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: 72ZVK

Calculation Name: 5D1X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1X

Chain ID: B

ChEMBL ID:

UniProt ID: Q2FZF0

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2083537.034584
FMO2-HF: Nuclear repulsion 2003084.245601
FMO2-HF: Total energy -80452.788982
FMO2-MP2: Total energy -80687.220956


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:GLN)


Summations of interaction energy for fragment #1(B:1:GLN)
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.
-0.4172.1370.081-0.945-1.6890.003
Interaction energy analysis for fragmet #1(B:1:GLN)
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 : 0.007
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].
3B3GLN0-0.020-0.0153.840-0.9690.582-0.003-0.629-0.9190.003
4B4LEU0-0.017-0.0116.297-0.130-0.1300.0000.0000.0000.000
5B5VAL00.0140.0059.7650.1050.1050.0000.0000.0000.000
6B6GLN0-0.018-0.03212.4970.0220.0220.0000.0000.0000.000
7B7SER00.0130.00516.111-0.023-0.0230.0000.0000.0000.000
8B8GLY00.0040.01719.475-0.016-0.0160.0000.0000.0000.000
9B9SER0-0.068-0.04521.3480.0030.0030.0000.0000.0000.000
10B10GLU-1-0.788-0.87924.578-0.061-0.0610.0000.0000.0000.000
11B11VAL0-0.074-0.04427.1490.0140.0140.0000.0000.0000.000
12B12LYS10.8230.91828.8790.0290.0290.0000.0000.0000.000
13B13LYS10.8760.93233.0430.0110.0110.0000.0000.0000.000
14B14PRO00.028-0.01036.075-0.002-0.0020.0000.0000.0000.000
15B15GLY00.0320.03937.0480.0020.0020.0000.0000.0000.000
16B16SER0-0.060-0.01734.331-0.005-0.0050.0000.0000.0000.000
17B17SER00.0570.00931.8710.0080.0080.0000.0000.0000.000
18B18VAL0-0.083-0.03526.689-0.008-0.0080.0000.0000.0000.000
19B19THR00.0420.02024.3700.0110.0110.0000.0000.0000.000
20B20LEU00.0060.02920.908-0.017-0.0170.0000.0000.0000.000
21B21SER00.002-0.02318.299-0.015-0.0150.0000.0000.0000.000
22B22CYS0-0.053-0.02513.6460.0020.0020.0000.0000.0000.000
23B23LYS10.8940.94711.4650.6350.6350.0000.0000.0000.000
24B24ALA00.0640.0489.1830.0070.0070.0000.0000.0000.000
25B25SER0-0.027-0.0216.6260.0270.0270.0000.0000.0000.000
26B26GLY00.0340.0013.069-0.284-0.1180.041-0.106-0.1010.000
27B27ASP-1-0.780-0.8633.9711.6081.9650.001-0.074-0.2840.000
28B28THR0-0.011-0.0056.668-0.287-0.2870.0000.0000.0000.000
29B29PHE0-0.001-0.00310.4110.1940.1940.0000.0000.0000.000
30B30ASN00.014-0.01411.8510.0830.0830.0000.0000.0000.000
31B31THR00.0160.00812.513-0.012-0.0120.0000.0000.0000.000
32B32HIS0-0.0160.0109.8160.2850.2850.0000.0000.0000.000
33B33THR00.022-0.02413.975-0.106-0.1060.0000.0000.0000.000
34B34TYR0-0.104-0.06411.2560.0840.0840.0000.0000.0000.000
35B35SER00.0180.00014.891-0.054-0.0540.0000.0000.0000.000
