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: 39K3L

Calculation Name: 4X2H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X2H

Chain ID: A

ChEMBL ID:

UniProt ID: G0SET4

Base Structure: X-ray

Registration Date: 2023-06-22

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2060510.248862
FMO2-HF: Nuclear repulsion 1984798.410915
FMO2-HF: Total energy -75711.837946
FMO2-MP2: Total energy -75931.998324


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(A:365:PRO)


Summations of interaction energy for fragment #1(A:365:PRO)
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.
-1.070.749-0.017-0.869-0.9330.001
Interaction energy analysis for fragmet #1(A:365:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.009
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].
3A367PRO0-0.0120.0023.871-1.0290.790-0.017-0.869-0.9330.001
4A368LEU00.0410.0246.117-0.075-0.0750.0000.0000.0000.000
5A369PRO0-0.001-0.0119.0720.0300.0300.0000.0000.0000.000
6A370GLN0-0.0280.00110.8880.0330.0330.0000.0000.0000.000
7A371LEU0-0.004-0.00614.767-0.001-0.0010.0000.0000.0000.000
8A372PRO00.011-0.00718.5000.0050.0050.0000.0000.0000.000
9A373SER00.0260.02421.858-0.002-0.0020.0000.0000.0000.000
10A374ASN00.0080.03022.2000.0000.0000.0000.0000.0000.000
11A375VAL00.039-0.00124.2870.0010.0010.0000.0000.0000.000
12A376ARG10.8240.90024.3570.0250.0250.0000.0000.0000.000
13A377ASP-1-0.802-0.92329.716-0.011-0.0110.0000.0000.0000.000
14A378GLY00.0060.01232.5640.0000.0000.0000.0000.0000.000
15A379GLU-1-0.910-0.96035.312-0.010-0.0100.0000.0000.0000.000
16A380ASN0-0.045-0.02738.7930.0010.0010.0000.0000.0000.000
17A381ASN0-0.029-0.00836.2620.0010.0010.0000.0000.0000.000
18A382VAL00.0570.03736.7340.0010.0010.0000.0000.0000.000
19A383ALA00.013-0.01131.8920.0010.0010.0000.0000.0000.000
20A384SER00.0010.00533.9270.0010.0010.0000.0000.0000.000
21A385THR0-0.025-0.01834.7820.0010.0010.0000.0000.0000.000
22A386PHE0-0.046-0.02233.6230.0010.0010.0000.0000.0000.000
23A387LEU00.0220.00730.0050.0010.0010.0000.0000.0000.000
24A388GLN00.0410.02834.2650.0020.0020.0000.0000.0000.000
25A389ALA00.0100.00436.4880.0010.0010.0000.0000.0000.000
26A390PHE0-0.015-0.01134.0130.0010.0010.0000.0000.0000.000
27A391PHE00.028-0.01729.6960.0010.0010.0000.0000.0000.000
28A392GLN00.0050.02935.2130.0010.0010.0000.0000.0000.000
29A393LEU0-0.0040.00038.6000.0010.0010.0000.0000.0000.000
30A394TRP00.021-0.00134.1100.0000.0000.0000.0000.0000.000
31A395ASP-1-0.737-0.82635.4160.0120.0120.0000.0000.0000.000
32A396HIS0-0.106-0.05138.3050.0010.0010.0000.0000.0000.000
33A397ASP-1-0.863-0.94242.1380.0050.0050.0000.0000.0000.000
34A398ARG10.7800.88436.754-0.011-0.0110.0000.0000.0000.000
35A399LEU00.0060.00041.2080.0000.0000.0000.0000.0000.000
36A400THR0-0.009-0.01244.066-0.001-0.0010.0000.0000.0000.000
37A401LEU0-0.013-0.00438.191-0.001-0.0010.0000.0000.0000.000
38A402ILE0-0.0130.00440.688-0.001-0.0010.0000.0000.0000.000
39A403PRO0-0.004-0.00943.308-0.001-0.0010.0000.0000.0000.000
40A404GLN0-0.0210.00643.541-0.001-0.0010.0000.0000.0000.000
