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: 9MG62

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 OptH
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 -1915643.557702
FMO2-HF: Nuclear repulsion 1843171.475686
FMO2-HF: Total energy -72472.082016
FMO2-MP2: Total energy -72683.934146


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.
18.24220.8060.106-1.094-1.576-0.004
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 : 0.981 / 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].
3B667TYR00.0260.0153.191-0.7561.8080.106-1.094-1.576-0.004
4B668ARG10.9760.9935.58025.55225.5520.0000.0000.0000.000
5B669GLU-1-0.843-0.9398.227-17.475-17.4750.0000.0000.0000.000
6B670VAL00.0090.0027.4241.7111.7110.0000.0000.0000.000
7B671GLU-1-0.894-0.9589.556-20.235-20.2350.0000.0000.0000.000
8B672LYS10.8330.92611.52818.79218.7920.0000.0000.0000.000
9B673LEU00.0360.01913.2111.1411.1410.0000.0000.0000.000
10B674LEU0-0.017-0.01012.2061.1401.1400.0000.0000.0000.000
11B675ARG10.9791.00014.36017.89317.8930.0000.0000.0000.000
12B676ALA00.0300.01617.4030.7470.7470.0000.0000.0000.000
13B677VAL0-0.030-0.02817.5590.6450.6450.0000.0000.0000.000
14B678ALA0-0.025-0.00819.1730.6330.6330.0000.0000.0000.000
15B679ASP-1-0.921-0.95220.948-11.120-11.1200.0000.0000.0000.000
16B680GLY0-0.059-0.03423.1280.4880.4880.0000.0000.0000.000
17B681ASP-1-0.868-0.93122.519-11.041-11.0410.0000.0000.0000.000
18B682LEU00.016-0.00823.030-0.388-0.3880.0000.0000.0000.000
19B683GLU-1-0.756-0.83624.241-10.200-10.2000.0000.0000.0000.000
20B684MET00.0180.02719.663-0.448-0.4480.0000.0000.0000.000
21B685VAL0-0.049-0.02419.402-0.568-0.5680.0000.0000.0000.000
22B686ARG10.7830.82919.9609.8489.8480.0000.0000.0000.000
23B687TYR0-0.021-0.00719.536-0.281-0.2810.0000.0000.0000.000
24B688LEU0-0.032-0.02615.717-0.364-0.3640.0000.0000.0000.000
25B689LEU0-0.054-0.02415.712-0.649-0.6490.0000.0000.0000.000
26B690GLU-1-0.959-0.95818.297-13.400-13.4000.0000.0000.0000.000
27B691TRP0-0.069-0.03820.4570.5420.5420.0000.0000.0000.000
28B692THR00.001-0.00323.9700.2040.2040.0000.0000.0000.000
29B733SER0-0.002-0.01112.2400.1230.1230.0000.0000.0000.000
30B734GLY00.005-0.00310.470-1.417-1.4170.0000.0000.0000.000
31B735LEU0-0.0240.00510.427-0.667-0.6670.0000.0000.0000.000
32B736GLY00.0690.02112.2880.8380.8380.0000.0000.0000.000
33B737VAL0-0.046-0.02314.504-0.469-0.4690.0000.0000.0000.000
34B738ASN0-0.031-0.03215.2760.1320.1320.0000.0000.0000.000
35B739VAL0-0.0020.0289.674-0.480-0.4800.0000.0000.0000.000
36B740THR0-0.0210.0568.9761.0031.0030.0000.0000.0000.000
37B741SER00.0330.0028.141-2.215-2.2150.0000.0000.0000.000
38B742GLN0-0.018-0.0165.7041.6881.6880.0000.0000.0000.000
39B743ASP-1-0.798-0.8957.642-20.382-20.3820.0000.0000.0000.000
40B744GLY0-0.025-0.08210.7071.2921.2920.0000.0000.0000.000
41B745SER0-0.080-0.05412.6421.5041.5040.0000.0000.0000.000
42B746SER00.010-0.01712.818-0.703-0.7030.0000.0000.0000.000
43B747PRO00.0750.01814.2960.4920.4920.0000.0000.0000.000
