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: GY551

Calculation Name: 1VKN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VKN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X2A2

Base Structure: X-ray

Registration Date: 2023-09-27

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 340
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5477495.919433
FMO2-HF: Nuclear repulsion 5344056.833107
FMO2-HF: Total energy -133439.086327
FMO2-MP2: Total energy -133828.738602


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-21.78-14.6942.308-3.407-5.986-0.029
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.023
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].
3A2ILE00.0320.0173.103-4.535-1.6111.430-1.453-2.900-0.005
4A3ARG10.7910.8942.5759.99111.2100.355-0.320-1.2540.000
5A4ALA00.0530.0235.145-0.089-0.034-0.001-0.001-0.0520.000
6A5GLY00.0280.0118.6000.5140.5140.0000.0000.0000.000
7A6ILE0-0.034-0.02111.694-0.022-0.0220.0000.0000.0000.000
8A7ILE00.0030.00415.2830.1320.1320.0000.0000.0000.000
9A8GLY00.0020.00118.2030.0140.0140.0000.0000.0000.000
10A9ALA00.020-0.00318.5360.0080.0080.0000.0000.0000.000
11A10THR00.0280.00620.3410.0280.0280.0000.0000.0000.000
12A11GLY0-0.034-0.00123.5990.0400.0400.0000.0000.0000.000
13A12TYR00.0360.00323.884-0.018-0.0180.0000.0000.0000.000
14A13THR00.0350.01722.0600.0110.0110.0000.0000.0000.000
15A14GLY00.0490.03919.600-0.055-0.0550.0000.0000.0000.000
16A15LEU00.0130.00319.386-0.018-0.0180.0000.0000.0000.000
17A16GLU-1-0.809-0.89320.768-0.275-0.2750.0000.0000.0000.000
18A17LEU0-0.015-0.00715.7020.0000.0000.0000.0000.0000.000
19A18VAL00.0030.00516.148-0.035-0.0350.0000.0000.0000.000
20A19ARG10.8430.90616.7050.2970.2970.0000.0000.0000.000
21A20LEU0-0.033-0.02216.8220.0700.0700.0000.0000.0000.000
22A21LEU00.0150.00110.988-0.007-0.0070.0000.0000.0000.000
23A22LYS10.8240.91812.8470.0090.0090.0000.0000.0000.000
24A23ASN0-0.074-0.03614.0020.0920.0920.0000.0000.0000.000
25A24HIS0-0.002-0.0039.4250.2850.2850.0000.0000.0000.000
26A25PRO00.0200.0179.4750.1020.1020.0000.0000.0000.000
27A26GLU-1-0.896-0.9625.604-0.705-0.7050.0000.0000.0000.000
28A27ALA0-0.0100.0016.376-1.446-1.4460.0000.0000.0000.000
29A28LYS10.9610.9824.486-2.429-2.270-0.001-0.008-0.1500.000
30A29ILE00.0170.0087.959-0.772-0.7720.0000.0000.0000.000
31A30THR0-0.057-0.0465.9330.3150.3150.0000.0000.0000.000
32A31TYR00.0260.0079.3420.1580.1580.0000.0000.0000.000
33A32LEU00.0410.03312.569-0.080-0.0800.0000.0000.0000.000
34A33SER00.0180.02116.1230.0740.0740.0000.0000.0000.000
35A34SER00.0220.00119.202-0.001-0.0010.0000.0000.0000.000
36A35ARG11.0071.00622.9050.2930.2930.0000.0000.0000.000
