Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: N1QVQ

Calculation Name: 1VAJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VAJ

Chain ID: A

ChEMBL ID:

UniProt ID: O57770

Base Structure: X-ray

Registration Date: 2023-06-20

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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2411615.568754
FMO2-HF: Nuclear repulsion 2330911.924598
FMO2-HF: Total energy -80703.644156
FMO2-MP2: Total energy -80942.320679


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:3:PHE)


Summations of interaction energy for fragment #1(A:3:PHE)
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.
-16.012-4.5475.402-5.665-11.198-0.027
Interaction energy analysis for fragmet #1(A:3:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.043
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].
3A5ILE0-0.035-0.0143.351-0.1671.798-0.002-0.803-1.1580.002
4A6LYS10.8980.9613.145-0.1491.1210.098-0.626-0.742-0.006
5A7ASP-1-0.765-0.8844.7020.5700.839-0.001-0.005-0.2620.000
6A8GLU-1-0.822-0.9256.507-1.081-1.0810.0000.0000.0000.000
7A9TRP0-0.022-0.0297.070-0.005-0.0050.0000.0000.0000.000
8A10GLY00.0660.0387.7570.1110.1110.0000.0000.0000.000
9A11GLU-1-0.936-0.9858.938-0.285-0.2850.0000.0000.0000.000
10A12PHE0-0.062-0.04211.7440.0660.0660.0000.0000.0000.000
11A13LEU00.012-0.00210.0450.0660.0660.0000.0000.0000.000
12A14VAL00.0330.02612.4830.0540.0540.0000.0000.0000.000
13A15ARG10.9500.97514.3650.3570.3570.0000.0000.0000.000
14A16LEU0-0.068-0.02116.6450.0290.0290.0000.0000.0000.000
15A17ALA00.0450.02017.3480.0240.0240.0000.0000.0000.000
16A18ARG10.7590.85518.9980.1180.1180.0000.0000.0000.000
17A19ARG10.9380.96521.0570.2060.2060.0000.0000.0000.000
18A20ALA0-0.002-0.00921.9730.0120.0120.0000.0000.0000.000
19A21ILE00.0280.02422.3700.0120.0120.0000.0000.0000.000
20A22GLU-1-0.846-0.92725.243-0.094-0.0940.0000.0000.0000.000
21A23GLU-1-0.927-0.96726.676-0.098-0.0980.0000.0000.0000.000
22A24TYR00.0270.02527.6900.0070.0070.0000.0000.0000.000
23A25LEU0-0.031-0.01628.9710.0070.0070.0000.0000.0000.000
24A26LYS10.8610.95429.1810.1020.1020.0000.0000.0000.000
25A27THR0-0.072-0.05931.9310.0050.0050.0000.0000.0000.000
26A28GLY0-0.0080.01232.7840.0030.0030.0000.0000.0000.000
27A29LYS10.8740.93331.1420.0870.0870.0000.0000.0000.000
28A30GLU-1-0.836-0.90325.870-0.128-0.1280.0000.0000.0000.000
29A31ILE0-0.087-0.04322.087-0.002-0.0020.0000.0000.0000.000
30A32GLU-1-0.879-0.93924.715-0.148-0.1480.0000.0000.0000.000
31A33PRO00.000-0.00219.835-0.009-0.0090.0000.0000.0000.000
32A34PRO0-0.060-0.00719.2020.0190.0190.0000.0000.0000.000
33A35LYS10.9540.97820.6830.2060.2060.0000.0000.0000.000
34A36ASP-1-0.938-0.97619.441-0.310-0.3100.0000.0000.0000.000
35A37THR00.017-0.02115.884-0.036-0.0360.0000.0000.0000.000
36A38PRO0-0.0100.00812.5240.0190.0190.0000.0000.0000.000
37A39PRO00.0420.01614.5810.0020.0020.0000.0000.0000.000
38A40GLU-1-0.856-0.94310.744-0.744-0.7440.0000.0000.0000.000
39A41LEU0-0.032-0.0139.795-0.019-0.0190.0000.0000.0000.000
40A42TRP0-0.008-0.00413.2130.0790.0790.0000.0000.0000.000
41A43GLU-1-0.908-0.94411.929-0.443-0.4430.0000.0000.0000.000
42A44LYS10.8730.95115.0030.1310.1310.0000.0000.0000.000