44B748LEU00.0360.02517.0220.5950.5950.0000.0000.0000.000
45B749HIS00.0120.04117.3700.2700.2700.0000.0000.0000.000
46B750VAL00.0160.02616.0510.4880.4880.0000.0000.0000.000
47B751ALA00.037-0.00319.2030.4650.4650.0000.0000.0000.000
48B752ALA0-0.0420.00122.1800.5630.5630.0000.0000.0000.000
49B753LEU0-0.015-0.01520.0620.4540.4540.0000.0000.0000.000
50B754HIS0-0.021-0.01619.7270.3040.3040.0000.0000.0000.000
51B755GLY00.0200.01624.5070.3330.3330.0000.0000.0000.000
52B756ARG10.8400.90924.04311.38911.3890.0000.0000.0000.000
53B757ALA00.018-0.00926.508-0.136-0.1360.0000.0000.0000.000
54B758ASP-1-0.871-0.93529.109-9.056-9.0560.0000.0000.0000.000
55B759LEU0-0.006-0.00722.334-0.057-0.0570.0000.0000.0000.000
56B760ILE0-0.0260.00024.401-0.232-0.2320.0000.0000.0000.000
57B761PRO00.0550.02325.916-0.159-0.1590.0000.0000.0000.000
58B762LEU0-0.0120.00425.523-0.035-0.0350.0000.0000.0000.000
59B763LEU00.0270.01219.868-0.225-0.2250.0000.0000.0000.000
60B764LEU00.009-0.00123.028-0.208-0.2080.0000.0000.0000.000
61B765LYS10.9100.96225.0619.2379.2370.0000.0000.0000.000
62B766HIS10.8070.90422.05311.19811.1980.0000.0000.0000.000
63B767GLY00.0630.04221.884-0.391-0.3910.0000.0000.0000.000
64B768ALA0-0.0140.00419.763-0.463-0.4630.0000.0000.0000.000
65B769ASN00.0200.00019.0831.0471.0470.0000.0000.0000.000
66B770ALA00.0470.00420.717-0.354-0.3540.0000.0000.0000.000
67B771GLY0-0.075-0.03422.9100.1240.1240.0000.0000.0000.000
68B772ALA00.000-0.00417.197-0.191-0.1910.0000.0000.0000.000
69B773ARG10.8070.90718.07813.08613.0860.0000.0000.0000.000
70B774ASN00.0760.04515.492-0.500-0.5000.0000.0000.0000.000
71B775ALA00.0600.01713.5620.3760.3760.0000.0000.0000.000
72B776ASP-1-0.877-0.93115.625-14.982-14.9820.0000.0000.0000.000
73B777GLN0-0.076-0.05117.6791.4031.4030.0000.0000.0000.000
74B778ALA00.0390.03220.0700.8050.8050.0000.0000.0000.000
75B779VAL0-0.050-0.02520.235-0.535-0.5350.0000.0000.0000.000
76B780PRO00.0530.00720.6900.2300.2300.0000.0000.0000.000
77B781LEU00.0090.01022.8170.2200.2200.0000.0000.0000.000
78B782HIS00.0080.01024.1590.0330.0330.0000.0000.0000.000
79B783LEU00.0060.03020.0600.2140.2140.0000.0000.0000.000
80B784ALA00.0440.01724.6810.2320.2320.0000.0000.0000.000
81B785CYS0-0.087-0.03427.3210.4380.4380.0000.0000.0000.000
82B786GLN0-0.022-0.02523.9760.0780.0780.0000.0000.0000.000
83B787GLN0-0.040-0.01425.6210.3570.3570.0000.0000.0000.000
84B788GLY00.0220.03029.0170.2010.2010.0000.0000.0000.000
85B789HIS0-0.0020.00827.2970.5200.5200.0000.0000.0000.000
86B790PHE00.0660.01831.367-0.118-0.1180.0000.0000.0000.000
87B791GLN00.0370.00532.689-0.091-0.0910.0000.0000.0000.000
88B792VAL00.0080.03126.865-0.058-0.0580.0000.0000.0000.000
89B793VAL00.0180.00829.747-0.136-0.1360.0000.0000.0000.000
90B794LYS10.9250.97131.1337.8557.8550.0000.0000.0000.000
91B795CYS0-0.017-0.00129.8550.0300.0300.0000.0000.0000.000
92B796LEU00.011-0.00425.448-0.112-0.1120.0000.0000.0000.000
93B797LEU0-0.077-0.03429.398-0.037-0.0370.0000.0000.0000.000
