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: K3833

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2305041.890761
FMO2-HF: Nuclear repulsion 2224443.759713
FMO2-HF: Total energy -80598.131048
FMO2-MP2: Total energy -80835.755965


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.
-33.53-26.91536.785-15.685-27.715-0.109
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 : -0.070 / q_NPA : -0.039
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].
3A3ILE00.0430.0223.835-0.3841.500-0.004-0.895-0.9850.002
4A4VAL0-0.086-0.0476.190-0.073-0.0730.0000.0000.0000.000
5A5GLU-1-0.854-0.9228.3920.0870.0870.0000.0000.0000.000
6A6VAL0-0.0060.00010.0980.0510.0510.0000.0000.0000.000
7A7TYR0-0.031-0.01012.759-0.031-0.0310.0000.0000.0000.000
8A8SER0-0.046-0.03416.2110.0200.0200.0000.0000.0000.000
9A9HIS00.0060.00018.4860.0020.0020.0000.0000.0000.000
10A10LEU0-0.038-0.02921.356-0.006-0.0060.0000.0000.0000.000
11A11ASN0-0.028-0.01022.799-0.001-0.0010.0000.0000.0000.000
12A12GLY00.0800.04220.008-0.010-0.0100.0000.0000.0000.000
13A13LEU0-0.005-0.00814.888-0.009-0.0090.0000.0000.0000.000
14A14GLU-1-0.796-0.88718.153-0.029-0.0290.0000.0000.0000.000
15A15TYR0-0.053-0.04121.199-0.010-0.0100.0000.0000.0000.000
16A16ILE00.0300.01316.012-0.007-0.0070.0000.0000.0000.000
17A17GLN0-0.035-0.02516.3150.0030.0030.0000.0000.0000.000
18A18VAL0-0.040-0.01020.034-0.006-0.0060.0000.0000.0000.000
19A19HIS0-0.084-0.04422.9300.0030.0030.0000.0000.0000.000
20A20LEU0-0.038-0.01219.897-0.001-0.0010.0000.0000.0000.000
21A21PRO00.0500.02818.613-0.019-0.0190.0000.0000.0000.000
22A22HIS0-0.008-0.00316.950-0.037-0.0370.0000.0000.0000.000
23A23ILE00.0110.00815.037-0.057-0.0570.0000.0000.0000.000
24A24TRP00.0210.01111.216-0.031-0.0310.0000.0000.0000.000
25A25GLU-1-0.880-0.94711.999-0.382-0.3820.0000.0000.0000.000
26A26GLU-1-0.784-0.87210.958-0.461-0.4610.0000.0000.0000.000
27A27ILE00.005-0.0058.977-0.177-0.1770.0000.0000.0000.000
28A28GLN0-0.071-0.0467.413-0.271-0.2710.0000.0000.0000.000
29A29GLU-1-0.852-0.9156.237-1.330-1.3300.0000.0000.0000.000
30A30ILE0-0.013-0.0056.118-0.632-0.6320.0000.0000.0000.000
31A31ILE00.0100.0162.320-2.016-0.9581.233-0.699-1.592-0.002
32A32VAL0-0.009-0.0021.927-13.738-15.25311.478-5.348-4.615-0.058
33A33SER0-0.051-0.0162.9413.2913.4550.2840.440-0.889-0.003
34A34ILE0-0.046-0.0212.2720.4262.5361.493-0.955-2.648-0.002
35A35ASP-1-0.818-0.9061.860-11.803-14.33111.365-4.509-4.328-0.047
36A36ALA00.0550.0092.358-0.0180.5312.450-0.826-2.1730.000
37A37GLU-1-0.861-0.9124.0350.2430.4130.004-0.061-0.1120.000
38A38ALA0-0.020-0.0057.3150.1810.1810.0000.0000.0000.000
39A39CYS0-0.037-0.0096.1950.2970.2970.0000.0000.0000.000
40A40ARG10.7420.8728.2020.1020.1020.0000.0000.0000.000
41A41THR00.009-0.0059.344-0.007-0.0070.0000.0000.0000.000
42A42LYS10.8640.94311.810-0.190-0.1900.0000.0000.0000.000
43A43GLU-1-0.789-0.88713.6280.0690.0690.0000.0000.0000.000
44A44SER0-0.019-0.02915.9820.0090.0090.0000.0000.0000.000
45A45LYS10.8290.88717.347-0.100-0.1000.0000.0000.0000.000
46A46GLU-1-0.735-0.80916.4390.1740.1740.0000.0000.0000.000
47A47LYS11.0000.98620.891-0.081-0.0810.0000.0000.0000.000
