FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8N5GY

Calculation Name: 4U9Q-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U9Q

Chain ID: B

ChEMBL ID:

UniProt ID: Q9KPS1

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 303
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4267793.732651
FMO2-HF: Nuclear repulsion 4154068.193459
FMO2-HF: Total energy -113725.539191
FMO2-MP2: Total energy -114061.044516


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:15:GLY)


Summations of interaction energy for fragment #1(B:15: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.
-4.478-0.2754.081-2.837-5.445-0.012
Interaction energy analysis for fragmet #1(B:15:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.025
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].
3B17PRO0-0.0080.0233.875-0.1871.016-0.008-0.583-0.6120.003
4B18SER00.006-0.0076.4710.5150.5150.0000.0000.0000.000
5B19GLN00.0370.0119.5230.2250.2250.0000.0000.0000.000
6B20VAL00.006-0.01312.3580.1670.1670.0000.0000.0000.000
7B21ILE0-0.038-0.00513.713-0.069-0.0690.0000.0000.0000.000
8B22SER0-0.0150.00813.9440.0570.0570.0000.0000.0000.000
9B23ASP-1-0.808-0.91716.398-0.319-0.3190.0000.0000.0000.000
10B24GLY0-0.003-0.00315.680-0.038-0.0380.0000.0000.0000.000
11B25LYS10.7780.89314.4240.1460.1460.0000.0000.0000.000
12B26ALA00.0330.00917.871-0.006-0.0060.0000.0000.0000.000
13B27ILE0-0.036-0.01318.4260.0240.0240.0000.0000.0000.000
14B28LYS10.9530.98122.1480.0310.0310.0000.0000.0000.000
15B29LYS10.8880.94424.3960.0060.0060.0000.0000.0000.000
16B30VAL00.0000.00223.776-0.009-0.0090.0000.0000.0000.000
17B31ALA0-0.016-0.01124.3450.0160.0160.0000.0000.0000.000
18B32LEU0-0.0060.02724.685-0.016-0.0160.0000.0000.0000.000
19B33LEU00.009-0.00721.0930.0200.0200.0000.0000.0000.000
20B34GLY0-0.019-0.00825.487-0.006-0.0060.0000.0000.0000.000
21B35GLU-1-0.815-0.91325.4960.0020.0020.0000.0000.0000.000
22B36GLU-1-0.842-0.90722.182-0.120-0.1200.0000.0000.0000.000
23B37TYR00.0360.02824.668-0.013-0.0130.0000.0000.0000.000
24B38VAL00.027-0.00126.7320.0130.0130.0000.0000.0000.000
25B39GLY0-0.028-0.01429.113-0.001-0.0010.0000.0000.0000.000
26B40MET0-0.0170.03530.6330.0060.0060.0000.0000.0000.000
27B41ARG10.8240.87931.7520.0260.0260.0000.0000.0000.000
28B42PRO00.0530.04133.7440.0000.0000.0000.0000.0000.000
29B43THR0-0.088-0.05036.2060.0070.0070.0000.0000.0000.000
30B44MET0-0.027-0.01034.327-0.003-0.0030.0000.0000.0000.000
31B45HIS0-0.002-0.01438.0790.0010.0010.0000.0000.0000.000
32B46VAL0-0.0070.02735.8570.0000.0000.0000.0000.0000.000
33B47ARG10.8170.87438.6580.0210.0210.0000.0000.0000.000
34B48VAL00.005-0.01335.512-0.003-0.0030.0000.0000.0000.000
35B49GLY00.0180.01037.6030.0030.0030.0000.0000.0000.000
