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: 7MJGK

Calculation Name: 1B6D-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B6D

Chain ID: B

ChEMBL ID:

UniProt ID:

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 OptAll
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2177679.548981
FMO2-HF: Nuclear repulsion 2096876.053679
FMO2-HF: Total energy -80803.495302
FMO2-MP2: Total energy -81039.69141


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(B:1:ASP)


Summations of interaction energy for fragment #1(B:1:ASP)
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.
-4.4051.2392.365-3.262-4.7450.033
Interaction energy analysis for fragmet #1(B:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.876 / q_NPA : -0.952
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].
3B3GLN0-0.062-0.0173.430-7.078-4.4740.056-1.108-1.5520.005
4B4MET00.0030.0145.229-3.072-3.009-0.001-0.006-0.0560.000
5B5THR0-0.005-0.0118.508-0.332-0.3320.0000.0000.0000.000
6B6GLN00.035-0.00711.8050.5290.5290.0000.0000.0000.000
7B7SER0-0.0390.00315.080-0.384-0.3840.0000.0000.0000.000
8B8PRO00.0420.02418.704-0.219-0.2190.0000.0000.0000.000
9B9SER00.0670.03618.7550.2100.2100.0000.0000.0000.000
10B10SER0-0.030-0.02519.7860.0930.0930.0000.0000.0000.000
11B11LEU00.0180.01923.265-0.126-0.1260.0000.0000.0000.000
12B12SER00.0360.01726.421-0.151-0.1510.0000.0000.0000.000
13B13ALA00.0090.01029.910-0.119-0.1190.0000.0000.0000.000
14B14SER00.005-0.00131.768-0.046-0.0460.0000.0000.0000.000
15B15VAL0-0.015-0.01134.5660.1590.1590.0000.0000.0000.000
16B16GLY00.0310.02035.231-0.260-0.2600.0000.0000.0000.000
17B17ASP-1-0.781-0.88332.3649.0289.0280.0000.0000.0000.000
18B18ARG10.9320.98229.878-9.621-9.6210.0000.0000.0000.000
19B19VAL0-0.0050.00625.7760.1030.1030.0000.0000.0000.000
20B20THR0-0.019-0.02324.048-0.098-0.0980.0000.0000.0000.000
21B21ILE0-0.048-0.01719.031-0.026-0.0260.0000.0000.0000.000
22B22THR00.000-0.00618.7080.0100.0100.0000.0000.0000.000
23B23CYS0-0.005-0.00612.8890.3140.3140.0000.0000.0000.000
24B24GLN00.0040.02812.998-0.452-0.4520.0000.0000.0000.000
25B25ALA00.0450.0218.8121.5431.5430.0000.0000.0000.000
26B26SER0-0.043-0.0134.851-1.880-1.807-0.001-0.023-0.0480.000
27B27GLN0-0.013-0.0105.4751.5991.5990.0000.0000.0000.000
28B28ASP-1-0.874-0.9389.09118.60318.6030.0000.0000.0000.000
29B29ILE00.0070.0078.8261.7881.7880.0000.0000.0000.000
30B30SER0-0.028-0.01811.521-1.085-1.0850.0000.0000.0000.000
31B31SER00.0500.01815.340-0.359-0.3590.0000.0000.0000.000
32B32TYR0-0.041-0.00412.595-1.141-1.1410.0000.0000.0000.000
33B33LEU00.011-0.00211.8451.9041.9040.0000.0000.0000.000
