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: VRVL1

Calculation Name: 1EQ6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EQ6

Chain ID: A

ChEMBL ID:

UniProt ID: P47123

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2051506.172976
FMO2-HF: Nuclear repulsion 1977608.987902
FMO2-HF: Total energy -73897.185074
FMO2-MP2: Total energy -74114.239737


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:30:SER)


Summations of interaction energy for fragment #1(A:30: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.
-19.551-16.0074.426-3.635-4.332-0.025
Interaction energy analysis for fragmet #1(A:30:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.018
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].
3A32ASN0-0.066-0.0333.8480.4672.372-0.012-0.947-0.9450.005
4A33ASN0-0.004-0.0346.4210.3930.3930.0000.0000.0000.000
5A34LYS10.9050.9499.3331.3391.3390.0000.0000.0000.000
6A35GLU-1-0.895-0.93512.575-0.283-0.2830.0000.0000.0000.000
7A36VAL0-0.036-0.01315.529-0.037-0.0370.0000.0000.0000.000
8A37GLU-1-0.930-0.97018.801-0.220-0.2200.0000.0000.0000.000
9A38LEU0-0.020-0.01120.737-0.030-0.0300.0000.0000.0000.000
10A39TYR0-0.019-0.06324.0970.0240.0240.0000.0000.0000.000
11A40GLY0-0.027-0.01027.7450.0210.0210.0000.0000.0000.000
12A41GLY00.0310.02125.7390.0130.0130.0000.0000.0000.000
13A42ALA0-0.036-0.00926.3290.0120.0120.0000.0000.0000.000
14A43ILE0-0.025-0.00822.4560.0240.0240.0000.0000.0000.000
15A44THR0-0.018-0.01119.328-0.012-0.0120.0000.0000.0000.000
16A45THR00.0100.00017.0360.0070.0070.0000.0000.0000.000
17A46VAL0-0.052-0.02611.589-0.019-0.0190.0000.0000.0000.000
18A47VAL00.0350.02313.5820.0250.0250.0000.0000.0000.000
19A48PRO00.0410.0289.824-0.098-0.0980.0000.0000.0000.000
20A49PRO0-0.050-0.0119.6170.3660.3660.0000.0000.0000.000
21A50GLY00.0640.02012.600-0.143-0.1430.0000.0000.0000.000
22A51PHE00.0130.02112.2540.0830.0830.0000.0000.0000.000
23A52ILE0-0.045-0.02316.5350.0340.0340.0000.0000.0000.000
24A53ASP-1-0.752-0.82920.277-0.407-0.4070.0000.0000.0000.000
25A54ALA00.0100.00122.7690.0210.0210.0000.0000.0000.000
26A55SER00.025-0.00325.4000.0350.0350.0000.0000.0000.000
27A56THR0-0.086-0.05325.6730.0220.0220.0000.0000.0000.000
28A57LEU0-0.068-0.03726.0790.0140.0140.0000.0000.0000.000
29A58ARG10.8010.88329.4980.3310.3310.0000.0000.0000.000
30A59GLU-1-0.913-0.94330.383-0.207-0.2070.0000.0000.0000.000
31A60VAL0-0.012-0.01027.496-0.013-0.0130.0000.0000.0000.000
32A61PRO0-0.003-0.00429.9180.0120.0120.0000.0000.0000.000
33A62ASP-1-0.881-0.93230.860-0.178-0.1780.0000.0000.0000.000
34A63THR0-0.054-0.03430.6150.0000.0000.0000.0000.0000.000
35A64GLN0-0.105-0.06027.104-0.018-0.0180.0000.0000.0000.000
36A65GLU-1-0.800-0.87923.389-0.326-0.3260.0000.0000.0000.000
37A66VAL0-0.022-0.01422.776-0.022-0.0220.0000.0000.0000.000
38A67TYR0-0.013-0.02118.528-0.039-0.0390.0000.0000.0000.000
39A68VAL0-0.027-0.02219.349-0.006-0.0060.0000.0000.0000.000
40A69ASN0-0.053-0.02913.462-0.033-0.0330.0000.0000.0000.000
