FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 6YYVZ

Calculation Name: 5X15-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X15

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FBS9

Base Structure: X-ray

Registration Date: 2023-09-21

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2075269.852327
FMO2-HF: Nuclear repulsion 1999933.083156
FMO2-HF: Total energy -75336.769171
FMO2-MP2: Total energy -75556.91602


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:34:ARG)


Summations of interaction energy for fragment #1(A:34: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.
-137.086-139.35712.933-5.996-4.665-0.001
Interaction energy analysis for fragmet #1(A:34:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.971 / q_NPA : 0.986
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].
3A36ASP-1-0.798-0.8973.844-27.409-25.702-0.016-0.895-0.7960.003
4A37GLY00.003-0.0046.3301.8031.8030.0000.0000.0000.000
5A38GLU-1-0.905-0.9517.451-15.481-15.4810.0000.0000.0000.000
6A39LEU0-0.0190.0009.6061.4081.4080.0000.0000.0000.000
7A40VAL00.0060.0047.3241.0591.0590.0000.0000.0000.000
8A41ARG10.8660.91810.49220.48020.4800.0000.0000.0000.000
9A42SER00.0340.01613.3910.7950.7950.0000.0000.0000.000
10A43LEU00.035-0.00312.5180.8380.8380.0000.0000.0000.000
11A44ASN0-0.066-0.03014.6371.3611.3610.0000.0000.0000.000
12A45ARG10.8840.94316.36813.00013.0000.0000.0000.0000.000
13A46VAL0-0.0070.01518.5700.5870.5870.0000.0000.0000.000
14A47SER0-0.012-0.02019.742-0.338-0.3380.0000.0000.0000.000
15A48SER00.007-0.00720.623-0.041-0.0410.0000.0000.0000.000
16A49ALA00.0440.02721.549-0.080-0.0800.0000.0000.0000.000
17A50THR0-0.029-0.03023.3290.3450.3450.0000.0000.0000.000
18A51ALA00.010-0.01018.468-0.059-0.0590.0000.0000.0000.000
19A52CYS0-0.086-0.04320.302-0.153-0.1530.0000.0000.0000.000
20A53ALA00.0190.00422.0660.1160.1160.0000.0000.0000.000
21A54LYS10.8620.92621.90611.28711.2870.0000.0000.0000.000
22A55LEU00.013-0.00216.908-0.148-0.1480.0000.0000.0000.000
23A56HIS0-0.009-0.00621.011-0.154-0.1540.0000.0000.0000.000
24A57GLU-1-0.931-0.95724.500-9.956-9.9560.0000.0000.0000.000
25A58LEU0-0.055-0.01619.179-0.022-0.0220.0000.0000.0000.000
26A59GLY0-0.042-0.01123.0010.0360.0360.0000.0000.0000.000
27A60ILE0-0.076-0.04418.187-0.265-0.2650.0000.0000.0000.000
28A61ARG10.9951.01022.37110.17710.1770.0000.0000.0000.000
29A62ARG10.7090.85422.46912.07312.0730.0000.0000.0000.000
30A63SER00.1130.05718.932-0.376-0.3760.0000.0000.0000.000
31A64TYR00.0560.04919.400-0.386-0.3860.0000.0000.0000.000
32A65LEU0-0.013-0.01017.6590.3430.3430.0000.0000.0000.000
33A66SER0-0.002-0.00321.7870.3570.3570.0000.0000.0000.000
34A67GLY00.0320.00625.518-0.017-0.0170.0000.0000.0000.000
35A68PRO0-0.074-0.03021.3810.2680.2680.0000.0000.0000.000
36A69THR0-0.038-0.01824.1700.1810.1810.0000.0000.0000.000
37A70ALA00.0380.01824.105-0.291-0.2910.0000.0000.0000.000
38A71LEU0-0.030-0.00424.5620.4930.4930.0000.0000.0000.000
39A72ASP-1-0.884-0.95825.056-10.661-10.6610.0000.0000.0000.000
40A73LEU0-0.020-0.01426.006-0.234-0.2340.0000.0000.0000.000
41A74GLY0-0.036-0.00526.3190.0000.0000.0000.0000.0000.000