34B34ASN0-0.024-0.00513.847-2.436-2.4360.0000.0000.0000.000
35B35TRP00.0400.00815.1510.8920.8920.0000.0000.0000.000
36B36TYR0-0.015-0.02914.680-1.291-1.2910.0000.0000.0000.000
37B37GLN00.0090.01519.148-0.211-0.2110.0000.0000.0000.000
38B38GLN0-0.0020.00419.7370.4250.4250.0000.0000.0000.000
39B39LYS10.8700.93122.414-11.050-11.0500.0000.0000.0000.000
40B40PRO00.0420.00125.2790.2720.2720.0000.0000.0000.000
41B41GLY00.0430.03525.440-0.417-0.4170.0000.0000.0000.000
42B42LYS10.8430.92124.913-11.381-11.3810.0000.0000.0000.000
43B43ALA00.0720.04021.8500.5330.5330.0000.0000.0000.000
44B44PRO0-0.001-0.00917.721-0.604-0.6040.0000.0000.0000.000
45B45LYS10.8940.96020.683-12.103-12.1030.0000.0000.0000.000
46B46LEU00.0190.01917.9710.1210.1210.0000.0000.0000.000
47B47LEU0-0.066-0.04220.844-0.821-0.8210.0000.0000.0000.000
48B48ILE0-0.0010.00720.653-0.641-0.6410.0000.0000.0000.000
49B49HIS00.0410.03417.3370.6430.6430.0000.0000.0000.000
50B50ALA00.0310.01117.920-0.625-0.6250.0000.0000.0000.000
51B51ALA00.0400.02617.612-0.676-0.6760.0000.0000.0000.000
52B52SER0-0.051-0.03918.808-0.179-0.1790.0000.0000.0000.000
53B53SER0-0.028-0.00922.073-0.810-0.8100.0000.0000.0000.000
54B54LEU0-0.041-0.02123.3760.4010.4010.0000.0000.0000.000
55B55GLU-1-0.873-0.94822.96312.58612.5860.0000.0000.0000.000
56B56THR0-0.020-0.01325.722-0.575-0.5750.0000.0000.0000.000
57B57GLY0-0.0020.00129.118-0.044-0.0440.0000.0000.0000.000
58B58VAL0-0.091-0.03426.149-0.143-0.1430.0000.0000.0000.000
59B59PRO00.0230.00229.421-0.121-0.1210.0000.0000.0000.000
60B60SER00.0470.01630.0820.1740.1740.0000.0000.0000.000
61B61ARG10.7320.84130.407-9.767-9.7670.0000.0000.0000.000
62B62PHE0-0.012-0.00525.8800.1210.1210.0000.0000.0000.000
63B63SER0-0.013-0.00126.084-0.328-0.3280.0000.0000.0000.000
64B64GLY00.0290.00522.0260.2620.2620.0000.0000.0000.000
65B65SER0-0.038-0.03021.209-0.721-0.7210.0000.0000.0000.000
66B66GLY00.0480.01818.8690.4510.4510.0000.0000.0000.000
67B67SER0-0.013-0.01217.728-0.282-0.2820.0000.0000.0000.000
68B68GLY0-0.0050.02014.919-0.338-0.3380.0000.0000.0000.000
69B69THR00.005-0.01612.3271.1751.1750.0000.0000.0000.000
70B70ASP-1-0.851-0.90613.64318.21018.2100.0000.0000.0000.000
71B71PHE0-0.004-0.00613.430-0.947-0.9470.0000.0000.0000.000
72B72SER0-0.029-0.01617.648-0.072-0.0720.0000.0000.0000.000
73B73PHE00.0060.00620.160-0.129-0.1290.0000.0000.0000.000
74B74THR0-0.032-0.02121.812-0.368-0.3680.0000.0000.0000.000
75B75ILE0-0.0090.01125.514-0.024-0.0240.0000.0000.0000.000
76B76SER0-0.036-0.05228.318-0.243-0.2430.0000.0000.0000.000
77B77SER0-0.004-0.00431.518-0.266-0.2660.0000.0000.0000.000
78B78LEU0-0.070-0.01429.3390.0820.0820.0000.0000.0000.000
