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: Q1M1Y

Calculation Name: 1VRR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VRR

Chain ID: A

ChEMBL ID:

UniProt ID: Q84AF2

Base Structure: X-ray

Registration Date: 2023-03-13

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2303112.811583
FMO2-HF: Nuclear repulsion 2222515.730749
FMO2-HF: Total energy -80597.080835
FMO2-MP2: Total energy -80834.801372


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.
-30.771-33.45552.239-19.777-29.778-0.104
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 : -0.072 / q_NPA : -0.047
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].
3A3ILE00.0450.0033.815-1.0691.372-0.025-1.239-1.1770.003
4A4VAL0-0.082-0.0285.9240.0730.0730.0000.0000.0000.000
5A5GLU-1-0.879-0.9468.1530.0180.0180.0000.0000.0000.000
6A6VAL0-0.013-0.00410.0810.0060.0060.0000.0000.0000.000
7A7TYR0-0.036-0.02112.546-0.008-0.0080.0000.0000.0000.000
8A8SER0-0.027-0.03415.9000.0050.0050.0000.0000.0000.000
9A9HIS0-0.0100.00218.5390.0070.0070.0000.0000.0000.000
10A10LEU0-0.040-0.02921.016-0.008-0.0080.0000.0000.0000.000
11A11ASN0-0.021-0.01522.766-0.003-0.0030.0000.0000.0000.000
12A12GLY00.0780.04520.049-0.009-0.0090.0000.0000.0000.000
13A13LEU00.001-0.00615.268-0.014-0.0140.0000.0000.0000.000
14A14GLU-1-0.824-0.89718.499-0.119-0.1190.0000.0000.0000.000
15A15TYR0-0.049-0.03321.638-0.008-0.0080.0000.0000.0000.000
16A16ILE00.0480.02016.238-0.007-0.0070.0000.0000.0000.000
17A17GLN0-0.030-0.02117.1010.0090.0090.0000.0000.0000.000
18A18VAL0-0.023-0.00220.234-0.005-0.0050.0000.0000.0000.000
19A19HIS0-0.075-0.03622.9880.0130.0130.0000.0000.0000.000
20A20LEU0-0.052-0.02919.8080.0000.0000.0000.0000.0000.000
21A21PRO00.0390.03118.703-0.037-0.0370.0000.0000.0000.000
22A22HIS00.0460.02217.342-0.046-0.0460.0000.0000.0000.000
23A23ILE0-0.009-0.00215.120-0.080-0.0800.0000.0000.0000.000
24A24TRP00.0290.01811.442-0.078-0.0780.0000.0000.0000.000
25A25GLU-1-0.902-0.94712.248-0.600-0.6000.0000.0000.0000.000
26A26GLU-1-0.791-0.88110.982-0.673-0.6730.0000.0000.0000.000
27A27ILE00.006-0.0049.221-0.255-0.2550.0000.0000.0000.000
28A28GLN0-0.051-0.0347.743-0.342-0.3420.0000.0000.0000.000
29A29GLU-1-0.856-0.9216.319-1.877-1.8770.0000.0000.0000.000
30A30ILE0-0.013-0.0155.813-1.019-1.0190.0000.0000.0000.000
31A31ILE0-0.020-0.0062.626-1.835-0.7700.418-0.395-1.0880.000
32A32VAL0-0.002-0.0142.091-13.139-12.6448.113-4.201-4.408-0.050
33A33SER0-0.111-0.0382.6042.8983.3901.773-0.563-1.702-0.009
34A34ILE0-0.030-0.0062.484-0.4772.0191.074-0.997-2.574-0.002
35A35ASP-1-0.823-0.8981.655-9.424-20.32223.699-8.401-4.400-0.055
36A36ALA00.049-0.0082.1190.6120.5743.957-1.106-2.8120.000
37A37GLU-1-0.858-0.9053.7440.4940.6450.0240.004-0.1790.000
38A38ALA0-0.0220.0036.9560.0800.0800.0000.0000.0000.000
39A39CYS0-0.064-0.0356.2090.2550.2550.0000.0000.0000.000
40A40ARG10.7430.8698.374-0.345-0.3450.0000.0000.0000.000
41A41THR00.0200.0039.537-0.086-0.0860.0000.0000.0000.000
42A42LYS10.9090.97212.129-0.393-0.3930.0000.0000.0000.000
43A43GLU-1-0.878-0.94113.9470.2030.2030.0000.0000.0000.000
44A44SER0-0.060-0.04215.824-0.024-0.0240.0000.0000.0000.000