37A36THR0-0.061-0.04325.9420.0180.0180.0000.0000.0000.000
38A37TYR00.0200.00225.2440.0280.0280.0000.0000.0000.000
39A38ALA00.0250.02823.2790.0140.0140.0000.0000.0000.000
40A39GLY00.0010.00122.9260.0230.0230.0000.0000.0000.000
41A40LYS10.9200.96624.4570.1220.1220.0000.0000.0000.000
42A41LYS10.9250.97721.607-0.108-0.1080.0000.0000.0000.000
43A42LEU00.0410.02219.506-0.012-0.0120.0000.0000.0000.000
44A43GLU-1-0.932-0.97122.2230.0940.0940.0000.0000.0000.000
45A44GLU-1-0.918-0.96924.2230.0040.0040.0000.0000.0000.000
46A45ILE0-0.080-0.02925.539-0.004-0.0040.0000.0000.0000.000
47A46PHE00.014-0.00825.083-0.008-0.0080.0000.0000.0000.000
48A47PRO00.0500.04125.326-0.001-0.0010.0000.0000.0000.000
49A48SER0-0.032-0.02125.9590.0160.0160.0000.0000.0000.000
50A49THR0-0.034-0.03221.1630.0110.0110.0000.0000.0000.000
51A50LEU0-0.0100.00421.1350.0110.0110.0000.0000.0000.000
52A51GLU-1-0.815-0.86116.2860.0250.0250.0000.0000.0000.000
53A52ASN00.000-0.00717.935-0.053-0.0530.0000.0000.0000.000
54A53SER00.004-0.03415.3620.0070.0070.0000.0000.0000.000
55A54ILE0-0.049-0.02417.541-0.031-0.0310.0000.0000.0000.000
56A55LEU0-0.047-0.02018.111-0.073-0.0730.0000.0000.0000.000
57A56SER0-0.023-0.02017.1240.0430.0430.0000.0000.0000.000
58A57GLU-1-0.919-0.97219.450-0.290-0.2900.0000.0000.0000.000
59A58PHE0-0.048-0.04417.014-0.010-0.0100.0000.0000.0000.000
60A59ASP-1-0.786-0.89518.291-0.433-0.4330.0000.0000.0000.000
61A60PRO00.0640.02817.035-0.092-0.0920.0000.0000.0000.000
62A61GLU-1-0.887-0.94115.759-0.605-0.6050.0000.0000.0000.000
63A62LYS10.8110.90714.2130.2700.2700.0000.0000.0000.000
64A63VAL00.0410.03212.289-0.120-0.1200.0000.0000.0000.000
65A64SER0-0.001-0.00310.832-0.360-0.3600.0000.0000.0000.000
66A65LYS10.9380.98510.2810.1810.1810.0000.0000.0000.000
67A66ASN0-0.103-0.0708.0080.0820.0820.0000.0000.0000.000
68A67CYS0-0.0460.0037.102-0.080-0.0800.0000.0000.0000.000
69A68ASP-1-0.747-0.8632.506-22.659-19.9300.525-1.625-1.630-0.024
70A69VAL0-0.011-0.0055.9500.8200.8200.0000.0000.0000.000
71A70LEU0-0.027-0.0098.9440.1530.1530.0000.0000.0000.000
72A71PHE00.0100.00611.3990.1120.1120.0000.0000.0000.000
73A72THR0-0.027-0.01815.1160.0630.0630.0000.0000.0000.000
74A73ALA0-0.002-0.00318.4630.0300.0300.0000.0000.0000.000
75A74LEU0-0.014-0.00721.2860.0540.0540.0000.0000.0000.000
76A75PRO0-0.043-0.02624.2180.0060.0060.0000.0000.0000.000
77A76ALA00.002-0.00626.825-0.025-0.0250.0000.0000.0000.000
78A77GLY00.008-0.00327.1690.0320.0320.0000.0000.0000.000
79A78ALA00.008-0.00125.066-0.010-0.0100.0000.0000.0000.000
80A79SER0-0.008-0.00920.051-0.033-0.0330.0000.0000.0000.000
81A80TYR0-0.037-0.04521.488-0.055-0.0550.0000.0000.0000.000
