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: MV77Z

Calculation Name: 3VXG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VXG

Chain ID: A

ChEMBL ID:

UniProt ID: Q76L36

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 304
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4659241.722441
FMO2-HF: Nuclear repulsion 4541641.895349
FMO2-HF: Total energy -117599.827093
FMO2-MP2: Total energy -117953.399883


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:4:SER)


Summations of interaction energy for fragment #1(A:4:SER)
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.
-43.109-45.42832.754-16.275-14.163-0.038
Interaction energy analysis for fragmet #1(A:4:SER)
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 : -0.042
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].
3A6LEU0-0.0420.0062.127-7.665-4.4605.065-3.946-4.3240.029
4A7LEU00.019-0.0012.314-7.246-5.8451.465-0.872-1.9940.018
5A8PRO0-0.0060.0082.146-5.934-5.7192.985-1.621-1.579-0.021
6A9LYS10.8930.9694.235-0.1760.0480.000-0.031-0.1930.000
7A10THR0-0.006-0.0262.222-0.4421.7431.096-1.457-1.8260.004
8A11PHE0-0.007-0.0184.9580.5670.643-0.001-0.004-0.0710.000
9A12ARG10.8830.9473.7280.4570.591-0.001-0.028-0.1060.000
10A13THR00.0350.0228.9890.1320.1320.0000.0000.0000.000
11A14LYS10.9060.96812.2660.0500.0500.0000.0000.0000.000
12A15SER0-0.049-0.04314.6690.0180.0180.0000.0000.0000.000
13A16GLY00.0010.00111.2940.0170.0170.0000.0000.0000.000
14A17LYS10.7890.8839.5810.1160.1160.0000.0000.0000.000
15A18GLU-1-0.789-0.8461.590-22.875-32.63422.145-8.316-4.070-0.068
16A19ILE0-0.0060.0075.6310.2450.2450.0000.0000.0000.000
17A20SER00.0260.0036.058-0.341-0.3410.0000.0000.0000.000
18A21ILE0-0.003-0.0018.4250.0660.0660.0000.0000.0000.000
19A22ALA00.0100.01311.354-0.008-0.0080.0000.0000.0000.000
20A23LEU0-0.044-0.01414.1970.0210.0210.0000.0000.0000.000
21A24GLY00.020-0.00617.7500.0010.0010.0000.0000.0000.000
22A25THR0-0.053-0.05820.0120.0030.0030.0000.0000.0000.000
23A26GLY00.0220.02523.3980.0040.0040.0000.0000.0000.000
24A27THR0-0.056-0.03525.3320.0010.0010.0000.0000.0000.000
25A28LYS10.8130.89728.3690.0310.0310.0000.0000.0000.000
26A29TRP00.002-0.00331.3320.0010.0010.0000.0000.0000.000
27A30LYS10.8880.95034.2300.0220.0220.0000.0000.0000.000
28A31GLN00.0120.01737.1170.0000.0000.0000.0000.0000.000
29A32ALA0-0.0030.00240.7410.0010.0010.0000.0000.0000.000
30A33GLN00.059-0.00433.899-0.001-0.0010.0000.0000.0000.000
31A34THR0-0.0050.00337.134-0.001-0.0010.0000.0000.0000.000
32A35ILE00.0090.02238.5750.0000.0000.0000.0000.0000.000
33A36ASN0-0.030-0.03434.510-0.002-0.0020.0000.0000.0000.000
34A37ASP-1-0.917-0.94834.950-0.024-0.0240.0000.0000.0000.000
35A38VAL00.0100.00632.092-0.001-0.0010.0000.0000.0000.000
