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: Z6Z3N

Calculation Name: 1AD0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AD0

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2290200.300275
FMO2-HF: Nuclear repulsion 2206334.924748
FMO2-HF: Total energy -83865.375527
FMO2-MP2: Total energy -84109.361588


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:1:GLU)


Summations of interaction energy for fragment #1(B:1:GLU)
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.
-93.539-94.73514.816-7.391-6.2290.065
Interaction energy analysis for fragmet #1(B:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.860 / q_NPA : -0.919
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].
3B3GLN0-0.027-0.0171.697-29.508-31.52514.811-7.088-5.7060.066
4B4LEU0-0.028-0.0314.652-6.322-6.250-0.001-0.010-0.0610.000
5B5LEU00.0150.0108.3391.5181.5180.0000.0000.0000.000
6B6GLU-1-0.772-0.87911.02521.49321.4930.0000.0000.0000.000
7B7SER0-0.043-0.02014.632-0.181-0.1810.0000.0000.0000.000
8B8GLY00.0390.00717.722-0.332-0.3320.0000.0000.0000.000
9B9GLY00.0160.01420.653-0.635-0.6350.0000.0000.0000.000
10B10GLY00.014-0.00322.4070.0710.0710.0000.0000.0000.000
11B11LEU0-0.028-0.00325.531-0.037-0.0370.0000.0000.0000.000
12B12VAL0-0.029-0.01128.693-0.016-0.0160.0000.0000.0000.000
13B13GLN00.0630.03131.421-0.199-0.1990.0000.0000.0000.000
14B14PRO0-0.005-0.01434.7330.1060.1060.0000.0000.0000.000
15B15GLY00.0010.00835.651-0.236-0.2360.0000.0000.0000.000
16B16GLY0-0.0180.00034.268-0.064-0.0640.0000.0000.0000.000
17B17SER0-0.022-0.04130.899-0.014-0.0140.0000.0000.0000.000
18B18LEU0-0.028-0.00524.919-0.024-0.0240.0000.0000.0000.000
19B19ARG10.8630.94322.707-12.663-12.6630.0000.0000.0000.000
20B20LEU00.0200.03419.7950.3070.3070.0000.0000.0000.000
21B21SER0-0.057-0.03818.229-0.119-0.1190.0000.0000.0000.000
22B22CYS0-0.053-0.02812.8450.0230.0230.0000.0000.0000.000
23B23ALA00.0270.04412.434-0.675-0.6750.0000.0000.0000.000
24B24THR0-0.049-0.0539.1521.6161.6160.0000.0000.0000.000
25B25SER00.0220.0096.495-0.147-0.1470.0000.0000.0000.000
26B26GLY00.0840.0393.7351.8422.0570.005-0.140-0.0810.000
27B27PHE0-0.039-0.0283.807-1.646-1.3510.001-0.127-0.168-0.001
28B28THR00.0140.0126.654-0.029-0.0290.0000.0000.0000.000
29B29PHE00.0730.04510.386-1.261-1.2610.0000.0000.0000.000
30B30THR0-0.067-0.05412.089-0.665-0.6650.0000.0000.0000.000
31B31ASP-1-0.827-0.90712.83515.62615.6260.0000.0000.0000.000
32B32TYR00.0070.00610.017-0.183-0.1830.0000.0000.0000.000
33B33TYR00.0090.01914.460-0.390-0.3900.0000.0000.0000.000
34B34MET0-0.0300.00812.0011.1911.1910.0000.0000.0000.000
35B35ASN00.034-0.00315.756-1.851-1.8510.0000.0000.0000.000
36B36TRP00.0060.00516.4421.1661.1660.0000.0000.0000.000
