FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: QVK9Y

Calculation Name: 2H56-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H56

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KC25

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 218
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2496526.924708
FMO2-HF: Nuclear repulsion 2411310.529064
FMO2-HF: Total energy -85216.395644
FMO2-MP2: Total energy -85466.691124


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.
-12.469-8.0586.168-4.409-6.17-0.033
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 : 0.000 / q_NPA : -0.013
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].
3A2ARG10.9530.9923.3651.5434.3460.326-1.163-1.966-0.001
4A3TYR00.0360.0035.1890.4380.623-0.001-0.014-0.1690.000
5A4PHE0-0.032-0.0107.936-0.551-0.5510.0000.0000.0000.000
6A5SER00.0290.00411.0620.2420.2420.0000.0000.0000.000
7A6THR00.0360.01113.547-0.064-0.0640.0000.0000.0000.000
8A7ASP-1-0.925-0.95515.798-0.633-0.6330.0000.0000.0000.000
9A8SER0-0.014-0.00312.427-0.135-0.1350.0000.0000.0000.000
10A9PRO00.0160.00212.7020.1280.1280.0000.0000.0000.000
11A10GLU-1-0.839-0.93710.577-1.745-1.7450.0000.0000.0000.000
12A11VAL00.0250.01714.6450.1000.1000.0000.0000.0000.000
13A12LYS10.9460.95916.7810.6080.6080.0000.0000.0000.000
14A13THR0-0.018-0.00618.0240.0720.0720.0000.0000.0000.000
15A14ILE0-0.062-0.01017.6530.0650.0650.0000.0000.0000.000
16A15VAL0-0.021-0.00520.3680.0600.0600.0000.0000.0000.000
17A16ALA0-0.0210.00622.7180.0450.0450.0000.0000.0000.000
18A17GLN0-0.053-0.03424.7120.0200.0200.0000.0000.0000.000
19A18ASP-1-0.768-0.85825.178-0.275-0.2750.0000.0000.0000.000
20A19SER00.0450.00326.191-0.004-0.0040.0000.0000.0000.000
21A20ARG10.8590.95228.2880.1650.1650.0000.0000.0000.000
22A21LEU00.0070.00621.3100.0180.0180.0000.0000.0000.000
23A22PHE00.0270.00823.6690.0010.0010.0000.0000.0000.000
24A23GLN0-0.028-0.02424.6300.0020.0020.0000.0000.0000.000
25A24PHE0-0.0270.00121.8540.0170.0170.0000.0000.0000.000
26A25ILE00.003-0.00619.0360.0200.0200.0000.0000.0000.000
27A26GLU-1-0.944-0.96720.946-0.274-0.2740.0000.0000.0000.000
28A27ILE0-0.064-0.02422.9220.0260.0260.0000.0000.0000.000
29A28ALA0-0.075-0.03520.4100.0310.0310.0000.0000.0000.000
30A29GLY00.0320.02218.3490.0430.0430.0000.0000.0000.000
31A30GLU-1-0.946-0.96412.114-0.133-0.1330.0000.0000.0000.000
32A31VAL0-0.047-0.01812.8580.1400.1400.0000.0000.0000.000
33A32GLN0-0.012-0.0239.295-0.143-0.1430.0000.0000.0000.000
34A33LEU0-0.014-0.0047.6410.0510.0510.0000.0000.0000.000
35A34PRO0-0.024-0.0235.249-0.134-0.1340.0000.0000.0000.000
36A35THR0-0.0080.0032.440-1.1600.3090.455-0.582-1.343-0.002