41A405PHE0-0.006-0.00739.998-0.001-0.0010.0000.0000.0000.000
42A406TYR0-0.027-0.02735.820-0.001-0.0010.0000.0000.0000.000
43A407ASP-1-0.736-0.85742.215-0.001-0.0010.0000.0000.0000.000
44A408SER00.008-0.01543.6370.0000.0000.0000.0000.0000.000
45A409GLU-1-0.815-0.88441.899-0.002-0.0020.0000.0000.0000.000
46A410THR0-0.050-0.00938.1540.0000.0000.0000.0000.0000.000
47A411THR0-0.004-0.00335.6420.0010.0010.0000.0000.0000.000
48A412PHE00.004-0.00933.4070.0000.0000.0000.0000.0000.000
49A413SER00.0030.00031.0060.0000.0000.0000.0000.0000.000
50A414VAL00.0020.00530.5930.0000.0000.0000.0000.0000.000
51A415VAL0-0.042-0.01225.8060.0000.0000.0000.0000.0000.000
52A416PHE00.009-0.00525.8980.0000.0000.0000.0000.0000.000
53A417ALA0-0.005-0.00120.2690.0000.0000.0000.0000.0000.000
54A418THR0-0.070-0.04920.6970.0080.0080.0000.0000.0000.000
55A419ASP-1-0.856-0.90622.6630.0320.0320.0000.0000.0000.000
56A420SER0-0.061-0.05424.5320.0060.0060.0000.0000.0000.000
57A421PRO00.0100.00226.957-0.003-0.0030.0000.0000.0000.000
58A422GLN00.010-0.00430.0460.0000.0000.0000.0000.0000.000
59A423ASP-1-0.727-0.80828.7030.0260.0260.0000.0000.0000.000
60A424PRO00.0560.04431.401-0.002-0.0020.0000.0000.0000.000
61A425ALA00.0510.02231.392-0.002-0.0020.0000.0000.0000.000
62A426SER00.0330.03230.788-0.003-0.0030.0000.0000.0000.000
63A427SER0-0.020-0.01332.842-0.002-0.0020.0000.0000.0000.000
64A428SER0-0.048-0.02435.809-0.002-0.0020.0000.0000.0000.000
65A429CYS00.025-0.00234.340-0.001-0.0010.0000.0000.0000.000
66A430SER0-0.0030.00335.465-0.001-0.0010.0000.0000.0000.000
67A431LYS10.8640.92437.670-0.017-0.0170.0000.0000.0000.000
68A432PHE00.0300.02139.267-0.001-0.0010.0000.0000.0000.000
69A433SER00.0290.00237.726-0.001-0.0010.0000.0000.0000.000
70A434ARG10.9220.97140.353-0.012-0.0120.0000.0000.0000.000
71A435ASN00.015-0.01043.0570.0000.0000.0000.0000.0000.000
72A436LEU00.0190.02241.484-0.001-0.0010.0000.0000.0000.000
73A437ASN0-0.044-0.03741.821-0.001-0.0010.0000.0000.0000.000
74A438ILE0-0.043-0.02745.7290.0000.0000.0000.0000.0000.000
75A439LEU0-0.023-0.00648.3550.0000.0000.0000.0000.0000.000
76A440SER0-0.010-0.00447.230-0.001-0.0010.0000.0000.0000.000
77A441PRO00.0200.01847.0020.0000.0000.0000.0000.0000.000
78A442ARG10.9070.94846.888-0.004-0.0040.0000.0000.0000.000
79A443HIS00.0680.06743.0360.0000.0000.0000.0000.0000.000
80A444PRO00.0480.01741.9570.0000.0000.0000.0000.0000.000
81A445SER00.025-0.00939.0730.0000.0000.0000.0000.0000.000
82A446THR0-0.046-0.02237.9300.0010.0010.0000.0000.0000.000
83A447LEU0-0.039-0.01937.6030.0010.0010.0000.0000.0000.000
84A448GLN0-0.008-0.01136.3610.0000.0000.0000.0000.0000.000
85A449ARG10.9100.96530.210-0.012-0.0120.0000.0000.0000.000
86A450LEU0-0.0260.00233.4880.0010.0010.0000.0000.0000.000
87A451PHE00.000-0.00635.5700.0000.0000.0000.0000.0000.000
88A452VAL00.022-0.00738.164-0.001-0.0010.0000.0000.0000.000
89A453GLY00.0260.03140.8760.0000.0000.0000.0000.0000.000
90A454SER0-0.026-0.02743.2060.0010.0010.0000.0000.0000.000
91A455ASN00.0070.00244.1240.0000.0000.0000.0000.0000.000
