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: 49M8N

Calculation Name: 5DUD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DUD

Chain ID: B

ChEMBL ID:

UniProt ID: P0AAV4

Base Structure: X-ray

Registration Date: 2023-09-20

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2315304.180093
FMO2-HF: Nuclear repulsion 2234760.119032
FMO2-HF: Total energy -80544.061062
FMO2-MP2: Total energy -80782.782054


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:3:ARG)


Summations of interaction energy for fragment #1(B:3:ARG)
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.
-264.472-270.5350.435-22.208-22.167-0.261
Interaction energy analysis for fragmet #1(B:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.798 / q_NPA : 0.883
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].
3B5ARG10.7980.8811.94516.45216.7399.970-4.554-5.702-0.044
4B6CYS00.0240.0144.4833.2493.350-0.001-0.017-0.0830.000
5B7TYR0-0.084-0.0436.9321.4851.4850.0000.0000.0000.000
6B8LEU00.0110.00910.6170.2430.2430.0000.0000.0000.000
7B9ILE0-0.031-0.01813.9790.1170.1170.0000.0000.0000.000
8B10GLY0-0.0040.00816.8170.7160.7160.0000.0000.0000.000
9B11GLU-1-0.886-0.94818.422-14.393-14.3930.0000.0000.0000.000
10B12THR0-0.016-0.03319.118-0.205-0.2050.0000.0000.0000.000
11B13ALA0-0.0170.00017.0370.0640.0640.0000.0000.0000.000
12B14VAL0-0.0120.00510.525-0.262-0.2620.0000.0000.0000.000
13B15VAL00.0070.00311.2450.9050.9050.0000.0000.0000.000
14B16LEU0-0.0030.0124.874-2.208-2.2080.0000.0000.0000.000
15B17GLU-1-0.844-0.9217.315-28.120-28.1200.0000.0000.0000.000
16B18LEU00.000-0.0073.860-8.208-7.8050.002-0.128-0.2760.000
17B19GLU-1-0.819-0.8871.863-54.539-54.65310.452-5.220-5.118-0.051
18B20PRO00.021-0.0054.6551.6951.776-0.001-0.009-0.0710.000
19B21PRO0-0.031-0.0115.9931.8631.8630.0000.0000.0000.000
20B22VAL00.0170.0147.376-1.200-1.2000.0000.0000.0000.000
21B23THR00.0060.0087.4140.6730.6730.0000.0000.0000.000
22B24LEU00.0240.02410.107-0.913-0.9130.0000.0000.0000.000
23B25ALA0-0.006-0.00310.7950.0360.0360.0000.0000.0000.000
24B26SER00.018-0.0067.234-1.132-1.1320.0000.0000.0000.000
25B27GLN00.007-0.0159.358-1.669-1.6690.0000.0000.0000.000
26B28LYS10.8240.90012.27316.87116.8710.0000.0000.0000.000
27B29ARG10.8330.9119.57526.93426.9340.0000.0000.0000.000
28B30ILE0-0.0030.0059.776-0.049-0.0490.0000.0000.0000.000
29B31TRP0-0.036-0.02012.7790.7110.7110.0000.0000.0000.000
30B32ARG10.7850.90014.62317.36917.3690.0000.0000.0000.000
31B33LEU00.002-0.0099.3170.3730.3730.0000.0000.0000.000
32B34ALA00.002-0.01213.4470.5040.5040.0000.0000.0000.000
33B35GLN0-0.052-0.03716.2260.3570.3570.0000.0000.0000.000
34B36ARG10.8770.92012.41421.92421.9240.0000.0000.0000.000