41A70SER0-0.070-0.05317.0130.1210.1210.0000.0000.0000.000
42A71ARG10.7780.8969.2552.3862.3860.0000.0000.0000.000
43A72ARG10.7880.87216.6290.7870.7870.0000.0000.0000.000
44A73ASP-1-0.844-0.91816.338-0.884-0.8840.0000.0000.0000.000
45A74GLU-1-0.900-0.94016.263-0.716-0.7160.0000.0000.0000.000
46A75GLU-1-0.943-0.96214.112-1.120-1.1200.0000.0000.0000.000
47A76GLU-1-0.916-0.95210.203-1.477-1.4770.0000.0000.0000.000
48A77PHE0-0.024-0.0277.236-0.021-0.0210.0000.0000.0000.000
49A78GLU-1-0.925-0.9712.262-5.028-4.3300.978-0.603-1.072-0.002
50A79ASP-1-0.810-0.9172.139-15.518-14.7953.462-2.079-2.106-0.028
51A80GLY0-0.019-0.0044.6161.0361.174-0.001-0.004-0.1330.000
52A81LEU0-0.063-0.0346.1200.8850.8850.0000.0000.0000.000
53A82ALA0-0.004-0.0089.303-0.137-0.1370.0000.0000.0000.000
54A83THR00.012-0.01912.449-0.137-0.1370.0000.0000.0000.000
55A84ASN0-0.029-0.00815.6220.0250.0250.0000.0000.0000.000
56A85GLU-1-0.755-0.85013.121-1.183-1.1830.0000.0000.0000.000
57A86SER0-0.022-0.01216.6760.0220.0220.0000.0000.0000.000
58A87ILE0-0.020-0.01014.6610.0010.0010.0000.0000.0000.000
59A88ILE00.0240.01418.8990.0120.0120.0000.0000.0000.000
60A89VAL0-0.019-0.00420.4470.0110.0110.0000.0000.0000.000
61A90ASP-1-0.743-0.86122.923-0.200-0.2000.0000.0000.0000.000
62A91LEU0-0.050-0.01726.4600.0140.0140.0000.0000.0000.000
63A92LEU00.0040.00929.0600.0070.0070.0000.0000.0000.000
64A93GLU-1-0.889-0.95331.345-0.080-0.0800.0000.0000.0000.000
65A94THR0-0.122-0.08732.752-0.002-0.0020.0000.0000.0000.000
66A95VAL00.0100.01732.1300.0040.0040.0000.0000.0000.000
67A96ASP-1-0.902-0.95034.655-0.034-0.0340.0000.0000.0000.000
68A97LYS10.7270.85433.6150.0220.0220.0000.0000.0000.000
69A98SER00.020-0.00933.815-0.002-0.0020.0000.0000.0000.000
70A99ASP-1-0.856-0.92430.9170.0370.0370.0000.0000.0000.000
71A100LEU0-0.0200.00324.780-0.010-0.0100.0000.0000.0000.000
72A101LYS10.8130.89926.688-0.050-0.0500.0000.0000.0000.000
73A102GLU-1-0.846-0.92828.203-0.020-0.0200.0000.0000.0000.000
74A103ALA00.0100.01329.677-0.012-0.0120.0000.0000.0000.000
75A104TRP0-0.017-0.02521.7910.0000.0000.0000.0000.0000.000
76A105GLN0-0.020-0.02826.917-0.004-0.0040.0000.0000.0000.000
77A106PHE0-0.030-0.00528.590-0.007-0.0070.0000.0000.0000.000
78A107HIS10.8360.87727.5580.0910.0910.0000.0000.0000.000
79A108VAL0-0.0170.00524.374-0.021-0.0210.0000.0000.0000.000
80A109GLU-1-0.820-0.87726.988-0.115-0.1150.0000.0000.0000.000
81A110ASP-1-0.821-0.90429.857-0.120-0.1200.0000.0000.0000.000
82A111LEU0-0.041-0.01924.491-0.015-0.0150.0000.0000.0000.000
83A112THR0-0.035-0.05326.861-0.016-0.0160.0000.0000.0000.000
84A113GLU-1-0.920-0.96529.183-0.105-0.1050.0000.0000.0000.000
85A114LEU0-0.052-0.00929.4450.0020.0020.0000.0000.0000.000
86A115ASN0-0.070-0.02428.009-0.020-0.0200.0000.0000.0000.000
87A116GLY0-0.061-0.03731.5540.0030.0030.0000.0000.0000.000
88A117THR0-0.019-0.04229.6950.0080.0080.0000.0000.0000.000
89A118THR0-0.087-0.05232.6100.0060.0060.0000.0000.0000.000
90A119LYS10.8100.89430.1150.0630.0630.0000.0000.0000.000
