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: 5N9QZ

Calculation Name: 1O65-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O65

Chain ID: A

ChEMBL ID:

UniProt ID: P32157

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2775650.45286
FMO2-HF: Nuclear repulsion 2686815.938193
FMO2-HF: Total energy -88834.514666
FMO2-MP2: Total energy -89093.587315


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:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-82.289-77.0760.985-2.51-3.688-0.004
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.996 / q_NPA : 0.999
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].
3A5LEU00.0040.0052.435-1.6593.3640.986-2.496-3.512-0.004
4A6VAL00.0420.0044.8363.4273.617-0.001-0.014-0.1760.000
5A7GLU-1-0.844-0.9077.040-24.617-24.6170.0000.0000.0000.000
6A8ARG10.8880.9388.47026.34326.3430.0000.0000.0000.000
7A9GLU-1-0.945-0.9628.515-28.054-28.0540.0000.0000.0000.000
8A10GLN0-0.056-0.02111.2272.2872.2870.0000.0000.0000.000
9A11MET00.0200.01811.4930.5040.5040.0000.0000.0000.000
10A12ARG10.9250.95614.35916.26916.2690.0000.0000.0000.000
11A13TYR0-0.021-0.01214.278-0.605-0.6050.0000.0000.0000.000
12A14PRO00.0170.00820.2720.3300.3300.0000.0000.0000.000
13A15VAL0-0.042-0.01623.670-0.281-0.2810.0000.0000.0000.000
14A16ASP-1-0.792-0.85925.534-10.509-10.5090.0000.0000.0000.000
15A17VAL00.026-0.00228.078-0.275-0.2750.0000.0000.0000.000
16A18TYR0-0.024-0.02730.1790.2880.2880.0000.0000.0000.000
17A19THR0-0.033-0.02732.070-0.140-0.1400.0000.0000.0000.000
18A20GLY00.0440.01734.6760.1690.1690.0000.0000.0000.000
19A21LYS10.7160.83137.0887.7517.7510.0000.0000.0000.000
20A34ALA0-0.014-0.01637.600-0.041-0.0410.0000.0000.0000.000
21A35LYS10.7480.88631.5549.4449.4440.0000.0000.0000.000
22A36ILE00.006-0.01436.666-0.013-0.0130.0000.0000.0000.000
23A37GLN00.0010.00633.485-0.282-0.2820.0000.0000.0000.000
24A38VAL0-0.058-0.02133.7040.2820.2820.0000.0000.0000.000
25A39ASP-1-0.860-0.93933.979-8.764-8.7640.0000.0000.0000.000
26A40GLY00.0030.01535.083-0.078-0.0780.0000.0000.0000.000
27A41GLU-1-0.877-0.93233.326-9.003-9.0030.0000.0000.0000.000
28A42LEU0-0.033-0.02331.7610.3080.3080.0000.0000.0000.000
29A43MET0-0.036-0.00331.887-0.281-0.2810.0000.0000.0000.000
30A44LEU00.0110.01725.6750.0930.0930.0000.0000.0000.000
31A45THR00.006-0.01129.905-0.130-0.1300.0000.0000.0000.000
32A46GLU-1-0.913-0.97228.453-9.603-9.6030.0000.0000.0000.000
33A47LEU0-0.036-0.04328.438-0.208-0.2080.0000.0000.0000.000
34A48GLY00.0610.04329.451-0.007-0.0070.0000.0000.0000.000
35A49LEU0-0.028-0.00729.1280.0650.0650.0000.0000.0000.000
36A50GLU-1-0.878-0.94331.981-7.940-7.9400.0000.0000.0000.000