43A45MET00.001-0.0018.414-0.083-0.0830.0000.0000.0000.000
44A46GLY00.0270.03713.5320.0200.0200.0000.0000.0000.000
45A47VAL0-0.023-0.02212.991-0.063-0.0630.0000.0000.0000.000
46A48PHE00.0270.00814.3050.0420.0420.0000.0000.0000.000
47A49VAL0-0.0280.00515.109-0.028-0.0280.0000.0000.0000.000
48A50THR00.018-0.00316.4030.0140.0140.0000.0000.0000.000
49A51LEU0-0.0020.01118.473-0.008-0.0080.0000.0000.0000.000
50A52ASN00.0230.01117.4900.0130.0130.0000.0000.0000.000
51A53ARG10.8950.92321.358-0.005-0.0050.0000.0000.0000.000
52A54TYR00.033-0.00120.2250.0040.0040.0000.0000.0000.000
53A55ASN0-0.048-0.02722.9190.0050.0050.0000.0000.0000.000
54A56VAL0-0.0290.00924.0500.0000.0000.0000.0000.0000.000
55A57PRO00.001-0.00323.6000.0030.0030.0000.0000.0000.000
56A58PRO00.0880.04419.587-0.005-0.0050.0000.0000.0000.000
57A59GLN00.0300.03221.435-0.010-0.0100.0000.0000.0000.000
58A60THR0-0.126-0.07823.211-0.005-0.0050.0000.0000.0000.000
59A61ALA0-0.010-0.00621.416-0.007-0.0070.0000.0000.0000.000
60A62LEU00.0210.03920.320-0.009-0.0090.0000.0000.0000.000
61A63ARG10.7450.85222.8540.0320.0320.0000.0000.0000.000
62A64GLY00.0300.02123.130-0.002-0.0020.0000.0000.0000.000
63A65CYS0-0.102-0.04618.4960.0000.0000.0000.0000.0000.000
64A66ILE00.0330.02820.8080.0090.0090.0000.0000.0000.000
65A67GLY00.049-0.00318.703-0.017-0.0170.0000.0000.0000.000
66A68PHE0-0.070-0.01518.3100.0160.0160.0000.0000.0000.000
67A69PRO00.0460.01917.313-0.021-0.0210.0000.0000.0000.000
68A70THR00.0150.00816.926-0.001-0.0010.0000.0000.0000.000
69A71PRO00.0330.02515.726-0.019-0.0190.0000.0000.0000.000
70A72ILE0-0.038-0.03217.596-0.002-0.0020.0000.0000.0000.000
71A73TYR0-0.015-0.00519.3720.0070.0070.0000.0000.0000.000
72A74PRO0-0.005-0.00117.632-0.020-0.0200.0000.0000.0000.000
73A75LEU00.0410.01710.6730.0180.0180.0000.0000.0000.000
74A76VAL00.0150.00515.1390.0280.0280.0000.0000.0000.000
75A77GLU-1-0.903-0.96916.570-0.159-0.1590.0000.0000.0000.000
76A78ALA0-0.007-0.00417.0170.0270.0270.0000.0000.0000.000
77A79THR0-0.001-0.01415.1340.0170.0170.0000.0000.0000.000
78A80ILE0-0.029-0.00717.4590.0240.0240.0000.0000.0000.000
79A81LYS10.8930.93620.6860.1520.1520.0000.0000.0000.000
80A82ALA00.0150.01619.1160.0170.0170.0000.0000.0000.000
81A83ALA0-0.0010.00819.7410.0160.0160.0000.0000.0000.000
82A84ILE00.0290.01821.3230.0150.0150.0000.0000.0000.000
83A85TYR00.019-0.00323.9750.0090.0090.0000.0000.0000.000
84A86SER0-0.080-0.03921.8200.0110.0110.0000.0000.0000.000
85A87ALA00.012-0.00123.9590.0100.0100.0000.0000.0000.000
86A88VAL0-0.066-0.04326.4300.0080.0080.0000.0000.0000.000
87A89ASP-1-0.915-0.94427.943-0.053-0.0530.0000.0000.0000.000
88A90ASP-1-0.709-0.82825.261-0.019-0.0190.0000.0000.0000.000
89A91PRO0-0.023-0.02827.9880.0030.0030.0000.0000.0000.000
90A92ARG10.7830.87023.2330.0100.0100.0000.0000.0000.000
91A93PHE0-0.030-0.01625.5800.0040.0040.0000.0000.0000.000
92A94PRO0-0.0330.00630.697-0.003-0.0030.0000.0000.0000.000
93A95PRO00.0580.01830.849-0.001-0.0010.0000.0000.0000.000
94A96VAL0-0.015-0.00626.8020.0030.0030.0000.0000.0000.000
95A97LYS10.9390.97330.2160.0300.0300.0000.0000.0000.000
96A98LEU00.0330.00329.659-0.002-0.0020.0000.0000.0000.000
97A99GLU-1-0.899-0.96430.487-0.049-0.0490.0000.0000.0000.000