48A48THR0-0.059-0.03220.594-0.005-0.0050.0000.0000.0000.000
49A49LYS10.8680.93914.211-0.175-0.1750.0000.0000.0000.000
50A50GLN0-0.009-0.00119.2100.0020.0020.0000.0000.0000.000
51A51GLY00.0310.01920.602-0.006-0.0060.0000.0000.0000.000
52A52GLN00.0010.00814.315-0.003-0.0030.0000.0000.0000.000
53A53ILE00.0100.00312.7950.0120.0120.0000.0000.0000.000
54A54LEU0-0.055-0.01810.930-0.011-0.0110.0000.0000.0000.000
55A55TYR00.044-0.0125.8540.0040.0040.0000.0000.0000.000
56A56SER0-0.009-0.0118.0490.0510.0510.0000.0000.0000.000
57A57PRO00.0150.0017.9710.1650.1650.0000.0000.0000.000
58A58VAL0-0.038-0.0079.0330.0910.0910.0000.0000.0000.000
59A59ALA00.0710.0409.6590.0290.0290.0000.0000.0000.000
60A60LEU0-0.004-0.0033.486-0.701-0.0960.360-0.164-0.8020.001
61A61ASN0-0.035-0.0296.6950.0220.0220.0000.0000.0000.000
62A62GLU-1-0.914-0.9559.3000.0070.0070.0000.0000.0000.000
63A63ALA00.0150.0116.414-0.154-0.1540.0000.0000.0000.000
64A64PHE0-0.004-0.0233.336-1.570-0.7580.429-0.295-0.9460.001
65A65LYS10.8080.8888.207-0.282-0.2820.0000.0000.0000.000
66A66GLU-1-0.903-0.95110.766-0.720-0.7200.0000.0000.0000.000
67A67LYS10.8580.9326.8091.9251.9250.0000.0000.0000.000
68A68LEU0-0.017-0.00410.1840.0040.0040.0000.0000.0000.000
69A69GLU-1-0.846-0.91912.5880.0010.0010.0000.0000.0000.000
70A70ALA0-0.045-0.01513.7960.0120.0120.0000.0000.0000.000
71A71LYS10.7730.88811.7750.5530.5530.0000.0000.0000.000
72A72GLY0-0.0060.00015.3480.0280.0280.0000.0000.0000.000
73A73TRP0-0.081-0.05614.4050.0700.0700.0000.0000.0000.000
74A74LYS10.8820.93117.4450.0040.0040.0000.0000.0000.000
75A75GLU-1-0.850-0.89819.7550.0640.0640.0000.0000.0000.000
76A76SER0-0.054-0.02020.626-0.021-0.0210.0000.0000.0000.000
77A77ARG10.9560.97322.546-0.056-0.0560.0000.0000.0000.000
78A78THR0-0.008-0.00325.232-0.012-0.0120.0000.0000.0000.000
79A79ASN00.0200.00628.1740.0120.0120.0000.0000.0000.000
80A80TYR0-0.001-0.00127.987-0.004-0.0040.0000.0000.0000.000
81A81TYR0-0.063-0.04733.4950.0030.0030.0000.0000.0000.000
82A82VAL0-0.0110.00233.3310.0000.0000.0000.0000.0000.000
83A83THR00.006-0.01736.470-0.002-0.0020.0000.0000.0000.000
84A84ALA00.0220.00738.7580.0020.0020.0000.0000.0000.000
85A85ASP-1-0.842-0.91040.7160.0300.0300.0000.0000.0000.000
86A86PRO00.0450.00739.6580.0000.0000.0000.0000.0000.000
87A87LYS10.8030.88340.768-0.025-0.0250.0000.0000.0000.000
88A88LEU00.0060.01943.084-0.001-0.0010.0000.0000.0000.000
89A89ILE00.0230.02636.3810.0000.0000.0000.0000.0000.000
90A90ARG10.9290.96338.409-0.036-0.0360.0000.0000.0000.000
91A91GLU-1-0.842-0.92040.4420.0240.0240.0000.0000.0000.000
92A92THR0-0.027-0.02540.163-0.001-0.0010.0000.0000.0000.000
93A93LEU0-0.038-0.01434.8840.0000.0000.0000.0000.0000.000
94A94SER0-0.0270.00036.4570.0010.0010.0000.0000.0000.000
95A95LEU0-0.0160.00238.830-0.003-0.0030.0000.0000.0000.000
96A96GLU-1-0.847-0.93336.6520.0200.0200.0000.0000.0000.000
97A97PRO0-0.010-0.00734.3640.0000.0000.0000.0000.0000.000
98A98GLU-1-0.785-0.87337.1130.0260.0260.0000.0000.0000.000
99A99GLU-1-0.804-0.88240.2480.0150.0150.0000.0000.0000.000
100A100GLN00.007-0.01535.7960.0020.0020.0000.0000.0000.000
