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: LJ4Q9

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2235121.226652
FMO2-HF: Nuclear repulsion 2155544.271597
FMO2-HF: Total energy -79576.955055
FMO2-MP2: Total energy -79807.833671


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.
-31.568-33.00128.26-11.331-15.497-0.01
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 : -0.033 / q_NPA : -0.011
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].
3A3THR0-0.012-0.0113.726-0.5180.938-0.003-0.681-0.7710.000
4A4GLU-1-0.841-0.9376.0480.0830.0830.0000.0000.0000.000
5A5THR0-0.055-0.0298.5630.1450.1450.0000.0000.0000.000
6A6GLU-1-0.795-0.8806.596-0.603-0.6030.0000.0000.0000.000
7A7GLY00.0600.0318.1490.2550.2550.0000.0000.0000.000
8A8ARG10.9310.9598.772-0.061-0.0610.0000.0000.0000.000
9A9ALA0-0.004-0.01211.8870.0180.0180.0000.0000.0000.000
10A10ALA00.0580.0249.4300.0210.0210.0000.0000.0000.000
11A11VAL00.0280.01211.554-0.011-0.0110.0000.0000.0000.000
12A12LYS10.8560.94413.964-0.315-0.3150.0000.0000.0000.000
13A13LEU0-0.0030.02113.824-0.047-0.0470.0000.0000.0000.000
14A14ALA00.0230.03414.915-0.029-0.0290.0000.0000.0000.000
15A15ARG10.8750.93416.763-0.288-0.2880.0000.0000.0000.000
16A16LYS10.9670.97319.539-0.267-0.2670.0000.0000.0000.000
17A17THR0-0.058-0.04418.677-0.027-0.0270.0000.0000.0000.000
18A18ILE00.0010.00320.000-0.024-0.0240.0000.0000.0000.000
19A19GLU-1-0.908-0.95923.0580.2100.2100.0000.0000.0000.000
20A20ILE0-0.031-0.01223.899-0.025-0.0250.0000.0000.0000.000
21A21PHE0-0.052-0.01725.226-0.019-0.0190.0000.0000.0000.000
22A22LEU0-0.012-0.00326.773-0.015-0.0150.0000.0000.0000.000
23A23SER0-0.0640.00828.832-0.020-0.0200.0000.0000.0000.000
24A24LYS10.8770.92229.904-0.207-0.2070.0000.0000.0000.000
25A25GLY00.0210.01330.646-0.003-0.0030.0000.0000.0000.000
26A26LYS10.9090.94028.482-0.227-0.2270.0000.0000.0000.000
27A27SER00.046-0.00124.087-0.011-0.0110.0000.0000.0000.000
28A28PRO0-0.0520.01223.4940.0020.0020.0000.0000.0000.000
29A29ARG00.0810.01819.9210.1040.1040.0000.0000.0000.000
30A30PRO0-0.077-0.04022.543-0.026-0.0260.0000.0000.0000.000
31A31ASP-1-0.905-0.96924.8730.2230.2230.0000.0000.0000.000
32A32ALA0-0.028-0.03125.523-0.017-0.0170.0000.0000.0000.000
33A33SER00.0090.06420.322-0.003-0.0030.0000.0000.0000.000
34A34GLY0-0.018-0.00622.293-0.007-0.0070.0000.0000.0000.000
35A35VAL0-0.060-0.02515.978-0.025-0.0250.0000.0000.0000.000
36A36GLU-1-0.935-0.96316.9730.1800.1800.0000.0000.0000.000
37A37LEU0-0.036-0.01413.3010.0140.0140.0000.0000.0000.000
38A38SER0-0.022-0.0319.4550.0560.0560.0000.0000.0000.000
39A39PRO00.055-0.00310.1920.1060.1060.0000.0000.0000.000
40A40VAL00.0430.0435.1840.1740.1740.0000.0000.0000.000
41A41PHE0-0.053-0.0387.9570.6040.6040.0000.0000.0000.000
42A42GLU-1-0.882-0.94310.5640.6580.6580.0000.0000.0000.000
43A43GLU-1-0.928-0.9605.2772.7462.7460.0000.0000.0000.000
44A44TYR0-0.045-0.0149.3910.0430.0430.0000.0000.0000.000
45A45ARG10.8240.8821.897-20.878-27.30714.118-4.173-3.5160.030
46A46GLY00.0170.0349.063-0.368-0.3680.0000.0000.0000.000
47A47VAL0-0.007-0.0238.8750.6050.6050.0000.0000.0000.000