79B79GLN00.0430.01032.034-0.455-0.4550.0000.0000.0000.000
80B80PRO00.042-0.00432.5710.2650.2650.0000.0000.0000.000
81B81GLU-1-0.827-0.87831.9089.2579.2570.0000.0000.0000.000
82B82ASP-1-0.766-0.86528.62810.66010.6600.0000.0000.0000.000
83B83LEU0-0.0480.00827.5780.4200.4200.0000.0000.0000.000
84B84ALA0-0.038-0.02524.483-0.091-0.0910.0000.0000.0000.000
85B85THR00.0040.01019.141-0.279-0.2790.0000.0000.0000.000
86B86TYR0-0.005-0.01519.868-0.116-0.1160.0000.0000.0000.000
87B87TYR0-0.019-0.02014.4170.1970.1970.0000.0000.0000.000
88B89GLN00.0200.01210.323-1.365-1.3650.0000.0000.0000.000
89B90GLN00.0260.0105.039-5.587-5.5870.0000.0000.0000.000
90B91TYR0-0.074-0.0699.4501.0421.0420.0000.0000.0000.000
91B92ASP-1-0.856-0.9208.63426.46226.4620.0000.0000.0000.000
92B93SER0-0.001-0.0046.801-0.668-0.6680.0000.0000.0000.000
93B94LEU0-0.031-0.0026.4791.0451.0450.0000.0000.0000.000
94B95PRO00.0010.0092.471-5.412-2.6942.312-2.095-2.9350.028
95B96LEU0-0.051-0.0245.246-5.866-5.879-0.001-0.0020.0170.000
96B97THR00.0020.0043.680-2.606-2.4070.000-0.028-0.1710.000
97B98PHE00.012-0.0026.522-3.577-3.5770.0000.0000.0000.000
98B99GLY00.0480.0228.7252.1992.1990.0000.0000.0000.000
99B100GLY0-0.049-0.02710.989-0.685-0.6850.0000.0000.0000.000
100B101GLY0-0.024-0.00613.047-0.933-0.9330.0000.0000.0000.000
101B102THR0-0.023-0.03016.2370.0120.0120.0000.0000.0000.000
102B103LYS10.8110.90819.658-11.943-11.9430.0000.0000.0000.000
103B104VAL00.0330.02622.833-0.298-0.2980.0000.0000.0000.000
104B105GLU-1-0.796-0.87425.91410.92310.9230.0000.0000.0000.000
105B106ILE00.0450.02329.127-0.085-0.0850.0000.0000.0000.000
106B107LYS10.8190.89132.713-9.199-9.1990.0000.0000.0000.000
107B108ARG10.8310.92134.228-9.000-9.0000.0000.0000.0000.000
108B109THR00.003-0.00937.4200.0340.0340.0000.0000.0000.000
109B110VAL0-0.0160.01635.5370.1540.1540.0000.0000.0000.000
110B111ALA0-0.0160.00136.108-0.240-0.2400.0000.0000.0000.000
111B112ALA00.0300.00935.3420.2940.2940.0000.0000.0000.000
112B113PRO0-0.0030.01232.369-0.106-0.1060.0000.0000.0000.000
113B114SER0-0.011-0.00135.010-0.156-0.1560.0000.0000.0000.000
114B115VAL00.0130.00733.1130.1750.1750.0000.0000.0000.000
115B116PHE0-0.043-0.02834.601-0.352-0.3520.0000.0000.0000.000
116B117ILE0-0.024-0.01832.9260.2810.2810.0000.0000.0000.000
117B118PHE0-0.003-0.00233.571-0.338-0.3380.0000.0000.0000.000
118B119PRO00.0220.02233.5880.3240.3240.0000.0000.0000.000
119B120PRO0-0.019-0.00432.4080.0070.0070.0000.0000.0000.000
120B121SER00.0320.00834.250-0.167-0.1670.0000.0000.0000.000
121B122ASP-1-0.845-0.93436.3888.0808.0800.0000.0000.0000.000
122B123GLU-1-0.791-0.88137.9328.1458.1450.0000.0000.0000.000
123B124GLN0-0.0090.01630.1830.5240.5240.0000.0000.0000.000
