Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: M3YRZ

Calculation Name: 1ZQ7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZQ7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PZK8

Base Structure: X-ray

Registration Date: 2023-06-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2238253.472559
FMO2-HF: Nuclear repulsion 2158673.916417
FMO2-HF: Total energy -79579.556142
FMO2-MP2: Total energy -79810.328409


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-30.471-30.14927.145-12.054-15.415-0.022
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.012
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].
3A3THR0-0.015-0.0493.448-1.4360.3190.019-0.850-0.925-0.001
4A4GLU-1-0.878-0.9556.008-0.143-0.1430.0000.0000.0000.000
5A5THR0-0.047-0.0238.4290.1610.1610.0000.0000.0000.000
6A6GLU-1-0.762-0.8277.364-0.328-0.3280.0000.0000.0000.000
7A7GLY00.0790.0268.1860.2670.2670.0000.0000.0000.000
8A8ARG10.8480.9198.825-0.024-0.0240.0000.0000.0000.000
9A9ALA00.0140.00311.8960.0200.0200.0000.0000.0000.000
10A10ALA00.0270.0159.2900.0320.0320.0000.0000.0000.000
11A11VAL00.013-0.00311.3820.0000.0000.0000.0000.0000.000
12A12LYS10.7600.87813.732-0.280-0.2800.0000.0000.0000.000
13A13LEU00.0000.01413.676-0.037-0.0370.0000.0000.0000.000
14A14ALA00.0180.01714.632-0.032-0.0320.0000.0000.0000.000
15A15ARG10.7250.83916.486-0.285-0.2850.0000.0000.0000.000
16A16LYS10.8720.92619.250-0.257-0.2570.0000.0000.0000.000
17A17THR0-0.048-0.03218.730-0.028-0.0280.0000.0000.0000.000
18A18ILE0-0.0120.00319.635-0.028-0.0280.0000.0000.0000.000
19A19GLU-1-0.811-0.91322.7860.2120.2120.0000.0000.0000.000
20A20ILE0-0.028-0.01723.683-0.025-0.0250.0000.0000.0000.000
21A21PHE0-0.034-0.01524.888-0.019-0.0190.0000.0000.0000.000
22A22LEU0-0.009-0.01625.970-0.015-0.0150.0000.0000.0000.000
23A23SER0-0.059-0.01428.705-0.021-0.0210.0000.0000.0000.000
24A24LYS10.8070.89328.733-0.228-0.2280.0000.0000.0000.000
25A25GLY00.0110.01830.770-0.003-0.0030.0000.0000.0000.000
26A26LYS10.7720.86527.945-0.260-0.2600.0000.0000.0000.000
27A27SER00.0810.03423.374-0.018-0.0180.0000.0000.0000.000
28A28PRO0-0.074-0.02323.563-0.011-0.0110.0000.0000.0000.000
29A29ARG00.0850.07819.9700.0550.0550.0000.0000.0000.000
30A30PRO00.0280.02222.882-0.022-0.0220.0000.0000.0000.000
31A31ASP-1-0.830-0.90425.4410.2320.2320.0000.0000.0000.000
32A32ALA0-0.015-0.01725.868-0.006-0.0060.0000.0000.0000.000
33A33SER00.0550.02620.230-0.003-0.0030.0000.0000.0000.000
34A34GLY0-0.030-0.00822.011-0.005-0.0050.0000.0000.0000.000
35A35VAL0-0.045-0.02315.964-0.023-0.0230.0000.0000.0000.000
36A36GLU-1-0.932-0.95616.9180.2030.2030.0000.0000.0000.000
37A37LEU0-0.038-0.01713.5700.0280.0280.0000.0000.0000.000
38A38SER0-0.002-0.0229.6160.0070.0070.0000.0000.0000.000
39A39PRO00.042-0.00211.3050.1280.1280.0000.0000.0000.000
40A40VAL00.0280.0245.5710.1360.1360.0000.0000.0000.000
41A41PHE0-0.020-0.0218.4510.5490.5490.0000.0000.0000.000
42A42GLU-1-0.876-0.94411.0220.7470.7470.0000.0000.0000.000
43A43GLU-1-0.860-0.9015.4424.0764.0760.0000.0000.0000.000
44A44TYR0-0.041-0.0149.6830.0480.0480.0000.0000.0000.000
45A45ARG10.7710.8531.878-20.697-28.76716.921-4.876-3.9760.022