37A36LYS10.9390.9692.000-6.847-7.4985.282-2.502-2.129-0.031
38A37PRO00.0320.0212.966-1.077-0.4890.107-0.144-0.5520.001
39A38ASN00.0300.0114.856-0.194-0.177-0.001-0.004-0.0110.000
40A39PRO00.0940.0558.6110.1470.1470.0000.0000.0000.000
41A40PHE00.0680.01910.8780.0750.0750.0000.0000.0000.000
42A41GLN0-0.013-0.0189.4590.0240.0240.0000.0000.0000.000
43A42SER00.0130.0018.9210.0660.0660.0000.0000.0000.000
44A43LEU00.0250.03111.1960.0420.0420.0000.0000.0000.000
45A44VAL0-0.0230.00214.7190.0350.0350.0000.0000.0000.000
46A45SER0-0.014-0.01612.5680.0660.0660.0000.0000.0000.000
47A46SER0-0.010-0.01313.397-0.005-0.0050.0000.0000.0000.000
48A47ILE0-0.054-0.02415.5200.0060.0060.0000.0000.0000.000
49A48VAL0-0.060-0.03717.6420.0060.0060.0000.0000.0000.000
50A49GLU-1-0.872-0.94413.8220.2730.2730.0000.0000.0000.000
51A50GLN0-0.0190.00718.6020.0120.0120.0000.0000.0000.000
52A51GLN0-0.048-0.04021.4190.0240.0240.0000.0000.0000.000
53A52LEU0-0.0320.00021.5410.0080.0080.0000.0000.0000.000
54A53SER00.0300.01421.1340.0130.0130.0000.0000.0000.000
55A54ILE00.1190.04514.287-0.005-0.0050.0000.0000.0000.000
56A55LYS10.9530.97218.224-0.295-0.2950.0000.0000.0000.000
57A56ALA0-0.010-0.00520.6880.0160.0160.0000.0000.0000.000
58A57ALA00.0390.01818.1630.0020.0020.0000.0000.0000.000
59A58SER00.0110.01816.8520.0160.0160.0000.0000.0000.000
60A59ALA0-0.0010.00217.9960.0190.0190.0000.0000.0000.000
61A60ILE0-0.057-0.02621.279-0.002-0.0020.0000.0000.0000.000
62A61TYR00.0210.01813.567-0.080-0.0800.0000.0000.0000.000
63A62GLY00.0320.02318.1180.0200.0200.0000.0000.0000.000
64A63ARG10.8790.93519.002-0.325-0.3250.0000.0000.0000.000
65A64VAL0-0.013-0.01119.253-0.029-0.0290.0000.0000.0000.000
66A65GLU-1-0.833-0.93214.0550.8390.8390.0000.0000.0000.000
67A66GLN0-0.041-0.02318.8090.0060.0060.0000.0000.0000.000
68A67LEU0-0.084-0.02622.015-0.024-0.0240.0000.0000.0000.000
69A68VAL0-0.033-0.02018.425-0.030-0.0300.0000.0000.0000.000
70A69GLY0-0.040-0.00121.073-0.005-0.0050.0000.0000.0000.000
71A70GLY0-0.023-0.01917.7570.0250.0250.0000.0000.0000.000
72A71ALA00.0120.01412.443-0.016-0.0160.0000.0000.0000.000
73A72LEU0-0.0210.00114.394-0.103-0.1030.0000.0000.0000.000
74A73GLU-1-0.951-0.98911.9870.5980.5980.0000.0000.0000.000
75A74LYS10.8740.92213.912-0.177-0.1770.0000.0000.0000.000
76A75PRO00.0530.02116.9350.0360.0360.0000.0000.0000.000
77A76GLU-1-0.725-0.84319.8490.1480.1480.0000.0000.0000.000
78A77GLN0-0.019-0.01117.2280.0120.0120.0000.0000.0000.000
79A78LEU00.0450.01019.8450.0120.0120.0000.0000.0000.000
80A79TYR0-0.0430.00623.111-0.009-0.0090.0000.0000.0000.000
81A80ARG10.8550.89322.928-0.177-0.1770.0000.0000.0000.000
