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: 7MGRK

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1916162.811734
FMO2-HF: Nuclear repulsion 1843688.794403
FMO2-HF: Total energy -72474.017331
FMO2-MP2: Total energy -72685.680915


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.
20.75822.8710.118-0.859-1.372-0.002
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 : 0.976 / 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].
3B667TYR00.0380.0193.105-1.6960.4170.118-0.859-1.372-0.002
4B668ARG10.8930.9505.82026.48326.4830.0000.0000.0000.000
5B669GLU-1-0.767-0.8828.270-17.505-17.5050.0000.0000.0000.000
6B670VAL00.0160.0017.8471.7911.7910.0000.0000.0000.000
7B671GLU-1-0.813-0.8909.972-18.089-18.0890.0000.0000.0000.000
8B672LYS10.7940.90011.68619.70619.7060.0000.0000.0000.000
9B673LEU00.0280.02013.6351.0351.0350.0000.0000.0000.000
10B674LEU00.005-0.00711.9530.9890.9890.0000.0000.0000.000
11B675ARG10.8650.92314.43817.69617.6960.0000.0000.0000.000
12B676ALA00.0110.01017.5450.7230.7230.0000.0000.0000.000
13B677VAL0-0.040-0.02918.1160.6680.6680.0000.0000.0000.000
14B678ALA0-0.022-0.01218.9510.5740.5740.0000.0000.0000.000
15B679ASP-1-0.885-0.96120.812-10.768-10.7680.0000.0000.0000.000
16B680GLY0-0.033-0.01723.2220.4890.4890.0000.0000.0000.000
17B681ASP-1-0.833-0.90822.956-11.070-11.0700.0000.0000.0000.000
18B682LEU00.013-0.01523.180-0.447-0.4470.0000.0000.0000.000
19B683GLU-1-0.784-0.84424.430-10.229-10.2290.0000.0000.0000.000
20B684MET00.0070.00819.739-0.472-0.4720.0000.0000.0000.000
21B685VAL0-0.030-0.02219.601-0.666-0.6660.0000.0000.0000.000
22B686ARG10.7520.83920.2109.7919.7910.0000.0000.0000.000
23B687TYR0-0.014-0.01119.477-0.278-0.2780.0000.0000.0000.000
24B688LEU0-0.030-0.02115.609-0.449-0.4490.0000.0000.0000.000
25B689LEU0-0.061-0.02315.819-0.883-0.8830.0000.0000.0000.000
26B690GLU-1-0.934-0.96018.509-13.242-13.2420.0000.0000.0000.000
27B691TRP0-0.063-0.03320.5620.5960.5960.0000.0000.0000.000
28B692THR0-0.008-0.00423.9310.3980.3980.0000.0000.0000.000
29B733SER00.0330.00311.8240.0040.0040.0000.0000.0000.000
30B734GLY00.001-0.00310.112-1.569-1.5690.0000.0000.0000.000
31B735LEU0-0.040-0.00110.543-0.503-0.5030.0000.0000.0000.000
32B736GLY00.0880.02212.5120.8110.8110.0000.0000.0000.000
33B737VAL0-0.037-0.01814.699-0.583-0.5830.0000.0000.0000.000
34B738ASN0-0.044-0.03115.6270.3350.3350.0000.0000.0000.000
35B739VAL0-0.0050.01910.078-0.625-0.6250.0000.0000.0000.000
36B740THR0-0.017-0.0169.7641.0021.0020.0000.0000.0000.000
37B741SER00.000-0.0258.572-2.226-2.2260.0000.0000.0000.000
38B742GLN0-0.031-0.0255.7941.2371.2370.0000.0000.0000.000
39B743ASP-1-0.788-0.8387.527-20.201-20.2010.0000.0000.0000.000
40B744GLY00.017-0.00610.5691.5241.5240.0000.0000.0000.000
41B745SER0-0.050-0.04612.3451.5891.5890.0000.0000.0000.000
42B746SER00.002-0.01813.040-0.761-0.7610.0000.0000.0000.000
43B747PRO00.0420.00314.3020.5430.5430.0000.0000.0000.000
44B748LEU00.0280.02317.2530.6080.6080.0000.0000.0000.000