48A48PHE00.0040.00710.852-0.325-0.3250.0000.0000.0000.000
49A49VAL0-0.0050.01112.6850.0920.0920.0000.0000.0000.000
50A50THR0-0.008-0.02615.310-0.050-0.0500.0000.0000.0000.000
51A51LEU00.0130.02417.501-0.003-0.0030.0000.0000.0000.000
52A52THR00.0360.01819.611-0.030-0.0300.0000.0000.0000.000
53A53GLU-1-0.840-0.94122.4100.1670.1670.0000.0000.0000.000
54A54GLY0-0.010-0.00125.940-0.010-0.0100.0000.0000.0000.000
55A55GLY0-0.042-0.02023.879-0.013-0.0130.0000.0000.0000.000
56A56LEU0-0.025-0.00824.297-0.006-0.0060.0000.0000.0000.000
57A57LEU0-0.033-0.00620.1710.0130.0130.0000.0000.0000.000
58A58ARG10.7730.88222.967-0.220-0.2200.0000.0000.0000.000
59A59GLY00.0370.02222.655-0.010-0.0100.0000.0000.0000.000
60A60CYS0-0.094-0.04816.7420.0250.0250.0000.0000.0000.000
61A61ILE0-0.0140.00218.396-0.038-0.0380.0000.0000.0000.000
62A62GLY00.0370.00015.4530.0600.0600.0000.0000.0000.000
63A63HIS0-0.076-0.01114.532-0.059-0.0590.0000.0000.0000.000
64A64PRO0-0.012-0.00913.1680.2020.2020.0000.0000.0000.000
65A65TYR00.0410.02112.6070.1510.1510.0000.0000.0000.000
66A66PRO0-0.0070.02010.5330.0590.0590.0000.0000.0000.000
67A67ASP-1-0.896-0.96312.4340.7170.7170.0000.0000.0000.000
68A68SER0-0.058-0.03414.459-0.160-0.1600.0000.0000.0000.000
69A69THR00.0340.01912.3720.2260.2260.0000.0000.0000.000
70A70LEU00.0450.0207.090-0.107-0.1070.0000.0000.0000.000
71A71LYN0-0.040-0.03411.009-0.138-0.1380.0000.0000.0000.000
72A72GLH00.019-0.02513.853-0.126-0.1260.0000.0000.0000.000
73A73ALA00.0320.03112.706-0.088-0.0880.0000.0000.0000.000
74A74ILE00.0030.01210.359-0.090-0.0900.0000.0000.0000.000
75A75LEU0-0.041-0.02714.376-0.116-0.1160.0000.0000.0000.000
76A76ASP-1-0.857-0.93918.0190.5050.5050.0000.0000.0000.000
77A77SER00.009-0.01115.673-0.064-0.0640.0000.0000.0000.000
78A78ALA00.008-0.00217.224-0.063-0.0630.0000.0000.0000.000
79A79ILE0-0.004-0.00418.672-0.063-0.0630.0000.0000.0000.000
80A80SER0-0.039-0.01721.022-0.064-0.0640.0000.0000.0000.000
81A81ALA0-0.029-0.00319.418-0.040-0.0400.0000.0000.0000.000
82A82ALA00.0380.02221.564-0.034-0.0340.0000.0000.0000.000
83A83THR0-0.061-0.05024.364-0.034-0.0340.0000.0000.0000.000
84A84ARG10.8700.93823.743-0.388-0.3880.0000.0000.0000.000
85A85ASP-1-0.693-0.83323.5710.3140.3140.0000.0000.0000.000
86A86PRO0-0.036-0.02325.887-0.021-0.0210.0000.0000.0000.000
87A87ARG10.8040.89421.216-0.305-0.3050.0000.0000.0000.000
88A88PHE0-0.033-0.01324.088-0.018-0.0180.0000.0000.0000.000
89A89PRO0-0.0170.01229.3320.0050.0050.0000.0000.0000.000
90A90THR00.019-0.01429.0780.0130.0130.0000.0000.0000.000
91A91VAL0-0.0330.00325.692-0.012-0.0120.0000.0000.0000.000
92A92GLU-1-0.918-0.96228.9830.1660.1660.0000.0000.0000.000
93A93GLN0-0.027-0.03929.7990.0090.0090.0000.0000.0000.000
94A94ASP-1-0.954-0.98729.8700.1440.1440.0000.0000.0000.000
95A95GLU-1-0.708-0.85328.8960.1720.1720.0000.0000.0000.000
96A96MET00.0390.03422.1100.0050.0050.0000.0000.0000.000
97A97LYS10.8290.93325.476-0.112-0.1120.0000.0000.0000.000
98A98ASN0-0.037-0.02727.750-0.015-0.0150.0000.0000.0000.000
99A99ILE00.0280.02622.265-0.001-0.0010.0000.0000.0000.000
100A100LEU0-0.065-0.02520.036-0.002-0.0020.0000.0000.0000.000
101A101VAL0-0.004-0.01715.8920.0230.0230.0000.0000.0000.000