92A456LEU00.0350.02541.7550.0010.0010.0000.0000.0000.000
93A457ILE0-0.0230.00138.4440.0010.0010.0000.0000.0000.000
94A458ALA00.0510.01740.6360.0010.0010.0000.0000.0000.000
95A459ASP-1-0.889-0.94443.1040.0070.0070.0000.0000.0000.000
96A460LEU0-0.0160.00836.1770.0010.0010.0000.0000.0000.000
97A461TRP0-0.005-0.02736.5070.0010.0010.0000.0000.0000.000
98A462LYS10.8000.90039.790-0.007-0.0070.0000.0000.0000.000
99A463VAL0-0.051-0.02339.7560.0000.0000.0000.0000.0000.000
100A464LEU0-0.0110.00834.2260.0010.0010.0000.0000.0000.000
101A465PRO00.0280.02934.550-0.001-0.0010.0000.0000.0000.000
102A466ALA00.0350.03836.628-0.001-0.0010.0000.0000.0000.000
103A467THR0-0.048-0.06233.0230.0010.0010.0000.0000.0000.000
104A468ARG10.8750.93133.886-0.015-0.0150.0000.0000.0000.000
105A469HIS10.8160.89529.972-0.010-0.0100.0000.0000.0000.000
106A470PRO0-0.0020.01728.5320.0000.0000.0000.0000.0000.000
107A471SER00.024-0.03131.853-0.001-0.0010.0000.0000.0000.000
108A472LEU00.0140.00530.6250.0000.0000.0000.0000.0000.000
109A473ASP-1-0.859-0.89730.9250.0000.0000.0000.0000.0000.000
110A474GLN0-0.051-0.01129.524-0.001-0.0010.0000.0000.0000.000
111A475THR00.024-0.00926.9580.0010.0010.0000.0000.0000.000
112A476SER0-0.016-0.00423.913-0.002-0.0020.0000.0000.0000.000
113A477GLN0-0.073-0.03223.1280.0020.0020.0000.0000.0000.000
114A478TRP0-0.054-0.03224.6510.0030.0030.0000.0000.0000.000
115A479LEU0-0.0110.00118.247-0.003-0.0030.0000.0000.0000.000
116A480ILE0-0.008-0.01422.4480.0020.0020.0000.0000.0000.000
117A481ASP-1-0.867-0.92621.260-0.022-0.0220.0000.0000.0000.000
118A482CYS0-0.090-0.02924.5180.0020.0020.0000.0000.0000.000
119A483HIS00.0390.01925.531-0.004-0.0040.0000.0000.0000.000
120A484THR00.0280.01329.3300.0010.0010.0000.0000.0000.000
121A485PHE0-0.032-0.01630.311-0.002-0.0020.0000.0000.0000.000
122A486PRO00.0410.01332.2600.0010.0010.0000.0000.0000.000
123A487HIS0-0.058-0.03234.451-0.001-0.0010.0000.0000.0000.000
124A488LEU00.0090.03635.2890.0010.0010.0000.0000.0000.000
125A489ALA00.0240.00537.9170.0000.0000.0000.0000.0000.000
126A490ASP-1-0.752-0.85741.433-0.006-0.0060.0000.0000.0000.000
127A491PRO0-0.071-0.02843.1460.0000.0000.0000.0000.0000.000
128A492THR0-0.072-0.07745.9810.0000.0000.0000.0000.0000.000
129A493GLY0-0.0100.00348.0040.0000.0000.0000.0000.0000.000
130A494MET0-0.048-0.01349.0250.0000.0000.0000.0000.0000.000
131A495ALA0-0.024-0.01045.6110.0000.0000.0000.0000.0000.000
132A496PRO0-0.033-0.02544.3350.0000.0000.0000.0000.0000.000
133A497TYR0-0.004-0.00840.0350.0000.0000.0000.0000.0000.000
134A498ALA00.0110.01440.5050.0000.0000.0000.0000.0000.000
135A499MET0-0.047-0.01235.943-0.001-0.0010.0000.0000.0000.000
136A500GLY00.031-0.00235.0000.0010.0010.0000.0000.0000.000
137A501LEU0-0.036-0.02031.435-0.001-0.0010.0000.0000.0000.000
138A502MET0-0.0100.01424.6300.0010.0010.0000.0000.0000.000
139A503ILE00.011-0.01228.267-0.002-0.0020.0000.0000.0000.000
140A504ASN00.0310.02521.3670.0040.0040.0000.0000.0000.000
141A505VAL00.0110.00425.176-0.002-0.0020.0000.0000.0000.000
