9320.9755.6041.8281.8280.0000.0000.0000.000
46B94THR0-0.103-0.0368.0970.0960.0960.0000.0000.0000.000
47B95ARG10.9370.95210.2750.6070.6070.0000.0000.0000.000
48B96ILE0-0.0300.00813.5800.0690.0690.0000.0000.0000.000
49B97PRO00.009-0.00216.1820.0070.0070.0000.0000.0000.000
50B98VAL0-0.0070.00218.9750.0170.0170.0000.0000.0000.000
51B99ARG10.8370.90721.3840.2610.2610.0000.0000.0000.000
52B100GLY00.1180.02925.7430.0030.0030.0000.0000.0000.000
53B101ALA0-0.038-0.00229.2000.0010.0010.0000.0000.0000.000
54B102ILE0-0.050-0.01932.1990.0020.0020.0000.0000.0000.000
55B103MET00.0100.01334.9150.0050.0050.0000.0000.0000.000
56B104LEU0-0.020-0.03438.2770.0010.0010.0000.0000.0000.000
57B105ASP-1-0.842-0.93641.245-0.072-0.0720.0000.0000.0000.000
58B106MET00.0490.02144.9910.0000.0000.0000.0000.0000.000
59B107SER00.0450.04046.8830.0000.0000.0000.0000.0000.000
60B108MET0-0.104-0.05042.573-0.003-0.0030.0000.0000.0000.000
61B109GLN00.0210.00944.001-0.002-0.0020.0000.0000.0000.000
62B110GLN0-0.0070.00343.512-0.002-0.0020.0000.0000.0000.000
63B111CYS0-0.039-0.01538.373-0.004-0.0040.0000.0000.0000.000
64B112VAL00.0440.03838.2950.0020.0020.0000.0000.0000.000
65B113LEU0-0.104-0.05035.590-0.008-0.0080.0000.0000.0000.000
66B114VAL00.1070.04034.0980.0080.0080.0000.0000.0000.000
67B115LYS10.9600.99134.6040.0930.0930.0000.0000.0000.000
68B123TRP0-0.085-0.05834.421-0.002-0.0020.0000.0000.0000.000
69B124GLY0-0.018-0.01931.687-0.007-0.0070.0000.0000.0000.000
70B125PHE00.003-0.00231.0390.0080.0080.0000.0000.0000.000
71B126PRO00.0200.03230.875-0.009-0.0090.0000.0000.0000.000
72B127LYS10.9140.94725.3310.2140.2140.0000.0000.0000.000
73B128GLY00.0680.05425.1280.0010.0010.0000.0000.0000.000
74B129LYS10.8870.93318.5230.3380.3380.0000.0000.0000.000
75B130ILE0-0.002-0.00719.7290.0110.0110.0000.0000.0000.000
76B131ASP-1-0.906-0.93820.688-0.199-0.1990.0000.0000.0000.000
77B132LYS10.9000.92318.6230.1140.1140.0000.0000.0000.000
78B133ASP-1-0.960-0.97521.044-0.116-0.1160.0000.0000.0000.000
79B134GLU-1-0.716-0.85623.072-0.154-0.1540.0000.0000.0000.000
80B135SER00.0050.00123.691-0.017-0.0170.0000.0000.0000.000
81B136ASP-1-0.914-0.96123.535-0.224-0.2240.0000.0000.0000.000
82B137VAL00.007-0.02225.768-0.001-0.0010.0000.0000.0000.000
83B138ASP-1-0.849-0.91928.413-0.114-0.1140.0000.0000.0000.000
84B139CYS0-0.0330.03525.245-0.003-0.0030.0000.0000.0000.000
85B140ALA0-0.037-0.03427.2770.0020.0020.0000.0000.0000.000
86B141ILE0-0.036-0.02029.5790.0060.0060.0000.0000.0000.000
87B142ARG10.8890.94925.5870.1710.1710.0000.0000.0000.000
88B143GLU-1-0.850-0.92826.607-0.173-0.1730.0000.0000.0000.000
89B144VAL0-0.031-0.02030.3800.0050.0050.0000.0000.0000.000
90B145TYR0-0.0220.01833.6400.0080.0080.0000.0000.0000.000
91B146GLU-1-0.890-0.95130.298-0.124-0.1240.0000.0000.0000.000
92B147GLU-1-0.921-0.95330.033-0.150-0.1500.0000.0000.0000.000
