FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 4JZRN

Calculation Name: 3DQP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DQP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CGI7

Base Structure: X-ray

Registration Date: 2023-09-23

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2635827.831508
FMO2-HF: Nuclear repulsion 2551243.389943
FMO2-HF: Total energy -84584.441565
FMO2-MP2: Total energy -84832.688382


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.
-19.538-10.30514.563-7.602-16.193-0.028
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 : 0.027 / 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].
3A3ILE00.0530.0292.325-0.9851.1552.569-1.185-3.5240.001
4A4PHE00.0090.0024.729-0.737-0.660-0.001-0.019-0.0560.000
5A5ILE0-0.009-0.0017.8280.2720.2720.0000.0000.0000.000
6A6VAL00.0390.01610.881-0.192-0.1920.0000.0000.0000.000
7A7GLY00.0500.01114.5700.0260.0260.0000.0000.0000.000
8A8SER0-0.026-0.02314.2710.0160.0160.0000.0000.0000.000
9A9THR0-0.036-0.02015.905-0.006-0.0060.0000.0000.0000.000
10A10GLY00.0180.01619.260-0.037-0.0370.0000.0000.0000.000
11A11ARG10.7840.84419.445-0.230-0.2300.0000.0000.0000.000
12A12VAL00.1000.04216.3090.0130.0130.0000.0000.0000.000
13A13GLY00.0330.03315.1530.0770.0770.0000.0000.0000.000
14A14LYS10.8370.91214.874-0.231-0.2310.0000.0000.0000.000
15A15SER0-0.035-0.01216.5600.0090.0090.0000.0000.0000.000
16A16LEU00.0480.02210.251-0.004-0.0040.0000.0000.0000.000
17A17LEU0-0.007-0.01311.1240.1120.1120.0000.0000.0000.000
18A18LYS10.9560.98312.716-0.395-0.3950.0000.0000.0000.000
19A19SER0-0.042-0.03312.3690.0600.0600.0000.0000.0000.000
20A20LEU00.0580.0216.6970.0390.0390.0000.0000.0000.000
21A21SER0-0.086-0.0319.2820.0550.0550.0000.0000.0000.000
22A22THR0-0.076-0.03211.641-0.092-0.0920.0000.0000.0000.000
23A23THR0-0.016-0.0186.8760.2360.2360.0000.0000.0000.000
24A24ASP-1-0.897-0.9525.1570.7350.7350.0000.0000.0000.000
25A25TYR0-0.009-0.0102.503-5.341-2.7464.051-1.878-4.7680.005
26A26GLN0-0.023-0.0063.479-2.042-1.2170.005-0.227-0.6040.001
27A27ILE00.0150.0095.167-0.140-0.1400.0000.0000.0000.000
28A28TYR0-0.004-0.0306.581-0.077-0.0770.0000.0000.0000.000
29A29ALA00.0290.0109.8520.1470.1470.0000.0000.0000.000
30A30GLY00.0550.03112.503-0.103-0.1030.0000.0000.0000.000
31A31ALA0-0.045-0.03114.8190.0440.0440.0000.0000.0000.000
32A32ARG10.9310.98818.331-0.183-0.1830.0000.0000.0000.000
33A33LYS10.8700.92321.485-0.148-0.1480.0000.0000.0000.000
34A34VAL00.0500.03118.5980.0210.0210.0000.0000.0000.000
35A35GLU-1-0.804-0.90120.0640.1430.1430.0000.0000.0000.000
36A36GLN0-0.054-0.02622.1760.0090.0090.0000.0000.0000.000
