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: 6N73Z

Calculation Name: 1V6Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V6Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SKI6

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2410285.371122
FMO2-HF: Nuclear repulsion 2326169.110827
FMO2-HF: Total energy -84116.260295
FMO2-MP2: Total energy -84367.828216


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
-92.78-99.82238.231-14.734-16.453-0.172
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.885
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].
3A4HIS00.0410.0163.896-2.914-1.643-0.001-0.529-0.7410.001
4A5ARG10.8160.8755.93122.50022.5000.0000.0000.0000.000
5A6ALA0-0.030-0.0119.5030.6340.6340.0000.0000.0000.000
6A7PHE00.0250.01611.4851.0521.0520.0000.0000.0000.000
7A8SER0-0.021-0.03613.825-0.580-0.5800.0000.0000.0000.000
8A9PRO00.0190.00015.9200.3790.3790.0000.0000.0000.000
9A10GLY00.0490.03019.7530.0890.0890.0000.0000.0000.000
10A11LEU0-0.077-0.01915.7640.1400.1400.0000.0000.0000.000
11A12THR0-0.004-0.00617.218-0.476-0.4760.0000.0000.0000.000
12A13GLY00.0580.03314.8670.6160.6160.0000.0000.0000.000
13A14VAL0-0.068-0.03213.933-0.800-0.8000.0000.0000.0000.000
14A15LEU00.0140.0248.9860.1350.1350.0000.0000.0000.000
15A16PRO00.0350.01613.4491.0231.0230.0000.0000.0000.000
16A17LEU00.0450.01813.483-1.754-1.7540.0000.0000.0000.000
17A18ARG10.8410.90413.48517.51117.5110.0000.0000.0000.000
18A19GLU-1-0.754-0.86711.119-22.034-22.0340.0000.0000.0000.000
19A20THR0-0.030-0.0019.260-3.344-3.3440.0000.0000.0000.000
20A21ARG10.9540.9918.66116.97716.9770.0000.0000.0000.000
21A22HIS0-0.0020.0007.650-0.663-0.6630.0000.0000.0000.000
22A23LEU00.0140.0073.556-4.547-4.0010.058-0.173-0.4310.001
23A24VAL00.020-0.0013.869-11.314-11.0740.000-0.063-0.1770.000
24A25GLU-1-0.943-0.9806.231-24.509-24.5090.0000.0000.0000.000
25A26VAL0-0.043-0.0197.236-0.441-0.4410.0000.0000.0000.000
26A27LEU0-0.026-0.0082.822-2.405-0.5200.191-0.799-1.2770.000
27A28ARG10.9020.9651.791-3.496-5.01410.651-4.910-4.223-0.068
28A29ALA00.0210.0081.857-4.335-4.0865.483-3.310-2.4220.001
29A30ARG10.8780.9392.65760.70957.5910.2333.201-0.316-0.002
30A31VAL00.0290.0135.366-3.174-3.153-0.0010.001-0.0200.000
31A32GLY00.0140.0147.7620.5580.5580.0000.0000.0000.000
32A33ASP-1-0.797-0.8901.805-116.962-123.91321.619-8.080-6.587-0.105
33A34ARG10.8210.8914.14635.12235.285-0.001-0.023-0.1390.000
34A35PHE0-0.043-0.0194.124-8.469-8.299-0.001-0.049-0.1200.000
35A36THR00.0090.0136.2104.6104.6100.0000.0000.0000.000
36A37VAL0-0.029-0.0029.783-1.405-1.4050.0000.0000.0000.000