46A46GLY00.0320.0408.915-0.266-0.2660.0000.0000.0000.000
47A47VAL0-0.020-0.0208.7040.6410.6410.0000.0000.0000.000
48A48PHE00.011-0.00610.724-0.343-0.3430.0000.0000.0000.000
49A49VAL0-0.0040.00912.3260.0880.0880.0000.0000.0000.000
50A50THR0-0.003-0.01414.975-0.054-0.0540.0000.0000.0000.000
51A51LEU00.0160.02717.397-0.001-0.0010.0000.0000.0000.000
52A52THR00.0330.00519.726-0.020-0.0200.0000.0000.0000.000
53A53GLU-1-0.798-0.89922.3120.1550.1550.0000.0000.0000.000
54A54GLY0-0.012-0.00425.769-0.007-0.0070.0000.0000.0000.000
55A55GLY0-0.023-0.00524.327-0.014-0.0140.0000.0000.0000.000
56A56LEU0-0.045-0.01724.398-0.005-0.0050.0000.0000.0000.000
57A57LEU0-0.019-0.01320.2560.0130.0130.0000.0000.0000.000
58A58ARG10.7490.83623.243-0.217-0.2170.0000.0000.0000.000
59A59GLY00.0420.03222.759-0.011-0.0110.0000.0000.0000.000
60A60CYS0-0.099-0.06417.0440.0230.0230.0000.0000.0000.000
61A61ILE0-0.004-0.00518.237-0.041-0.0410.0000.0000.0000.000
62A62GLY00.0400.01115.2630.0650.0650.0000.0000.0000.000
63A63HIS0-0.063-0.01814.363-0.043-0.0430.0000.0000.0000.000
64A64PRO00.006-0.00613.3570.2080.2080.0000.0000.0000.000
65A65TYR00.0220.01812.8630.1100.1100.0000.0000.0000.000
66A66PRO0-0.0030.00510.9330.0800.0800.0000.0000.0000.000
67A67ASP-1-0.884-0.95612.6870.7640.7640.0000.0000.0000.000
68A68SER0-0.087-0.05914.462-0.184-0.1840.0000.0000.0000.000
69A69THR0-0.0040.01212.4970.1980.1980.0000.0000.0000.000
70A70LEU00.0330.0217.022-0.142-0.1420.0000.0000.0000.000
71A71LYN0-0.034-0.02411.027-0.158-0.1580.0000.0000.0000.000
72A72GLH0-0.056-0.07614.032-0.100-0.1000.0000.0000.0000.000
73A73ALA00.0370.02412.635-0.089-0.0890.0000.0000.0000.000
74A74ILE00.0010.00910.221-0.085-0.0850.0000.0000.0000.000
75A75LEU0-0.050-0.02114.276-0.122-0.1220.0000.0000.0000.000
76A76ASP-1-0.811-0.90017.9470.4980.4980.0000.0000.0000.000
77A77SER00.0230.01715.549-0.075-0.0750.0000.0000.0000.000
78A78ALA00.0100.01016.942-0.058-0.0580.0000.0000.0000.000
79A79ILE00.0150.00318.471-0.057-0.0570.0000.0000.0000.000
80A80SER0-0.041-0.02320.624-0.064-0.0640.0000.0000.0000.000
81A81ALA0-0.035-0.01419.140-0.042-0.0420.0000.0000.0000.000
82A82ALA00.0160.01521.277-0.038-0.0380.0000.0000.0000.000
83A83THR0-0.058-0.06024.041-0.036-0.0360.0000.0000.0000.000
84A84ARG10.8190.90223.035-0.436-0.4360.0000.0000.0000.000
85A85ASP-1-0.696-0.80723.5220.3220.3220.0000.0000.0000.000
86A86PRO0-0.032-0.01825.405-0.022-0.0220.0000.0000.0000.000
87A87ARG10.7770.86220.991-0.342-0.3420.0000.0000.0000.000
88A88PHE0-0.0130.00124.308-0.018-0.0180.0000.0000.0000.000
89A89PRO0-0.0150.00529.3090.0040.0040.0000.0000.0000.000
90A90THR00.0380.00728.8190.0130.0130.0000.0000.0000.000
91A91VAL0-0.0420.01825.332-0.013-0.0130.0000.0000.0000.000
92A92GLU-1-0.888-0.96628.5690.1680.1680.0000.0000.0000.000
93A93GLN0-0.020-0.01529.6840.0060.0060.0000.0000.0000.000
94A94ASP-1-0.882-0.92829.8440.1310.1310.0000.0000.0000.000
95A95GLU-1-0.747-0.84928.6580.1710.1710.0000.0000.0000.000
96A96MET00.0530.02821.9010.0030.0030.0000.0000.0000.000
97A97LYS10.7610.89625.496-0.119-0.1190.0000.0000.0000.000
98A98ASN0-0.075-0.06627.570-0.021-0.0210.0000.0000.0000.000
99A99ILE0-0.0050.02722.129-0.003-0.0030.0000.0000.0000.000
