FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 3J7YL

Calculation Name: 2HYX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HYX

Chain ID: A

ChEMBL ID:

UniProt ID: P9WG63

Base Structure: X-ray

Registration Date: 2023-09-22

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 332
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4759835.255618
FMO2-HF: Nuclear repulsion 4635965.110743
FMO2-HF: Total energy -123870.144875
FMO2-MP2: Total energy -124237.325157


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:-3:GLY)


Summations of interaction energy for fragment #1(A:-3:GLY)
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.
0.4392.268-0.019-1.016-0.7950.004
Interaction energy analysis for fragmet #1(A:-3:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.012
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].
3A-1MET0-0.029-0.0153.7990.2962.125-0.019-1.016-0.7950.004
4A366GLU-1-0.885-0.9357.092-0.608-0.6080.0000.0000.0000.000
5A367ILE0-0.0430.0019.0990.1720.1720.0000.0000.0000.000
6A368ARG10.9130.92512.7650.0710.0710.0000.0000.0000.000
7A369GLU-1-0.806-0.90113.973-0.150-0.1500.0000.0000.0000.000
8A370GLN00.0270.03611.553-0.036-0.0360.0000.0000.0000.000
9A371LEU00.0150.02313.159-0.010-0.0100.0000.0000.0000.000
10A372ASN0-0.048-0.0328.842-0.385-0.3850.0000.0000.0000.000
11A373LEU00.0050.00711.2390.0530.0530.0000.0000.0000.000
12A374GLY00.0080.01110.851-0.223-0.2230.0000.0000.0000.000
13A375GLY00.0160.00712.1320.0650.0650.0000.0000.0000.000
14A376ILE0-0.0030.00013.283-0.118-0.1180.0000.0000.0000.000
15A377VAL00.0290.02015.5070.0430.0430.0000.0000.0000.000
16A378ASN0-0.013-0.01318.0020.0290.0290.0000.0000.0000.000
17A379ALA00.035-0.01021.631-0.004-0.0040.0000.0000.0000.000
18A380GLN0-0.029-0.04024.3720.0100.0100.0000.0000.0000.000
19A381ASN00.0200.01119.431-0.016-0.0160.0000.0000.0000.000
20A382ALA0-0.004-0.00220.360-0.031-0.0310.0000.0000.0000.000
21A383GLN00.009-0.00220.506-0.016-0.0160.0000.0000.0000.000
22A384LEU00.0370.03819.0800.0090.0090.0000.0000.0000.000
23A385SER0-0.004-0.00816.337-0.002-0.0020.0000.0000.0000.000
24A386ASN0-0.077-0.03818.144-0.044-0.0440.0000.0000.0000.000
25A387CYS0-0.118-0.02720.4540.0280.0280.0000.0000.0000.000
26A388SER0-0.027-0.04918.104-0.044-0.0440.0000.0000.0000.000
27A389ASP-1-0.861-0.95915.587-0.249-0.2490.0000.0000.0000.000
28A390GLY00.011-0.00618.1990.0300.0300.0000.0000.0000.000
29A391ALA0-0.0340.00821.6160.0230.0230.0000.0000.0000.000
30A392ALA00.021-0.02223.4590.0110.0110.0000.0000.0000.000
31A393GLN0-0.043-0.01826.6580.0200.0200.0000.0000.0000.000
32A394LEU0-0.020-0.01027.037-0.012-0.0120.0000.0000.0000.000
33A395GLU-1-0.792-0.85822.588-0.256-0.2560.0000.0000.0000.000
34A396SER0-0.050-0.03926.2080.0120.0120.0000.0000.0000.000
