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: 43MMN

Calculation Name: 3C9B-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C9B

Chain ID: B

ChEMBL ID:

UniProt ID: P53853

Base Structure: X-ray

Registration Date: 2023-06-21

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2460014.997501
FMO2-HF: Nuclear repulsion 2375816.077642
FMO2-HF: Total energy -84198.919859
FMO2-MP2: Total energy -84447.273192


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:17:GLY)


Summations of interaction energy for fragment #1(B:17:GLY)
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.
-2.0620.0790.052-0.861-1.3340
Interaction energy analysis for fragmet #1(B:17:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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].
3B19ALA00.0460.0233.869-1.2160.058-0.001-0.578-0.6960.001
4B20LYS10.7380.8462.9131.2212.0880.053-0.283-0.638-0.001
5B21CYS00.0140.0044.8410.4620.4620.0000.0000.0000.000
6B22GLU-1-0.931-0.9596.767-0.099-0.0990.0000.0000.0000.000
7B23GLU-1-0.804-0.8778.023-0.792-0.7920.0000.0000.0000.000
8B24GLU-1-0.930-0.9667.226-1.400-1.4000.0000.0000.0000.000
9B25VAL0-0.009-0.00310.7060.1580.1580.0000.0000.0000.000
10B26ASP-1-0.905-0.94912.820-0.223-0.2230.0000.0000.0000.000
11B27ALA0-0.033-0.01713.8520.0700.0700.0000.0000.0000.000
12B28ILE00.003-0.00613.4140.0650.0650.0000.0000.0000.000
13B29GLU-1-0.918-0.95816.668-0.215-0.2150.0000.0000.0000.000
14B30ARG10.8510.92218.6050.2240.2240.0000.0000.0000.000
15B31GLU-1-0.959-0.97018.729-0.273-0.2730.0000.0000.0000.000
16B32VAL0-0.008-0.01720.4380.0340.0340.0000.0000.0000.000
17B33GLU-1-0.822-0.87122.728-0.115-0.1150.0000.0000.0000.000
18B34LEU00.0210.01124.0800.0190.0190.0000.0000.0000.000
19B35TYR00.0310.02324.9150.0240.0240.0000.0000.0000.000
20B36ARG10.8050.86425.9300.1470.1470.0000.0000.0000.000
21B37LEU00.0120.00728.2250.0120.0120.0000.0000.0000.000
22B38ASN0-0.033-0.03228.3810.0160.0160.0000.0000.0000.000
23B39LYS10.8390.92229.9010.1230.1230.0000.0000.0000.000
24B40MET0-0.012-0.00132.6200.0070.0070.0000.0000.0000.000
25B41LYS10.9270.97434.4470.0840.0840.0000.0000.0000.000
26B42PRO0-0.0060.00035.7640.0060.0060.0000.0000.0000.000
27B43VAL00.0370.01237.4360.0050.0050.0000.0000.0000.000
28B44TYR00.0260.00435.5810.0050.0050.0000.0000.0000.000
29B45GLU-1-0.811-0.88839.888-0.066-0.0660.0000.0000.0000.000
30B46LYS10.7920.88841.5180.0670.0670.0000.0000.0000.000
31B47ARG10.7670.87441.5600.0580.0580.0000.0000.0000.000
32B48ASP-1-0.726-0.85043.168-0.053-0.0530.0000.0000.0000.000
33B49ALA0-0.0060.00345.9770.0020.0020.0000.0000.0000.000
34B50TYR0-0.010-0.00247.5930.0010.0010.0000.0000.0000.000
35B51ILE0-0.069-0.02845.9150.0020.0020.0000.0000.0000.000
36B52ASP-1-0.909-0.95449.967-0.040-0.0400.0000.0000.0000.000
37B53GLU-1-0.973-0.97851.973-0.035-0.0350.0000.0000.0000.000
38B54ILE0-0.087-0.03751.6530.0020.0020.0000.0000.0000.000
39B55ALA0-0.010-0.01554.7450.0000.0000.0000.0000.0000.000
40B56GLU-1-0.877-0.94256.336-0.024-0.0240.0000.0000.0000.000
41B57PHE00.018-0.00447.3000.0000.0000.0000.0000.0000.000
42B58TRP00.0540.00744.2660.0000.0000.0000.0000.0000.000
43B59LYS10.8450.94950.8450.0240.0240.0000.0000.0000.000
44B60ILE00.0170.01452.9080.0010.0010.0000.0000.0000.000