36B50ASP-1-0.813-0.87638.867-0.024-0.0240.0000.0000.0000.000
37B51GLU-1-0.777-0.87737.567-0.030-0.0300.0000.0000.0000.000
38B52VAL0-0.087-0.05433.6430.0010.0010.0000.0000.0000.000
39B53LYS10.8630.93235.5420.0580.0580.0000.0000.0000.000
40B54LYS10.8350.91430.8080.1210.1210.0000.0000.0000.000
41B55ALA00.001-0.02632.6100.0020.0020.0000.0000.0000.000
42B56GLN00.0240.03934.0950.0020.0020.0000.0000.0000.000
43B57ILE00.0020.00034.872-0.003-0.0030.0000.0000.0000.000
44B58LEU00.0100.00831.1740.0050.0050.0000.0000.0000.000
45B59PHE0-0.037-0.04930.0260.0090.0090.0000.0000.0000.000
46B60GLU-1-0.736-0.84935.681-0.052-0.0520.0000.0000.0000.000
47B61ASP-1-0.780-0.89435.067-0.039-0.0390.0000.0000.0000.000
48B62LYS10.8860.94036.9340.0220.0220.0000.0000.0000.000
49B63LYS10.8450.91036.8490.0270.0270.0000.0000.0000.000
50B64ASN0-0.0130.00234.7070.0010.0010.0000.0000.0000.000
51B65PRO00.0270.00638.167-0.003-0.0030.0000.0000.0000.000
52B66GLY00.0800.05140.422-0.002-0.0020.0000.0000.0000.000
53B67VAL0-0.024-0.01433.549-0.004-0.0040.0000.0000.0000.000
54B68LYS10.8470.93235.7890.0580.0580.0000.0000.0000.000
55B69PHE0-0.046-0.02629.881-0.007-0.0070.0000.0000.0000.000
56B70THR00.005-0.01131.3110.0070.0070.0000.0000.0000.000
57B71SER00.011-0.00530.281-0.006-0.0060.0000.0000.0000.000
58B72PRO0-0.004-0.00626.141-0.003-0.0030.0000.0000.0000.000
59B73VAL0-0.030-0.00827.136-0.011-0.0110.0000.0000.0000.000
60B74SER00.0350.03330.0400.0070.0070.0000.0000.0000.000
61B75GLY00.027-0.00431.860-0.003-0.0030.0000.0000.0000.000
62B76LYS10.8050.90033.2490.0260.0260.0000.0000.0000.000
63B77VAL0-0.039-0.01933.143-0.001-0.0010.0000.0000.0000.000
64B78VAL00.0020.00430.3530.0040.0040.0000.0000.0000.000
65B79GLU-1-0.777-0.87627.9820.0140.0140.0000.0000.0000.000
66B80ILE0-0.034-0.01631.829-0.007-0.0070.0000.0000.0000.000
67B81ASN0-0.038-0.01327.8400.0110.0110.0000.0000.0000.000
68B82ARG10.8640.91130.9100.0000.0000.0000.0000.0000.000
69B83GLY00.0720.05330.9560.0070.0070.0000.0000.0000.000
70B84ALA00.0310.00331.852-0.003-0.0030.0000.0000.0000.000
71B85LYS10.9360.95133.948-0.019-0.0190.0000.0000.0000.000
72B86ARG10.9811.00235.748-0.013-0.0130.0000.0000.0000.000
73B87VAL0-0.0080.01730.746-0.006-0.0060.0000.0000.0000.000
74B88LEU00.003-0.00230.3870.0050.0050.0000.0000.0000.000
75B89GLN0-0.070-0.04726.9730.0030.0030.0000.0000.0000.000
76B90SER00.022-0.01525.856-0.004-0.0040.0000.0000.0000.000
77B91VAL0-0.051-0.01127.9850.0090.0090.0000.0000.0000.000
78B92VAL0-0.048-0.01926.726-0.011-0.0110.0000.0000.0000.000
79B93ILE00.0140.00628.5600.0070.0070.0000.0000.0000.000
80B94GLU-1-0.942-0.97328.505-0.024-0.0240.0000.0000.0000.000
81B95VAL0-0.019-0.01426.631-0.001-0.0010.0000.0000.0000.000