37A37VAL00.0080.00315.5480.0280.0280.0000.0000.0000.000
38A38PRO0-0.069-0.01816.318-0.033-0.0330.0000.0000.0000.000
39A39GLN00.012-0.00316.4260.0220.0220.0000.0000.0000.000
40A40TYR00.0800.02113.6750.0080.0080.0000.0000.0000.000
41A41ASN00.0110.00113.122-0.010-0.0100.0000.0000.0000.000
42A42ASN0-0.0050.0037.355-0.301-0.3010.0000.0000.0000.000
43A43VAL0-0.0240.0049.026-0.033-0.0330.0000.0000.0000.000
44A44LYS10.9130.9539.9970.0630.0630.0000.0000.0000.000
45A45ALA0-0.0020.00912.8770.0460.0460.0000.0000.0000.000
46A46VAL00.0000.00313.089-0.063-0.0630.0000.0000.0000.000
47A47HIS00.0040.00016.0770.0520.0520.0000.0000.0000.000
48A48PHE00.0610.00616.248-0.001-0.0010.0000.0000.0000.000
49A49ASP-1-0.870-0.93318.9260.1790.1790.0000.0000.0000.000
50A50VAL0-0.0080.00020.1970.0090.0090.0000.0000.0000.000
51A51ASP-1-0.809-0.89822.3000.1280.1280.0000.0000.0000.000
52A52TRP0-0.053-0.00719.360-0.005-0.0050.0000.0000.0000.000
53A53THR00.020-0.01523.8510.0120.0120.0000.0000.0000.000
54A54PRO00.0640.01520.5980.0080.0080.0000.0000.0000.000
55A55GLU-1-0.810-0.88719.9730.0680.0680.0000.0000.0000.000
56A56GLU-1-0.889-0.90921.2130.0730.0730.0000.0000.0000.000
57A57MET0-0.051-0.01617.8440.0050.0050.0000.0000.0000.000
58A58ALA00.0570.02416.0670.0150.0150.0000.0000.0000.000
59A59LYS10.8570.94015.777-0.035-0.0350.0000.0000.0000.000
60A60GLN0-0.053-0.03415.353-0.062-0.0620.0000.0000.0000.000
61A61LEU0-0.032-0.01011.7170.0020.0020.0000.0000.0000.000
62A62HIS00.0390.02010.8990.0050.0050.0000.0000.0000.000
63A63GLY00.0380.0249.592-0.059-0.0590.0000.0000.0000.000
64A64MET0-0.084-0.0116.420-0.478-0.4780.0000.0000.0000.000
65A65ASP-1-0.796-0.8852.215-7.691-4.4553.901-3.284-3.853-0.034
66A66ALA0-0.002-0.0073.596-0.0570.5890.425-0.214-0.8570.000
67A67ILE0-0.034-0.0085.221-0.575-0.573-0.001-0.0070.0070.000
68A68ILE00.0190.0146.456-0.035-0.0350.0000.0000.0000.000
69A69ASN00.0260.0359.749-0.192-0.1920.0000.0000.0000.000
70A70VAL00.019-0.00213.338-0.028-0.0280.0000.0000.0000.000
71A71SER0-0.082-0.06015.824-0.082-0.0820.0000.0000.0000.000
72A72GLY00.0400.01318.756-0.002-0.0020.0000.0000.0000.000
73A73SER0-0.098-0.07322.334-0.010-0.0100.0000.0000.0000.000
74A74GLY00.0230.00925.626-0.017-0.0170.0000.0000.0000.000
75A75GLY00.0240.00227.559-0.014-0.0140.0000.0000.0000.000
76A76LYS10.8740.93929.323-0.162-0.1620.0000.0000.0000.000
77A77SER00.014-0.01027.740-0.013-0.0130.0000.0000.0000.000
78A78LEU00.0080.02427.3170.0070.0070.0000.0000.0000.000
79A79LEU00.0590.02226.8600.0100.0100.0000.0000.0000.000
80A80LYS10.8700.90427.399-0.123-0.1230.0000.0000.0000.000
81A81VAL0-0.043-0.01022.3090.0050.0050.0000.0000.0000.000
82A82ASP-1-0.767-0.87222.4110.2620.2620.0000.0000.0000.000
