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: N9MMQ

Calculation Name: 3WHR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WHR

Chain ID: B

ChEMBL ID:

UniProt ID: P54422

Base Structure: X-ray

Registration Date: 2023-09-20

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1657928.340213
FMO2-HF: Nuclear repulsion 1588690.117225
FMO2-HF: Total energy -69238.222988
FMO2-MP2: Total energy -69440.281998


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:403:THR)


Summations of interaction energy for fragment #1(B:403:THR)
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.
-25.11-21.46223.245-9-17.892-0.065
Interaction energy analysis for fragmet #1(B:403:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.015
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].
3B405HIS00.0750.0773.226-2.2410.4910.095-1.290-1.537-0.001
4B406PHE0-0.0050.0055.0200.1210.140-0.001-0.003-0.0140.000
5B407THR0-0.029-0.0258.699-0.001-0.0010.0000.0000.0000.000
6B408VAL00.0170.00211.8590.0140.0140.0000.0000.0000.000
7B409ALA00.0280.02415.461-0.004-0.0040.0000.0000.0000.000
8B410ASP-1-0.786-0.88018.773-0.043-0.0430.0000.0000.0000.000
9B411ARG10.9340.95722.1170.0240.0240.0000.0000.0000.000
10B412TRP0-0.085-0.05224.9890.0040.0040.0000.0000.0000.000
11B413GLY00.0290.03023.9740.0000.0000.0000.0000.0000.000
12B414ASN0-0.082-0.04020.448-0.003-0.0030.0000.0000.0000.000
13B415VAL00.009-0.00915.9960.0040.0040.0000.0000.0000.000
14B416VAL0-0.0170.00212.260-0.011-0.0110.0000.0000.0000.000
15B417SER00.0290.01210.5120.0070.0070.0000.0000.0000.000
16B418TYR0-0.026-0.0157.6680.0110.0110.0000.0000.0000.000
17B419THR00.009-0.0162.4560.153-0.4362.012-0.407-1.015-0.001
18B420THR0-0.035-0.0243.124-0.853-0.0920.060-0.282-0.539-0.001
19B421THR00.0270.0031.922-15.103-14.48713.993-7.510-7.099-0.052
20B422ILE0-0.0050.0152.9311.9091.3380.1550.917-0.501-0.002
21B423GLU-1-0.779-0.8663.5420.0200.4000.001-0.134-0.2470.000
22B424GLN0-0.054-0.0263.209-2.432-1.2560.027-0.627-0.576-0.005
23B425LEU0-0.014-0.0134.2270.0890.264-0.001-0.008-0.1670.000
24B426PHE0-0.044-0.0336.040-0.164-0.1640.0000.0000.0000.000
25B427GLY00.0240.0246.554-0.079-0.0790.0000.0000.0000.000
26B428THR0-0.032-0.0397.9510.0940.0940.0000.0000.0000.000
27B429GLY0-0.0180.00910.9980.0490.0490.0000.0000.0000.000
28B430ILE0-0.054-0.02312.7750.0360.0360.0000.0000.0000.000
29B431MET0-0.0130.00813.995-0.014-0.0140.0000.0000.0000.000
30B432VAL0-0.019-0.01316.130-0.003-0.0030.0000.0000.0000.000
31B433PRO00.0050.00318.6180.0140.0140.0000.0000.0000.000
32B434ASP-1-0.907-0.96521.784-0.032-0.0320.0000.0000.0000.000
33B435TYR0-0.054-0.03319.761-0.001-0.0010.0000.0000.0000.000
34B436GLY0-0.009-0.00717.932-0.001-0.0010.0000.0000.0000.000
35B437VAL0-0.023-0.00913.4140.0260.0260.0000.0000.0000.000
36B438ILE0-0.0050.00010.036-0.011-0.0110.0000.0000.0000.000
37B439LEU0-0.0080.00111.080-0.056-0.0560.0000.0000.0000.000
