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: 85ZZY

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1658089.123309
FMO2-HF: Nuclear repulsion 1588851.407983
FMO2-HF: Total energy -69237.715326
FMO2-MP2: Total energy -69439.834723


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.
-15.024-21.91839.132-12.906-19.328-0.039
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 : -0.004 / q_NPA : 0.025
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].
3B405HIS00.0770.0803.180-2.845-0.1820.123-1.220-1.5660.000
4B406PHE0-0.0060.0044.9760.3400.365-0.001-0.003-0.0200.000
5B407THR0-0.032-0.0278.655-0.039-0.0390.0000.0000.0000.000
6B408VAL00.0280.00511.8400.0610.0610.0000.0000.0000.000
7B409ALA00.0330.02615.440-0.020-0.0200.0000.0000.0000.000
8B410ASP-1-0.785-0.88518.764-0.109-0.1090.0000.0000.0000.000
9B411ARG10.9370.95522.1050.0620.0620.0000.0000.0000.000
10B412TRP0-0.085-0.04924.8250.0090.0090.0000.0000.0000.000
11B413GLY00.0220.02623.9890.0020.0020.0000.0000.0000.000
12B414ASN0-0.077-0.03220.441-0.020-0.0200.0000.0000.0000.000
13B415VAL00.007-0.00916.0070.0020.0020.0000.0000.0000.000
14B416VAL0-0.0190.00312.192-0.010-0.0100.0000.0000.0000.000
15B417SER00.0240.00610.536-0.055-0.0550.0000.0000.0000.000
16B418TYR0-0.028-0.0107.3860.0250.0250.0000.0000.0000.000
17B419THR0-0.007-0.0252.4310.018-0.5332.105-0.446-1.108-0.002
18B420THR0-0.042-0.0253.063-0.2800.5030.067-0.298-0.552-0.001
19B421THR00.031-0.0301.657-11.803-21.63330.286-11.439-9.017-0.022
20B422ILE0-0.0180.0132.939-0.732-1.1860.1490.790-0.485-0.002
21B423GLU-1-0.738-0.8583.618-0.1340.1860.000-0.109-0.2110.000
22B424GLN0-0.113-0.0483.246-1.352-0.2600.025-0.587-0.529-0.005
23B425LEU0-0.010-0.0133.9380.4960.696-0.001-0.017-0.1830.000
24B426PHE0-0.045-0.0306.035-0.494-0.4940.0000.0000.0000.000
25B427GLY00.0270.0246.492-0.319-0.3190.0000.0000.0000.000
26B428THR0-0.030-0.0367.883-0.211-0.2110.0000.0000.0000.000
27B429GLY0-0.0180.00810.923-0.121-0.1210.0000.0000.0000.000
28B430ILE0-0.057-0.02412.707-0.084-0.0840.0000.0000.0000.000
29B431MET0-0.0090.00913.8830.0610.0610.0000.0000.0000.000
30B432VAL0-0.030-0.01916.011-0.067-0.0670.0000.0000.0000.000
31B433PRO00.0050.00318.4860.0040.0040.0000.0000.0000.000
32B434ASP-1-0.905-0.96221.6550.2240.2240.0000.0000.0000.000
33B435TYR0-0.057-0.03619.832-0.020-0.0200.0000.0000.0000.000
34B436GLY0-0.009-0.00817.7870.0120.0120.0000.0000.0000.000
35B437VAL0-0.019-0.00713.3530.0740.0740.0000.0000.0000.000
36B438ILE0-0.0010.0059.735-0.054-0.0540.0000.0000.0000.000
37B439LEU0-0.011-0.00510.9370.0770.0770.0000.0000.0000.000
38B440ASN00.0310.0278.115-0.005-0.0050.0000.0000.0000.000
39B441ASN00.005-0.0097.9040.0750.0750.0000.0000.0000.000
40B442GLU-1-0.808-0.9425.7541.3341.3340.0000.0000.0000.000
41B443LEU0-0.040-0.0139.297-0.179-0.1790.0000.0000.0000.000