93B148THR0-0.133-0.11334.6350.0060.0060.0000.0000.0000.000
94B149GLY00.0280.01937.7010.0060.0060.0000.0000.0000.000
95B150PHE0-0.082-0.04338.8810.0060.0060.0000.0000.0000.000
96B151ASP-1-0.788-0.87138.058-0.091-0.0910.0000.0000.0000.000
97B152CYS0-0.048-0.03035.4180.0020.0020.0000.0000.0000.000
98B153SER00.050-0.00636.592-0.003-0.0030.0000.0000.0000.000
99B154SER0-0.061-0.03137.616-0.001-0.0010.0000.0000.0000.000
100B155ARG10.9270.95839.4680.0790.0790.0000.0000.0000.000
101B156ILE0-0.0400.00832.195-0.002-0.0020.0000.0000.0000.000
102B157ASN00.0500.01735.7120.0000.0000.0000.0000.0000.000
103B158PRO00.0480.01531.750-0.007-0.0070.0000.0000.0000.000
104B159ASN0-0.005-0.01631.193-0.014-0.0140.0000.0000.0000.000
105B160GLU-1-0.918-0.94233.443-0.107-0.1070.0000.0000.0000.000
106B161PHE0-0.008-0.01928.187-0.005-0.0050.0000.0000.0000.000
107B162ILE0-0.077-0.02828.8410.0040.0040.0000.0000.0000.000
108B163ASP-1-0.823-0.88923.455-0.278-0.2780.0000.0000.0000.000
109B164MET0-0.027-0.01124.1450.0080.0080.0000.0000.0000.000
110B165THR00.0000.01417.483-0.018-0.0180.0000.0000.0000.000
111B166ILE00.000-0.01120.3200.0140.0140.0000.0000.0000.000
112B167ARG10.9530.98017.5800.3510.3510.0000.0000.0000.000
113B168GLY00.0880.05314.529-0.057-0.0570.0000.0000.0000.000
114B169GLN0-0.058-0.03415.014-0.034-0.0340.0000.0000.0000.000
115B170ASN0-0.038-0.01617.3530.0620.0620.0000.0000.0000.000
116B171VAL00.0140.00619.4780.0070.0070.0000.0000.0000.000
117B172ARG10.8930.94123.0120.2230.2230.0000.0000.0000.000
118B173LEU0-0.056-0.01225.9100.0060.0060.0000.0000.0000.000
119B174TYR00.0660.02828.0490.0010.0010.0000.0000.0000.000
120B175ILE0-0.060-0.03232.0540.0030.0030.0000.0000.0000.000
121B176ILE00.0330.01535.1160.0050.0050.0000.0000.0000.000
122B177PRO0-0.034-0.01938.3170.0010.0010.0000.0000.0000.000
123B178GLY00.007-0.01041.7510.0020.0020.0000.0000.0000.000
124B179ILE0-0.077-0.01940.7940.0030.0030.0000.0000.0000.000
125B180SER00.0320.02144.1870.0010.0010.0000.0000.0000.000
126B181LEU00.0730.03746.361-0.002-0.0020.0000.0000.0000.000
127B182ASP-1-0.919-0.94347.990-0.057-0.0570.0000.0000.0000.000
128B183THR0-0.144-0.10443.6340.0020.0020.0000.0000.0000.000
129B184ARG10.9730.97644.5470.0630.0630.0000.0000.0000.000
130B185PHE00.0660.04240.512-0.001-0.0010.0000.0000.0000.000
131B186GLU-1-0.857-0.92642.537-0.064-0.0640.0000.0000.0000.000
132B187SER0-0.0060.01441.2710.0000.0000.0000.0000.0000.000
133B188ARG10.8400.89543.3280.0670.0670.0000.0000.0000.000
134B189THR0-0.072-0.03441.508-0.003-0.0030.0000.0000.0000.000
135B190ARG10.9070.95637.4740.0940.0940.0000.0000.0000.000
136B191LYS10.9200.95735.5870.0780.0780.0000.0000.0000.000
137B192GLU-1-0.839-0.92133.215-0.099-0.0990.0000.0000.0000.000
138B193ILE00.0480.03932.550-0.006-0.0060.0000.0000.0000.000
139B194SER0-0.057-0.01935.6400.0080.0080.0000.0000.0000.000
140B195LYS10.9100.92938.2490.0830.0830.0000.0000.0000.000
