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: J39L9

Calculation Name: 3PUF-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: B

ChEMBL ID:

UniProt ID: O75792

Base Structure: X-ray

Registration Date: 2023-06-19

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2051523.335742
FMO2-HF: Nuclear repulsion 1974814.662015
FMO2-HF: Total energy -76708.673727
FMO2-MP2: Total energy -76934.082311


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:13:MET)


Summations of interaction energy for fragment #1(B:13: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.
-3.4610.0360.77-1.513-2.753-0.007
Interaction energy analysis for fragmet #1(B:13:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.009
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].
3B15GLN0-0.008-0.0212.714-3.458-0.2180.770-1.485-2.524-0.007
4B16HIS0-0.054-0.0474.0791.2081.4650.000-0.028-0.2290.000
5B17VAL00.0460.0336.636-0.202-0.2020.0000.0000.0000.000
6B18PHE00.010-0.0128.7510.1800.1800.0000.0000.0000.000
7B19LEU00.0070.01511.965-0.042-0.0420.0000.0000.0000.000
8B20VAL0-0.013-0.00413.9180.0530.0530.0000.0000.0000.000
9B21SER00.0160.00016.7950.0070.0070.0000.0000.0000.000
10B22GLU-1-0.935-0.97219.531-0.238-0.2380.0000.0000.0000.000
11B23TYR0-0.045-0.04120.918-0.016-0.0160.0000.0000.0000.000
12B24LEU0-0.0480.00116.491-0.005-0.0050.0000.0000.0000.000
13B35LEU00.0050.00814.2710.0090.0090.0000.0000.0000.000
14B36MET0-0.044-0.02013.019-0.035-0.0350.0000.0000.0000.000
15B37PHE00.0130.0039.1580.0050.0050.0000.0000.0000.000
16B38VAL0-0.011-0.01513.2520.0640.0640.0000.0000.0000.000
17B39LYS10.9470.97916.252-0.453-0.4530.0000.0000.0000.000
18B40LEU0-0.003-0.00717.7510.0010.0010.0000.0000.0000.000
19B41VAL00.0420.02921.3520.0170.0170.0000.0000.0000.000
20B42ASN00.009-0.00323.501-0.035-0.0350.0000.0000.0000.000
21B43PRO0-0.017-0.01624.8890.0030.0030.0000.0000.0000.000
22B44CYS0-0.047-0.00828.1160.0030.0030.0000.0000.0000.000
23B45SER00.0210.00026.158-0.001-0.0010.0000.0000.0000.000
24B46GLY0-0.0060.00827.7920.0060.0060.0000.0000.0000.000
25B47GLU-1-0.928-0.96324.0010.2350.2350.0000.0000.0000.000
26B48GLY0-0.039-0.03320.618-0.009-0.0090.0000.0000.0000.000
27B49ALA00.0100.00419.0370.0020.0020.0000.0000.0000.000
28B50ILE0-0.039-0.02012.8060.0110.0110.0000.0000.0000.000
29B51TYR00.0140.00516.269-0.045-0.0450.0000.0000.0000.000
30B52LEU0-0.030-0.00313.1530.0140.0140.0000.0000.0000.000
31B53PHE00.0100.00416.073-0.011-0.0110.0000.0000.0000.000
32B54ASN00.028-0.00117.485-0.015-0.0150.0000.0000.0000.000
33B55MET00.0460.00818.6850.0200.0200.0000.0000.0000.000
34B56CYS0-0.009-0.00621.2960.0120.0120.0000.0000.0000.000
35B57LEU00.0180.01023.2480.0050.0050.0000.0000.0000.000
36B58GLN0-0.058-0.02824.1170.0160.0160.0000.0000.0000.000
37B59GLN00.0540.05222.622-0.006-0.0060.0000.0000.0000.000
38B60LEU00.0270.01120.9160.0000.0000.0000.0000.0000.000
39B61PHE0-0.014-0.01418.302-0.012-0.0120.0000.0000.0000.000
40B62GLU-1-0.764-0.85519.1240.0440.0440.0000.0000.0000.000