37B37VAL0-0.009-0.00717.870-0.783-0.7830.0000.0000.0000.000
38B38ARG10.7830.87419.204-10.937-10.9370.0000.0000.0000.000
39B39GLN00.0260.01320.2460.5090.5090.0000.0000.0000.000
40B40ALA00.0640.04522.7700.0890.0890.0000.0000.0000.000
41B41PRO00.0320.00824.9670.2270.2270.0000.0000.0000.000
42B42GLY00.0230.02425.067-0.525-0.5250.0000.0000.0000.000
43B43LYS10.8480.91425.776-11.495-11.4950.0000.0000.0000.000
44B44GLY00.0460.02624.6260.5170.5170.0000.0000.0000.000
45B45LEU0-0.008-0.00418.8540.0330.0330.0000.0000.0000.000
46B46GLU-1-0.783-0.84522.72010.72810.7280.0000.0000.0000.000
47B47TRP0-0.035-0.02220.2470.1220.1220.0000.0000.0000.000
48B48LEU00.0060.00022.152-0.547-0.5470.0000.0000.0000.000
49B49GLY00.0590.00922.324-0.628-0.6280.0000.0000.0000.000
50B50PHE0-0.072-0.03020.0780.7310.7310.0000.0000.0000.000
51B51ILE0-0.020-0.00819.236-0.669-0.6690.0000.0000.0000.000
52B52GLY00.0450.02019.4790.7420.7420.0000.0000.0000.000
53B52ASN0-0.025-0.00517.086-0.276-0.2760.0000.0000.0000.000
54B52LYS10.8590.90518.651-12.502-12.5020.0000.0000.0000.000
55B52ALA00.0020.01320.518-0.517-0.5170.0000.0000.0000.000
56B53ASN00.0290.01522.464-0.553-0.5530.0000.0000.0000.000
57B54GLY00.0670.04724.262-0.190-0.1900.0000.0000.0000.000
58B55TYR0-0.069-0.04420.3640.3340.3340.0000.0000.0000.000
59B56THR00.0500.01724.038-0.051-0.0510.0000.0000.0000.000
60B57THR0-0.026-0.01023.8650.4390.4390.0000.0000.0000.000
61B58GLU-1-0.828-0.89224.84710.03210.0320.0000.0000.0000.000
62B59TYR00.0190.00425.1570.5000.5000.0000.0000.0000.000
63B60SER00.0450.02326.856-0.315-0.3150.0000.0000.0000.000
64B61ALA00.021-0.00928.497-0.092-0.0920.0000.0000.0000.000
65B62SER0-0.009-0.01328.747-0.203-0.2030.0000.0000.0000.000
66B63VAL00.0070.00126.557-0.032-0.0320.0000.0000.0000.000
67B64LYS10.8190.92530.006-9.961-9.9610.0000.0000.0000.000
68B65GLY00.0200.02131.288-0.299-0.2990.0000.0000.0000.000
69B66ARG10.7750.86530.764-9.870-9.8700.0000.0000.0000.000
70B67PHE00.000-0.01525.7780.1600.1600.0000.0000.0000.000
71B68THR0-0.050-0.03226.847-0.304-0.3040.0000.0000.0000.000
72B69ILE0-0.0020.02020.7970.3320.3320.0000.0000.0000.000
73B70SER0-0.007-0.01422.076-0.442-0.4420.0000.0000.0000.000
74B71ARG10.7880.88915.214-15.466-15.4660.0000.0000.0000.000
75B72ASP-1-0.760-0.84118.89713.10513.1050.0000.0000.0000.000
76B73LYS10.9540.96616.582-14.058-14.0580.0000.0000.0000.000
77B74SER0-0.082-0.06216.9130.4920.4920.0000.0000.0000.000
78B75LYS10.8950.92916.787-13.707-13.7070.0000.0000.0000.000
79B76SER00.0030.02312.1820.8720.8720.0000.0000.0000.000
80B77THR00.0240.02013.3631.5821.5820.0000.0000.0000.000
81B78LEU0-0.042-0.01815.292-1.143-1.1430.0000.0000.0000.000
82B79TYR00.016-0.02317.1500.2620.2620.0000.0000.0000.000