83A83LEU00.0090.02622.6380.0120.0120.0000.0000.0000.000
84A84TYR00.0120.00622.9690.0110.0110.0000.0000.0000.000
85A85GLY00.021-0.00721.976-0.001-0.0010.0000.0000.0000.000
86A86ALA0-0.0150.00018.5530.0220.0220.0000.0000.0000.000
87A87VAL00.0510.01318.4320.0200.0200.0000.0000.0000.000
88A88LYS10.7630.88520.011-0.170-0.1700.0000.0000.0000.000
89A89LEU00.0240.00613.823-0.012-0.0120.0000.0000.0000.000
90A90MET0-0.0410.01215.4430.0140.0140.0000.0000.0000.000
91A91GLN00.0420.00616.367-0.019-0.0190.0000.0000.0000.000
92A92ALA0-0.055-0.03216.700-0.031-0.0310.0000.0000.0000.000
93A93ALA00.0000.00112.305-0.021-0.0210.0000.0000.0000.000
94A94GLU-1-0.808-0.90113.7870.0720.0720.0000.0000.0000.000
95A95LYS10.7780.86216.149-0.114-0.1140.0000.0000.0000.000
96A96ALA0-0.055-0.01813.228-0.032-0.0320.0000.0000.0000.000
97A97GLU-1-0.966-0.97812.588-0.161-0.1610.0000.0000.0000.000
98A98VAL0-0.056-0.0117.834-0.027-0.0270.0000.0000.0000.000
99A99LYS10.8420.8949.3940.1770.1770.0000.0000.0000.000
100A100ARG10.8530.9353.963-0.239-0.069-0.001-0.016-0.1530.000
101A101PHE00.014-0.0027.1350.4770.4770.0000.0000.0000.000
102A102ILE00.0280.0136.392-0.149-0.1490.0000.0000.0000.000
103A103LEU0-0.018-0.01110.4210.0410.0410.0000.0000.0000.000
104A104LEU00.0120.01814.123-0.042-0.0420.0000.0000.0000.000
105A105SER0-0.056-0.07416.471-0.044-0.0440.0000.0000.0000.000
106A106THR0-0.039-0.02419.9320.0140.0140.0000.0000.0000.000
107A107ILE00.0400.02822.881-0.010-0.0100.0000.0000.0000.000
108A108PHE00.0720.03024.588-0.011-0.0110.0000.0000.0000.000
109A109SER0-0.040-0.01721.993-0.016-0.0160.0000.0000.0000.000
110A110LEU0-0.004-0.01021.056-0.008-0.0080.0000.0000.0000.000
111A111GLN0-0.030-0.02025.1690.0000.0000.0000.0000.0000.000
112A112PRO00.0560.01228.3410.0000.0000.0000.0000.0000.000
113A113GLU-1-0.895-0.95230.6040.1030.1030.0000.0000.0000.000
114A114LYS10.8240.92228.542-0.121-0.1210.0000.0000.0000.000
115A115TRP0-0.092-0.02728.0920.0010.0010.0000.0000.0000.000
116A116ILE0-0.010-0.01133.153-0.006-0.0060.0000.0000.0000.000
117A117GLY00.0460.02436.2790.0030.0030.0000.0000.0000.000
118A118ALA00.030-0.00536.8760.0060.0060.0000.0000.0000.000
119A119GLY0-0.0050.00834.7460.0020.0020.0000.0000.0000.000
120A120PHE00.0460.02429.1960.0080.0080.0000.0000.0000.000
121A121ASP-1-0.896-0.94433.6520.1020.1020.0000.0000.0000.000
122A122ALA0-0.039-0.02035.4790.0000.0000.0000.0000.0000.000
123A123LEU0-0.022-0.00729.4920.0060.0060.0000.0000.0000.000
124A124LYS10.8530.92631.131-0.102-0.1020.0000.0000.0000.000
125A125ASP-1-0.864-0.93231.9600.1210.1210.0000.0000.0000.000
126A126TYR0-0.061-0.04123.4490.0090.0090.0000.0000.0000.000
