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: JL469

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2059751.133792
FMO2-HF: Nuclear repulsion 1984039.506581
FMO2-HF: Total energy -75711.627212
FMO2-MP2: Total energy -75931.784787


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.
-1.2820.72-0.023-0.878-1.1010.003
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 : 0.002 / q_NPA : -0.008
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].
3A367PRO0-0.023-0.0073.821-1.3880.614-0.023-0.878-1.1010.003
4A368LEU00.0310.0145.7210.0780.0780.0000.0000.0000.000
5A369PRO00.004-0.0038.7590.0130.0130.0000.0000.0000.000
6A370GLN0-0.0100.00510.7560.0150.0150.0000.0000.0000.000
7A371LEU0-0.016-0.00714.1940.0100.0100.0000.0000.0000.000
8A372PRO00.001-0.01017.792-0.001-0.0010.0000.0000.0000.000
9A373SER00.0410.03221.067-0.003-0.0030.0000.0000.0000.000
10A374ASN0-0.0200.01822.1280.0020.0020.0000.0000.0000.000
11A375VAL00.0520.00324.125-0.001-0.0010.0000.0000.0000.000
12A376ARG10.8740.92924.1970.0240.0240.0000.0000.0000.000
13A377ASP-1-0.800-0.92429.558-0.012-0.0120.0000.0000.0000.000
14A378GLY0-0.0160.00232.4190.0010.0010.0000.0000.0000.000
15A379GLU-1-0.925-0.96535.258-0.007-0.0070.0000.0000.0000.000
16A380ASN0-0.014-0.01738.5900.0010.0010.0000.0000.0000.000
17A381ASN0-0.038-0.00435.7570.0000.0000.0000.0000.0000.000
18A382VAL00.0540.01736.3900.0000.0000.0000.0000.0000.000
19A383ALA00.010-0.00631.4050.0000.0000.0000.0000.0000.000
20A384SER00.0260.01633.5320.0000.0000.0000.0000.0000.000
21A385THR0-0.024-0.01034.6490.0010.0010.0000.0000.0000.000
22A386PHE0-0.039-0.02733.3690.0010.0010.0000.0000.0000.000
23A387LEU00.0130.01129.6360.0000.0000.0000.0000.0000.000
24A388GLN00.0240.01534.1040.0000.0000.0000.0000.0000.000
25A389ALA0-0.007-0.00336.4110.0010.0010.0000.0000.0000.000
26A390PHE0-0.011-0.01233.6380.0000.0000.0000.0000.0000.000
27A391PHE00.061-0.00229.3540.0000.0000.0000.0000.0000.000
28A392GLN00.0240.03835.0410.0000.0000.0000.0000.0000.000
29A393LEU00.015-0.00238.3050.0000.0000.0000.0000.0000.000
30A394TRP0-0.024-0.00734.2160.0000.0000.0000.0000.0000.000
31A395ASP-1-0.748-0.83735.443-0.005-0.0050.0000.0000.0000.000
32A396HIS0-0.096-0.04338.1900.0010.0010.0000.0000.0000.000
33A397ASP-1-0.904-0.96141.812-0.004-0.0040.0000.0000.0000.000
34A398ARG10.8220.91336.6590.0070.0070.0000.0000.0000.000
35A399LEU00.023-0.00841.124-0.001-0.0010.0000.0000.0000.000
36A400THR0-0.0060.00143.6510.0000.0000.0000.0000.0000.000
37A401LEU0-0.015-0.00837.9510.0000.0000.0000.0000.0000.000
38A402ILE0-0.044-0.01540.3820.0000.0000.0000.0000.0000.000
39A403PRO00.003-0.00243.0740.0000.0000.0000.0000.0000.000
40A404GLN0-0.0060.02343.2690.0000.0000.0000.0000.0000.000
41A405PHE00.019-0.00339.6790.0000.0000.0000.0000.0000.000
42A406TYR0-0.044-0.02835.471-0.001-0.0010.0000.0000.0000.000
43A407ASP-1-0.711-0.85141.722-0.009-0.0090.0000.0000.0000.000
44A408SER0-0.009-0.01543.0800.0000.0000.0000.0000.0000.000
