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: Z67QN

Calculation Name: 1O63-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O63

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0D2

Base Structure: X-ray

Registration Date: 2023-06-22

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

DOI:


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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2264138.411249
FMO2-HF: Nuclear repulsion 2183940.773499
FMO2-HF: Total energy -80197.63775
FMO2-MP2: Total energy -80432.156543


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:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-35.294-19.48223.17-15.358-23.624-0.103
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.025
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].
3A4LEU00.0530.0142.742-1.7000.7840.698-1.124-2.0590.005
4A5ALA0-0.034-0.0095.309-0.0070.039-0.001-0.002-0.0430.000
5A6ILE00.020-0.0157.996-0.022-0.0220.0000.0000.0000.000
6A7PRO0-0.0160.00511.1430.0420.0420.0000.0000.0000.000
7A8LYS10.8210.89414.805-0.025-0.0250.0000.0000.0000.000
8A9GLY0-0.047-0.02917.4420.0160.0160.0000.0000.0000.000
9A10ARG10.8470.88020.1500.0630.0630.0000.0000.0000.000
10A11LEU00.0350.00716.762-0.007-0.0070.0000.0000.0000.000
11A12GLU-1-0.855-0.91815.304-0.144-0.1440.0000.0000.0000.000
12A13GLU-1-0.886-0.96515.557-0.209-0.2090.0000.0000.0000.000
13A14LYS10.9270.97416.5400.1550.1550.0000.0000.0000.000
14A15VAL00.0000.00410.697-0.036-0.0360.0000.0000.0000.000
15A16MET00.0010.00311.614-0.100-0.1000.0000.0000.0000.000
16A17THR0-0.027-0.01813.112-0.068-0.0680.0000.0000.0000.000
17A18TYR0-0.013-0.01211.298-0.027-0.0270.0000.0000.0000.000
18A19LEU00.0480.0146.654-0.064-0.0640.0000.0000.0000.000
19A20LYS10.9741.0059.6490.2370.2370.0000.0000.0000.000
20A21LYS10.8520.90812.4740.2870.2870.0000.0000.0000.000
21A22THR0-0.0380.0068.013-0.071-0.0710.0000.0000.0000.000
22A23GLY0-0.001-0.0149.543-0.097-0.0970.0000.0000.0000.000
23A24VAL0-0.064-0.0146.368-0.085-0.0850.0000.0000.0000.000
24A25ILE0-0.005-0.0069.1030.2190.2190.0000.0000.0000.000
25A26PHE0-0.024-0.0388.215-0.108-0.1080.0000.0000.0000.000
26A27GLU-1-0.930-0.95011.530-0.185-0.1850.0000.0000.0000.000
27A28ARG10.7930.86012.593-0.018-0.0180.0000.0000.0000.000
28A29GLU-1-0.846-0.91612.901-0.339-0.3390.0000.0000.0000.000
29A30SER0-0.0040.00815.1500.0440.0440.0000.0000.0000.000
30A31SER00.012-0.01616.473-0.024-0.0240.0000.0000.0000.000
31A32ILE00.008-0.00915.909-0.019-0.0190.0000.0000.0000.000
32A33LEU0-0.0180.00910.3520.0370.0370.0000.0000.0000.000
33A34ARG10.8720.93410.5940.2200.2200.0000.0000.0000.000
34A35GLU-1-0.797-0.8578.2870.0310.0310.0000.0000.0000.000
35A36GLY00.0770.0267.1670.0720.0720.0000.0000.0000.000
36A37LYS10.9290.9796.5051.0521.0520.0000.0000.0000.000
37A38ASP-1-0.891-0.9503.913-2.183-1.8000.001-0.123-0.2600.000
38A39ILE0-0.026-0.0072.149-10.923-8.4143.982-3.174-3.316-0.035
39A40VAL0-0.0020.0113.5241.5201.9970.004-0.102-0.3790.000
40A41CYS0-0.042-0.0145.775-0.288-0.2880.0000.0000.0000.000
41A42PHE00.0350.0127.7610.1280.1280.0000.0000.0000.000
42A43MET0-0.046-0.00510.522-0.052-0.0520.0000.0000.0000.000