36B36TRP00.0010.00316.1560.0100.0100.0000.0000.0000.000
37B37VAL0-0.009-0.00617.6360.0080.0080.0000.0000.0000.000
38B38ARG10.8320.91019.610-0.102-0.1020.0000.0000.0000.000
39B39GLN0-0.010-0.01221.2730.0220.0220.0000.0000.0000.000
40B40ALA00.0260.02423.816-0.006-0.0060.0000.0000.0000.000
41B41PRO00.036-0.00926.4530.0140.0140.0000.0000.0000.000
42B42GLY00.0050.02027.277-0.003-0.0030.0000.0000.0000.000
43B43GLN0-0.030-0.01426.607-0.006-0.0060.0000.0000.0000.000
44B44ARG10.9790.99025.021-0.158-0.1580.0000.0000.0000.000
45B45LEU00.0080.00118.674-0.010-0.0100.0000.0000.0000.000
46B46GLU-1-0.795-0.86922.6610.1230.1230.0000.0000.0000.000
47B47TRP0-0.009-0.00818.966-0.013-0.0130.0000.0000.0000.000
48B48ILE0-0.015-0.00121.800-0.016-0.0160.0000.0000.0000.000
49B49GLY00.0890.02421.860-0.017-0.0170.0000.0000.0000.000
50B50GLY0-0.035-0.00619.6690.0230.0230.0000.0000.0000.000
51B51ILE0-0.034-0.01818.801-0.027-0.0270.0000.0000.0000.000
52B52MET00.0450.04317.2190.0310.0310.0000.0000.0000.000
53B52PRO0-0.010-0.01316.480-0.035-0.0350.0000.0000.0000.000
54B53ILE0-0.046-0.03218.576-0.033-0.0330.0000.0000.0000.000
55B54PHE00.0230.01220.355-0.006-0.0060.0000.0000.0000.000
56B55ALA0-0.041-0.00122.562-0.005-0.0050.0000.0000.0000.000
57B56ALA00.0320.03523.4980.0000.0000.0000.0000.0000.000
58B57SER0-0.030-0.04023.1450.0130.0130.0000.0000.0000.000
59B58LYS10.9110.94724.198-0.095-0.0950.0000.0000.0000.000
60B59SER00.0500.01824.4780.0080.0080.0000.0000.0000.000
61B60ALA00.0030.00926.2280.0010.0010.0000.0000.0000.000
62B61PRO00.011-0.01027.696-0.010-0.0100.0000.0000.0000.000
63B62HIS0-0.006-0.01428.167-0.011-0.0110.0000.0000.0000.000
64B63LEU0-0.026-0.01127.304-0.006-0.0060.0000.0000.0000.000
65B64GLN0-0.079-0.04630.427-0.005-0.0050.0000.0000.0000.000
66B65ASP-1-0.910-0.93931.6600.0390.0390.0000.0000.0000.000
67B66ARG10.8130.87631.878-0.055-0.0550.0000.0000.0000.000
68B67LEU0-0.004-0.00425.121-0.003-0.0030.0000.0000.0000.000
69B68THR00.0550.03827.4380.0080.0080.0000.0000.0000.000
70B69ILE0-0.0110.00321.148-0.006-0.0060.0000.0000.0000.000
71B70THR00.0210.02123.233-0.003-0.0030.0000.0000.0000.000
72B71ALA00.0300.00918.3650.0030.0030.0000.0000.0000.000
73B72ASN0-0.0060.00318.853-0.029-0.0290.0000.0000.0000.000
74B73LYS10.9430.95217.1520.0770.0770.0000.0000.0000.000
75B74ALA00.0300.02516.292-0.059-0.0590.0000.0000.0000.000
76B75THR00.0130.01116.850-0.095-0.0950.0000.0000.0000.000
77B76ARG10.8960.9569.7001.1051.1050.0000.0000.0000.000
78B77THR0-0.036-0.00913.333-0.044-0.0440.0000.0000.0000.000
79B78ALA00.0110.00715.9140.0280.0280.0000.0000.0000.000
80B79TYR00.019-0.02117.548-0.028-0.0280.0000.0000.0000.000
81B80MET0-0.0100.01420.9550.0300.0300.0000.0000.0000.000
