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: Z6Z7N

Calculation Name: 4X0R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X0R

Chain ID: B

ChEMBL ID:

UniProt ID: P20592

Base Structure: X-ray

Registration Date: 2023-06-22

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2548174.388472
FMO2-HF: Nuclear repulsion 2457694.870924
FMO2-HF: Total energy -90479.517549
FMO2-MP2: Total energy -90741.789751


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:GLU)


Summations of interaction energy for fragment #1(B:3:GLU)
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.
-161.394-161.58831.929-17.195-14.5410.133
Interaction energy analysis for fragmet #1(B:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.778 / q_NPA : -0.877
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].
3B5ASP-1-0.888-0.9382.27826.86530.5593.599-3.114-4.179-0.035
4B6LYS10.8390.8901.753-155.912-159.93428.331-14.073-10.2370.168
5B7MET00.0000.0004.889-3.939-3.805-0.001-0.008-0.1250.000
6B8PHE00.0570.0166.630-2.945-2.9450.0000.0000.0000.000
7B9PHE0-0.044-0.0078.458-1.961-1.9610.0000.0000.0000.000
8B10LEU00.0080.00010.235-2.324-2.3240.0000.0000.0000.000
9B11ILE00.0200.01310.906-1.763-1.7630.0000.0000.0000.000
10B12GLU-1-0.789-0.87512.50519.50619.5060.0000.0000.0000.000
11B13LYS10.8070.89914.509-18.295-18.2950.0000.0000.0000.000
12B14ILE0-0.0090.00316.456-1.240-1.2400.0000.0000.0000.000
13B15LYS10.8290.89315.678-20.052-20.0520.0000.0000.0000.000
14B16MET0-0.025-0.00518.278-0.825-0.8250.0000.0000.0000.000
15B17PHE0-0.0030.00320.539-0.828-0.8280.0000.0000.0000.000
16B18ASN00.027-0.00722.041-0.723-0.7230.0000.0000.0000.000
17B19GLN00.0210.00721.039-0.857-0.8570.0000.0000.0000.000
18B20ASP-1-0.823-0.89224.90512.22812.2280.0000.0000.0000.000
19B21ILE0-0.036-0.01326.527-0.530-0.5300.0000.0000.0000.000
20B22GLU-1-0.747-0.83327.7619.8019.8010.0000.0000.0000.000
21B23LYS10.9060.95226.243-12.364-12.3640.0000.0000.0000.000
22B24LEU0-0.065-0.02031.030-0.413-0.4130.0000.0000.0000.000
23B25VAL0-0.009-0.00132.220-0.388-0.3880.0000.0000.0000.000
24B26GLU-1-0.935-0.95932.2519.4339.4330.0000.0000.0000.000
25B27GLY0-0.040-0.01735.320-0.220-0.2200.0000.0000.0000.000
26B28GLU-1-0.845-0.94032.7509.1139.1130.0000.0000.0000.000
27B29GLU-1-0.814-0.89431.8899.3089.3080.0000.0000.0000.000
28B30VAL0-0.034-0.02029.162-0.208-0.2080.0000.0000.0000.000
29B31VAL0-0.027-0.01332.3510.1490.1490.0000.0000.0000.000
30B32ARG10.8120.88134.734-8.874-8.8740.0000.0000.0000.000
31B33GLU-1-0.866-0.93036.6877.9217.9210.0000.0000.0000.000
32B34ASN0-0.054-0.02439.623-0.356-0.3560.0000.0000.0000.000
33B35GLU-1-0.822-0.90135.8949.1669.1660.0000.0000.0000.000