83B80LEU00.0120.00720.162-0.149-0.1490.0000.0000.0000.000
84B81GLN0-0.0050.00022.4900.2520.2520.0000.0000.0000.000
85B82MET0-0.023-0.00524.7380.0310.0310.0000.0000.0000.000
86B82ASN00.0600.02928.015-0.075-0.0750.0000.0000.0000.000
87B82THR00.0200.01731.8390.0480.0480.0000.0000.0000.000
88B82LEU00.0000.01728.1360.0240.0240.0000.0000.0000.000
89B83GLN0-0.030-0.02932.190-0.432-0.4320.0000.0000.0000.000
90B84ALA00.0640.03532.0920.3160.3160.0000.0000.0000.000
91B85GLU-1-0.861-0.92831.8039.3319.3310.0000.0000.0000.000
92B86ASP-1-0.760-0.82428.38810.55410.5540.0000.0000.0000.000
93B87SER0-0.019-0.00527.1270.5370.5370.0000.0000.0000.000
94B88ALA0-0.020-0.01423.878-0.104-0.1040.0000.0000.0000.000
95B89ILE00.0200.02018.3160.0070.0070.0000.0000.0000.000
96B90TYR0-0.033-0.03719.598-0.272-0.2720.0000.0000.0000.000
97B91TYR00.020-0.00614.6190.7030.7030.0000.0000.0000.000
98B93THR00.007-0.02812.0111.1071.1070.0000.0000.0000.000
99B94ARG10.8160.8807.685-26.533-26.5330.0000.0000.0000.000
100B95ASP-1-0.787-0.90312.54615.83115.8310.0000.0000.0000.000
101B96ARG10.9130.95611.427-19.238-19.2380.0000.0000.0000.000
102B97GLY0-0.024-0.02313.795-0.120-0.1200.0000.0000.0000.000
103B98LEU0-0.044-0.02417.1020.0530.0530.0000.0000.0000.000
104B99ARG10.8680.93020.360-11.756-11.7560.0000.0000.0000.000
105B100PHE0-0.0210.00116.721-0.304-0.3040.0000.0000.0000.000
106B100TYR00.0340.00212.546-0.463-0.4630.0000.0000.0000.000
107B100PHE0-0.023-0.00214.6010.3640.3640.0000.0000.0000.000
108B101ASP-1-0.758-0.8549.94924.68024.6800.0000.0000.0000.000
109B102TYR00.0110.0204.097-0.328-0.0890.000-0.026-0.2130.000
110B103TRP0-0.021-0.0248.584-3.408-3.4080.0000.0000.0000.000
111B104GLY00.0450.0388.5003.3593.3590.0000.0000.0000.000
112B105GLN0-0.034-0.0279.7211.4241.4240.0000.0000.0000.000
113B106GLY0-0.011-0.00712.281-1.458-1.4580.0000.0000.0000.000
114B107THR0-0.055-0.03215.542-0.167-0.1670.0000.0000.0000.000
115B108LEU0-0.021-0.00518.489-0.407-0.4070.0000.0000.0000.000
116B109VAL0-0.0030.00321.981-0.135-0.1350.0000.0000.0000.000
117B110THR0-0.073-0.04225.098-0.114-0.1140.0000.0000.0000.000
118B111VAL00.0110.01528.674-0.116-0.1160.0000.0000.0000.000
119B112SER00.002-0.01131.675-0.328-0.3280.0000.0000.0000.000
120B113SER00.0450.01934.7430.1170.1170.0000.0000.0000.000
121B114ALA0-0.045-0.00535.521-0.158-0.1580.0000.0000.0000.000
122B115SER00.017-0.00335.1910.1590.1590.0000.0000.0000.000
123B116THR0-0.017-0.01130.9170.0020.0020.0000.0000.0000.000
124B117LYS10.8360.93232.710-8.803-8.8030.0000.0000.0000.000
125B118GLY00.0600.03531.1580.3170.3170.0000.0000.0000.000
126B119PRO0-0.079-0.02128.912-0.289-0.2890.0000.0000.0000.000
127B120SER00.0090.00432.220-0.154-0.1540.0000.0000.0000.000