37A38PHE00.0550.00212.5371.2481.2480.0000.0000.0000.000
38A39ASP-1-0.835-0.91616.020-15.593-15.5930.0000.0000.0000.000
39A40GLY00.0190.01919.3340.5240.5240.0000.0000.0000.000
40A41GLU-1-0.904-0.92421.720-11.531-11.5310.0000.0000.0000.000
41A42ARG10.7390.81919.72115.34815.3480.0000.0000.0000.000
42A43GLU-1-0.784-0.87314.748-20.056-20.0560.0000.0000.0000.000
43A44ALA00.0150.01514.6020.9170.9170.0000.0000.0000.000
44A45LEU0-0.0290.0109.010-1.916-1.9160.0000.0000.0000.000
45A46ALA00.0260.0009.7552.0842.0840.0000.0000.0000.000
46A47GLU-1-0.750-0.8537.708-28.378-28.3780.0000.0000.0000.000
47A48VAL0-0.009-0.0025.0523.4993.4990.0000.0000.0000.000
48A49VAL0-0.034-0.0197.9210.5910.5910.0000.0000.0000.000
49A50ASP-1-0.812-0.92110.822-20.030-20.0300.0000.0000.0000.000
50A51LEU0-0.008-0.0056.626-2.110-2.1100.0000.0000.0000.000
51A52GLY0-0.0090.02210.058-0.150-0.1500.0000.0000.0000.000
52A53PRO0-0.037-0.01012.9540.1640.1640.0000.0000.0000.000
53A54PRO0-0.024-0.03713.5461.3701.3700.0000.0000.0000.000
54A55LEU0-0.002-0.0016.2980.1730.1730.0000.0000.0000.000
55A56ARG10.9360.96410.82319.64419.6440.0000.0000.0000.000
56A57TYR0-0.024-0.0129.736-2.609-2.6090.0000.0000.0000.000
57A58ARG10.8610.92211.42323.61723.6170.0000.0000.0000.000
58A59VAL00.0380.01012.269-1.903-1.9030.0000.0000.0000.000
59A60LEU0-0.097-0.04110.3720.6390.6390.0000.0000.0000.000
60A61GLU-1-0.814-0.89014.553-18.193-18.1930.0000.0000.0000.000
61A62GLU-1-0.787-0.86415.857-16.578-16.5780.0000.0000.0000.000
62A63ARG10.8100.86811.91820.63820.6380.0000.0000.0000.000
63A64ARG10.9450.96618.53312.64912.6490.0000.0000.0000.000
64A65PRO00.0440.02718.504-0.511-0.5110.0000.0000.0000.000
65A66GLU-1-0.954-0.96315.533-15.512-15.5120.0000.0000.0000.000
66A67ARG10.7810.85519.57012.71612.7160.0000.0000.0000.000
67A68GLU-1-0.774-0.89022.376-10.287-10.2870.0000.0000.0000.000
68A69VAL0-0.0060.00022.223-0.416-0.4160.0000.0000.0000.000
69A70GLY00.0180.01721.746-0.283-0.2830.0000.0000.0000.000
70A71VAL0-0.040-0.01022.5670.1250.1250.0000.0000.0000.000
71A72GLU-1-0.806-0.86225.939-8.778-8.7780.0000.0000.0000.000
72A73VAL00.0100.00528.2680.0140.0140.0000.0000.0000.000
73A74VAL0-0.007-0.00431.0930.1180.1180.0000.0000.0000.000
74A75LEU00.0150.00634.9230.0830.0830.0000.0000.0000.000
75A76TYR00.0300.00437.1210.2310.2310.0000.0000.0000.000
76A77VAL00.0050.00140.5090.0230.0230.0000.0000.0000.000
77A78ALA00.0230.01542.6510.1130.1130.0000.0000.0000.000
78A79LEU0-0.048-0.02346.170-0.086-0.0860.0000.0000.0000.000
79A80LEU00.0230.01744.8540.1030.1030.0000.0000.0000.000
80A81LYS10.9470.96749.0585.5625.5620.0000.0000.0000.000