38B440ASN00.0180.0217.9400.0770.0770.0000.0000.0000.000
39B441ASN0-0.021-0.0288.1110.0930.0930.0000.0000.0000.000
40B442GLU-1-0.781-0.9344.814-3.557-3.474-0.001-0.002-0.0790.000
41B443LEU0-0.033-0.0098.6790.1380.1380.0000.0000.0000.000
42B444THR0-0.009-0.01010.0290.0690.0690.0000.0000.0000.000
43B445ASP-1-0.896-0.9327.151-0.209-0.2090.0000.0000.0000.000
44B446PHE0-0.094-0.04010.4280.0690.0690.0000.0000.0000.000
45B447ASP-1-0.874-0.93214.073-0.024-0.0240.0000.0000.0000.000
46B448ALA0-0.017-0.01516.832-0.016-0.0160.0000.0000.0000.000
47B449ILE0-0.062-0.03318.5770.0000.0000.0000.0000.0000.000
48B450PRO0-0.006-0.00221.4720.0020.0020.0000.0000.0000.000
49B451GLY00.0280.00122.7830.0100.0100.0000.0000.0000.000
50B452GLY00.0120.01322.0430.0060.0060.0000.0000.0000.000
51B453ALA00.004-0.01319.685-0.010-0.0100.0000.0000.0000.000
52B454ASN0-0.043-0.03013.570-0.048-0.0480.0000.0000.0000.000
53B455GLU-1-0.809-0.85916.864-0.093-0.0930.0000.0000.0000.000
54B456VAL00.0520.03117.006-0.016-0.0160.0000.0000.0000.000
55B457GLN0-0.041-0.04218.7930.0160.0160.0000.0000.0000.000
56B458PRO00.0120.00719.492-0.026-0.0260.0000.0000.0000.000
57B459ASN0-0.056-0.04019.4910.0010.0010.0000.0000.0000.000
58B460LYS10.7830.91017.1770.1210.1210.0000.0000.0000.000
59B461ARG10.9360.95513.0520.2430.2430.0000.0000.0000.000
60B462PRO00.0220.02810.1440.0590.0590.0000.0000.0000.000
61B463LEU0-0.010-0.00911.071-0.057-0.0570.0000.0000.0000.000
62B464SER00.0690.0366.2510.0720.0720.0000.0000.0000.000
63B465SER0-0.004-0.0116.4030.0300.0300.0000.0000.0000.000
64B466MET0-0.039-0.0102.749-1.089-0.4050.654-0.264-1.074-0.001
65B467THR0-0.006-0.0095.302-0.143-0.133-0.001-0.001-0.0080.000
66B468PRO0-0.0190.0196.8540.0210.0210.0000.0000.0000.000
67B469THR0-0.010-0.0199.037-0.008-0.0080.0000.0000.0000.000
68B470ILE0-0.019-0.02412.547-0.006-0.0060.0000.0000.0000.000
69B471LEU00.0020.00815.7210.0020.0020.0000.0000.0000.000
70B472PHE00.019-0.00418.762-0.006-0.0060.0000.0000.0000.000
71B473LYS10.8610.91522.257-0.004-0.0040.0000.0000.0000.000
72B474ASP-1-0.805-0.88825.6130.0020.0020.0000.0000.0000.000
73B475ASP-1-0.927-0.96626.531-0.012-0.0120.0000.0000.0000.000
74B476LYS10.8930.95725.2220.0060.0060.0000.0000.0000.000
75B477PRO0-0.0080.01319.9030.0040.0040.0000.0000.0000.000
76B478VAL00.028-0.00620.7650.0000.0000.0000.0000.0000.000
77B479LEU00.0130.01016.1850.0040.0040.0000.0000.0000.000
78B480THR0-0.0160.01211.835-0.005-0.0050.0000.0000.0000.000
79B481VAL0-0.0030.00610.8800.0100.0100.0000.0000.0000.000
80B482GLY00.0710.0177.501-0.028-0.0280.0000.0000.0000.000
81B483SER00.026-0.0155.475-0.177-0.1770.0000.0000.0000.000
82B484PRO0-0.0130.0122.2300.026-0.9975.813-1.738-3.0530.000
83B485GLY00.0640.0232.5460.934-1.3880.2182.845-0.741-0.003
84B486GLY00.0780.0603.806-1.645-1.2550.000-0.112-0.2780.001
85B487ALA00.0620.0175.538-0.272-0.244-0.0010.001-0.0280.000
86B488THR0-0.074-0.0577.496-0.181-0.1810.0000.0000.0000.000