100A100LEU0-0.0210.00319.659-0.003-0.0030.0000.0000.0000.000
101A101VAL00.009-0.00815.9790.0210.0210.0000.0000.0000.000
102A102GLU-1-0.840-0.92113.8220.3280.3280.0000.0000.0000.000
103A103VAL0-0.012-0.0139.666-0.006-0.0060.0000.0000.0000.000
104A104THR0-0.0090.0108.207-0.009-0.0090.0000.0000.0000.000
105A105ILE0-0.052-0.0224.704-0.346-0.263-0.001-0.014-0.0680.000
106A106LEU00.0290.0195.0370.7231.019-0.001-0.025-0.2700.000
107A107THR00.0130.0011.9131.9061.8534.297-1.414-2.8300.003
108A108GLN0-0.037-0.0384.263-2.879-2.7710.002-0.071-0.0390.000
109A109PRO0-0.051-0.0256.759-0.341-0.3410.0000.0000.0000.000
110A110GLU-1-0.928-0.9597.459-0.422-0.4220.0000.0000.0000.000
111A111LYS10.8230.91010.589-0.316-0.3160.0000.0000.0000.000
112A112ILE00.0560.01612.622-0.081-0.0810.0000.0000.0000.000
113A113ASN0-0.068-0.03514.7690.0460.0460.0000.0000.0000.000
114A114ALA00.0040.00817.616-0.042-0.0420.0000.0000.0000.000
115A115SER0-0.042-0.04719.4460.0380.0380.0000.0000.0000.000
116A116PRO00.042-0.00321.662-0.017-0.0170.0000.0000.0000.000
117A117LYS10.8160.90123.3430.0560.0560.0000.0000.0000.000
118A118GLU-1-0.741-0.82919.754-0.177-0.1770.0000.0000.0000.000
119A119LEU0-0.0180.00517.468-0.029-0.0290.0000.0000.0000.000
120A120PRO00.006-0.00616.887-0.024-0.0240.0000.0000.0000.000
121A121ASP-1-0.822-0.91316.992-0.276-0.2760.0000.0000.0000.000
122A122LYS10.7250.85914.2260.2240.2240.0000.0000.0000.000
123A123VAL0-0.0070.00412.314-0.041-0.0410.0000.0000.0000.000
124A124GLU-1-0.844-0.9199.148-1.363-1.3630.0000.0000.0000.000
125A125ILE00.0020.00310.270-0.088-0.0880.0000.0000.0000.000
126A126GLY00.0430.02410.663-0.037-0.0370.0000.0000.0000.000
127A127LYS10.7510.8764.8222.3692.3690.0000.0000.0000.000
128A128HIS00.0350.0135.754-0.059-0.0590.0000.0000.0000.000
129A129GLY00.0120.0207.9300.1120.1120.0000.0000.0000.000
130A130LEU0-0.031-0.0179.813-0.026-0.0260.0000.0000.0000.000
131A131ILE00.015-0.00412.5080.0800.0800.0000.0000.0000.000
132A132VAL0-0.019-0.00815.146-0.062-0.0620.0000.0000.0000.000
133A133LYS10.8580.91118.547-0.312-0.3120.0000.0000.0000.000
134A134GLN00.012-0.00220.778-0.046-0.0460.0000.0000.0000.000
135A135GLY0-0.007-0.00424.458-0.004-0.0040.0000.0000.0000.000
136A136TYR00.006-0.01223.6920.0280.0280.0000.0000.0000.000
137A137CYS0-0.0270.01124.2580.0170.0170.0000.0000.0000.000
138A138GLN00.0450.00018.1980.0320.0320.0000.0000.0000.000
139A139GLY0-0.0110.00319.592-0.004-0.0040.0000.0000.0000.000
140A140LEU0-0.0100.00613.428-0.016-0.0160.0000.0000.0000.000
141A141LEU0-0.037-0.01914.444-0.026-0.0260.0000.0000.0000.000
142A142LEU00.0160.01211.0680.0240.0240.0000.0000.0000.000
143A143PRO00.0390.0096.906-0.013-0.0130.0000.0000.0000.000
144A144GLN00.0370.0289.786-0.071-0.0710.0000.0000.0000.000
145A145VAL0-0.044-0.02512.415-0.009-0.0090.0000.0000.0000.000
146A146ALA00.0450.01714.397-0.007-0.0070.0000.0000.0000.000
147A147PRO00.0200.02812.3100.0010.0010.0000.0000.0000.000
148A148GLU-1-0.827-0.90815.3140.0390.0390.0000.0000.0000.000
149A149ASN0-0.136-0.07917.6310.0250.0250.0000.0000.0000.000
150A150ASP-1-0.963-0.96819.710-0.113-0.1130.0000.0000.0000.000
151A151MET0-0.0420.01718.3030.0260.0260.0000.0000.0000.000
152A152ASP-1-0.772-0.90018.086-0.175-0.1750.0000.0000.0000.000