45B749HIS0-0.0060.01117.3040.2270.2270.0000.0000.0000.000
46B750VAL00.0250.02215.6830.4940.4940.0000.0000.0000.000
47B751ALA00.0340.01418.9210.4540.4540.0000.0000.0000.000
48B752ALA0-0.035-0.02422.1410.5190.5190.0000.0000.0000.000
49B753LEU00.003-0.00119.6670.4430.4430.0000.0000.0000.000
50B754HIS0-0.039-0.02919.0800.2630.2630.0000.0000.0000.000
51B755GLY00.0150.01124.1730.2780.2780.0000.0000.0000.000
52B756ARG10.8570.95224.31611.40211.4020.0000.0000.0000.000
53B757ALA00.003-0.02326.631-0.183-0.1830.0000.0000.0000.000
54B758ASP-1-0.888-0.94129.144-9.283-9.2830.0000.0000.0000.000
55B759LEU0-0.0080.00222.587-0.049-0.0490.0000.0000.0000.000
56B760ILE0-0.032-0.00424.583-0.253-0.2530.0000.0000.0000.000
57B761PRO00.0570.01326.320-0.157-0.1570.0000.0000.0000.000
58B762LEU0-0.0140.00226.308-0.036-0.0360.0000.0000.0000.000
59B763LEU00.0240.01820.116-0.292-0.2920.0000.0000.0000.000
60B764LEU00.0120.00223.211-0.227-0.2270.0000.0000.0000.000
61B765LYS10.9180.96725.3499.2399.2390.0000.0000.0000.000
62B766HIS10.8330.90722.14011.40011.4000.0000.0000.0000.000
63B767GLY00.0300.02222.096-0.393-0.3930.0000.0000.0000.000
64B768ALA0-0.0310.00720.282-0.436-0.4360.0000.0000.0000.000
65B769ASN00.0360.00519.3001.0501.0500.0000.0000.0000.000
66B770ALA00.0540.00821.376-0.323-0.3230.0000.0000.0000.000
67B771GLY0-0.062-0.02123.3190.2300.2300.0000.0000.0000.000
68B772ALA0-0.017-0.00617.739-0.204-0.2040.0000.0000.0000.000
69B773ARG10.7910.88317.93413.30713.3070.0000.0000.0000.000
70B774ASN00.0260.01015.164-0.322-0.3220.0000.0000.0000.000
71B775ALA00.0340.00913.5860.3740.3740.0000.0000.0000.000
72B776ASP-1-0.855-0.90715.462-14.576-14.5760.0000.0000.0000.000
73B777GLN0-0.058-0.03517.6911.4921.4920.0000.0000.0000.000
74B778ALA00.0260.02420.1290.6980.6980.0000.0000.0000.000
75B779VAL0-0.012-0.00520.050-0.581-0.5810.0000.0000.0000.000
76B780PRO00.014-0.00220.7550.2800.2800.0000.0000.0000.000
77B781LEU00.0440.02422.8190.2160.2160.0000.0000.0000.000
78B782HIS0-0.019-0.00924.0560.0980.0980.0000.0000.0000.000
79B783LEU00.0140.01419.6020.2400.2400.0000.0000.0000.000
80B784ALA00.0070.00424.2960.2180.2180.0000.0000.0000.000
81B785CYS0-0.069-0.03127.0850.4110.4110.0000.0000.0000.000
82B786GLN0-0.020-0.01423.6020.0730.0730.0000.0000.0000.000
83B787GLN0-0.0180.00625.1570.3750.3750.0000.0000.0000.000
84B788GLY00.0590.04428.9400.2080.2080.0000.0000.0000.000
85B789HIS0-0.0040.00826.6270.5630.5630.0000.0000.0000.000
86B790PHE00.0390.00230.965-0.129-0.1290.0000.0000.0000.000
87B791GLN00.0490.01732.803-0.033-0.0330.0000.0000.0000.000
88B792VAL0-0.0130.02026.650-0.056-0.0560.0000.0000.0000.000
89B793VAL00.001-0.00929.679-0.117-0.1170.0000.0000.0000.000
90B794LYS10.8890.92431.0657.8077.8070.0000.0000.0000.000
91B795CYS00.0150.01030.2820.0270.0270.0000.0000.0000.000
92B796LEU0-0.0150.00325.524-0.111-0.1110.0000.0000.0000.000
93B797LEU0-0.036-0.02029.591-0.029-0.0290.0000.0000.0000.000