41B63VAL0-0.040-0.02513.300-0.038-0.0380.0000.0000.0000.000
42B64LYS10.8880.94816.6850.0150.0150.0000.0000.0000.000
43B65VAL0-0.051-0.03914.116-0.036-0.0360.0000.0000.0000.000
44B66PHE00.0200.02816.3210.0270.0270.0000.0000.0000.000
45B67LYS10.8250.88616.018-0.083-0.0830.0000.0000.0000.000
46B68GLU-1-0.788-0.87318.303-0.024-0.0240.0000.0000.0000.000
47B69LYS10.9200.94319.485-0.161-0.1610.0000.0000.0000.000
48B70HIS0-0.003-0.00619.884-0.011-0.0110.0000.0000.0000.000
49B71HIS00.0300.01117.306-0.054-0.0540.0000.0000.0000.000
50B72SER0-0.068-0.03814.0450.0540.0540.0000.0000.0000.000
51B73TRP0-0.010-0.01111.219-0.046-0.0460.0000.0000.0000.000
52B74PHE00.0310.01212.169-0.038-0.0380.0000.0000.0000.000
53B75ILE00.0020.0078.1750.0960.0960.0000.0000.0000.000
54B76ASN00.0080.00710.323-0.114-0.1140.0000.0000.0000.000
55B77GLN00.0040.01011.6740.1180.1180.0000.0000.0000.000
56B78SER0-0.014-0.0047.702-0.240-0.2400.0000.0000.0000.000
57B79VAL00.0550.0229.1360.1550.1550.0000.0000.0000.000
58B80GLN0-0.018-0.0046.261-0.680-0.6800.0000.0000.0000.000
59B81SER00.015-0.0099.1930.0810.0810.0000.0000.0000.000
60B82GLY0-0.0020.01310.8140.0480.0480.0000.0000.0000.000
61B83GLY00.1010.05212.4730.0340.0340.0000.0000.0000.000
62B84LEU0-0.097-0.03711.5120.0370.0370.0000.0000.0000.000
63B85LEU00.0160.02712.273-0.120-0.1200.0000.0000.0000.000
64B86HIS00.0190.00310.4760.0860.0860.0000.0000.0000.000
65B87PHE00.0480.01913.843-0.069-0.0690.0000.0000.0000.000
66B88ALA0-0.0010.00715.0900.0410.0410.0000.0000.0000.000
67B89THR00.0450.02317.108-0.022-0.0220.0000.0000.0000.000
68B90PRO0-0.010-0.01020.9360.0190.0190.0000.0000.0000.000
69B91VAL00.0310.02222.4800.0070.0070.0000.0000.0000.000
70B92ASP-1-0.846-0.91125.195-0.006-0.0060.0000.0000.0000.000
71B93PRO00.020-0.01627.2120.0100.0100.0000.0000.0000.000
72B94LEU00.0090.00028.4680.0110.0110.0000.0000.0000.000
73B95PHE00.0240.01528.8270.0050.0050.0000.0000.0000.000
74B96LEU00.0210.00923.8790.0070.0070.0000.0000.0000.000
75B97LEU0-0.007-0.00628.5910.0080.0080.0000.0000.0000.000
76B98LEU00.0070.00331.4700.0040.0040.0000.0000.0000.000
77B99HIS00.0000.01730.0870.0090.0090.0000.0000.0000.000
78B100TYR0-0.047-0.05527.5320.0040.0040.0000.0000.0000.000
79B101LEU00.0100.00733.196-0.001-0.0010.0000.0000.0000.000
80B102ILE0-0.015-0.01235.393-0.002-0.0020.0000.0000.0000.000
81B103LYS10.8820.94630.337-0.122-0.1220.0000.0000.0000.000
82B104ALA00.0570.03236.6450.0010.0010.0000.0000.0000.000
83B105ASP-1-0.904-0.93838.8650.0510.0510.0000.0000.0000.000
84B106LYS10.8060.89139.728-0.069-0.0690.0000.0000.0000.000
85B107GLU-1-0.923-0.92640.8630.0700.0700.0000.0000.0000.000
86B108GLY00.1190.05542.891-0.001-0.0010.0000.0000.0000.000
87B109LYS10.8180.89545.551-0.043-0.0430.0000.0000.0000.000
88B110PHE0-0.061-0.04644.2260.0010.0010.0000.0000.0000.000
89B111GLN00.0750.05840.1110.0010.0010.0000.0000.0000.000
90B112PRO00.0180.03139.523-0.004-0.0040.0000.0000.0000.000
91B113LEU00.047-0.00333.1240.0040.0040.0000.0000.0000.000