42B444THR0-0.008-0.01210.361-0.028-0.0280.0000.0000.0000.000
43B445ASP-1-0.889-0.9246.760-0.277-0.2770.0000.0000.0000.000
44B446PHE0-0.104-0.04910.284-0.100-0.1000.0000.0000.0000.000
45B447ASP-1-0.908-0.95113.897-0.141-0.1410.0000.0000.0000.000
46B448ALA0-0.026-0.02516.5110.0250.0250.0000.0000.0000.000
47B449ILE0-0.064-0.03318.4740.0130.0130.0000.0000.0000.000
48B450PRO0-0.004-0.00221.138-0.017-0.0170.0000.0000.0000.000
49B451GLY00.0260.00122.540-0.001-0.0010.0000.0000.0000.000
50B452GLY00.0200.01821.452-0.006-0.0060.0000.0000.0000.000
51B453ALA00.009-0.01119.0580.0050.0050.0000.0000.0000.000
52B454ASN0-0.013-0.01012.858-0.001-0.0010.0000.0000.0000.000
53B455GLU-1-0.817-0.87016.514-0.038-0.0380.0000.0000.0000.000
54B456VAL00.0630.03317.069-0.009-0.0090.0000.0000.0000.000
55B457GLN0-0.040-0.03918.7870.0070.0070.0000.0000.0000.000
56B458PRO00.0090.00319.6530.0080.0080.0000.0000.0000.000
57B459ASN0-0.044-0.03019.848-0.001-0.0010.0000.0000.0000.000
58B460LYS10.7850.91816.9260.0910.0910.0000.0000.0000.000
59B461ARG10.9320.95212.9780.1990.1990.0000.0000.0000.000
60B462PRO00.0260.03310.236-0.037-0.0370.0000.0000.0000.000
61B463LEU0-0.013-0.01410.787-0.062-0.0620.0000.0000.0000.000
62B464SER00.0720.0455.902-0.214-0.2140.0000.0000.0000.000
63B465SER0-0.010-0.0186.1950.2930.2930.0000.0000.0000.000
64B466MET0-0.037-0.0152.774-1.168-0.4460.435-0.220-0.937-0.001
65B467THR0-0.011-0.0095.3640.5220.536-0.001-0.001-0.0110.000
66B468PRO0-0.0170.0176.7480.1010.1010.0000.0000.0000.000
67B469THR0-0.005-0.0169.0750.1430.1430.0000.0000.0000.000
68B470ILE0-0.008-0.01812.6190.0020.0020.0000.0000.0000.000
69B471LEU0-0.0020.00415.7820.0120.0120.0000.0000.0000.000
70B472PHE00.0240.00018.8200.0130.0130.0000.0000.0000.000
71B473LYS10.9590.97622.3150.1700.1700.0000.0000.0000.000
72B474ASP-1-0.908-0.95225.664-0.140-0.1400.0000.0000.0000.000
73B475ASP-1-0.948-0.97026.606-0.149-0.1490.0000.0000.0000.000
74B476LYS10.9210.96325.2680.1360.1360.0000.0000.0000.000
75B477PRO0-0.0100.01519.986-0.011-0.0110.0000.0000.0000.000
76B478VAL00.0350.00420.8180.0160.0160.0000.0000.0000.000
77B479LEU00.0120.00816.1560.0050.0050.0000.0000.0000.000
78B480THR0-0.0270.00411.792-0.016-0.0160.0000.0000.0000.000
79B481VAL0-0.0040.00210.8700.0210.0210.0000.0000.0000.000
80B482GLY00.0670.0127.537-0.019-0.0190.0000.0000.0000.000
81B483SER00.032-0.0115.4800.3230.3230.0000.0000.0000.000
82B484PRO0-0.0170.0132.306-1.260-2.1095.519-1.707-2.962-0.001
83B485GLY00.0670.0272.4922.5140.2280.2912.707-0.711-0.004
84B486GLY00.0650.0613.4290.4430.7430.001-0.066-0.2350.000
85B487ALA00.0650.0195.022-0.268-0.237-0.0010.001-0.0300.000
86B488THR0-0.078-0.0627.4260.0660.0660.0000.0000.0000.000
87B489ILE0-0.0290.0002.871-0.672-0.1470.135-0.158-0.502-0.001
88B490ILE00.0440.0177.1710.1950.1950.0000.0000.0000.000
89B491SER00.008-0.00410.2210.1570.1570.0000.0000.0000.000
