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: LZ699

Calculation Name: 5CGY-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CGY

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2281104.466526
FMO2-HF: Nuclear repulsion 2195566.688565
FMO2-HF: Total energy -85537.777961
FMO2-MP2: Total energy -85787.966465


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:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
2.8375.030.016-0.796-1.4120.002
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.006
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].
3H3GLN0-0.016-0.0083.698-1.4330.022-0.004-0.535-0.9160.002
4H4LEU0-0.0040.0005.4450.8050.8050.0000.0000.0000.000
5H5VAL00.0100.0008.7060.1140.1140.0000.0000.0000.000
6H6GLN00.008-0.01611.2140.1000.1000.0000.0000.0000.000
7H7SER0-0.0100.01414.9870.0190.0190.0000.0000.0000.000
8H8GLY00.0340.01818.387-0.004-0.0040.0000.0000.0000.000
9H9SER0-0.030-0.02220.2030.0040.0040.0000.0000.0000.000
10H10GLU-1-0.765-0.86023.096-0.365-0.3650.0000.0000.0000.000
11H11LEU0-0.058-0.02926.0830.0180.0180.0000.0000.0000.000
12H12LYS10.8250.89828.5700.3520.3520.0000.0000.0000.000
13H13LYS10.9030.96832.4300.2170.2170.0000.0000.0000.000
14H14PRO00.0250.00135.531-0.007-0.0070.0000.0000.0000.000
15H15GLY0-0.023-0.01137.0780.0090.0090.0000.0000.0000.000
16H16ALA0-0.0080.00334.5000.0020.0020.0000.0000.0000.000
17H17SER0-0.013-0.01231.3010.0000.0000.0000.0000.0000.000
18H18VAL0-0.011-0.00825.8240.0010.0010.0000.0000.0000.000
19H19LYS10.8640.92723.3960.4200.4200.0000.0000.0000.000
20H20VAL00.0170.03920.571-0.012-0.0120.0000.0000.0000.000
21H21SER0-0.001-0.02017.7470.0040.0040.0000.0000.0000.000
22H22CYS0-0.0200.00713.785-0.046-0.0460.0000.0000.0000.000
23H23LYS10.8660.9529.8221.5831.5830.0000.0000.0000.000
24H24ALA00.0500.0279.477-0.351-0.3510.0000.0000.0000.000
25H25SER0-0.056-0.0355.521-0.294-0.2940.0000.0000.0000.000
26H26GLY00.0690.0243.649-1.875-1.5350.013-0.193-0.1600.000
27H27TYR00.0060.0144.1763.8724.2700.007-0.068-0.3360.000
28H28SER0-0.002-0.0066.964-0.510-0.5100.0000.0000.0000.000
29H29PHE00.0460.01310.683-0.006-0.0060.0000.0000.0000.000
30H30THR00.0430.00812.3660.0040.0040.0000.0000.0000.000
31H31SER0-0.051-0.01212.9820.0750.0750.0000.0000.0000.000
32H32TYR0-0.024-0.04510.7450.1060.1060.0000.0000.0000.000
33H33SER0-0.0090.02013.426-0.137-0.1370.0000.0000.0000.000
34H34ILE0-0.034-0.00312.980-0.121-0.1210.0000.0000.0000.000
35H35ASN00.0170.00615.8020.1390.1390.0000.0000.0000.000
36H36TRP00.017-0.00517.312-0.130-0.1300.0000.0000.0000.000
37H37VAL00.0020.00618.8680.0660.0660.0000.0000.0000.000
38H38ARG10.8010.89821.1360.2650.2650.0000.0000.0000.000
39H39GLN0-0.008-0.01222.728-0.021-0.0210.0000.0000.0000.000
40H40ALA00.0220.02225.021-0.012-0.0120.0000.0000.0000.000