81A82GLY00.0130.00450.419-0.078-0.0780.0000.0000.0000.000
82A83ASP-1-0.869-0.94347.861-6.299-6.2990.0000.0000.0000.000
83A84LYS10.8070.90046.0476.2246.2240.0000.0000.0000.000
84A85LEU0-0.010-0.00744.053-0.143-0.1430.0000.0000.0000.000
85A86ALA00.0280.00942.693-0.149-0.1490.0000.0000.0000.000
86A87GLU-1-0.819-0.88641.364-7.219-7.2190.0000.0000.0000.000
87A88VAL0-0.010-0.00239.554-0.208-0.2080.0000.0000.0000.000
88A89VAL00.0120.00438.159-0.188-0.1880.0000.0000.0000.000
89A90ARG10.8160.91536.9047.7817.7810.0000.0000.0000.000
90A91ALA00.0590.02935.263-0.248-0.2480.0000.0000.0000.000
91A92ALA0-0.007-0.01933.720-0.263-0.2630.0000.0000.0000.000
92A93THR0-0.059-0.03432.580-0.218-0.2180.0000.0000.0000.000
93A94GLU-1-0.903-0.95530.680-9.386-9.3860.0000.0000.0000.000
94A95LEU0-0.056-0.01529.184-0.369-0.3690.0000.0000.0000.000
95A96GLY00.0520.03727.750-0.087-0.0870.0000.0000.0000.000
96A97ALA00.0100.00428.664-0.029-0.0290.0000.0000.0000.000
97A98THR0-0.010-0.03729.004-0.056-0.0560.0000.0000.0000.000
98A99ARG10.7670.86132.0248.3628.3620.0000.0000.0000.000
99A100ILE00.001-0.00335.605-0.012-0.0120.0000.0000.0000.000
100A101GLN0-0.029-0.02938.5710.0780.0780.0000.0000.0000.000
101A102PRO00.0010.00041.6980.0430.0430.0000.0000.0000.000
102A103LEU00.0020.00843.8180.0750.0750.0000.0000.0000.000
103A104VAL0-0.0060.00447.0380.0380.0380.0000.0000.0000.000
104A105THR00.003-0.00548.164-0.007-0.0070.0000.0000.0000.000
105A106ARG10.8810.91651.3455.4645.4640.0000.0000.0000.000
106A107HIS00.0240.00452.2050.1440.1440.0000.0000.0000.000
107A108SER0-0.040-0.01250.712-0.012-0.0120.0000.0000.0000.000
108A109VAL00.0240.02252.3220.1040.1040.0000.0000.0000.000
109A110PRO0-0.029-0.00651.7990.1110.1110.0000.0000.0000.000
110A111LYS10.8300.89353.4275.4815.4810.0000.0000.0000.000
111A112GLU-1-0.906-0.94653.119-5.403-5.4030.0000.0000.0000.000
112A113MET0-0.036-0.02246.293-0.095-0.0950.0000.0000.0000.000
113A114GLY00.0570.04551.9240.0080.0080.0000.0000.0000.000
114A115GLU-1-0.777-0.90049.913-6.349-6.3490.0000.0000.0000.000
115A116GLY0-0.0030.00250.240-0.115-0.1150.0000.0000.0000.000
116A117LYS10.9040.94848.3646.1156.1150.0000.0000.0000.000
117A118LEU00.0330.01545.233-0.149-0.1490.0000.0000.0000.000
118A119ARG10.8760.92745.4736.0466.0460.0000.0000.0000.000
119A120ARG10.8690.94443.0366.9636.9630.0000.0000.0000.000
120A121LEU00.021-0.00243.062-0.145-0.1450.0000.0000.0000.000
121A122ARG10.9180.95541.1096.6726.6720.0000.0000.0000.000
122A123ALA0-0.0020.00240.457-0.186-0.1860.0000.0000.0000.000
123A124VAL0-0.060-0.02839.502-0.146-0.1460.0000.0000.0000.000
124A125ALA00.0610.03537.051-0.190-0.1900.0000.0000.0000.000