82A81ASP-1-0.864-0.93823.173-0.484-0.4840.0000.0000.0000.000
83A82LEU0-0.016-0.00418.037-0.011-0.0110.0000.0000.0000.000
84A83VAL00.0170.00017.420-0.050-0.0500.0000.0000.0000.000
85A84ARG10.8970.95718.5520.4780.4780.0000.0000.0000.000
86A85GLU-1-0.934-0.96219.873-0.581-0.5810.0000.0000.0000.000
87A86LEU0-0.053-0.01514.348-0.010-0.0100.0000.0000.0000.000
88A87LYS10.9140.94214.4490.8310.8310.0000.0000.0000.000
89A88GLY00.0090.00411.175-0.080-0.0800.0000.0000.0000.000
90A89VAL0-0.0070.0199.314-0.470-0.4700.0000.0000.0000.000
91A90LYS10.8600.9419.0103.5153.5150.0000.0000.0000.000
92A91ILE00.0020.00211.503-0.077-0.0770.0000.0000.0000.000
93A92ILE00.0030.01112.7030.0780.0780.0000.0000.0000.000
94A93ASP-1-0.782-0.90515.892-0.708-0.7080.0000.0000.0000.000
95A94LEU0-0.032-0.02518.0960.0470.0470.0000.0000.0000.000
96A95GLY0-0.053-0.01221.3700.0780.0780.0000.0000.0000.000
97A96ALA00.002-0.02824.151-0.024-0.0240.0000.0000.0000.000
98A97ASP-1-0.783-0.88623.629-0.544-0.5440.0000.0000.0000.000
99A98PHE00.0790.03420.8920.0040.0040.0000.0000.0000.000
100A99ARG10.7720.89523.9180.5260.5260.0000.0000.0000.000
101A100PHE0-0.003-0.00825.7910.0090.0090.0000.0000.0000.000
102A101ASP-1-0.781-0.87328.062-0.545-0.5450.0000.0000.0000.000
103A102ASP-1-0.836-0.91129.467-0.356-0.3560.0000.0000.0000.000
104A103PRO00.0120.00030.0710.0050.0050.0000.0000.0000.000
105A104GLY00.0220.00431.6360.0110.0110.0000.0000.0000.000
106A105VAL00.0310.02133.9000.0160.0160.0000.0000.0000.000
107A106TYR0-0.016-0.00628.4280.0190.0190.0000.0000.0000.000
108A107ARG10.9320.96832.5500.3120.3120.0000.0000.0000.000
109A108GLU-1-0.967-0.97034.819-0.249-0.2490.0000.0000.0000.000
110A109TRP00.013-0.00834.8710.0170.0170.0000.0000.0000.000
111A110TYR0-0.104-0.07730.8770.0040.0040.0000.0000.0000.000
112A111GLY0-0.0180.01634.0870.0000.0000.0000.0000.0000.000
113A112LYS10.8210.91428.1250.4460.4460.0000.0000.0000.000
114A113GLU-1-0.948-0.97632.893-0.337-0.3370.0000.0000.0000.000
115A114LEU0-0.0110.00327.276-0.008-0.0080.0000.0000.0000.000
116A115SER00.0460.02129.278-0.004-0.0040.0000.0000.0000.000
117A116GLY00.0370.01527.945-0.030-0.0300.0000.0000.0000.000
118A117TYR0-0.018-0.02925.735-0.055-0.0550.0000.0000.0000.000
119A118GLU-1-0.901-0.95326.066-0.482-0.4820.0000.0000.0000.000
120A119ASN0-0.057-0.03324.552-0.020-0.0200.0000.0000.0000.000
121A120ILE0-0.050-0.00320.607-0.070-0.0700.0000.0000.0000.000
122A121LYS10.9110.95517.9691.0811.0810.0000.0000.0000.000
123A122ARG10.7870.88919.4340.5320.5320.0000.0000.0000.000
124A123VAL00.0200.01819.2770.0480.0480.0000.0000.0000.000
125A124TYR0-0.022-0.03621.508-0.038-0.0380.0000.0000.0000.000
