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: K31V3

Calculation Name: 1WNH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WNH

Chain ID: A

ChEMBL ID:

UniProt ID: P70202

Base Structure: X-ray

Registration Date: 2023-06-21

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2743930.833933
FMO2-HF: Nuclear repulsion 2654404.236501
FMO2-HF: Total energy -89526.597431
FMO2-MP2: Total energy -89785.554645


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:-2:ALA)


Summations of interaction energy for fragment #1(A:-2:ALA)
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.
-10.206-5.0240.672-3.032-2.821-0.02
Interaction energy analysis for fragmet #1(A:-2:ALA)
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 : 0.024
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].
3A0THR00.0240.0142.946-1.4400.8580.059-1.143-1.2140.004
4A1MET0-0.034-0.0165.4510.6310.6310.0000.0000.0000.000
5A2GLU-1-0.847-0.9279.191-0.909-0.9090.0000.0000.0000.000
6A3ILE0-0.059-0.02911.1800.0770.0770.0000.0000.0000.000
7A4PRO0-0.006-0.01314.1290.0350.0350.0000.0000.0000.000
8A5PRO00.0760.03916.570-0.008-0.0080.0000.0000.0000.000
9A6THR0-0.002-0.00317.6340.0100.0100.0000.0000.0000.000
10A7HIS00.0150.02417.4670.0200.0200.0000.0000.0000.000
11A8TYR00.0480.00019.264-0.004-0.0040.0000.0000.0000.000
12A9ALA00.0070.00215.9630.0200.0200.0000.0000.0000.000
13A10ALA00.0360.02415.525-0.010-0.0100.0000.0000.0000.000
14A11SER0-0.041-0.01416.4590.0410.0410.0000.0000.0000.000
15A12ARG10.8960.94219.2870.2690.2690.0000.0000.0000.000
16A13ALA00.0350.03014.7020.0270.0270.0000.0000.0000.000
17A14ALA00.0540.01316.8170.0340.0340.0000.0000.0000.000
18A15SER0-0.034-0.00918.0770.0380.0380.0000.0000.0000.000
19A16VAL0-0.0210.00218.0490.0280.0280.0000.0000.0000.000
20A17ALA00.0240.00016.5550.0290.0290.0000.0000.0000.000
21A18GLU-1-0.863-0.92918.554-0.073-0.0730.0000.0000.0000.000
22A19ASN0-0.027-0.01022.0170.0250.0250.0000.0000.0000.000
23A20CYS0-0.049-0.01620.0100.0220.0220.0000.0000.0000.000
24A21ILE00.0380.02519.4760.0180.0180.0000.0000.0000.000
25A22ASN00.017-0.00422.7780.0210.0210.0000.0000.0000.000
26A23TYR0-0.037-0.00525.3110.0080.0080.0000.0000.0000.000
27A24GLN0-0.035-0.02821.0110.0140.0140.0000.0000.0000.000
28A25GLN0-0.032-0.01724.5140.0070.0070.0000.0000.0000.000
29A26GLY0-0.0020.00927.247-0.001-0.0010.0000.0000.0000.000
30A27THR0-0.047-0.04129.8670.0040.0040.0000.0000.0000.000
31A28PRO0-0.034-0.01933.569-0.005-0.0050.0000.0000.0000.000
32A29HIS10.8370.90236.1590.0030.0030.0000.0000.0000.000
33A30LYS10.9240.98628.905-0.012-0.0120.0000.0000.0000.000
34A31LEU0-0.021-0.01130.0580.0000.0000.0000.0000.0000.000
35A32PHE0-0.010-0.00925.5950.0020.0020.0000.0000.0000.000