37A51GLY00.0360.02535.547-0.009-0.0090.0000.0000.0000.000
38A52ASP-1-0.706-0.83332.492-9.002-9.0020.0000.0000.0000.000
39A53GLU-1-0.906-0.91835.451-7.576-7.5760.0000.0000.0000.000
40A54GLN00.0080.01535.062-0.046-0.0460.0000.0000.0000.000
41A55ALA00.0160.00136.9520.0600.0600.0000.0000.0000.000
42A56GLU-1-0.701-0.80838.605-7.297-7.2970.0000.0000.0000.000
43A57LYS10.7820.86538.3297.2167.2160.0000.0000.0000.000
44A58LYS10.8400.88037.5167.4137.4130.0000.0000.0000.000
45A59VAL0-0.039-0.00232.754-0.065-0.0650.0000.0000.0000.000
46A60HIS00.0740.04232.505-0.228-0.2280.0000.0000.0000.000
47A61GLY00.0260.00128.829-0.118-0.1180.0000.0000.0000.000
48A62GLY0-0.024-0.00928.110-0.261-0.2610.0000.0000.0000.000
49A63PRO00.0820.04127.191-0.138-0.1380.0000.0000.0000.000
50A64ASP-1-0.849-0.91423.787-11.531-11.5310.0000.0000.0000.000
51A65ARG10.8570.92524.2189.0739.0730.0000.0000.0000.000
52A66ALA00.0280.04526.0810.2460.2460.0000.0000.0000.000
53A67LEU00.0090.01224.5060.2250.2250.0000.0000.0000.000
54A68CYS0-0.033-0.01124.528-0.521-0.5210.0000.0000.0000.000
55A69HIS00.0820.05621.4340.3360.3360.0000.0000.0000.000
56A70TYR0-0.028-0.02623.664-0.132-0.1320.0000.0000.0000.000
57A71PRO0-0.0220.00120.6730.1770.1770.0000.0000.0000.000
58A72ARG10.8450.88323.15512.08312.0830.0000.0000.0000.000
59A73GLU-1-0.844-0.92420.834-14.307-14.3070.0000.0000.0000.000
60A74HIS10.7030.81921.13913.71013.7100.0000.0000.0000.000
61A75TYR00.030-0.00926.0940.3500.3500.0000.0000.0000.000
62A76LEU0-0.0020.01626.6300.3330.3330.0000.0000.0000.000
63A77TYR0-0.133-0.10127.093-0.052-0.0520.0000.0000.0000.000
64A78TRP00.0480.00028.0360.2200.2200.0000.0000.0000.000
65A79ALA00.0420.02431.7410.2940.2940.0000.0000.0000.000
66A80ARG10.8960.94728.26110.97210.9720.0000.0000.0000.000
67A81GLU-1-0.892-0.91831.440-9.866-9.8660.0000.0000.0000.000
68A82PHE0-0.044-0.02534.1050.1820.1820.0000.0000.0000.000
69A83PRO00.0070.00837.4150.0390.0390.0000.0000.0000.000
70A84GLU-1-0.932-0.97939.099-7.439-7.4390.0000.0000.0000.000
71A85GLN0-0.036-0.00239.0250.1530.1530.0000.0000.0000.000
72A86ALA0-0.001-0.00637.117-0.195-0.1950.0000.0000.0000.000
73A87GLU-1-0.911-0.96636.984-7.865-7.8650.0000.0000.0000.000
74A88LEU0-0.0120.00037.887-0.055-0.0550.0000.0000.0000.000
75A89PHE0-0.066-0.03432.713-0.280-0.2800.0000.0000.0000.000
76A90VAL00.0030.00532.924-0.252-0.2520.0000.0000.0000.000
77A91ALA0-0.0050.03329.9690.0450.0450.0000.0000.0000.000
78A92PRO0-0.029-0.00631.4160.2150.2150.0000.0000.0000.000
79A93ALA00.0350.01132.4380.0730.0730.0000.0000.0000.000
80A94PHE0-0.003-0.01029.4260.1360.1360.0000.0000.0000.000
81A95GLY0-0.009-0.01230.678-0.134-0.1340.0000.0000.0000.000
