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: GYQL1

Calculation Name: 12E8-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 12E8

Chain ID: H

ChEMBL ID:

UniProt ID:

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 OptHSide
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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2212262.209561
FMO2-HF: Nuclear repulsion 2128454.260069
FMO2-HF: Total energy -83807.949492
FMO2-MP2: Total energy -84052.66625


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(H:1:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
37.99140.7090.05-1.281-1.4850.003
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.884 / q_NPA : -0.950
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].
3H3GLN0-0.038-0.0223.300-7.297-4.7320.052-1.235-1.3810.003
4H4LEU00.0260.0205.573-2.299-2.2990.0000.0000.0000.000
5H5GLN0-0.027-0.0128.944-1.642-1.6420.0000.0000.0000.000
6H6GLN00.024-0.01610.893-0.250-0.2500.0000.0000.0000.000
7H7SER00.0320.03614.667-0.048-0.0480.0000.0000.0000.000
8H8GLY00.003-0.00217.5000.1140.1140.0000.0000.0000.000
9H9ALA0-0.040-0.02319.494-0.212-0.2120.0000.0000.0000.000
10H10GLU-1-0.909-0.93722.52911.11611.1160.0000.0000.0000.000
11H11VAL0-0.025-0.01525.756-0.107-0.1070.0000.0000.0000.000
12H12VAL0-0.002-0.00728.793-0.188-0.1880.0000.0000.0000.000
13H13ARG10.9790.98231.499-8.124-8.1240.0000.0000.0000.000
14H14SER00.020-0.01334.9040.1800.1800.0000.0000.0000.000
15H15GLY0-0.052-0.02136.330-0.208-0.2080.0000.0000.0000.000
16H16ALA0-0.063-0.02333.722-0.058-0.0580.0000.0000.0000.000
17H17SER00.005-0.01831.2180.0240.0240.0000.0000.0000.000
18H18VAL0-0.0060.00925.726-0.097-0.0970.0000.0000.0000.000
19H19LYS10.8850.94223.609-11.684-11.6840.0000.0000.0000.000
20H20LEU00.0130.02220.4430.0670.0670.0000.0000.0000.000
21H21SER00.009-0.00617.6990.0810.0810.0000.0000.0000.000
22H22CYS0-0.0020.02314.0650.2990.2990.0000.0000.0000.000
23H23THR00.006-0.00811.272-0.456-0.4560.0000.0000.0000.000
24H24ALA00.0100.0139.5711.2231.2230.0000.0000.0000.000
25H25SER0-0.014-0.0055.464-1.977-1.9770.0000.0000.0000.000
26H26GLY00.004-0.0054.0382.9082.894-0.001-0.0400.0550.000
27H27PHE0-0.035-0.0234.9003.8714.038-0.001-0.006-0.1590.000
28H28ASN0-0.0040.0078.069-2.685-2.6850.0000.0000.0000.000
29H29ILE00.013-0.00811.8640.4580.4580.0000.0000.0000.000
30H30LYS10.7620.87413.959-16.762-16.7620.0000.0000.0000.000
31H31ASP-1-0.835-0.90214.71517.87417.8740.0000.0000.0000.000
32H32TYR0-0.061-0.0439.8292.2792.2790.0000.0000.0000.000
33H33TYR00.0280.03215.460-1.012-1.0120.0000.0000.0000.000
34H34ILE0-0.040-0.03714.2141.2091.2090.0000.0000.0000.000
35H35HIS00.0420.02616.727-1.727-1.7270.0000.0000.0000.000
36H36TRP00.0160.00117.4870.7850.7850.0000.0000.0000.000