98A100GLU-1-0.788-0.87928.471-0.032-0.0320.0000.0000.0000.000
99A101MET0-0.0280.00023.5880.0030.0030.0000.0000.0000.000
100A102ASP-1-0.864-0.91226.098-0.068-0.0680.0000.0000.0000.000
101A103ASN0-0.113-0.07426.8420.0020.0020.0000.0000.0000.000
102A104LEU00.0230.02123.3810.0080.0080.0000.0000.0000.000
103A105VAL0-0.0130.00118.440-0.009-0.0090.0000.0000.0000.000
104A106VAL0-0.017-0.02117.0170.0050.0050.0000.0000.0000.000
105A107GLU-1-0.850-0.93712.9370.0130.0130.0000.0000.0000.000
106A108VAL0-0.013-0.00211.885-0.009-0.0090.0000.0000.0000.000
107A109SER0-0.001-0.00710.5280.0170.0170.0000.0000.0000.000
108A110VAL00.0150.0008.1890.0210.0210.0000.0000.0000.000
109A111LEU0-0.017-0.0108.833-0.017-0.0170.0000.0000.0000.000
110A112THR0-0.022-0.0067.829-0.105-0.1050.0000.0000.0000.000
111A113PRO0-0.029-0.03610.4370.0000.0000.0000.0000.0000.000
112A114PRO00.0190.01113.9560.0560.0560.0000.0000.0000.000
113A115GLU-1-0.959-0.97214.6700.4150.4150.0000.0000.0000.000
114A116LEU0-0.038-0.02617.6230.0010.0010.0000.0000.0000.000
115A117ILE0-0.026-0.00819.8040.0230.0230.0000.0000.0000.000
116A118GLU-1-0.953-0.97522.0340.1780.1780.0000.0000.0000.000
117A119GLY0-0.049-0.04024.8330.0100.0100.0000.0000.0000.000
118A120PRO00.0060.00127.891-0.005-0.0050.0000.0000.0000.000
119A121PRO00.0720.03628.4700.0120.0120.0000.0000.0000.000
120A122GLU-1-0.836-0.93328.2220.1150.1150.0000.0000.0000.000
121A123GLU-1-1.012-1.01726.8700.1570.1570.0000.0000.0000.000
122A124ARG10.7790.88523.994-0.098-0.0980.0000.0000.0000.000
123A125PRO00.0670.03222.3280.0220.0220.0000.0000.0000.000
124A126ARG10.9400.96921.277-0.149-0.1490.0000.0000.0000.000
125A127LYS10.8720.95419.883-0.180-0.1800.0000.0000.0000.000
126A128ILE0-0.0040.02317.0650.0380.0380.0000.0000.0000.000
127A129LYS10.9170.95512.328-0.510-0.5100.0000.0000.0000.000
128A130VAL00.0590.04213.8600.0270.0270.0000.0000.0000.000
129A131GLY0-0.008-0.00411.8090.0190.0190.0000.0000.0000.000
130A132ARG10.6840.8009.175-0.484-0.4840.0000.0000.0000.000
131A133ASP-1-0.774-0.86610.2470.4290.4290.0000.0000.0000.000
132A134GLY00.0380.03913.011-0.031-0.0310.0000.0000.0000.000
133A135LEU0-0.009-0.02014.7710.0280.0280.0000.0000.0000.000
134A136ILE0-0.003-0.00918.287-0.024-0.0240.0000.0000.0000.000
135A137VAL00.0110.00921.1020.0140.0140.0000.0000.0000.000
136A138GLU-1-0.892-0.95724.5550.0310.0310.0000.0000.0000.000
137A139LYS10.9540.98027.356-0.045-0.0450.0000.0000.0000.000
138A140GLY0-0.0200.00031.065-0.004-0.0040.0000.0000.0000.000
139A141ILE0-0.021-0.02331.924-0.001-0.0010.0000.0000.0000.000
140A142TYR0-0.052-0.00930.915-0.005-0.0050.0000.0000.0000.000
141A143SER00.013-0.01125.1560.0050.0050.0000.0000.0000.000
142A144GLY00.0140.01624.935-0.008-0.0080.0000.0000.0000.000
143A145LEU0-0.033-0.00317.5600.0080.0080.0000.0000.0000.000
144A146LEU0-0.026-0.00919.171-0.015-0.0150.0000.0000.0000.000
145A147LEU00.002-0.00614.1350.0160.0160.0000.0000.0000.000
146A148PRO00.0440.01510.8270.0040.0040.0000.0000.0000.000
147A149GLN00.004-0.01512.3590.0360.0360.0000.0000.0000.000
148A150VAL0-0.0050.01213.624-0.003-0.0030.0000.0000.0000.000
149A151PRO00.0270.01815.725-0.004-0.0040.0000.0000.0000.000
150A152VAL0-0.032-0.00912.7130.0050.0050.0000.0000.0000.000