35B37LEU0-0.045-0.02512.8330.0250.0250.0000.0000.0000.000
36B38VAL00.0190.00816.8080.4430.4430.0000.0000.0000.000
37B39ASP-1-0.934-0.94420.361-13.470-13.4700.0000.0000.0000.000
38B40MET0-0.052-0.01416.2790.2380.2380.0000.0000.0000.000
39B41PRO00.024-0.00221.906-0.176-0.1760.0000.0000.0000.000
40B42ASN0-0.031-0.02118.442-0.492-0.4920.0000.0000.0000.000
41B43VAL00.0360.04217.297-0.414-0.4140.0000.0000.0000.000
42B44VAL0-0.078-0.04320.2710.8480.8480.0000.0000.0000.000
43B45GLU-1-0.880-0.94020.672-12.898-12.8980.0000.0000.0000.000
44B46ALA0-0.010-0.00816.874-0.961-0.9610.0000.0000.0000.000
45B47ILE0-0.0010.00817.2900.5420.5420.0000.0000.0000.000
46B48PRO00.0020.00315.453-1.094-1.0940.0000.0000.0000.000
47B49GLY00.0380.01014.3161.4121.4120.0000.0000.0000.000
48B50MET0-0.040-0.01612.694-0.551-0.5510.0000.0000.0000.000
49B51ASN00.0170.0126.2820.5590.5590.0000.0000.0000.000
50B52ASN0-0.058-0.0308.280-2.551-2.5510.0000.0000.0000.000
51B53ILE00.0300.01110.6131.9281.9280.0000.0000.0000.000
52B54THR00.0120.02112.037-1.508-1.5080.0000.0000.0000.000
53B55VAL0-0.012-0.01112.9340.8560.8560.0000.0000.0000.000
54B56ILE00.0140.00915.593-0.273-0.2730.0000.0000.0000.000
55B57LEU00.018-0.00115.6870.2140.2140.0000.0000.0000.000
56B58ARG10.8660.91019.57013.07013.0700.0000.0000.0000.000
57B59ASN0-0.061-0.03721.5250.6920.6920.0000.0000.0000.000
58B60PRO00.0480.03319.502-0.531-0.5310.0000.0000.0000.000
59B61GLU-1-0.846-0.90019.994-13.592-13.5920.0000.0000.0000.000
60B62SER0-0.060-0.04921.095-0.030-0.0300.0000.0000.0000.000
61B63LEU0-0.010-0.01416.926-0.550-0.5500.0000.0000.0000.000
62B64ALA0-0.0040.01915.550-1.342-1.3420.0000.0000.0000.000
63B65LEU0-0.004-0.01114.265-1.206-1.2060.0000.0000.0000.000
64B66ASP-1-0.770-0.87312.891-22.003-22.0030.0000.0000.0000.000
65B67ALA00.0090.01411.647-2.168-2.1680.0000.0000.0000.000
66B68ILE0-0.009-0.0118.040-2.457-2.4570.0000.0000.0000.000
67B69GLU-1-0.840-0.9097.107-29.431-29.4310.0000.0000.0000.000
68B70ARG10.7150.8438.04517.14317.1430.0000.0000.0000.000
69B71LEU00.0210.0098.259-0.786-0.7860.0000.0000.0000.000
70B72GLN00.0480.0271.828-26.698-29.77310.158-3.661-3.422-0.045
71B73ARG10.8480.9124.41623.85923.946-0.001-0.012-0.0740.000
72B74TRP00.013-0.0136.6641.4091.4090.0000.0000.0000.000
73B75TRP00.0020.0103.0607.5958.2380.074-0.152-0.5640.001
74B76GLU-1-0.839-0.9301.865-117.810-122.28119.782-8.455-6.857-0.122
75B77GLU-1-0.890-0.9055.415-19.811-19.8110.0000.0000.0000.000
76B78SER0-0.049-0.0337.5913.0513.0510.0000.0000.0000.000
77B79GLU-1-0.787-0.87710.153-19.111-19.1110.0000.0000.0000.000
78B80ALA0-0.018-0.01313.6890.6100.6100.0000.0000.0000.000
79B81LEU0-0.002-0.00513.8370.2440.2440.0000.0000.0000.000