92B114ASP-1-0.876-0.93534.0150.0640.0640.0000.0000.0000.000
93B115GLN0-0.049-0.04034.6220.0060.0060.0000.0000.0000.000
94B116VAL0-0.0290.01034.8340.0040.0040.0000.0000.0000.000
95B117VAL0-0.069-0.04229.3840.0060.0060.0000.0000.0000.000
96B118VAL00.0360.02530.9040.0040.0040.0000.0000.0000.000
97B119ASP-1-0.805-0.92426.9610.1640.1640.0000.0000.0000.000
98B120ASN0-0.023-0.00527.3150.0010.0010.0000.0000.0000.000
99B121VAL0-0.0090.01424.3450.0180.0180.0000.0000.0000.000
100B122PHE0-0.045-0.02421.2810.0350.0350.0000.0000.0000.000
101B123PRO00.0640.01922.270-0.021-0.0210.0000.0000.0000.000
102B124ASN0-0.049-0.02519.051-0.032-0.0320.0000.0000.0000.000
103B125CYS00.0160.02022.517-0.018-0.0180.0000.0000.0000.000
104B126ILE00.0750.02525.511-0.015-0.0150.0000.0000.0000.000
105B127LEU0-0.034-0.01720.466-0.013-0.0130.0000.0000.0000.000
106B128LEU0-0.008-0.00225.084-0.014-0.0140.0000.0000.0000.000
107B129LEU00.0390.01927.629-0.009-0.0090.0000.0000.0000.000
108B130LYS10.8420.93027.425-0.024-0.0240.0000.0000.0000.000
109B131LEU00.0340.03225.924-0.010-0.0100.0000.0000.0000.000
110B132PRO0-0.0080.00528.4050.0020.0020.0000.0000.0000.000
111B133GLY0-0.013-0.01131.478-0.002-0.0020.0000.0000.0000.000
112B134LEU00.0540.02231.6890.0000.0000.0000.0000.0000.000
113B135GLU-1-0.771-0.84234.6820.0170.0170.0000.0000.0000.000
114B136LYS10.9790.97237.7600.0170.0170.0000.0000.0000.000
115B137LEU0-0.0030.00931.700-0.001-0.0010.0000.0000.0000.000
116B138LEU00.0560.02135.1980.0020.0020.0000.0000.0000.000
117B139HIS0-0.063-0.01537.756-0.001-0.0010.0000.0000.0000.000
118B140HIS0-0.062-0.02938.1760.0010.0010.0000.0000.0000.000
119B141VAL00.0200.01036.4750.0010.0010.0000.0000.0000.000
120B142THR0-0.045-0.02538.8290.0050.0050.0000.0000.0000.000
121B143GLU-1-0.826-0.88341.6780.0180.0180.0000.0000.0000.000
122B144GLU-1-0.830-0.91843.2320.0190.0190.0000.0000.0000.000
123B145LYS10.8540.92845.075-0.027-0.0270.0000.0000.0000.000
124B146GLY00.0570.01645.9320.0020.0020.0000.0000.0000.000
125B147ASN0-0.033-0.03347.477-0.003-0.0030.0000.0000.0000.000
126B148PRO00.039-0.00346.6290.0010.0010.0000.0000.0000.000
127B149GLU-1-0.916-0.93447.5260.0110.0110.0000.0000.0000.000
128B150ILE0-0.041-0.01646.3360.0000.0000.0000.0000.0000.000
129B151ASP-1-0.904-0.96842.4300.0230.0230.0000.0000.0000.000
130B152ASN0-0.083-0.04841.182-0.001-0.0010.0000.0000.0000.000
131B153LYN0-0.0430.01941.8830.0010.0010.0000.0000.0000.000
132B154LYS10.7950.89840.699-0.015-0.0150.0000.0000.0000.000
133B155TYR0-0.015-0.01440.9720.0040.0040.0000.0000.0000.000
134B156TYR0-0.004-0.04538.723-0.003-0.0030.0000.0000.0000.000
135B157LYS10.8500.91541.710-0.044-0.0440.0000.0000.0000.000
136B158TYR00.0210.01238.929-0.003-0.0030.0000.0000.0000.000
137B159SER0-0.012-0.00941.5570.0010.0010.0000.0000.0000.000
138B160LYS10.8970.94042.232-0.044-0.0440.0000.0000.0000.000
139B161GLU-1-0.808-0.90343.8730.0160.0160.0000.0000.0000.000
140B162LYS10.8630.92743.030-0.020-0.0200.0000.0000.0000.000