36A39SER00.0520.02331.7010.0010.0010.0000.0000.0000.000
37A40THR00.037-0.00331.761-0.002-0.0020.0000.0000.0000.000
38A41GLU-1-0.933-0.94630.956-0.038-0.0380.0000.0000.0000.000
39A42LEU0-0.017-0.00725.627-0.003-0.0030.0000.0000.0000.000
40A43VAL0-0.004-0.00727.132-0.005-0.0050.0000.0000.0000.000
41A44ASP-1-0.813-0.91527.271-0.044-0.0440.0000.0000.0000.000
42A45ASN0-0.026-0.01424.294-0.003-0.0030.0000.0000.0000.000
43A46ILE00.006-0.00321.832-0.007-0.0070.0000.0000.0000.000
44A47LEU00.0020.00622.606-0.008-0.0080.0000.0000.0000.000
45A48LEU0-0.041-0.00723.877-0.005-0.0050.0000.0000.0000.000
46A49GLY00.0440.00520.844-0.004-0.0040.0000.0000.0000.000
47A50LEU0-0.0010.00718.400-0.013-0.0130.0000.0000.0000.000
48A51LYS10.9420.97719.8060.0490.0490.0000.0000.0000.000
49A52LEU0-0.096-0.05720.4100.0010.0010.0000.0000.0000.000
50A53GLY00.0190.02016.8570.0000.0000.0000.0000.0000.000
51A54PHE0-0.0120.00115.021-0.030-0.0300.0000.0000.0000.000
52A55ARG10.8720.92112.5060.1850.1850.0000.0000.0000.000
53A56HIS00.0050.02310.896-0.002-0.0020.0000.0000.0000.000
54A57ILE0-0.0030.01314.1180.0190.0190.0000.0000.0000.000
55A58ASP-1-0.783-0.87816.699-0.082-0.0820.0000.0000.0000.000
56A59THR0-0.005-0.01818.4780.0090.0090.0000.0000.0000.000
57A60ALA00.0200.00521.6700.0000.0000.0000.0000.0000.000
58A61GLU-1-0.745-0.82524.394-0.015-0.0150.0000.0000.0000.000
59A62ALA0-0.030-0.03527.5910.0010.0010.0000.0000.0000.000
60A63TYR0-0.0050.01921.5980.0040.0040.0000.0000.0000.000
61A64ASN0-0.031-0.01928.0500.0020.0020.0000.0000.0000.000
62A65THR00.0840.04626.167-0.001-0.0010.0000.0000.0000.000
63A66GLN00.0330.03225.634-0.005-0.0050.0000.0000.0000.000
64A67LYS10.9050.95026.9360.0240.0240.0000.0000.0000.000
65A68GLU-1-0.755-0.87427.956-0.035-0.0350.0000.0000.0000.000
66A69VAL00.0190.00722.073-0.003-0.0030.0000.0000.0000.000
67A70GLY00.0380.02724.983-0.003-0.0030.0000.0000.0000.000
68A71GLU-1-0.915-0.95926.868-0.029-0.0290.0000.0000.0000.000
69A72ALA00.0020.00024.5910.0000.0000.0000.0000.0000.000
70A73LEU0-0.028-0.02320.592-0.004-0.0040.0000.0000.0000.000
71A74LYS10.8760.95924.3700.0310.0310.0000.0000.0000.000
72A75ARG10.8550.92627.7820.0410.0410.0000.0000.0000.000
73A76THR0-0.031-0.00522.1780.0000.0000.0000.0000.0000.000
74A77ASP-1-0.883-0.92924.829-0.045-0.0450.0000.0000.0000.000
75A78VAL0-0.127-0.06018.195-0.003-0.0030.0000.0000.0000.000
76A79PRO00.0570.02419.5460.0030.0030.0000.0000.0000.000
77A80ARG10.8940.93317.3700.0570.0570.0000.0000.0000.000
78A81GLU-1-0.853-0.94617.591-0.058-0.0580.0000.0000.0000.000
79A82ASP-1-0.839-0.87914.829-0.173-0.1730.0000.0000.0000.000
80A83ILE0-0.047-0.01914.342-0.047-0.0470.0000.0000.0000.000
81A84TRP0-0.034-0.02211.412-0.008-0.0080.0000.0000.0000.000
