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: MVQRZ

Calculation Name: 2PX7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PX7

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLX2

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2051256.125552
FMO2-HF: Nuclear repulsion 1978070.613334
FMO2-HF: Total energy -73185.512218
FMO2-MP2: Total energy -73404.286266


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.
-7.934-3.04912.507-7.827-9.565-0.054
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 : -0.088 / q_NPA : -0.027
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].
3A3VAL0-0.030-0.0463.8282.0533.800-0.009-0.847-0.8910.003
4A4SER0-0.032-0.0046.280-0.124-0.1240.0000.0000.0000.000
5A5VAL00.0220.0148.734-0.010-0.0100.0000.0000.0000.000
6A6LEU0-0.005-0.00511.2180.0640.0640.0000.0000.0000.000
7A7ILE00.022-0.00113.6390.0050.0050.0000.0000.0000.000
8A8PRO0-0.004-0.00217.0360.0260.0260.0000.0000.0000.000
9A9ALA0-0.054-0.02520.6670.0130.0130.0000.0000.0000.000
10A10ALA00.0620.01822.2470.0070.0070.0000.0000.0000.000
11A11GLY0-0.014-0.00125.4790.0080.0080.0000.0000.0000.000
12A19GLY00.022-0.00231.4650.0010.0010.0000.0000.0000.000
13A20PRO00.0060.00826.6890.0000.0000.0000.0000.0000.000
14A21LYS10.9130.95524.6170.0730.0730.0000.0000.0000.000
15A22ALA00.0230.00521.7870.0000.0000.0000.0000.0000.000
16A23PHE0-0.003-0.00922.462-0.004-0.0040.0000.0000.0000.000
17A24LEU00.0140.01625.1770.0080.0080.0000.0000.0000.000
18A25GLN0-0.009-0.01924.241-0.001-0.0010.0000.0000.0000.000
19A26VAL00.0320.01722.3470.0020.0020.0000.0000.0000.000
20A27GLY00.0250.01322.6110.0000.0000.0000.0000.0000.000
21A28GLY0-0.0130.00223.1080.0070.0070.0000.0000.0000.000
22A29ARG10.9380.97914.3640.0110.0110.0000.0000.0000.000
23A30THR0-0.0080.01121.318-0.003-0.0030.0000.0000.0000.000
24A31LEU0-0.024-0.01219.863-0.005-0.0050.0000.0000.0000.000
25A32LEU00.0130.00517.269-0.014-0.0140.0000.0000.0000.000
26A33GLU-1-0.880-0.94316.654-0.107-0.1070.0000.0000.0000.000
27A34TRP0-0.030-0.03015.327-0.008-0.0080.0000.0000.0000.000
28A35THR0-0.044-0.01613.816-0.014-0.0140.0000.0000.0000.000
29A36LEU00.0440.00912.116-0.062-0.0620.0000.0000.0000.000
30A37ALA0-0.072-0.02810.923-0.072-0.0720.0000.0000.0000.000
31A38ALA0-0.032-0.0149.2850.0380.0380.0000.0000.0000.000
32A39PHE00.004-0.0067.4460.0370.0370.0000.0000.0000.000
33A40ARG10.9630.9817.076-0.384-0.3840.0000.0000.0000.000
34A41ASP-1-0.863-0.9352.148-0.5891.9053.473-2.347-3.620-0.019
35A42ALA0-0.050-0.0212.740-9.144-5.8610.753-2.139-1.897-0.025
36A43ALA0-0.041-0.0113.753-0.3810.1400.007-0.144-0.3840.000
37A44GLU-1-0.775-0.8784.384-0.179-0.074-0.001-0.013-0.0910.000
38A45VAL00.0070.0178.127-0.089-0.0890.0000.0000.0000.000
39A46LEU00.0040.01010.6920.0670.0670.0000.0000.0000.000
40A47VAL00.010-0.00414.289-0.012-0.0120.0000.0000.0000.000
41A48ALA0-0.026-0.00717.2440.0200.0200.0000.0000.0000.000
42A49LEU0-0.004-0.01220.904-0.003-0.0030.0000.0000.0000.000
43A50PRO0-0.026-0.00423.6290.0040.0040.0000.0000.0000.000
44A51PRO00.0610.02527.3850.0000.0000.0000.0000.0000.000
45A52GLY0-0.0060.00829.1210.0030.0030.0000.0000.0000.000
