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: N9ZVQ

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2059878.44777
FMO2-HF: Nuclear repulsion 1984167.273272
FMO2-HF: Total energy -75711.174498
FMO2-MP2: Total energy -75931.334066


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.
-1.5830.664-0.023-1.024-1.20.004
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 : 0.001
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].
3A367PRO0-0.027-0.0103.821-1.7200.527-0.023-1.024-1.2000.004
4A368LEU00.0320.0135.7060.1150.1150.0000.0000.0000.000
5A369PRO00.003-0.0018.713-0.002-0.0020.0000.0000.0000.000
6A370GLN0-0.0040.00510.9640.0070.0070.0000.0000.0000.000
7A371LEU0-0.022-0.00914.1760.0120.0120.0000.0000.0000.000
8A372PRO00.002-0.00817.768-0.005-0.0050.0000.0000.0000.000
9A373SER00.0450.03521.049-0.002-0.0020.0000.0000.0000.000
10A374ASN0-0.0180.02122.2060.0020.0020.0000.0000.0000.000
11A375VAL00.041-0.00124.084-0.002-0.0020.0000.0000.0000.000
12A376ARG10.8670.92424.1760.0100.0100.0000.0000.0000.000
13A377ASP-1-0.798-0.93029.507-0.006-0.0060.0000.0000.0000.000
14A378GLY0-0.027-0.00332.3700.0000.0000.0000.0000.0000.000
15A379GLU-1-0.928-0.96635.205-0.001-0.0010.0000.0000.0000.000
16A380ASN0-0.023-0.01938.5390.0010.0010.0000.0000.0000.000
17A381ASN00.0060.01935.7180.0000.0000.0000.0000.0000.000
18A382VAL00.0310.00236.3270.0000.0000.0000.0000.0000.000
19A383ALA00.0170.00531.388-0.001-0.0010.0000.0000.0000.000
20A384SER00.0260.01633.504-0.001-0.0010.0000.0000.0000.000
21A385THR0-0.032-0.01434.6230.0000.0000.0000.0000.0000.000
22A386PHE0-0.022-0.01433.4030.0000.0000.0000.0000.0000.000
23A387LEU00.0100.00329.726-0.001-0.0010.0000.0000.0000.000
24A388GLN00.0290.01634.085-0.001-0.0010.0000.0000.0000.000
25A389ALA0-0.014-0.00736.3990.0000.0000.0000.0000.0000.000
26A390PHE0-0.009-0.01433.2890.0000.0000.0000.0000.0000.000
27A391PHE00.053-0.00529.464-0.001-0.0010.0000.0000.0000.000
28A392GLN00.0320.04135.0390.0000.0000.0000.0000.0000.000
29A393LEU00.004-0.01238.3060.0000.0000.0000.0000.0000.000
30A394TRP0-0.026-0.01234.062-0.001-0.0010.0000.0000.0000.000
31A395ASP-1-0.739-0.85135.534-0.011-0.0110.0000.0000.0000.000
32A396HIS0-0.108-0.04738.2000.0000.0000.0000.0000.0000.000
33A397ASP-1-0.904-0.96541.805-0.007-0.0070.0000.0000.0000.000
34A398ARG10.8280.93236.8440.0130.0130.0000.0000.0000.000
35A399LEU00.007-0.01841.1230.0000.0000.0000.0000.0000.000
36A400THR00.0050.00943.6460.0000.0000.0000.0000.0000.000
37A401LEU0-0.015-0.00737.8620.0000.0000.0000.0000.0000.000
38A402ILE0-0.045-0.01140.6360.0000.0000.0000.0000.0000.000
39A403PRO0-0.004-0.00743.0550.0000.0000.0000.0000.0000.000
40A404GLN0-0.0060.01743.2670.0010.0010.0000.0000.0000.000
41A405PHE00.0310.00239.6430.0000.0000.0000.0000.0000.000
42A406TYR0-0.041-0.01935.5650.0000.0000.0000.0000.0000.000
43A407ASP-1-0.750-0.88741.692-0.010-0.0100.0000.0000.0000.000
44A408SER0-0.052-0.05043.0480.0000.0000.0000.0000.0000.000