80B82GLU-1-0.846-0.91916.545-15.137-15.1370.0000.0000.0000.000
81B83PRO00.0190.03618.2790.3900.3900.0000.0000.0000.000
82B84GLU-1-0.781-0.86920.534-13.777-13.7770.0000.0000.0000.000
83B85SER0-0.049-0.04722.1590.1120.1120.0000.0000.0000.000
84B86ARG10.7700.86923.22213.21813.2180.0000.0000.0000.000
85B87PHE00.001-0.00225.966-0.325-0.3250.0000.0000.0000.000
86B88ILE0-0.010-0.00228.7290.3160.3160.0000.0000.0000.000
87B89GLU-1-0.813-0.88730.703-9.224-9.2240.0000.0000.0000.000
88B90ILE0-0.019-0.00830.3340.0990.0990.0000.0000.0000.000
89B91PRO0-0.031-0.00734.2150.0360.0360.0000.0000.0000.000
90B92VAL0-0.001-0.00534.154-0.026-0.0260.0000.0000.0000.000
91B93VAL00.006-0.00337.5850.1450.1450.0000.0000.0000.000
92B94TYR00.018-0.01633.0970.0450.0450.0000.0000.0000.000
93B95GLY00.005-0.00339.5360.2030.2030.0000.0000.0000.000
94B96GLY0-0.009-0.00741.4370.0340.0340.0000.0000.0000.000
95B97ALA0-0.009-0.02443.489-0.079-0.0790.0000.0000.0000.000
96B98GLY00.0140.01741.345-0.063-0.0630.0000.0000.0000.000
97B99GLY0-0.0110.00138.773-0.232-0.2320.0000.0000.0000.000
98B100PRO0-0.010-0.00839.5810.0510.0510.0000.0000.0000.000
99B101ASP-1-0.756-0.85036.840-7.709-7.7090.0000.0000.0000.000
100B102LEU0-0.0250.01036.909-0.074-0.0740.0000.0000.0000.000
101B103ALA00.0210.00338.454-0.048-0.0480.0000.0000.0000.000
102B104VAL0-0.017-0.00137.5350.0640.0640.0000.0000.0000.000
103B105VAL00.012-0.00133.163-0.089-0.0890.0000.0000.0000.000
104B106ALA0-0.024-0.01035.402-0.094-0.0940.0000.0000.0000.000
105B107ALA00.0100.00337.611-0.009-0.0090.0000.0000.0000.000
106B108HIS0-0.090-0.05333.9890.1640.1640.0000.0000.0000.000
107B109CYS0-0.0330.00031.627-0.113-0.1130.0000.0000.0000.000
108B110GLY00.0010.02134.266-0.044-0.0440.0000.0000.0000.000
109B111LEU0-0.027-0.01434.2750.0800.0800.0000.0000.0000.000
110B112SER00.0280.00738.2560.0500.0500.0000.0000.0000.000
111B113GLU-1-0.822-0.93938.863-7.103-7.1030.0000.0000.0000.000
112B114LYS10.8900.95538.7586.5706.5700.0000.0000.0000.000
113B115GLN00.0430.01936.907-0.180-0.1800.0000.0000.0000.000
114B116VAL00.0050.00934.250-0.209-0.2090.0000.0000.0000.000
115B117VAL0-0.011-0.00233.788-0.227-0.2270.0000.0000.0000.000
116B118GLU-1-0.877-0.93634.850-7.500-7.5000.0000.0000.0000.000
117B119LEU00.0130.02229.721-0.163-0.1630.0000.0000.0000.000
118B120HIS00.0090.01029.047-0.036-0.0360.0000.0000.0000.000
119B121SER00.010-0.00930.275-0.227-0.2270.0000.0000.0000.000
120B122SER0-0.089-0.05431.3580.0270.0270.0000.0000.0000.000
121B123VAL0-0.052-0.01225.075-0.120-0.1200.0000.0000.0000.000
122B124GLU-1-0.897-0.92625.233-10.707-10.7070.0000.0000.0000.000
123B125TYR0-0.049-0.05023.442-0.444-0.4440.0000.0000.0000.000