141B196ILE00.0530.02438.354-0.006-0.0060.0000.0000.0000.000
142B197GLU-1-0.937-0.95440.257-0.078-0.0780.0000.0000.0000.000
143B198TRP00.0600.03341.119-0.008-0.0080.0000.0000.0000.000
144B199HIS10.8810.93140.6040.0970.0970.0000.0000.0000.000
145B200ASN00.0510.03742.695-0.002-0.0020.0000.0000.0000.000
146B201LEU00.021-0.00239.328-0.003-0.0030.0000.0000.0000.000
147B202MET0-0.035-0.03241.747-0.004-0.0040.0000.0000.0000.000
148B203ASP-1-0.845-0.93144.339-0.076-0.0760.0000.0000.0000.000
149B204LEU0-0.042-0.00937.953-0.003-0.0030.0000.0000.0000.000
150B205PRO0-0.007-0.01036.9260.0020.0020.0000.0000.0000.000
151B206THR00.021-0.02135.1440.0050.0050.0000.0000.0000.000
152B207PHE00.0100.05338.3650.0010.0010.0000.0000.0000.000
153B208LYS10.9620.93940.1150.0830.0830.0000.0000.0000.000
154B209LYS10.8220.95542.5600.0850.0850.0000.0000.0000.000
155B210ASN00.0920.03543.930-0.002-0.0020.0000.0000.0000.000
156B211LYS10.9440.98537.4690.1100.1100.0000.0000.0000.000
157B212PRO00.0740.04239.577-0.006-0.0060.0000.0000.0000.000
158B213GLN00.1050.02833.530-0.003-0.0030.0000.0000.0000.000
159B214THR00.0060.02237.0910.0070.0070.0000.0000.0000.000
160B215MET00.0630.02438.245-0.003-0.0030.0000.0000.0000.000
161B216LYS10.8030.89535.6470.1170.1170.0000.0000.0000.000
162B217ASN00.0540.01532.499-0.012-0.0120.0000.0000.0000.000
163B218LYS10.9481.00033.4340.0900.0900.0000.0000.0000.000
164B219PHE00.0230.00534.5910.0000.0000.0000.0000.0000.000
165B220TYR0-0.004-0.01426.384-0.006-0.0060.0000.0000.0000.000
166B221MET00.0280.01827.742-0.015-0.0150.0000.0000.0000.000
167B222VAL00.0070.01329.580-0.005-0.0050.0000.0000.0000.000
168B223ILE0-0.023-0.03432.0150.0000.0000.0000.0000.0000.000
169B224PRO00.0250.01927.7300.0090.0090.0000.0000.0000.000
170B225PHE00.0890.04226.7020.0030.0030.0000.0000.0000.000
171B226LEU0-0.038-0.00631.6420.0100.0100.0000.0000.0000.000
172B227ALA0-0.0020.00233.7990.0070.0070.0000.0000.0000.000
173B228PRO00.0390.00431.1470.0090.0090.0000.0000.0000.000
174B229LEU00.0520.03234.0850.0060.0060.0000.0000.0000.000
175B230LYS10.9110.97236.2960.1010.1010.0000.0000.0000.000
176B231LYS10.9520.97434.9240.1260.1260.0000.0000.0000.000
177B232TRP0-0.056-0.03235.8840.0070.0070.0000.0000.0000.000
178B233ILE00.0560.01338.4480.0050.0050.0000.0000.0000.000
179B234LYS10.9100.96341.5400.0840.0840.0000.0000.0000.000
180B235LYS10.9640.98336.7450.1120.1120.0000.0000.0000.000
181B236ARG10.9480.99540.4960.0900.0900.0000.0000.0000.000
182B237ASN00.029-0.00443.6900.0050.0050.0000.0000.0000.000
183B238ILE0-0.0260.00545.3620.0030.0030.0000.0000.0000.000
184B239ALA0-0.004-0.00344.8200.0030.0030.0000.0000.0000.000
185B240ASN0-0.023-0.02246.6290.0020.0020.0000.0000.0000.000
186B241ASN0-0.077-0.03749.0460.0050.0050.0000.0000.0000.000
187B242THR0-0.0180.00549.6400.0010.0010.0000.0000.0000.000
188B243THR00.0270.02352.2060.0000.0000.0000.0000.0000.000