128B121VAL0-0.010-0.01630.4570.1900.1900.0000.0000.0000.000
129B122PHE0-0.012-0.01333.523-0.229-0.2290.0000.0000.0000.000
130B123PRO00.0100.01034.6340.2590.2590.0000.0000.0000.000
131B124LEU0-0.042-0.01233.570-0.241-0.2410.0000.0000.0000.000
132B125ALA00.0450.00835.7220.2650.2650.0000.0000.0000.000
133B126PRO00.0170.02338.223-0.156-0.1560.0000.0000.0000.000
134B127CYS0-0.007-0.01841.131-0.033-0.0330.0000.0000.0000.000
135B128SER0-0.013-0.00243.983-0.158-0.1580.0000.0000.0000.000
136B129ARG10.8400.91140.677-7.635-7.6350.0000.0000.0000.000
137B130SER00.035-0.00441.8840.0480.0480.0000.0000.0000.000
138B131THR0-0.022-0.03743.8930.0720.0720.0000.0000.0000.000
139B132SER0-0.0440.00345.159-0.052-0.0520.0000.0000.0000.000
140B133GLU-1-0.812-0.87440.1577.6047.6040.0000.0000.0000.000
141B134SER00.0030.00938.5880.0960.0960.0000.0000.0000.000
142B135THR0-0.085-0.03333.6220.3230.3230.0000.0000.0000.000
143B136ALA00.0570.03635.579-0.215-0.2150.0000.0000.0000.000
144B137ALA0-0.011-0.01533.4320.3420.3420.0000.0000.0000.000
145B138LEU0-0.0160.00532.391-0.330-0.3300.0000.0000.0000.000
146B139GLY00.042-0.00531.1230.3420.3420.0000.0000.0000.000
147B140CYS0-0.0530.00326.8930.0970.0970.0000.0000.0000.000
148B141LEU00.0230.03830.9180.2700.2700.0000.0000.0000.000
149B142VAL0-0.016-0.01528.136-0.128-0.1280.0000.0000.0000.000
150B143LYS10.9110.92131.362-8.320-8.3200.0000.0000.0000.000
151B144ASP-1-0.806-0.88834.0098.3638.3630.0000.0000.0000.000
152B145TYR0-0.022-0.03027.417-0.262-0.2620.0000.0000.0000.000
153B146PHE00.0280.01031.1180.0160.0160.0000.0000.0000.000
154B147PRO00.0240.02327.422-0.172-0.1720.0000.0000.0000.000
155B148GLU-1-0.783-0.87725.23812.58612.5860.0000.0000.0000.000
156B149PRO0-0.015-0.01020.882-0.038-0.0380.0000.0000.0000.000
157B150VAL0-0.018-0.01923.808-0.180-0.1800.0000.0000.0000.000
158B151THR0-0.029-0.00718.8210.6710.6710.0000.0000.0000.000
159B152VAL0-0.017-0.02721.689-0.626-0.6260.0000.0000.0000.000
160B153SER0-0.0010.00920.2130.7870.7870.0000.0000.0000.000
161B154TRP00.0030.00622.217-0.918-0.9180.0000.0000.0000.000
162B155ASN0-0.015-0.02723.3090.3850.3850.0000.0000.0000.000
163B156SER0-0.011-0.01522.4760.0670.0670.0000.0000.0000.000
164B157GLY00.0270.02519.1910.6840.6840.0000.0000.0000.000
165B158ALA0-0.039-0.01119.8420.4710.4710.0000.0000.0000.000
166B159LEU0-0.056-0.02522.228-0.459-0.4590.0000.0000.0000.000
167B160THR00.0310.00618.176-0.043-0.0430.0000.0000.0000.000
168B161SER00.0340.01321.345-0.152-0.1520.0000.0000.0000.000
169B162GLY00.0490.02023.080-0.392-0.3920.0000.0000.0000.000
170B163VAL0-0.061-0.02322.882-0.520-0.5200.0000.0000.0000.000
171B164HIS00.0020.00623.8990.5080.5080.0000.0000.0000.000
172B165THR0-0.0020.00123.132-0.703-0.7030.0000.0000.0000.000