45B61VAL0-0.010-0.00746.8870.0000.0000.0000.0000.0000.000
46B62LEU0-0.044-0.03547.0800.0000.0000.0000.0000.0000.000
47B63SER0-0.081-0.04350.1490.0020.0020.0000.0000.0000.000
48B64GLN0-0.079-0.03949.8430.0020.0020.0000.0000.0000.000
49B65HIS0-0.058-0.03642.8720.0020.0020.0000.0000.0000.000
50B66VAL00.0280.00445.5920.0010.0010.0000.0000.0000.000
51B67SER0-0.024-0.00442.7290.0020.0020.0000.0000.0000.000
52B68PHE00.0660.02145.6750.0010.0010.0000.0000.0000.000
53B69ALA00.0360.00946.7630.0010.0010.0000.0000.0000.000
54B70ASN0-0.090-0.03947.3040.0030.0030.0000.0000.0000.000
55B71TYR0-0.039-0.01141.6230.0010.0010.0000.0000.0000.000
56B72ILE0-0.048-0.00547.5590.0000.0000.0000.0000.0000.000
57B73ARG10.8760.93150.7770.0160.0160.0000.0000.0000.000
58B74ALA00.0630.02254.512-0.001-0.0010.0000.0000.0000.000
59B75SER0-0.061-0.04657.3080.0000.0000.0000.0000.0000.000
60B76ASP-1-0.725-0.84752.945-0.020-0.0200.0000.0000.0000.000
61B77PHE00.0480.02352.708-0.001-0.0010.0000.0000.0000.000
62B78LYS10.8970.95256.1690.0170.0170.0000.0000.0000.000
63B79TYR0-0.034-0.04055.5340.0000.0000.0000.0000.0000.000
64B80ILE00.0160.01251.267-0.001-0.0010.0000.0000.0000.000
65B81ASP-1-0.823-0.90753.799-0.024-0.0240.0000.0000.0000.000
66B82THR0-0.104-0.05856.0790.0000.0000.0000.0000.0000.000
67B83ILE0-0.049-0.01149.754-0.001-0.0010.0000.0000.0000.000
68B84ASP-1-0.791-0.86953.012-0.033-0.0330.0000.0000.0000.000
69B85LYS10.9210.95747.9520.0400.0400.0000.0000.0000.000
70B86ILE0-0.023-0.01144.0580.0010.0010.0000.0000.0000.000
71B87LYS10.7910.89439.6360.0640.0640.0000.0000.0000.000
72B88VAL0-0.0110.00536.8910.0020.0020.0000.0000.0000.000
73B89GLU-1-0.844-0.89636.825-0.070-0.0700.0000.0000.0000.000
74B90TRP00.041-0.00431.2970.0040.0040.0000.0000.0000.000
75B91LEU0-0.002-0.00531.398-0.004-0.0040.0000.0000.0000.000
76B92ALA0-0.0040.00426.686-0.003-0.0030.0000.0000.0000.000
77B93LEU0-0.057-0.02927.890-0.010-0.0100.0000.0000.0000.000
78B94GLU-1-0.968-0.97830.508-0.088-0.0880.0000.0000.0000.000
79B95SER0-0.058-0.04827.8370.0030.0030.0000.0000.0000.000
80B96GLU-1-0.860-0.93223.003-0.144-0.1440.0000.0000.0000.000
81B97MET0-0.078-0.03623.948-0.008-0.0080.0000.0000.0000.000
82B98TYR0-0.0340.01325.8110.0120.0120.0000.0000.0000.000
83B99ASP-1-0.732-0.84824.567-0.137-0.1370.0000.0000.0000.000
84B100THR00.007-0.01324.2290.0060.0060.0000.0000.0000.000
85B101ARG10.7540.84124.4870.1060.1060.0000.0000.0000.000
86B102ASP-1-0.789-0.87928.811-0.081-0.0810.0000.0000.0000.000
87B103PHE0-0.002-0.00530.851-0.002-0.0020.0000.0000.0000.000
88B104SER0-0.028-0.01734.3440.0030.0030.0000.0000.0000.000
89B105ILE0-0.0180.00337.993-0.001-0.0010.0000.0000.0000.000
90B106THR0-0.046-0.03641.0910.0020.0020.0000.0000.0000.000
91B107PHE00.0300.00744.1460.0000.0000.0000.0000.0000.000
92B108HIS10.7360.80747.6220.0320.0320.0000.0000.0000.000
93B109PHE00.0050.00350.0890.0000.0000.0000.0000.0000.000
94B110HIS00.0670.02554.249-0.001-0.0010.0000.0000.0000.000
95B111GLY00.0000.00757.5900.0010.0010.0000.0000.0000.000
96B112ILE0-0.061-0.04759.1500.0000.0000.0000.0000.0000.000
97B113GLU-1-0.895-0.94662.537-0.019-0.0190.0000.0000.0000.000
98B114GLY00.0060.00365.3850.0010.0010.0000.0000.0000.000