124B126VAL00.0270.00919.0320.0200.0200.0000.0000.0000.000
125B127VAL0-0.024-0.00520.911-0.225-0.2250.0000.0000.0000.000
126B128TRP00.0080.00512.325-0.984-0.9840.0000.0000.0000.000
127B129PHE00.0080.00317.061-1.056-1.0560.0000.0000.0000.000
128B130LEU00.0160.01519.1960.6840.6840.0000.0000.0000.000
129B131GLY00.0600.02021.801-0.589-0.5890.0000.0000.0000.000
130B132PHE0-0.0240.00523.5590.4890.4890.0000.0000.0000.000
131B133GLN0-0.0030.00126.0550.6530.6530.0000.0000.0000.000
132B134PRO00.0310.00727.983-0.329-0.3290.0000.0000.0000.000
133B135GLY00.0630.02528.0590.3260.3260.0000.0000.0000.000
134B136PHE0-0.068-0.01524.2510.2050.2050.0000.0000.0000.000
135B137PRO0-0.0120.00224.129-0.514-0.5140.0000.0000.0000.000
136B138TYR0-0.007-0.00519.6990.3040.3040.0000.0000.0000.000
137B139LEU0-0.0150.00120.387-0.546-0.5460.0000.0000.0000.000
138B140GLY0-0.003-0.00618.4540.2320.2320.0000.0000.0000.000
139B141SER0-0.039-0.03317.9630.0830.0830.0000.0000.0000.000
140B142LEU00.0130.03120.2230.3510.3510.0000.0000.0000.000
141B143PRO00.0350.01423.194-0.228-0.2280.0000.0000.0000.000
142B144GLU-1-0.887-0.94424.039-10.506-10.5060.0000.0000.0000.000
143B145GLN0-0.040-0.01725.4490.0340.0340.0000.0000.0000.000
144B146LEU00.000-0.01728.0900.3130.3130.0000.0000.0000.000
145B147HIS0-0.066-0.02721.896-0.020-0.0200.0000.0000.0000.000
146B148THR00.0500.01627.3930.2680.2680.0000.0000.0000.000
147B149PRO0-0.019-0.01529.283-0.250-0.2500.0000.0000.0000.000
148B150ARG10.8540.93923.94011.04111.0410.0000.0000.0000.000
149B151ARG10.7380.85131.3457.7457.7450.0000.0000.0000.000
150B152ALA00.0270.03534.9480.2040.2040.0000.0000.0000.000
151B153GLU-1-0.737-0.85035.896-7.501-7.5010.0000.0000.0000.000
152B154PRO0-0.0110.00737.9890.0130.0130.0000.0000.0000.000
153B155ARG10.8180.87139.7377.1457.1450.0000.0000.0000.000
154B156LEU0-0.013-0.00340.8520.1680.1680.0000.0000.0000.000
155B157LEU0-0.025-0.00838.626-0.172-0.1720.0000.0000.0000.000
156B158VAL0-0.0080.00434.5470.1930.1930.0000.0000.0000.000
157B159PRO00.0160.00337.537-0.081-0.0810.0000.0000.0000.000
158B160ALA00.0290.03936.461-0.185-0.1850.0000.0000.0000.000
159B161GLY00.0570.03735.5850.2330.2330.0000.0000.0000.000
160B162SER0-0.042-0.04635.3930.1080.1080.0000.0000.0000.000
161B163VAL00.0060.01031.417-0.311-0.3110.0000.0000.0000.000
162B164GLY00.0270.00131.0250.3040.3040.0000.0000.0000.000
163B165ILE0-0.0030.02227.912-0.322-0.3220.0000.0000.0000.000
164B166GLY00.0390.00127.2280.3130.3130.0000.0000.0000.000
165B167GLY0-0.0070.02525.138-0.416-0.4160.0000.0000.0000.000
166B168PRO00.0380.02320.4780.1960.1960.0000.0000.0000.000
167B169GLN0-0.067-0.05319.627-0.748-0.7480.0000.0000.0000.000
168B170THR00.0340.00923.4750.5690.5690.0000.0000.0000.000