124B125LEU00.010-0.00133.5000.2230.2230.0000.0000.0000.000
125B126LYS10.7860.87735.267-8.012-8.0120.0000.0000.0000.000
126B127SER0-0.043-0.02032.389-0.021-0.0210.0000.0000.0000.000
127B128GLY00.0000.00131.6520.3560.3560.0000.0000.0000.000
128B129THR0-0.051-0.02327.5270.4000.4000.0000.0000.0000.000
129B130ALA0-0.008-0.01729.292-0.378-0.3780.0000.0000.0000.000
130B131SER00.0140.00927.5940.4540.4540.0000.0000.0000.000
131B132VAL0-0.045-0.00928.907-0.425-0.4250.0000.0000.0000.000
132B133VAL00.0130.00828.7790.3910.3910.0000.0000.0000.000
133B134CYS0-0.051-0.01329.256-0.063-0.0630.0000.0000.0000.000
134B135LEU0-0.0050.00629.3800.3380.3380.0000.0000.0000.000
135B136LEU00.0310.02128.737-0.415-0.4150.0000.0000.0000.000
136B137ASN0-0.015-0.03231.6430.3550.3550.0000.0000.0000.000
137B138ASN00.0200.02734.275-0.156-0.1560.0000.0000.0000.000
138B139PHE0-0.0070.00328.024-0.205-0.2050.0000.0000.0000.000
139B140TYR00.006-0.01231.0870.2870.2870.0000.0000.0000.000
140B141PRO00.0240.01129.546-0.303-0.3030.0000.0000.0000.000
141B142ARG10.8570.88222.503-12.764-12.7640.0000.0000.0000.000
142B143GLU-1-0.980-0.97825.87611.42411.4240.0000.0000.0000.000
143B144ALA00.0130.00025.961-0.513-0.5130.0000.0000.0000.000
144B145LYS10.8290.91524.654-10.349-10.3490.0000.0000.0000.000
145B146VAL00.0260.01325.318-0.586-0.5860.0000.0000.0000.000
146B147GLN0-0.011-0.01624.5370.1550.1550.0000.0000.0000.000
147B148TRP00.0030.00025.003-0.741-0.7410.0000.0000.0000.000
148B149LYS10.8710.92527.774-9.514-9.5140.0000.0000.0000.000
149B150VAL00.003-0.00129.619-0.183-0.1830.0000.0000.0000.000
150B151ASP-1-0.803-0.90131.9788.7338.7330.0000.0000.0000.000
151B152ASN0-0.045-0.03033.8600.0160.0160.0000.0000.0000.000
152B153ALA00.0460.04229.9920.0750.0750.0000.0000.0000.000
153B154LEU0-0.011-0.00425.2530.0570.0570.0000.0000.0000.000
154B155GLN0-0.047-0.02025.0390.4070.4070.0000.0000.0000.000
155B156SER00.001-0.00720.0420.3200.3200.0000.0000.0000.000
156B157GLY00.0220.01117.629-0.083-0.0830.0000.0000.0000.000
157B158ASN00.0050.00018.5840.5780.5780.0000.0000.0000.000
158B159SER00.0320.00820.600-0.629-0.6290.0000.0000.0000.000
159B160GLN0-0.054-0.02016.5511.2991.2990.0000.0000.0000.000
160B161GLU-1-0.813-0.89020.20712.19112.1910.0000.0000.0000.000
161B162SER0-0.015-0.01320.9450.5790.5790.0000.0000.0000.000
162B163VAL0-0.0090.00223.082-0.621-0.6210.0000.0000.0000.000
163B164THR0-0.0100.00624.6950.3360.3360.0000.0000.0000.000
164B165GLU-1-0.813-0.89924.81812.04412.0440.0000.0000.0000.000
165B166GLN00.0040.00227.112-0.318-0.3180.0000.0000.0000.000
166B167ASP-1-0.841-0.92830.51910.05610.0560.0000.0000.0000.000