94B798ASP-1-0.839-0.92532.446-8.009-8.0090.0000.0000.0000.000
95B799SER0-0.108-0.04129.1800.0790.0790.0000.0000.0000.000
96B800ASN0-0.026-0.02530.024-0.081-0.0810.0000.0000.0000.000
97B801ALA0-0.023-0.00427.782-0.229-0.2290.0000.0000.0000.000
98B802LYS10.8810.92328.5949.5549.5540.0000.0000.0000.000
99B803PRO00.0660.04429.380-0.360-0.3600.0000.0000.0000.000
100B804ASN0-0.0130.00731.763-0.044-0.0440.0000.0000.0000.000
101B805LYS10.9190.95525.01211.03811.0380.0000.0000.0000.000
102B806LYS10.9060.94727.8069.5169.5160.0000.0000.0000.000
103B807ASP-1-0.698-0.75323.085-12.002-12.0020.0000.0000.0000.000
104B808LEU00.0640.02919.6600.5410.5410.0000.0000.0000.000
105B809SER0-0.080-0.02824.1820.3760.3760.0000.0000.0000.000
106B810GLY00.011-0.02926.8370.4850.4850.0000.0000.0000.000
107B811ASN00.0350.02228.0150.8300.8300.0000.0000.0000.000
108B812THR00.0330.02928.419-0.291-0.2910.0000.0000.0000.000
109B813PRO00.045-0.00428.7460.0310.0310.0000.0000.0000.000
110B814LEU00.0280.02730.5260.0530.0530.0000.0000.0000.000
111B815ILE0-0.028-0.01632.2650.1640.1640.0000.0000.0000.000
112B816TYR0-0.087-0.11125.4650.0660.0660.0000.0000.0000.000
113B817ALA00.0280.01731.1930.0640.0640.0000.0000.0000.000
114B818CYS0-0.060-0.01233.5010.2440.2440.0000.0000.0000.000
115B819SER0-0.011-0.00732.6990.0610.0610.0000.0000.0000.000
116B820GLY00.0230.00333.0290.0590.0590.0000.0000.0000.000
117B821GLY0-0.003-0.00733.8700.0750.0750.0000.0000.0000.000
118B822HIS00.001-0.00131.6950.3990.3990.0000.0000.0000.000
119B823HIS00.035-0.00636.563-0.017-0.0170.0000.0000.0000.000
120B824GLU-1-0.942-0.96238.186-7.584-7.5840.0000.0000.0000.000
121B825LEU0-0.036-0.01632.697-0.043-0.0430.0000.0000.0000.000
122B826VAL00.0000.00837.025-0.075-0.0750.0000.0000.0000.000
123B827ALA00.0430.01639.079-0.018-0.0180.0000.0000.0000.000
124B828LEU00.0060.01735.3400.0230.0230.0000.0000.0000.000
125B829LEU00.0490.00032.753-0.081-0.0810.0000.0000.0000.000
126B830LEU0-0.053-0.02036.793-0.038-0.0380.0000.0000.0000.000
127B831GLN0-0.004-0.00439.958-0.069-0.0690.0000.0000.0000.000
128B832HIS0-0.0190.01035.739-0.019-0.0190.0000.0000.0000.000
129B833GLY0-0.0060.00036.760-0.159-0.1590.0000.0000.0000.000
130B834ALA0-0.046-0.03035.667-0.142-0.1420.0000.0000.0000.000
131B835SER0-0.066-0.04836.5230.2360.2360.0000.0000.0000.000
132B836ILE00.0260.01337.927-0.200-0.2000.0000.0000.0000.000
133B837ASN00.0320.01440.3450.0080.0080.0000.0000.0000.000
134B838ALA0-0.0270.00135.269-0.043-0.0430.0000.0000.0000.000
135B839SER00.0390.00936.110-0.018-0.0180.0000.0000.0000.000
136B840ASN0-0.023-0.01631.274-0.067-0.0670.0000.0000.0000.000
137B841ASN00.0130.00228.0620.4880.4880.0000.0000.0000.000
138B842LYS10.9130.95931.7399.5299.5290.0000.0000.0000.000
139B843GLY0-0.010-0.01734.7500.2570.2570.0000.0000.0000.000
140B844ASN0-0.065-0.03235.7770.4370.4370.0000.0000.0000.000
141B845THR00.0510.02936.209-0.202-0.2020.0000.0000.0000.000
142B846ALA00.043-0.00536.859-0.037-0.0370.0000.0000.0000.000