46A53ALA0-0.076-0.03126.6110.0030.0030.0000.0000.0000.000
47A54GLU-1-0.915-0.96826.257-0.071-0.0710.0000.0000.0000.000
48A55PRO0-0.022-0.00320.815-0.004-0.0040.0000.0000.0000.000
49A56PRO0-0.0100.00320.0860.0080.0080.0000.0000.0000.000
50A57LYS10.9450.95820.0000.0650.0650.0000.0000.0000.000
51A58GLY00.004-0.00117.7200.0040.0040.0000.0000.0000.000
52A59LEU00.0000.01415.259-0.010-0.0100.0000.0000.0000.000
53A60GLY00.0090.00611.0540.0100.0100.0000.0000.0000.000
54A61ALA0-0.026-0.02311.072-0.084-0.0840.0000.0000.0000.000
55A62VAL00.0040.02013.0920.0420.0420.0000.0000.0000.000
56A63PHE00.010-0.00715.400-0.012-0.0120.0000.0000.0000.000
57A64LEU00.0350.00918.4270.0140.0140.0000.0000.0000.000
58A65GLU-1-0.922-0.94621.568-0.072-0.0720.0000.0000.0000.000
59A66GLY0-0.010-0.01424.474-0.002-0.0020.0000.0000.0000.000
60A67GLY0-0.058-0.03425.1450.0080.0080.0000.0000.0000.000
61A68ALA00.0150.00228.186-0.002-0.0020.0000.0000.0000.000
62A69THR00.0610.03329.270-0.002-0.0020.0000.0000.0000.000
63A70ARG10.9010.93520.3250.1450.1450.0000.0000.0000.000
64A71GLN00.0690.03024.360-0.010-0.0100.0000.0000.0000.000
65A72ALA00.0160.01025.135-0.003-0.0030.0000.0000.0000.000
66A73SER00.000-0.01122.8120.0000.0000.0000.0000.0000.000
67A74VAL0-0.0070.00219.911-0.006-0.0060.0000.0000.0000.000
68A75ALA0-0.022-0.00320.647-0.005-0.0050.0000.0000.0000.000
69A76ARG10.9030.94922.3480.0810.0810.0000.0000.0000.000
70A77LEU0-0.003-0.00317.2860.0030.0030.0000.0000.0000.000
71A78LEU0-0.009-0.00517.500-0.001-0.0010.0000.0000.0000.000
72A79GLU-1-1.010-0.99918.320-0.056-0.0560.0000.0000.0000.000
73A80ALA0-0.011-0.00217.1730.0120.0120.0000.0000.0000.000
74A81ALA0-0.0260.00913.9680.0050.0050.0000.0000.0000.000
75A82SER0-0.027-0.02711.5440.0550.0550.0000.0000.0000.000
76A83LEU0-0.0300.0037.2450.0670.0670.0000.0000.0000.000
77A84PRO00.0000.01010.820-0.078-0.0780.0000.0000.0000.000
78A85LEU0-0.021-0.00310.213-0.041-0.0410.0000.0000.0000.000
79A86VAL00.0020.00311.336-0.003-0.0030.0000.0000.0000.000
80A87LEU00.003-0.0018.7580.0040.0040.0000.0000.0000.000
81A88VAL00.0060.02412.8380.0100.0100.0000.0000.0000.000
82A89HIS00.0590.00714.287-0.005-0.0050.0000.0000.0000.000
83A90ASP-1-0.828-0.89816.374-0.124-0.1240.0000.0000.0000.000
84A91VAL00.0490.00318.336-0.001-0.0010.0000.0000.0000.000
85A92ALA0-0.056-0.02919.3750.0110.0110.0000.0000.0000.000
86A93ARG10.8920.96418.0380.1340.1340.0000.0000.0000.000
87A94PRO00.0550.03516.832-0.024-0.0240.0000.0000.0000.000
88A95PHE0-0.0150.00615.521-0.003-0.0030.0000.0000.0000.000
89A96VAL0-0.0100.00211.8320.0120.0120.0000.0000.0000.000
90A97SER0-0.014-0.04411.5900.0080.0080.0000.0000.0000.000
91A98ARG11.0060.9721.6090.559-2.7068.284-2.337-2.682-0.013
92A99GLY0-0.013-0.0037.744-0.067-0.0670.0000.0000.0000.000
93A100LEU0-0.0010.01410.200-0.063-0.0630.0000.0000.0000.000
94A101VAL00.0310.0127.085-0.010-0.0100.0000.0000.0000.000
95A102ALA00.0160.0136.427-0.116-0.1160.0000.0000.0000.000
96A103ARG10.8870.9457.8310.0200.0200.0000.0000.0000.000
97A104VAL0-0.033-0.01411.4830.0020.0020.0000.0000.0000.000
98A105LEU0-0.007-0.0126.1940.0410.0410.0000.0000.0000.000
99A106GLU-1-0.853-0.9149.693-0.221-0.2210.0000.0000.0000.000