37H37VAL0-0.031-0.01618.717-0.602-0.6020.0000.0000.0000.000
38H38LYS10.8570.94120.557-10.375-10.3750.0000.0000.0000.000
39H39GLN00.0470.02420.9130.4110.4110.0000.0000.0000.000
40H40ARG10.8270.89723.739-9.754-9.7540.0000.0000.0000.000
41H41PRO00.0570.01626.8150.1730.1730.0000.0000.0000.000
42H42GLU-1-0.936-0.96327.91510.18210.1820.0000.0000.0000.000
43H43LYS10.8670.93127.530-9.856-9.8560.0000.0000.0000.000
44H44GLY00.0220.01325.2570.3960.3960.0000.0000.0000.000
45H45LEU0-0.023-0.00919.388-0.274-0.2740.0000.0000.0000.000
46H46GLU-1-0.832-0.90423.39710.27310.2730.0000.0000.0000.000
47H47TRP0-0.025-0.01921.324-0.078-0.0780.0000.0000.0000.000
48H48ILE0-0.047-0.02422.973-0.581-0.5810.0000.0000.0000.000
49H49GLY00.0470.01223.241-0.624-0.6240.0000.0000.0000.000
50H50TRP0-0.070-0.04220.9840.9080.9080.0000.0000.0000.000
51H51ILE00.009-0.00620.143-0.701-0.7010.0000.0000.0000.000
52H52ASP-1-0.787-0.89320.46015.13615.1360.0000.0000.0000.000
53H52PRO0-0.080-0.06217.368-0.609-0.6090.0000.0000.0000.000
54H53GLU-1-0.855-0.90720.41814.53514.5350.0000.0000.0000.000
55H54ILE0-0.041-0.01821.803-0.545-0.5450.0000.0000.0000.000
56H55GLY0-0.065-0.02224.047-0.500-0.5000.0000.0000.0000.000
57H56ASP-1-0.892-0.94225.59310.80410.8040.0000.0000.0000.000
58H57THR0-0.060-0.04124.8050.4860.4860.0000.0000.0000.000
59H58GLU-1-0.881-0.92325.83310.99010.9900.0000.0000.0000.000
60H59TYR0-0.0060.01126.2960.4870.4870.0000.0000.0000.000
61H60VAL00.0380.02528.138-0.407-0.4070.0000.0000.0000.000
62H61PRO00.035-0.00929.860-0.104-0.1040.0000.0000.0000.000
63H62LYS10.7710.87630.486-10.219-10.2190.0000.0000.0000.000
64H63PHE0-0.002-0.02027.867-0.071-0.0710.0000.0000.0000.000
65H64GLN00.0740.04330.8840.2740.2740.0000.0000.0000.000
66H65GLY0-0.026-0.00232.715-0.263-0.2630.0000.0000.0000.000
67H66LYS10.7200.87929.879-9.440-9.4400.0000.0000.0000.000
68H67ALA00.034-0.00826.5130.1070.1070.0000.0000.0000.000
69H68THR0-0.045-0.01727.423-0.309-0.3090.0000.0000.0000.000
70H69MET0-0.0110.00922.8120.3420.3420.0000.0000.0000.000
71H70THR00.000-0.00823.141-0.350-0.3500.0000.0000.0000.000
72H71ALA00.0160.00219.4080.5860.5860.0000.0000.0000.000
73H72ASP-1-0.767-0.85919.13413.63113.6310.0000.0000.0000.000
74H73THR00.0270.01317.1320.5960.5960.0000.0000.0000.000
75H74SER0-0.065-0.01916.3660.7390.7390.0000.0000.0000.000
76H75SER0-0.094-0.07316.0240.5600.5600.0000.0000.0000.000
77H76ASN00.0300.01012.1960.7030.7030.0000.0000.0000.000
78H77THR0-0.0100.00713.5631.1001.1000.0000.0000.0000.000
79H78ALA00.0180.02016.172-0.802-0.8020.0000.0000.0000.000
80H79TYR0-0.019-0.04718.2490.0420.0420.0000.0000.0000.000
81H80LEU00.0210.02721.077-0.257-0.2570.0000.0000.0000.000
82H81GLN0-0.034-0.00823.1480.0290.0290.0000.0000.0000.000
83H82LEU00.0390.02125.294-0.135-0.1350.0000.0000.0000.000