82A85VAL0-0.009-0.01214.2880.0010.0010.0000.0000.0000.000
83A86THR00.0390.01214.9320.0090.0090.0000.0000.0000.000
84A87THR0-0.007-0.02317.5760.0010.0010.0000.0000.0000.000
85A88LYS10.8160.88919.3990.0690.0690.0000.0000.0000.000
86A89TYR00.0550.03723.0990.0010.0010.0000.0000.0000.000
87A90SER0-0.013-0.01826.370-0.002-0.0020.0000.0000.0000.000
88A91PRO00.0030.00627.9530.0020.0020.0000.0000.0000.000
89A92GLY00.0670.01430.9180.0020.0020.0000.0000.0000.000
90A93TRP0-0.045-0.02425.6560.0000.0000.0000.0000.0000.000
91A94GLY00.0150.01431.6440.0000.0000.0000.0000.0000.000
92A95SER0-0.032-0.01734.5880.0000.0000.0000.0000.0000.000
93A96ILE0-0.0130.00735.9870.0020.0020.0000.0000.0000.000
94A97LYS10.8240.90836.5000.0060.0060.0000.0000.0000.000
95A98ALA0-0.0090.00633.175-0.001-0.0010.0000.0000.0000.000
96A99TYR00.002-0.00333.5560.0010.0010.0000.0000.0000.000
97A100SER0-0.020-0.02532.0870.0010.0010.0000.0000.0000.000
98A101LYS10.8700.92234.3780.0030.0030.0000.0000.0000.000
99A102SER00.026-0.00833.5500.0020.0020.0000.0000.0000.000
100A103PRO00.0270.01328.038-0.002-0.0020.0000.0000.0000.000
101A104SER00.0450.02428.983-0.001-0.0010.0000.0000.0000.000
102A105ASP-1-0.875-0.89930.610-0.001-0.0010.0000.0000.0000.000
103A106SER0-0.068-0.05728.473-0.003-0.0030.0000.0000.0000.000
104A107ILE00.0140.00825.174-0.003-0.0030.0000.0000.0000.000
105A108ASP-1-0.775-0.86927.4740.0010.0010.0000.0000.0000.000
106A109LYS10.8010.90030.1480.0160.0160.0000.0000.0000.000
107A110ALA0-0.019-0.00825.203-0.003-0.0030.0000.0000.0000.000
108A111LEU0-0.0030.00524.540-0.004-0.0040.0000.0000.0000.000
109A112ALA0-0.021-0.00427.241-0.002-0.0020.0000.0000.0000.000
110A113GLN0-0.088-0.05628.978-0.002-0.0020.0000.0000.0000.000
111A114LEU00.006-0.01022.846-0.003-0.0030.0000.0000.0000.000
112A115GLY0-0.068-0.02826.193-0.004-0.0040.0000.0000.0000.000
113A116VAL0-0.060-0.01622.586-0.002-0.0020.0000.0000.0000.000
114A117ASP-1-0.846-0.92724.092-0.007-0.0070.0000.0000.0000.000
115A118TYR0-0.006-0.02217.2630.0110.0110.0000.0000.0000.000
116A119VAL00.0020.00219.914-0.013-0.0130.0000.0000.0000.000
117A120ASP-1-0.751-0.86314.360-0.081-0.0810.0000.0000.0000.000
118A121LEU00.0180.01313.3510.0220.0220.0000.0000.0000.000
119A122PHE00.0240.00716.598-0.010-0.0100.0000.0000.0000.000
120A123LEU0-0.027-0.00616.4550.0100.0100.0000.0000.0000.000
121A124ILE00.0300.01420.564-0.001-0.0010.0000.0000.0000.000
122A125HIS0-0.002-0.01622.562-0.004-0.0040.0000.0000.0000.000
123A126SER00.010-0.00324.235-0.003-0.0030.0000.0000.0000.000
124A127PRO00.0400.02424.3850.0040.0040.0000.0000.0000.000
125A128PHE0-0.048-0.02426.5080.0030.0030.0000.0000.0000.000
126A129PHE0-0.041-0.00627.717-0.001-0.0010.0000.0000.0000.000