91A120TRP00.0170.00225.259-0.010-0.0100.0000.0000.0000.000
92A121GLU-1-0.902-0.94025.476-0.014-0.0140.0000.0000.0000.000
93A122ALA00.0260.00823.234-0.024-0.0240.0000.0000.0000.000
94A123LEU0-0.030-0.01919.5630.0240.0240.0000.0000.0000.000
95A124GLN0-0.051-0.03114.8680.0130.0130.0000.0000.0000.000
96A125GLU-1-0.822-0.89319.3540.0030.0030.0000.0000.0000.000
97A126ASP-1-0.807-0.85917.0360.2660.2660.0000.0000.0000.000
98A127THR0-0.030-0.01219.921-0.038-0.0380.0000.0000.0000.000
99A128VAL0-0.024-0.00417.2270.0390.0390.0000.0000.0000.000
100A129GLN0-0.006-0.01019.6810.0160.0160.0000.0000.0000.000
101A130GLN00.0400.00922.928-0.039-0.0390.0000.0000.0000.000
102A131GLY0-0.0120.00326.460-0.003-0.0030.0000.0000.0000.000
103A132THR00.000-0.00425.141-0.010-0.0100.0000.0000.0000.000
104A133LYS10.8910.94819.579-0.013-0.0130.0000.0000.0000.000
105A134PHE00.005-0.00121.5480.0430.0430.0000.0000.0000.000
106A135THR00.005-0.01116.404-0.028-0.0280.0000.0000.0000.000
107A136GLY00.0450.01318.7190.0490.0490.0000.0000.0000.000
108A137LEU0-0.058-0.01514.667-0.063-0.0630.0000.0000.0000.000
109A138VAL00.0150.01418.8680.0440.0440.0000.0000.0000.000
110A139MET00.0140.01221.677-0.050-0.0500.0000.0000.0000.000
111A140GLU-1-0.779-0.85323.938-0.134-0.1340.0000.0000.0000.000
112A141VAL0-0.032-0.02727.2370.0000.0000.0000.0000.0000.000
113A142ALA0-0.046-0.02129.7610.0100.0100.0000.0000.0000.000
114A143ASN00.0890.03432.1770.0060.0060.0000.0000.0000.000
115A144LYS10.9520.97834.7270.1190.1190.0000.0000.0000.000
116A145TRP0-0.0100.00434.2560.0080.0080.0000.0000.0000.000
117A146GLY0-0.027-0.00737.5610.0040.0040.0000.0000.0000.000
118A147LYS10.7740.87235.6260.1040.1040.0000.0000.0000.000
119A148PRO00.0640.04730.704-0.009-0.0090.0000.0000.0000.000
120A149ASP-1-0.888-0.94429.506-0.148-0.1480.0000.0000.0000.000
121A150LEU0-0.099-0.04530.803-0.002-0.0020.0000.0000.0000.000
122A151ALA0-0.015-0.01829.550-0.003-0.0030.0000.0000.0000.000
123A152GLN0-0.054-0.03521.8190.0190.0190.0000.0000.0000.000
124A153THR00.0470.02423.107-0.002-0.0020.0000.0000.0000.000
125A154VAL00.0050.00221.689-0.041-0.0410.0000.0000.0000.000
126A155VAL0-0.015-0.00117.8580.0440.0440.0000.0000.0000.000
127A156ILE00.0160.00119.381-0.056-0.0560.0000.0000.0000.000
128A157GLY00.0060.00816.6170.0540.0540.0000.0000.0000.000
129A158VAL00.0310.00917.647-0.031-0.0310.0000.0000.0000.000
130A159ALA0-0.029-0.01618.5150.0440.0440.0000.0000.0000.000
131A160LEU0-0.0240.01220.652-0.015-0.0150.0000.0000.0000.000
132A161ILE0-0.025-0.02119.9980.0320.0320.0000.0000.0000.000
133A162ARG10.8040.86924.1720.0210.0210.0000.0000.0000.000
134A163LEU0-0.0060.01125.8880.0180.0180.0000.0000.0000.000
135A164THR00.030-0.00729.295-0.004-0.0040.0000.0000.0000.000
136A165GLN0-0.104-0.04732.300-0.002-0.0020.0000.0000.0000.000
137A166PHE0-0.010-0.02131.1800.0020.0020.0000.0000.0000.000
138A167ASP-1-0.867-0.88933.944-0.060-0.0600.0000.0000.0000.000
139A168THR00.0200.01329.210-0.011-0.0110.0000.0000.0000.000
140A169ASP-1-0.754-0.83328.699-0.052-0.0520.0000.0000.0000.000