94B798ASP-1-0.794-0.87132.642-7.925-7.9250.0000.0000.0000.000
95B799SER0-0.073-0.03429.8910.1230.1230.0000.0000.0000.000
96B800ASN0-0.0050.00130.526-0.207-0.2070.0000.0000.0000.000
97B801ALA00.0090.00828.218-0.192-0.1920.0000.0000.0000.000
98B802LYS10.8400.90629.0349.4729.4720.0000.0000.0000.000
99B803PRO00.0780.03829.647-0.354-0.3540.0000.0000.0000.000
100B804ASN0-0.038-0.00531.504-0.081-0.0810.0000.0000.0000.000
101B805LYS10.9430.96525.91010.76610.7660.0000.0000.0000.000
102B806LYS10.9250.96727.7469.4279.4270.0000.0000.0000.000
103B807ASP-1-0.719-0.79323.169-11.720-11.7200.0000.0000.0000.000
104B808LEU00.0430.00419.5740.4770.4770.0000.0000.0000.000
105B809SER0-0.071-0.04223.9650.3620.3620.0000.0000.0000.000
106B810GLY00.011-0.00726.6780.4840.4840.0000.0000.0000.000
107B811ASN00.0180.00227.7390.7350.7350.0000.0000.0000.000
108B812THR00.0270.01028.164-0.268-0.2680.0000.0000.0000.000
109B813PRO00.0300.00528.3070.0740.0740.0000.0000.0000.000
110B814LEU00.0590.03830.3160.0650.0650.0000.0000.0000.000
111B815ILE0-0.016-0.00132.1650.1570.1570.0000.0000.0000.000
112B816TYR0-0.054-0.05325.5030.0450.0450.0000.0000.0000.000
113B817ALA00.0290.02031.1930.0800.0800.0000.0000.0000.000
114B818CYS0-0.068-0.02933.6010.2300.2300.0000.0000.0000.000
115B819SER0-0.021-0.01532.7490.0530.0530.0000.0000.0000.000
116B820GLY00.0260.00632.9950.0110.0110.0000.0000.0000.000
117B821GLY00.0290.01833.7920.0640.0640.0000.0000.0000.000
118B822HIS0-0.0260.00331.4470.4110.4110.0000.0000.0000.000
119B823HIS0-0.025-0.04236.3640.0580.0580.0000.0000.0000.000
120B824GLU-1-0.882-0.93638.283-7.488-7.4880.0000.0000.0000.000
121B825LEU0-0.048-0.02332.517-0.023-0.0230.0000.0000.0000.000
122B826VAL0-0.022-0.00236.756-0.059-0.0590.0000.0000.0000.000
123B827ALA00.0540.02238.953-0.011-0.0110.0000.0000.0000.000
124B828LEU0-0.0020.00935.1020.0160.0160.0000.0000.0000.000
125B829LEU00.011-0.01632.547-0.095-0.0950.0000.0000.0000.000
126B830LEU0-0.037-0.01636.619-0.044-0.0440.0000.0000.0000.000
127B831GLN0-0.023-0.00839.880-0.047-0.0470.0000.0000.0000.000
128B832HIS0-0.032-0.00835.8570.0370.0370.0000.0000.0000.000
129B833GLY00.0100.01136.831-0.179-0.1790.0000.0000.0000.000
130B834ALA0-0.063-0.03035.646-0.138-0.1380.0000.0000.0000.000
131B835SER0-0.011-0.03436.3840.2660.2660.0000.0000.0000.000
132B836ILE00.0060.00737.847-0.175-0.1750.0000.0000.0000.000
133B837ASN00.0100.01340.1550.0310.0310.0000.0000.0000.000
134B838ALA0-0.030-0.00535.284-0.027-0.0270.0000.0000.0000.000
135B839SER00.0220.00335.806-0.022-0.0220.0000.0000.0000.000
136B840ASN0-0.043-0.02930.949-0.102-0.1020.0000.0000.0000.000
137B841ASN00.001-0.00727.8130.4950.4950.0000.0000.0000.000
138B842LYS10.8520.91431.7989.0539.0530.0000.0000.0000.000
139B843GLY0-0.017-0.01134.4860.2530.2530.0000.0000.0000.000
140B844ASN0-0.057-0.03635.7060.3300.3300.0000.0000.0000.000
141B845THR00.043-0.01035.958-0.227-0.2270.0000.0000.0000.000
142B846ALA00.0320.00036.736-0.064-0.0640.0000.0000.0000.000