102A102GLU-1-0.938-0.98114.3240.3730.3730.0000.0000.0000.000
103A103VAL00.0060.0009.840-0.005-0.0050.0000.0000.0000.000
104A104THR0-0.019-0.0038.3490.0060.0060.0000.0000.0000.000
105A105ILE0-0.021-0.0114.806-0.188-0.1880.0000.0000.0000.000
106A106LEU0-0.0080.0025.2861.0071.0070.0000.0000.0000.000
107A107THR00.006-0.0062.4060.8770.3295.328-1.286-3.4940.005
108A108GLN0-0.027-0.0154.405-3.137-3.0120.002-0.076-0.0510.000
109A109PRO0-0.037-0.0196.820-0.546-0.5460.0000.0000.0000.000
110A110GLU-1-0.902-0.9406.886-0.745-0.7450.0000.0000.0000.000
111A111LYS10.8400.92410.246-0.257-0.2570.0000.0000.0000.000
112A112ILE00.0420.02512.496-0.085-0.0850.0000.0000.0000.000
113A113ASN0-0.074-0.04914.6000.0840.0840.0000.0000.0000.000
114A114ALA00.0260.01217.639-0.039-0.0390.0000.0000.0000.000
115A115SER0-0.027-0.00119.6910.0360.0360.0000.0000.0000.000
116A116PRO00.0630.00521.642-0.019-0.0190.0000.0000.0000.000
117A117LYS10.8640.91822.5430.0650.0650.0000.0000.0000.000
118A118GLU-1-0.834-0.92119.846-0.199-0.1990.0000.0000.0000.000
119A119LEU0-0.0160.00916.944-0.034-0.0340.0000.0000.0000.000
120A120PRO00.004-0.00616.961-0.035-0.0350.0000.0000.0000.000
121A121ASP-1-0.902-0.94217.527-0.282-0.2820.0000.0000.0000.000
122A122LYS10.8320.91314.0240.3000.3000.0000.0000.0000.000
123A123VAL0-0.0140.00512.511-0.080-0.0800.0000.0000.0000.000
124A124GLU-1-0.869-0.9309.698-1.293-1.2930.0000.0000.0000.000
125A125ILE00.0130.00210.740-0.074-0.0740.0000.0000.0000.000
126A126GLY00.008-0.00110.824-0.047-0.0470.0000.0000.0000.000
127A127LYS10.8480.9455.2472.1282.1280.0000.0000.0000.000
128A128HIS00.0290.0036.3480.1070.1070.0000.0000.0000.000
129A129GLY00.0360.0338.4230.1150.1150.0000.0000.0000.000
130A130LEU0-0.046-0.03210.117-0.024-0.0240.0000.0000.0000.000
131A131ILE00.0390.01212.7650.0720.0720.0000.0000.0000.000
132A132VAL0-0.030-0.00514.993-0.051-0.0510.0000.0000.0000.000
133A133LYS10.9210.95318.297-0.281-0.2810.0000.0000.0000.000
134A134GLN00.0140.00020.365-0.047-0.0470.0000.0000.0000.000
135A135GLY0-0.0130.00024.026-0.006-0.0060.0000.0000.0000.000
136A136TYR0-0.020-0.03123.7230.0260.0260.0000.0000.0000.000
137A137CYS0-0.0250.00724.5860.0100.0100.0000.0000.0000.000
138A138GLN00.0590.00417.6790.0390.0390.0000.0000.0000.000
139A139GLY00.0140.00619.233-0.011-0.0110.0000.0000.0000.000
140A140LEU0-0.032-0.00413.382-0.007-0.0070.0000.0000.0000.000
141A141LEU0-0.047-0.01114.806-0.009-0.0090.0000.0000.0000.000
142A142LEU00.014-0.00311.2590.0210.0210.0000.0000.0000.000
143A143PRO00.0580.0167.335-0.004-0.0040.0000.0000.0000.000
144A144GLN00.0560.04110.151-0.089-0.0890.0000.0000.0000.000
145A145VAL0-0.056-0.02912.5200.0000.0000.0000.0000.0000.000
146A146ALA00.0370.01114.113-0.006-0.0060.0000.0000.0000.000
147A147PRO0-0.0030.00212.3830.0030.0030.0000.0000.0000.000
148A148GLU-1-0.842-0.92315.3110.0250.0250.0000.0000.0000.000
149A149ASN0-0.154-0.09117.5950.0320.0320.0000.0000.0000.000
150A150ASP-1-0.983-0.97519.590-0.120-0.1200.0000.0000.0000.000
151A151MET0-0.0490.00718.1070.0270.0270.0000.0000.0000.000
152A152ASP-1-0.810-0.90417.990-0.182-0.1820.0000.0000.0000.000