143B847LEU00.0330.02037.779-0.008-0.0080.0000.0000.0000.000
144B848HIS0-0.017-0.00139.141-0.050-0.0500.0000.0000.0000.000
145B849GLU-1-0.812-0.91334.619-8.770-8.7700.0000.0000.0000.000
146B850ALA0-0.0020.00837.7760.0010.0010.0000.0000.0000.000
147B851VAL0-0.035-0.00639.8200.1210.1210.0000.0000.0000.000
148B852ILE0-0.052-0.03238.0560.0810.0810.0000.0000.0000.000
149B853GLU-1-0.974-0.99235.413-8.492-8.4920.0000.0000.0000.000
150B854LYS10.8830.95139.1607.1927.1920.0000.0000.0000.000
151B855HIS00.0400.04136.5870.3140.3140.0000.0000.0000.000
152B856VAL00.020-0.00441.8430.0290.0290.0000.0000.0000.000
153B857PHE00.0520.02143.5770.0360.0360.0000.0000.0000.000
154B858VAL00.0040.01139.0860.0150.0150.0000.0000.0000.000
155B859VAL0-0.024-0.00942.2610.0180.0180.0000.0000.0000.000
156B860GLU-1-0.918-0.96644.641-6.209-6.2090.0000.0000.0000.000
157B861LEU0-0.017-0.00742.8690.0700.0700.0000.0000.0000.000
158B862LEU0-0.021-0.02440.105-0.007-0.0070.0000.0000.0000.000
159B863LEU0-0.0100.00544.2690.0280.0280.0000.0000.0000.000
160B864LEU0-0.0030.01747.8190.0800.0800.0000.0000.0000.000
161B865HIS0-0.081-0.04144.9470.0620.0620.0000.0000.0000.000
162B866GLY0-0.005-0.00346.601-0.057-0.0570.0000.0000.0000.000
163B867ALA0-0.074-0.03743.709-0.036-0.0360.0000.0000.0000.000
164B868SER0-0.027-0.01745.1190.1540.1540.0000.0000.0000.000
165B869VAL00.0820.02645.609-0.140-0.1400.0000.0000.0000.000
166B870GLN0-0.042-0.02647.6560.1070.1070.0000.0000.0000.000
167B871VAL0-0.035-0.00641.507-0.028-0.0280.0000.0000.0000.000
168B872LEU00.0280.00944.2230.0060.0060.0000.0000.0000.000
169B873ASN0-0.0250.00339.240-0.132-0.1320.0000.0000.0000.000
170B874LYS10.9330.93034.3829.1089.1080.0000.0000.0000.000
171B875ARG10.8570.93438.3967.8197.8190.0000.0000.0000.000
172B876GLN0-0.021-0.00742.1250.2110.2110.0000.0000.0000.000
173B877ARG10.9751.00641.2987.3657.3650.0000.0000.0000.000
174B878THR0-0.044-0.00844.023-0.134-0.1340.0000.0000.0000.000
175B879ALA00.036-0.00144.230-0.014-0.0140.0000.0000.0000.000
176B880VAL00.0990.04745.184-0.025-0.0250.0000.0000.0000.000
177B881ASP-1-0.820-0.88247.185-6.595-6.5950.0000.0000.0000.000
178B882CYS0-0.122-0.07543.286-0.210-0.2100.0000.0000.0000.000
179B883ALA00.0280.02644.974-0.108-0.1080.0000.0000.0000.000
180B884GLU-1-0.924-0.97247.344-6.598-6.5980.0000.0000.0000.000
181B885GLN00.0150.00049.3770.1250.1250.0000.0000.0000.000
182B886ASN0-0.006-0.01352.938-0.023-0.0230.0000.0000.0000.000
183B887SER0-0.0040.01649.646-0.024-0.0240.0000.0000.0000.000
184B888LYS11.0231.00650.6345.9005.9000.0000.0000.0000.000
185B889ILE00.0160.00045.0810.0380.0380.0000.0000.0000.000
186B890MET0-0.0220.00149.3500.0120.0120.0000.0000.0000.000
187B891GLU-1-0.958-0.97751.611-5.495-5.4950.0000.0000.0000.000
188B892LEU0-0.034-0.02849.0480.0530.0530.0000.0000.0000.000
189B893LEU0-0.062-0.03447.108-0.011-0.0110.0000.0000.0000.000
190B894GLN0-0.0330.00651.201-0.004-0.0040.0000.0000.0000.000
191B895VAL0-0.034-0.00453.4610.0630.0630.0000.0000.0000.000