45A45LYS10.9620.96817.252-0.205-0.2050.0000.0000.0000.000
46A46GLU-1-0.799-0.86616.6540.2720.2720.0000.0000.0000.000
47A47LYS11.0140.99021.219-0.129-0.1290.0000.0000.0000.000
48A48THR0-0.056-0.03820.776-0.003-0.0030.0000.0000.0000.000
49A49LYS10.8670.94014.590-0.288-0.2880.0000.0000.0000.000
50A50GLN0-0.023-0.01219.2820.0050.0050.0000.0000.0000.000
51A51GLY00.0250.01920.920-0.003-0.0030.0000.0000.0000.000
52A52GLN00.0340.03214.585-0.012-0.0120.0000.0000.0000.000
53A53ILE00.009-0.00812.7180.0050.0050.0000.0000.0000.000
54A54LEU0-0.065-0.02311.016-0.003-0.0030.0000.0000.0000.000
55A55TYR00.0500.0035.943-0.010-0.0100.0000.0000.0000.000
56A56SER0-0.042-0.0298.255-0.073-0.0730.0000.0000.0000.000
57A57PRO00.0240.0137.8080.2340.2340.0000.0000.0000.000
58A58VAL0-0.013-0.0088.8670.0760.0760.0000.0000.0000.000
59A59ALA00.0560.0399.183-0.039-0.0390.0000.0000.0000.000
60A60LEU00.018-0.0113.178-0.647-0.2130.979-0.226-1.1860.001
61A61ASN0-0.050-0.0356.477-0.0220.026-0.001-0.001-0.0450.000
62A62GLU-1-0.933-0.9589.1750.1060.1060.0000.0000.0000.000
63A63ALA0-0.0060.0016.342-0.212-0.2120.0000.0000.0000.000
64A64PHE00.003-0.0203.861-1.072-0.4330.096-0.177-0.5590.000
65A65LYS10.8150.9028.333-0.340-0.3400.0000.0000.0000.000
66A66GLU-1-0.901-0.93811.267-0.675-0.6750.0000.0000.0000.000
67A67LYS10.8900.9457.1012.0312.0310.0000.0000.0000.000
68A68LEU0-0.005-0.00210.152-0.031-0.0310.0000.0000.0000.000
69A69GLU-1-0.851-0.93112.574-0.014-0.0140.0000.0000.0000.000
70A70ALA0-0.045-0.00514.1310.0100.0100.0000.0000.0000.000
71A71LYS10.7960.88811.9430.7690.7690.0000.0000.0000.000
72A72GLY0-0.016-0.00615.8240.0170.0170.0000.0000.0000.000
73A73TRP0-0.096-0.05314.3070.0810.0810.0000.0000.0000.000
74A74LYS10.9780.99517.4020.0620.0620.0000.0000.0000.000
75A75GLU-1-0.845-0.90719.6990.0510.0510.0000.0000.0000.000
76A76SER0-0.075-0.03720.611-0.018-0.0180.0000.0000.0000.000
77A77ARG10.9200.95322.886-0.051-0.0510.0000.0000.0000.000
78A78THR0-0.006-0.00525.517-0.013-0.0130.0000.0000.0000.000
79A79ASN00.003-0.00228.3190.0150.0150.0000.0000.0000.000
80A80TYR00.0140.00427.666-0.005-0.0050.0000.0000.0000.000
81A81TYR0-0.051-0.03633.3660.0060.0060.0000.0000.0000.000
82A82VAL0-0.022-0.00232.825-0.001-0.0010.0000.0000.0000.000
83A83THR00.021-0.01736.031-0.001-0.0010.0000.0000.0000.000
84A84ALA00.0180.00438.5960.0010.0010.0000.0000.0000.000
85A85ASP-1-0.868-0.92240.3750.0270.0270.0000.0000.0000.000
86A86PRO00.0700.01539.7720.0000.0000.0000.0000.0000.000
87A87LYS10.8700.91640.758-0.020-0.0200.0000.0000.0000.000
88A88LEU00.0290.03742.617-0.001-0.0010.0000.0000.0000.000
89A89ILE00.0200.02036.183-0.001-0.0010.0000.0000.0000.000
90A90ARG10.9050.94538.202-0.026-0.0260.0000.0000.0000.000
91A91GLU-1-0.913-0.95140.2790.0160.0160.0000.0000.0000.000
92A92THR0-0.015-0.01839.826-0.001-0.0010.0000.0000.0000.000
93A93LEU0-0.043-0.01434.8430.0000.0000.0000.0000.0000.000
94A94SER0-0.012-0.00136.3670.0000.0000.0000.0000.0000.000
95A95LEU0-0.0250.00538.695-0.003-0.0030.0000.0000.0000.000
96A96GLU-1-0.849-0.92536.8550.0040.0040.0000.0000.0000.000
97A97PRO00.016-0.00434.6030.0020.0020.0000.0000.0000.000
98A98GLU-1-0.825-0.90137.2370.0220.0220.0000.0000.0000.000