45A409GLU-1-0.816-0.88641.641-0.011-0.0110.0000.0000.0000.000
46A410THR0-0.051-0.00937.4960.0000.0000.0000.0000.0000.000
47A411THR0-0.022-0.00834.8700.0000.0000.0000.0000.0000.000
48A412PHE00.0260.00032.8970.0000.0000.0000.0000.0000.000
49A413SER00.001-0.00230.7520.0000.0000.0000.0000.0000.000
50A414VAL00.0090.01230.2150.0000.0000.0000.0000.0000.000
51A415VAL0-0.037-0.01325.5380.0000.0000.0000.0000.0000.000
52A416PHE00.011-0.00326.0100.0000.0000.0000.0000.0000.000
53A417ALA0-0.0040.00320.433-0.001-0.0010.0000.0000.0000.000
54A418THR0-0.050-0.03121.008-0.003-0.0030.0000.0000.0000.000
55A419ASP-1-0.930-0.95722.902-0.013-0.0130.0000.0000.0000.000
56A420SER0-0.018-0.00225.5570.0020.0020.0000.0000.0000.000
57A421PRO00.0350.00326.5080.0000.0000.0000.0000.0000.000
58A422GLN0-0.014-0.01429.7080.0000.0000.0000.0000.0000.000
59A423ASP-1-0.727-0.81928.479-0.011-0.0110.0000.0000.0000.000
60A424PRO00.0440.03231.2230.0000.0000.0000.0000.0000.000
61A425ALA00.0420.01131.2480.0000.0000.0000.0000.0000.000
62A426SER00.0390.03430.8850.0000.0000.0000.0000.0000.000
63A427SER0-0.0130.00032.8530.0000.0000.0000.0000.0000.000
64A428SER0-0.061-0.03035.7850.0000.0000.0000.0000.0000.000
65A429CYS00.0350.01034.2930.0000.0000.0000.0000.0000.000
66A430SER0-0.009-0.00435.4690.0000.0000.0000.0000.0000.000
67A431LYS10.9070.94437.6980.0060.0060.0000.0000.0000.000
68A432PHE00.0230.02139.1140.0000.0000.0000.0000.0000.000
69A433SER00.014-0.00837.7740.0000.0000.0000.0000.0000.000
70A434ARG10.9270.97340.3770.0060.0060.0000.0000.0000.000
71A435ASN00.004-0.02143.0880.0000.0000.0000.0000.0000.000
72A436LEU00.0230.03041.6130.0000.0000.0000.0000.0000.000
73A437ASN0-0.010-0.00541.7760.0000.0000.0000.0000.0000.000
74A438ILE0-0.058-0.02845.7320.0000.0000.0000.0000.0000.000
75A439LEU0-0.025-0.00748.3180.0000.0000.0000.0000.0000.000
76A440SER0-0.033-0.02247.0160.0000.0000.0000.0000.0000.000
77A441PRO00.0450.02046.722-0.001-0.0010.0000.0000.0000.000
78A442ARG10.9060.95646.3430.0080.0080.0000.0000.0000.000
79A443HIS00.0750.06442.478-0.001-0.0010.0000.0000.0000.000
80A444PRO00.0240.00541.7730.0000.0000.0000.0000.0000.000
81A445SER00.040-0.01138.871-0.001-0.0010.0000.0000.0000.000
82A446THR0-0.045-0.01937.701-0.001-0.0010.0000.0000.0000.000
83A447LEU0-0.014-0.01337.227-0.001-0.0010.0000.0000.0000.000
84A448GLN0-0.0230.00036.161-0.001-0.0010.0000.0000.0000.000
85A449ARG10.9060.96430.1730.0180.0180.0000.0000.0000.000
86A450LEU00.0010.00333.237-0.001-0.0010.0000.0000.0000.000
87A451PHE0-0.009-0.00835.4890.0010.0010.0000.0000.0000.000
88A452VAL00.0210.00538.0650.0000.0000.0000.0000.0000.000
89A453GLY00.0270.02640.5510.0010.0010.0000.0000.0000.000
90A454SER00.005-0.01742.4780.0000.0000.0000.0000.0000.000
91A455ASN0-0.005-0.00743.9460.0000.0000.0000.0000.0000.000
92A456LEU00.0310.02141.6160.0000.0000.0000.0000.0000.000
93A457ILE0-0.012-0.00138.2990.0000.0000.0000.0000.0000.000
94A458ALA00.0370.02540.4230.0000.0000.0000.0000.0000.000