127A127TYR0-0.013-0.02126.9830.0150.0150.0000.0000.0000.000
128A128ILE00.0140.00927.6260.0040.0040.0000.0000.0000.000
129A129ALA0-0.048-0.02526.7660.0000.0000.0000.0000.0000.000
130A130LYS10.8790.93619.399-0.340-0.3400.0000.0000.0000.000
131A131HIS00.0080.00423.227-0.001-0.0010.0000.0000.0000.000
132A132PHE0-0.005-0.01124.686-0.004-0.0040.0000.0000.0000.000
133A133ALA0-0.0110.00320.907-0.004-0.0040.0000.0000.0000.000
134A134ASP-1-0.725-0.81619.7710.2960.2960.0000.0000.0000.000
135A135LEU0-0.036-0.01120.663-0.011-0.0110.0000.0000.0000.000
136A136TYR0-0.0060.00920.284-0.012-0.0120.0000.0000.0000.000
137A137LEU00.037-0.00314.457-0.005-0.0050.0000.0000.0000.000
138A138THR0-0.065-0.05017.936-0.020-0.0200.0000.0000.0000.000
139A139LYS10.8450.93019.578-0.120-0.1200.0000.0000.0000.000
140A140GLU-1-0.942-0.95921.5550.0640.0640.0000.0000.0000.000
141A141THR0-0.075-0.03116.9210.0190.0190.0000.0000.0000.000
142A142ASN0-0.036-0.02816.791-0.028-0.0280.0000.0000.0000.000
143A143LEU0-0.0140.00112.053-0.036-0.0360.0000.0000.0000.000
144A144ASP-1-0.814-0.8968.868-0.154-0.1540.0000.0000.0000.000
145A145TYR00.004-0.0059.1250.0950.0950.0000.0000.0000.000
146A146THR00.0130.00010.162-0.067-0.0670.0000.0000.0000.000
147A147ILE0-0.032-0.00412.0170.1020.1020.0000.0000.0000.000
148A148ILE00.0140.01214.483-0.040-0.0400.0000.0000.0000.000
149A149GLN0-0.040-0.04416.270-0.007-0.0070.0000.0000.0000.000
150A150PRO00.004-0.00818.733-0.025-0.0250.0000.0000.0000.000
151A151GLY00.0610.04121.374-0.019-0.0190.0000.0000.0000.000
152A152ALA0-0.036-0.02224.4410.0190.0190.0000.0000.0000.000
153A153LEU00.0130.00521.1750.0040.0040.0000.0000.0000.000
154A154THR0-0.038-0.03424.892-0.013-0.0130.0000.0000.0000.000
155A155GLU-1-0.820-0.88624.6470.2890.2890.0000.0000.0000.000
156A156GLU-1-0.889-0.91426.0820.1910.1910.0000.0000.0000.000
157A157GLU-1-0.933-0.98423.8040.2990.2990.0000.0000.0000.000
158A158ALA0-0.065-0.01520.349-0.004-0.0040.0000.0000.0000.000
159A159THR0-0.020-0.03422.412-0.022-0.0220.0000.0000.0000.000
160A160GLY0-0.008-0.00119.604-0.015-0.0150.0000.0000.0000.000
161A161LEU0-0.052-0.01920.296-0.004-0.0040.0000.0000.0000.000
162A162ILE0-0.016-0.01017.6480.0050.0050.0000.0000.0000.000
163A163ASP-1-0.795-0.88022.0250.1510.1510.0000.0000.0000.000
164A164ILE00.000-0.01717.7850.0210.0210.0000.0000.0000.000
165A165ASN0-0.004-0.00619.4070.0020.0020.0000.0000.0000.000
166A166ASP-1-0.746-0.84822.5920.1460.1460.0000.0000.0000.000
167A167GLU-1-0.834-0.91325.7000.1130.1130.0000.0000.0000.000
168A168VAL0-0.042-0.00827.194-0.006-0.0060.0000.0000.0000.000
169A169SER0-0.031-0.01026.8530.0210.0210.0000.0000.0000.000