82B96ALA00.000-0.01029.9250.0050.0050.0000.0000.0000.000
83B97GLY00.0020.01833.3210.0000.0000.0000.0000.0000.000
84B98ASP-1-0.905-0.96532.810-0.085-0.0850.0000.0000.0000.000
85B99ASP-1-0.810-0.87534.328-0.066-0.0660.0000.0000.0000.000
86B100GLN0-0.004-0.03935.360-0.007-0.0070.0000.0000.0000.000
87B101VAL0-0.038-0.00836.8980.0070.0070.0000.0000.0000.000
88B102THR0-0.014-0.00337.220-0.005-0.0050.0000.0000.0000.000
89B103PHE0-0.061-0.04436.0470.0040.0040.0000.0000.0000.000
90B104ASP-1-0.894-0.93640.415-0.075-0.0750.0000.0000.0000.000
91B105LYS10.7970.89739.8830.0990.0990.0000.0000.0000.000
92B106PHE0-0.012-0.01540.2360.0060.0060.0000.0000.0000.000
93B107GLU-1-0.819-0.89140.329-0.106-0.1060.0000.0000.0000.000
94B108ALA00.0370.00037.6390.0010.0010.0000.0000.0000.000
95B109ASN0-0.037-0.02539.082-0.002-0.0020.0000.0000.0000.000
96B110GLN00.0700.03941.9870.0020.0020.0000.0000.0000.000
97B111LEU00.0000.02436.2330.0030.0030.0000.0000.0000.000
98B112ALA00.0090.00739.6400.0010.0010.0000.0000.0000.000
99B113SER0-0.103-0.06140.6920.0050.0050.0000.0000.0000.000
100B114LEU0-0.0130.01639.6510.0050.0050.0000.0000.0000.000
101B115ASN00.007-0.00643.337-0.001-0.0010.0000.0000.0000.000
102B116ARG10.9700.98440.7210.0810.0810.0000.0000.0000.000
103B117ASP-1-0.814-0.91141.221-0.072-0.0720.0000.0000.0000.000
104B118ALA0-0.0040.01742.8970.0010.0010.0000.0000.0000.000
105B119ILE0-0.0100.00037.138-0.002-0.0020.0000.0000.0000.000
106B120LYS10.7980.89738.0800.0680.0680.0000.0000.0000.000
107B121THR0-0.005-0.01738.4890.0000.0000.0000.0000.0000.000
108B122GLN00.000-0.00237.5450.0040.0040.0000.0000.0000.000
109B123LEU0-0.0090.00532.749-0.005-0.0050.0000.0000.0000.000
110B124VAL0-0.045-0.01634.688-0.003-0.0030.0000.0000.0000.000
111B125GLU-1-0.857-0.94636.359-0.062-0.0620.0000.0000.0000.000
112B126SER00.0000.00034.147-0.001-0.0010.0000.0000.0000.000
113B127GLY00.0070.01332.781-0.004-0.0040.0000.0000.0000.000
114B128LEU0-0.0190.00828.156-0.006-0.0060.0000.0000.0000.000
115B129TRP00.016-0.00330.203-0.012-0.0120.0000.0000.0000.000
116B130THR0-0.039-0.03428.350-0.007-0.0070.0000.0000.0000.000
117B131ALA0-0.0170.00326.310-0.006-0.0060.0000.0000.0000.000
118B132PHE0-0.019-0.00226.476-0.014-0.0140.0000.0000.0000.000
119B133ARG10.9090.95121.5240.1710.1710.0000.0000.0000.000
120B134THR0-0.015-0.01628.699-0.007-0.0070.0000.0000.0000.000
121B135ARG10.8970.96724.7650.1590.1590.0000.0000.0000.000
122B136PRO00.0500.02530.307-0.001-0.0010.0000.0000.0000.000
123B137PHE00.0440.00130.720-0.001-0.0010.0000.0000.0000.000
124B138SER0-0.040-0.01025.8300.0000.0000.0000.0000.0000.000
125B139LYS10.8910.95827.8310.0560.0560.0000.0000.0000.000
126B140VAL00.0390.03329.615-0.006-0.0060.0000.0000.0000.000
