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: 5JZLZ

Calculation Name: 2ZCX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZCX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FBX0

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2155977.683075
FMO2-HF: Nuclear repulsion 2078301.680003
FMO2-HF: Total energy -77676.003072
FMO2-MP2: Total energy -77905.517628


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:19:GLN)


Summations of interaction energy for fragment #1(A:19: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.
-12.681-8.4478.468-3.371-9.3320.011
Interaction energy analysis for fragmet #1(A:19:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.021
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].
3A21LYS10.8870.9292.512-3.958-2.1860.2940.026-2.0930.005
4A22GLN00.0460.0111.966-5.020-3.9016.284-2.670-4.7330.013
5A23GLN00.0580.0202.075-2.317-1.0941.891-0.721-2.394-0.007
6A24ARG10.9390.9775.262-0.213-0.093-0.001-0.006-0.1120.000
7A25GLU-1-0.846-0.9206.5182.1352.1350.0000.0000.0000.000
8A26GLU-1-0.920-0.9547.242-1.111-1.1110.0000.0000.0000.000
9A27ALA00.0150.0118.929-0.141-0.1410.0000.0000.0000.000
10A28ILE0-0.047-0.03610.6270.0030.0030.0000.0000.0000.000
11A29LEU0-0.035-0.01310.902-0.011-0.0110.0000.0000.0000.000
12A30ASP-1-0.782-0.86713.229-0.285-0.2850.0000.0000.0000.000
13A31ALA00.0120.01814.993-0.012-0.0120.0000.0000.0000.000
14A32ALA0-0.045-0.03316.5410.0000.0000.0000.0000.0000.000
15A33ARG10.8010.86213.277-0.043-0.0430.0000.0000.0000.000
16A34GLU-1-0.936-0.95618.910-0.135-0.1350.0000.0000.0000.000
17A35LEU0-0.016-0.00820.8300.0000.0000.0000.0000.0000.000
18A36GLY00.003-0.01822.2840.0030.0030.0000.0000.0000.000
19A37THR0-0.105-0.06222.803-0.011-0.0110.0000.0000.0000.000
20A38GLU-1-0.903-0.92325.195-0.011-0.0110.0000.0000.0000.000
21A39ARG10.8280.90126.750-0.035-0.0350.0000.0000.0000.000
22A40GLY00.0340.04427.7560.0070.0070.0000.0000.0000.000
23A41ILE00.031-0.00723.3020.0100.0100.0000.0000.0000.000
24A42ARG10.7600.87426.770-0.036-0.0360.0000.0000.0000.000
25A43GLU-1-0.871-0.94428.4770.0770.0770.0000.0000.0000.000
26A44ILE0-0.0350.01922.6480.0040.0040.0000.0000.0000.000
27A45THR0-0.004-0.01524.9800.0350.0350.0000.0000.0000.000
28A46LEU00.012-0.01218.635-0.005-0.0050.0000.0000.0000.000
29A47THR0-0.028-0.03520.8170.0220.0220.0000.0000.0000.000
30A48ASP-1-0.787-0.87822.3960.1190.1190.0000.0000.0000.000
31A49ILE00.0320.03517.162-0.014-0.0140.0000.0000.0000.000
32A50ALA0-0.052-0.02217.897-0.008-0.0080.0000.0000.0000.000
33A51ALA0-0.026-0.03018.865-0.014-0.0140.0000.0000.0000.000
34A52THR0-0.018-0.01318.947-0.026-0.0260.0000.0000.0000.000
35A53VAL0-0.033-0.01513.868-0.026-0.0260.0000.0000.0000.000
36A54GLY0-0.0070.02215.889-0.014-0.0140.0000.0000.0000.000
37A55MET0-0.107-0.04612.1830.0140.0140.0000.0000.0000.000
38A56HIS00.0570.02217.1480.0110.0110.0000.0000.0000.000
39A57LYS11.0311.00117.885-0.271-0.2710.0000.0000.0000.000
40A58SER0-0.003-0.00418.8800.0330.0330.0000.0000.0000.000
41A59ALA00.0090.00114.0430.0590.0590.0000.0000.0000.000
42A60LEU00.0430.02014.1060.1040.1040.0000.0000.0000.000
43A61LEU0-0.019-0.01115.0190.0580.0580.0000.0000.0000.000
44A62ARG10.8670.95012.925-0.824-0.8240.0000.0000.0000.000