36A33LEU0-0.0260.00726.566-0.004-0.0040.0000.0000.0000.000
37A34VAL0-0.009-0.01621.4170.0030.0030.0000.0000.0000.000
38A35GLN0-0.037-0.00323.882-0.002-0.0020.0000.0000.0000.000
39A36THR0-0.031-0.03521.874-0.004-0.0040.0000.0000.0000.000
40A37VAL00.0060.00816.8920.0060.0060.0000.0000.0000.000
41A38GLN0-0.080-0.06017.403-0.008-0.0080.0000.0000.0000.000
42A39GLN0-0.039-0.0359.4270.1090.1090.0000.0000.0000.000
43A40ALA00.0070.00212.1130.0440.0440.0000.0000.0000.000
44A41SER00.0090.0246.8450.0320.0320.0000.0000.0000.000
45A42LYS10.9470.9829.0410.8650.8650.0000.0000.0000.000
46A43GLU-1-0.893-0.9642.633-9.263-6.3790.613-1.889-1.607-0.024
47A44ASP-1-0.943-0.9546.352-0.367-0.3670.0000.0000.0000.000
48A45ILE00.0190.0095.376-0.197-0.1970.0000.0000.0000.000
49A46PRO00.0490.0107.1610.2400.2400.0000.0000.0000.000
50A47GLY0-0.031-0.01710.2650.0970.0970.0000.0000.0000.000
51A48ARG10.8200.90910.0970.0380.0380.0000.0000.0000.000
52A49GLY00.0290.01911.2650.0600.0600.0000.0000.0000.000
53A50HIS0-0.101-0.0469.813-0.168-0.1680.0000.0000.0000.000
54A51LYS10.9160.9585.651-0.162-0.1620.0000.0000.0000.000
55A52TYR0-0.066-0.0548.322-0.350-0.3500.0000.0000.0000.000
56A53HIS0-0.060-0.0217.0010.2010.2010.0000.0000.0000.000
57A54LEU00.005-0.0099.088-0.041-0.0410.0000.0000.0000.000
58A55LYS10.9490.98912.1110.1810.1810.0000.0000.0000.000
59A56PHE00.0340.00714.980-0.032-0.0320.0000.0000.0000.000
60A57SER00.0570.05618.5890.0180.0180.0000.0000.0000.000
61A58VAL0-0.030-0.01221.895-0.013-0.0130.0000.0000.0000.000
62A59GLU-1-0.919-0.96724.271-0.054-0.0540.0000.0000.0000.000
63A60GLU-1-0.753-0.87427.991-0.024-0.0240.0000.0000.0000.000
64A61ILE00.000-0.02430.1840.0010.0010.0000.0000.0000.000
65A62ILE0-0.109-0.03132.8630.0000.0000.0000.0000.0000.000
66A63GLN0-0.021-0.03334.976-0.001-0.0010.0000.0000.0000.000
67A64LYS10.8720.94434.1020.0290.0290.0000.0000.0000.000
68A65GLN0-0.058-0.02734.3340.0010.0010.0000.0000.0000.000
69A66VAL00.0010.01928.2660.0010.0010.0000.0000.0000.000
70A67THR0-0.013-0.01126.280-0.007-0.0070.0000.0000.0000.000
71A68VAL0-0.0090.00123.4990.0060.0060.0000.0000.0000.000
72A69ASN00.0200.00619.547-0.030-0.0300.0000.0000.0000.000
73A70CYS0-0.0300.00118.2460.0340.0340.0000.0000.0000.000
74A71THR0-0.024-0.00512.032-0.038-0.0380.0000.0000.0000.000
75A72ALA0-0.016-0.01713.1110.0600.0600.0000.0000.0000.000
76A73GLU-1-0.866-0.9367.2320.2430.2430.0000.0000.0000.000
77A74VAL0-0.0020.00011.0270.0940.0940.0000.0000.0000.000
78A75LEU0-0.044-0.0129.532-0.146-0.1460.0000.0000.0000.000
79A76TYR00.0360.01712.0230.0870.0870.0000.0000.0000.000
80A77PRO00.0090.00613.681-0.059-0.0590.0000.0000.0000.000
81A78GLN00.0190.00815.621-0.001-0.0010.0000.0000.0000.000
82A79MET00.0180.01016.7640.0390.0390.0000.0000.0000.000