167B168SER0-0.0080.00031.955-0.281-0.2810.0000.0000.0000.000
168B169LYS10.8040.89329.422-10.369-10.3690.0000.0000.0000.000
169B170ASP-1-0.912-0.94633.3918.4238.4230.0000.0000.0000.000
170B171SER00.0100.00034.272-0.265-0.2650.0000.0000.0000.000
171B172THR0-0.084-0.05433.7270.0230.0230.0000.0000.0000.000
172B173TYR0-0.052-0.03727.5040.3330.3330.0000.0000.0000.000
173B174SER00.0340.00830.041-0.395-0.3950.0000.0000.0000.000
174B175LEU0-0.031-0.00324.7990.3030.3030.0000.0000.0000.000
175B176SER00.0230.01626.582-0.496-0.4960.0000.0000.0000.000
176B177SER0-0.011-0.03124.6070.5180.5180.0000.0000.0000.000
177B178THR00.003-0.00824.384-0.762-0.7620.0000.0000.0000.000
178B179LEU0-0.0010.01523.9870.6010.6010.0000.0000.0000.000
179B180THR00.005-0.01323.833-0.428-0.4280.0000.0000.0000.000
180B181LEU0-0.036-0.00924.6930.3420.3420.0000.0000.0000.000
181B182SER00.045-0.00927.149-0.264-0.2640.0000.0000.0000.000
182B183LYS10.8590.90728.956-8.761-8.7610.0000.0000.0000.000
183B184ALA00.0520.01932.266-0.232-0.2320.0000.0000.0000.000
184B185ASP-1-0.833-0.87728.80810.67810.6780.0000.0000.0000.000
185B186TYR00.0280.01431.204-0.140-0.1400.0000.0000.0000.000
186B187GLU-1-0.822-0.90232.6848.2998.2990.0000.0000.0000.000
187B188LYS10.8550.92730.919-10.311-10.3110.0000.0000.0000.000
188B189HIS10.8410.94230.699-9.854-9.8540.0000.0000.0000.000
189B190LYS10.9200.95535.808-8.033-8.0330.0000.0000.0000.000
190B191VAL0-0.009-0.00136.735-0.127-0.1270.0000.0000.0000.000
191B192TYR00.004-0.00431.0750.3760.3760.0000.0000.0000.000
192B193ALA00.018-0.00732.762-0.263-0.2630.0000.0000.0000.000
193B195GLU-1-0.838-0.90230.5019.5559.5550.0000.0000.0000.000
194B196VAL00.0290.00629.7180.4190.4190.0000.0000.0000.000
195B197THR00.0040.00029.501-0.264-0.2640.0000.0000.0000.000
196B198HIS00.0640.01329.7340.1260.1260.0000.0000.0000.000
197B199GLN00.0420.01931.722-0.166-0.1660.0000.0000.0000.000
198B200GLY00.0160.01233.666-0.243-0.2430.0000.0000.0000.000
199B201LEU0-0.085-0.03434.003-0.228-0.2280.0000.0000.0000.000
200B202SER00.0140.00436.6170.0870.0870.0000.0000.0000.000
201B203SER0-0.023-0.02137.252-0.127-0.1270.0000.0000.0000.000
202B204PRO0-0.020-0.00632.834-0.002-0.0020.0000.0000.0000.000
203B205VAL00.0380.03234.753-0.204-0.2040.0000.0000.0000.000
204B206THR0-0.013-0.00434.5250.3430.3430.0000.0000.0000.000
205B207LYS10.9180.97334.964-8.407-8.4070.0000.0000.0000.000
206B208SER00.020-0.00735.0790.2620.2620.0000.0000.0000.000
207B209PHE0-0.026-0.00334.003-0.204-0.2040.0000.0000.0000.000
208B210ASN00.0460.01137.8270.2630.2630.0000.0000.0000.000
209B211ARG10.8200.91536.794-8.343-8.3430.0000.0000.0000.000
210B212GLY00.0060.00539.307-0.127-0.1270.0000.0000.0000.000