82B81GLU-1-0.928-0.96623.246-0.044-0.0440.0000.0000.0000.000
83B82LEU0-0.029-0.00726.9010.0100.0100.0000.0000.0000.000
84B82THR00.0330.01328.858-0.008-0.0080.0000.0000.0000.000
85B82SER00.013-0.00232.6180.0070.0070.0000.0000.0000.000
86B82LEU0-0.063-0.02029.8860.0060.0060.0000.0000.0000.000
87B83THR00.0570.02833.579-0.004-0.0040.0000.0000.0000.000
88B84SER00.0390.00333.311-0.001-0.0010.0000.0000.0000.000
89B85ASP-1-0.918-0.95632.7130.0690.0690.0000.0000.0000.000
90B86ASP-1-0.778-0.83429.6620.0640.0640.0000.0000.0000.000
91B87SER0-0.087-0.02928.2990.0010.0010.0000.0000.0000.000
92B88GLY00.0520.01726.2050.0090.0090.0000.0000.0000.000
93B89VAL0-0.044-0.01019.735-0.018-0.0180.0000.0000.0000.000
94B90TYR00.001-0.02320.7070.0170.0170.0000.0000.0000.000
95B91TYR0-0.028-0.01715.396-0.015-0.0150.0000.0000.0000.000
96B93ALA00.0390.01611.6430.0350.0350.0000.0000.0000.000
97B94ARG10.8090.9015.697-1.896-1.8960.0000.0000.0000.000
98B95ASP-1-0.757-0.87610.3410.6530.6530.0000.0000.0000.000
99B96GLY0-0.087-0.0328.7110.1050.1050.0000.0000.0000.000
100B97ARG10.9470.9699.083-1.483-1.4830.0000.0000.0000.000
101B98GLY00.0160.00610.948-0.140-0.1400.0000.0000.0000.000
102B99ALA00.0050.01013.783-0.037-0.0370.0000.0000.0000.000
103B100LEU0-0.039-0.03012.4670.0180.0180.0000.0000.0000.000
104B101GLN00.0210.0385.940-0.016-0.0160.0000.0000.0000.000
105B102TYR0-0.005-0.0193.0540.5931.0730.042-0.136-0.3850.000
106B103TRP00.037-0.0087.737-0.210-0.2100.0000.0000.0000.000
107B104GLY00.0190.0249.2320.0000.0000.0000.0000.0000.000
108B105GLN00.0130.00811.7350.0580.0580.0000.0000.0000.000
109B106GLY00.0320.03013.9940.0200.0200.0000.0000.0000.000
110B107THR0-0.080-0.05617.023-0.049-0.0490.0000.0000.0000.000
111B108LEU00.0140.01720.2040.0100.0100.0000.0000.0000.000
112B109VAL00.0360.01823.586-0.021-0.0210.0000.0000.0000.000
113B110THR0-0.020-0.01626.4020.0130.0130.0000.0000.0000.000
114B111VAL00.0160.01130.036-0.010-0.0100.0000.0000.0000.000
115B112SER00.0520.02633.1460.0050.0050.0000.0000.0000.000
116B113SER00.0790.02236.292-0.005-0.0050.0000.0000.0000.000
117B114ALA0-0.0200.01839.122-0.005-0.0050.0000.0000.0000.000
118B119SER00.000-0.02038.576-0.002-0.0020.0000.0000.0000.000
119B120THR0-0.029-0.01336.3820.0050.0050.0000.0000.0000.000
120B121LYS10.9060.96538.227-0.007-0.0070.0000.0000.0000.000
121B122GLY00.0400.02138.6100.0020.0020.0000.0000.0000.000
122B123PRO0-0.0020.00837.6500.0020.0020.0000.0000.0000.000
123B124SER0-0.054-0.02540.345-0.004-0.0040.0000.0000.0000.000
124B125VAL0-0.002-0.00740.6230.0040.0040.0000.0000.0000.000
125B126PHE00.0170.01043.400-0.003-0.0030.0000.0000.0000.000
126B127PRO00.0200.00944.6870.0030.0030.0000.0000.0000.000