126A125GLY00.040-0.00320.614-0.009-0.0090.0000.0000.0000.000
127A126LEU00.0160.00721.2910.0040.0040.0000.0000.0000.000
128A127PRO00.0020.00419.6240.0260.0260.0000.0000.0000.000
129A128GLU-1-0.773-0.88821.668-0.563-0.5630.0000.0000.0000.000
130A129LEU0-0.031-0.00724.8970.0410.0410.0000.0000.0000.000
131A130HIS10.7980.87722.9970.5980.5980.0000.0000.0000.000
132A131ARG10.8050.85919.1880.5770.5770.0000.0000.0000.000
133A132GLU-1-0.918-0.96618.889-0.853-0.8530.0000.0000.0000.000
134A133GLU-1-0.935-0.96819.800-0.715-0.7150.0000.0000.0000.000
135A134ILE0-0.057-0.02916.060-0.076-0.0760.0000.0000.0000.000
136A135LYS10.9210.97514.8090.8350.8350.0000.0000.0000.000
137A136ASN0-0.030-0.00514.174-0.249-0.2490.0000.0000.0000.000
138A137ALA0-0.0090.01316.2740.0400.0400.0000.0000.0000.000
139A138GLN0-0.006-0.01312.172-0.330-0.3300.0000.0000.0000.000
140A139VAL00.0100.00714.588-0.141-0.1410.0000.0000.0000.000
141A140VAL00.0080.01016.4530.0970.0970.0000.0000.0000.000
142A141GLY00.0130.00618.395-0.011-0.0110.0000.0000.0000.000
143A142ASN0-0.045-0.03419.774-0.017-0.0170.0000.0000.0000.000
144A143PRO00.0020.02521.4900.0460.0460.0000.0000.0000.000
145A144GLY0-0.013-0.00124.939-0.002-0.0020.0000.0000.0000.000
146A145CYS0-0.020-0.00527.7130.0040.0040.0000.0000.0000.000
147A146TYR00.001-0.02628.9090.0120.0120.0000.0000.0000.000
148A147PRO00.0290.02329.4440.0150.0150.0000.0000.0000.000
149A148THR00.0340.03226.260-0.007-0.0070.0000.0000.0000.000
150A149SER0-0.0260.00728.8850.0180.0180.0000.0000.0000.000
151A150VAL00.0580.02631.8460.0160.0160.0000.0000.0000.000
152A151ILE00.0060.00429.7060.0140.0140.0000.0000.0000.000
153A152LEU00.0130.00727.1180.0080.0080.0000.0000.0000.000
154A153ALA0-0.0100.01231.3630.0150.0150.0000.0000.0000.000
155A154LEU00.0460.03234.8430.0180.0180.0000.0000.0000.000
156A155ALA00.0040.02731.9820.0080.0080.0000.0000.0000.000
157A156PRO0-0.0020.00433.6660.0030.0030.0000.0000.0000.000
158A157ALA00.0450.01535.6300.0090.0090.0000.0000.0000.000
159A158LEU0-0.045-0.01836.4300.0090.0090.0000.0000.0000.000
160A159LYS10.9400.98132.4970.3110.3110.0000.0000.0000.000
161A160HIS0-0.035-0.02736.333-0.006-0.0060.0000.0000.0000.000
162A161ASN0-0.026-0.00839.5110.0070.0070.0000.0000.0000.000
163A162LEU00.0360.02540.5210.0100.0100.0000.0000.0000.000
164A163VAL0-0.042-0.01741.9270.0080.0080.0000.0000.0000.000
165A164ASP-1-0.876-0.93344.510-0.181-0.1810.0000.0000.0000.000
166A165PRO0-0.036-0.03841.481-0.002-0.0020.0000.0000.0000.000
167A166GLU-1-0.937-0.95143.168-0.184-0.1840.0000.0000.0000.000
168A167THR0-0.026-0.02445.126-0.003-0.0030.0000.0000.0000.000