42A75ASN0-0.051-0.02521.098-0.438-0.4380.0000.0000.0000.000
43A76LYS10.8380.92318.49212.67612.6760.0000.0000.0000.000
44A77VAL0-0.037-0.01213.904-0.282-0.2820.0000.0000.0000.000
45A78THR0-0.0150.02412.3630.3450.3450.0000.0000.0000.000
46A79GLY00.012-0.0098.831-0.224-0.2240.0000.0000.0000.000
47A80PRO0-0.0130.0034.3840.8710.968-0.001-0.006-0.0890.000
48A81ALA00.0200.0187.2231.1261.1260.0000.0000.0000.000
49A82ARG10.8010.8904.61435.63235.738-0.001-0.001-0.1040.000
50A83THR0-0.036-0.03410.0751.8721.8720.0000.0000.0000.000
51A84LEU00.0260.01312.812-0.115-0.1150.0000.0000.0000.000
52A85GLN0-0.005-0.00615.9040.7090.7090.0000.0000.0000.000
53A86PHE0-0.005-0.01418.7460.0430.0430.0000.0000.0000.000
54A87MET0-0.0030.01221.8170.1800.1800.0000.0000.0000.000
55A88PRO00.038-0.00224.8690.1450.1450.0000.0000.0000.000
56A89GLN0-0.083-0.04428.312-0.366-0.3660.0000.0000.0000.000
57A90ARG10.9010.95129.53910.16510.1650.0000.0000.0000.000
58A91GLU-1-0.901-0.94231.114-9.236-9.2360.0000.0000.0000.000
59A92ASP-1-0.900-0.93531.372-9.142-9.1420.0000.0000.0000.000
60A93VAL0-0.116-0.07027.6880.2160.2160.0000.0000.0000.000
61A105SER00.0450.00522.5980.0350.0350.0000.0000.0000.000
62A106THR0-0.019-0.02219.188-0.257-0.2570.0000.0000.0000.000
63A107ALA00.0290.03417.620-0.650-0.6500.0000.0000.0000.000
64A108LEU00.0460.01016.278-0.955-0.9550.0000.0000.0000.000
65A109TRP0-0.011-0.02616.661-0.329-0.3290.0000.0000.0000.000
66A110ALA0-0.0230.00013.225-0.343-0.3430.0000.0000.0000.000
67A111VAL00.0560.04111.958-1.471-1.4710.0000.0000.0000.000
68A112LEU00.0060.00911.899-1.349-1.3490.0000.0000.0000.000
69A113GLU-1-0.918-0.95112.492-18.225-18.2250.0000.0000.0000.000
70A114GLU-1-0.880-0.9157.247-36.423-36.4230.0000.0000.0000.000
71A115VAL0-0.055-0.0158.048-2.895-2.8950.0000.0000.0000.000
72A116GLN0-0.037-0.0311.964-10.282-14.46312.951-5.094-3.676-0.004
73A117PRO0-0.046-0.0317.0050.5030.5030.0000.0000.0000.000
74A118GLY00.0000.0017.664-1.026-1.0260.0000.0000.0000.000
75A119ASP-1-0.821-0.9076.012-34.320-34.3200.0000.0000.0000.000
76A120VAL0-0.012-0.0038.4632.3802.3800.0000.0000.0000.000
77A121LEU0-0.0360.00610.991-1.197-1.1970.0000.0000.0000.000
78A122VAL00.0230.01113.2971.3571.3570.0000.0000.0000.000
79A123VAL00.008-0.00515.462-0.508-0.5080.0000.0000.0000.000
80A124GLN00.0260.01818.312-0.075-0.0750.0000.0000.0000.000
81A125ALA00.030-0.00520.7020.0230.0230.0000.0000.0000.000
82A126TYR0-0.036-0.03623.5120.4980.4980.0000.0000.0000.000
83A127GLY00.0300.01326.0010.4060.4060.0000.0000.0000.000
84A128SER0-0.046-0.03827.8110.5090.5090.0000.0000.0000.000
85A129ALA0-0.052-0.04229.526-0.151-0.1510.0000.0000.0000.000
86A130PHE00.007-0.00531.4080.3160.3160.0000.0000.0000.000
87A131THR00.0230.02727.407-0.039-0.0390.0000.0000.0000.000
88A132GLY0-0.0040.00427.351-0.107-0.1070.0000.0000.0000.000
89A133CYS0-0.078-0.03621.849-0.159-0.1590.0000.0000.0000.000
90A134LEU00.0240.00518.505-0.388-0.3880.0000.0000.0000.000
91A135GLY00.0200.00623.1120.4920.4920.0000.0000.0000.000
92A136ASP-1-0.836-0.93724.319-11.240-11.2400.0000.0000.0000.000
93A137MET0-0.028-0.01725.077-0.135-0.1350.0000.0000.0000.000
94A138LEU0-0.024-0.01920.350-0.276-0.2760.0000.0000.0000.000