100A107ALA00.0400.01210.6870.0560.0560.0000.0000.0000.000
101A108ALA0-0.0320.00012.8030.0440.0440.0000.0000.0000.000
102A109GLN0-0.024-0.0197.6250.1500.1500.0000.0000.0000.000
103A110ARG10.8400.92713.2500.2550.2550.0000.0000.0000.000
104A111SER0-0.038-0.03716.2340.0360.0360.0000.0000.0000.000
105A112GLY00.0400.01517.0780.0270.0270.0000.0000.0000.000
106A113ALA0-0.005-0.01818.3860.0010.0010.0000.0000.0000.000
107A114ALA0-0.0280.00615.7060.0160.0160.0000.0000.0000.000
108A115VAL00.0330.00617.128-0.026-0.0260.0000.0000.0000.000
109A116PRO00.0070.03016.1280.0190.0190.0000.0000.0000.000
110A117VAL0-0.009-0.00818.4230.0080.0080.0000.0000.0000.000
111A118LEU0-0.0070.00821.1590.0050.0050.0000.0000.0000.000
112A119PRO00.0110.00023.770-0.002-0.0020.0000.0000.0000.000
113A120VAL00.0190.01327.3160.0000.0000.0000.0000.0000.000
114A121PRO0-0.036-0.00928.7150.0030.0030.0000.0000.0000.000
115A122ASP-1-0.861-0.91730.802-0.017-0.0170.0000.0000.0000.000
116A123THR0-0.050-0.05034.329-0.002-0.0020.0000.0000.0000.000
117A124LEU00.0210.02633.755-0.001-0.0010.0000.0000.0000.000
118A125MET0-0.025-0.01537.0240.0010.0010.0000.0000.0000.000
119A126ALA0-0.021-0.01139.606-0.002-0.0020.0000.0000.0000.000
120A127PRO00.001-0.05240.8590.0010.0010.0000.0000.0000.000
121A128GLU-1-0.954-0.96944.106-0.021-0.0210.0000.0000.0000.000
122A129GLY00.012-0.00646.7810.0010.0010.0000.0000.0000.000
123A130GLU-1-1.015-0.89746.889-0.016-0.0160.0000.0000.0000.000
124A131ALA0-0.195-0.12945.3410.0000.0000.0000.0000.0000.000
125A132TYR00.038-0.07943.4260.0010.0010.0000.0000.0000.000
126A133GLY00.2400.17245.746-0.001-0.0010.0000.0000.0000.000
127A134ARG10.9510.99041.6270.0280.0280.0000.0000.0000.000
128A135VAL0-0.0080.00040.566-0.001-0.0010.0000.0000.0000.000
129A136VAL0-0.052-0.02537.3720.0000.0000.0000.0000.0000.000
130A137PRO00.0430.00737.6750.0000.0000.0000.0000.0000.000
131A138ARG10.9580.98532.1390.0180.0180.0000.0000.0000.000
132A139GLU-1-0.881-0.94732.634-0.026-0.0260.0000.0000.0000.000
133A140ALA0-0.051-0.01832.464-0.003-0.0030.0000.0000.0000.000
134A141PHE0-0.022-0.00631.362-0.004-0.0040.0000.0000.0000.000
135A142ARG10.8430.91725.8990.0510.0510.0000.0000.0000.000
136A143LEU00.0060.01225.417-0.001-0.0010.0000.0000.0000.000
137A144VAL00.0330.01822.519-0.003-0.0030.0000.0000.0000.000
138A145GLN0-0.042-0.03019.0120.0000.0000.0000.0000.0000.000
139A146THR0-0.059-0.02716.8100.0030.0030.0000.0000.0000.000
140A147PRO00.026-0.00511.7740.0270.0270.0000.0000.0000.000
141A148GLN0-0.044-0.03914.9330.0150.0150.0000.0000.0000.000
142A149GLY00.0260.01714.097-0.032-0.0320.0000.0000.0000.000
143A150PHE00.008-0.00614.8040.0430.0430.0000.0000.0000.000
144A151PHE00.0410.04915.307-0.025-0.0250.0000.0000.0000.000
145A152THR0-0.027-0.05114.013-0.003-0.0030.0000.0000.0000.000
146A153ALA00.003-0.01016.8980.0100.0100.0000.0000.0000.000
147A154LEU00.0200.03319.9330.0090.0090.0000.0000.0000.000
148A155LEU00.0220.01718.6910.0090.0090.0000.0000.0000.000
149A156ARG10.8760.92717.4920.0800.0800.0000.0000.0000.000
150A157GLU-1-0.915-0.95022.606-0.056-0.0560.0000.0000.0000.000
151A158ALA0-0.008-0.00424.3540.0060.0060.0000.0000.0000.000