45A409GLU-1-0.919-0.95441.874-0.011-0.0110.0000.0000.0000.000
46A410THR0-0.0220.01237.4370.0000.0000.0000.0000.0000.000
47A411THR0-0.033-0.01235.2790.0000.0000.0000.0000.0000.000
48A412PHE00.0310.00032.9630.0000.0000.0000.0000.0000.000
49A413SER0-0.022-0.01830.8520.0000.0000.0000.0000.0000.000
50A414VAL00.0160.01630.2030.0000.0000.0000.0000.0000.000
51A415VAL0-0.036-0.00825.6420.0000.0000.0000.0000.0000.000
52A416PHE00.0160.00026.0260.0000.0000.0000.0000.0000.000
53A417ALA0-0.0020.00320.420-0.002-0.0020.0000.0000.0000.000
54A418THR0-0.064-0.03721.024-0.005-0.0050.0000.0000.0000.000
55A419ASP-1-0.915-0.95322.926-0.033-0.0330.0000.0000.0000.000
56A420SER0-0.033-0.00325.0040.0000.0000.0000.0000.0000.000
57A421PRO00.0360.00126.2960.0020.0020.0000.0000.0000.000
58A422GLN0-0.011-0.01429.5220.0010.0010.0000.0000.0000.000
59A423ASP-1-0.729-0.82028.496-0.027-0.0270.0000.0000.0000.000
60A424PRO00.0460.03631.2580.0000.0000.0000.0000.0000.000
61A425ALA00.027-0.00531.2610.0010.0010.0000.0000.0000.000
62A426SER00.0150.01830.9250.0010.0010.0000.0000.0000.000
63A427SER0-0.011-0.00732.8740.0010.0010.0000.0000.0000.000
64A428SER0-0.038-0.01635.9440.0010.0010.0000.0000.0000.000
65A429CYS00.0410.01734.2880.0010.0010.0000.0000.0000.000
66A430SER0-0.0010.00335.4280.0000.0000.0000.0000.0000.000
67A431LYS10.9000.94337.7130.0160.0160.0000.0000.0000.000
68A432PHE00.0170.01739.1430.0010.0010.0000.0000.0000.000
69A433SER00.0270.00437.7150.0000.0000.0000.0000.0000.000
70A434ARG10.9390.98040.3800.0140.0140.0000.0000.0000.000
71A435ASN00.000-0.02243.0960.0010.0010.0000.0000.0000.000
72A436LEU00.0140.02441.6210.0010.0010.0000.0000.0000.000
73A437ASN0-0.003-0.00141.9200.0000.0000.0000.0000.0000.000
74A438ILE0-0.066-0.03245.7310.0000.0000.0000.0000.0000.000
75A439LEU0-0.028-0.00948.3260.0010.0010.0000.0000.0000.000
76A440SER0-0.032-0.01946.9160.0010.0010.0000.0000.0000.000
77A441PRO00.0400.01946.711-0.001-0.0010.0000.0000.0000.000
78A442ARG10.9060.95246.3320.0110.0110.0000.0000.0000.000
79A443HIS00.0700.05842.1670.0000.0000.0000.0000.0000.000
80A444PRO00.0290.00841.721-0.001-0.0010.0000.0000.0000.000
81A445SER00.043-0.00938.901-0.001-0.0010.0000.0000.0000.000
82A446THR0-0.048-0.01837.684-0.001-0.0010.0000.0000.0000.000
83A447LEU0-0.016-0.01537.196-0.001-0.0010.0000.0000.0000.000
84A448GLN0-0.0150.00536.134-0.001-0.0010.0000.0000.0000.000
85A449ARG10.8960.95730.5400.0270.0270.0000.0000.0000.000
86A450LEU00.0040.01533.214-0.001-0.0010.0000.0000.0000.000
87A451PHE0-0.009-0.01535.4650.0010.0010.0000.0000.0000.000
88A452VAL00.0190.00638.0400.0000.0000.0000.0000.0000.000
89A453GLY00.0200.02140.5220.0010.0010.0000.0000.0000.000
90A454SER00.001-0.02242.4550.0000.0000.0000.0000.0000.000
91A455ASN00.003-0.00243.9230.0000.0000.0000.0000.0000.000
92A456LEU00.0290.02541.5770.0000.0000.0000.0000.0000.000
93A457ILE0-0.0040.00238.411-0.001-0.0010.0000.0000.0000.000
94A458ALA00.0270.01940.4140.0000.0000.0000.0000.0000.000