95A139VAL00.0840.05119.617-0.790-0.7900.0000.0000.0000.000
96A140ARG10.9350.98319.73911.00511.0050.0000.0000.0000.000
97A141TYR0-0.110-0.10215.427-0.302-0.3020.0000.0000.0000.000
98A142PHE00.0430.04412.784-0.827-0.8270.0000.0000.0000.000
99A143LYN00.0650.05315.114-0.696-0.6960.0000.0000.0000.000
100A144ARG10.8890.94416.81715.15715.1570.0000.0000.0000.000
101A145LYS10.8590.94712.03121.27021.2700.0000.0000.0000.000
102A146GLY00.0000.01312.176-1.418-1.4180.0000.0000.0000.000
103A147GLY0-0.003-0.01011.284-1.479-1.4790.0000.0000.0000.000
104A148ALA0-0.020-0.00611.4501.1561.1560.0000.0000.0000.000
105A149GLY00.0600.01813.2331.1831.1830.0000.0000.0000.000
106A150ILE0-0.043-0.01814.386-0.982-0.9820.0000.0000.0000.000
107A151VAL00.0220.01616.4280.8530.8530.0000.0000.0000.000
108A152VAL0-0.007-0.01118.257-0.573-0.5730.0000.0000.0000.000
109A153ASP-1-0.819-0.90121.042-11.738-11.7380.0000.0000.0000.000
110A154GLY00.0390.01823.2470.2490.2490.0000.0000.0000.000
111A155ARG10.9091.01725.6159.7669.7660.0000.0000.0000.000
112A156ILE00.0510.02322.321-0.414-0.4140.0000.0000.0000.000
113A157ARG10.8420.92126.15610.77210.7720.0000.0000.0000.000
114A158ASP-1-0.877-0.93427.612-10.146-10.1460.0000.0000.0000.000
115A159ALA00.0620.02228.933-0.182-0.1820.0000.0000.0000.000
116A160PRO0-0.019-0.02329.932-0.080-0.0800.0000.0000.0000.000
117A161ARG10.9360.97429.4389.3439.3430.0000.0000.0000.000
118A162VAL00.0240.01024.148-0.146-0.1460.0000.0000.0000.000
119A163ARG10.9170.95925.5789.4629.4620.0000.0000.0000.000
120A164GLU-1-0.967-0.96027.244-9.447-9.4470.0000.0000.0000.000
121A165LEU0-0.104-0.05923.312-0.165-0.1650.0000.0000.0000.000
122A166GLY00.020-0.01022.3250.0550.0550.0000.0000.0000.000
123A167VAL0-0.055-0.02617.315-0.450-0.4500.0000.0000.0000.000
124A168PRO00.0490.06118.0520.3860.3860.0000.0000.0000.000
125A169ILE0-0.027-0.04018.825-0.788-0.7880.0000.0000.0000.000
126A170TRP00.003-0.00718.3380.3350.3350.0000.0000.0000.000
127A171CYS0-0.043-0.01121.694-0.352-0.3520.0000.0000.0000.000
128A172THR00.0280.00324.4630.3840.3840.0000.0000.0000.000
129A173GLY00.012-0.02027.7790.4640.4640.0000.0000.0000.000
130A174THR0-0.065-0.03228.323-0.250-0.2500.0000.0000.0000.000
131A175THR0-0.008-0.00229.9480.2820.2820.0000.0000.0000.000
132A176PRO00.0280.00631.449-0.206-0.2060.0000.0000.0000.000
133A177HIS0-0.011-0.00931.8100.1360.1360.0000.0000.0000.000
134A178TYR0-0.010-0.00828.335-0.236-0.2360.0000.0000.0000.000
135A179ALA00.0110.00424.7910.1500.1500.0000.0000.0000.000
136A180SER00.0470.01526.6890.0370.0370.0000.0000.0000.000
137A181GLN0-0.0320.00228.3280.1100.1100.0000.0000.0000.000
138A182SER00.006-0.02531.1240.4330.4330.0000.0000.0000.000
139A183GLU-1-0.799-0.87231.095-10.040-10.0400.0000.0000.0000.000
140A184LEU0-0.0440.00026.142-0.252-0.2520.0000.0000.0000.000
141A185PHE00.012-0.00125.2630.1310.1310.0000.0000.0000.000
142A186PRO0-0.040-0.02220.493-0.188-0.1880.0000.0000.0000.000
143A187TRP00.0110.01219.8660.4850.4850.0000.0000.0000.000
144A188ALA0-0.022-0.00915.557-0.366-0.3660.0000.0000.0000.000
145A189TYR0-0.086-0.0768.5292.1062.1060.0000.0000.0000.000
146A190ASP-1-0.785-0.8948.492-33.282-33.2820.0000.0000.0000.000