35A398GLY00.0830.04624.462-0.012-0.0120.0000.0000.0000.000
36A399THR0-0.064-0.03426.7910.0110.0110.0000.0000.0000.000
37A400ALA00.0200.01126.581-0.015-0.0150.0000.0000.0000.000
38A401PRO00.0140.01722.8790.0100.0100.0000.0000.0000.000
39A402ASP-1-0.832-0.90126.001-0.140-0.1400.0000.0000.0000.000
40A403LEU00.0100.01526.483-0.012-0.0120.0000.0000.0000.000
41A404LYS10.8420.92425.5760.1900.1900.0000.0000.0000.000
42A405GLY00.023-0.00326.9370.0010.0010.0000.0000.0000.000
43A406ILE0-0.0260.01227.4470.0050.0050.0000.0000.0000.000
44A407THR0-0.065-0.03229.1370.0070.0070.0000.0000.0000.000
45A408GLY00.0270.00931.6640.0060.0060.0000.0000.0000.000
46A409TRP00.0350.03032.465-0.005-0.0050.0000.0000.0000.000
47A410LEU00.0010.00034.1170.0060.0060.0000.0000.0000.000
48A411ASN0-0.021-0.00936.471-0.002-0.0020.0000.0000.0000.000
49A412THR00.0200.00137.146-0.001-0.0010.0000.0000.0000.000
50A413PRO00.0410.00940.0670.0030.0030.0000.0000.0000.000
51A414GLY0-0.017-0.00942.844-0.003-0.0030.0000.0000.0000.000
52A415ASN0-0.056-0.03738.6830.0010.0010.0000.0000.0000.000
53A416LYS10.9520.99139.0210.0420.0420.0000.0000.0000.000
54A417PRO00.0260.00935.1940.0000.0000.0000.0000.0000.000
55A418ILE00.0110.01635.0570.0030.0030.0000.0000.0000.000
56A419ASP-1-0.798-0.87734.189-0.118-0.1180.0000.0000.0000.000
57A420LEU00.0700.03528.9850.0060.0060.0000.0000.0000.000
58A421LYS10.8150.89432.8230.1270.1270.0000.0000.0000.000
59A422SER0-0.079-0.05436.1670.0050.0050.0000.0000.0000.000
60A423LEU0-0.030-0.02034.2970.0060.0060.0000.0000.0000.000
61A424ARG10.9310.99832.7760.1260.1260.0000.0000.0000.000
62A425GLY0-0.022-0.01438.0660.0060.0060.0000.0000.0000.000
63A426LYS10.9030.94437.9110.0670.0670.0000.0000.0000.000
64A427VAL00.0130.02633.505-0.006-0.0060.0000.0000.0000.000
65A428VAL0-0.031-0.03331.4450.0080.0080.0000.0000.0000.000
66A429LEU00.0180.02327.904-0.010-0.0100.0000.0000.0000.000
67A430ILE0-0.045-0.02325.4250.0100.0100.0000.0000.0000.000
68A431ASP-1-0.814-0.91525.678-0.070-0.0700.0000.0000.0000.000
69A432PHE0-0.037-0.01621.7840.0020.0020.0000.0000.0000.000
70A433TRP00.002-0.02523.4630.0160.0160.0000.0000.0000.000
71A434ALA00.0370.01123.311-0.007-0.0070.0000.0000.0000.000
72A435TYR0-0.034-0.05825.2110.0060.0060.0000.0000.0000.000
73A436SER0-0.059-0.04026.0770.0090.0090.0000.0000.0000.000
74A437CYS00.0190.02621.6320.0110.0110.0000.0000.0000.000
75A438ILE00.0510.02024.018-0.010-0.0100.0000.0000.0000.000
76A439ASN00.0540.01620.2570.0040.0040.0000.0000.0000.000
77A440CYS0-0.021-0.01023.072-0.018-0.0180.0000.0000.0000.000
78A441GLN0-0.067-0.04025.603-0.005-0.0050.0000.0000.0000.000
79A442ARG10.7550.83923.839-0.074-0.0740.0000.0000.0000.000
80A443ALA00.0100.00325.840-0.005-0.0050.0000.0000.0000.000
81A444ILE00.0410.00728.001-0.007-0.0070.0000.0000.0000.000