87B489ILE0-0.0280.0042.722-0.710-0.1660.219-0.164-0.599-0.001
88B490ILE00.0420.0187.063-0.191-0.1910.0000.0000.0000.000
89B491SER00.007-0.00410.115-0.092-0.0920.0000.0000.0000.000
90B492SER00.0580.0368.907-0.091-0.0910.0000.0000.0000.000
91B493VAL0-0.0070.0128.675-0.069-0.0690.0000.0000.0000.000
92B494LEU0-0.027-0.00811.435-0.049-0.0490.0000.0000.0000.000
93B495GLN00.008-0.01514.339-0.047-0.0470.0000.0000.0000.000
94B496THR00.0120.00812.848-0.026-0.0260.0000.0000.0000.000
95B497ILE0-0.010-0.01114.599-0.023-0.0230.0000.0000.0000.000
96B498LEU0-0.013-0.00717.299-0.014-0.0140.0000.0000.0000.000
97B499TYR00.0260.00817.846-0.014-0.0140.0000.0000.0000.000
98B500HIS0-0.046-0.03618.908-0.014-0.0140.0000.0000.0000.000
99B501ILE0-0.074-0.03720.184-0.008-0.0080.0000.0000.0000.000
100B502GLU-1-0.964-0.97022.5680.0470.0470.0000.0000.0000.000
101B503TYR0-0.049-0.03323.392-0.004-0.0040.0000.0000.0000.000
102B504GLY0-0.0190.00924.680-0.003-0.0030.0000.0000.0000.000
103B505MET0-0.053-0.01021.965-0.003-0.0030.0000.0000.0000.000
104B506GLU-1-0.770-0.87422.1520.0460.0460.0000.0000.0000.000
105B507LEU00.0200.01316.3500.0050.0050.0000.0000.0000.000
106B508LYS10.7930.86516.543-0.069-0.0690.0000.0000.0000.000
107B509ALA00.015-0.00218.5900.0090.0090.0000.0000.0000.000
108B510ALA0-0.021-0.00818.4330.0070.0070.0000.0000.0000.000
109B511VAL0-0.064-0.04013.2850.0140.0140.0000.0000.0000.000
110B512GLU-1-0.757-0.84015.1220.1180.1180.0000.0000.0000.000
111B513GLU-1-0.906-0.92517.5640.0930.0930.0000.0000.0000.000
112B514PRO0-0.040-0.00917.2380.0170.0170.0000.0000.0000.000
113B515ARG10.7410.82810.970-0.215-0.2150.0000.0000.0000.000
114B516ILE0-0.034-0.04016.194-0.007-0.0070.0000.0000.0000.000
115B517TYR0-0.021-0.01712.2300.0570.0570.0000.0000.0000.000
116B518THR0-0.009-0.01115.195-0.021-0.0210.0000.0000.0000.000
117B519ASN00.0490.04914.7980.0140.0140.0000.0000.0000.000
118B520SER0-0.020-0.01716.912-0.027-0.0270.0000.0000.0000.000
119B521MET00.0340.01120.2550.0060.0060.0000.0000.0000.000
120B522SER00.001-0.00620.934-0.007-0.0070.0000.0000.0000.000
121B523SER0-0.074-0.02715.7940.0020.0020.0000.0000.0000.000
122B524TYR00.010-0.01818.0550.0090.0090.0000.0000.0000.000
123B525ARG10.8770.94810.506-0.338-0.3380.0000.0000.0000.000
124B526TYR0-0.028-0.04016.4030.0010.0010.0000.0000.0000.000
125B527GLU-1-0.690-0.80413.3820.2170.2170.0000.0000.0000.000
126B528ASP-1-0.922-0.98517.2500.0870.0870.0000.0000.0000.000
127B529GLY00.0430.03020.1730.0020.0020.0000.0000.0000.000
128B530VAL0-0.022-0.00520.068-0.007-0.0070.0000.0000.0000.000
129B531PRO0-0.0010.00222.895-0.004-0.0040.0000.0000.0000.000
130B532LYS11.0290.99926.659-0.063-0.0630.0000.0000.0000.000
131B533ASP-1-0.878-0.93628.0340.0560.0560.0000.0000.0000.000
132B534VAL00.002-0.00226.029-0.003-0.0030.0000.0000.0000.000
133B535LEU00.0360.02522.545-0.001-0.0010.0000.0000.0000.000
134B536SER0-0.053-0.03026.583-0.002-0.0020.0000.0000.0000.000
135B537LYS10.9250.96830.079-0.052-0.0520.0000.0000.0000.000