141A170VAL0-0.0010.00123.656-0.014-0.0140.0000.0000.0000.000
142A171VAL0-0.0030.00024.0010.0140.0140.0000.0000.0000.000
143A172ILE0-0.012-0.00417.809-0.026-0.0260.0000.0000.0000.000
144A173SER0-0.033-0.01619.9860.0270.0270.0000.0000.0000.000
145A174ILE00.0210.00114.269-0.051-0.0510.0000.0000.0000.000
146A175ASN0-0.010-0.00117.7950.0600.0600.0000.0000.0000.000
147A176VAL00.021-0.00715.173-0.097-0.0970.0000.0000.0000.000
148A177PRO00.0130.01117.8470.0650.0650.0000.0000.0000.000
149A178LEU0-0.0150.01217.483-0.063-0.0630.0000.0000.0000.000
150A179THR00.010-0.01917.4090.0350.0350.0000.0000.0000.000
151A180LYS10.9570.97420.1100.2520.2520.0000.0000.0000.000
152A181GLU-1-0.835-0.90918.874-0.382-0.3820.0000.0000.0000.000
153A182GLU-1-0.720-0.81214.642-0.648-0.6480.0000.0000.0000.000
154A183ALA00.0320.01518.6680.0370.0370.0000.0000.0000.000
155A184SER0-0.117-0.07222.0140.0410.0410.0000.0000.0000.000
156A185GLN0-0.021-0.03516.215-0.038-0.0380.0000.0000.0000.000
157A186ALA00.0390.02220.2250.0370.0370.0000.0000.0000.000
158A187SER0-0.016-0.01521.4930.0280.0280.0000.0000.0000.000
159A188ASN0-0.149-0.07023.2310.0270.0270.0000.0000.0000.000
160A189LYS10.9030.94523.1600.0290.0290.0000.0000.0000.000
161A190GLU-1-0.848-0.88718.548-0.025-0.0250.0000.0000.0000.000
162A191LEU00.018-0.00214.026-0.031-0.0310.0000.0000.0000.000
163A192PRO0-0.0020.00614.8030.0140.0140.0000.0000.0000.000
164A193ALA00.0240.0049.370-0.015-0.0150.0000.0000.0000.000
165A194ARG10.7820.8509.6250.7800.7800.0000.0000.0000.000
166A195CYS0-0.0090.00210.943-0.071-0.0710.0000.0000.0000.000
167A196HIS0-0.0010.0037.497-0.117-0.1170.0000.0000.0000.000
168A197ALA0-0.014-0.0067.1580.1390.1390.0000.0000.0000.000
169A198VAL00.0350.0068.198-0.068-0.0680.0000.0000.0000.000
170A199TYR0-0.022-0.03211.2880.0470.0470.0000.0000.0000.000
171A200GLN0-0.028-0.0114.4840.8820.962-0.001-0.002-0.0760.000
172A201LEU00.0320.0188.8970.0810.0810.0000.0000.0000.000
173A202LEU0-0.0320.00210.1530.1270.1270.0000.0000.0000.000
174A203GLN00.014-0.00311.7050.1770.1770.0000.0000.0000.000
175A204GLU-1-0.875-0.9158.225-0.876-0.8760.0000.0000.0000.000
176A205MET00.0100.01211.8280.0440.0440.0000.0000.0000.000
177A206VAL00.0440.02514.8300.0610.0610.0000.0000.0000.000
178A207ARG10.8300.92010.912-0.221-0.2210.0000.0000.0000.000
179A208LYS10.8440.89810.0990.4730.4730.0000.0000.0000.000
180A209PHE00.0450.04315.926-0.030-0.0300.0000.0000.0000.000
181A210HIS0-0.086-0.04418.0760.0640.0640.0000.0000.0000.000
182A211VAL00.0360.01921.780-0.025-0.0250.0000.0000.0000.000
183A212VAL0-0.050-0.01723.9940.0230.0230.0000.0000.0000.000
184A213ASP-1-0.850-0.90726.456-0.079-0.0790.0000.0000.0000.000
185A214THR0-0.022-0.01230.050-0.009-0.0090.0000.0000.0000.000
186A215SER0-0.111-0.08631.986-0.001-0.0010.0000.0000.0000.000
187A216LEU0-0.0060.01229.023-0.001-0.0010.0000.0000.0000.000
188A217PHE00.0130.01328.502-0.003-0.0030.0000.0000.0000.000
189A218ALA0-0.062-0.03234.5850.0150.0150.0000.0000.0000.000