90B492SER00.0470.0339.1220.1390.1390.0000.0000.0000.000
91B493VAL0-0.018-0.0018.7120.0830.0830.0000.0000.0000.000
92B494LEU0-0.022-0.00611.4830.0970.0970.0000.0000.0000.000
93B495GLN0-0.006-0.02614.4490.1040.1040.0000.0000.0000.000
94B496THR00.0250.02512.9350.0540.0540.0000.0000.0000.000
95B497ILE0-0.009-0.01014.7590.0510.0510.0000.0000.0000.000
96B498LEU0-0.017-0.01017.3360.0420.0420.0000.0000.0000.000
97B499TYR00.0440.01317.9570.0380.0380.0000.0000.0000.000
98B500HIS0-0.068-0.04618.9350.0230.0230.0000.0000.0000.000
99B501ILE0-0.071-0.03420.3180.0210.0210.0000.0000.0000.000
100B502GLU-1-0.977-0.97722.601-0.180-0.1800.0000.0000.0000.000
101B503TYR0-0.030-0.02523.3230.0240.0240.0000.0000.0000.000
102B504GLY0-0.0230.00724.7150.0150.0150.0000.0000.0000.000
103B505MET0-0.039-0.00121.6380.0120.0120.0000.0000.0000.000
104B506GLU-1-0.746-0.86422.158-0.202-0.2020.0000.0000.0000.000
105B507LEU00.002-0.00216.404-0.002-0.0020.0000.0000.0000.000
106B508LYS10.8000.87916.5620.1800.1800.0000.0000.0000.000
107B509ALA00.0170.00218.542-0.011-0.0110.0000.0000.0000.000
108B510ALA0-0.028-0.01318.376-0.005-0.0050.0000.0000.0000.000
109B511VAL0-0.066-0.04313.262-0.032-0.0320.0000.0000.0000.000
110B512GLU-1-0.734-0.83715.082-0.264-0.2640.0000.0000.0000.000
111B513GLU-1-0.927-0.93317.514-0.179-0.1790.0000.0000.0000.000
112B514PRO0-0.047-0.00917.256-0.036-0.0360.0000.0000.0000.000
113B515ARG10.7840.88710.7480.5040.5040.0000.0000.0000.000
114B516ILE0-0.025-0.03216.1920.0430.0430.0000.0000.0000.000
115B517TYR0-0.013-0.01112.231-0.096-0.0960.0000.0000.0000.000
116B518THR0-0.023-0.02815.1570.0500.0500.0000.0000.0000.000
117B519ASN00.0470.03914.330-0.004-0.0040.0000.0000.0000.000
118B520SER00.003-0.00716.4570.0150.0150.0000.0000.0000.000
119B521MET00.0430.01619.742-0.002-0.0020.0000.0000.0000.000
120B522SER0-0.044-0.02721.2420.0070.0070.0000.0000.0000.000
121B523SER0-0.037-0.00615.4810.0270.0270.0000.0000.0000.000
122B524TYR00.004-0.02318.009-0.031-0.0310.0000.0000.0000.000
123B525ARG10.9140.95610.1810.2410.2410.0000.0000.0000.000
124B526TYR0-0.014-0.02116.362-0.024-0.0240.0000.0000.0000.000
125B527GLU-1-0.685-0.80813.586-0.307-0.3070.0000.0000.0000.000
126B528ASP-1-0.927-0.98117.243-0.068-0.0680.0000.0000.0000.000
127B529GLY00.0440.02620.180-0.013-0.0130.0000.0000.0000.000
128B530VAL0-0.020-0.00220.0830.0000.0000.0000.0000.0000.000
129B531PRO0-0.0010.00322.8890.0160.0160.0000.0000.0000.000
130B532LYS11.0290.99526.6510.0450.0450.0000.0000.0000.000
131B533ASP-1-0.882-0.94528.017-0.069-0.0690.0000.0000.0000.000
132B534VAL0-0.005-0.00325.9050.0010.0010.0000.0000.0000.000
133B535LEU00.0340.02022.515-0.001-0.0010.0000.0000.0000.000
134B536SER0-0.039-0.01126.5550.0040.0040.0000.0000.0000.000
135B537LYS10.9410.97430.0480.0910.0910.0000.0000.0000.000
136B538LEU0-0.012-0.01224.8770.0020.0020.0000.0000.0000.000
