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: M937Z

Calculation Name: 4B93-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B93

Chain ID: B

ChEMBL ID:

UniProt ID: Q96NW4

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1916009.302281
FMO2-HF: Nuclear repulsion 1843536.148168
FMO2-HF: Total energy -72473.154113
FMO2-MP2: Total energy -72684.986433


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:665:LYS)


Summations of interaction energy for fragment #1(B:665:LYS)
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.
18.75221.4520.258-1.199-1.759-0.004
Interaction energy analysis for fragmet #1(B:665:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.978 / q_NPA : 0.957
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].
3B667TYR00.0120.0072.879-1.1961.5040.258-1.199-1.759-0.004
4B668ARG10.9690.9905.60525.08625.0860.0000.0000.0000.000
5B669GLU-1-0.799-0.9028.292-17.301-17.3010.0000.0000.0000.000
6B670VAL00.0190.0067.3391.6191.6190.0000.0000.0000.000
7B671GLU-1-0.799-0.8929.586-17.951-17.9510.0000.0000.0000.000
8B672LYS10.7770.88511.53819.37419.3740.0000.0000.0000.000
9B673LEU00.0240.01413.2401.0991.0990.0000.0000.0000.000
10B674LEU0-0.018-0.00812.1971.0601.0600.0000.0000.0000.000
11B675ARG10.8720.93114.16117.62717.6270.0000.0000.0000.000
12B676ALA00.0230.01317.4190.7400.7400.0000.0000.0000.000
13B677VAL0-0.029-0.03017.5900.6340.6340.0000.0000.0000.000
14B678ALA0-0.0160.00319.1370.6230.6230.0000.0000.0000.000
15B679ASP-1-0.907-0.95020.928-10.891-10.8910.0000.0000.0000.000
16B680GLY0-0.069-0.03523.1300.4750.4750.0000.0000.0000.000
17B681ASP-1-0.854-0.92322.676-10.945-10.9450.0000.0000.0000.000
18B682LEU00.027-0.00423.054-0.398-0.3980.0000.0000.0000.000
19B683GLU-1-0.771-0.85324.273-10.091-10.0910.0000.0000.0000.000
20B684MET00.0140.01919.764-0.495-0.4950.0000.0000.0000.000
21B685VAL0-0.048-0.02819.324-0.569-0.5690.0000.0000.0000.000
22B686ARG10.7810.84820.0009.6969.6960.0000.0000.0000.000
23B687TYR0-0.023-0.00919.856-0.246-0.2460.0000.0000.0000.000
24B688LEU0-0.026-0.02615.884-0.422-0.4220.0000.0000.0000.000
25B689LEU0-0.052-0.02715.564-0.651-0.6510.0000.0000.0000.000
26B690GLU-1-0.970-0.96218.347-13.330-13.3300.0000.0000.0000.000
27B691TRP0-0.062-0.03420.3970.5400.5400.0000.0000.0000.000
28B692THR00.0030.00024.0170.1920.1920.0000.0000.0000.000
29B733SER00.0290.00212.0510.1060.1060.0000.0000.0000.000
30B734GLY0-0.003-0.00810.563-1.423-1.4230.0000.0000.0000.000
31B735LEU0-0.0280.00410.366-0.650-0.6500.0000.0000.0000.000
32B736GLY00.0770.02212.3340.7870.7870.0000.0000.0000.000
33B737VAL0-0.039-0.02114.505-0.446-0.4460.0000.0000.0000.000
34B738ASN0-0.048-0.04015.2390.1800.1800.0000.0000.0000.000
35B739VAL0-0.0090.0219.661-0.496-0.4960.0000.0000.0000.000
36B740THR0-0.0360.0258.9660.9450.9450.0000.0000.0000.000
37B741SER00.016-0.0278.075-2.085-2.0850.0000.0000.0000.000
38B742GLN0-0.025-0.0225.7071.2001.2000.0000.0000.0000.000
39B743ASP-1-0.790-0.8557.634-20.424-20.4240.0000.0000.0000.000
40B744GLY00.023-0.02810.7001.2431.2430.0000.0000.0000.000