82A81VAL00.0010.03323.9720.0080.0080.0000.0000.0000.000
83A82SER00.0370.02027.098-0.013-0.0130.0000.0000.0000.000
84A83ASP-1-0.772-0.90128.6120.0890.0890.0000.0000.0000.000
85A84GLU-1-0.910-0.93829.8890.1310.1310.0000.0000.0000.000
86A85ALA00.0080.00728.5160.0090.0090.0000.0000.0000.000
87A86LEU00.0560.01523.3650.0160.0160.0000.0000.0000.000
88A87ARG10.9150.95026.721-0.096-0.0960.0000.0000.0000.000
89A88GLN0-0.066-0.02529.3300.0160.0160.0000.0000.0000.000
90A89ALA0-0.0180.01324.6970.0120.0120.0000.0000.0000.000
91A90GLY00.004-0.00925.6410.0240.0240.0000.0000.0000.000
92A91VAL0-0.0210.00822.836-0.006-0.0060.0000.0000.0000.000
93A92SER00.001-0.01225.355-0.016-0.0160.0000.0000.0000.000
94A93LYS11.0610.99827.298-0.053-0.0530.0000.0000.0000.000
95A94ARG10.9550.98328.010-0.019-0.0190.0000.0000.0000.000
96A95LYS10.8570.93822.289-0.152-0.1520.0000.0000.0000.000
97A96ILE00.0200.02323.943-0.006-0.0060.0000.0000.0000.000
98A97GLU-1-0.885-0.94125.684-0.021-0.0210.0000.0000.0000.000
99A98TYR0-0.010-0.01122.875-0.010-0.0100.0000.0000.0000.000
100A99ILE00.0530.03020.043-0.018-0.0180.0000.0000.0000.000
101A100ARG10.8170.88522.115-0.096-0.0960.0000.0000.0000.000
102A101HIS00.0100.02724.595-0.013-0.0130.0000.0000.0000.000
103A102VAL00.0410.01717.889-0.021-0.0210.0000.0000.0000.000
104A103CYS0-0.078-0.03321.040-0.011-0.0110.0000.0000.0000.000
105A104GLU-1-0.906-0.94622.090-0.089-0.0890.0000.0000.0000.000
106A105HIS0-0.013-0.02322.245-0.030-0.0300.0000.0000.0000.000
107A106VAL0-0.0050.00417.717-0.022-0.0220.0000.0000.0000.000
108A107GLU-1-0.970-1.00220.720-0.013-0.0130.0000.0000.0000.000
109A108SER0-0.093-0.02723.305-0.004-0.0040.0000.0000.0000.000
110A109GLY00.0200.00322.774-0.002-0.0020.0000.0000.0000.000
111A110ARG10.8610.94423.3100.1170.1170.0000.0000.0000.000
112A111LEU0-0.031-0.01918.024-0.026-0.0260.0000.0000.0000.000
113A112ASP-1-0.802-0.90418.101-0.471-0.4710.0000.0000.0000.000
114A113PHE0-0.001-0.03612.993-0.026-0.0260.0000.0000.0000.000
115A114THR0-0.019-0.00313.753-0.145-0.1450.0000.0000.0000.000
116A115GLU-1-0.957-0.96314.815-0.514-0.5140.0000.0000.0000.000
117A116LEU0-0.057-0.04415.529-0.022-0.0220.0000.0000.0000.000
118A117GLU-1-0.892-0.93410.099-1.680-1.6800.0000.0000.0000.000
119A118GLY00.002-0.01113.3060.0130.0130.0000.0000.0000.000
120A119ALA0-0.062-0.00816.1390.0640.0640.0000.0000.0000.000
121A120GLU-1-0.830-0.93217.625-0.702-0.7020.0000.0000.0000.000
122A121ALA00.022-0.00318.1860.0260.0260.0000.0000.0000.000
123A122THR0-0.028-0.02619.1090.0400.0400.0000.0000.0000.000
124A123THR00.0120.02121.2380.0290.0290.0000.0000.0000.000
125A124VAL00.0260.02116.0150.0440.0440.0000.0000.0000.000