101A101LYS10.8470.92640.028-0.025-0.0250.0000.0000.0000.000
102A102LYS10.8220.90841.574-0.015-0.0150.0000.0000.0000.000
103A103VAL0-0.012-0.01144.084-0.001-0.0010.0000.0000.0000.000
104A104ILE0-0.040-0.02239.7890.0000.0000.0000.0000.0000.000
105A105GLU-1-0.849-0.94544.0720.0250.0250.0000.0000.0000.000
106A106ALA0-0.061-0.02346.512-0.001-0.0010.0000.0000.0000.000
107A107ALA0-0.036-0.01547.374-0.001-0.0010.0000.0000.0000.000
108A108GLY0-0.046-0.02249.2990.0000.0000.0000.0000.0000.000
109A109LYS10.8110.91244.134-0.027-0.0270.0000.0000.0000.000
110A110GLU-1-0.889-0.94440.7110.0390.0390.0000.0000.0000.000
111A111ALA00.0370.02140.2170.0010.0010.0000.0000.0000.000
112A112LEU00.0040.01035.6340.0000.0000.0000.0000.0000.000
113A113LYS10.8550.91731.362-0.049-0.0490.0000.0000.0000.000
114A114SER0-0.0010.00129.6010.0060.0060.0000.0000.0000.000
115A115TYR0-0.056-0.04624.284-0.007-0.0070.0000.0000.0000.000
116A116ASN00.0010.01923.408-0.001-0.0010.0000.0000.0000.000
117A117GLN0-0.025-0.04020.039-0.027-0.0270.0000.0000.0000.000
118A118THR00.003-0.01817.1500.0140.0140.0000.0000.0000.000
119A119ASP-1-0.810-0.89915.6630.1230.1230.0000.0000.0000.000
120A120PHE0-0.0100.01212.056-0.033-0.0330.0000.0000.0000.000
121A121VAL0-0.024-0.02316.3930.0160.0160.0000.0000.0000.000
122A122LYS10.8350.91116.6110.1950.1950.0000.0000.0000.000
123A123ASP-1-0.833-0.92220.056-0.097-0.0970.0000.0000.0000.000
124A124ARG10.7710.85822.1750.0050.0050.0000.0000.0000.000
125A125VAL00.0210.01716.6710.0110.0110.0000.0000.0000.000
126A126ALA00.009-0.00817.722-0.008-0.0080.0000.0000.0000.000
127A127ILE0-0.012-0.00311.1670.0140.0140.0000.0000.0000.000
128A128GLU-1-0.801-0.87413.2590.2490.2490.0000.0000.0000.000
129A129VAL00.0280.0077.1880.0850.0850.0000.0000.0000.000
130A130GLN00.0110.0179.8050.0530.0530.0000.0000.0000.000
131A131PHE0-0.023-0.0333.507-0.570-0.1880.010-0.072-0.3200.000
132A132GLY00.0450.0269.159-0.086-0.0860.0000.0000.0000.000
133A133LYS10.8630.92412.978-0.186-0.1860.0000.0000.0000.000
134A134TYR00.0730.01314.658-0.020-0.0200.0000.0000.0000.000
135A135SER0-0.030-0.00815.6470.0030.0030.0000.0000.0000.000
136A136PHE0-0.040-0.01315.764-0.022-0.0220.0000.0000.0000.000
137A137VAL00.0840.05213.209-0.009-0.0090.0000.0000.0000.000
138A138ALA0-0.0130.00016.049-0.022-0.0220.0000.0000.0000.000
139A139TYR00.0120.00719.721-0.021-0.0210.0000.0000.0000.000
140A140ASP-1-0.742-0.86716.0600.2620.2620.0000.0000.0000.000
141A141LEU0-0.021-0.01216.484-0.026-0.0260.0000.0000.0000.000
142A142PHE0-0.039-0.02919.665-0.022-0.0220.0000.0000.0000.000
143A143VAL0-0.054-0.01722.478-0.016-0.0160.0000.0000.0000.000
144A144LYS10.7630.88217.482-0.237-0.2370.0000.0000.0000.000
145A145HIS00.0310.01016.156-0.054-0.0540.0000.0000.0000.000
146A146MET0-0.0140.00521.702-0.020-0.0200.0000.0000.0000.000
147A147ALA00.0140.00525.055-0.012-0.0120.0000.0000.0000.000
148A148PHE0-0.022-0.01321.179-0.011-0.0110.0000.0000.0000.000
149A149TYR00.0200.01225.102-0.009-0.0090.0000.0000.0000.000
150A150VAL0-0.022-0.02126.739-0.008-0.0080.0000.0000.0000.000
151A151SER0-0.106-0.06328.557-0.005-0.0050.0000.0000.0000.000
152A152ASP-1-0.855-0.90929.3770.0030.0030.0000.0000.0000.000