99B115ASP-1-0.804-0.85362.678-0.017-0.0170.0000.0000.0000.000
100B116PHE0-0.022-0.02754.3850.0000.0000.0000.0000.0000.000
101B117LYS10.8450.92657.8490.0230.0230.0000.0000.0000.000
102B118GLU-1-0.827-0.87956.141-0.030-0.0300.0000.0000.0000.000
103B119GLN00.0120.00952.9970.0000.0000.0000.0000.0000.000
104B120GLN00.0200.00548.513-0.001-0.0010.0000.0000.0000.000
105B121VAL0-0.029-0.00546.5970.0000.0000.0000.0000.0000.000
106B122THR00.0350.02041.567-0.001-0.0010.0000.0000.0000.000
107B123LYS10.7720.90240.7400.0380.0380.0000.0000.0000.000
108B124VAL00.0420.02535.601-0.002-0.0020.0000.0000.0000.000
109B125PHE0-0.023-0.01135.4720.0060.0060.0000.0000.0000.000
110B126GLN00.0690.04131.114-0.003-0.0030.0000.0000.0000.000
111B127ILE00.0010.00826.0280.0090.0090.0000.0000.0000.000
112B128LYS10.7810.88828.3510.0510.0510.0000.0000.0000.000
113B129LYS10.9040.93921.0860.1030.1030.0000.0000.0000.000
114B130GLY0-0.016-0.00626.6660.0020.0020.0000.0000.0000.000
115B131LYS10.7090.84027.9050.0300.0300.0000.0000.0000.000
116B132ASP-1-0.775-0.87526.196-0.038-0.0380.0000.0000.0000.000
117B133ASP-1-0.875-0.93224.8620.0180.0180.0000.0000.0000.000
118B134GLN0-0.120-0.08718.4090.0010.0010.0000.0000.0000.000
119B135GLU-1-0.797-0.87117.949-0.018-0.0180.0000.0000.0000.000
120B136ASP-1-0.881-0.91420.880-0.092-0.0920.0000.0000.0000.000
121B137GLY0-0.001-0.00623.643-0.013-0.0130.0000.0000.0000.000
122B138ILE0-0.032-0.02126.4700.0050.0050.0000.0000.0000.000
123B139LEU00.0310.02630.190-0.003-0.0030.0000.0000.0000.000
124B140THR0-0.097-0.05332.4530.0070.0070.0000.0000.0000.000
125B141SER0-0.001-0.03734.876-0.002-0.0020.0000.0000.0000.000
126B142GLU-1-0.890-0.93836.341-0.044-0.0440.0000.0000.0000.000
127B143PRO0-0.070-0.04240.1380.0000.0000.0000.0000.0000.000
128B144VAL00.0130.01843.976-0.001-0.0010.0000.0000.0000.000
129B145PRO0-0.053-0.03145.8520.0020.0020.0000.0000.0000.000
130B146ILE00.0230.02349.502-0.001-0.0010.0000.0000.0000.000
131B147GLU-1-0.857-0.92051.672-0.021-0.0210.0000.0000.0000.000
132B148TRP0-0.017-0.03251.8750.0010.0010.0000.0000.0000.000
133B149PRO00.0180.01856.5230.0000.0000.0000.0000.0000.000
134B150GLN00.0250.01559.7390.0010.0010.0000.0000.0000.000
135B151SER0-0.071-0.05962.3920.0010.0010.0000.0000.0000.000
136B152TYR0-0.099-0.08655.7830.0010.0010.0000.0000.0000.000
137B153ASP-1-0.753-0.88259.962-0.016-0.0160.0000.0000.0000.000
138B154SER0-0.093-0.04461.7920.0010.0010.0000.0000.0000.000
139B155ILE0-0.079-0.05957.0190.0010.0010.0000.0000.0000.000
140B156ASN00.0660.05856.867-0.001-0.0010.0000.0000.0000.000
141B157PRO0-0.020-0.00552.6530.0010.0010.0000.0000.0000.000
142B158ASP-1-0.771-0.84653.851-0.018-0.0180.0000.0000.0000.000
143B159LEU0-0.0180.00756.5940.0010.0010.0000.0000.0000.000
144B160ILE0-0.049-0.01757.6400.0010.0010.0000.0000.0000.000
145B161LYS10.9540.97859.7980.0120.0120.0000.0000.0000.000
146B162ASP-1-0.850-0.92460.967-0.008-0.0080.0000.0000.0000.000
147B163LYS10.8660.92154.7060.0140.0140.0000.0000.0000.000
148B164ARG10.9800.99357.3880.0060.0060.0000.0000.0000.000
149B165SER00.0440.03359.7180.0010.0010.0000.0000.0000.000
150B166PRO00.0200.00561.6510.0000.0000.0000.0000.0000.000
151B167GLU-1-0.811-0.88162.992-0.007-0.0070.0000.0000.0000.000
