Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 2LLMR

Calculation Name: 4O7H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4O7H

Chain ID: A

ChEMBL ID:

UniProt ID:

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2880945.541383
FMO2-HF: Nuclear repulsion 2791956.41258
FMO2-HF: Total energy -88989.128803
FMO2-MP2: Total energy -89251.764895


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-13.483-6.7774.186-3.237-7.654-0.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : 0.005
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].
3A3ARG10.8400.8972.911-2.0931.8930.443-2.304-2.125-0.007
4A4LEU0-0.019-0.0064.9640.8940.996-0.001-0.011-0.0910.000
5A5TYR00.0530.0328.3130.0650.0650.0000.0000.0000.000
6A6HIS0-0.004-0.03010.6900.1690.1690.0000.0000.0000.000
7A7HIS00.1010.04313.3570.0770.0770.0000.0000.0000.000
8A8GLY00.0640.03016.1610.0010.0010.0000.0000.0000.000
9A9LEU0-0.014-0.01417.7670.0360.0360.0000.0000.0000.000
10A10SER00.0320.03717.8250.0250.0250.0000.0000.0000.000
11A11PRO00.0340.01018.559-0.035-0.0350.0000.0000.0000.000
12A12ALA00.0340.00918.913-0.018-0.0180.0000.0000.0000.000
13A13ALA00.0450.02014.403-0.064-0.0640.0000.0000.0000.000
14A14ARG10.8350.90414.1440.3080.3080.0000.0000.0000.000
15A15LYS10.8490.88115.3320.4770.4770.0000.0000.0000.000
16A16VAL00.0300.00911.3160.0070.0070.0000.0000.0000.000
17A17ARG10.7890.87110.2210.7070.7070.0000.0000.0000.000
18A18VAL0-0.001-0.00311.6240.0040.0040.0000.0000.0000.000
19A19ALA0-0.002-0.01214.0260.0460.0460.0000.0000.0000.000
20A20LEU00.0180.0177.6120.0450.0450.0000.0000.0000.000
21A21ALA00.0030.01110.4180.0500.0500.0000.0000.0000.000
22A22GLU-1-0.797-0.85411.314-0.234-0.2340.0000.0000.0000.000
23A23LYS10.7700.87912.6620.6430.6430.0000.0000.0000.000
24A24ARG10.7930.89110.7560.3680.3680.0000.0000.0000.000
25A25LEU0-0.0110.0167.8810.0430.0430.0000.0000.0000.000
26A26ASP-1-0.907-0.9523.198-1.321-0.8880.053-0.087-0.3980.000
27A27TYR0-0.035-0.0272.425-0.987-0.5090.939-0.370-1.048-0.001
28A28GLU-1-0.809-0.8692.591-4.334-3.3662.395-0.180-3.183-0.006
29A29ALA0-0.031-0.0243.632-0.690-0.6130.0140.033-0.1220.000
30A30VAL00.010-0.0016.8160.4020.4020.0000.0000.0000.000
31A31ILE0-0.040-0.0249.489-0.027-0.0270.0000.0000.0000.000
32A32GLU-1-0.817-0.89513.273-0.750-0.7500.0000.0000.0000.000
33A33GLU-1-0.887-0.95615.501-0.301-0.3010.0000.0000.0000.000
34A34THR00.0070.00818.3820.0300.0300.0000.0000.0000.000
35A35TRP0-0.080-0.04220.6630.0110.0110.0000.0000.0000.000
36A36ILE0-0.055-0.02521.9050.0460.0460.0000.0000.0000.000
37A37ARG10.8300.88521.8960.2840.2840.0000.0000.0000.000
38A38ASN00.028-0.01416.2830.0540.0540.0000.0000.0000.000
39A39GLU-1-0.802-0.88019.962-0.372-0.3720.0000.0000.0000.000