153A153LYS10.8530.92725.990-0.045-0.0450.0000.0000.0000.000
154A154ILE0-0.090-0.02419.897-0.002-0.0020.0000.0000.0000.000
155A155ASP-1-0.785-0.84423.169-0.008-0.0080.0000.0000.0000.000
156A156VAL0-0.029-0.01918.3290.0040.0040.0000.0000.0000.000
157A157GLY00.0280.02018.422-0.006-0.0060.0000.0000.0000.000
158A158VAL0-0.043-0.02811.946-0.009-0.0090.0000.0000.0000.000
159A159GLU-1-0.813-0.92312.6050.4020.4020.0000.0000.0000.000
160A160ILE0-0.0020.0026.4320.0200.0200.0000.0000.0000.000
161A161LEU0-0.011-0.0137.9400.0620.0620.0000.0000.0000.000
162A162PRO0-0.0030.0135.0870.1320.1320.0000.0000.0000.000
163A163MET00.0410.0376.039-0.139-0.1390.0000.0000.0000.000
164A164LYS10.8590.9238.123-0.228-0.2280.0000.0000.0000.000
165A165GLU-1-0.852-0.8937.1780.1740.1740.0000.0000.0000.000
166A166LEU0-0.0010.0262.475-0.370-0.2741.105-0.186-1.015-0.001
167A167SER00.024-0.0106.712-0.010-0.0100.0000.0000.0000.000
168A168LYS10.8080.9129.016-0.147-0.1470.0000.0000.0000.000
169A169GLU-1-0.857-0.8978.2990.0900.0900.0000.0000.0000.000
170A170MET00.0100.0116.7080.0140.0140.0000.0000.0000.000
171A171SER0-0.016-0.04110.320-0.035-0.0350.0000.0000.0000.000
172A172SER0-0.076-0.04813.2750.0220.0220.0000.0000.0000.000
173A173GLY0-0.013-0.00515.9160.0030.0030.0000.0000.0000.000
174A174ILE0-0.0020.0139.440-0.017-0.0170.0000.0000.0000.000
175A175SER00.0190.00810.799-0.034-0.0340.0000.0000.0000.000
176A176TYR00.002-0.01310.2030.0010.0010.0000.0000.0000.000
177A177TYR00.016-0.0079.620-0.035-0.0350.0000.0000.0000.000
178A178GLU-1-0.744-0.88211.4430.2320.2320.0000.0000.0000.000
179A179GLY0-0.057-0.02114.266-0.031-0.0310.0000.0000.0000.000
180A180GLU-1-0.855-0.93213.8520.2240.2240.0000.0000.0000.000
181A181LEU00.0340.01915.104-0.024-0.0240.0000.0000.0000.000
182A182TYR0-0.031-0.01216.958-0.027-0.0270.0000.0000.0000.000
183A183ASN0-0.056-0.04818.280-0.035-0.0350.0000.0000.0000.000
184A184VAL00.0070.03119.071-0.011-0.0110.0000.0000.0000.000
185A185ILE00.0260.00920.754-0.015-0.0150.0000.0000.0000.000
186A186ARG10.8260.91522.553-0.121-0.1210.0000.0000.0000.000
187A187GLN0-0.070-0.03823.825-0.013-0.0130.0000.0000.0000.000
188A188GLY0-0.0060.00927.008-0.005-0.0050.0000.0000.0000.000
189A189ARG10.9650.95625.204-0.028-0.0280.0000.0000.0000.000
190A190GLY00.0170.00026.188-0.005-0.0050.0000.0000.0000.000
191A191VAL0-0.0340.01926.403-0.003-0.0030.0000.0000.0000.000
192A192PRO00.0570.02222.2560.0030.0030.0000.0000.0000.000
193A193ALA0-0.002-0.01125.304-0.002-0.0020.0000.0000.0000.000
194A194VAL00.011-0.00222.712-0.005-0.0050.0000.0000.0000.000
195A195PRO00.0040.01822.5370.0100.0100.0000.0000.0000.000
196A196LEU0-0.024-0.01218.1740.0110.0110.0000.0000.0000.000
197A197VAL00.0160.00913.442-0.021-0.0210.0000.0000.0000.000
198A198LEU0-0.0010.01613.3870.0470.0470.0000.0000.0000.000
199A199ILE00.013-0.0067.741-0.073-0.0730.0000.0000.0000.000
200A200GLY00.0410.0187.9770.2230.2230.0000.0000.0000.000
201A201ILE00.014-0.0012.726-1.247-0.7592.549-0.492-2.5450.002
202A202ALA00.026-0.0123.046-1.607-0.4790.253-0.429-0.952-0.004
203A203PRO0-0.0310.0062.210-2.734-1.5223.776-1.194-3.7930.002