34B36THR00.0200.01340.265-0.036-0.0360.0000.0000.0000.000
35B37ARG10.8480.93134.697-8.946-8.9460.0000.0000.0000.000
36B38LEU0-0.029-0.04735.551-0.285-0.2850.0000.0000.0000.000
37B39TYR00.007-0.01237.780-0.345-0.3450.0000.0000.0000.000
38B40ASN0-0.037-0.01240.957-0.241-0.2410.0000.0000.0000.000
39B41LYS10.8260.92637.302-8.706-8.7060.0000.0000.0000.000
40B42ILE00.0320.03339.842-0.135-0.1350.0000.0000.0000.000
41B43ARG10.9360.95742.945-7.574-7.5740.0000.0000.0000.000
42B44GLU-1-0.851-0.91246.7496.2866.2860.0000.0000.0000.000
43B45ASP-1-0.829-0.92247.2136.5026.5020.0000.0000.0000.000
44B46PHE00.025-0.00844.491-0.124-0.1240.0000.0000.0000.000
45B47LYS10.8450.90849.692-6.470-6.4700.0000.0000.0000.000
46B48ASN0-0.046-0.00952.124-0.203-0.2030.0000.0000.0000.000
47B49TRP00.0610.01752.051-0.158-0.1580.0000.0000.0000.000
48B50VAL00.0110.00553.427-0.132-0.1320.0000.0000.0000.000
49B51GLY00.0180.01755.872-0.127-0.1270.0000.0000.0000.000
50B52ILE0-0.0020.00555.644-0.152-0.1520.0000.0000.0000.000
51B53LEU0-0.0200.00156.591-0.129-0.1290.0000.0000.0000.000
52B54ALA00.0170.00759.402-0.111-0.1110.0000.0000.0000.000
53B55THR0-0.045-0.03361.844-0.140-0.1400.0000.0000.0000.000
54B56ASN00.002-0.01161.429-0.173-0.1730.0000.0000.0000.000
55B57THR00.0320.01263.053-0.052-0.0520.0000.0000.0000.000
56B58GLN00.0030.00565.083-0.032-0.0320.0000.0000.0000.000
57B59LYS10.8920.95365.243-5.005-5.0050.0000.0000.0000.000
58B60VAL00.016-0.00267.036-0.076-0.0760.0000.0000.0000.000
59B61LYS10.8910.94867.930-4.771-4.7710.0000.0000.0000.000
60B62ASN00.0300.02471.084-0.049-0.0490.0000.0000.0000.000
61B63ILE0-0.0030.00872.484-0.060-0.0600.0000.0000.0000.000
62B64ILE0-0.013-0.01572.023-0.056-0.0560.0000.0000.0000.000
63B65HIS0-0.035-0.01574.8530.0020.0020.0000.0000.0000.000
64B66GLU-1-0.900-0.95577.1043.9923.9920.0000.0000.0000.000
65B67GLU-1-0.855-0.90777.0144.0214.0210.0000.0000.0000.000
66B68VAL00.002-0.00477.788-0.050-0.0500.0000.0000.0000.000
67B69GLU-1-0.761-0.86480.3693.8543.8540.0000.0000.0000.000
68B70LYS10.7710.88980.639-4.054-4.0540.0000.0000.0000.000
69B71TYR0-0.031-0.03879.851-0.057-0.0570.0000.0000.0000.000
70B72GLU-1-0.879-0.95083.7423.8433.8430.0000.0000.0000.000
71B73LYS10.8510.90685.086-3.855-3.8550.0000.0000.0000.000
72B74GLN0-0.081-0.03986.431-0.008-0.0080.0000.0000.0000.000
73B75ALA0-0.037-0.00788.289-0.036-0.0360.0000.0000.0000.000
74B76ALA0-0.046-0.00590.204-0.042-0.0420.0000.0000.0000.000
75B87LYS10.9010.91573.681-4.343-4.3430.0000.0000.0000.000
76B88THR00.0190.00274.8430.0660.0660.0000.0000.0000.000
77B89PHE00.0560.01973.6030.0540.0540.0000.0000.0000.000
78B90GLU-1-0.780-0.85570.7264.5284.5280.0000.0000.0000.000