147A191VAL0-0.048-0.00710.701-0.900-0.9000.0000.0000.0000.000
148A192PRO00.0090.00313.0220.0750.0750.0000.0000.0000.000
149A193VAL0-0.0010.01314.7710.6770.6770.0000.0000.0000.000
150A194ALA0-0.047-0.02817.1290.0340.0340.0000.0000.0000.000
151A195ALA00.0200.01918.5330.6260.6260.0000.0000.0000.000
152A196GLY00.0070.00320.260-0.240-0.2400.0000.0000.0000.000
153A197GLY0-0.020-0.01622.8380.1040.1040.0000.0000.0000.000
154A198VAL0-0.058-0.03217.4130.2970.2970.0000.0000.0000.000
155A199LEU00.0050.01015.768-0.074-0.0740.0000.0000.0000.000
156A200THR00.0140.00512.633-0.282-0.2820.0000.0000.0000.000
157A201LEU0-0.006-0.00511.0130.1200.1200.0000.0000.0000.000
158A202PRO0-0.004-0.0017.496-0.165-0.1650.0000.0000.0000.000
159A203GLY0-0.019-0.0025.038-2.308-2.3080.0000.0000.0000.000
160A204ASP-1-0.857-0.9325.875-23.429-23.4290.0000.0000.0000.000
161A205LEU0-0.015-0.0157.987-0.723-0.7230.0000.0000.0000.000
162A206VAL0-0.008-0.00210.5011.4321.4320.0000.0000.0000.000
163A207VAL00.0150.00113.647-0.209-0.2090.0000.0000.0000.000
164A208ALA0-0.039-0.02116.0620.7980.7980.0000.0000.0000.000
165A209ASP-1-0.709-0.86718.187-12.052-12.0520.0000.0000.0000.000
166A210ASP-1-0.807-0.91521.659-10.816-10.8160.0000.0000.0000.000
167A211ASP-1-0.933-0.95224.810-10.207-10.2070.0000.0000.0000.000
168A212GLY0-0.038-0.02223.4700.1760.1760.0000.0000.0000.000
169A213ALA0-0.011-0.00618.258-0.332-0.3320.0000.0000.0000.000
170A214VAL0-0.001-0.01318.0370.4320.4320.0000.0000.0000.000
171A215VAL0-0.035-0.01213.269-0.633-0.6330.0000.0000.0000.000
172A216VAL00.005-0.00613.4300.7440.7440.0000.0000.0000.000
173A217PRO00.0110.00611.503-1.372-1.3720.0000.0000.0000.000
174A218VAL00.010-0.0146.1200.6450.6450.0000.0000.0000.000
175A219SER0-0.098-0.0279.4850.5350.5350.0000.0000.0000.000
176A220LYS10.8290.88912.40715.34215.3420.0000.0000.0000.000
177A221ALA00.0430.03011.4700.7420.7420.0000.0000.0000.000
178A222GLN00.0230.00113.5090.1970.1970.0000.0000.0000.000
179A223GLU-1-0.819-0.88915.316-14.005-14.0050.0000.0000.0000.000
180A224ILE0-0.012-0.00817.1300.8970.8970.0000.0000.0000.000
181A225VAL0-0.027-0.00915.0220.6380.6380.0000.0000.0000.000
182A226ASP-1-0.832-0.92418.181-13.883-13.8830.0000.0000.0000.000
183A227SER00.0030.00920.9170.7260.7260.0000.0000.0000.000
184A228ALA0-0.011-0.01521.3240.5680.5680.0000.0000.0000.000
185A229PHE00.0250.01719.3250.4050.4050.0000.0000.0000.000
186A230ASP-1-0.911-0.94924.180-10.262-10.2620.0000.0000.0000.000
187A231HIS0-0.070-0.03326.1530.2860.2860.0000.0000.0000.000
188A232GLU-1-0.795-0.88923.962-11.054-11.0540.0000.0000.0000.000
189A233GLN0-0.0110.00627.3220.3510.3510.0000.0000.0000.000
190A234TRP00.001-0.00429.7600.5090.5090.0000.0000.0000.000
191A235GLU-1-0.867-0.92430.585-9.127-9.1270.0000.0000.0000.000
192A236GLU-1-0.827-0.89930.699-8.796-8.7960.0000.0000.0000.000
193A237PHE0-0.029-0.02032.6710.3400.3400.0000.0000.0000.000
194A238SER0-0.130-0.08235.4490.2540.2540.0000.0000.0000.000
195A239ARG10.8500.90129.0549.4659.4650.0000.0000.0000.000
196A240MET00.0020.01136.8520.1390.1390.0000.0000.0000.000
197A241ARG10.8280.93038.9207.3297.3290.0000.0000.0000.000
198A242ILE0-0.0160.00540.0800.1530.1530.0000.0000.0000.000