43A44VAL00.0260.01612.8920.0250.0250.0000.0000.0000.000
44A45ARG10.9840.99115.331-0.064-0.0640.0000.0000.0000.000
45A46PRO00.0840.03616.7050.0250.0250.0000.0000.0000.000
46A47PHE00.0510.02117.0400.0160.0160.0000.0000.0000.000
47A48ASP-1-0.931-0.96816.7650.1760.1760.0000.0000.0000.000
48A49VAL0-0.0130.00711.4190.0510.0510.0000.0000.0000.000
49A50PRO00.0480.00912.8730.0690.0690.0000.0000.0000.000
50A51THR00.0120.02114.4020.0360.0360.0000.0000.0000.000
51A52TYR00.0340.01211.1070.0410.0410.0000.0000.0000.000
52A53LEU0-0.037-0.0058.0470.1170.1170.0000.0000.0000.000
53A54VAL0-0.007-0.00311.0010.0690.0690.0000.0000.0000.000
54A55HIS0-0.085-0.04914.084-0.016-0.0160.0000.0000.0000.000
55A56GLY0-0.0120.00210.5560.0180.0180.0000.0000.0000.000
56A57VAL0-0.045-0.0169.4880.2120.2120.0000.0000.0000.000
57A58ALA0-0.032-0.0276.4780.2120.2120.0000.0000.0000.000
58A59ASP-1-0.759-0.8522.3782.5274.8223.497-2.676-3.116-0.028
59A60ILE00.0170.0042.587-1.319-0.3490.417-0.195-1.1920.001
60A61GLY00.0280.0155.643-0.113-0.1130.0000.0000.0000.000
61A62PHE00.0110.0077.438-0.027-0.0270.0000.0000.0000.000
62A63CYS0-0.038-0.01911.8920.0250.0250.0000.0000.0000.000
63A64GLY00.0880.03715.647-0.015-0.0150.0000.0000.0000.000
64A65THR00.024-0.00818.9150.0130.0130.0000.0000.0000.000
65A66ASP-1-0.885-0.94321.1470.0230.0230.0000.0000.0000.000
66A67VAL0-0.045-0.02217.9760.0120.0120.0000.0000.0000.000
67A68LEU0-0.003-0.01715.8450.0160.0160.0000.0000.0000.000
68A69LEU0-0.0030.01119.8290.0080.0080.0000.0000.0000.000
69A70GLU-1-0.817-0.88223.3880.0610.0610.0000.0000.0000.000
70A71LYS10.8270.90918.957-0.166-0.1660.0000.0000.0000.000
71A72GLU-1-0.805-0.87820.5250.0840.0840.0000.0000.0000.000
72A73THR0-0.074-0.04316.4640.0270.0270.0000.0000.0000.000
73A74SER00.0120.00516.736-0.010-0.0100.0000.0000.0000.000
74A75LEU0-0.056-0.02511.2350.0140.0140.0000.0000.0000.000
75A76ILE00.0370.02511.112-0.043-0.0430.0000.0000.0000.000
76A77GLN00.0460.02511.4830.0030.0030.0000.0000.0000.000
77A78PRO0-0.085-0.0239.021-0.010-0.0100.0000.0000.0000.000
78A79PHE00.0690.0299.202-0.020-0.0200.0000.0000.0000.000
79A80PHE0-0.0010.00214.1470.0200.0200.0000.0000.0000.000
80A81ILE0-0.003-0.00112.180-0.024-0.0240.0000.0000.0000.000
81A82PRO00.0460.02316.4370.0210.0210.0000.0000.0000.000
82A83THR0-0.007-0.01319.0400.0120.0120.0000.0000.0000.000
83A84ASN00.0070.01021.3330.0090.0090.0000.0000.0000.000
84A85ILE0-0.045-0.02320.063-0.006-0.0060.0000.0000.0000.000
85A86SER0-0.008-0.00323.8350.0030.0030.0000.0000.0000.000
86A87ARG10.8340.90426.6270.0300.0300.0000.0000.0000.000
87A88MET00.0210.03127.1260.0020.0020.0000.0000.0000.000
88A89VAL0-0.035-0.01829.810-0.001-0.0010.0000.0000.0000.000
89A90LEU00.0570.03533.6580.0040.0040.0000.0000.0000.000
90A91ALA0-0.026-0.02636.816-0.004-0.0040.0000.0000.0000.000
91A92GLY00.0630.02939.2310.0030.0030.0000.0000.0000.000
92A93PRO0-0.0100.00942.707-0.002-0.0020.0000.0000.0000.000
93A94LYS10.8640.91045.1610.0120.0120.0000.0000.0000.000
94A95GLY0-0.0080.01246.7750.0000.0000.0000.0000.0000.000
95A96ARG10.8980.96147.950-0.005-0.0050.0000.0000.0000.000
96A97GLY00.0470.02946.9200.0000.0000.0000.0000.0000.000
97A98ILE0-0.037-0.02743.0060.0010.0010.0000.0000.0000.000