41B745SER0-0.065-0.06012.5311.5911.5910.0000.0000.0000.000
42B746SER00.002-0.00512.749-0.686-0.6860.0000.0000.0000.000
43B747PRO00.0710.01114.1490.5220.5220.0000.0000.0000.000
44B748LEU00.0240.02616.9850.5930.5930.0000.0000.0000.000
45B749HIS00.0150.01817.2240.2220.2220.0000.0000.0000.000
46B750VAL00.0240.03016.0460.4900.4900.0000.0000.0000.000
47B751ALA00.0470.01019.1480.4570.4570.0000.0000.0000.000
48B752ALA0-0.046-0.00522.1370.5580.5580.0000.0000.0000.000
49B753LEU0-0.014-0.01219.8110.4490.4490.0000.0000.0000.000
50B754HIS0-0.030-0.03119.4130.2410.2410.0000.0000.0000.000
51B755GLY00.0110.01824.5030.3220.3220.0000.0000.0000.000
52B756ARG10.8270.89924.06811.26111.2610.0000.0000.0000.000
53B757ALA00.020-0.01126.479-0.141-0.1410.0000.0000.0000.000
54B758ASP-1-0.887-0.94129.075-9.070-9.0700.0000.0000.0000.000
55B759LEU0-0.007-0.00322.349-0.056-0.0560.0000.0000.0000.000
56B760ILE0-0.027-0.00324.140-0.249-0.2490.0000.0000.0000.000
57B761PRO00.0620.02525.887-0.171-0.1710.0000.0000.0000.000
58B762LEU00.0020.01225.743-0.050-0.0500.0000.0000.0000.000
59B763LEU00.0290.02519.751-0.230-0.2300.0000.0000.0000.000
60B764LEU00.010-0.00423.010-0.215-0.2150.0000.0000.0000.000
61B765LYS10.9170.96425.0319.1879.1870.0000.0000.0000.000
62B766HIS10.7930.88922.11411.13511.1350.0000.0000.0000.000
63B767GLY00.0600.03721.879-0.391-0.3910.0000.0000.0000.000
64B768ALA0-0.0240.00119.720-0.463-0.4630.0000.0000.0000.000
65B769ASN00.0170.00218.9501.0081.0080.0000.0000.0000.000
66B770ALA00.046-0.00120.645-0.337-0.3370.0000.0000.0000.000
67B771GLY0-0.058-0.03022.8190.1370.1370.0000.0000.0000.000
68B772ALA0-0.0030.00217.118-0.202-0.2020.0000.0000.0000.000
69B773ARG10.7930.88717.97813.00713.0070.0000.0000.0000.000
70B774ASN00.0480.01115.376-0.389-0.3890.0000.0000.0000.000
71B775ALA00.0420.01413.5560.3240.3240.0000.0000.0000.000
72B776ASP-1-0.856-0.91015.615-14.843-14.8430.0000.0000.0000.000
73B777GLN0-0.066-0.04617.8101.3841.3840.0000.0000.0000.000
74B778ALA00.0400.03920.0600.8070.8070.0000.0000.0000.000
75B779VAL0-0.038-0.01520.124-0.535-0.5350.0000.0000.0000.000
76B780PRO00.0490.01220.4270.2090.2090.0000.0000.0000.000
77B781LEU00.0030.00822.7310.2150.2150.0000.0000.0000.000
78B782HIS00.0100.00524.1720.0570.0570.0000.0000.0000.000
79B783LEU00.0140.03120.0120.2410.2410.0000.0000.0000.000
80B784ALA00.0420.01824.6730.2320.2320.0000.0000.0000.000
81B785CYS0-0.074-0.03427.2940.4380.4380.0000.0000.0000.000
82B786GLN0-0.031-0.02723.9090.0720.0720.0000.0000.0000.000
83B787GLN0-0.034-0.01225.4970.3630.3630.0000.0000.0000.000
84B788GLY00.0260.03529.0130.1990.1990.0000.0000.0000.000
85B789HIS0-0.0030.00427.0860.5350.5350.0000.0000.0000.000
86B790PHE00.0570.01431.335-0.126-0.1260.0000.0000.0000.000
87B791GLN00.0460.01132.780-0.088-0.0880.0000.0000.0000.000
88B792VAL00.0050.03226.781-0.054-0.0540.0000.0000.0000.000
89B793VAL00.0200.00629.686-0.136-0.1360.0000.0000.0000.000
90B794LYS10.8700.92131.0627.7937.7930.0000.0000.0000.000
91B795CYS00.0140.00630.0050.0320.0320.0000.0000.0000.000