83A80GLY0-0.004-0.00419.6950.0080.0080.0000.0000.0000.000
84A81GLN0-0.029-0.00219.1340.0270.0270.0000.0000.0000.000
85A82GLY0-0.032-0.01721.718-0.009-0.0090.0000.0000.0000.000
86A83SER0-0.057-0.02319.1990.0110.0110.0000.0000.0000.000
87A84ALA00.0550.03320.225-0.019-0.0190.0000.0000.0000.000
88A85PRO0-0.015-0.00916.4580.0050.0050.0000.0000.0000.000
89A86GLU-1-0.895-0.93013.7810.1010.1010.0000.0000.0000.000
90A87VAL0-0.014-0.01914.298-0.051-0.0510.0000.0000.0000.000
91A88ASN0-0.0230.00112.2210.0430.0430.0000.0000.0000.000
92A89PHE0-0.004-0.01914.270-0.049-0.0490.0000.0000.0000.000
93A90THR0-0.0130.00415.2180.0220.0220.0000.0000.0000.000
94A91PHE00.0460.00017.505-0.032-0.0320.0000.0000.0000.000
95A92GLU-1-0.924-0.96119.4120.0190.0190.0000.0000.0000.000
96A93GLY00.0090.00120.4110.0130.0130.0000.0000.0000.000
97A94GLU-1-0.938-0.97424.1340.0690.0690.0000.0000.0000.000
98A95ILE0-0.018-0.00125.095-0.009-0.0090.0000.0000.0000.000
99A96GLY00.0300.00928.078-0.007-0.0070.0000.0000.0000.000
100A97LYS10.9000.94131.711-0.019-0.0190.0000.0000.0000.000
101A98ASN00.0710.04031.759-0.007-0.0070.0000.0000.0000.000
102A99PRO00.0260.03534.4780.0010.0010.0000.0000.0000.000
103A100ASP-1-0.846-0.94537.2580.0220.0220.0000.0000.0000.000
104A101GLU-1-0.982-0.98239.3290.0090.0090.0000.0000.0000.000
105A102GLU-1-0.885-0.95540.090-0.007-0.0070.0000.0000.0000.000
106A103ASP-1-0.778-0.89136.8050.0010.0010.0000.0000.0000.000
107A104ASN00.011-0.00740.4410.0000.0000.0000.0000.0000.000
108A105THR0-0.039-0.00943.269-0.001-0.0010.0000.0000.0000.000
109A106PHE0-0.036-0.03040.202-0.001-0.0010.0000.0000.0000.000
110A107TYR0-0.017-0.04942.367-0.001-0.0010.0000.0000.0000.000
111A108GLN00.0240.00044.099-0.001-0.0010.0000.0000.0000.000
112A109SER0-0.065-0.02347.164-0.001-0.0010.0000.0000.0000.000
113A110LEU0-0.011-0.01943.342-0.001-0.0010.0000.0000.0000.000
114A111MET0-0.0060.00646.5400.0000.0000.0000.0000.0000.000
115A112SER0-0.038-0.01448.9710.0000.0000.0000.0000.0000.000
116A113LEU0-0.083-0.01949.037-0.001-0.0010.0000.0000.0000.000
117A114LYS10.9260.96652.4810.0030.0030.0000.0000.0000.000
118A115ARG10.9260.95654.6180.0080.0080.0000.0000.0000.000
119A116PRO00.0770.03149.9660.0000.0000.0000.0000.0000.000
120A117LEU00.0040.01945.390-0.001-0.0010.0000.0000.0000.000
121A118GLU-1-0.947-0.97948.046-0.013-0.0130.0000.0000.0000.000
122A119ALA0-0.061-0.03046.1220.0000.0000.0000.0000.0000.000
123A120GLN00.016-0.01145.4740.0000.0000.0000.0000.0000.000
124A121ASP-1-0.907-0.93644.074-0.034-0.0340.0000.0000.0000.000
125A122ILE0-0.0060.03741.1000.0010.0010.0000.0000.0000.000
126A123PRO00.028-0.03039.033-0.001-0.0010.0000.0000.0000.000
127A124ASP-1-0.776-0.87942.218-0.037-0.0370.0000.0000.0000.000
128A125ASN0-0.049-0.04043.853-0.004-0.0040.0000.0000.0000.000