84H82SER00.0610.02528.762-0.079-0.0790.0000.0000.0000.000
85H82SER0-0.007-0.01432.482-0.008-0.0080.0000.0000.0000.000
86H82LEU0-0.054-0.01129.529-0.050-0.0500.0000.0000.0000.000
87H83THR00.004-0.00533.502-0.370-0.3700.0000.0000.0000.000
88H84SER00.0660.02233.3050.1680.1680.0000.0000.0000.000
89H85GLU-1-0.799-0.87532.8229.0539.0530.0000.0000.0000.000
90H86ASP-1-0.807-0.89329.5989.8409.8400.0000.0000.0000.000
91H87THR00.0360.03328.2430.3880.3880.0000.0000.0000.000
92H88ALA0-0.063-0.03425.091-0.139-0.1390.0000.0000.0000.000
93H89VAL00.0160.02519.385-0.059-0.0590.0000.0000.0000.000
94H90TYR0-0.050-0.05520.642-0.140-0.1400.0000.0000.0000.000
95H91TYR00.0060.01515.2350.3570.3570.0000.0000.0000.000
96H93ASN0-0.023-0.02412.7401.0261.0260.0000.0000.0000.000
97H94ALA00.0310.00711.407-1.071-1.0710.0000.0000.0000.000
98H95GLY00.0350.00812.5731.5951.5950.0000.0000.0000.000
99H96HIS0-0.0250.00011.3570.8190.8190.0000.0000.0000.000
100H97ASP-1-0.781-0.88815.06216.11316.1130.0000.0000.0000.000
101H98TYR0-0.057-0.01414.626-0.583-0.5830.0000.0000.0000.000
102H99ASP-1-0.878-0.92616.51818.61918.6190.0000.0000.0000.000
103H100ARG10.9400.94618.792-13.321-13.3210.0000.0000.0000.000
104H100GLY00.0030.00119.127-0.715-0.7150.0000.0000.0000.000
105H100ARG10.7980.90413.586-21.443-21.4430.0000.0000.0000.000
106H100PHE00.0140.00614.1710.2620.2620.0000.0000.0000.000
107H101PRO0-0.038-0.0139.106-0.004-0.0040.0000.0000.0000.000
108H102TYR00.0270.0095.8174.6294.6290.0000.0000.0000.000
109H103TRP0-0.002-0.0059.073-3.900-3.9000.0000.0000.0000.000
110H104GLY00.0560.0259.5321.7901.7900.0000.0000.0000.000
111H105GLN0-0.030-0.01911.6340.6530.6530.0000.0000.0000.000
112H106GLY0-0.016-0.00113.081-0.930-0.9300.0000.0000.0000.000
113H107THR0-0.027-0.02416.5380.1430.1430.0000.0000.0000.000
114H108LEU0-0.038-0.01119.499-0.298-0.2980.0000.0000.0000.000
115H109VAL00.0250.02022.787-0.157-0.1570.0000.0000.0000.000
116H110THR00.004-0.01525.829-0.051-0.0510.0000.0000.0000.000
117H111VAL0-0.0040.00929.223-0.149-0.1490.0000.0000.0000.000
118H112SER00.004-0.00632.338-0.219-0.2190.0000.0000.0000.000
119H113ALA0-0.026-0.01535.8320.0280.0280.0000.0000.0000.000
120H114ALA00.0220.03338.298-0.204-0.2040.0000.0000.0000.000
121H115LYS10.9300.96038.703-6.902-6.9020.0000.0000.0000.000
122H116THR0-0.030-0.01936.334-0.024-0.0240.0000.0000.0000.000
123H117THR0-0.0110.00338.899-0.248-0.2480.0000.0000.0000.000
124H118PRO00.0330.01739.8580.1950.1950.0000.0000.0000.000
125H119PRO0-0.0230.00339.267-0.082-0.0820.0000.0000.0000.000
126H120SER00.0040.00641.812-0.122-0.1220.0000.0000.0000.000
127H121VAL0-0.003-0.01342.0610.1100.1100.0000.0000.0000.000
128H122TYR0-0.024-0.02544.636-0.158-0.1580.0000.0000.0000.000