153A153SER00.014-0.02816.7390.0150.0150.0000.0000.0000.000
154A154ILE0-0.050-0.01918.0480.0310.0310.0000.0000.0000.000
155A155ASP-1-0.838-0.91220.627-0.055-0.0550.0000.0000.0000.000
156A156PHE00.0070.00412.3850.0460.0460.0000.0000.0000.000
157A157LEU0-0.0050.00416.9230.0530.0530.0000.0000.0000.000
158A158SER00.0080.00719.0280.0420.0420.0000.0000.0000.000
159A159HIS00.0280.00120.2190.0210.0210.0000.0000.0000.000
160A160THR00.005-0.00916.5370.0430.0430.0000.0000.0000.000
161A161CYS0-0.096-0.02119.3830.0350.0350.0000.0000.0000.000
162A162MET00.0050.01322.2260.0140.0140.0000.0000.0000.000
163A163LYS10.9040.97219.476-0.278-0.2780.0000.0000.0000.000
164A164ALA0-0.030-0.01721.1930.0260.0260.0000.0000.0000.000
165A165GLY0-0.031-0.01022.8500.0030.0030.0000.0000.0000.000
166A166LEU0-0.090-0.04223.412-0.015-0.0150.0000.0000.0000.000
167A167SER0-0.023-0.03626.770-0.006-0.0060.0000.0000.0000.000
168A168PRO00.0780.02225.4040.0030.0030.0000.0000.0000.000
169A169ASP-1-0.866-0.90824.9430.0220.0220.0000.0000.0000.000
170A170ALA00.015-0.00824.466-0.007-0.0070.0000.0000.0000.000
171A171TRP00.047-0.01021.004-0.006-0.0060.0000.0000.0000.000
172A172VAL0-0.061-0.02022.850-0.016-0.0160.0000.0000.0000.000
173A173LYS10.8510.91125.560-0.033-0.0330.0000.0000.0000.000
174A174GLY0-0.0090.00024.2800.0050.0050.0000.0000.0000.000
175A175ALA0-0.0230.01422.5520.0120.0120.0000.0000.0000.000
176A176GLU-1-0.928-0.97718.8350.2000.2000.0000.0000.0000.000
177A177VAL00.0370.01514.6470.0320.0320.0000.0000.0000.000
178A178TYR0-0.058-0.02612.422-0.043-0.0430.0000.0000.0000.000
179A179CYS00.0090.0189.0470.0430.0430.0000.0000.0000.000
180A180PHE00.0050.0066.4340.1510.1510.0000.0000.0000.000
181A181GLU-1-0.843-0.9322.327-8.512-7.3652.193-1.268-2.072-0.011
182A182GLY00.021-0.0073.2622.1572.7510.032-0.175-0.451-0.001
183A183GLN00.0400.0472.319-6.451-4.2916.591-3.659-5.093-0.033
184A184ILE00.0180.0085.0350.1640.226-0.001-0.013-0.0490.000
185A185PHE00.0380.0385.512-0.213-0.2130.0000.0000.0000.000
186A186LYS10.9610.96810.686-0.217-0.2170.0000.0000.0000.000
187A187GLU-1-0.815-0.91214.4480.2280.2280.0000.0000.0000.000
188A188LYS10.8790.94517.665-0.050-0.0500.0000.0000.0000.000
189A189GLU-1-0.942-0.98919.8720.0600.0600.0000.0000.0000.000
190A190PRO00.0220.02421.3830.0220.0220.0000.0000.0000.000
191A191ASP-1-0.984-0.99021.1610.1740.1740.0000.0000.0000.000
192A192GLY0-0.0160.00721.481-0.019-0.0190.0000.0000.0000.000
193A193GLU-1-0.981-1.01417.6790.0510.0510.0000.0000.0000.000
194A194VAL0-0.046-0.02012.5440.0250.0250.0000.0000.0000.000
195A195ILE00.0000.01013.552-0.045-0.0450.0000.0000.0000.000
196A196GLU-1-0.886-0.9686.1520.8730.8730.0000.0000.0000.000
197A197GLU-1-0.949-0.95010.187-0.245-0.2450.0000.0000.0000.000
198A198LYS10.8910.9217.1090.7170.7170.0000.0000.0000.000
199A199PHE0-0.061-0.0207.086-0.348-0.3480.0000.0000.0000.000
200A200LEU0-0.020-0.0115.9450.2250.2250.0000.0000.0000.000
201A201GLU-1-0.913-0.9539.422-0.381-0.3810.0000.0000.0000.000
202A202HIS0-0.049-0.01512.436-0.037-0.0370.0000.0000.0000.000
203A203HIS0-0.051-0.02915.739-0.024-0.0240.0000.0000.0000.000
204A204HIS0-0.0020.00413.0980.0400.0400.0000.0000.0000.000