151A153GLU-1-0.947-0.97416.1220.0500.0500.0000.0000.0000.000
152A154TRP0-0.054-0.04218.103-0.010-0.0100.0000.0000.0000.000
153A155GLY0-0.060-0.00719.685-0.005-0.0050.0000.0000.0000.000
154A156TRP00.0220.01320.205-0.001-0.0010.0000.0000.0000.000
155A157ASP-1-0.839-0.91319.8690.1510.1510.0000.0000.0000.000
156A158GLU-1-0.853-0.96818.1800.2240.2240.0000.0000.0000.000
157A159GLU-1-0.940-0.97320.9880.1090.1090.0000.0000.0000.000
158A160GLU-1-0.880-0.93923.7670.0990.0990.0000.0000.0000.000
159A161PHE0-0.019-0.01516.479-0.010-0.0100.0000.0000.0000.000
160A162LEU0-0.014-0.00721.748-0.008-0.0080.0000.0000.0000.000
161A163ALA00.0150.01823.610-0.011-0.0110.0000.0000.0000.000
162A164GLU-1-0.893-0.95523.4600.0570.0570.0000.0000.0000.000
163A165THR0-0.067-0.04621.560-0.010-0.0100.0000.0000.0000.000
164A166CYS0-0.086-0.02623.861-0.008-0.0080.0000.0000.0000.000
165A167TRP00.0400.02427.321-0.009-0.0090.0000.0000.0000.000
166A168LYS10.8740.95123.232-0.030-0.0300.0000.0000.0000.000
167A169ALA0-0.009-0.00726.723-0.008-0.0080.0000.0000.0000.000
168A170GLY0-0.054-0.01328.163-0.005-0.0050.0000.0000.0000.000
169A171LEU0-0.064-0.04029.620-0.002-0.0020.0000.0000.0000.000
170A172PRO0-0.004-0.00531.6780.0010.0010.0000.0000.0000.000
171A173PRO00.0520.00729.9860.0030.0030.0000.0000.0000.000
172A174ASP-1-0.876-0.93229.5730.0700.0700.0000.0000.0000.000
173A175CYS0-0.0080.01130.3200.0010.0010.0000.0000.0000.000
174A176TRP00.0570.01126.7490.0040.0040.0000.0000.0000.000
175A177LEU00.0070.01328.6540.0080.0080.0000.0000.0000.000
176A178ASP-1-0.912-0.94231.3780.0640.0640.0000.0000.0000.000
177A179GLU-1-0.923-0.96831.2580.0750.0750.0000.0000.0000.000
178A180ASP-1-0.959-0.98031.4200.0630.0630.0000.0000.0000.000
179A181THR0-0.118-0.05627.927-0.007-0.0070.0000.0000.0000.000
180A182LYS10.8820.94125.587-0.057-0.0570.0000.0000.0000.000
181A183VAL00.0370.01521.669-0.007-0.0070.0000.0000.0000.000
182A184TYR00.0080.00019.0670.0110.0110.0000.0000.0000.000
183A185LYS10.8920.95615.515-0.397-0.3970.0000.0000.0000.000
184A186PHE0-0.018-0.00312.459-0.001-0.0010.0000.0000.0000.000
185A187THR00.0510.0287.993-0.036-0.0360.0000.0000.0000.000
186A188ALA00.033-0.0068.304-0.080-0.0800.0000.0000.0000.000
187A189GLU-1-0.810-0.8732.683-9.722-5.5151.323-2.735-2.795-0.028
188A190ILE0-0.0030.0025.847-0.056-0.0560.0000.0000.0000.000
189A191PHE0-0.032-0.0014.8490.2860.2860.0000.0000.0000.000
190A192GLU-1-0.803-0.91610.122-0.028-0.0280.0000.0000.0000.000
191A193GLU-1-0.776-0.84913.400-0.095-0.0950.0000.0000.0000.000
192A194GLU-1-0.871-0.95314.460-0.013-0.0130.0000.0000.0000.000
193A195TYR0-0.022-0.02116.4810.0080.0080.0000.0000.0000.000
194A196PRO0-0.0140.00120.107-0.013-0.0130.0000.0000.0000.000
195A197ARG10.7580.86621.3900.0860.0860.0000.0000.0000.000
196A198GLY00.0050.01619.897-0.007-0.0070.0000.0000.0000.000
197A199PRO0-0.071-0.03515.507-0.019-0.0190.0000.0000.0000.000
198A200ILE0-0.0190.01011.7130.0170.0170.0000.0000.0000.000
199A201LYS10.8890.9519.5940.0310.0310.0000.0000.0000.000
200A202ARG10.8150.9002.741-5.065-1.3113.984-1.496-6.2410.005
201A203LYS10.8440.9197.222-0.134-0.1340.0000.0000.0000.000
202A204PRO0-0.042-0.0134.942-0.012-0.0120.0000.0000.0000.000
203A205LEU00.0090.0086.650-0.026-0.0260.0000.0000.0000.000