92B796LEU00.004-0.00225.267-0.111-0.1110.0000.0000.0000.000
93B797LEU0-0.074-0.02929.334-0.041-0.0410.0000.0000.0000.000
94B798ASP-1-0.807-0.89032.373-7.945-7.9450.0000.0000.0000.000
95B799SER0-0.084-0.03029.1540.0590.0590.0000.0000.0000.000
96B800ASN00.003-0.00229.963-0.182-0.1820.0000.0000.0000.000
97B801ALA00.0030.00127.639-0.215-0.2150.0000.0000.0000.000
98B802LYS10.8130.88828.4959.4749.4740.0000.0000.0000.000
99B803PRO00.0680.04229.281-0.349-0.3490.0000.0000.0000.000
100B804ASN0-0.039-0.00831.656-0.024-0.0240.0000.0000.0000.000
101B805LYS10.9320.96625.26810.83910.8390.0000.0000.0000.000
102B806LYS10.9200.95527.7779.4599.4590.0000.0000.0000.000
103B807ASP-1-0.720-0.78923.170-11.857-11.8570.0000.0000.0000.000
104B808LEU00.0760.02819.8390.5040.5040.0000.0000.0000.000
105B809SER0-0.087-0.04024.1730.3830.3830.0000.0000.0000.000
106B810GLY00.010-0.02826.8300.4720.4720.0000.0000.0000.000
107B811ASN00.0240.00827.9570.7760.7760.0000.0000.0000.000
108B812THR00.0190.00728.409-0.277-0.2770.0000.0000.0000.000
109B813PRO00.0540.01628.4220.0530.0530.0000.0000.0000.000
110B814LEU00.0350.03030.5160.0550.0550.0000.0000.0000.000
111B815ILE0-0.015-0.00932.3770.1520.1520.0000.0000.0000.000
112B816TYR0-0.054-0.04325.5020.1050.1050.0000.0000.0000.000
113B817ALA00.0180.01431.1860.0670.0670.0000.0000.0000.000
114B818CYS0-0.052-0.01433.4940.2400.2400.0000.0000.0000.000
115B819SER0-0.031-0.01632.7390.0390.0390.0000.0000.0000.000
116B820GLY00.0210.00333.0250.0590.0590.0000.0000.0000.000
117B821GLY00.001-0.00333.8660.0700.0700.0000.0000.0000.000
118B822HIS0-0.011-0.01031.5320.4050.4050.0000.0000.0000.000
119B823HIS00.020-0.01336.5580.0100.0100.0000.0000.0000.000
120B824GLU-1-0.932-0.95738.187-7.447-7.4470.0000.0000.0000.000
121B825LEU0-0.031-0.01532.680-0.044-0.0440.0000.0000.0000.000
122B826VAL0-0.014-0.00236.970-0.075-0.0750.0000.0000.0000.000
123B827ALA00.0410.01939.058-0.023-0.0230.0000.0000.0000.000
124B828LEU00.0130.01635.2600.0130.0130.0000.0000.0000.000
125B829LEU00.0440.00032.627-0.081-0.0810.0000.0000.0000.000
126B830LEU0-0.064-0.02436.702-0.043-0.0430.0000.0000.0000.000
127B831GLN00.001-0.00439.862-0.067-0.0670.0000.0000.0000.000
128B832HIS0-0.0150.01235.5960.0030.0030.0000.0000.0000.000
129B833GLY0-0.0080.00236.668-0.159-0.1590.0000.0000.0000.000
130B834ALA0-0.051-0.02935.536-0.145-0.1450.0000.0000.0000.000
131B835SER0-0.051-0.03736.4340.2630.2630.0000.0000.0000.000
132B836ILE00.0330.01437.875-0.198-0.1980.0000.0000.0000.000
133B837ASN00.0140.00440.3350.0330.0330.0000.0000.0000.000
134B838ALA0-0.0240.00435.249-0.044-0.0440.0000.0000.0000.000
135B839SER00.0350.00136.101-0.008-0.0080.0000.0000.0000.000
136B840ASN0-0.047-0.03531.252-0.112-0.1120.0000.0000.0000.000
137B841ASN00.0240.01528.0940.4760.4760.0000.0000.0000.000
138B842LYS10.8530.91632.1149.1759.1750.0000.0000.0000.000
139B843GLY0-0.019-0.02134.7070.2570.2570.0000.0000.0000.000
140B844ASN0-0.050-0.02535.7450.4200.4200.0000.0000.0000.000
141B845THR00.0510.01836.201-0.201-0.2010.0000.0000.0000.000