152B168GLY00.0470.01661.205-0.001-0.0010.0000.0000.0000.000
153B169LYS10.8950.93257.3140.0040.0040.0000.0000.0000.000
154B170LYS10.7990.88357.0420.0060.0060.0000.0000.0000.000
155B171LYS10.9350.97958.6070.0100.0100.0000.0000.0000.000
156B172TYR00.0710.02650.738-0.001-0.0010.0000.0000.0000.000
157B173ARG10.9230.95752.4820.0070.0070.0000.0000.0000.000
158B174GLN0-0.023-0.00853.377-0.001-0.0010.0000.0000.0000.000
159B175GLY00.1000.05754.392-0.001-0.0010.0000.0000.0000.000
160B176MET0-0.055-0.02448.454-0.002-0.0020.0000.0000.0000.000
161B177LYS10.9010.94449.2270.0130.0130.0000.0000.0000.000
162B178THR0-0.038-0.00551.0070.0000.0000.0000.0000.0000.000
163B179ILE00.0520.02247.5250.0000.0000.0000.0000.0000.000
164B180PHE00.0290.00948.827-0.001-0.0010.0000.0000.0000.000
165B181GLY0-0.035-0.01549.2230.0000.0000.0000.0000.0000.000
166B182TRP0-0.058-0.01641.3620.0000.0000.0000.0000.0000.000
167B183PHE00.0890.02844.364-0.001-0.0010.0000.0000.0000.000
168B184ARG10.7730.84245.0970.0200.0200.0000.0000.0000.000
169B185TRP0-0.0370.00936.5480.0000.0000.0000.0000.0000.000
170B186THR0-0.024-0.03139.215-0.001-0.0010.0000.0000.0000.000
171B187GLY00.1450.07837.156-0.003-0.0030.0000.0000.0000.000
172B188LEU0-0.055-0.03735.0470.0010.0010.0000.0000.0000.000
173B189LYS10.8380.92038.0930.0270.0270.0000.0000.0000.000
174B190PRO00.1060.04238.4350.0000.0000.0000.0000.0000.000
175B191GLY00.0110.00841.2240.0020.0020.0000.0000.0000.000
176B192LYS10.7890.88644.3820.0090.0090.0000.0000.0000.000
177B193GLU-1-0.744-0.83241.040-0.025-0.0250.0000.0000.0000.000
178B194PHE00.0220.01544.0740.0020.0020.0000.0000.0000.000
179B195PRO0-0.067-0.05443.7100.0000.0000.0000.0000.0000.000
180B196HIS00.0610.03740.398-0.001-0.0010.0000.0000.0000.000
181B197GLY00.0370.01540.949-0.002-0.0020.0000.0000.0000.000
182B198ASP-1-0.787-0.88135.849-0.033-0.0330.0000.0000.0000.000
183B199SER00.010-0.01037.297-0.003-0.0030.0000.0000.0000.000
184B200LEU0-0.038-0.00638.267-0.001-0.0010.0000.0000.0000.000
185B201ALA0-0.015-0.00937.606-0.001-0.0010.0000.0000.0000.000
186B202SER00.039-0.00933.957-0.002-0.0020.0000.0000.0000.000
187B203LEU0-0.068-0.01536.603-0.002-0.0020.0000.0000.0000.000
188B204PHE00.016-0.01439.8010.0000.0000.0000.0000.0000.000
189B205SER00.0060.00035.3720.0000.0000.0000.0000.0000.000
190B206GLU-1-0.873-0.91833.174-0.068-0.0680.0000.0000.0000.000
191B207GLU-1-0.846-0.91036.049-0.040-0.0400.0000.0000.0000.000
192B208ILE0-0.042-0.01939.4580.0000.0000.0000.0000.0000.000
193B209TYR0-0.022-0.05638.7240.0000.0000.0000.0000.0000.000
194B210PRO00.0280.02336.9180.0000.0000.0000.0000.0000.000
195B211PHE0-0.039-0.03336.0520.0000.0000.0000.0000.0000.000
196B212CYS0-0.0100.03741.8410.0020.0020.0000.0000.0000.000
197B213VAL00.0530.00844.9260.0020.0020.0000.0000.0000.000
198B214LYS10.8790.95340.5060.0520.0520.0000.0000.0000.000
199B215TYR00.0320.00142.2710.0010.0010.0000.0000.0000.000
200B216TYR00.0160.01147.9320.0020.0020.0000.0000.0000.000
201B217ALA0-0.020-0.02249.0800.0020.0020.0000.0000.0000.000
202B218GLU-1-0.952-0.96348.445-0.030-0.0300.0000.0000.0000.000
203B219ALA00.0300.01051.1700.0020.0020.0000.0000.0000.000
204B220GLN0-0.064-0.00153.7210.0010.0010.0000.0000.0000.000
205B221ARG10.8960.95052.2020.0290.0290.0000.0000.0000.000