136B538LEU0-0.003-0.00724.829-0.003-0.0030.0000.0000.0000.000
137B539ASN00.017-0.00625.9380.0030.0030.0000.0000.0000.000
138B540GLY0-0.030-0.00128.724-0.003-0.0030.0000.0000.0000.000
139B541MET0-0.068-0.03630.404-0.003-0.0030.0000.0000.0000.000
140B542GLY00.0000.01729.922-0.002-0.0020.0000.0000.0000.000
141B543HIS00.0140.03424.6710.0070.0070.0000.0000.0000.000
142B544LYS10.8460.91224.146-0.073-0.0730.0000.0000.0000.000
143B545PHE00.0270.01919.8900.0070.0070.0000.0000.0000.000
144B546GLY00.0590.03221.423-0.011-0.0110.0000.0000.0000.000
145B547THR0-0.033-0.02822.7970.0010.0010.0000.0000.0000.000
146B548SER0-0.036-0.01620.618-0.004-0.0040.0000.0000.0000.000
147B549PRO00.0170.03218.6810.0060.0060.0000.0000.0000.000
148B550VAL0-0.068-0.04813.6160.0010.0010.0000.0000.0000.000
149B551ASP-1-0.838-0.91311.6030.1880.1880.0000.0000.0000.000
150B552ILE0-0.118-0.07010.1360.0590.0590.0000.0000.0000.000
151B553GLY00.0120.0306.761-0.009-0.0090.0000.0000.0000.000
152B554ASN0-0.029-0.0236.633-0.199-0.1990.0000.0000.0000.000
153B555VAL0-0.040-0.0157.233-0.065-0.0650.0000.0000.0000.000
154B556GLN0-0.048-0.0277.7130.0320.0320.0000.0000.0000.000
155B557SER0-0.056-0.04710.4780.0030.0030.0000.0000.0000.000
156B558ILE0-0.012-0.01413.271-0.001-0.0010.0000.0000.0000.000
157B559SER0-0.0090.01016.3550.0020.0020.0000.0000.0000.000
158B560ILE0-0.039-0.03519.491-0.004-0.0040.0000.0000.0000.000
159B561ASP-1-0.779-0.86222.4380.0090.0090.0000.0000.0000.000
160B562HIS0-0.041-0.06123.670-0.002-0.0020.0000.0000.0000.000
161B563GLU-1-0.987-0.97028.1820.0060.0060.0000.0000.0000.000
162B564ASN0-0.095-0.07629.965-0.001-0.0010.0000.0000.0000.000
163B565GLY0-0.0390.00228.6470.0000.0000.0000.0000.0000.000
164B566THR0-0.066-0.03326.5980.0000.0000.0000.0000.0000.000
165B567PHE00.0200.00420.944-0.001-0.0010.0000.0000.0000.000
166B568LYS10.8680.92820.303-0.030-0.0300.0000.0000.0000.000
167B569GLY00.0160.01217.076-0.004-0.0040.0000.0000.0000.000
168B570VAL0-0.027-0.01914.7710.0050.0050.0000.0000.0000.000
169B571ALA00.0040.00212.703-0.011-0.0110.0000.0000.0000.000
170B572ASP-1-0.705-0.82410.8950.1820.1820.0000.0000.0000.000
171B573SER0-0.052-0.06313.020-0.002-0.0020.0000.0000.0000.000
172B574SER00.0260.0109.865-0.015-0.0150.0000.0000.0000.000
173B575ARG10.8020.8953.1900.3060.8610.003-0.221-0.3370.001
174B576ASN0-0.0010.00111.426-0.019-0.0190.0000.0000.0000.000
175B577GLY0-0.0150.00412.640-0.006-0.0060.0000.0000.0000.000
176B578ALA00.012-0.00813.3900.0040.0040.0000.0000.0000.000
177B579ALA0-0.0140.00915.154-0.013-0.0130.0000.0000.0000.000
178B580ILE0-0.004-0.01817.1570.0060.0060.0000.0000.0000.000
179B581GLY00.0120.02219.926-0.006-0.0060.0000.0000.0000.000
180B582ILE0-0.014-0.01821.6800.0010.0010.0000.0000.0000.000
181B583ASN00.0220.00924.597-0.001-0.0010.0000.0000.0000.000
182B584LEU0-0.026-0.01327.1680.0010.0010.0000.0000.0000.000
183B585LYS11.0001.00930.1190.0100.0100.0000.0000.0000.000