170A170ALA00.001-0.01027.449-0.012-0.0120.0000.0000.0000.000
171A171SER00.0030.00026.9180.0110.0110.0000.0000.0000.000
172A172ASN0-0.005-0.01622.105-0.001-0.0010.0000.0000.0000.000
173A173THR00.0450.03922.4630.0250.0250.0000.0000.0000.000
174A174ILE00.009-0.02219.5490.0390.0390.0000.0000.0000.000
175A175GLY00.0080.01718.5650.0590.0590.0000.0000.0000.000
176A176ASP-1-0.668-0.80217.5100.4010.4010.0000.0000.0000.000
177A177VAL0-0.0100.00816.8050.0420.0420.0000.0000.0000.000
178A178ALA0-0.038-0.01014.3760.0820.0820.0000.0000.0000.000
179A179ASP-1-0.779-0.87312.8890.8920.8920.0000.0000.0000.000
180A180THR0-0.002-0.02212.8160.0390.0390.0000.0000.0000.000
181A181ILE0-0.031-0.02410.1960.0390.0390.0000.0000.0000.000
182A182LYS10.8110.9018.476-0.660-0.6600.0000.0000.0000.000
183A183GLU-1-0.796-0.8787.7290.8330.8330.0000.0000.0000.000
184A184LEU0-0.009-0.0058.324-0.166-0.1660.0000.0000.0000.000
185A185VAL0-0.064-0.0252.8090.384-0.7373.591-0.552-1.9170.000
186A186MET0-0.0040.0183.597-2.232-1.5690.024-0.220-0.468-0.001
187A187THR0-0.019-0.0055.571-0.289-0.2890.0000.0000.0000.000
188A188ASP-1-0.856-0.9195.253-1.486-1.4860.0000.0000.0000.000
189A189HIS0-0.041-0.0197.7330.0730.0730.0000.0000.0000.000
190A190SER00.008-0.0179.2370.0860.0860.0000.0000.0000.000
191A191ILE0-0.0210.0176.9790.1080.1080.0000.0000.0000.000
192A192GLY0-0.015-0.00210.847-0.035-0.0350.0000.0000.0000.000
193A193LYS10.7640.90013.604-0.010-0.0100.0000.0000.0000.000
194A194VAL0-0.003-0.01014.8950.0520.0520.0000.0000.0000.000
195A195ILE00.0000.00613.728-0.027-0.0270.0000.0000.0000.000
196A196SER00.0180.00917.7150.0290.0290.0000.0000.0000.000
197A197MET0-0.0160.01018.2740.0130.0130.0000.0000.0000.000
198A198HIS10.8330.89721.265-0.195-0.1950.0000.0000.0000.000
199A199ASN00.003-0.02923.1470.0080.0080.0000.0000.0000.000
200A200GLY0-0.039-0.02224.724-0.017-0.0170.0000.0000.0000.000
201A201LYS10.7810.88425.518-0.161-0.1610.0000.0000.0000.000
202A202THR00.0330.03321.058-0.011-0.0110.0000.0000.0000.000
203A203ALA00.0360.01719.5140.0260.0260.0000.0000.0000.000
204A204ILE0-0.028-0.01614.412-0.004-0.0040.0000.0000.0000.000
205A205LYS10.8260.89210.442-0.331-0.3310.0000.0000.0000.000
206A206GLU-1-0.826-0.90315.0630.1220.1220.0000.0000.0000.000
207A207ALA00.004-0.00218.139-0.026-0.0260.0000.0000.0000.000
208A208LEU0-0.008-0.00511.993-0.016-0.0160.0000.0000.0000.000
209A209GLU-1-0.969-0.98015.0680.0310.0310.0000.0000.0000.000
210A210SER0-0.016-0.02416.077-0.034-0.0340.0000.0000.0000.000
211A211LEU00.0080.00515.125-0.013-0.0130.0000.0000.0000.000
212A212LEU0-0.044-0.03714.367-0.026-0.0260.0000.0000.0000.000
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