79B91ILE0-0.0210.00669.7030.0780.0780.0000.0000.0000.000
80B92ILE00.0330.02069.6950.0700.0700.0000.0000.0000.000
81B93VAL0-0.0090.00166.2440.0700.0700.0000.0000.0000.000
82B94HIS00.0030.00964.8040.0640.0640.0000.0000.0000.000
83B95GLN00.029-0.00564.7040.0430.0430.0000.0000.0000.000
84B96TYR0-0.018-0.00961.7620.0740.0740.0000.0000.0000.000
85B97ILE0-0.0140.00459.9530.0910.0910.0000.0000.0000.000
86B98GLN00.0380.01559.8600.1070.1070.0000.0000.0000.000
87B99GLN0-0.065-0.03060.1320.0690.0690.0000.0000.0000.000
88B100LEU0-0.050-0.02357.8180.0380.0380.0000.0000.0000.000
89B101VAL00.0060.00555.0170.1130.1130.0000.0000.0000.000
90B102GLU-1-0.854-0.92354.3595.9485.9480.0000.0000.0000.000
91B103PRO0-0.037-0.02553.8450.1170.1170.0000.0000.0000.000
92B104ALA0-0.0040.00952.0100.1260.1260.0000.0000.0000.000
93B105LEU00.0140.00549.8130.1710.1710.0000.0000.0000.000
94B106SER00.0190.01249.0190.1260.1260.0000.0000.0000.000
95B107MET0-0.059-0.01047.8440.1290.1290.0000.0000.0000.000
96B108LEU0-0.020-0.00943.6550.1830.1830.0000.0000.0000.000
97B109GLN0-0.025-0.02644.1720.2090.2090.0000.0000.0000.000
98B110LYS10.9490.98444.069-6.659-6.6590.0000.0000.0000.000
99B111ALA0-0.005-0.01542.8550.1730.1730.0000.0000.0000.000
100B112MET0-0.0280.00039.6730.2700.2700.0000.0000.0000.000
101B113GLU-1-0.869-0.92639.2567.3677.3670.0000.0000.0000.000
102B114ILE0-0.060-0.02839.2210.2340.2340.0000.0000.0000.000
103B115ILE0-0.024-0.01435.5960.2440.2440.0000.0000.0000.000
104B116GLN00.0000.00535.1620.1370.1370.0000.0000.0000.000
105B117GLN0-0.035-0.02734.2240.1750.1750.0000.0000.0000.000
106B118ALA0-0.010-0.00133.9700.2770.2770.0000.0000.0000.000
107B119PHE00.0500.00530.7360.4030.4030.0000.0000.0000.000
108B120ILE0-0.0060.00029.4360.4720.4720.0000.0000.0000.000
109B121ASN0-0.004-0.00129.4570.3680.3680.0000.0000.0000.000
110B122VAL00.0100.00826.3120.3680.3680.0000.0000.0000.000
111B123ALA00.0280.01025.1610.5720.5720.0000.0000.0000.000
112B124LYS10.9090.95624.689-9.840-9.8400.0000.0000.0000.000
113B125LYS10.8690.93224.700-12.359-12.3590.0000.0000.0000.000
114B126HIS0-0.037-0.02121.1301.1471.1470.0000.0000.0000.000
115B127PHE00.0450.00818.8491.0071.0070.0000.0000.0000.000
116B128GLY00.0200.02321.770-0.052-0.0520.0000.0000.0000.000
117B129GLU-1-0.919-0.95919.59614.19114.1910.0000.0000.0000.000
118B130PHE0-0.056-0.02315.6780.5080.5080.0000.0000.0000.000
119B131PHE00.0620.02320.296-0.244-0.2440.0000.0000.0000.000
120B132ASN00.0080.00119.868-0.965-0.9650.0000.0000.0000.000
121B133LEU00.0310.03217.596-0.286-0.2860.0000.0000.0000.000
122B134ASN0-0.010-0.01221.261-0.404-0.4040.0000.0000.0000.000
123B135GLN0-0.016-0.00724.353-0.291-0.2910.0000.0000.0000.000