82A445PRO00.0090.01230.372-0.005-0.0050.0000.0000.0000.000
83A446HIS10.8330.91529.9020.0060.0060.0000.0000.0000.000
84A447VAL00.0390.04028.930-0.004-0.0040.0000.0000.0000.000
85A448VAL0-0.030-0.02032.159-0.004-0.0040.0000.0000.0000.000
86A449GLY00.0270.02535.404-0.001-0.0010.0000.0000.0000.000
87A450TRP0-0.023-0.01628.848-0.002-0.0020.0000.0000.0000.000
88A451TYR0-0.014-0.00735.683-0.002-0.0020.0000.0000.0000.000
89A452GLN0-0.069-0.04937.2290.0000.0000.0000.0000.0000.000
90A453ALA0-0.0020.01839.1070.0010.0010.0000.0000.0000.000
91A454TYR0-0.021-0.04936.087-0.001-0.0010.0000.0000.0000.000
92A455LYS10.9531.00439.9260.0320.0320.0000.0000.0000.000
93A456ASP-1-0.940-0.97040.763-0.041-0.0410.0000.0000.0000.000
94A457SER0-0.083-0.05641.6260.0010.0010.0000.0000.0000.000
95A458GLY0-0.051-0.03240.801-0.003-0.0030.0000.0000.0000.000
96A459LEU0-0.0060.02033.702-0.005-0.0050.0000.0000.0000.000
97A460ALA0-0.054-0.02735.6950.0060.0060.0000.0000.0000.000
98A461VAL00.0290.00631.434-0.005-0.0050.0000.0000.0000.000
99A462ILE0-0.013-0.01030.1370.0050.0050.0000.0000.0000.000
100A463GLY00.0650.03928.767-0.007-0.0070.0000.0000.0000.000
101A464VAL0-0.045-0.02624.9430.0060.0060.0000.0000.0000.000
102A465HIS00.0370.02525.4330.0080.0080.0000.0000.0000.000
103A466THR00.004-0.01020.576-0.003-0.0030.0000.0000.0000.000
104A467PRO0-0.077-0.02222.8040.0090.0090.0000.0000.0000.000
105A468GLH0-0.056-0.05419.342-0.014-0.0140.0000.0000.0000.000
106A469TYR0-0.009-0.00121.4010.0190.0190.0000.0000.0000.000
107A470ALA00.0260.00224.179-0.016-0.0160.0000.0000.0000.000
108A471PHE00.002-0.00226.842-0.012-0.0120.0000.0000.0000.000
109A472GLU-1-0.759-0.86024.7140.0220.0220.0000.0000.0000.000
110A473LYS10.8850.93323.8750.0210.0210.0000.0000.0000.000
111A474VAL0-0.042-0.01029.245-0.006-0.0060.0000.0000.0000.000
112A475PRO00.0700.02332.9110.0020.0020.0000.0000.0000.000
113A476GLY00.0160.00434.7560.0000.0000.0000.0000.0000.000
114A477ASN0-0.054-0.03432.4650.0010.0010.0000.0000.0000.000
115A478VAL00.0630.04130.2940.0020.0020.0000.0000.0000.000
116A479ALA0-0.021-0.00132.7660.0000.0000.0000.0000.0000.000
117A480LYS10.9520.97936.216-0.011-0.0110.0000.0000.0000.000
118A481GLY00.0270.03132.9440.0030.0030.0000.0000.0000.000
119A482ALA00.027-0.00433.8290.0000.0000.0000.0000.0000.000
120A483ALA0-0.034-0.01834.641-0.001-0.0010.0000.0000.0000.000
121A484ASN0-0.080-0.05435.7530.0020.0020.0000.0000.0000.000
122A485LEU0-0.0040.01230.7880.0020.0020.0000.0000.0000.000
123A486GLY00.0000.01435.185-0.003-0.0030.0000.0000.0000.000
124A487ILE0-0.034-0.01031.805-0.004-0.0040.0000.0000.0000.000
125A488SER0-0.007-0.01336.1130.0000.0000.0000.0000.0000.000
126A489TYR0-0.053-0.03330.3850.0020.0020.0000.0000.0000.000
127A490PRO00.009-0.00334.5370.0030.0030.0000.0000.0000.000