125A126LEU00.0110.00335.874-0.258-0.2580.0000.0000.0000.000
126A127GLU-1-0.827-0.90236.114-7.906-7.9060.0000.0000.0000.000
127A128ALA00.0520.02035.229-0.182-0.1820.0000.0000.0000.000
128A129ALA00.0400.03632.015-0.282-0.2820.0000.0000.0000.000
129A130LYS10.9080.95631.2278.1708.1700.0000.0000.0000.000
130A131GLN0-0.050-0.03231.997-0.236-0.2360.0000.0000.0000.000
131A132SER0-0.016-0.01129.238-0.198-0.1980.0000.0000.0000.000
132A133GLY00.0070.00827.706-0.410-0.4100.0000.0000.0000.000
133A134ARG10.7530.86526.8599.7289.7280.0000.0000.0000.000
134A135VAL0-0.051-0.02626.6750.1720.1720.0000.0000.0000.000
135A136VAL0-0.035-0.00627.7530.3660.3660.0000.0000.0000.000
136A137VAL0-0.013-0.00730.3360.0280.0280.0000.0000.0000.000
137A138PRO0-0.021-0.00732.6980.1330.1330.0000.0000.0000.000
138A139GLU-1-0.825-0.88734.711-7.772-7.7720.0000.0000.0000.000
139A140VAL0-0.027-0.00137.5290.0740.0740.0000.0000.0000.000
140A141LEU00.0250.01740.0510.1520.1520.0000.0000.0000.000
141A142PRO00.014-0.01242.9880.0460.0460.0000.0000.0000.000
142A143PRO0-0.0140.00446.078-0.079-0.0790.0000.0000.0000.000
143A144ILE00.0140.01944.7310.1100.1100.0000.0000.0000.000
144A145PRO0-0.009-0.01848.663-0.024-0.0240.0000.0000.0000.000
145A146LEU00.0620.04046.112-0.058-0.0580.0000.0000.0000.000
146A147LYS10.9450.96647.3435.5425.5420.0000.0000.0000.000
147A148ALA0-0.047-0.02647.6840.0210.0210.0000.0000.0000.000
148A149VAL00.0100.02741.776-0.098-0.0980.0000.0000.0000.000
149A150PRO00.0000.01440.1690.1320.1320.0000.0000.0000.000
150A151GLN00.003-0.02140.580-0.131-0.1310.0000.0000.0000.000
151A152VAL0-0.044-0.01935.985-0.100-0.1000.0000.0000.0000.000
152A153ALA0-0.003-0.00332.6710.0330.0330.0000.0000.0000.000
153A154GLN00.019-0.01328.347-0.073-0.0730.0000.0000.0000.000
154A155GLY00.0150.01833.512-0.005-0.0050.0000.0000.0000.000
155A156LEU0-0.0220.00631.7610.0390.0390.0000.0000.0000.000
156A157VAL00.0190.00236.2450.0500.0500.0000.0000.0000.000
157A158ALA00.0020.01439.426-0.008-0.0080.0000.0000.0000.000
158A159HIS00.0380.00840.4190.1490.1490.0000.0000.0000.000
159A160VAL00.000-0.00442.861-0.094-0.0940.0000.0000.0000.000
160A161GLY0-0.0030.00345.3900.0230.0230.0000.0000.0000.000
161A162ALA0-0.0180.01440.2390.0010.0010.0000.0000.0000.000
162A163THR0-0.032-0.03140.365-0.065-0.0650.0000.0000.0000.000
163A164ALA00.0330.03035.709-0.144-0.1440.0000.0000.0000.000
164A165ARG10.8730.90732.9968.3978.3970.0000.0000.0000.000
165A166VAL00.1070.04429.647-0.041-0.0410.0000.0000.0000.000
166A167ARG10.9420.96727.1649.6349.6340.0000.0000.0000.000
167A168GLU-1-0.885-0.93028.547-8.867-8.8670.0000.0000.0000.000