169A168ILE0-0.0200.01040.2060.0030.0030.0000.0000.0000.000
170A169LEU00.0150.00243.343-0.004-0.0040.0000.0000.0000.000
171A170VAL0-0.012-0.01438.054-0.002-0.0020.0000.0000.0000.000
172A171ASP-1-0.842-0.92141.470-0.171-0.1710.0000.0000.0000.000
173A172ALA00.0200.00237.3630.0000.0000.0000.0000.0000.000
174A173LYS10.8170.90638.4990.1830.1830.0000.0000.0000.000
175A174SER00.019-0.00934.355-0.016-0.0160.0000.0000.0000.000
176A175GLY00.0120.02135.1790.0120.0120.0000.0000.0000.000
177A176VAL00.0570.01434.945-0.019-0.0190.0000.0000.0000.000
178A177SER0-0.035-0.03530.120-0.019-0.0190.0000.0000.0000.000
179A178GLY00.0080.00330.737-0.026-0.0260.0000.0000.0000.000
180A179ALA0-0.041-0.01332.012-0.014-0.0140.0000.0000.0000.000
181A180GLY0-0.013-0.00630.007-0.009-0.0090.0000.0000.0000.000
182A181ARG10.7710.84427.4820.2980.2980.0000.0000.0000.000
183A182LYS10.9030.96531.1480.2550.2550.0000.0000.0000.000
184A183GLU-1-0.747-0.84533.261-0.223-0.2230.0000.0000.0000.000
185A184LYS10.9290.96436.6180.1870.1870.0000.0000.0000.000
186A185VAL00.0830.01540.181-0.003-0.0030.0000.0000.0000.000
187A186ASP-1-0.857-0.91742.146-0.146-0.1460.0000.0000.0000.000
188A187TYR0-0.067-0.05837.725-0.006-0.0060.0000.0000.0000.000
189A188LEU00.0150.03539.217-0.001-0.0010.0000.0000.0000.000
190A189PHE00.0240.00340.365-0.001-0.0010.0000.0000.0000.000
191A190SER0-0.016-0.03542.1230.0010.0010.0000.0000.0000.000
192A191GLU-1-0.957-0.95044.245-0.109-0.1090.0000.0000.0000.000
193A192VAL0-0.058-0.02240.375-0.002-0.0020.0000.0000.0000.000
194A193ASN0-0.021-0.02043.552-0.004-0.0040.0000.0000.0000.000
195A194GLU-1-0.941-0.97044.490-0.086-0.0860.0000.0000.0000.000
196A195SER00.0160.02245.6170.0020.0020.0000.0000.0000.000
197A196LEU0-0.023-0.01343.700-0.008-0.0080.0000.0000.0000.000
198A197ARG10.9310.97141.1620.1640.1640.0000.0000.0000.000
199A198PRO00.0150.00343.568-0.010-0.0100.0000.0000.0000.000
200A199TYR0-0.018-0.00236.1740.0010.0010.0000.0000.0000.000
201A200ASN0-0.024-0.02238.2900.0020.0020.0000.0000.0000.000
202A201VAL00.0420.01441.694-0.009-0.0090.0000.0000.0000.000
203A202ALA00.0190.02643.3170.0020.0020.0000.0000.0000.000
204A203LYS10.8870.96540.9100.2300.2300.0000.0000.0000.000
205A204HIS00.0440.01133.951-0.003-0.0030.0000.0000.0000.000
206A205ARG10.9650.97632.0920.3350.3350.0000.0000.0000.000
207A206HIS00.006-0.01630.329-0.006-0.0060.0000.0000.0000.000
208A207VAL00.0410.04233.940-0.011-0.0110.0000.0000.0000.000
209A208PRO00.0440.02634.758-0.005-0.0050.0000.0000.0000.000
210A209GLU-1-0.751-0.85128.412-0.483-0.4830.0000.0000.0000.000
211A210MET0-0.018-0.01032.199-0.006-0.0060.0000.0000.0000.000
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