45A63TYR0-0.100-0.0437.2670.1720.1720.0000.0000.0000.000
46A64PHE00.0430.01212.0060.0830.0830.0000.0000.0000.000
47A65GLU-1-0.828-0.88815.6540.4790.4790.0000.0000.0000.000
48A66THR00.001-0.01119.136-0.045-0.0450.0000.0000.0000.000
49A67ARG10.9040.94419.687-0.173-0.1730.0000.0000.0000.000
50A68GLU-1-0.817-0.90621.1780.2800.2800.0000.0000.0000.000
51A69GLN00.0040.00616.9280.0240.0240.0000.0000.0000.000
52A70ILE0-0.018-0.00116.0150.0470.0470.0000.0000.0000.000
53A71PHE00.0530.01217.606-0.001-0.0010.0000.0000.0000.000
54A72LEU0-0.0060.04019.927-0.027-0.0270.0000.0000.0000.000
55A73LYS10.8860.93511.066-1.392-1.3920.0000.0000.0000.000
56A74ILE00.0240.01516.352-0.016-0.0160.0000.0000.0000.000
57A75THR0-0.017-0.02717.865-0.065-0.0650.0000.0000.0000.000
58A76ALA0-0.007-0.01216.978-0.037-0.0370.0000.0000.0000.000
59A77GLU-1-0.928-0.96312.7860.4340.4340.0000.0000.0000.000
60A78GLY00.0400.03016.674-0.068-0.0680.0000.0000.0000.000
61A79TRP00.0250.00120.102-0.038-0.0380.0000.0000.0000.000
62A80LYS10.8880.95313.535-0.359-0.3590.0000.0000.0000.000
63A81GLU-1-0.820-0.86617.815-0.164-0.1640.0000.0000.0000.000
64A82TRP00.0450.01319.166-0.019-0.0190.0000.0000.0000.000
65A83SER0-0.020-0.03121.561-0.024-0.0240.0000.0000.0000.000
66A84ALA00.0000.00619.420-0.014-0.0140.0000.0000.0000.000
67A85GLU-1-0.771-0.84621.527-0.178-0.1780.0000.0000.0000.000
68A86LEU0-0.024-0.01723.799-0.007-0.0070.0000.0000.0000.000
69A87CYS0-0.036-0.04224.4210.0040.0040.0000.0000.0000.000
70A88ALA0-0.044-0.01223.728-0.004-0.0040.0000.0000.0000.000
71A89ARG10.8690.90925.7850.1390.1390.0000.0000.0000.000
72A90LEU00.0100.00229.1010.0040.0040.0000.0000.0000.000
73A91ARG10.8430.91823.8200.1150.1150.0000.0000.0000.000
74A92GLU-1-0.946-0.95629.376-0.160-0.1600.0000.0000.0000.000
75A93LEU0-0.054-0.02332.3610.0030.0030.0000.0000.0000.000
76A94PRO0-0.043-0.02135.2820.0020.0020.0000.0000.0000.000
77A95GLY0-0.025-0.03438.1330.0050.0050.0000.0000.0000.000
78A96ALA00.0550.02638.8420.0030.0030.0000.0000.0000.000
79A97ALA0-0.0210.00040.4250.0030.0030.0000.0000.0000.000
80A98PRO00.0590.02139.908-0.003-0.0030.0000.0000.0000.000
81A99ASP-1-0.821-0.90839.871-0.023-0.0230.0000.0000.0000.000
82A100ALA0-0.032-0.00938.608-0.002-0.0020.0000.0000.0000.000
83A101VAL00.0390.02234.588-0.005-0.0050.0000.0000.0000.000
84A102GLY00.0160.00535.1900.0010.0010.0000.0000.0000.000
85A103GLN0-0.012-0.00535.803-0.002-0.0020.0000.0000.0000.000
86A104VAL00.0160.01430.885-0.005-0.0050.0000.0000.0000.000
87A105PHE00.0060.00331.370-0.002-0.0020.0000.0000.0000.000
88A106ALA0-0.013-0.01531.9310.0030.0030.0000.0000.0000.000
89A107ALA00.0500.03132.8270.0010.0010.0000.0000.0000.000
90A108THR0-0.048-0.02927.539-0.002-0.0020.0000.0000.0000.000
91A109LEU0-0.014-0.00528.0890.0000.0000.0000.0000.0000.000
92A110ALA00.0120.00229.8050.0050.0050.0000.0000.0000.000
93A111ALA0-0.030-0.00128.657-0.001-0.0010.0000.0000.0000.000
94A112ARG10.6900.79122.7880.0970.0970.0000.0000.0000.000
95A113PRO00.0800.04527.1530.0200.0200.0000.0000.0000.000
96A114LEU00.0460.02921.5580.0180.0180.0000.0000.0000.000
97A115PHE00.007-0.00623.2160.0230.0230.0000.0000.0000.000
98A116CYS0-0.017-0.00524.9740.0200.0200.0000.0000.0000.000
99A117ASP-1-0.789-0.87027.6310.0600.0600.0000.0000.0000.000