169B171GLY00.0480.02025.101-0.476-0.4760.0000.0000.0000.000
170B172VAL0-0.002-0.01327.5030.3420.3420.0000.0000.0000.000
171B173TYR00.0120.00529.968-0.404-0.4040.0000.0000.0000.000
172B174PRO0-0.0030.01230.2640.3140.3140.0000.0000.0000.000
173B175LEU00.008-0.01033.0570.2630.2630.0000.0000.0000.000
174B176ALA0-0.005-0.00135.399-0.028-0.0280.0000.0000.0000.000
175B177THR00.024-0.00533.4810.0340.0340.0000.0000.0000.000
176B178PRO00.0150.01034.7760.0760.0760.0000.0000.0000.000
177B179GLY00.011-0.00432.604-0.318-0.3180.0000.0000.0000.000
178B180GLY00.0420.02431.8100.2290.2290.0000.0000.0000.000
179B181TRP0-0.045-0.03125.1610.0770.0770.0000.0000.0000.000
180B182GLN0-0.009-0.00131.4750.4560.4560.0000.0000.0000.000
181B183LEU00.010-0.00633.238-0.209-0.2090.0000.0000.0000.000
182B184ILE0-0.010-0.02032.0760.2490.2490.0000.0000.0000.000
183B185GLY00.0570.01136.1850.1830.1830.0000.0000.0000.000
184B186HIS0-0.090-0.01736.745-0.089-0.0890.0000.0000.0000.000
185B187THR00.0190.01734.8160.0130.0130.0000.0000.0000.000
186B188SER0-0.011-0.01337.747-0.059-0.0590.0000.0000.0000.000
187B189LEU00.0130.01235.0640.0790.0790.0000.0000.0000.000
188B190SER00.0280.00435.868-0.185-0.1850.0000.0000.0000.000
189B191LEU00.0200.02129.536-0.061-0.0610.0000.0000.0000.000
190B192PHE0-0.003-0.00632.222-0.261-0.2610.0000.0000.0000.000
191B193ASP-1-0.839-0.92833.972-7.848-7.8480.0000.0000.0000.000
192B194PRO0-0.039-0.02237.172-0.051-0.0510.0000.0000.0000.000
193B195ALA0-0.018-0.01538.1370.0310.0310.0000.0000.0000.000
194B196ARG10.7530.88734.8868.8518.8510.0000.0000.0000.000
195B197ASP-1-0.879-0.94837.694-8.334-8.3340.0000.0000.0000.000
196B198GLU-1-0.787-0.84132.152-10.227-10.2270.0000.0000.0000.000
197B199PRO0-0.048-0.01933.1230.0270.0270.0000.0000.0000.000
198B200ILE0-0.023-0.02828.6450.0090.0090.0000.0000.0000.000
199B201LEU00.0100.01631.100-0.109-0.1090.0000.0000.0000.000
200B202LEU0-0.0150.00326.459-0.091-0.0910.0000.0000.0000.000
201B203ARG10.7680.84524.36410.82210.8220.0000.0000.0000.000
202B204PRO0-0.015-0.02719.0780.0330.0330.0000.0000.0000.000
203B205GLY00.0390.01819.974-0.049-0.0490.0000.0000.0000.000
204B206ASP-1-0.752-0.84520.681-11.766-11.7660.0000.0000.0000.000
205B207SER0-0.033-0.02423.746-0.162-0.1620.0000.0000.0000.000
206B208VAL0-0.001-0.01325.1950.3810.3810.0000.0000.0000.000
207B209ARG10.8920.92727.3578.8678.8670.0000.0000.0000.000
208B210PHE00.0120.01128.5730.1840.1840.0000.0000.0000.000
209B211VAL0-0.001-0.00532.7250.0880.0880.0000.0000.0000.000
210B212PRO0-0.005-0.00936.0920.1430.1430.0000.0000.0000.000
211B213GLN0-0.0210.00138.7890.1490.1490.0000.0000.0000.000
212B214LYS10.8430.92341.5737.0327.0320.0000.0000.0000.000