40A40SER0-0.003-0.00215.841-0.003-0.0030.0000.0000.0000.000
41A41PHE0-0.031-0.00513.923-0.074-0.0740.0000.0000.0000.000
42A42LEU00.005-0.00416.759-0.037-0.0370.0000.0000.0000.000
43A43ALA0-0.056-0.02017.6440.0090.0090.0000.0000.0000.000
44A44MET0-0.0420.00112.039-0.089-0.0890.0000.0000.0000.000
45A45ASN0-0.013-0.01915.7750.0230.0230.0000.0000.0000.000
46A46PRO00.0220.01118.1370.0400.0400.0000.0000.0000.000
47A47GLU-1-0.990-0.99021.427-0.468-0.4680.0000.0000.0000.000
48A48GLY0-0.033-0.02420.4820.0290.0290.0000.0000.0000.000
49A49GLU-1-0.916-0.95819.908-0.479-0.4790.0000.0000.0000.000
50A50VAL0-0.0660.00014.867-0.104-0.1040.0000.0000.0000.000
51A51PRO0-0.062-0.04913.6170.0950.0950.0000.0000.0000.000
52A52VAL00.0040.00012.2370.0870.0870.0000.0000.0000.000
53A53LEU0-0.035-0.0158.155-0.233-0.2330.0000.0000.0000.000
54A54VAL00.0080.0126.4450.4190.4190.0000.0000.0000.000
55A55GLU-1-0.710-0.8056.207-3.830-3.8300.0000.0000.0000.000
56A56ALA0-0.008-0.0102.687-1.007-0.5080.341-0.298-0.5420.000
57A57ASP-1-0.904-0.9554.095-0.773-0.6100.002-0.020-0.1450.000
58A58GLY0-0.008-0.0026.5250.2950.2950.0000.0000.0000.000
59A59LEU0-0.0240.0037.9900.1540.1540.0000.0000.0000.000
60A60THR0-0.003-0.0119.794-0.423-0.4230.0000.0000.0000.000
61A61ILE0-0.048-0.01611.8790.2550.2550.0000.0000.0000.000
62A62THR00.0670.01414.171-0.183-0.1830.0000.0000.0000.000
63A63ASP-1-0.734-0.86616.843-0.511-0.5110.0000.0000.0000.000
64A64GLY00.0110.00917.169-0.055-0.0550.0000.0000.0000.000
65A65TRP0-0.101-0.06818.0710.0100.0100.0000.0000.0000.000
66A66ALA00.0230.01319.1350.0070.0070.0000.0000.0000.000
67A67ILE0-0.019-0.00512.970-0.029-0.0290.0000.0000.0000.000
68A68CYS0-0.069-0.03615.684-0.009-0.0090.0000.0000.0000.000
69A69GLU-1-0.778-0.86717.383-0.385-0.3850.0000.0000.0000.000
70A70TYR00.0290.00110.8400.0950.0950.0000.0000.0000.000
71A71LEU0-0.018-0.02911.1850.0070.0070.0000.0000.0000.000
72A72GLU-1-0.774-0.85115.158-0.363-0.3630.0000.0000.0000.000
73A73GLU-1-0.988-0.99118.417-0.418-0.4180.0000.0000.0000.000
74A74VAL0-0.030-0.01112.7000.0650.0650.0000.0000.0000.000
75A75TYR0-0.074-0.0589.4520.0680.0680.0000.0000.0000.000
76A76PRO00.0230.02615.171-0.001-0.0010.0000.0000.0000.000
77A77GLU-1-0.920-0.95617.596-0.221-0.2210.0000.0000.0000.000
78A78PRO0-0.042-0.02015.660-0.023-0.0230.0000.0000.0000.000
79A79SER0-0.001-0.00918.260-0.047-0.0470.0000.0000.0000.000
80A80LEU0-0.024-0.02616.5840.0170.0170.0000.0000.0000.000
81A81LEU0-0.060-0.03920.8650.0120.0120.0000.0000.0000.000
82A82GLY00.0640.02723.8940.0250.0250.0000.0000.0000.000
83A83GLY0-0.0070.00326.278-0.011-0.0110.0000.0000.0000.000
84A84PRO00.0310.00128.492-0.002-0.0020.0000.0000.0000.000
85A85ALA00.0580.01931.020-0.011-0.0110.0000.0000.0000.000
86A86ALA00.001-0.00532.044-0.009-0.0090.0000.0000.0000.000