82A96GLU-1-0.828-0.90727.107-10.454-10.4540.0000.0000.0000.000
83A97ASN0-0.036-0.04127.5320.1380.1380.0000.0000.0000.000
84A98LEU0-0.0030.00823.4470.1150.1150.0000.0000.0000.000
85A99SER00.0210.01025.399-0.221-0.2210.0000.0000.0000.000
86A100THR00.0560.02521.324-0.047-0.0470.0000.0000.0000.000
87A101ASP-1-0.830-0.88222.431-12.317-12.3170.0000.0000.0000.000
88A102GLY0-0.001-0.01118.604-0.289-0.2890.0000.0000.0000.000
89A103LEU0-0.0260.00015.260-1.360-1.3600.0000.0000.0000.000
90A104THR00.012-0.01616.0000.8180.8180.0000.0000.0000.000
91A105GLU-1-0.696-0.84815.606-15.406-15.4060.0000.0000.0000.000
92A106SER00.0040.00013.781-0.127-0.1270.0000.0000.0000.000
93A107ASN0-0.062-0.02311.011-1.129-1.1290.0000.0000.0000.000
94A108VAL00.0380.04111.548-1.081-1.0810.0000.0000.0000.000
95A109TYR0-0.055-0.0406.924-1.219-1.2190.0000.0000.0000.000
96A110MET0-0.034-0.00211.1461.4271.4270.0000.0000.0000.000
97A111GLY00.0570.04611.622-1.136-1.1360.0000.0000.0000.000
98A112ASP-1-0.749-0.83510.401-24.210-24.2100.0000.0000.0000.000
99A113ILE0-0.001-0.00112.8371.5071.5070.0000.0000.0000.000
100A114PHE00.024-0.00414.753-1.140-1.1400.0000.0000.0000.000
101A115ARG10.8660.90617.38215.04415.0440.0000.0000.0000.000
102A116TRP0-0.011-0.02020.201-0.350-0.3500.0000.0000.0000.000
103A117GLY00.0410.03323.3190.4610.4610.0000.0000.0000.000
104A118GLU-1-0.962-0.98725.354-10.585-10.5850.0000.0000.0000.000
105A119ALA0-0.055-0.01825.1650.0600.0600.0000.0000.0000.000
106A120LEU0-0.024-0.01919.456-0.623-0.6230.0000.0000.0000.000
107A121ILE0-0.0040.01219.6060.5510.5510.0000.0000.0000.000
108A122GLN0-0.016-0.02114.743-0.162-0.1620.0000.0000.0000.000
109A123VAL0-0.0470.00815.2320.8480.8480.0000.0000.0000.000
110A124SER00.0210.00016.735-0.433-0.4330.0000.0000.0000.000
111A125GLN0-0.008-0.01019.0260.4250.4250.0000.0000.0000.000
112A126PRO00.0610.04518.3080.0430.0430.0000.0000.0000.000
113A127ARG10.8190.91920.55311.03511.0350.0000.0000.0000.000
114A128SER0-0.005-0.02724.178-0.238-0.2380.0000.0000.0000.000
115A129PRO0-0.0100.02726.5280.3880.3880.0000.0000.0000.000
116A130CYS0-0.032-0.02729.3750.2460.2460.0000.0000.0000.000
117A131TYR00.0870.04232.8470.0780.0780.0000.0000.0000.000
118A132LYS10.8830.93636.1047.9687.9680.0000.0000.0000.000
119A133LEU00.0280.00931.0200.1130.1130.0000.0000.0000.000
120A134ASN00.0270.01435.656-0.159-0.1590.0000.0000.0000.000
121A135TYR0-0.028-0.02438.0010.1400.1400.0000.0000.0000.000
122A136HIS0-0.086-0.01836.2710.2710.2710.0000.0000.0000.000
123A137PHE00.010-0.00633.2030.0260.0260.0000.0000.0000.000
124A138ASP-1-0.933-0.95438.675-7.044-7.0440.0000.0000.0000.000