99A99GLU-1-0.796-0.88940.4400.0080.0080.0000.0000.0000.000
100A100GLN0-0.016-0.01535.4730.0030.0030.0000.0000.0000.000
101A101LYS10.8760.93239.905-0.022-0.0220.0000.0000.0000.000
102A102LYS10.8250.90741.440-0.007-0.0070.0000.0000.0000.000
103A103VAL0-0.002-0.01044.0010.0000.0000.0000.0000.0000.000
104A104ILE0-0.054-0.02139.6390.0010.0010.0000.0000.0000.000
105A105GLU-1-0.819-0.92543.7550.0240.0240.0000.0000.0000.000
106A106ALA0-0.0440.00546.268-0.001-0.0010.0000.0000.0000.000
107A107ALA0-0.073-0.05447.522-0.001-0.0010.0000.0000.0000.000
108A108GLY0-0.066-0.03349.3160.0010.0010.0000.0000.0000.000
109A109LYS10.8210.92543.961-0.024-0.0240.0000.0000.0000.000
110A110GLU-1-0.897-0.94540.7780.0410.0410.0000.0000.0000.000
111A111ALA00.0180.00939.9810.0010.0010.0000.0000.0000.000
112A112LEU0-0.0060.00535.4620.0010.0010.0000.0000.0000.000
113A113LYS10.8590.92430.904-0.048-0.0480.0000.0000.0000.000
114A114SER00.0130.01229.3980.0080.0080.0000.0000.0000.000
115A115TYR0-0.049-0.04924.140-0.012-0.0120.0000.0000.0000.000
116A116ASN00.0000.02223.1850.0010.0010.0000.0000.0000.000
117A117GLN0-0.025-0.02420.134-0.025-0.0250.0000.0000.0000.000
118A118THR00.019-0.01817.5280.0100.0100.0000.0000.0000.000
119A119ASP-1-0.848-0.92915.4970.1290.1290.0000.0000.0000.000
120A120PHE0-0.0050.01811.863-0.034-0.0340.0000.0000.0000.000
121A121VAL0-0.022-0.02116.5780.0100.0100.0000.0000.0000.000
122A122LYS10.8060.89116.5270.3100.3100.0000.0000.0000.000
123A123ASP-1-0.884-0.94620.187-0.174-0.1740.0000.0000.0000.000
124A124ARG10.7560.85022.4660.0510.0510.0000.0000.0000.000
125A125VAL00.0270.02716.7350.0060.0060.0000.0000.0000.000
126A126ALA00.023-0.00318.037-0.001-0.0010.0000.0000.0000.000
127A127ILE0-0.0120.00411.3500.0110.0110.0000.0000.0000.000
128A128GLU-1-0.798-0.88213.2130.2150.2150.0000.0000.0000.000
129A129VAL0-0.0060.0147.0650.0600.0600.0000.0000.0000.000
130A130GLN0-0.003-0.0119.4930.0060.0060.0000.0000.0000.000
131A131PHE0-0.005-0.0173.790-0.311-0.0750.001-0.037-0.1990.000
132A132GLY00.0290.0139.388-0.036-0.0360.0000.0000.0000.000
133A133LYS10.8380.91713.121-0.233-0.2330.0000.0000.0000.000
134A134TYR00.1100.02614.575-0.016-0.0160.0000.0000.0000.000
135A135SER0-0.036-0.00915.541-0.009-0.0090.0000.0000.0000.000
136A136PHE0-0.035-0.02815.644-0.026-0.0260.0000.0000.0000.000
137A137VAL00.0690.06413.312-0.007-0.0070.0000.0000.0000.000
138A138ALA00.0080.01416.031-0.025-0.0250.0000.0000.0000.000
139A139TYR0-0.022-0.00619.424-0.023-0.0230.0000.0000.0000.000
140A140ASP-1-0.735-0.86015.5490.2350.2350.0000.0000.0000.000
141A141LEU0-0.040-0.02516.514-0.028-0.0280.0000.0000.0000.000
142A142PHE0-0.047-0.04219.768-0.020-0.0200.0000.0000.0000.000
143A143VAL0-0.048-0.01422.463-0.012-0.0120.0000.0000.0000.000
144A144LYS10.7850.88317.418-0.203-0.2030.0000.0000.0000.000
145A145HIS00.0230.01416.033-0.050-0.0500.0000.0000.0000.000
146A146MET0-0.0240.00221.517-0.020-0.0200.0000.0000.0000.000
147A147ALA00.0240.02124.855-0.011-0.0110.0000.0000.0000.000
148A148PHE0-0.027-0.01821.290-0.011-0.0110.0000.0000.0000.000
149A149TYR00.0400.00324.862-0.008-0.0080.0000.0000.0000.000
150A150VAL0-0.006-0.01326.543-0.007-0.0070.0000.0000.0000.000
151A151SER0-0.136-0.07328.860-0.002-0.0020.0000.0000.0000.000