173B166PHE00.0010.01224.6040.3580.3580.0000.0000.0000.000
174B167PRO00.0170.00425.8430.1880.1880.0000.0000.0000.000
175B168ALA0-0.0010.00226.833-0.453-0.4530.0000.0000.0000.000
176B169VAL0-0.014-0.00629.036-0.065-0.0650.0000.0000.0000.000
177B170LEU0-0.021-0.01032.599-0.002-0.0020.0000.0000.0000.000
178B171GLN0-0.028-0.01834.472-0.359-0.3590.0000.0000.0000.000
179B172SER00.0310.00337.7720.0710.0710.0000.0000.0000.000
180B173SER0-0.005-0.00239.430-0.082-0.0820.0000.0000.0000.000
181B173GLY00.0190.01437.687-0.032-0.0320.0000.0000.0000.000
182B174LEU0-0.057-0.01734.9190.2400.2400.0000.0000.0000.000
183B175TYR00.0310.01130.008-0.146-0.1460.0000.0000.0000.000
184B176SER0-0.019-0.01632.364-0.254-0.2540.0000.0000.0000.000
185B177LEU00.0010.02325.7730.0270.0270.0000.0000.0000.000
186B178SER00.0350.00529.804-0.313-0.3130.0000.0000.0000.000
187B179SER0-0.007-0.00225.3860.3040.3040.0000.0000.0000.000
188B180VAL00.019-0.00228.070-0.461-0.4610.0000.0000.0000.000
189B181VAL00.004-0.00127.0050.5270.5270.0000.0000.0000.000
190B182THR00.0010.01228.931-0.396-0.3960.0000.0000.0000.000
191B183VAL0-0.014-0.01829.6400.3900.3900.0000.0000.0000.000
192B184PRO00.0460.03431.661-0.295-0.2950.0000.0000.0000.000
193B185SER00.059-0.01234.6550.1110.1110.0000.0000.0000.000
194B186SER0-0.007-0.00337.271-0.083-0.0830.0000.0000.0000.000
195B187SER0-0.038-0.01933.9220.0890.0890.0000.0000.0000.000
196B188LEU0-0.0080.01235.8770.0880.0880.0000.0000.0000.000
197B189GLY00.0350.01138.073-0.263-0.2630.0000.0000.0000.000
198B190THR0-0.074-0.02637.288-0.211-0.2110.0000.0000.0000.000
199B191LYS10.9140.95329.117-10.773-10.7730.0000.0000.0000.000
200B192THR0-0.0110.00431.196-0.062-0.0620.0000.0000.0000.000
201B193TYR00.0420.02229.5430.5440.5440.0000.0000.0000.000
202B194THR00.027-0.00328.595-0.536-0.5360.0000.0000.0000.000
203B196ASN0-0.020-0.02323.317-0.090-0.0900.0000.0000.0000.000
204B197VAL00.012-0.00524.3150.4310.4310.0000.0000.0000.000
205B198ASP-1-0.831-0.91121.81914.22314.2230.0000.0000.0000.000
206B199HIS00.0580.04023.6780.2450.2450.0000.0000.0000.000
207B200LYS10.9160.93418.754-15.749-15.7490.0000.0000.0000.000
208B201PRO0-0.0090.00623.803-0.251-0.2510.0000.0000.0000.000
209B202SER0-0.012-0.03326.513-0.464-0.4640.0000.0000.0000.000
210B203ASN0-0.056-0.02526.628-0.057-0.0570.0000.0000.0000.000
211B204THR00.0090.01927.709-0.283-0.2830.0000.0000.0000.000
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214B207ASP-1-0.778-0.87926.22512.77412.7740.0000.0000.0000.000
215B208LYS10.9230.97829.176-9.512-9.5120.0000.0000.0000.000
216B209ARG10.9210.94731.429-8.957-8.9570.0000.0000.0000.000
217B210VAL0-0.027-0.01832.228-0.201-0.2010.0000.0000.0000.000
218B211GLU-1-0.843-0.89934.6198.5308.5300.0000.0000.0000.000