87A87MET00.0080.02928.260-0.002-0.0020.0000.0000.0000.000
88A88ARG10.9480.97023.5930.3030.3030.0000.0000.0000.000
89A89ALA0-0.009-0.00728.497-0.017-0.0170.0000.0000.0000.000
90A90GLU-1-0.725-0.80631.132-0.192-0.1920.0000.0000.0000.000
91A91VAL00.0050.00124.651-0.005-0.0050.0000.0000.0000.000
92A92ARG10.8370.88224.5380.3340.3340.0000.0000.0000.000
93A93ARG10.7830.87227.7530.1870.1870.0000.0000.0000.000
94A94LEU0-0.013-0.00828.7400.0010.0010.0000.0000.0000.000
95A95VAL00.004-0.00123.709-0.003-0.0030.0000.0000.0000.000
96A96ALA00.0170.01126.282-0.006-0.0060.0000.0000.0000.000
97A97TRP0-0.067-0.03628.7120.0120.0120.0000.0000.0000.000
98A98PHE0-0.004-0.02126.6770.0120.0120.0000.0000.0000.000
99A99ASP-1-0.665-0.81323.478-0.430-0.4300.0000.0000.0000.000
100A100ARG10.9250.97826.4950.2520.2520.0000.0000.0000.000
101A101LYS10.8110.89330.0220.1850.1850.0000.0000.0000.000
102A102PHE00.0210.00328.5710.0100.0100.0000.0000.0000.000
103A103ASN00.0230.00826.389-0.004-0.0040.0000.0000.0000.000
104A104ARG10.8310.89329.0200.2490.2490.0000.0000.0000.000
105A105GLU-1-0.844-0.87732.213-0.170-0.1700.0000.0000.0000.000
106A106VAL0-0.002-0.01131.1540.0160.0160.0000.0000.0000.000
107A107THR00.016-0.01325.4090.0140.0140.0000.0000.0000.000
108A108GLU-1-0.812-0.87628.622-0.268-0.2680.0000.0000.0000.000
109A109PRO0-0.043-0.01029.7400.0040.0040.0000.0000.0000.000
110A110LEU0-0.012-0.01430.6300.0090.0090.0000.0000.0000.000
111A111VAL00.0550.02724.7980.0090.0090.0000.0000.0000.000
112A112ARG10.8480.91928.0980.2090.2090.0000.0000.0000.000
113A113GLU-1-0.771-0.86029.750-0.165-0.1650.0000.0000.0000.000
114A114LYS10.8110.88731.0020.1620.1620.0000.0000.0000.000
115A115LEU0-0.034-0.00925.0330.0090.0090.0000.0000.0000.000
116A116LEU00.0490.01524.8560.0060.0060.0000.0000.0000.000
117A117LYS10.7870.87427.3360.1680.1680.0000.0000.0000.000
118A118ARG10.9000.96029.3690.1490.1490.0000.0000.0000.000
119A119VAL0-0.025-0.00123.7690.0100.0100.0000.0000.0000.000
120A120ILE00.0170.02526.5030.0050.0050.0000.0000.0000.000
121A121SER0-0.002-0.01828.8880.0080.0080.0000.0000.0000.000
122A122GLY0-0.013-0.00931.6330.0090.0090.0000.0000.0000.000
123A123GLY00.0200.03033.2450.0030.0030.0000.0000.0000.000
124A124ALA0-0.023-0.01835.805-0.003-0.0030.0000.0000.0000.000
125A125PRO00.0390.01835.271-0.005-0.0050.0000.0000.0000.000
126A126ASP-1-0.816-0.90436.961-0.127-0.1270.0000.0000.0000.000
127A127SER00.005-0.03138.485-0.002-0.0020.0000.0000.0000.000
128A128ARG10.8770.93940.6490.1070.1070.0000.0000.0000.000
129A129GLN00.0690.05536.291-0.011-0.0110.0000.0000.0000.000
130A130ILE00.0460.02935.216-0.004-0.0040.0000.0000.0000.000
131A131ARG10.8660.92137.2160.1140.1140.0000.0000.0000.000
132A132ALA00.0290.02738.7280.0020.0020.0000.0000.0000.000