129A126PHE0-0.057-0.03344.600-0.002-0.0020.0000.0000.0000.000
130A127GLY00.0220.02642.080-0.001-0.0010.0000.0000.0000.000
131A128ASN0-0.083-0.03642.7030.0010.0010.0000.0000.0000.000
132A129VAL00.010-0.00141.1550.0000.0000.0000.0000.0000.000
133A130SER00.0000.01444.5550.0000.0000.0000.0000.0000.000
134A131PRO00.0520.00445.3370.0000.0000.0000.0000.0000.000
135A132GLN00.023-0.00645.160-0.001-0.0010.0000.0000.0000.000
136A133MET00.0370.02743.9620.0020.0020.0000.0000.0000.000
137A134LYS10.8730.96339.2870.0320.0320.0000.0000.0000.000
138A135PRO00.0340.02139.424-0.002-0.0020.0000.0000.0000.000
139A136VAL00.0320.02739.0150.0010.0010.0000.0000.0000.000
140A137GLN00.0420.02337.2190.0010.0010.0000.0000.0000.000
141A138HIS0-0.008-0.02035.351-0.002-0.0020.0000.0000.0000.000
142A139LEU00.0530.03834.229-0.001-0.0010.0000.0000.0000.000
143A140ALA00.0100.00934.4550.0000.0000.0000.0000.0000.000
144A141TRP00.020-0.01431.1530.0000.0000.0000.0000.0000.000
145A142VAL00.0050.01529.955-0.004-0.0040.0000.0000.0000.000
146A143ALA0-0.011-0.00929.4840.0000.0000.0000.0000.0000.000
147A144CYS0-0.061-0.03930.095-0.003-0.0030.0000.0000.0000.000
148A145GLY00.0770.05526.800-0.008-0.0080.0000.0000.0000.000
149A146TYR0-0.023-0.01625.478-0.009-0.0090.0000.0000.0000.000
150A147VAL0-0.007-0.00625.956-0.005-0.0050.0000.0000.0000.000
151A148MET00.005-0.00225.893-0.009-0.0090.0000.0000.0000.000
152A149TRP0-0.028-0.00819.074-0.004-0.0040.0000.0000.0000.000
153A150GLN0-0.048-0.03221.897-0.012-0.0120.0000.0000.0000.000
154A151ASN0-0.031-0.03023.413-0.002-0.0020.0000.0000.0000.000
155A152SER0-0.021-0.01321.004-0.010-0.0100.0000.0000.0000.000
156A153THR00.0240.01219.641-0.006-0.0060.0000.0000.0000.000
157A154GLU-1-0.805-0.89814.925-0.495-0.4950.0000.0000.0000.000
158A155ASP-1-0.931-0.96518.988-0.243-0.2430.0000.0000.0000.000
159A156THR0-0.057-0.00522.3300.0210.0210.0000.0000.0000.000
160A157TRP0-0.003-0.03222.692-0.027-0.0270.0000.0000.0000.000
161A158TYR0-0.050-0.01624.7820.0120.0120.0000.0000.0000.000
162A159LYS11.0051.01226.5880.1150.1150.0000.0000.0000.000
163A160MET00.0240.02629.3570.0020.0020.0000.0000.0000.000
164A161LEU0-0.036-0.00932.1770.0000.0000.0000.0000.0000.000
165A162LYS10.8310.89835.3730.0450.0450.0000.0000.0000.000
166A163ILE00.0060.01237.9240.0000.0000.0000.0000.0000.000
167A164GLN00.000-0.01139.9210.0000.0000.0000.0000.0000.000
168A165THR0-0.022-0.03242.3170.0030.0030.0000.0000.0000.000
169A166VAL00.0100.00842.045-0.001-0.0010.0000.0000.0000.000
170A167LYS10.9680.98443.7160.0180.0180.0000.0000.0000.000
171A168GLN00.0200.00144.9570.0000.0000.0000.0000.0000.000
172A169VAL0-0.020-0.01344.5310.0000.0000.0000.0000.0000.000
173A170GLN0-0.061-0.04446.8600.0020.0020.0000.0000.0000.000