41H41PRO0-0.027-0.03428.3580.0020.0020.0000.0000.0000.000
42H42GLY0-0.0110.00428.9600.0170.0170.0000.0000.0000.000
43H43GLN0-0.052-0.00528.6940.0300.0300.0000.0000.0000.000
44H44GLY00.0320.02126.198-0.016-0.0160.0000.0000.0000.000
45H45PRO0-0.030-0.03021.7830.0020.0020.0000.0000.0000.000
46H46GLU-1-0.752-0.86424.036-0.272-0.2720.0000.0000.0000.000
47H47TRP0-0.004-0.01820.213-0.011-0.0110.0000.0000.0000.000
48H48MET0-0.036-0.00923.1790.0140.0140.0000.0000.0000.000
49H49GLY00.0270.00923.0670.0330.0330.0000.0000.0000.000
50H50TRP0-0.054-0.01119.472-0.050-0.0500.0000.0000.0000.000
51H51ILE0-0.025-0.02019.1250.0300.0300.0000.0000.0000.000
52H52ASP-1-0.729-0.83118.861-0.235-0.2350.0000.0000.0000.000
53H53THR0-0.061-0.02415.0370.0310.0310.0000.0000.0000.000
54H54ASN0-0.050-0.02618.197-0.004-0.0040.0000.0000.0000.000
55H55THR0-0.067-0.06620.086-0.001-0.0010.0000.0000.0000.000
56H56GLY00.0070.00722.1360.0030.0030.0000.0000.0000.000
57H57ASN0-0.035-0.02723.350-0.012-0.0120.0000.0000.0000.000
58H58PRO0-0.0050.00323.706-0.017-0.0170.0000.0000.0000.000
59H59THR0-0.023-0.02124.5210.0390.0390.0000.0000.0000.000
60H60TYR00.0010.01124.963-0.032-0.0320.0000.0000.0000.000
61H61ALA00.0370.01826.9100.0220.0220.0000.0000.0000.000
62H62GLN0-0.032-0.04428.4870.0050.0050.0000.0000.0000.000
63H63ASP-1-0.884-0.92831.638-0.191-0.1910.0000.0000.0000.000
64H64PHE0-0.033-0.02728.217-0.011-0.0110.0000.0000.0000.000
65H65ALA00.0000.00130.523-0.010-0.0100.0000.0000.0000.000
66H66GLY00.0170.01031.9660.0170.0170.0000.0000.0000.000
67H67ARG10.7360.84132.8300.2430.2430.0000.0000.0000.000
68H68PHE0-0.020-0.00927.291-0.013-0.0130.0000.0000.0000.000
69H69VAL00.0110.00727.1780.0140.0140.0000.0000.0000.000
70H70PHE00.0130.01322.344-0.036-0.0360.0000.0000.0000.000
71H71SER0-0.021-0.01522.3160.0370.0370.0000.0000.0000.000
72H72LEU00.008-0.00217.987-0.062-0.0620.0000.0000.0000.000
73H73ASP-1-0.828-0.88618.522-0.433-0.4330.0000.0000.0000.000
74H74THR00.016-0.00116.751-0.094-0.0940.0000.0000.0000.000
75H75SER0-0.060-0.03616.265-0.031-0.0310.0000.0000.0000.000
76H76VAL00.0170.01115.103-0.028-0.0280.0000.0000.0000.000
77H77THR0-0.034-0.00910.635-0.171-0.1710.0000.0000.0000.000
78H78THR0-0.005-0.00112.488-0.267-0.2670.0000.0000.0000.000
79H79ALA00.0110.01415.0690.1420.1420.0000.0000.0000.000
80H80TYR0-0.030-0.03717.344-0.078-0.0780.0000.0000.0000.000
81H81LEU00.0110.02220.3080.0410.0410.0000.0000.0000.000
82H82GLN00.0020.00522.967-0.020-0.0200.0000.0000.0000.000
83H83ILE00.0200.01225.6460.0160.0160.0000.0000.0000.000
84H84SER00.0260.00329.0980.0050.0050.0000.0000.0000.000
85H85SER0-0.017-0.00732.8800.0060.0060.0000.0000.0000.000
86H86LEU0-0.0030.01629.9270.0090.0090.0000.0000.0000.000
87H87LYS10.9310.95233.8890.2190.2190.0000.0000.0000.000