142B846ALA00.0340.00536.844-0.034-0.0340.0000.0000.0000.000
143B847LEU00.0440.02237.771-0.008-0.0080.0000.0000.0000.000
144B848HIS0-0.0080.00539.131-0.065-0.0650.0000.0000.0000.000
145B849GLU-1-0.737-0.85034.519-8.713-8.7130.0000.0000.0000.000
146B850ALA00.0030.01237.771-0.002-0.0020.0000.0000.0000.000
147B851VAL0-0.027-0.00339.8150.1180.1180.0000.0000.0000.000
148B852ILE0-0.061-0.03437.9980.0760.0760.0000.0000.0000.000
149B853GLU-1-0.970-0.99135.674-8.358-8.3580.0000.0000.0000.000
150B854LYS10.7810.89039.1577.0337.0330.0000.0000.0000.000
151B855HIS00.0520.04636.6260.3010.3010.0000.0000.0000.000
152B856VAL00.027-0.00441.8390.0280.0280.0000.0000.0000.000
153B857PHE00.0400.01943.5380.0400.0400.0000.0000.0000.000
154B858VAL00.0070.01139.0210.0150.0150.0000.0000.0000.000
155B859VAL0-0.026-0.00942.2550.0170.0170.0000.0000.0000.000
156B860GLU-1-0.890-0.95944.634-6.100-6.1000.0000.0000.0000.000
157B861LEU0-0.0130.00242.6810.0700.0700.0000.0000.0000.000
158B862LEU0-0.011-0.01340.104-0.008-0.0080.0000.0000.0000.000
159B863LEU0-0.0110.00344.2610.0270.0270.0000.0000.0000.000
160B864LEU0-0.0030.01847.8110.0790.0790.0000.0000.0000.000
161B865HIS0-0.099-0.05444.8990.0570.0570.0000.0000.0000.000
162B866GLY0-0.006-0.00446.511-0.056-0.0560.0000.0000.0000.000
163B867ALA0-0.074-0.03443.748-0.038-0.0380.0000.0000.0000.000
164B868SER0-0.019-0.01645.1190.1500.1500.0000.0000.0000.000
165B869VAL00.0660.01945.600-0.134-0.1340.0000.0000.0000.000
166B870GLN0-0.036-0.02247.6380.0790.0790.0000.0000.0000.000
167B871VAL0-0.0210.00341.415-0.030-0.0300.0000.0000.0000.000
168B872LEU00.0240.01044.2160.0080.0080.0000.0000.0000.000
169B873ASN0-0.043-0.01739.249-0.101-0.1010.0000.0000.0000.000
170B874LYS10.9070.91934.0159.0449.0440.0000.0000.0000.000
171B875ARG10.8830.94938.0067.8037.8030.0000.0000.0000.000
172B876GLN0-0.030-0.01441.9050.2130.2130.0000.0000.0000.000
173B877ARG10.9520.98641.6427.2407.2400.0000.0000.0000.000
174B878THR0-0.030-0.02744.017-0.156-0.1560.0000.0000.0000.000
175B879ALA00.0230.00344.229-0.011-0.0110.0000.0000.0000.000
176B880VAL00.0980.05045.178-0.018-0.0180.0000.0000.0000.000
177B881ASP-1-0.816-0.85947.250-6.537-6.5370.0000.0000.0000.000
178B882CYS0-0.107-0.07043.288-0.203-0.2030.0000.0000.0000.000
179B883ALA00.0390.03444.971-0.105-0.1050.0000.0000.0000.000
180B884GLU-1-0.831-0.91146.842-6.630-6.6300.0000.0000.0000.000
181B885GLN00.0390.01149.3760.0780.0780.0000.0000.0000.000
182B886ASN0-0.015-0.02052.936-0.016-0.0160.0000.0000.0000.000
183B887SER00.0000.02149.627-0.013-0.0130.0000.0000.0000.000
184B888LYS10.9320.95850.8855.8205.8200.0000.0000.0000.000
185B889ILE00.0270.00445.0840.0380.0380.0000.0000.0000.000
186B890MET0-0.0100.00649.3460.0060.0060.0000.0000.0000.000
187B891GLU-1-0.877-0.93251.607-5.505-5.5050.0000.0000.0000.000
188B892LEU0-0.029-0.01849.2920.0580.0580.0000.0000.0000.000
189B893LEU0-0.062-0.03747.022-0.008-0.0080.0000.0000.0000.000
190B894GLN0-0.093-0.03251.1950.0580.0580.0000.0000.0000.000
191B895VAL0-0.0130.00853.5690.0670.0670.0000.0000.0000.000