128A491ILE00.0100.01930.849-0.003-0.0030.0000.0000.0000.000
129A492ALA00.0010.00329.4190.0010.0010.0000.0000.0000.000
130A493LEU00.0120.00428.751-0.002-0.0020.0000.0000.0000.000
131A494ASP-1-0.702-0.86423.109-0.138-0.1380.0000.0000.0000.000
132A495ASN00.024-0.00624.635-0.001-0.0010.0000.0000.0000.000
133A496ASN0-0.0190.00024.4660.0160.0160.0000.0000.0000.000
134A497TYR00.0370.02219.836-0.010-0.0100.0000.0000.0000.000
135A498ALA00.0120.03320.924-0.031-0.0310.0000.0000.0000.000
136A499THR0-0.003-0.01622.635-0.025-0.0250.0000.0000.0000.000
137A500TRP00.0180.01315.520-0.012-0.0120.0000.0000.0000.000
138A501THR0-0.050-0.04217.185-0.045-0.0450.0000.0000.0000.000
139A502ASN0-0.097-0.04518.595-0.060-0.0600.0000.0000.0000.000
140A503TYR00.007-0.02220.436-0.015-0.0150.0000.0000.0000.000
141A504ARG10.8330.93612.8540.7150.7150.0000.0000.0000.000
142A505ASN00.0920.05515.271-0.077-0.0770.0000.0000.0000.000
143A506ARG10.7840.8717.5720.9340.9340.0000.0000.0000.000
144A507TYR0-0.016-0.00810.4200.0000.0000.0000.0000.0000.000
145A508TRP0-0.0210.02816.050-0.017-0.0170.0000.0000.0000.000
146A509PRO0-0.002-0.02419.2470.0280.0280.0000.0000.0000.000
147A510ALA00.0240.00718.868-0.011-0.0110.0000.0000.0000.000
148A511GLU-1-0.852-0.93020.898-0.072-0.0720.0000.0000.0000.000
149A512TYR00.007-0.01918.653-0.015-0.0150.0000.0000.0000.000
150A513LEU0-0.020-0.00424.6350.0160.0160.0000.0000.0000.000
151A514ILE0-0.019-0.01228.005-0.013-0.0130.0000.0000.0000.000
152A515ASP-1-0.689-0.80530.151-0.123-0.1230.0000.0000.0000.000
153A516ALA00.0500.02833.343-0.001-0.0010.0000.0000.0000.000
154A517THR0-0.047-0.04334.1910.0020.0020.0000.0000.0000.000
155A518GLY0-0.054-0.04932.743-0.003-0.0030.0000.0000.0000.000
156A519THR0-0.040-0.01729.290-0.015-0.0150.0000.0000.0000.000
157A520VAL0-0.016-0.00424.0110.0140.0140.0000.0000.0000.000
158A521ARG10.8680.90527.2070.1350.1350.0000.0000.0000.000
159A522HIS00.0500.03324.6270.0090.0090.0000.0000.0000.000
160A523ILE00.0150.01119.4430.0090.0090.0000.0000.0000.000
161A524LYS10.8720.96520.2630.0740.0740.0000.0000.0000.000
162A525PHE0-0.032-0.02814.0820.0090.0090.0000.0000.0000.000
163A526GLY00.0120.00918.1660.0170.0170.0000.0000.0000.000
164A527GLU-1-0.809-0.89018.9800.0420.0420.0000.0000.0000.000
165A528GLY00.0400.02221.8060.0110.0110.0000.0000.0000.000
166A529ASP-1-0.885-0.94522.907-0.059-0.0590.0000.0000.0000.000
167A530TYR0-0.032-0.01925.676-0.016-0.0160.0000.0000.0000.000
168A531ASN00.0370.00328.534-0.005-0.0050.0000.0000.0000.000
169A532VAL00.0310.05325.574-0.001-0.0010.0000.0000.0000.000
170A533THR00.0520.02426.027-0.003-0.0030.0000.0000.0000.000
171A534GLU-1-0.733-0.83228.529-0.042-0.0420.0000.0000.0000.000
172A535THR0-0.051-0.04631.6670.0020.0020.0000.0000.0000.000
173A536LEU00.0120.01027.6600.0000.0000.0000.0000.0000.000