98A99PRO00.0200.01346.1940.0000.0000.0000.0000.0000.000
99A100GLU-1-0.864-0.92648.0140.0090.0090.0000.0000.0000.000
100A101GLY0-0.021-0.00149.6660.0010.0010.0000.0000.0000.000
101A102GLU-1-0.814-0.87445.3120.0270.0270.0000.0000.0000.000
102A103LYS10.8120.89842.841-0.016-0.0160.0000.0000.0000.000
103A104ARG10.8240.88742.690-0.015-0.0150.0000.0000.0000.000
104A105ILE0-0.002-0.00237.338-0.003-0.0030.0000.0000.0000.000
105A106ALA00.0280.02737.6560.0040.0040.0000.0000.0000.000
106A107THR00.007-0.03132.449-0.002-0.0020.0000.0000.0000.000
107A108LYS10.8000.90628.015-0.009-0.0090.0000.0000.0000.000
108A109PHE0-0.066-0.03425.1620.0060.0060.0000.0000.0000.000
109A110PRO00.0370.01929.321-0.004-0.0040.0000.0000.0000.000
110A111ASN00.003-0.02026.741-0.005-0.0050.0000.0000.0000.000
111A112VAL00.0020.00027.041-0.004-0.0040.0000.0000.0000.000
112A113THR0-0.016-0.01429.640-0.005-0.0050.0000.0000.0000.000
113A114GLN0-0.058-0.04132.838-0.004-0.0040.0000.0000.0000.000
114A115ARG10.8590.90525.873-0.060-0.0600.0000.0000.0000.000
115A116TYR0-0.050-0.05132.816-0.003-0.0030.0000.0000.0000.000
116A117CYS0-0.023-0.01634.728-0.006-0.0060.0000.0000.0000.000
117A118GLU-1-0.836-0.89834.2140.0420.0420.0000.0000.0000.000
118A119SER0-0.111-0.06535.131-0.003-0.0030.0000.0000.0000.000
119A120LYS10.8610.91037.235-0.010-0.0100.0000.0000.0000.000
120A121GLY0-0.0270.00940.344-0.001-0.0010.0000.0000.0000.000
121A122TRP0-0.035-0.03240.6850.0000.0000.0000.0000.0000.000
122A123HIS00.0380.03041.7750.0030.0030.0000.0000.0000.000
123A125ARG10.8400.89241.266-0.027-0.0270.0000.0000.0000.000
124A126ILE0-0.002-0.00434.980-0.002-0.0020.0000.0000.0000.000
125A127ILE0-0.029-0.01838.1020.0030.0030.0000.0000.0000.000
126A128PRO00.0120.00232.904-0.003-0.0030.0000.0000.0000.000
127A129LEU00.0100.00733.4960.0000.0000.0000.0000.0000.000
128A130LYS10.9200.94028.178-0.057-0.0570.0000.0000.0000.000
129A131GLY00.002-0.00530.145-0.001-0.0010.0000.0000.0000.000
130A132SER0-0.012-0.00932.2180.0020.0020.0000.0000.0000.000
131A133VAL0-0.0050.00533.0690.0010.0010.0000.0000.0000.000
132A134GLU-1-0.841-0.91535.6640.0020.0020.0000.0000.0000.000
133A135LEU00.0050.00238.309-0.001-0.0010.0000.0000.0000.000
134A136ALA00.0030.00139.6330.0010.0010.0000.0000.0000.000
135A137PRO00.0150.00340.6830.0000.0000.0000.0000.0000.000
136A138ILE0-0.020-0.00443.9490.0000.0000.0000.0000.0000.000
137A139ALA0-0.026-0.00544.2400.0000.0000.0000.0000.0000.000
138A140GLY0-0.0050.00446.1560.0010.0010.0000.0000.0000.000
139A141LEU0-0.059-0.00940.2980.0020.0020.0000.0000.0000.000
140A142SER0-0.056-0.05740.8800.0020.0020.0000.0000.0000.000
141A143ASP-1-0.836-0.89543.3860.0130.0130.0000.0000.0000.000
142A144LEU0-0.022-0.01740.720-0.002-0.0020.0000.0000.0000.000
143A145ILE0-0.0210.00436.2570.0030.0030.0000.0000.0000.000
144A146VAL00.0450.02932.132-0.002-0.0020.0000.0000.0000.000
145A147ASP-1-0.788-0.87430.7130.0130.0130.0000.0000.0000.000
146A148ILE0-0.001-0.00325.708-0.003-0.0030.0000.0000.0000.000
147A149THR0-0.023-0.00529.969-0.002-0.0020.0000.0000.0000.000
148A150GLU-1-0.774-0.86126.610-0.058-0.0580.0000.0000.0000.000
149A151THR00.014-0.00730.303-0.001-0.0010.0000.0000.0000.000
150A152GLY00.0420.03233.6730.0010.0010.0000.0000.0000.000