127A130THR00.0120.00232.6190.0020.0020.0000.0000.0000.000
128A131THR00.033-0.00135.157-0.001-0.0010.0000.0000.0000.000
129A132GLU-1-0.790-0.87836.430-0.005-0.0050.0000.0000.0000.000
130A133GLN0-0.065-0.03635.1790.0010.0010.0000.0000.0000.000
131A134THR00.0520.00731.725-0.001-0.0010.0000.0000.0000.000
132A135HIS0-0.046-0.01034.6750.0020.0020.0000.0000.0000.000
133A136GLY0-0.008-0.00437.3030.0010.0010.0000.0000.0000.000
134A137TYR0-0.0020.00431.7580.0020.0020.0000.0000.0000.000
135A138THR00.018-0.01231.586-0.002-0.0020.0000.0000.0000.000
136A139LEU00.014-0.00225.0040.0000.0000.0000.0000.0000.000
137A140GLU-1-0.771-0.86927.2880.0070.0070.0000.0000.0000.000
138A141GLN00.0860.05428.1720.0010.0010.0000.0000.0000.000
139A142ALA0-0.029-0.01727.8750.0010.0010.0000.0000.0000.000
140A143TRP0-0.033-0.02218.727-0.007-0.0070.0000.0000.0000.000
141A144GLU-1-0.882-0.94625.0020.0300.0300.0000.0000.0000.000
142A145ALA0-0.010-0.00627.4200.0030.0030.0000.0000.0000.000
143A146LEU0-0.042-0.02721.520-0.001-0.0010.0000.0000.0000.000
144A147VAL0-0.0020.00022.5390.0060.0060.0000.0000.0000.000
145A148GLU-1-0.842-0.90324.0820.0500.0500.0000.0000.0000.000
146A149ALA0-0.019-0.00424.5400.0010.0010.0000.0000.0000.000
147A150LYS10.8440.92116.183-0.140-0.1400.0000.0000.0000.000
148A151LYS10.8380.90322.385-0.049-0.0490.0000.0000.0000.000
149A152ALA0-0.045-0.01224.6280.0020.0020.0000.0000.0000.000
150A153GLY0-0.022-0.00322.296-0.004-0.0040.0000.0000.0000.000
151A154LYS10.8260.89823.131-0.017-0.0170.0000.0000.0000.000
152A155VAL0-0.007-0.00519.366-0.012-0.0120.0000.0000.0000.000
153A156ARG10.7650.88212.5190.0380.0380.0000.0000.0000.000
154A157GLU-1-0.858-0.93312.3640.2510.2510.0000.0000.0000.000
155A158ILE00.0220.01816.138-0.026-0.0260.0000.0000.0000.000
156A159GLY00.039-0.01016.4750.0140.0140.0000.0000.0000.000
157A160ILE0-0.049-0.01117.5860.0000.0000.0000.0000.0000.000
158A161SER0-0.004-0.00318.181-0.010-0.0100.0000.0000.0000.000
159A162ASN0-0.018-0.01420.4650.0040.0040.0000.0000.0000.000
160A163ALA00.0120.01819.9500.0050.0050.0000.0000.0000.000
161A164ALA00.0540.01120.743-0.008-0.0080.0000.0000.0000.000
162A165ILE00.012-0.00320.2270.0050.0050.0000.0000.0000.000
163A166PRO00.0490.01522.1350.0050.0050.0000.0000.0000.000
164A167HIS00.0230.01923.2820.0030.0030.0000.0000.0000.000
165A168LEU0-0.007-0.00817.5150.0050.0050.0000.0000.0000.000
166A169GLU-1-0.949-0.96721.1440.0050.0050.0000.0000.0000.000
167A170LYS10.8580.91623.3620.0040.0040.0000.0000.0000.000
168A171LEU0-0.0040.00620.2810.0030.0030.0000.0000.0000.000
169A172PHE0-0.0010.00216.8370.0050.0050.0000.0000.0000.000
170A173ALA0-0.025-0.00821.8540.0070.0070.0000.0000.0000.000
171A174ALA0-0.0110.00525.2330.0010.0010.0000.0000.0000.000