142A506ASN00.0050.01220.8140.0060.0060.0000.0000.0000.000
143A507GLY00.0740.04022.875-0.003-0.0030.0000.0000.0000.000
144A508GLN0-0.055-0.03122.5470.0030.0030.0000.0000.0000.000
145A509CYS0-0.041-0.01825.761-0.003-0.0030.0000.0000.0000.000
146A510GLU-1-0.805-0.85829.2490.0210.0210.0000.0000.0000.000
147A511GLU-1-0.777-0.88530.7270.0200.0200.0000.0000.0000.000
148A512ALA00.0030.00533.0490.0020.0020.0000.0000.0000.000
149A513ASP-1-0.811-0.88334.9540.0230.0230.0000.0000.0000.000
150A514ILE0-0.006-0.02936.7090.0000.0000.0000.0000.0000.000
151A515SER0-0.121-0.07638.097-0.001-0.0010.0000.0000.0000.000
152A516GLN0-0.015-0.01137.7390.0000.0000.0000.0000.0000.000
153A517ASN0-0.057-0.02240.210-0.001-0.0010.0000.0000.0000.000
154A518LEU00.0180.01836.9480.0000.0000.0000.0000.0000.000
155A519TYR00.0110.00333.9970.0000.0000.0000.0000.0000.000
156A520GLY00.0090.00131.1840.0010.0010.0000.0000.0000.000
157A521THR0-0.015-0.01026.001-0.002-0.0020.0000.0000.0000.000
158A522ARG10.6830.78126.464-0.023-0.0230.0000.0000.0000.000
159A523THR00.0280.00320.235-0.003-0.0030.0000.0000.0000.000
160A524PHE0-0.086-0.04923.7170.0000.0000.0000.0000.0000.000
161A525SER00.0500.01221.0920.0010.0010.0000.0000.0000.000
162A526ARG10.7410.83323.787-0.005-0.0050.0000.0000.0000.000
163A527CYS00.0080.02625.683-0.003-0.0030.0000.0000.0000.000
164A528PHE00.006-0.00227.5550.0010.0010.0000.0000.0000.000
165A529ILE0-0.016-0.01029.268-0.002-0.0020.0000.0000.0000.000
166A530LEU00.0210.01232.6590.0010.0010.0000.0000.0000.000
167A531GLY00.0550.00935.504-0.001-0.0010.0000.0000.0000.000
168A532PRO00.0230.02738.3360.0010.0010.0000.0000.0000.000
169A533SER0-0.032-0.03242.1330.0000.0000.0000.0000.0000.000
170A534LYS10.8360.89744.5210.0010.0010.0000.0000.0000.000
171A535PRO00.016-0.00647.6500.0000.0000.0000.0000.0000.000
172A536GLY0-0.0020.00550.9950.0000.0000.0000.0000.0000.000
173A537ALA0-0.0110.00946.8980.0000.0000.0000.0000.0000.000
174A538PRO00.000-0.00147.5360.0000.0000.0000.0000.0000.000
175A539HIS10.8400.92543.5760.0010.0010.0000.0000.0000.000
176A540PRO00.0680.04144.0460.0000.0000.0000.0000.0000.000
177A541TYR0-0.015-0.00338.8750.0000.0000.0000.0000.0000.000
178A542ARG10.7820.86540.4590.0040.0040.0000.0000.0000.000
179A543VAL00.0240.01435.419-0.001-0.0010.0000.0000.0000.000
180A544LEU0-0.0070.01236.2590.0000.0000.0000.0000.0000.000
181A545SER0-0.015-0.02032.6320.0010.0010.0000.0000.0000.000
182A546ASP-1-0.743-0.82132.0960.0040.0040.0000.0000.0000.000
183A547GLN00.0100.00728.2020.0000.0000.0000.0000.0000.000
184A548LEU00.0080.00827.8950.0000.0000.0000.0000.0000.000
185A549THR0-0.003-0.00522.5070.0010.0010.0000.0000.0000.000
186A550LEU00.0010.00724.7060.0010.0010.0000.0000.0000.000
187A551HIS00.0700.02417.378-0.002-0.0020.0000.0000.0000.000
188A552THR00.014-0.00120.282-0.004-0.0040.0000.0000.0000.000
189A553TRP00.0500.04623.102-0.001-0.0010.0000.0000.0000.000
190A554LYS10.8750.92123.100-0.048-0.0480.0000.0000.0000.000
191A555PRO00.0220.02127.450-0.002-0.0020.0000.0000.0000.000
192A556GLN0-0.0130.00329.9920.0030.0030.0000.0000.0000.000