127B128LEU0-0.046-0.02542.7660.0000.0000.0000.0000.0000.000
128B129ALA00.0460.01946.2480.0020.0020.0000.0000.0000.000
129B130PRO00.0110.01447.9200.0020.0020.0000.0000.0000.000
130B136SER00.001-0.01249.953-0.003-0.0030.0000.0000.0000.000
131B137SER00.0420.03052.3780.0010.0010.0000.0000.0000.000
132B137LYS10.9020.95854.522-0.024-0.0240.0000.0000.0000.000
133B137SER0-0.021-0.01353.7180.0010.0010.0000.0000.0000.000
134B137THR0-0.009-0.02049.248-0.001-0.0010.0000.0000.0000.000
135B137SER0-0.036-0.02147.4720.0010.0010.0000.0000.0000.000
136B137GLY00.0610.04246.2440.0000.0000.0000.0000.0000.000
137B138GLY0-0.0240.00744.0540.0030.0030.0000.0000.0000.000
138B139THR0-0.031-0.04045.001-0.001-0.0010.0000.0000.0000.000
139B140ALA00.0690.02345.716-0.003-0.0030.0000.0000.0000.000
140B141ALA0-0.0620.00743.5510.0030.0030.0000.0000.0000.000
141B142LEU00.0300.04642.476-0.003-0.0030.0000.0000.0000.000
142B143GLY00.0560.01141.3420.0050.0050.0000.0000.0000.000
143B144CYS0-0.096-0.00138.430-0.005-0.0050.0000.0000.0000.000
144B145LEU0-0.002-0.00540.0180.0040.0040.0000.0000.0000.000
145B146VAL0-0.007-0.00736.944-0.005-0.0050.0000.0000.0000.000
146B147LYS10.8910.92039.294-0.022-0.0220.0000.0000.0000.000
147B148ASP-1-0.792-0.88241.4630.0170.0170.0000.0000.0000.000
148B149TYR0-0.037-0.00933.392-0.006-0.0060.0000.0000.0000.000
149B150PHE00.1120.05834.6040.0050.0050.0000.0000.0000.000
150B151PRO0-0.074-0.03931.554-0.007-0.0070.0000.0000.0000.000
151B152GLU-1-0.758-0.90929.3620.0540.0540.0000.0000.0000.000
152B153PRO0-0.054-0.01827.1360.0030.0030.0000.0000.0000.000
153B154VAL00.0370.03129.176-0.011-0.0110.0000.0000.0000.000
154B155THR0-0.040-0.01727.5580.0070.0070.0000.0000.0000.000
155B156VAL0-0.004-0.01530.666-0.008-0.0080.0000.0000.0000.000
156B157SER0-0.0180.00031.6810.0070.0070.0000.0000.0000.000
157B158TRP00.0600.02133.605-0.006-0.0060.0000.0000.0000.000
158B159ASN00.0340.00835.9520.0000.0000.0000.0000.0000.000
159B160SER0-0.015-0.01034.089-0.004-0.0040.0000.0000.0000.000
160B161GLY0-0.025-0.00631.754-0.005-0.0050.0000.0000.0000.000
161B162ALA0-0.033-0.00732.2170.0060.0060.0000.0000.0000.000
162B163LEU0-0.024-0.00334.7790.0030.0030.0000.0000.0000.000
163B164THR00.0410.00929.9790.0000.0000.0000.0000.0000.000
164B165SER0-0.016-0.00832.8370.0110.0110.0000.0000.0000.000
165B166GLY00.0290.01234.574-0.005-0.0050.0000.0000.0000.000
166B167VAL0-0.049-0.02033.330-0.004-0.0040.0000.0000.0000.000
167B168HIS00.0160.01133.3250.0120.0120.0000.0000.0000.000
168B169THR00.001-0.00731.534-0.010-0.0100.0000.0000.0000.000
169B170PHE0-0.0170.00931.8930.0090.0090.0000.0000.0000.000
170B171PRO00.0130.00130.076-0.005-0.0050.0000.0000.0000.000
171B172ALA0-0.0200.00231.925-0.004-0.0040.0000.0000.0000.000