174A171ARG10.8150.90540.790-0.010-0.0100.0000.0000.0000.000
175A172ASN00.0140.00547.500-0.001-0.0010.0000.0000.0000.000
176A173ASP-1-0.870-0.92844.0370.0170.0170.0000.0000.0000.000
177A174ASP-1-0.845-0.91644.3880.0180.0180.0000.0000.0000.000
178A175PHE0-0.087-0.02537.4980.0000.0000.0000.0000.0000.000
179A176ILE00.0240.02441.315-0.002-0.0020.0000.0000.0000.000
180A177GLU-1-0.851-0.91140.7230.0030.0030.0000.0000.0000.000
181A178LEU0-0.045-0.02140.072-0.001-0.0010.0000.0000.0000.000
182A179ASP-1-0.876-0.91339.918-0.017-0.0170.0000.0000.0000.000
183A180TYR00.013-0.02237.866-0.001-0.0010.0000.0000.0000.000
184A181THR0-0.0020.00939.128-0.001-0.0010.0000.0000.0000.000
185A182ILE0-0.031-0.03033.5460.0010.0010.0000.0000.0000.000
186A183LEU0-0.042-0.01236.668-0.001-0.0010.0000.0000.0000.000
187A184LEU00.0220.01229.8100.0000.0000.0000.0000.0000.000
188A185HIS0-0.038-0.04731.8840.0030.0030.0000.0000.0000.000
189A186ASP-1-0.745-0.88927.638-0.148-0.1480.0000.0000.0000.000
190A187ILE0-0.032-0.03126.9780.0020.0020.0000.0000.0000.000
191A188ALA0-0.072-0.02025.412-0.006-0.0060.0000.0000.0000.000
192A189SER0-0.013-0.00727.426-0.003-0.0030.0000.0000.0000.000
193A190GLN0-0.0300.00830.2070.0140.0140.0000.0000.0000.000
194A191GLU-1-0.912-0.94831.909-0.099-0.0990.0000.0000.0000.000
195A192ILE00.010-0.00833.3540.0000.0000.0000.0000.0000.000
196A193ILE0-0.070-0.03631.2480.0020.0020.0000.0000.0000.000
197A194PRO0-0.008-0.00534.6840.0010.0010.0000.0000.0000.000
198A195TRP00.005-0.01529.911-0.004-0.0040.0000.0000.0000.000
199A196GLN0-0.028-0.02835.9090.0020.0020.0000.0000.0000.000
200A197MET0-0.037-0.01233.836-0.001-0.0010.0000.0000.0000.000
201A198GLN00.0090.04236.118-0.001-0.0010.0000.0000.0000.000
202A199VAL0-0.007-0.02235.0540.0020.0020.0000.0000.0000.000
203A200LEU0-0.017-0.00936.1220.0010.0010.0000.0000.0000.000
204A201TRP00.018-0.01035.350-0.001-0.0010.0000.0000.0000.000
205A202HIS00.0700.03237.1470.0010.0010.0000.0000.0000.000
206A203PRO0-0.0030.00437.0300.0020.0020.0000.0000.0000.000
207A204GLN0-0.0200.00536.7630.0030.0030.0000.0000.0000.000
208A205TYR0-0.048-0.03534.0120.0030.0030.0000.0000.0000.000
209A206GLY00.0580.04932.6430.0020.0020.0000.0000.0000.000
210A207THR0-0.002-0.02231.540-0.002-0.0020.0000.0000.0000.000
211A208LYS10.9550.98431.333-0.020-0.0200.0000.0000.0000.000
212A209VAL00.0130.01430.736-0.002-0.0020.0000.0000.0000.000
213A210LYS10.8460.94032.194-0.006-0.0060.0000.0000.0000.000
214A211HIS00.007-0.01234.2670.0040.0040.0000.0000.0000.000
215A212ASN00.0340.01230.461-0.007-0.0070.0000.0000.0000.000
216A213SER0-0.0250.00733.4540.0000.0000.0000.0000.0000.000
217A214ARG11.0271.02731.0210.0750.0750.0000.0000.0000.000
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