88H88ALA00.0680.02433.899-0.013-0.0130.0000.0000.0000.000
89H89GLY00.0160.00533.560-0.010-0.0100.0000.0000.0000.000
90H90ASP-1-0.769-0.85230.214-0.265-0.2650.0000.0000.0000.000
91H91THR0-0.0190.00528.902-0.028-0.0280.0000.0000.0000.000
92H92ALA00.0110.00325.9530.0170.0170.0000.0000.0000.000
93H93VAL0-0.0090.01720.225-0.015-0.0150.0000.0000.0000.000
94H94TYR0-0.008-0.03721.3350.0360.0360.0000.0000.0000.000
95H95TYR00.0310.00816.587-0.059-0.0590.0000.0000.0000.000
96H97ALA00.0110.00013.174-0.123-0.1230.0000.0000.0000.000
97H98THR00.019-0.0028.9930.1060.1060.0000.0000.0000.000
98H99TYR00.003-0.02710.180-0.024-0.0240.0000.0000.0000.000
99H100TYR00.016-0.0066.035-0.299-0.2990.0000.0000.0000.000
100H101VAL0-0.006-0.0155.6420.2550.2550.0000.0000.0000.000
101H102ASP-1-0.916-0.9545.2751.8421.8420.0000.0000.0000.000
102H103LEU0-0.061-0.0288.281-0.040-0.0400.0000.0000.0000.000
103H104TRP0-0.046-0.02710.991-0.046-0.0460.0000.0000.0000.000
104H105GLY0-0.0010.01512.862-0.052-0.0520.0000.0000.0000.000
105H106SER0-0.0040.00712.3120.0390.0390.0000.0000.0000.000
106H107TYR00.0370.02314.067-0.040-0.0400.0000.0000.0000.000
107H108ARG10.8230.91714.340-0.030-0.0300.0000.0000.0000.000
108H109GLN00.0390.01015.638-0.099-0.0990.0000.0000.0000.000
109H110ASP-1-0.794-0.87717.925-0.142-0.1420.0000.0000.0000.000
110H111TYR00.0280.00718.388-0.045-0.0450.0000.0000.0000.000
111H112TYR00.0050.00416.965-0.022-0.0220.0000.0000.0000.000
112H113GLY0-0.0110.01613.743-0.010-0.0100.0000.0000.0000.000
113H114MET0-0.044-0.05014.544-0.108-0.1080.0000.0000.0000.000
114H115ASP-1-0.789-0.85810.457-0.349-0.3490.0000.0000.0000.000
115H116VAL0-0.033-0.0196.815-0.087-0.0870.0000.0000.0000.000
116H117TRP0-0.019-0.0209.9250.0700.0700.0000.0000.0000.000
117H118GLY00.0120.00910.799-0.282-0.2820.0000.0000.0000.000
118H119HIS0-0.038-0.0359.5350.3630.3630.0000.0000.0000.000
119H120GLY0-0.0020.01613.8630.1390.1390.0000.0000.0000.000
120H121THR0-0.062-0.03917.062-0.043-0.0430.0000.0000.0000.000
121H122LEU00.0050.01019.8900.0450.0450.0000.0000.0000.000
122H123VAL00.0080.00823.281-0.003-0.0030.0000.0000.0000.000
123H124THR0-0.002-0.00526.1900.0220.0220.0000.0000.0000.000
124H125VAL0-0.028-0.01229.7360.0050.0050.0000.0000.0000.000
125H126SER00.0290.00633.0140.0180.0180.0000.0000.0000.000
126H127SER0-0.015-0.03235.4780.0000.0000.0000.0000.0000.000
127H128ALA0-0.0200.00936.9290.0080.0080.0000.0000.0000.000
128H129SER0-0.013-0.01238.224-0.004-0.0040.0000.0000.0000.000
129H130THR0-0.002-0.00738.881-0.001-0.0010.0000.0000.0000.000
130H131LYS10.8740.96640.2200.1460.1460.0000.0000.0000.000
131H132GLY00.0760.04442.092-0.006-0.0060.0000.0000.0000.000
132H133PRO0-0.056-0.02443.0690.0020.0020.0000.0000.0000.000
133H134SER0-0.009-0.00545.0350.0050.0050.0000.0000.0000.000
134H135VAL00.0110.00947.069-0.002-0.0020.0000.0000.0000.000