172B173VAL0-0.0040.00333.8030.0060.0060.0000.0000.0000.000
173B174LEU0-0.032-0.01535.451-0.006-0.0060.0000.0000.0000.000
174B175GLN0-0.024-0.02637.4490.0020.0020.0000.0000.0000.000
175B176SER00.0550.00541.0380.0000.0000.0000.0000.0000.000
176B177SER0-0.020-0.00743.5400.0000.0000.0000.0000.0000.000
177B178GLY00.0200.02439.659-0.003-0.0030.0000.0000.0000.000
178B179LEU0-0.083-0.03538.781-0.003-0.0030.0000.0000.0000.000
179B180TYR00.005-0.00132.1930.0010.0010.0000.0000.0000.000
180B181SER0-0.014-0.00937.720-0.007-0.0070.0000.0000.0000.000
181B182LEU00.0170.01632.8400.0050.0050.0000.0000.0000.000
182B183SER00.013-0.00236.921-0.005-0.0050.0000.0000.0000.000
183B184SER0-0.0030.00634.8940.0050.0050.0000.0000.0000.000
184B185VAL00.026-0.00637.122-0.006-0.0060.0000.0000.0000.000
185B186VAL00.0030.00737.6460.0050.0050.0000.0000.0000.000
186B187THR0-0.045-0.03439.548-0.003-0.0030.0000.0000.0000.000
187B188VAL00.0340.00041.1610.0010.0010.0000.0000.0000.000
188B189PRO00.0490.02642.9910.0000.0000.0000.0000.0000.000
189B190SER00.0280.01446.115-0.003-0.0030.0000.0000.0000.000
190B191SER0-0.031-0.04049.359-0.002-0.0020.0000.0000.0000.000
191B192SER0-0.024-0.03148.771-0.003-0.0030.0000.0000.0000.000
192B193LEU0-0.042-0.00945.346-0.002-0.0020.0000.0000.0000.000
193B194GLY00.0200.02849.2300.0000.0000.0000.0000.0000.000
194B195THR0-0.028-0.01349.873-0.001-0.0010.0000.0000.0000.000
195B196GLN0-0.0040.00542.913-0.001-0.0010.0000.0000.0000.000
196B197THR00.0360.03145.5400.0010.0010.0000.0000.0000.000
197B198TYR00.027-0.00741.7580.0010.0010.0000.0000.0000.000
198B199ILE00.0200.00439.811-0.001-0.0010.0000.0000.0000.000
199B201ASN0-0.034-0.03235.093-0.002-0.0020.0000.0000.0000.000
200B202VAL00.0620.02335.0190.0040.0040.0000.0000.0000.000
201B203ASN0-0.011-0.00730.283-0.012-0.0120.0000.0000.0000.000
202B204HIS00.0460.01432.8590.0060.0060.0000.0000.0000.000
203B205LYS10.9340.96129.4850.0240.0240.0000.0000.0000.000
204B206PRO0-0.011-0.00332.673-0.007-0.0070.0000.0000.0000.000
205B207SER00.0180.01136.0370.0000.0000.0000.0000.0000.000
206B208ASN0-0.054-0.02934.170-0.002-0.0020.0000.0000.0000.000
207B209THR00.004-0.00837.9820.0010.0010.0000.0000.0000.000
208B210LYS10.9320.97337.1560.0240.0240.0000.0000.0000.000
209B211VAL00.0230.02040.859-0.002-0.0020.0000.0000.0000.000
210B212ASP-1-0.818-0.89743.2130.0130.0130.0000.0000.0000.000
211B213LYN0-0.028-0.01242.6240.0010.0010.0000.0000.0000.000
212B214LYS10.8950.94046.634-0.006-0.0060.0000.0000.0000.000
213B215VAL0-0.007-0.01150.1210.0020.0020.0000.0000.0000.000
214B216GLU-1-0.897-0.95752.3980.0140.0140.0000.0000.0000.000
215B217PRO0-0.056-0.01055.5950.0010.0010.0000.0000.0000.000