125A139ILE00.0070.02736.6340.0250.0250.0000.0000.0000.000
126A140SER0-0.001-0.01838.355-0.094-0.0940.0000.0000.0000.000
127A141ASP-1-0.912-0.96236.364-8.459-8.4590.0000.0000.0000.000
128A142ILE00.0640.04532.624-0.320-0.3200.0000.0000.0000.000
129A143ALA0-0.025-0.01331.778-0.395-0.3950.0000.0000.0000.000
130A144GLN0-0.025-0.01830.706-0.122-0.1220.0000.0000.0000.000
131A145LEU00.0540.03130.326-0.447-0.4470.0000.0000.0000.000
132A146MET0-0.024-0.00927.485-0.332-0.3320.0000.0000.0000.000
133A147GLN00.0620.04026.175-0.376-0.3760.0000.0000.0000.000
134A148ASN00.0060.01425.537-0.503-0.5030.0000.0000.0000.000
135A149THR0-0.037-0.01725.400-0.480-0.4800.0000.0000.0000.000
136A150GLY00.0030.00921.966-0.615-0.6150.0000.0000.0000.000
137A151LYS10.8400.94721.77912.21612.2160.0000.0000.0000.000
138A152VAL0-0.026-0.01021.9870.6240.6240.0000.0000.0000.000
139A153GLY00.0570.02921.6800.4310.4310.0000.0000.0000.000
140A154TRP0-0.058-0.04718.765-0.266-0.2660.0000.0000.0000.000
141A155LEU0-0.037-0.01421.1100.4810.4810.0000.0000.0000.000
142A156TYR00.010-0.02018.071-0.947-0.9470.0000.0000.0000.000
143A157SER0-0.0070.00220.8780.4910.4910.0000.0000.0000.000
144A158VAL00.008-0.00622.000-0.479-0.4790.0000.0000.0000.000
145A159ILE0-0.061-0.02719.2560.2600.2600.0000.0000.0000.000
146A160ALA0-0.009-0.01922.7520.3310.3310.0000.0000.0000.000
147A161PRO0-0.003-0.00225.248-0.142-0.1420.0000.0000.0000.000
148A162GLY00.0420.01628.301-0.005-0.0050.0000.0000.0000.000
149A163LYS10.8640.91929.6608.6498.6490.0000.0000.0000.000
150A164VAL0-0.0100.01726.816-0.346-0.3460.0000.0000.0000.000
151A165SER0-0.007-0.05828.5380.2930.2930.0000.0000.0000.000
152A166ALA00.0360.02828.490-0.395-0.3950.0000.0000.0000.000
153A167ASP-1-0.866-0.89728.990-9.894-9.8940.0000.0000.0000.000
154A168ALA0-0.057-0.01425.938-0.325-0.3250.0000.0000.0000.000
155A169PRO0-0.014-0.00821.663-0.077-0.0770.0000.0000.0000.000
156A170LEU00.0050.00019.421-0.102-0.1020.0000.0000.0000.000
157A171GLU-1-0.823-0.90717.545-15.289-15.2890.0000.0000.0000.000
158A172LEU0-0.068-0.00410.1020.1310.1310.0000.0000.0000.000
159A173VAL0-0.027-0.02213.820-0.494-0.4940.0000.0000.0000.000
160A174SER0-0.049-0.02510.840-0.111-0.1110.0000.0000.0000.000
161A175ARG10.7670.8446.07829.24529.2450.0000.0000.0000.000
162A176VAL0-0.004-0.0057.506-1.377-1.3770.0000.0000.0000.000
163A177SER0-0.056-0.0517.8871.4291.4290.0000.0000.0000.000
164A178ASP-1-0.872-0.9315.604-27.660-27.6600.0000.0000.0000.000
165A179VAL00.0060.0096.8400.6730.6730.0000.0000.0000.000
166A180THR00.002-0.0199.9051.0771.0770.0000.0000.0000.000
167A181VAL00.0400.00711.7781.2691.2690.0000.0000.0000.000