126A125ILE0-0.006-0.01219.3350.0480.0480.0000.0000.0000.000
127A126GLU-1-0.927-0.93920.933-0.287-0.2870.0000.0000.0000.000
128A127LYS10.9110.95720.5580.3830.3830.0000.0000.0000.000
129A128LEU00.002-0.00916.1810.0390.0390.0000.0000.0000.000
130A129THR0-0.076-0.06920.4700.0480.0480.0000.0000.0000.000
131A130ALA0-0.0240.01023.3690.0330.0330.0000.0000.0000.000
132A131ILE0-0.044-0.01120.1730.0310.0310.0000.0000.0000.000
133A132LYS10.9050.93924.0230.0490.0490.0000.0000.0000.000
134A133GLY0-0.045-0.03823.7730.0080.0080.0000.0000.0000.000
135A134ILE0-0.035-0.01218.5800.0130.0130.0000.0000.0000.000
136A135GLY00.0580.03521.888-0.006-0.0060.0000.0000.0000.000
137A136GLN0-0.011-0.02521.365-0.003-0.0030.0000.0000.0000.000
138A137TRP0-0.023-0.00618.455-0.026-0.0260.0000.0000.0000.000
139A138THR0-0.008-0.00517.670-0.019-0.0190.0000.0000.0000.000
140A139ALA00.0230.01216.733-0.033-0.0330.0000.0000.0000.000
141A140GLU-1-0.780-0.88816.411-0.428-0.4280.0000.0000.0000.000
142A141MET0-0.016-0.00814.626-0.111-0.1110.0000.0000.0000.000
143A142PHE0-0.046-0.01012.035-0.097-0.0970.0000.0000.0000.000
144A143MET00.0060.00311.593-0.114-0.1140.0000.0000.0000.000
145A144MET0-0.046-0.00211.183-0.179-0.1790.0000.0000.0000.000
146A145PHE0-0.024-0.0228.661-0.237-0.2370.0000.0000.0000.000
147A146SER0-0.100-0.0597.190-0.076-0.0760.0000.0000.0000.000
148A147LEU00.0250.0157.408-0.258-0.2580.0000.0000.0000.000
149A148GLY00.0080.0276.849-0.260-0.2600.0000.0000.0000.000
150A149ARG10.7910.9017.9010.9530.9530.0000.0000.0000.000
151A150LEU0-0.011-0.0259.3590.1340.1340.0000.0000.0000.000
152A151ASP-1-0.792-0.86812.590-0.875-0.8750.0000.0000.0000.000
153A152VAL0-0.0050.00914.8950.1070.1070.0000.0000.0000.000
154A153LEU00.0400.00217.3660.0180.0180.0000.0000.0000.000
155A154SER0-0.024-0.01419.4400.0530.0530.0000.0000.0000.000
156A155VAL00.022-0.01021.2120.0450.0450.0000.0000.0000.000
157A156GLY0-0.061-0.03824.0810.0280.0280.0000.0000.0000.000
158A157ASP-1-0.704-0.83920.120-0.126-0.1260.0000.0000.0000.000
159A158VAL00.012-0.00822.895-0.003-0.0030.0000.0000.0000.000
160A159GLY0-0.0010.01421.8240.0150.0150.0000.0000.0000.000
161A160LEU00.0250.00319.1350.0020.0020.0000.0000.0000.000
162A161GLN0-0.074-0.04722.8490.0170.0170.0000.0000.0000.000
163A162ARG10.8380.93125.6610.0080.0080.0000.0000.0000.000
164A163GLY00.0730.04024.6060.0090.0090.0000.0000.0000.000
165A164ALA00.0010.00025.645-0.005-0.0050.0000.0000.0000.000
166A165LYS10.9140.94027.6270.0790.0790.0000.0000.0000.000
167A166TRP0-0.0330.00427.318-0.008-0.0080.0000.0000.0000.000
168A167LEU00.0480.03224.9780.0050.0050.0000.0000.0000.000