124B136THR0-0.006-0.01522.785-0.230-0.2300.0000.0000.0000.000
125B137VAL00.0340.03622.582-0.418-0.4180.0000.0000.0000.000
126B138GLN00.0290.00425.474-0.224-0.2240.0000.0000.0000.000
127B139SER0-0.062-0.03127.801-0.348-0.3480.0000.0000.0000.000
128B140THR00.001-0.01526.432-0.243-0.2430.0000.0000.0000.000
129B141ILE0-0.010-0.01028.097-0.234-0.2340.0000.0000.0000.000
130B142GLU-1-0.800-0.87330.8958.1828.1820.0000.0000.0000.000
131B143ASP-1-0.816-0.89731.6798.9578.9570.0000.0000.0000.000
132B144ILE00.0020.00429.297-0.245-0.2450.0000.0000.0000.000
133B145LYS10.8390.91733.705-8.496-8.4960.0000.0000.0000.000
134B146VAL00.0010.01236.280-0.283-0.2830.0000.0000.0000.000
135B147LYS10.8150.89433.372-9.191-9.1910.0000.0000.0000.000
136B148HIS0-0.042-0.01934.962-0.048-0.0480.0000.0000.0000.000
137B149THR00.041-0.01938.929-0.173-0.1730.0000.0000.0000.000
138B150ALA00.0180.02041.748-0.201-0.2010.0000.0000.0000.000
139B151LYS10.8220.91137.694-8.309-8.3090.0000.0000.0000.000
140B152ALA00.0100.00742.722-0.166-0.1660.0000.0000.0000.000
141B153GLU-1-0.821-0.90444.4916.2566.2560.0000.0000.0000.000
142B154ASN0-0.079-0.05146.339-0.288-0.2880.0000.0000.0000.000
143B155MET00.0080.00346.184-0.166-0.1660.0000.0000.0000.000
144B156ILE00.0050.01647.854-0.137-0.1370.0000.0000.0000.000
145B157GLN0-0.033-0.03950.669-0.255-0.2550.0000.0000.0000.000
146B158LEU0-0.083-0.04450.746-0.150-0.1500.0000.0000.0000.000
147B159GLN0-0.0080.00252.316-0.014-0.0140.0000.0000.0000.000
148B160PHE00.0510.01553.958-0.119-0.1190.0000.0000.0000.000
149B161ARG10.9460.98552.649-5.948-5.9480.0000.0000.0000.000
150B162MET0-0.005-0.00554.105-0.105-0.1050.0000.0000.0000.000
151B163GLU-1-0.789-0.87857.7845.4075.4070.0000.0000.0000.000
152B164GLN0-0.035-0.03160.098-0.173-0.1730.0000.0000.0000.000
153B165MET0-0.057-0.02461.502-0.134-0.1340.0000.0000.0000.000
154B166VAL00.014-0.00360.071-0.082-0.0820.0000.0000.0000.000
155B167PHE0-0.024-0.00363.221-0.075-0.0750.0000.0000.0000.000
156B168LYS10.7930.90565.605-4.849-4.8490.0000.0000.0000.000
157B180SER0-0.011-0.01881.587-0.001-0.0010.0000.0000.0000.000
158B181VAL0-0.0030.00483.280-0.025-0.0250.0000.0000.0000.000
159B182SER0-0.020-0.01180.3110.0610.0610.0000.0000.0000.000
160B183SER00.0460.01281.264-0.039-0.0390.0000.0000.0000.000
161B184PHE00.0330.01280.5640.0570.0570.0000.0000.0000.000
162B185THR00.0900.04979.5500.0570.0570.0000.0000.0000.000
163B186GLU-1-0.901-0.92077.5444.2254.2250.0000.0000.0000.000
164B187ILE0-0.022-0.01775.5690.0750.0750.0000.0000.0000.000
165B188GLY00.0420.01774.7890.0730.0730.0000.0000.0000.000
166B189ILE0-0.0120.00674.2640.0750.0750.0000.0000.0000.000
167B190HIS0-0.025-0.02971.8680.1420.1420.0000.0000.0000.000