151A153ARG10.8160.90835.7750.0300.0300.0000.0000.0000.000
152A154THR00.0820.03334.4980.0000.0000.0000.0000.0000.000
153A155LEU00.0210.02135.6930.0020.0020.0000.0000.0000.000
154A156LYS10.9870.99438.8250.0180.0180.0000.0000.0000.000
155A157GLU-1-0.915-0.95038.840-0.019-0.0190.0000.0000.0000.000
156A158ASN0-0.027-0.01739.8750.0030.0030.0000.0000.0000.000
157A159ASN0-0.054-0.02542.9040.0010.0010.0000.0000.0000.000
158A160LEU0-0.0060.00639.5010.0020.0020.0000.0000.0000.000
159A161GLU-1-0.838-0.92641.862-0.012-0.0120.0000.0000.0000.000
160A162ILE0-0.021-0.02435.8490.0020.0020.0000.0000.0000.000
161A163LEU0-0.025-0.02039.368-0.001-0.0010.0000.0000.0000.000
162A164ASP-1-0.757-0.85137.360-0.001-0.0010.0000.0000.0000.000
163A165GLU-1-0.833-0.89132.826-0.021-0.0210.0000.0000.0000.000
164A166ILE0-0.060-0.02530.7550.0010.0010.0000.0000.0000.000
165A167PHE00.043-0.00125.4070.0020.0020.0000.0000.0000.000
166A168VAL0-0.037-0.00925.207-0.001-0.0010.0000.0000.0000.000
167A169ILE0-0.032-0.01522.3620.0050.0050.0000.0000.0000.000
168A170ARG10.9250.95919.7530.0500.0500.0000.0000.0000.000
169A171THR0-0.001-0.00414.1860.0110.0110.0000.0000.0000.000
170A172HIS00.0250.04014.902-0.012-0.0120.0000.0000.0000.000
171A173VAL00.0520.0248.3690.0050.0050.0000.0000.0000.000
172A174VAL0-0.016-0.01910.2560.0130.0130.0000.0000.0000.000
173A175VAL00.009-0.0055.8500.0400.0400.0000.0000.0000.000
174A176ASN00.0250.0247.236-0.246-0.2460.0000.0000.0000.000
175A177PRO00.0700.0188.2810.0810.0810.0000.0000.0000.000
176A178VAL0-0.014-0.01310.105-0.053-0.0530.0000.0000.0000.000
177A179SER0-0.005-0.0264.860-0.251-0.2510.0000.0000.0000.000
178A180TYR00.0320.0256.263-0.066-0.0660.0000.0000.0000.000
179A181ARG10.9260.9648.013-0.604-0.6040.0000.0000.0000.000
180A182THR0-0.070-0.0637.8070.0080.0080.0000.0000.0000.000
181A183LYS10.8240.9192.032-9.763-9.5525.785-2.949-3.0470.009
182A184ARG10.9410.9944.833-0.552-0.470-0.001-0.001-0.0790.000
183A185GLU-1-0.878-0.9536.598-0.464-0.4640.0000.0000.0000.000
184A186GLU-1-0.801-0.8872.387-9.337-5.7865.163-3.411-5.303-0.048
185A187VAL0-0.031-0.0332.542-2.320-0.9751.237-0.752-1.830-0.002
186A188VAL0-0.015-0.0073.5980.0690.1460.0110.058-0.1470.000
187A189SER00.0500.0415.899-0.003-0.0030.0000.0000.0000.000
188A190PHE0-0.010-0.0142.525-1.508-0.2472.378-0.879-2.761-0.005
189A191LEU0-0.043-0.0474.3390.1450.266-0.001-0.028-0.0920.000
190A192GLU-1-0.918-0.9516.802-0.434-0.4340.0000.0000.0000.000
191A193LYS10.9440.9747.6871.2001.2000.0000.0000.0000.000
192A194LEU0-0.047-0.0266.5740.0870.0870.0000.0000.0000.000
193A195GLN00.0100.0019.1740.1030.1030.0000.0000.0000.000
194A196GLU-1-0.886-0.93612.044-0.445-0.4450.0000.0000.0000.000
195A197VAL0-0.038-0.02011.8510.0420.0420.0000.0000.0000.000
196A198ILE0-0.056-0.03710.8750.0510.0510.0000.0000.0000.000
197A199GLU-1-0.935-0.95514.365-0.165-0.1650.0000.0000.0000.000
198A200HIS00.0590.04417.1580.0200.0200.0000.0000.0000.000
199A201ASP-1-0.869-0.87916.918-0.226-0.2260.0000.0000.0000.000
200A202SER0-0.085-0.06218.0490.0260.0260.0000.0000.0000.000
201A203ASN0-0.077-0.03619.9610.0310.0310.0000.0000.0000.000
202A204GLU-1-1.057-1.05921.424-0.139-0.1390.0000.0000.0000.000