169A168TYR0-0.140-0.11925.903-0.006-0.0060.0000.0000.0000.000
170A169GLY0-0.0220.00731.5110.0010.0010.0000.0000.0000.000
171A170ASN00.0330.01234.239-0.003-0.0030.0000.0000.0000.000
172A171GLY00.0820.04332.7740.0130.0130.0000.0000.0000.000
173A172GLU-1-0.960-0.96433.851-0.049-0.0490.0000.0000.0000.000
174A173GLY00.0260.00934.710-0.012-0.0120.0000.0000.0000.000
175A174ASP-1-0.886-0.95933.152-0.124-0.1240.0000.0000.0000.000
176A175GLY00.0880.03129.850-0.012-0.0120.0000.0000.0000.000
177A176LYS10.9871.00728.8420.1570.1570.0000.0000.0000.000
178A177LYS10.9140.95029.6200.1180.1180.0000.0000.0000.000
179A178LEU0-0.039-0.00630.437-0.015-0.0150.0000.0000.0000.000
180A179LEU00.0620.03123.445-0.015-0.0150.0000.0000.0000.000
181A180ILE0-0.026-0.00826.617-0.025-0.0250.0000.0000.0000.000
182A181TYR0-0.081-0.04428.407-0.019-0.0190.0000.0000.0000.000
183A182HIS10.9020.93227.4270.2210.2210.0000.0000.0000.000
184A183GLY00.0710.04624.215-0.015-0.0150.0000.0000.0000.000
185A184LYS10.8900.94423.9350.2340.2340.0000.0000.0000.000
186A185ALA0-0.022-0.00125.560-0.013-0.0130.0000.0000.0000.000
187A186TRP0-0.043-0.01120.306-0.010-0.0100.0000.0000.0000.000
188A187ALA00.0180.06619.896-0.068-0.0680.0000.0000.0000.000
189A188PRO0-0.036-0.02217.3140.0350.0350.0000.0000.0000.000
190A189TYR00.021-0.02813.574-0.159-0.1590.0000.0000.0000.000
191A190GLU-1-0.800-0.92316.482-0.644-0.6440.0000.0000.0000.000
192A191THR0-0.001-0.01912.4980.1210.1210.0000.0000.0000.000
193A192VAL00.0280.01012.3650.0630.0630.0000.0000.0000.000
194A193ALA00.0260.01614.9380.1020.1020.0000.0000.0000.000
195A194CYS0-0.065-0.03616.9480.0990.0990.0000.0000.0000.000
196A195LEU00.0010.01111.9530.0910.0910.0000.0000.0000.000
197A196TYR0-0.003-0.01516.2210.0720.0720.0000.0000.0000.000
198A197LEU0-0.043-0.01019.3990.0670.0670.0000.0000.0000.000
199A198TRP0-0.006-0.02815.1800.0440.0440.0000.0000.0000.000
200A199LYS10.9320.97216.4230.0210.0210.0000.0000.0000.000
201A200ALA0-0.013-0.00420.2740.0350.0350.0000.0000.0000.000
202A201ALA0-0.039-0.03322.5330.0220.0220.0000.0000.0000.000
203A202GLY00.0020.00822.1910.0180.0180.0000.0000.0000.000
204A203THR00.0770.02722.102-0.004-0.0040.0000.0000.0000.000
205A204PHE00.0130.00122.378-0.003-0.0030.0000.0000.0000.000
206A205ALA0-0.020-0.01426.424-0.003-0.0030.0000.0000.0000.000
207A206GLU-1-1.038-1.00925.3860.1140.1140.0000.0000.0000.000
208A207GLU-1-0.972-0.97828.6760.0730.0730.0000.0000.0000.000
209A208TYR0-0.018-0.00829.175-0.010-0.0100.0000.0000.0000.000
210A209ARG10.8070.89331.9590.0460.0460.0000.0000.0000.000
211A210SER0-0.022-0.03432.367-0.007-0.0070.0000.0000.0000.000
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