95A459ASP-1-0.908-0.96342.851-0.011-0.0110.0000.0000.0000.000
96A460LEU0-0.032-0.01135.7610.0000.0000.0000.0000.0000.000
97A461TRP00.000-0.02336.2330.0000.0000.0000.0000.0000.000
98A462LYS10.8660.94739.3280.0110.0110.0000.0000.0000.000
99A463VAL0-0.049-0.01039.1260.0000.0000.0000.0000.0000.000
100A464LEU0-0.036-0.00434.059-0.001-0.0010.0000.0000.0000.000
101A465PRO00.0200.02734.1780.0010.0010.0000.0000.0000.000
102A466ALA00.0400.02836.2950.0000.0000.0000.0000.0000.000
103A467THR0-0.024-0.03932.968-0.001-0.0010.0000.0000.0000.000
104A468ARG10.9250.97834.0100.0080.0080.0000.0000.0000.000
105A469HIS10.7950.88529.8270.0130.0130.0000.0000.0000.000
106A470PRO00.0130.02328.4740.0010.0010.0000.0000.0000.000
107A471SER00.0390.00931.748-0.001-0.0010.0000.0000.0000.000
108A472LEU00.0150.00430.2940.0000.0000.0000.0000.0000.000
109A473ASP-1-0.879-0.92630.963-0.001-0.0010.0000.0000.0000.000
110A474GLN0-0.049-0.02229.0690.0010.0010.0000.0000.0000.000
111A475THR00.0520.00926.774-0.002-0.0020.0000.0000.0000.000
112A476SER0-0.009-0.00323.588-0.001-0.0010.0000.0000.0000.000
113A477GLN0-0.090-0.04023.080-0.002-0.0020.0000.0000.0000.000
114A478TRP0-0.089-0.04424.573-0.004-0.0040.0000.0000.0000.000
115A479LEU0-0.0030.00818.0870.0010.0010.0000.0000.0000.000
116A480ILE0-0.013-0.02422.250-0.002-0.0020.0000.0000.0000.000
117A481ASP-1-0.838-0.91220.542-0.020-0.0200.0000.0000.0000.000
118A482CYS0-0.090-0.03524.107-0.001-0.0010.0000.0000.0000.000
119A483HIS0-0.006-0.00126.0770.0030.0030.0000.0000.0000.000
120A484THR00.0360.02128.741-0.001-0.0010.0000.0000.0000.000
121A485PHE0-0.045-0.01930.0790.0000.0000.0000.0000.0000.000
122A486PRO00.0590.01131.9850.0000.0000.0000.0000.0000.000
123A487HIS0-0.055-0.02934.306-0.001-0.0010.0000.0000.0000.000
124A488LEU00.0180.04234.892-0.001-0.0010.0000.0000.0000.000
125A489ALA00.0330.00837.7990.0010.0010.0000.0000.0000.000
126A490ASP-1-0.763-0.87941.391-0.007-0.0070.0000.0000.0000.000
127A491PRO0-0.057-0.01942.9330.0000.0000.0000.0000.0000.000
128A492THR0-0.064-0.05145.7290.0000.0000.0000.0000.0000.000
129A493GLY0-0.023-0.00847.6700.0000.0000.0000.0000.0000.000
130A494MET0-0.053-0.01749.1700.0000.0000.0000.0000.0000.000
131A495ALA0-0.027-0.00945.6730.0000.0000.0000.0000.0000.000
132A496PRO0-0.028-0.01344.2630.0000.0000.0000.0000.0000.000
133A497TYR0-0.022-0.02739.9700.0000.0000.0000.0000.0000.000
134A498ALA00.0160.01840.2710.0010.0010.0000.0000.0000.000
135A499MET0-0.051-0.01835.598-0.001-0.0010.0000.0000.0000.000
136A500GLY00.028-0.00334.4890.0000.0000.0000.0000.0000.000
137A501LEU0-0.041-0.01831.2340.0010.0010.0000.0000.0000.000
138A502MET0-0.0130.00325.387-0.001-0.0010.0000.0000.0000.000
139A503ILE00.016-0.00327.8100.0010.0010.0000.0000.0000.000
140A504ASN00.0090.00621.3930.0000.0000.0000.0000.0000.000
141A505VAL00.0060.00524.4890.0010.0010.0000.0000.0000.000
142A506ASN00.0100.01820.139-0.006-0.0060.0000.0000.0000.000
143A507GLY00.0640.03122.4250.0030.0030.0000.0000.0000.000