135H136PHE0-0.011-0.01048.9730.0060.0060.0000.0000.0000.000
136H137PRO00.0360.02150.442-0.003-0.0030.0000.0000.0000.000
137H138LEU0-0.029-0.00347.541-0.001-0.0010.0000.0000.0000.000
138H139ALA00.0590.02152.1510.0020.0020.0000.0000.0000.000
139H140PRO00.0130.03154.954-0.001-0.0010.0000.0000.0000.000
140H141SER00.0250.00853.8020.0020.0020.0000.0000.0000.000
141H142SER00.0210.00055.096-0.001-0.0010.0000.0000.0000.000
142H143LYS10.8950.94357.6960.0510.0510.0000.0000.0000.000
143H144SER00.0610.04261.2780.0000.0000.0000.0000.0000.000
144H145THR0-0.063-0.04863.0040.0010.0010.0000.0000.0000.000
145H146SER00.0760.06261.7460.0020.0020.0000.0000.0000.000
146H147GLY00.0390.01061.768-0.001-0.0010.0000.0000.0000.000
147H148GLY00.0230.01758.276-0.002-0.0020.0000.0000.0000.000
148H149THR00.0270.02953.3650.0010.0010.0000.0000.0000.000
149H150ALA0-0.037-0.02054.6800.0000.0000.0000.0000.0000.000
150H151ALA00.0100.00450.265-0.001-0.0010.0000.0000.0000.000
151H152LEU0-0.0120.00851.7160.0010.0010.0000.0000.0000.000
152H153GLY00.037-0.00149.159-0.002-0.0020.0000.0000.0000.000
153H154CYS0-0.0520.00447.9140.0030.0030.0000.0000.0000.000
154H155LEU00.0280.03844.897-0.005-0.0050.0000.0000.0000.000
155H156VAL0-0.019-0.02043.0960.0040.0040.0000.0000.0000.000
156H157LYS10.9030.92743.0030.1270.1270.0000.0000.0000.000
157H158ASP-1-0.810-0.88742.367-0.140-0.1400.0000.0000.0000.000
158H159TYR0-0.043-0.04637.4540.0090.0090.0000.0000.0000.000
159H160PHE00.0290.01933.553-0.010-0.0100.0000.0000.0000.000
160H161PRO00.0200.01633.8400.0090.0090.0000.0000.0000.000
161H162GLU-1-0.742-0.86132.999-0.186-0.1860.0000.0000.0000.000
162H163PRO0-0.040-0.01533.824-0.007-0.0070.0000.0000.0000.000
163H164VAL0-0.017-0.01635.7690.0100.0100.0000.0000.0000.000
164H165THR0-0.064-0.03138.288-0.002-0.0020.0000.0000.0000.000
165H166VAL00.009-0.01740.6560.0040.0040.0000.0000.0000.000
166H167SER0-0.0160.00443.390-0.001-0.0010.0000.0000.0000.000
167H168TRP00.0270.00146.1520.0020.0020.0000.0000.0000.000
168H169ASN0-0.004-0.01649.5550.0000.0000.0000.0000.0000.000
169H170SER0-0.012-0.01350.6080.0040.0040.0000.0000.0000.000
170H171GLY00.0000.00348.000-0.001-0.0010.0000.0000.0000.000
171H172ALA0-0.032-0.00648.9490.0010.0010.0000.0000.0000.000
172H173LEU0-0.046-0.01150.3480.0030.0030.0000.0000.0000.000
173H174THR00.0390.00445.867-0.003-0.0030.0000.0000.0000.000
174H175SER00.0250.00546.603-0.002-0.0020.0000.0000.0000.000
175H176GLY00.0390.02147.5180.0010.0010.0000.0000.0000.000
176H177VAL0-0.062-0.01344.514-0.002-0.0020.0000.0000.0000.000
177H178HIS00.0140.01338.6290.0000.0000.0000.0000.0000.000
178H179THR0-0.0050.00239.8870.0040.0040.0000.0000.0000.000
179H180PHE0-0.0180.00438.487-0.004-0.0040.0000.0000.0000.000
180H181PRO00.0380.00033.5120.0000.0000.0000.0000.0000.000