153A153SER0-0.002-0.00416.1530.0240.0240.0000.0000.0000.000
154A154ILE0-0.051-0.02817.8140.0350.0350.0000.0000.0000.000
155A155ASP-1-0.841-0.91120.493-0.026-0.0260.0000.0000.0000.000
156A156PHE0-0.0110.00012.0300.0470.0470.0000.0000.0000.000
157A157LEU00.0100.01616.8560.0580.0580.0000.0000.0000.000
158A158SER0-0.020-0.01318.9820.0420.0420.0000.0000.0000.000
159A159HIS00.031-0.00320.0430.0280.0280.0000.0000.0000.000
160A160THR00.004-0.01016.3720.0450.0450.0000.0000.0000.000
161A161CYS0-0.088-0.02019.2010.0350.0350.0000.0000.0000.000
162A162MET0-0.0030.01022.3600.0140.0140.0000.0000.0000.000
163A163LYS10.8860.94619.029-0.290-0.2900.0000.0000.0000.000
164A164ALA0-0.020-0.00221.1480.0350.0350.0000.0000.0000.000
165A165GLY0-0.040-0.01322.7380.0040.0040.0000.0000.0000.000
166A166LEU0-0.080-0.03723.646-0.015-0.0150.0000.0000.0000.000
167A167SER0-0.009-0.03726.960-0.007-0.0070.0000.0000.0000.000
168A168PRO00.0590.01425.3370.0040.0040.0000.0000.0000.000
169A169ASP-1-0.790-0.85725.0270.0380.0380.0000.0000.0000.000
170A170ALA0-0.004-0.00724.649-0.007-0.0070.0000.0000.0000.000
171A171TRP00.0850.01321.020-0.004-0.0040.0000.0000.0000.000
172A172VAL0-0.044-0.01522.838-0.015-0.0150.0000.0000.0000.000
173A173LYS10.7780.86525.617-0.048-0.0480.0000.0000.0000.000
174A174GLY0-0.0090.00823.8370.0020.0020.0000.0000.0000.000
175A175ALA0-0.047-0.01423.1420.0150.0150.0000.0000.0000.000
176A176GLU-1-0.841-0.88519.2300.2690.2690.0000.0000.0000.000
177A177VAL00.0330.01115.0450.0240.0240.0000.0000.0000.000
178A178TYR0-0.060-0.04912.671-0.039-0.0390.0000.0000.0000.000
179A179CYS00.0510.0448.801-0.004-0.0040.0000.0000.0000.000
180A180PHE0-0.033-0.0196.8330.2100.2100.0000.0000.0000.000
181A181GLU-1-0.768-0.8802.458-8.175-7.1122.305-1.230-2.138-0.012
182A182GLY00.013-0.0172.5571.5392.6710.491-0.475-1.148-0.004
183A183GLN0-0.0190.0122.412-6.406-2.4713.112-3.086-3.961-0.030
184A184ILE00.0310.0075.1990.1300.2030.000-0.013-0.0600.000
185A185PHE00.0240.0475.470-0.257-0.2570.0000.0000.0000.000
186A186LYS10.8540.90210.266-0.224-0.2240.0000.0000.0000.000
187A187GLU-1-0.767-0.87214.0990.1930.1930.0000.0000.0000.000
188A188LYS10.8120.89217.2620.0120.0120.0000.0000.0000.000
189A189GLU-1-0.940-0.98219.2500.0230.0230.0000.0000.0000.000
190A190PRO00.0210.01221.1720.0180.0180.0000.0000.0000.000
191A191ASP-1-0.833-0.91220.5310.1870.1870.0000.0000.0000.000
192A192GLY0-0.0040.01720.990-0.009-0.0090.0000.0000.0000.000
193A193GLU-1-0.827-0.91017.286-0.016-0.0160.0000.0000.0000.000
194A194VAL0-0.048-0.02612.5650.0330.0330.0000.0000.0000.000
195A195ILE00.0050.01512.836-0.064-0.0640.0000.0000.0000.000
196A196GLU-1-0.821-0.9065.5550.1830.1830.0000.0000.0000.000
197A197GLU-1-0.891-0.92410.313-0.345-0.3450.0000.0000.0000.000
198A198LYS10.8320.8736.9640.9780.9780.0000.0000.0000.000
199A199PHE0-0.0390.0046.894-0.354-0.3540.0000.0000.0000.000
200A200LEU0-0.006-0.0195.9350.2470.2470.0000.0000.0000.000
201A201GLU-1-0.905-0.9609.398-0.361-0.3610.0000.0000.0000.000
202A202HIS0-0.061-0.02712.669-0.049-0.0490.0000.0000.0000.000
203A203HIS0-0.089-0.05116.054-0.022-0.0220.0000.0000.0000.000
204A204HIS0-0.062-0.04512.8880.0570.0570.0000.0000.0000.000