141B163THR00.015-0.00638.440-0.002-0.0020.0000.0000.0000.000
142B164LEU00.0120.00740.273-0.001-0.0010.0000.0000.0000.000
143B165LYS10.8490.92742.491-0.017-0.0170.0000.0000.0000.000
144B166TRP0-0.038-0.02133.036-0.003-0.0030.0000.0000.0000.000
145B167LEU00.003-0.01535.832-0.003-0.0030.0000.0000.0000.000
146B168GLU-1-0.890-0.94238.9260.0060.0060.0000.0000.0000.000
147B169LYS10.8900.94439.822-0.002-0.0020.0000.0000.0000.000
148B170LYS10.8270.92032.4260.0040.0040.0000.0000.0000.000
149B171VAL00.0450.03536.304-0.004-0.0040.0000.0000.0000.000
150B172ASN00.0260.01138.461-0.003-0.0030.0000.0000.0000.000
151B173GLN0-0.018-0.00734.6690.0000.0000.0000.0000.0000.000
152B174THR00.009-0.01332.912-0.005-0.0050.0000.0000.0000.000
153B175VAL00.0370.02035.566-0.005-0.0050.0000.0000.0000.000
154B176ALA0-0.028-0.01038.465-0.003-0.0030.0000.0000.0000.000
155B177ALA00.001-0.00233.337-0.005-0.0050.0000.0000.0000.000
156B178LEU00.0040.00333.708-0.006-0.0060.0000.0000.0000.000
157B179LYS10.8870.93735.8060.0180.0180.0000.0000.0000.000
158B180THR0-0.051-0.02135.479-0.002-0.0020.0000.0000.0000.000
159B181ASN0-0.062-0.04231.189-0.012-0.0120.0000.0000.0000.000
160B182ASN0-0.062-0.01033.818-0.006-0.0060.0000.0000.0000.000
161B183VAL00.0020.00632.332-0.001-0.0010.0000.0000.0000.000
162B184ASN0-0.0160.00734.6400.0010.0010.0000.0000.0000.000
163B205GLU-1-0.880-0.94345.242-0.013-0.0130.0000.0000.0000.000
164B206GLU-1-0.846-0.92544.5400.0120.0120.0000.0000.0000.000
165B207ASP-1-0.853-0.93542.765-0.007-0.0070.0000.0000.0000.000
166B208TYR00.005-0.00837.3580.0010.0010.0000.0000.0000.000
167B209ILE0-0.0090.00439.3520.0010.0010.0000.0000.0000.000
168B210ARG10.8480.90740.266-0.013-0.0130.0000.0000.0000.000
169B211TYR0-0.0070.01432.1210.0050.0050.0000.0000.0000.000
170B212ALA00.003-0.00835.6420.0020.0020.0000.0000.0000.000
171B213HIS0-0.062-0.03235.6100.0010.0010.0000.0000.0000.000
172B214GLY00.0540.02535.4260.0050.0050.0000.0000.0000.000
173B215LEU0-0.0080.01429.3480.0040.0040.0000.0000.0000.000
174B216ILE0-0.007-0.01931.0170.0040.0040.0000.0000.0000.000
175B217SER0-0.058-0.03632.5950.0060.0060.0000.0000.0000.000
176B218ASP-1-0.875-0.92328.0650.0670.0670.0000.0000.0000.000
177B219TYR0-0.141-0.09525.0560.0050.0050.0000.0000.0000.000
178B220ILE0-0.050-0.02429.6940.0020.0020.0000.0000.0000.000
179B221PRO00.0230.02532.8390.0020.0020.0000.0000.0000.000
180B222LYS10.9000.92533.975-0.071-0.0710.0000.0000.0000.000
181B223GLU-1-0.869-0.94736.3910.0790.0790.0000.0000.0000.000
182B224LEU0-0.045-0.03036.604-0.006-0.0060.0000.0000.0000.000
183B225SER00.0170.01136.557-0.008-0.0080.0000.0000.0000.000
184B226ASP-1-0.794-0.88238.5430.0510.0510.0000.0000.0000.000
185B227ASP-1-0.825-0.89742.0170.0400.0400.0000.0000.0000.000
186B228LEU0-0.020-0.01138.202-0.003-0.0030.0000.0000.0000.000
187B229SER0-0.067-0.02042.191-0.003-0.0030.0000.0000.0000.000
188B230LYS10.8540.91543.735-0.046-0.0460.0000.0000.0000.000
189B231TYR0-0.0250.01044.818-0.002-0.0020.0000.0000.0000.000