129H123PRO00.0050.00245.8930.1480.1480.0000.0000.0000.000
130H124LEU0-0.012-0.00844.390-0.083-0.0830.0000.0000.0000.000
131H125ALA00.0130.00747.6760.0960.0960.0000.0000.0000.000
132H126PRO00.0120.01649.918-0.037-0.0370.0000.0000.0000.000
133H127GLY00.0770.03452.119-0.090-0.0900.0000.0000.0000.000
134H128SER0-0.037-0.01955.7350.0260.0260.0000.0000.0000.000
135H129ALA0-0.010-0.00356.849-0.115-0.1150.0000.0000.0000.000
136H130ALA0-0.006-0.00758.1350.0670.0670.0000.0000.0000.000
137H131GLN00.009-0.00957.501-0.033-0.0330.0000.0000.0000.000
138H132THR0-0.058-0.02057.815-0.003-0.0030.0000.0000.0000.000
139H133ASN00.0480.01950.2560.0240.0240.0000.0000.0000.000
140H134SER00.0160.01950.210-0.003-0.0030.0000.0000.0000.000
141H135MET0-0.033-0.00545.220-0.022-0.0220.0000.0000.0000.000
142H136VAL00.0400.03647.439-0.074-0.0740.0000.0000.0000.000
143H137THR0-0.027-0.02843.0180.1120.1120.0000.0000.0000.000
144H138LEU0-0.022-0.00244.503-0.148-0.1480.0000.0000.0000.000
145H139GLY00.0600.00642.7250.2070.2070.0000.0000.0000.000
146H140CYS0-0.109-0.01140.837-0.084-0.0840.0000.0000.0000.000
147H141LEU00.0000.01941.4770.1730.1730.0000.0000.0000.000
148H142VAL0-0.0090.00238.564-0.154-0.1540.0000.0000.0000.000
149H143LYS10.9430.94040.437-6.751-6.7510.0000.0000.0000.000
150H144GLY00.0230.01841.762-0.109-0.1090.0000.0000.0000.000
151H145TYR00.0490.03634.739-0.120-0.1200.0000.0000.0000.000
152H146PHE00.0570.04134.4620.1740.1740.0000.0000.0000.000
153H147PRO0-0.009-0.00432.279-0.218-0.2180.0000.0000.0000.000
154H148GLU-1-0.839-0.90030.4819.5949.5940.0000.0000.0000.000
155H149PRO00.006-0.01428.3580.0740.0740.0000.0000.0000.000
156H150VAL00.011-0.01631.364-0.199-0.1990.0000.0000.0000.000
157H151THR0-0.020-0.00530.4400.2480.2480.0000.0000.0000.000
158H152VAL0-0.021-0.02533.165-0.257-0.2570.0000.0000.0000.000
159H153THR0-0.027-0.01133.9240.2530.2530.0000.0000.0000.000
160H154TRP00.0300.01236.427-0.313-0.3130.0000.0000.0000.000
161H155ASN0-0.007-0.02339.1640.0460.0460.0000.0000.0000.000
162H156SER0-0.010-0.01138.496-0.042-0.0420.0000.0000.0000.000
163H157GLY0-0.0050.00535.5270.1420.1420.0000.0000.0000.000
164H158SER0-0.019-0.00835.9040.1030.1030.0000.0000.0000.000
165H159LEU0-0.055-0.01438.493-0.008-0.0080.0000.0000.0000.000
166H160SER00.0280.00833.2220.0370.0370.0000.0000.0000.000
167H161SER00.0220.01334.5840.1420.1420.0000.0000.0000.000
168H162GLY00.022-0.00635.818-0.202-0.2020.0000.0000.0000.000
169H163VAL0-0.040-0.01634.906-0.188-0.1880.0000.0000.0000.000
170H164HIS0-0.038-0.00134.4160.3810.3810.0000.0000.0000.000
171H165THR00.0240.00832.835-0.376-0.3760.0000.0000.0000.000
172H166PHE0-0.024-0.00232.6370.2840.2840.0000.0000.0000.000
173H167PRO00.0390.00930.260-0.041-0.0410.0000.0000.0000.000
174H168ALA0-0.0120.01232.298-0.282-0.2820.0000.0000.0000.000