168A182GLN0-0.001-0.00214.9430.1320.1320.0000.0000.0000.000
169A183GLU-1-0.746-0.83710.983-22.035-22.0350.0000.0000.0000.000
170A184ALA00.0100.00515.2640.9420.9420.0000.0000.0000.000
171A185ALA00.001-0.00316.9840.8710.8710.0000.0000.0000.000
172A186ALA00.0260.00818.2510.7300.7300.0000.0000.0000.000
173A187ILE0-0.008-0.02015.5390.6790.6790.0000.0000.0000.000
174A188ALA0-0.032-0.01919.9220.6460.6460.0000.0000.0000.000
175A189TRP0-0.046-0.04322.6810.5370.5370.0000.0000.0000.000
176A190HIS0-0.046-0.02422.320-0.046-0.0460.0000.0000.0000.000
177A191MET0-0.0620.01020.727-0.019-0.0190.0000.0000.0000.000
178A192PRO00.001-0.00123.7800.3240.3240.0000.0000.0000.000
179A193PHE0-0.023-0.01924.588-0.338-0.3380.0000.0000.0000.000
180A194ASP-1-0.780-0.89320.395-13.406-13.4060.0000.0000.0000.000
181A195ASP-1-0.824-0.88722.180-11.641-11.6410.0000.0000.0000.000
182A196ASP-1-0.864-0.91818.623-13.538-13.5380.0000.0000.0000.000
183A197GLN0-0.036-0.03415.706-1.602-1.6020.0000.0000.0000.000
184A198TYR0-0.008-0.01117.711-0.166-0.1660.0000.0000.0000.000
185A199HIS0-0.0020.00416.7860.4560.4560.0000.0000.0000.000
186A200ARG10.8000.8969.28421.57821.5780.0000.0000.0000.000
187A201LEU00.004-0.00414.463-0.500-0.5000.0000.0000.0000.000
188A202LEU0-0.080-0.04816.2650.0160.0160.0000.0000.0000.000
189A203SER0-0.051-0.02413.8800.4140.4140.0000.0000.0000.000
190A204ALA0-0.039-0.00412.369-0.822-0.8220.0000.0000.0000.000
191A205ALA00.0200.00012.5571.0691.0690.0000.0000.0000.000
192A206GLY00.0370.01114.288-0.247-0.2470.0000.0000.0000.000
193A207LEU0-0.0520.00317.1300.5760.5760.0000.0000.0000.000
194A208SER0-0.001-0.01118.6340.5880.5880.0000.0000.0000.000
195A209LYS10.8950.91922.24511.09111.0910.0000.0000.0000.000
196A210SER0-0.068-0.03024.9640.1600.1600.0000.0000.0000.000
197A211TRP00.0920.03920.0640.0940.0940.0000.0000.0000.000
198A212THR00.0330.01521.990-0.114-0.1140.0000.0000.0000.000
199A213ARG10.9120.96323.0669.2079.2070.0000.0000.0000.000
200A214THR0-0.049-0.02625.3010.3390.3390.0000.0000.0000.000
201A215MET00.0570.04320.8230.1870.1870.0000.0000.0000.000
202A216GLN00.0380.00523.9770.1300.1300.0000.0000.0000.000
203A217LYS10.8670.91725.6899.1089.1080.0000.0000.0000.000
204A218ARG10.7730.87724.70311.31911.3190.0000.0000.0000.000
205A219ARG10.8060.87021.51812.12912.1290.0000.0000.0000.000
206A220LEU0-0.055-0.01926.8140.2460.2460.0000.0000.0000.000
207A221SER0-0.096-0.05330.2670.2740.2740.0000.0000.0000.000
208A222GLY00.0300.02129.7900.2490.2490.0000.0000.0000.000
209A223LYS10.8850.93030.6148.2928.2920.0000.0000.0000.000
210A224ILE00.0430.02826.823-0.158-0.1580.0000.0000.0000.000
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