168A169VAL0-0.043-0.01630.7400.1720.1720.0000.0000.0000.000
169A170LEU0-0.041-0.00926.4490.0950.0950.0000.0000.0000.000
170A171ASP-1-0.794-0.87325.960-10.314-10.3140.0000.0000.0000.000
171A172PRO0-0.011-0.00721.8390.1600.1600.0000.0000.0000.000
172A173GLU-1-0.915-0.95920.980-12.236-12.2360.0000.0000.0000.000
173A174LYS10.8280.91023.6039.4629.4620.0000.0000.0000.000
174A175PRO00.0050.00327.159-0.121-0.1210.0000.0000.0000.000
175A176LEU0-0.004-0.00129.1640.1490.1490.0000.0000.0000.000
176A177ALA0-0.0070.01231.2380.0890.0890.0000.0000.0000.000
177A178LEU00.012-0.00632.2540.0020.0020.0000.0000.0000.000
178A179ALA00.0110.01336.3260.1100.1100.0000.0000.0000.000
179A180VAL0-0.023-0.02239.338-0.019-0.0190.0000.0000.0000.000
180A181GLY00.0320.02442.0350.0920.0920.0000.0000.0000.000
181A182PRO0-0.018-0.02445.707-0.092-0.0920.0000.0000.0000.000
182A183GLU-1-0.813-0.91448.316-6.197-6.1970.0000.0000.0000.000
183A184GLY0-0.028-0.00450.0160.0200.0200.0000.0000.0000.000
184A185GLY0-0.0020.00548.0090.0430.0430.0000.0000.0000.000
185A186PHE0-0.003-0.01843.3440.0850.0850.0000.0000.0000.000
186A187ALA0-0.032-0.01148.9300.0250.0250.0000.0000.0000.000
187A188GLU-1-0.905-0.95550.340-5.673-5.6730.0000.0000.0000.000
188A189GLU-1-0.757-0.88150.442-5.646-5.6460.0000.0000.0000.000
189A190GLU-1-0.845-0.92348.933-5.987-5.9870.0000.0000.0000.000
190A191VAL0-0.008-0.00144.922-0.131-0.1310.0000.0000.0000.000
191A192ALA00.0800.04845.835-0.108-0.1080.0000.0000.0000.000
192A193LEU0-0.083-0.03346.560-0.036-0.0360.0000.0000.0000.000
193A194LEU00.000-0.00942.325-0.082-0.0820.0000.0000.0000.000
194A195GLU-1-0.853-0.93242.397-6.687-6.6870.0000.0000.0000.000
195A196ALA0-0.043-0.01542.749-0.094-0.0940.0000.0000.0000.000
196A197ARG10.7610.88641.7386.4366.4360.0000.0000.0000.000
197A198GLY00.0690.03438.817-0.131-0.1310.0000.0000.0000.000
198A199PHE0-0.087-0.05137.689-0.229-0.2290.0000.0000.0000.000
199A200THR00.0270.01236.2710.1750.1750.0000.0000.0000.000
200A201PRO0-0.005-0.00838.017-0.139-0.1390.0000.0000.0000.000
201A202VAL0-0.018-0.00334.664-0.124-0.1240.0000.0000.0000.000
202A203SER0-0.013-0.01237.8680.1370.1370.0000.0000.0000.000
203A204LEU00.008-0.00436.571-0.210-0.2100.0000.0000.0000.000
204A205GLY0-0.029-0.00438.959-0.052-0.0520.0000.0000.0000.000
205A206ARG10.9370.95940.8977.2057.2050.0000.0000.0000.000
206A207ARG10.9440.96439.7317.5237.5230.0000.0000.0000.000
207A208ILE00.0630.04644.615-0.082-0.0820.0000.0000.0000.000
208A209LEU0-0.014-0.01040.594-0.098-0.0980.0000.0000.0000.000
209A210ARG10.7890.86543.4067.1047.1040.0000.0000.0000.000
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