133A133GLY00.0730.04235.119-0.001-0.0010.0000.0000.0000.000
134A134ARG10.8910.91835.5940.1250.1250.0000.0000.0000.000
135A135ALA0-0.065-0.02537.0670.0040.0040.0000.0000.0000.000
136A136ASN0-0.005-0.00936.4160.0100.0100.0000.0000.0000.000
137A137VAL00.0050.00532.349-0.003-0.0030.0000.0000.0000.000
138A138HIS00.0360.03535.084-0.002-0.0020.0000.0000.0000.000
139A139THR0-0.039-0.02937.9250.0050.0050.0000.0000.0000.000
140A140HIS0-0.007-0.01332.803-0.003-0.0030.0000.0000.0000.000
141A141LEU00.0300.03132.045-0.005-0.0050.0000.0000.0000.000
142A142ARG10.9781.00234.8850.1250.1250.0000.0000.0000.000
143A143TYR0-0.026-0.00533.7880.0010.0010.0000.0000.0000.000
144A144ILE00.0190.00830.1160.0000.0000.0000.0000.0000.000
145A145SER00.006-0.00433.6650.0030.0030.0000.0000.0000.000
146A146TRP0-0.0040.00036.2210.0070.0070.0000.0000.0000.000
147A147LEU0-0.066-0.04132.5460.0040.0040.0000.0000.0000.000
148A148ILE0-0.043-0.01330.5740.0000.0000.0000.0000.0000.000
149A149ASP-1-0.890-0.91634.187-0.096-0.0960.0000.0000.0000.000
150A150ARG10.8780.94237.1300.1200.1200.0000.0000.0000.000
151A151ARG10.7440.85632.8960.1710.1710.0000.0000.0000.000
152A152ARG10.9280.97929.3010.1280.1280.0000.0000.0000.000
153A153TRP00.0230.01025.442-0.004-0.0040.0000.0000.0000.000
154A154LEU0-0.022-0.01927.5790.0070.0070.0000.0000.0000.000
155A155ALA0-0.005-0.00428.1310.0080.0080.0000.0000.0000.000
156A156GLY0-0.020-0.01030.0830.0050.0050.0000.0000.0000.000
157A157ASP-1-0.879-0.94230.115-0.168-0.1680.0000.0000.0000.000
158A158MET0-0.015-0.00623.9870.0140.0140.0000.0000.0000.000
159A159LEU0-0.0060.00420.695-0.005-0.0050.0000.0000.0000.000
160A160THR0-0.008-0.00422.542-0.014-0.0140.0000.0000.0000.000
161A161TYR00.074-0.00316.980-0.005-0.0050.0000.0000.0000.000
162A162ALA0-0.0270.01821.786-0.005-0.0050.0000.0000.0000.000
163A163ASP-1-0.735-0.88223.567-0.243-0.2430.0000.0000.0000.000
164A164ILE00.0380.02517.5500.0050.0050.0000.0000.0000.000
165A165THR0-0.001-0.01121.071-0.021-0.0210.0000.0000.0000.000
166A166ALA00.0170.02022.5040.0050.0050.0000.0000.0000.000
167A167ALA00.0190.01422.3550.0130.0130.0000.0000.0000.000
168A168CYS0-0.0280.00419.021-0.005-0.0050.0000.0000.0000.000
169A169HIS0-0.0020.00021.4080.0200.0200.0000.0000.0000.000
170A170LEU00.0010.00024.4850.0160.0160.0000.0000.0000.000
171A171SER0-0.0040.00721.5390.0090.0090.0000.0000.0000.000
172A172LEU0-0.0010.00221.4890.0180.0180.0000.0000.0000.000
173A173ILE0-0.041-0.02524.4970.0200.0200.0000.0000.0000.000
174A174ASP-1-0.796-0.88926.204-0.153-0.1530.0000.0000.0000.000
175A175TYR00.007-0.00222.0290.0140.0140.0000.0000.0000.000
176A176ALA0-0.032-0.01826.1920.0150.0150.0000.0000.0000.000
177A177GLY0-0.022-0.00929.3100.0140.0140.0000.0000.0000.000