100A118LEU0-0.054-0.03121.9240.0180.0180.0000.0000.0000.000
101A119LEU0-0.041-0.00826.0200.0250.0250.0000.0000.0000.000
102A120ALA0-0.017-0.00527.8000.0070.0070.0000.0000.0000.000
103A121GLN00.0240.01026.7800.0230.0230.0000.0000.0000.000
104A122ALA00.0150.00525.5680.0170.0170.0000.0000.0000.000
105A123PRO0-0.039-0.02627.0390.0220.0220.0000.0000.0000.000
106A124LEU00.0340.01329.9070.0060.0060.0000.0000.0000.000
107A125ASN0-0.018-0.00324.6040.0090.0090.0000.0000.0000.000
108A126LEU0-0.043-0.02924.9530.0260.0260.0000.0000.0000.000
109A127GLU-1-0.895-0.91926.2140.1840.1840.0000.0000.0000.000
110A128ARG10.8440.88128.564-0.193-0.1930.0000.0000.0000.000
111A129ASN0-0.0350.00226.1290.0040.0040.0000.0000.0000.000
112A130VAL0-0.010-0.00221.3890.0300.0300.0000.0000.0000.000
113A131SER0-0.011-0.00620.798-0.011-0.0110.0000.0000.0000.000
114A132VAL00.0550.00723.1720.0090.0090.0000.0000.0000.000
115A133GLU-1-0.802-0.88720.2860.4720.4720.0000.0000.0000.000
116A134SER00.0050.01019.0030.0690.0690.0000.0000.0000.000
117A135VAL00.0140.00619.987-0.010-0.0100.0000.0000.0000.000
118A136ARG10.8500.90822.320-0.421-0.4210.0000.0000.0000.000
119A137SER0-0.006-0.00917.3910.0000.0000.0000.0000.0000.000
120A138PHE00.0200.01019.541-0.024-0.0240.0000.0000.0000.000
121A139LYS10.9400.97020.427-0.262-0.2620.0000.0000.0000.000
122A140ILE00.0280.02420.603-0.033-0.0330.0000.0000.0000.000
123A141ALA00.0160.00118.074-0.029-0.0290.0000.0000.0000.000
124A142THR0-0.056-0.04019.981-0.051-0.0510.0000.0000.0000.000
125A143LEU0-0.008-0.02422.829-0.035-0.0350.0000.0000.0000.000
126A144ASP-1-0.859-0.89721.1980.1600.1600.0000.0000.0000.000
127A145GLU-1-0.808-0.87219.5420.0580.0580.0000.0000.0000.000
128A146VAL0-0.030-0.00423.498-0.027-0.0270.0000.0000.0000.000
129A147GLY00.0370.02626.416-0.017-0.0170.0000.0000.0000.000
130A148ARG10.7740.85319.523-0.103-0.1030.0000.0000.0000.000
131A149ILE00.016-0.00425.449-0.017-0.0170.0000.0000.0000.000
132A150GLY00.0400.01528.004-0.009-0.0090.0000.0000.0000.000
133A151ALA0-0.060-0.03328.926-0.005-0.0050.0000.0000.0000.000
134A152GLU-1-0.772-0.87128.251-0.072-0.0720.0000.0000.0000.000
135A153LEU00.0050.01331.491-0.005-0.0050.0000.0000.0000.000
136A154ARG10.8240.90831.412-0.045-0.0450.0000.0000.0000.000
137A155ARG10.8100.91831.5040.0590.0590.0000.0000.0000.000
138A156LEU0-0.079-0.02533.224-0.003-0.0030.0000.0000.0000.000
139A157LEU0-0.011-0.02637.019-0.002-0.0020.0000.0000.0000.000
140A158GLY0-0.0050.02138.6910.0030.0030.0000.0000.0000.000
141A159VAL0-0.020-0.00437.0550.0030.0030.0000.0000.0000.000
142A160ASP-1-0.792-0.90638.0130.0450.0450.0000.0000.0000.000
143A161GLU-1-0.896-0.94433.4300.0780.0780.0000.0000.0000.000
144A162THR0-0.036-0.04135.5800.0070.0070.0000.0000.0000.000
145A163GLN00.0690.03537.6640.0000.0000.0000.0000.0000.000
146A164ALA0-0.0160.00433.666-0.002-0.0020.0000.0000.0000.000
147A165VAL0-0.006-0.01032.1030.0010.0010.0000.0000.0000.000
148A166ASP-1-0.866-0.92334.0480.0610.0610.0000.0000.0000.000
149A167VAL0-0.0280.00034.600-0.001-0.0010.0000.0000.0000.000
150A168ILE00.0130.00829.205-0.002-0.0020.0000.0000.0000.000
151A169ALA0-0.0090.00832.1620.0020.0020.0000.0000.0000.000
152A170THR0-0.012-0.01233.3810.0020.0020.0000.0000.0000.000