127B141PRO00.0160.01131.4570.0080.0080.0000.0000.0000.000
128B142ALA00.0380.03434.5480.0010.0010.0000.0000.0000.000
129B143ILE00.0290.02437.962-0.003-0.0030.0000.0000.0000.000
130B144ASP-1-0.878-0.93839.691-0.058-0.0580.0000.0000.0000.000
131B145SER0-0.069-0.04638.774-0.002-0.0020.0000.0000.0000.000
132B146THR00.012-0.01739.129-0.001-0.0010.0000.0000.0000.000
133B147SER00.006-0.01735.912-0.001-0.0010.0000.0000.0000.000
134B148GLU-1-0.904-0.92637.930-0.087-0.0870.0000.0000.0000.000
135B149ALA0-0.0010.00133.690-0.004-0.0040.0000.0000.0000.000
136B150ILE00.0240.02230.418-0.001-0.0010.0000.0000.0000.000
137B151PHE0-0.034-0.04027.290-0.008-0.0080.0000.0000.0000.000
138B152VAL00.0460.02725.585-0.006-0.0060.0000.0000.0000.000
139B153THR0-0.041-0.02121.1570.0000.0000.0000.0000.0000.000
140B154ALA00.017-0.00421.546-0.018-0.0180.0000.0000.0000.000
141B155MET0-0.063-0.02418.560-0.018-0.0180.0000.0000.0000.000
142B156ASP-1-0.807-0.89213.884-0.596-0.5960.0000.0000.0000.000
143B157THR00.002-0.01514.9340.0040.0040.0000.0000.0000.000
144B158ASN0-0.045-0.00810.1670.1070.1070.0000.0000.0000.000
145B159PRO00.0370.0077.367-0.165-0.1650.0000.0000.0000.000
146B160LEU0-0.026-0.0212.723-1.044-0.1610.415-0.451-0.848-0.002
147B161ALA00.0480.0666.3260.1090.1090.0000.0000.0000.000
148B162ALA00.0250.0019.979-0.211-0.2110.0000.0000.0000.000
149B163GLU-1-0.902-0.95212.459-0.587-0.5870.0000.0000.0000.000
150B164PRO0-0.039-0.01715.0930.0440.0440.0000.0000.0000.000
151B165THR00.001-0.01418.4770.0600.0600.0000.0000.0000.000
152B166VAL00.0000.01616.0490.0520.0520.0000.0000.0000.000
153B167VAL00.0210.00517.3870.0400.0400.0000.0000.0000.000
154B168ILE0-0.006-0.00920.1210.0440.0440.0000.0000.0000.000
155B169ASN0-0.049-0.02522.1990.0510.0510.0000.0000.0000.000
156B170GLU-1-0.796-0.85721.001-0.357-0.3570.0000.0000.0000.000
157B171GLN0-0.016-0.00624.2700.0390.0390.0000.0000.0000.000
158B172SER0-0.011-0.02126.4950.0110.0110.0000.0000.0000.000
159B173GLU-1-0.920-0.95328.337-0.152-0.1520.0000.0000.0000.000
160B174ALA00.0340.02328.4320.0080.0080.0000.0000.0000.000
161B175PHE00.006-0.01625.2090.0020.0020.0000.0000.0000.000
162B176VAL0-0.012-0.00828.4250.0070.0070.0000.0000.0000.000
163B177ALA00.0540.03031.8030.0090.0090.0000.0000.0000.000
164B178GLY00.0530.02430.5640.0090.0090.0000.0000.0000.000
165B179LEU0-0.076-0.04228.9280.0080.0080.0000.0000.0000.000
166B180ASP-1-0.767-0.85132.266-0.128-0.1280.0000.0000.0000.000
167B181VAL00.0340.04534.3600.0090.0090.0000.0000.0000.000
168B182LEU0-0.039-0.03729.9780.0060.0060.0000.0000.0000.000
169B183SER0-0.085-0.05734.6530.0080.0080.0000.0000.0000.000
170B184ALA00.0770.05537.3620.0060.0060.0000.0000.0000.000
171B185LEU0-0.037-0.01234.2310.0060.0060.0000.0000.0000.000