181H182ALA0-0.0100.00335.1990.0070.0070.0000.0000.0000.000
182H183VAL0-0.0040.00734.709-0.012-0.0120.0000.0000.0000.000
183H184LEU0-0.015-0.00831.5650.0050.0050.0000.0000.0000.000
184H185GLN0-0.054-0.03435.2570.0040.0040.0000.0000.0000.000
185H186SER00.0400.00336.828-0.007-0.0070.0000.0000.0000.000
186H187SER00.0130.01337.897-0.006-0.0060.0000.0000.0000.000
187H188GLY00.0270.00235.595-0.002-0.0020.0000.0000.0000.000
188H189LEU0-0.073-0.02136.320-0.005-0.0050.0000.0000.0000.000
189H190TYR00.0650.02331.227-0.001-0.0010.0000.0000.0000.000
190H191SER0-0.009-0.01137.9050.0150.0150.0000.0000.0000.000
191H192LEU00.0330.04438.204-0.005-0.0050.0000.0000.0000.000
192H193SER0-0.003-0.02240.7060.0100.0100.0000.0000.0000.000
193H194SER0-0.0120.00442.354-0.002-0.0020.0000.0000.0000.000
194H195VAL00.016-0.01044.6570.0040.0040.0000.0000.0000.000
195H196VAL00.0190.01846.744-0.001-0.0010.0000.0000.0000.000
196H197THR0-0.017-0.01247.8640.0020.0020.0000.0000.0000.000
197H198VAL00.004-0.00150.4480.0010.0010.0000.0000.0000.000
198H199PRO00.0590.01754.0380.0000.0000.0000.0000.0000.000
199H200SER0-0.035-0.03657.4080.0000.0000.0000.0000.0000.000
200H201SER00.0180.00259.2050.0000.0000.0000.0000.0000.000
201H202SER0-0.0050.00958.1140.0020.0020.0000.0000.0000.000
202H203LEU0-0.028-0.01956.526-0.002-0.0020.0000.0000.0000.000
203H204GLY00.0260.01060.0050.0020.0020.0000.0000.0000.000
204H205THR0-0.081-0.04162.2410.0010.0010.0000.0000.0000.000
205H206GLN00.0580.04458.1240.0010.0010.0000.0000.0000.000
206H207THR0-0.009-0.00158.286-0.001-0.0010.0000.0000.0000.000
207H208TYR00.0010.00053.498-0.001-0.0010.0000.0000.0000.000
208H209ILE00.021-0.00953.1150.0000.0000.0000.0000.0000.000
209H211ASN00.043-0.00248.3640.0010.0010.0000.0000.0000.000
210H212VAL00.0020.01244.301-0.005-0.0050.0000.0000.0000.000
211H213ASN0-0.015-0.01242.0440.0070.0070.0000.0000.0000.000
212H214HIS00.018-0.00638.7320.0020.0020.0000.0000.0000.000
213H215LYS11.0020.99738.6930.1550.1550.0000.0000.0000.000
214H216PRO00.0140.01137.0350.0040.0040.0000.0000.0000.000
215H217SER00.0150.00439.572-0.003-0.0030.0000.0000.0000.000
216H218ASN0-0.053-0.03043.0450.0070.0070.0000.0000.0000.000
217H219THR00.0020.02144.5130.0060.0060.0000.0000.0000.000
218H220LYS10.9220.94445.5990.1100.1100.0000.0000.0000.000
219H221VAL0-0.004-0.00648.2600.0030.0030.0000.0000.0000.000
220H222ASP-1-0.838-0.88949.775-0.092-0.0920.0000.0000.0000.000
221H223LYS10.8520.90851.8150.0940.0940.0000.0000.0000.000
222H224ARG10.8700.92453.4310.0650.0650.0000.0000.0000.000
223H225VAL0-0.044-0.02452.322-0.002-0.0020.0000.0000.0000.000
224H226GLU-1-0.798-0.88455.785-0.063-0.0630.0000.0000.0000.000
225H227PRO0-0.019-0.00358.143-0.003-0.0030.0000.0000.0000.000
226H228LYS10.8300.91059.5050.0660.0660.0000.0000.0000.000