95A459ASP-1-0.868-0.92942.854-0.007-0.0070.0000.0000.0000.000
96A460LEU0-0.033-0.00835.8710.0000.0000.0000.0000.0000.000
97A461TRP0-0.001-0.02836.2990.0000.0000.0000.0000.0000.000
98A462LYS10.8190.90939.3280.0070.0070.0000.0000.0000.000
99A463VAL0-0.053-0.01839.3440.0010.0010.0000.0000.0000.000
100A464LEU0-0.0260.00533.9620.0000.0000.0000.0000.0000.000
101A465PRO00.0290.03234.1730.0010.0010.0000.0000.0000.000
102A466ALA00.0320.03336.2780.0000.0000.0000.0000.0000.000
103A467THR0-0.045-0.06332.8500.0000.0000.0000.0000.0000.000
104A468ARG10.8730.93433.9820.0000.0000.0000.0000.0000.000
105A469HIS10.7990.88629.8860.0080.0080.0000.0000.0000.000
106A470PRO00.0030.01628.4300.0010.0010.0000.0000.0000.000
107A471SER00.026-0.03331.730-0.001-0.0010.0000.0000.0000.000
108A472LEU0-0.0010.00030.4430.0000.0000.0000.0000.0000.000
109A473ASP-1-0.867-0.89430.965-0.002-0.0020.0000.0000.0000.000
110A474GLN0-0.048-0.02129.1160.0010.0010.0000.0000.0000.000
111A475THR00.0530.01026.805-0.001-0.0010.0000.0000.0000.000
112A476SER0-0.0070.00123.594-0.002-0.0020.0000.0000.0000.000
113A477GLN0-0.089-0.03923.0660.0010.0010.0000.0000.0000.000
114A478TRP0-0.073-0.03824.577-0.002-0.0020.0000.0000.0000.000
115A479LEU00.0010.01018.0620.0000.0000.0000.0000.0000.000
116A480ILE0-0.011-0.01822.261-0.001-0.0010.0000.0000.0000.000
117A481ASP-1-0.848-0.91720.697-0.030-0.0300.0000.0000.0000.000
118A482CYS0-0.088-0.03524.1450.0010.0010.0000.0000.0000.000
119A483HIS0-0.011-0.00626.2290.0000.0000.0000.0000.0000.000
120A484THR00.0380.01928.7980.0000.0000.0000.0000.0000.000
121A485PHE0-0.045-0.01930.143-0.001-0.0010.0000.0000.0000.000
122A486PRO00.0580.01332.0920.0010.0010.0000.0000.0000.000
123A487HIS0-0.058-0.02834.378-0.001-0.0010.0000.0000.0000.000
124A488LEU00.0200.03834.8010.0000.0000.0000.0000.0000.000
125A489ALA00.0290.00537.8640.0000.0000.0000.0000.0000.000
126A490ASP-1-0.748-0.86341.456-0.009-0.0090.0000.0000.0000.000
127A491PRO0-0.063-0.02143.0310.0000.0000.0000.0000.0000.000
128A492THR0-0.071-0.06745.7860.0010.0010.0000.0000.0000.000
129A493GLY0-0.020-0.00447.7310.0000.0000.0000.0000.0000.000
130A494MET0-0.052-0.01349.1770.0000.0000.0000.0000.0000.000
131A495ALA0-0.039-0.01845.8620.0000.0000.0000.0000.0000.000
132A496PRO0-0.019-0.01544.3490.0000.0000.0000.0000.0000.000
133A497TYR0-0.016-0.01940.057-0.001-0.0010.0000.0000.0000.000
134A498ALA00.0140.01840.3390.0010.0010.0000.0000.0000.000
135A499MET0-0.053-0.02035.751-0.001-0.0010.0000.0000.0000.000
136A500GLY00.0300.00234.5540.0010.0010.0000.0000.0000.000
137A501LEU0-0.048-0.02231.0580.0000.0000.0000.0000.0000.000
138A502MET0-0.0100.01224.8990.0000.0000.0000.0000.0000.000
139A503ILE00.017-0.00327.8360.0000.0000.0000.0000.0000.000
140A504ASN00.0080.00821.2600.0010.0010.0000.0000.0000.000
141A505VAL00.0010.00324.5170.0000.0000.0000.0000.0000.000
142A506ASN00.0080.01620.380-0.002-0.0020.0000.0000.0000.000
143A507GLY00.0700.03222.4310.0010.0010.0000.0000.0000.000