143B847LEU00.0520.02737.649-0.005-0.0050.0000.0000.0000.000
144B848HIS0-0.0020.00939.043-0.073-0.0730.0000.0000.0000.000
145B849GLU-1-0.730-0.83434.041-8.724-8.7240.0000.0000.0000.000
146B850ALA0-0.0050.00737.6890.0060.0060.0000.0000.0000.000
147B851VAL0-0.026-0.00639.8470.1040.1040.0000.0000.0000.000
148B852ILE0-0.064-0.03738.3310.0830.0830.0000.0000.0000.000
149B853GLU-1-0.960-0.98435.524-8.408-8.4080.0000.0000.0000.000
150B854LYS10.7790.88538.8857.0607.0600.0000.0000.0000.000
151B855HIS00.0630.05236.4280.3250.3250.0000.0000.0000.000
152B856VAL00.010-0.01041.6430.0260.0260.0000.0000.0000.000
153B857PHE00.0590.02643.5380.0560.0560.0000.0000.0000.000
154B858VAL0-0.0050.01638.9550.0150.0150.0000.0000.0000.000
155B859VAL0-0.022-0.01042.1270.0150.0150.0000.0000.0000.000
156B860GLU-1-0.869-0.94644.550-6.047-6.0470.0000.0000.0000.000
157B861LEU00.0020.00242.7680.0790.0790.0000.0000.0000.000
158B862LEU0-0.014-0.01040.0600.0150.0150.0000.0000.0000.000
159B863LEU0-0.021-0.00844.1820.0280.0280.0000.0000.0000.000
160B864LEU0-0.0250.00347.7830.0930.0930.0000.0000.0000.000
161B865HIS0-0.080-0.05044.7280.0300.0300.0000.0000.0000.000
162B866GLY00.0010.00646.274-0.059-0.0590.0000.0000.0000.000
163B867ALA0-0.056-0.02843.551-0.056-0.0560.0000.0000.0000.000
164B868SER0-0.008-0.01245.0030.1540.1540.0000.0000.0000.000
165B869VAL00.0690.02045.472-0.148-0.1480.0000.0000.0000.000
166B870GLN0-0.027-0.01647.7580.0300.0300.0000.0000.0000.000
167B871VAL0-0.028-0.00441.457-0.011-0.0110.0000.0000.0000.000
168B872LEU00.0230.01744.124-0.026-0.0260.0000.0000.0000.000
169B873ASN0-0.027-0.00839.011-0.084-0.0840.0000.0000.0000.000
170B874LYS10.9130.92533.3949.0959.0950.0000.0000.0000.000
171B875ARG10.8720.94937.6627.8597.8590.0000.0000.0000.000
172B876GLN0-0.031-0.02441.5800.2290.2290.0000.0000.0000.000
173B877ARG10.9360.99042.0117.1607.1600.0000.0000.0000.000
174B878THR0-0.008-0.02443.804-0.148-0.1480.0000.0000.0000.000
175B879ALA00.0300.00544.378-0.078-0.0780.0000.0000.0000.000
176B880VAL00.0700.03945.323-0.014-0.0140.0000.0000.0000.000
177B881ASP-1-0.811-0.87647.187-6.551-6.5510.0000.0000.0000.000
178B882CYS0-0.099-0.05443.260-0.172-0.1720.0000.0000.0000.000
179B883ALA00.0350.03044.801-0.115-0.1150.0000.0000.0000.000
180B884GLU-1-0.804-0.89546.451-6.651-6.6510.0000.0000.0000.000
181B885GLN00.0460.03049.2150.0580.0580.0000.0000.0000.000
182B886ASN0-0.036-0.03552.894-0.015-0.0150.0000.0000.0000.000
183B887SER0-0.0060.00749.9000.0080.0080.0000.0000.0000.000
184B888LYS10.9150.95650.6535.8725.8720.0000.0000.0000.000
185B889ILE00.0090.00544.9400.0110.0110.0000.0000.0000.000
186B890MET0-0.017-0.00249.0900.0060.0060.0000.0000.0000.000
187B891GLU-1-0.896-0.94351.454-5.555-5.5550.0000.0000.0000.000
188B892LEU0-0.027-0.01349.0410.0550.0550.0000.0000.0000.000
189B893LEU0-0.049-0.02546.9680.0030.0030.0000.0000.0000.000
190B894GLN0-0.083-0.03751.1430.0680.0680.0000.0000.0000.000
191B895VAL0-0.054-0.01253.0910.1020.1020.0000.0000.0000.000