152A159HIS0-0.026-0.03722.9070.0150.0150.0000.0000.0000.000
153A160ALA0-0.056-0.01826.1900.0070.0070.0000.0000.0000.000
154A161TYR0-0.012-0.02728.4610.0080.0080.0000.0000.0000.000
155A162ALA00.0270.01029.0430.0040.0040.0000.0000.0000.000
156A163ARG10.9540.97926.2050.0700.0700.0000.0000.0000.000
157A164ARG10.9090.95331.8210.0520.0520.0000.0000.0000.000
158A165LYS10.8870.95534.1640.0480.0480.0000.0000.0000.000
159A166GLY00.0230.03234.7870.0020.0020.0000.0000.0000.000
160A167LEU0-0.048-0.00731.0760.0010.0010.0000.0000.0000.000
161A168GLU-1-0.934-0.97131.120-0.063-0.0630.0000.0000.0000.000
162A169ALA00.001-0.00228.5330.0040.0040.0000.0000.0000.000
163A170SER0-0.046-0.01628.041-0.004-0.0040.0000.0000.0000.000
164A171ASP-1-0.848-0.91522.939-0.118-0.1180.0000.0000.0000.000
165A172ASP-1-0.735-0.88120.915-0.147-0.1470.0000.0000.0000.000
166A173ALA00.0230.01222.2190.0050.0050.0000.0000.0000.000
167A174GLN0-0.038-0.05623.4770.0140.0140.0000.0000.0000.000
168A175LEU0-0.033-0.00625.2310.0080.0080.0000.0000.0000.000
169A176VAL0-0.007-0.00322.0440.0060.0060.0000.0000.0000.000
170A177GLN00.0190.01225.5360.0050.0050.0000.0000.0000.000
171A178ALA0-0.043-0.01728.0770.0060.0060.0000.0000.0000.000
172A179LEU0-0.055-0.02826.2680.0060.0060.0000.0000.0000.000
173A180GLY0-0.0290.00130.0390.0040.0040.0000.0000.0000.000
174A181TYR0-0.073-0.04921.3670.0070.0070.0000.0000.0000.000
175A182PRO0-0.029-0.00524.569-0.001-0.0010.0000.0000.0000.000
176A183VAL00.019-0.00421.399-0.012-0.0120.0000.0000.0000.000
177A184ALA0-0.0030.01119.5230.0110.0110.0000.0000.0000.000
178A185LEU0-0.021-0.01820.456-0.011-0.0110.0000.0000.0000.000
179A186VAL0-0.008-0.00315.3550.0040.0040.0000.0000.0000.000
180A187GLU-1-0.928-0.96217.401-0.038-0.0380.0000.0000.0000.000
181A188GLY00.0330.00317.062-0.016-0.0160.0000.0000.0000.000
182A189GLU-1-0.809-0.90314.841-0.005-0.0050.0000.0000.0000.000
183A190ALA0-0.0050.00718.641-0.009-0.0090.0000.0000.0000.000
184A191THR00.0420.01316.8830.0020.0020.0000.0000.0000.000
185A192ALA0-0.0160.01916.613-0.003-0.0030.0000.0000.0000.000
186A193PHE0-0.025-0.00918.440-0.014-0.0140.0000.0000.0000.000
187A194LYS10.9250.95521.4020.0830.0830.0000.0000.0000.000
188A195ILE00.0250.00622.8610.0080.0080.0000.0000.0000.000
189A196THR0-0.105-0.05525.357-0.009-0.0090.0000.0000.0000.000
190A197HIS00.0200.00728.5440.0020.0020.0000.0000.0000.000
191A198PRO00.0370.00130.5030.0000.0000.0000.0000.0000.000
192A199GLN00.021-0.00631.7370.0000.0000.0000.0000.0000.000
193A200ASP-1-0.768-0.86927.066-0.039-0.0390.0000.0000.0000.000
194A201LEU0-0.024-0.01126.7930.0000.0000.0000.0000.0000.000
195A202VAL00.0250.01527.5500.0030.0030.0000.0000.0000.000
196A203LEU00.0030.00526.0740.0050.0050.0000.0000.0000.000
197A204ALA0-0.029-0.02523.4370.0040.0040.0000.0000.0000.000
198A205GLU-1-0.867-0.95823.706-0.016-0.0160.0000.0000.0000.000
199A206ALA0-0.104-0.03825.8450.0070.0070.0000.0000.0000.000
200A207LEU0-0.007-0.00719.5750.0070.0070.0000.0000.0000.000
201A208ALA00.0050.01020.6130.0090.0090.0000.0000.0000.000
202A209ARG10.9010.95721.146-0.004-0.0040.0000.0000.0000.000
203A210VAL0-0.0230.00918.2360.0080.0080.0000.0000.0000.000