168B191LEU0-0.0030.00270.2800.0970.0970.0000.0000.0000.000
169B192ASN0-0.031-0.03069.4080.1300.1300.0000.0000.0000.000
170B193ALA00.0040.01368.4450.0790.0790.0000.0000.0000.000
171B194TYR00.0780.03763.3620.0960.0960.0000.0000.0000.000
172B195PHE00.0150.00464.6880.1140.1140.0000.0000.0000.000
173B196LEU0-0.0220.01064.1200.1030.1030.0000.0000.0000.000
174B197GLU-1-0.936-0.99061.9945.1855.1850.0000.0000.0000.000
175B198THR0-0.022-0.02760.3280.1280.1280.0000.0000.0000.000
176B199SER0-0.042-0.02359.2440.1130.1130.0000.0000.0000.000
177B200LYS10.9330.96858.122-5.104-5.1040.0000.0000.0000.000
178B201ARG10.8440.92055.835-5.277-5.2770.0000.0000.0000.000
179B202LEU00.0210.00554.5640.1480.1480.0000.0000.0000.000
180B203ALA0-0.006-0.01353.7860.1130.1130.0000.0000.0000.000
181B204ASN0-0.075-0.03351.1810.1810.1810.0000.0000.0000.000
182B205GLN00.0270.00549.8110.2000.2000.0000.0000.0000.000
183B206ILE0-0.0030.00049.2840.1190.1190.0000.0000.0000.000
184B207PRO00.0030.00347.2470.1440.1440.0000.0000.0000.000
185B208PHE00.0190.01045.5060.1700.1700.0000.0000.0000.000
186B209ILE0-0.0100.00444.3360.2000.2000.0000.0000.0000.000
187B210ILE00.0090.00443.0880.1970.1970.0000.0000.0000.000
188B211GLN0-0.021-0.02441.1730.0690.0690.0000.0000.0000.000
189B212TYR0-0.031-0.02339.1020.2640.2640.0000.0000.0000.000
190B213PHE00.0170.00238.7350.2110.2110.0000.0000.0000.000
191B214MET00.0080.01038.0200.2090.2090.0000.0000.0000.000
192B215LEU0-0.042-0.00835.3420.1720.1720.0000.0000.0000.000
193B216ARG10.7870.83131.629-9.314-9.3140.0000.0000.0000.000
194B217GLU-1-0.743-0.85133.9788.4448.4440.0000.0000.0000.000
195B218ASN0-0.069-0.02933.4330.4240.4240.0000.0000.0000.000
196B219GLY00.0700.02730.6860.3010.3010.0000.0000.0000.000
197B220ASP-1-0.837-0.88029.25110.12610.1260.0000.0000.0000.000
198B221SER0-0.059-0.04928.8750.3910.3910.0000.0000.0000.000
199B222LEU00.0230.01726.8060.3410.3410.0000.0000.0000.000
200B223GLN0-0.037-0.03324.8730.8660.8660.0000.0000.0000.000
201B224LYS10.9570.96623.836-9.724-9.7240.0000.0000.0000.000
202B225ALA00.0100.01224.1400.3600.3600.0000.0000.0000.000
203B226MET0-0.020-0.00120.5030.2710.2710.0000.0000.0000.000
204B227MET0-0.008-0.00818.3000.8860.8860.0000.0000.0000.000
205B228GLN0-0.058-0.02619.7720.3530.3530.0000.0000.0000.000
206B229ILE00.0470.02417.8400.3870.3870.0000.0000.0000.000
207B230LEU0-0.0270.00314.0460.7000.7000.0000.0000.0000.000
208B231GLN0-0.050-0.02314.8761.5411.5410.0000.0000.0000.000
209B232GLU-1-0.810-0.89115.75514.32514.3250.0000.0000.0000.000
210B233LYS10.8700.92311.255-18.450-18.4500.0000.0000.0000.000
211B234ASN0-0.022-0.00912.1660.8930.8930.0000.0000.0000.000
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