172A175SER0-0.054-0.02721.6590.0030.0030.0000.0000.0000.000
173A176PRO0-0.0210.00523.6770.0010.0010.0000.0000.0000.000
174A177SER0-0.023-0.05821.7920.0010.0010.0000.0000.0000.000
175A178PRO00.056-0.00417.614-0.004-0.0040.0000.0000.0000.000
176A179GLU-1-0.908-0.90517.0660.1570.1570.0000.0000.0000.000
177A180TYR0-0.049-0.03417.539-0.001-0.0010.0000.0000.0000.000
178A181TYR00.0230.02116.329-0.020-0.0200.0000.0000.0000.000
179A182PRO0-0.0200.00216.5440.0090.0090.0000.0000.0000.000
180A183VAL00.0190.00411.4910.0100.0100.0000.0000.0000.000
181A184VAL0-0.027-0.01311.387-0.010-0.0100.0000.0000.0000.000
182A185ASN0-0.005-0.02413.5040.0150.0150.0000.0000.0000.000
183A186GLN0-0.054-0.03315.222-0.007-0.0070.0000.0000.0000.000
184A187ILE00.0030.01416.8070.0120.0120.0000.0000.0000.000
185A188GLU-1-0.754-0.85718.954-0.055-0.0550.0000.0000.0000.000
186A189PHE0-0.009-0.01216.680-0.003-0.0030.0000.0000.0000.000
187A190HIS0-0.009-0.02619.5500.0000.0000.0000.0000.0000.000
188A191PRO00.0270.01120.642-0.001-0.0010.0000.0000.0000.000
189A192PHE00.0000.01822.5080.0000.0000.0000.0000.0000.000
190A193LEU0-0.011-0.00123.2030.0040.0040.0000.0000.0000.000
191A194GLN00.0290.03319.701-0.013-0.0130.0000.0000.0000.000
192A195ASN0-0.033-0.03718.994-0.015-0.0150.0000.0000.0000.000
193A196GLN00.0580.03920.7150.0060.0060.0000.0000.0000.000
194A197SER00.0370.02421.9660.0070.0070.0000.0000.0000.000
195A198LYS10.9870.97222.1970.0330.0330.0000.0000.0000.000
196A199ASN0-0.037-0.01720.3260.0000.0000.0000.0000.0000.000
197A200ILE00.0400.03517.808-0.007-0.0070.0000.0000.0000.000
198A201VAL00.0580.03413.593-0.002-0.0020.0000.0000.0000.000
199A202ARG10.9220.94713.8900.0830.0830.0000.0000.0000.000
200A203PHE00.0220.01814.480-0.011-0.0110.0000.0000.0000.000
201A204CYS0-0.054-0.03413.0710.0180.0180.0000.0000.0000.000
202A205GLN0-0.029-0.0169.5130.0130.0130.0000.0000.0000.000
203A206GLU-1-0.882-0.93510.183-0.135-0.1350.0000.0000.0000.000
204A207HIS10.8340.92712.6420.0600.0600.0000.0000.0000.000
205A208GLY00.0240.0289.2910.0490.0490.0000.0000.0000.000
206A209ILE0-0.061-0.02110.2870.0750.0750.0000.0000.0000.000
207A210LEU0-0.021-0.0077.174-0.056-0.0560.0000.0000.0000.000
208A211VAL00.0180.0099.6420.0260.0260.0000.0000.0000.000
209A212GLU-1-0.809-0.90911.412-0.160-0.1600.0000.0000.0000.000
210A213ALA0-0.006-0.00313.6030.0120.0120.0000.0000.0000.000
211A214PHE00.001-0.00616.269-0.002-0.0020.0000.0000.0000.000
212A215SER0-0.008-0.02219.2230.0030.0030.0000.0000.0000.000
213A216PRO00.0500.03317.2470.0040.0040.0000.0000.0000.000
214A217LEU0-0.034-0.02319.6700.0030.0030.0000.0000.0000.000
215A218ALA00.0390.02522.4780.0040.0040.0000.0000.0000.000
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