174A537VAL00.0100.00631.148-0.002-0.0020.0000.0000.0000.000
175A538ARG10.8370.89133.4030.0480.0480.0000.0000.0000.000
176A539GLN0-0.008-0.00433.426-0.004-0.0040.0000.0000.0000.000
177A540LEU00.0480.01731.1630.0000.0000.0000.0000.0000.000
178A541LEU0-0.041-0.01435.6720.0010.0010.0000.0000.0000.000
179A542ASN0-0.011-0.01338.6200.0070.0070.0000.0000.0000.000
180A543ASP-1-0.927-0.96336.212-0.095-0.0950.0000.0000.0000.000
181A544ALA0-0.076-0.02938.7190.0000.0000.0000.0000.0000.000
182A545LYS10.8470.93540.4570.0590.0590.0000.0000.0000.000
183A546PRO00.0610.02943.3490.0030.0030.0000.0000.0000.000
184A547GLY0-0.019-0.00244.7630.0030.0030.0000.0000.0000.000
185A548VAL0-0.071-0.02242.2960.0040.0040.0000.0000.0000.000
186A549LYS10.9350.96645.0380.0360.0360.0000.0000.0000.000
187A550LEU00.0080.00439.8620.0000.0000.0000.0000.0000.000
188A551PRO00.0260.03242.0580.0020.0020.0000.0000.0000.000
189A552GLN00.0400.00942.264-0.005-0.0050.0000.0000.0000.000
190A553PRO00.0020.00336.9290.0000.0000.0000.0000.0000.000
191A554SER00.0890.05636.2040.0040.0040.0000.0000.0000.000
192A555SER0-0.059-0.03534.0340.0050.0050.0000.0000.0000.000
193A556THR0-0.111-0.06736.0050.0040.0040.0000.0000.0000.000
194A557THR0-0.016-0.01939.2450.0030.0030.0000.0000.0000.000
195A558THR0-0.059-0.02134.5770.0020.0020.0000.0000.0000.000
196A559PRO00.0280.01735.047-0.002-0.0020.0000.0000.0000.000
197A560ASP-1-0.795-0.87728.7040.0030.0030.0000.0000.0000.000
198A561LEU0-0.055-0.03430.5860.0050.0050.0000.0000.0000.000
199A562THR0-0.009-0.02324.0480.0070.0070.0000.0000.0000.000
200A563PRO0-0.040-0.01124.2320.0040.0040.0000.0000.0000.000
201A564ARG10.9690.98322.799-0.154-0.1540.0000.0000.0000.000
202A565ALA00.0380.01418.5350.0110.0110.0000.0000.0000.000
203A566ALA0-0.037-0.02518.5120.0230.0230.0000.0000.0000.000
204A567LEU0-0.007-0.00120.0990.0050.0050.0000.0000.0000.000
205A568THR0-0.012-0.01019.2170.0230.0230.0000.0000.0000.000
206A569PRO00.0270.01015.563-0.033-0.0330.0000.0000.0000.000
207A570GLU-1-0.775-0.84917.3070.1500.1500.0000.0000.0000.000
208A571THR0-0.0170.00517.7970.0490.0490.0000.0000.0000.000
209A572TYR0-0.020-0.04114.883-0.041-0.0410.0000.0000.0000.000
210A573PHE00.0280.01320.1050.0250.0250.0000.0000.0000.000
211A574GLY00.0160.03020.988-0.008-0.0080.0000.0000.0000.000
212A575VAL00.024-0.01419.8000.0380.0380.0000.0000.0000.000
213A576GLY0-0.0020.00317.3870.0320.0320.0000.0000.0000.000
214A577LYS10.8430.92514.834-0.179-0.1790.0000.0000.0000.000
215A578VAL0-0.0520.00015.5060.0570.0570.0000.0000.0000.000
216A579VAL00.0240.00712.5960.0610.0610.0000.0000.0000.000
217A580ASN0-0.049-0.04715.6540.0490.0490.0000.0000.0000.000
218A581TYR00.0450.03418.677-0.059-0.0590.0000.0000.0000.000
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