175H169VAL0-0.007-0.00133.6030.1650.1650.0000.0000.0000.000
176H170LEU0-0.002-0.00535.013-0.159-0.1590.0000.0000.0000.000
177H171GLN0-0.013-0.00637.924-0.146-0.1460.0000.0000.0000.000
178H172SER0-0.009-0.02341.697-0.040-0.0400.0000.0000.0000.000
179H173ASP-1-0.908-0.94839.3317.1937.1930.0000.0000.0000.000
180H174LEU0-0.0260.01539.0990.1450.1450.0000.0000.0000.000
181H175TYR0-0.047-0.04031.704-0.075-0.0750.0000.0000.0000.000
182H176THR0-0.052-0.04837.970-0.228-0.2280.0000.0000.0000.000
183H177LEU00.0210.03334.2030.1500.1500.0000.0000.0000.000
184H178SER00.010-0.00737.825-0.301-0.3010.0000.0000.0000.000
185H179SER00.003-0.00236.4930.1790.1790.0000.0000.0000.000
186H180SER00.0260.00538.419-0.221-0.2210.0000.0000.0000.000
187H181VAL00.0240.00938.8240.2220.2220.0000.0000.0000.000
188H182THR0-0.0050.00640.710-0.230-0.2300.0000.0000.0000.000
189H183VAL00.0320.02641.9930.1430.1430.0000.0000.0000.000
190H184PRO00.0480.00044.572-0.102-0.1020.0000.0000.0000.000
191H185SER00.021-0.00347.536-0.073-0.0730.0000.0000.0000.000
192H186SER0-0.022-0.00550.842-0.051-0.0510.0000.0000.0000.000
193H187THR0-0.047-0.02847.633-0.030-0.0300.0000.0000.0000.000
194H188TRP0-0.0020.03648.7510.0090.0090.0000.0000.0000.000
195H189PRO0-0.025-0.02850.828-0.042-0.0420.0000.0000.0000.000
196H190SER0-0.043-0.03052.903-0.001-0.0010.0000.0000.0000.000
197H191GLU-1-0.879-0.93948.5226.3126.3120.0000.0000.0000.000
198H192THR0-0.034-0.03047.620-0.001-0.0010.0000.0000.0000.000
199H193VAL00.0560.04344.0440.1140.1140.0000.0000.0000.000
200H194THR0-0.013-0.01444.127-0.171-0.1710.0000.0000.0000.000
201H196ASN00.030-0.00338.495-0.011-0.0110.0000.0000.0000.000
202H197VAL00.0120.00537.8290.2390.2390.0000.0000.0000.000
203H198ALA0-0.026-0.00934.899-0.182-0.1820.0000.0000.0000.000
204H199HIS00.0400.03334.9610.0130.0130.0000.0000.0000.000
205H200PRO00.018-0.00331.207-0.179-0.1790.0000.0000.0000.000
206H201ALA00.0090.01333.343-0.102-0.1020.0000.0000.0000.000
207H202SER0-0.009-0.03134.639-0.157-0.1570.0000.0000.0000.000
208H203SER0-0.047-0.01836.951-0.171-0.1710.0000.0000.0000.000
209H204THR0-0.0080.01138.288-0.263-0.2630.0000.0000.0000.000
210H205LYS10.9400.95435.536-7.790-7.7900.0000.0000.0000.000
211H206VAL0-0.0010.00040.442-0.200-0.2000.0000.0000.0000.000
212H207ASP-1-0.831-0.89342.1227.2717.2710.0000.0000.0000.000
213H208LYS10.8850.93844.277-6.512-6.5120.0000.0000.0000.000
214H209LYS10.9420.97445.927-5.866-5.8660.0000.0000.0000.000
215H210ILE0-0.002-0.00945.635-0.102-0.1020.0000.0000.0000.000
216H211VAL0-0.035-0.01749.205-0.039-0.0390.0000.0000.0000.000
217H212PRO00.017-0.00752.9300.0220.0220.0000.0000.0000.000
218H213ARG10.7930.88555.129-5.408-5.4080.0000.0000.0000.000
219H214ASP-1-0.809-0.87554.2395.6375.6370.0000.0000.0000.000