144A508GLN0-0.030-0.02022.2790.0000.0000.0000.0000.0000.000
145A509CYS0-0.037-0.01925.6960.0020.0020.0000.0000.0000.000
146A510GLU-1-0.889-0.92729.182-0.010-0.0100.0000.0000.0000.000
147A511GLU-1-0.764-0.87430.568-0.022-0.0220.0000.0000.0000.000
148A512ALA0-0.011-0.00232.9130.0000.0000.0000.0000.0000.000
149A513ASP-1-0.815-0.90234.845-0.016-0.0160.0000.0000.0000.000
150A514ILE0-0.013-0.02636.7310.0010.0010.0000.0000.0000.000
151A515SER0-0.111-0.05637.7110.0010.0010.0000.0000.0000.000
152A516GLN00.0140.00337.8790.0010.0010.0000.0000.0000.000
153A517ASN0-0.055-0.02340.0260.0010.0010.0000.0000.0000.000
154A518LEU0-0.0040.00336.7860.0010.0010.0000.0000.0000.000
155A519TYR00.008-0.00134.180-0.001-0.0010.0000.0000.0000.000
156A520GLY00.0100.00531.3420.0010.0010.0000.0000.0000.000
157A521THR0-0.014-0.00525.7780.0010.0010.0000.0000.0000.000
158A522ARG10.6770.76126.5230.0250.0250.0000.0000.0000.000
159A523THR00.0100.01120.2090.0020.0020.0000.0000.0000.000
160A524PHE0-0.078-0.03823.631-0.002-0.0020.0000.0000.0000.000
161A525SER00.030-0.00521.047-0.002-0.0020.0000.0000.0000.000
162A526ARG10.7670.85423.7520.0190.0190.0000.0000.0000.000
163A527CYS0-0.0020.02325.4260.0010.0010.0000.0000.0000.000
164A528PHE00.011-0.00427.2530.0010.0010.0000.0000.0000.000
165A529ILE0-0.0010.00528.9940.0000.0000.0000.0000.0000.000
166A530LEU0-0.010-0.00932.2570.0000.0000.0000.0000.0000.000
167A531GLY00.0580.00635.3790.0000.0000.0000.0000.0000.000
168A532PRO00.0190.02338.1690.0000.0000.0000.0000.0000.000
169A533SER0-0.039-0.05041.8050.0000.0000.0000.0000.0000.000
170A534LYS10.9400.97244.0680.0090.0090.0000.0000.0000.000
171A535PRO00.0420.00247.1280.0000.0000.0000.0000.0000.000
172A536GLY0-0.017-0.00350.4810.0000.0000.0000.0000.0000.000
173A537ALA0-0.0280.00346.4460.0000.0000.0000.0000.0000.000
174A538PRO0-0.005-0.00146.6910.0000.0000.0000.0000.0000.000
175A539HIS10.8540.93343.5940.0060.0060.0000.0000.0000.000
176A540PRO00.0520.04543.4680.0000.0000.0000.0000.0000.000
177A541TYR00.0080.01038.8750.0000.0000.0000.0000.0000.000
178A542ARG10.8200.90039.9580.0100.0100.0000.0000.0000.000
179A543VAL00.0240.00434.9770.0000.0000.0000.0000.0000.000
180A544LEU0-0.0390.00635.6240.0000.0000.0000.0000.0000.000
181A545SER00.001-0.00731.339-0.001-0.0010.0000.0000.0000.000
182A546ASP-1-0.711-0.81131.836-0.017-0.0170.0000.0000.0000.000
183A547GLN00.0000.00127.8140.0000.0000.0000.0000.0000.000
184A548LEU00.0170.01127.853-0.001-0.0010.0000.0000.0000.000
185A549THR0-0.017-0.01622.515-0.001-0.0010.0000.0000.0000.000
186A550LEU0-0.014-0.00625.0060.0000.0000.0000.0000.0000.000
187A551HIS00.0770.02517.8710.0010.0010.0000.0000.0000.000
188A552THR0-0.046-0.03220.4690.0040.0040.0000.0000.0000.000
189A553TRP00.0560.02123.3880.0020.0020.0000.0000.0000.000
190A554LYS10.9090.94522.7630.0320.0320.0000.0000.0000.000
191A555PRO00.0310.02627.2410.0020.0020.0000.0000.0000.000
192A556GLN00.0140.02229.560-0.001-0.0010.0000.0000.0000.000