137B539ASN00.0390.00525.890-0.013-0.0130.0000.0000.0000.000
138B540GLY0-0.039-0.00628.6810.0050.0050.0000.0000.0000.000
139B541MET0-0.078-0.03830.2690.0030.0030.0000.0000.0000.000
140B542GLY0-0.0030.01029.832-0.001-0.0010.0000.0000.0000.000
141B543HIS00.0190.04824.591-0.005-0.0050.0000.0000.0000.000
142B544LYS10.8440.91623.9680.1070.1070.0000.0000.0000.000
143B545PHE00.0200.02119.737-0.001-0.0010.0000.0000.0000.000
144B546GLY00.0470.02221.3780.0150.0150.0000.0000.0000.000
145B547THR0-0.035-0.04022.752-0.005-0.0050.0000.0000.0000.000
146B548SER0-0.052-0.02120.6170.0080.0080.0000.0000.0000.000
147B549PRO00.0280.03618.710-0.008-0.0080.0000.0000.0000.000
148B550VAL0-0.098-0.05613.6030.0300.0300.0000.0000.0000.000
149B551ASP-1-0.824-0.90511.727-0.150-0.1500.0000.0000.0000.000
150B552ILE0-0.146-0.08410.128-0.026-0.0260.0000.0000.0000.000
151B553GLY00.0090.0206.771-0.040-0.0400.0000.0000.0000.000
152B554ASN0-0.041-0.0356.6620.0470.0470.0000.0000.0000.000
153B555VAL0-0.054-0.0187.167-0.254-0.2540.0000.0000.0000.000
154B556GLN0-0.040-0.0197.7080.3050.3050.0000.0000.0000.000
155B557SER0-0.053-0.04010.459-0.061-0.0610.0000.0000.0000.000
156B558ILE0-0.013-0.01213.2500.0600.0600.0000.0000.0000.000
157B559SER0-0.0170.00416.338-0.014-0.0140.0000.0000.0000.000
158B560ILE0-0.039-0.03719.5760.0160.0160.0000.0000.0000.000
159B561ASP-1-0.779-0.86822.438-0.135-0.1350.0000.0000.0000.000
160B562HIS0-0.053-0.07623.7200.0230.0230.0000.0000.0000.000
161B563GLU-1-0.981-0.96828.192-0.103-0.1030.0000.0000.0000.000
162B564ASN0-0.083-0.05929.9460.0160.0160.0000.0000.0000.000
163B565GLY0-0.0430.00128.6400.0070.0070.0000.0000.0000.000
164B566THR0-0.061-0.03026.5020.0040.0040.0000.0000.0000.000
165B567PHE00.0170.00420.908-0.010-0.0100.0000.0000.0000.000
166B568LYS10.8570.92120.1950.1970.1970.0000.0000.0000.000
167B569GLY00.0110.00617.033-0.027-0.0270.0000.0000.0000.000
168B570VAL0-0.024-0.01714.7200.0390.0390.0000.0000.0000.000
169B571ALA00.0080.00112.628-0.060-0.0600.0000.0000.0000.000
170B572ASP-1-0.725-0.86710.849-0.426-0.4260.0000.0000.0000.000
171B573SER0-0.065-0.06212.9390.0430.0430.0000.0000.0000.000
172B574SER00.0530.02810.0140.0490.0490.0000.0000.0000.000
173B575ARG10.8040.9023.4090.1670.5680.000-0.133-0.2690.000
174B576ASN00.0000.00211.563-0.075-0.0750.0000.0000.0000.000
175B577GLY0-0.0160.00312.5290.0250.0250.0000.0000.0000.000
176B578ALA00.016-0.00613.2760.0110.0110.0000.0000.0000.000
177B579ALA0-0.0130.00915.062-0.029-0.0290.0000.0000.0000.000
178B580ILE0-0.005-0.01717.0750.0270.0270.0000.0000.0000.000
179B581GLY00.0070.02019.848-0.013-0.0130.0000.0000.0000.000
180B582ILE0-0.014-0.01621.4140.0180.0180.0000.0000.0000.000
181B583ASN00.0330.01524.541-0.010-0.0100.0000.0000.0000.000
182B584LEU0-0.037-0.02227.2740.0090.0090.0000.0000.0000.000
183B585LYS10.9981.00930.0680.0400.0400.0000.0000.0000.000