152A152ASP-1-0.864-0.91029.411-0.033-0.0330.0000.0000.0000.000
153A153LYS10.8810.94726.425-0.015-0.0150.0000.0000.0000.000
154A154ILE0-0.091-0.00319.917-0.008-0.0080.0000.0000.0000.000
155A155ASP-1-0.762-0.84522.953-0.059-0.0590.0000.0000.0000.000
156A156VAL0-0.048-0.03318.5370.0010.0010.0000.0000.0000.000
157A157GLY00.0090.00218.737-0.006-0.0060.0000.0000.0000.000
158A158VAL0-0.048-0.03512.309-0.011-0.0110.0000.0000.0000.000
159A159GLU-1-0.798-0.91312.3440.3090.3090.0000.0000.0000.000
160A160ILE0-0.013-0.0076.465-0.011-0.0110.0000.0000.0000.000
161A161LEU0-0.011-0.0148.1020.0760.0760.0000.0000.0000.000
162A162PRO00.0100.0194.8580.0540.0540.0000.0000.0000.000
163A163MET00.0360.0265.979-0.131-0.1310.0000.0000.0000.000
164A164LYS10.8730.9318.188-0.224-0.2240.0000.0000.0000.000
165A165GLU-1-0.849-0.9127.4950.4050.4050.0000.0000.0000.000
166A166LEU00.0340.0362.531-0.345-0.2841.200-0.188-1.0730.000
167A167SER00.0260.0116.7850.0030.0030.0000.0000.0000.000
168A168LYS10.8580.9438.896-0.309-0.3090.0000.0000.0000.000
169A169GLU-1-0.888-0.9318.5370.3630.3630.0000.0000.0000.000
170A170MET00.0090.0286.3950.0360.0360.0000.0000.0000.000
171A171SER0-0.009-0.03710.100-0.061-0.0610.0000.0000.0000.000
172A172SER0-0.051-0.02713.0010.0120.0120.0000.0000.0000.000
173A173GLY0-0.029-0.01515.4230.0090.0090.0000.0000.0000.000
174A174ILE00.0130.0119.270-0.024-0.0240.0000.0000.0000.000
175A175SER00.0190.02411.970-0.013-0.0130.0000.0000.0000.000
176A176TYR0-0.008-0.01710.0560.0420.0420.0000.0000.0000.000
177A177TYR00.0510.0179.565-0.039-0.0390.0000.0000.0000.000
178A178GLU-1-0.746-0.88011.4430.2460.2460.0000.0000.0000.000
179A179GLY0-0.031-0.01314.227-0.027-0.0270.0000.0000.0000.000
180A180GLU-1-0.834-0.92914.0660.1990.1990.0000.0000.0000.000
181A181LEU00.0230.01915.029-0.024-0.0240.0000.0000.0000.000
182A182TYR0-0.021-0.00616.778-0.024-0.0240.0000.0000.0000.000
183A183ASN0-0.056-0.03118.521-0.031-0.0310.0000.0000.0000.000
184A184VAL00.0220.03218.925-0.009-0.0090.0000.0000.0000.000
185A185ILE00.001-0.00320.389-0.012-0.0120.0000.0000.0000.000
186A186ARG10.8220.90622.729-0.108-0.1080.0000.0000.0000.000
187A187GLN0-0.099-0.04723.955-0.011-0.0110.0000.0000.0000.000
188A188GLY00.0230.01227.186-0.004-0.0040.0000.0000.0000.000
189A189ARG10.9860.97325.4500.0060.0060.0000.0000.0000.000
190A190GLY00.0200.00526.492-0.008-0.0080.0000.0000.0000.000
191A191VAL0-0.0690.00626.336-0.001-0.0010.0000.0000.0000.000
192A192PRO00.0520.01522.3970.0040.0040.0000.0000.0000.000
193A193ALA00.017-0.00625.258-0.005-0.0050.0000.0000.0000.000
194A194VAL00.013-0.00422.547-0.003-0.0030.0000.0000.0000.000
195A195PRO00.0230.02922.6380.0080.0080.0000.0000.0000.000
196A196LEU0-0.031-0.01717.9070.0100.0100.0000.0000.0000.000
197A197VAL00.0190.01513.687-0.019-0.0190.0000.0000.0000.000
198A198LEU0-0.0240.00513.2110.0330.0330.0000.0000.0000.000
199A199ILE00.0200.0057.808-0.065-0.0650.0000.0000.0000.000
200A200GLY00.0290.0017.8720.1680.1680.0000.0000.0000.000
201A201ILE00.0190.0122.732-1.676-1.2212.832-0.559-2.7280.004
202A202ALA00.012-0.0293.358-1.066-0.1130.100-0.330-0.724-0.002
203A203PRO0-0.0760.0152.006-0.684-2.3987.999-1.361-4.9240.006