172B186THR0-0.053-0.03536.2100.0070.0070.0000.0000.0000.000
173B187THR0-0.064-0.06037.9560.0060.0060.0000.0000.0000.000
174B188GLY00.0240.01439.2760.0050.0050.0000.0000.0000.000
175B189LYS10.8290.90036.0920.1060.1060.0000.0000.0000.000
176B190VAL00.0070.01931.202-0.001-0.0010.0000.0000.0000.000
177B191TYR0-0.016-0.01330.242-0.002-0.0020.0000.0000.0000.000
178B192VAL00.0550.02426.413-0.011-0.0110.0000.0000.0000.000
179B193CYS0-0.060-0.02124.6260.0060.0060.0000.0000.0000.000
180B194LYS10.8710.93222.4450.2380.2380.0000.0000.0000.000
181B195LYS10.9740.96315.9160.5810.5810.0000.0000.0000.000
182B196GLY00.018-0.00421.9480.0150.0150.0000.0000.0000.000
183B197THR0-0.0060.01020.3790.0250.0250.0000.0000.0000.000
184B198SER00.0100.01023.5630.0160.0160.0000.0000.0000.000
185B199LEU00.008-0.00622.599-0.028-0.0280.0000.0000.0000.000
186B200PRO00.0060.01426.5720.0190.0190.0000.0000.0000.000
187B201ARG10.8150.89529.4590.1580.1580.0000.0000.0000.000
188B202SER00.005-0.02032.1710.0100.0100.0000.0000.0000.000
189B203GLN0-0.024-0.02534.4080.0040.0040.0000.0000.0000.000
190B204GLN0-0.0120.00237.4660.0110.0110.0000.0000.0000.000
191B205PRO00.008-0.00138.063-0.005-0.0050.0000.0000.0000.000
192B206ASN0-0.053-0.02838.667-0.002-0.0020.0000.0000.0000.000
193B207VAL00.0250.02032.717-0.004-0.0040.0000.0000.0000.000
194B208GLU-1-0.814-0.89933.545-0.124-0.1240.0000.0000.0000.000
195B209GLU-1-0.829-0.89829.169-0.216-0.2160.0000.0000.0000.000
196B210HIS10.7730.88128.4970.1700.1700.0000.0000.0000.000
197B211VAL00.0480.02825.517-0.015-0.0150.0000.0000.0000.000
198B212PHE0-0.019-0.01322.7170.0200.0200.0000.0000.0000.000
199B213ASP-1-0.815-0.91420.901-0.324-0.3240.0000.0000.0000.000
200B214GLY00.0030.04317.9310.0210.0210.0000.0000.0000.000
201B215PRO0-0.062-0.04713.287-0.040-0.0400.0000.0000.0000.000
202B216HIS0-0.005-0.01715.439-0.039-0.0390.0000.0000.0000.000
203B217PRO0-0.038-0.00914.5390.0080.0080.0000.0000.0000.000
204B218ALA00.0170.01116.1960.0210.0210.0000.0000.0000.000
205B232SER0-0.042-0.03034.1320.0020.0020.0000.0000.0000.000
206B233ALA0-0.041-0.04535.0480.0020.0020.0000.0000.0000.000
207B234ASP-1-0.886-0.93137.481-0.053-0.0530.0000.0000.0000.000
208B235HIS00.0640.03538.734-0.005-0.0050.0000.0000.0000.000
209B236VAL0-0.048-0.01634.379-0.006-0.0060.0000.0000.0000.000
210B237ALA00.0390.05132.031-0.002-0.0020.0000.0000.0000.000
211B238TRP00.0210.00431.311-0.001-0.0010.0000.0000.0000.000
212B239SER0-0.085-0.04426.091-0.010-0.0100.0000.0000.0000.000
213B240ILE00.0470.02825.6330.0060.0060.0000.0000.0000.000
214B241ASN0-0.022-0.01420.668-0.028-0.0280.0000.0000.0000.000
215B242TYR00.1050.03016.1390.0230.0230.0000.0000.0000.000
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