144A508GLN0-0.038-0.02822.3470.0010.0010.0000.0000.0000.000
145A509CYS0-0.046-0.02225.6750.0000.0000.0000.0000.0000.000
146A510GLU-1-0.800-0.86129.1520.0010.0010.0000.0000.0000.000
147A511GLU-1-0.788-0.89630.565-0.010-0.0100.0000.0000.0000.000
148A512ALA0-0.0020.00732.8840.0010.0010.0000.0000.0000.000
149A513ASP-1-0.797-0.88334.891-0.003-0.0030.0000.0000.0000.000
150A514ILE0-0.013-0.02736.6910.0010.0010.0000.0000.0000.000
151A515SER0-0.122-0.07137.9990.0000.0000.0000.0000.0000.000
152A516GLN00.0060.00038.0690.0010.0010.0000.0000.0000.000
153A517ASN0-0.064-0.02840.2490.0000.0000.0000.0000.0000.000
154A518LEU00.0080.01036.8710.0010.0010.0000.0000.0000.000
155A519TYR00.003-0.00134.184-0.001-0.0010.0000.0000.0000.000
156A520GLY00.0070.00431.3710.0010.0010.0000.0000.0000.000
157A521THR0-0.031-0.02426.1120.0000.0000.0000.0000.0000.000
158A522ARG10.6720.77226.3900.0110.0110.0000.0000.0000.000
159A523THR00.0140.01320.1680.0010.0010.0000.0000.0000.000
160A524PHE0-0.069-0.03923.608-0.001-0.0010.0000.0000.0000.000
161A525SER00.0440.00920.990-0.001-0.0010.0000.0000.0000.000
162A526ARG10.7550.84323.7600.0150.0150.0000.0000.0000.000
163A527CYS00.0220.02625.412-0.001-0.0010.0000.0000.0000.000
164A528PHE0-0.004-0.00927.2830.0010.0010.0000.0000.0000.000
165A529ILE0-0.0110.00128.993-0.001-0.0010.0000.0000.0000.000
166A530LEU0-0.008-0.00832.3020.0010.0010.0000.0000.0000.000
167A531GLY00.0560.01235.424-0.001-0.0010.0000.0000.0000.000
168A532PRO00.0170.02138.2190.0010.0010.0000.0000.0000.000
169A533SER0-0.041-0.04341.8570.0000.0000.0000.0000.0000.000
170A534LYS10.8200.89144.1140.0090.0090.0000.0000.0000.000
171A535PRO00.033-0.00347.1750.0000.0000.0000.0000.0000.000
172A536GLY0-0.019-0.00450.5290.0000.0000.0000.0000.0000.000
173A537ALA0-0.0240.00646.4810.0000.0000.0000.0000.0000.000
174A538PRO00.0010.00146.7750.0000.0000.0000.0000.0000.000
175A539HIS10.8370.91843.5910.0070.0070.0000.0000.0000.000
176A540PRO00.0670.04343.5250.0000.0000.0000.0000.0000.000
177A541TYR00.0020.00638.7070.0000.0000.0000.0000.0000.000
178A542ARG10.7870.86440.0620.0110.0110.0000.0000.0000.000
179A543VAL00.0220.00335.027-0.001-0.0010.0000.0000.0000.000
180A544LEU0-0.0290.00935.7470.0000.0000.0000.0000.0000.000
181A545SER0-0.007-0.01532.2480.0000.0000.0000.0000.0000.000
182A546ASP-1-0.741-0.81431.856-0.014-0.0140.0000.0000.0000.000
183A547GLN00.0040.00727.811-0.001-0.0010.0000.0000.0000.000
184A548LEU00.0170.01127.873-0.001-0.0010.0000.0000.0000.000
185A549THR0-0.010-0.01022.343-0.001-0.0010.0000.0000.0000.000
186A550LEU0-0.013-0.00725.0050.0000.0000.0000.0000.0000.000
187A551HIS00.0770.02017.5240.0000.0000.0000.0000.0000.000
188A552THR0-0.021-0.01320.6880.0020.0020.0000.0000.0000.000
189A553TRP00.0370.01223.3530.0010.0010.0000.0000.0000.000
190A554LYS10.9190.95022.9800.0020.0020.0000.0000.0000.000
191A555PRO00.0370.02727.4450.0000.0000.0000.0000.0000.000
192A556GLN00.0050.02029.9250.0010.0010.0000.0000.0000.000