153A171ALA0-0.023-0.01032.596-0.003-0.0030.0000.0000.0000.000
154A172THR0-0.018-0.02828.4370.0010.0010.0000.0000.0000.000
155A173SER0-0.014-0.01531.3080.0050.0050.0000.0000.0000.000
156A174LEU0-0.037-0.01333.816-0.001-0.0010.0000.0000.0000.000
157A175ALA0-0.001-0.00631.802-0.005-0.0050.0000.0000.0000.000
158A176GLY00.0400.01931.799-0.004-0.0040.0000.0000.0000.000
159A177ALA00.011-0.00132.540-0.001-0.0010.0000.0000.0000.000
160A178LEU0-0.030-0.02336.113-0.004-0.0040.0000.0000.0000.000
161A179TRP00.0400.00631.649-0.004-0.0040.0000.0000.0000.000
162A180GLN0-0.068-0.03731.7100.0040.0040.0000.0000.0000.000
163A181MET0-0.067-0.03735.497-0.002-0.0020.0000.0000.0000.000
164A182ALA0-0.0090.00736.735-0.003-0.0030.0000.0000.0000.000
165A183THR0-0.079-0.04033.661-0.005-0.0050.0000.0000.0000.000
166A184PRO00.0020.00736.2900.0060.0060.0000.0000.0000.000
167A185GLY00.0610.03737.5360.0040.0040.0000.0000.0000.000
168A186PRO00.017-0.00937.003-0.002-0.0020.0000.0000.0000.000
169A187HIS00.0650.02339.914-0.007-0.0070.0000.0000.0000.000
170A188ILE00.0160.01742.006-0.001-0.0010.0000.0000.0000.000
171A189GLN00.0540.04137.991-0.005-0.0050.0000.0000.0000.000
172A190THR0-0.044-0.02842.940-0.004-0.0040.0000.0000.0000.000
173A191LEU00.0030.00745.670-0.001-0.0010.0000.0000.0000.000
174A192TYR0-0.009-0.02243.0240.0000.0000.0000.0000.0000.000
175A193ARG10.8930.93741.4060.0150.0150.0000.0000.0000.000
176A194SER0-0.072-0.01248.455-0.001-0.0010.0000.0000.0000.000
177A195ASP-1-0.759-0.85551.1880.0060.0060.0000.0000.0000.000
178A196PRO00.0340.00552.4010.0000.0000.0000.0000.0000.000
179A197ARG10.7990.86554.531-0.009-0.0090.0000.0000.0000.000
180A198LEU0-0.034-0.00949.3470.0020.0020.0000.0000.0000.000
181A199ALA00.0550.03749.1230.0000.0000.0000.0000.0000.000
182A200HIS0-0.019-0.02048.504-0.001-0.0010.0000.0000.0000.000
183A201ALA0-0.045-0.01446.2700.0020.0020.0000.0000.0000.000
184A202VAL0-0.030-0.00943.9680.0010.0010.0000.0000.0000.000
185A203VAL0-0.061-0.03239.680-0.001-0.0010.0000.0000.0000.000
186A204GLU-1-0.904-0.94140.079-0.031-0.0310.0000.0000.0000.000
187A205VAL00.007-0.01834.3080.0020.0020.0000.0000.0000.000
188A206GLU-1-0.843-0.93135.610-0.056-0.0560.0000.0000.0000.000
189A207PRO00.008-0.00137.2210.0020.0020.0000.0000.0000.000
190A208ARG10.9000.95640.767-0.004-0.0040.0000.0000.0000.000
191A209LEU00.0260.02133.7720.0030.0030.0000.0000.0000.000
192A210ASN00.0360.00938.5010.0020.0020.0000.0000.0000.000
193A211ARG10.9190.95939.5380.0160.0160.0000.0000.0000.000
194A212VAL0-0.021-0.00840.5860.0010.0010.0000.0000.0000.000
195A213LEU00.0330.01735.2590.0030.0030.0000.0000.0000.000
196A214GLY00.0410.03539.5340.0000.0000.0000.0000.0000.000
197A215ALA0-0.032-0.02841.7750.0010.0010.0000.0000.0000.000
198A216LEU0-0.029-0.00539.1060.0020.0020.0000.0000.0000.000
199A217LEU00.0290.00337.2050.0020.0020.0000.0000.0000.000
200A218ARG10.8510.91341.6120.0140.0140.0000.0000.0000.000
201A219GLY00.0180.02045.1340.0000.0000.0000.0000.0000.000
202A220ILE0-0.053-0.02240.7550.0020.0020.0000.0000.0000.000
203A221ALA00.000-0.00743.5420.0010.0010.0000.0000.0000.000
204A222ASP-1-1.012-0.98745.075-0.008-0.0080.0000.0000.0000.000
205A223GLY0-0.077-0.04046.5290.0020.0020.0000.0000.0000.000