178A178ASP-1-0.864-0.92031.302-0.141-0.1410.0000.0000.0000.000
179A179VAL00.0340.01429.576-0.002-0.0020.0000.0000.0000.000
180A180PRO0-0.046-0.00232.9000.0060.0060.0000.0000.0000.000
181A181TRP00.049-0.02028.3590.0010.0010.0000.0000.0000.000
182A182GLU-1-0.825-0.89834.903-0.097-0.0970.0000.0000.0000.000
183A183ASP-1-0.919-0.95338.119-0.096-0.0960.0000.0000.0000.000
184A184HIS0-0.097-0.06535.986-0.002-0.0020.0000.0000.0000.000
185A185PRO00.0730.03035.783-0.008-0.0080.0000.0000.0000.000
186A186GLN0-0.016-0.01235.436-0.003-0.0030.0000.0000.0000.000
187A187ALA0-0.003-0.00832.597-0.007-0.0070.0000.0000.0000.000
188A188LYS10.8240.90231.1860.0870.0870.0000.0000.0000.000
189A189GLU-1-0.900-0.95630.611-0.111-0.1110.0000.0000.0000.000
190A190TRP0-0.046-0.01825.894-0.007-0.0070.0000.0000.0000.000
191A191TYR0-0.050-0.03724.158-0.024-0.0240.0000.0000.0000.000
192A192ALA00.0460.02725.756-0.013-0.0130.0000.0000.0000.000
193A193LEU0-0.0010.01625.756-0.001-0.0010.0000.0000.0000.000
194A194VAL0-0.056-0.03621.588-0.010-0.0100.0000.0000.0000.000
195A195LYS10.7970.89721.2630.1340.1340.0000.0000.0000.000
196A196SER00.018-0.00221.0990.0040.0040.0000.0000.0000.000
197A197ARG10.7890.88718.7820.2890.2890.0000.0000.0000.000
198A198PRO0-0.021-0.02915.099-0.013-0.0130.0000.0000.0000.000
199A199SER0-0.044-0.03913.616-0.006-0.0060.0000.0000.0000.000
200A200PHE00.0570.01114.495-0.068-0.0680.0000.0000.0000.000
201A201ARG10.9831.00214.8520.1350.1350.0000.0000.0000.000
202A202PRO00.0210.00011.6120.0360.0360.0000.0000.0000.000
203A203LEU0-0.0150.00314.3380.0110.0110.0000.0000.0000.000
204A204LEU0-0.0450.01217.1800.0280.0280.0000.0000.0000.000
205A205THR00.006-0.00515.9040.0260.0260.0000.0000.0000.000
206A206GLU-1-0.838-0.86312.745-0.444-0.4440.0000.0000.0000.000
207A207THR0-0.055-0.03817.4850.0100.0100.0000.0000.0000.000
208A208ILE00.0370.02419.369-0.022-0.0220.0000.0000.0000.000
209A209SER0-0.0340.01021.5240.0260.0260.0000.0000.0000.000
210A210PRO00.0780.03323.996-0.018-0.0180.0000.0000.0000.000
211A211ILE0-0.030-0.03025.8710.0180.0180.0000.0000.0000.000
212A212ARG10.8370.92123.4330.1160.1160.0000.0000.0000.000
213A213PRO00.0590.04623.923-0.001-0.0010.0000.0000.0000.000
214A214PRO00.0070.00327.0390.0170.0170.0000.0000.0000.000
215A215ARG10.9630.96628.2860.0550.0550.0000.0000.0000.000
216A216HIS00.008-0.00729.1550.0150.0150.0000.0000.0000.000
217A217TYR0-0.055-0.02620.656-0.010-0.0100.0000.0000.0000.000
218A218ALA00.008-0.01122.731-0.015-0.0150.0000.0000.0000.000
219A219ASP-1-0.894-0.94124.143-0.072-0.0720.0000.0000.0000.000
220A220LEU0-0.002-0.01022.144-0.013-0.0130.0000.0000.0000.000
221A221ASP-1-0.923-0.94726.212-0.073-0.0730.0000.0000.0000.000
222A222PHE0-0.063-0.02728.3830.0030.0030.0000.0000.0000.000