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: R56K8

Calculation Name: 3H25-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H25

Chain ID: A

ChEMBL ID:

UniProt ID: Q52349

Base Structure: X-ray

Registration Date: 2023-06-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2035902.40542
FMO2-HF: Nuclear repulsion 1961893.215702
FMO2-HF: Total energy -74009.189718
FMO2-MP2: Total energy -74224.312931


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
-180.28-180.27432.587-17.679-14.9130.158
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.810 / q_NPA : -0.890
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].
3A6THR00.0010.0082.262-15.018-10.7782.618-2.986-3.8720.036
4A7LEU00.0160.0152.858-15.645-12.8410.276-1.282-1.7980.010
5A8GLN00.021-0.0201.882-17.570-20.23610.515-4.545-3.3030.004
6A9ALA0-0.0240.0075.730-5.048-5.0480.0000.0000.0000.000
7A10ILE00.0550.0256.867-3.709-3.7090.0000.0000.0000.000
8A11GLY00.0180.0098.421-3.006-3.0060.0000.0000.0000.000
9A12ARG10.8050.8939.798-25.829-25.8290.0000.0000.0000.000
10A13GLN00.0410.01411.781-0.597-0.5970.0000.0000.0000.000
11A14LEU0-0.001-0.00111.955-1.484-1.4840.0000.0000.0000.000
12A15LYS10.9480.97414.072-18.394-18.3940.0000.0000.0000.000
13A16ALA0-0.046-0.02315.819-1.025-1.0250.0000.0000.0000.000
14A17MET0-0.035-0.01317.653-0.423-0.4230.0000.0000.0000.000
15A18GLY0-0.007-0.00218.788-0.764-0.7640.0000.0000.0000.000
16A19CYS0-0.055-0.00520.535-0.522-0.5220.0000.0000.0000.000
17A20GLU-1-0.919-0.95019.99212.99812.9980.0000.0000.0000.000
18A21ARG10.7320.82320.234-12.964-12.9640.0000.0000.0000.000
19A22PHE00.009-0.00817.932-0.113-0.1130.0000.0000.0000.000
20A23ASP-1-0.775-0.88720.36813.92813.9280.0000.0000.0000.000
21A24ILE0-0.037-0.02414.6450.6320.6320.0000.0000.0000.000
22A25GLY00.0470.02517.852-0.524-0.5240.0000.0000.0000.000
23A26VAL0-0.069-0.05115.5211.4261.4260.0000.0000.0000.000
24A27ARG10.9250.95117.958-14.467-14.4670.0000.0000.0000.000
25A28ASP-1-0.721-0.80519.42414.59214.5920.0000.0000.0000.000
26A29ALA00.0300.00220.022-0.602-0.6020.0000.0000.0000.000
27A30THR0-0.059-0.04521.754-0.539-0.5390.0000.0000.0000.000
28A31THR0-0.035-0.05825.088-0.491-0.4910.0000.0000.0000.000
29A32GLY0-0.0230.00724.709-0.388-0.3880.0000.0000.0000.000
30A33GLN00.0400.01725.2770.0530.0530.0000.0000.0000.000
31A34MET0-0.058-0.01221.0010.9430.9430.0000.0000.0000.000
32A35MET0-0.0290.00520.478-0.240-0.2400.0000.0000.0000.000
33A36ASN00.0390.02420.9700.7050.7050.0000.0000.0000.000
34A37ARG10.8830.94218.100-17.066-17.0660.0000.0000.0000.000
35A38GLU-1-0.811-0.88019.77013.37813.3780.0000.0000.0000.000
36A39TRP0-0.041-0.03715.3160.6020.6020.0000.0000.0000.000
37A40SER00.039-0.00718.7390.3040.3040.0000.0000.0000.000
38A41ALA00.0500.01615.4051.0331.0330.0000.0000.0000.000
39A42ALA00.0020.00213.8991.5961.5960.0000.0000.0000.000
40A43GLU-1-0.744-0.82913.91716.32616.3260.0000.0000.0000.000
41A44VAL00.0030.00812.3311.1521.1520.0000.0000.0000.000
42A45LEU0-0.025-0.0088.6642.2592.2590.0000.0000.0000.000
43A46GLN0-0.0030.0149.5612.6632.6630.0000.0000.0000.000
44A47ASN0-0.040-0.03211.6520.6150.6150.0000.0000.0000.000
45A48THR0-0.002-0.0115.9591.0001.0000.0000.0000.0000.000
46A49PRO0-0.004-0.0088.0592.9292.9290.0000.0000.0000.000
47A50TRP00.0390.0229.024-0.406-0.4060.0000.0000.0000.000
48A51LEU00.0300.02010.007-0.752-0.7520.0000.0000.0000.000
49A52LYS10.8790.9211.754-134.012-138.38419.178-8.866-5.9400.108
50A53ARG10.9000.9588.715-22.165-22.1650.0000.0000.0000.000
51A54MET0-0.009-0.00411.813-1.984-1.9840.0000.0000.0000.000
52A55ASN00.0110.01210.3631.2711.2710.0000.0000.0000.000
53A56ALA00.0020.00010.824-1.248-1.2480.0000.0000.0000.000
54A57GLN0-0.036-0.03812.626-1.499-1.4990.0000.0000.0000.000
55A58GLY00.0210.03015.335-1.279-1.2790.0000.0000.0000.000
56A59ASN0-0.062-0.03715.847-1.763-1.7630.0000.0000.0000.000
57A60ASP-1-0.728-0.85014.94719.63519.6350.0000.0000.0000.000
58A61VAL0-0.022-0.01911.894-0.373-0.3730.0000.0000.0000.000
59A62TYR0-0.008-0.01114.7970.1870.1870.0000.0000.0000.000
60A63ILE0-0.025-0.01314.9530.5880.5880.0000.0000.0000.000
61A64ARG10.8550.92517.686-13.553-13.5530.0000.0000.0000.000
62A65PRO00.0200.00620.8520.3950.3950.0000.0000.0000.000
63A66ALA00.0000.01322.828-0.318-0.3180.0000.0000.0000.000
64A67GLU-1-0.816-0.89524.49510.52610.5260.0000.0000.0000.000
65A68GLN00.000-0.01728.230-0.250-0.2500.0000.0000.0000.000
66A69GLU-1-0.811-0.88224.16012.61512.6150.0000.0000.0000.000
67A70ARG10.8070.88427.191-10.391-10.3910.0000.0000.0000.000
68A71HIS00.0890.04925.530-0.117-0.1170.0000.0000.0000.000
69A72GLY0-0.008-0.00927.491-0.408-0.4080.0000.0000.0000.000
70A73LEU0-0.065-0.03121.539-0.088-0.0880.0000.0000.0000.000
71A74VAL00.0220.00326.158-0.118-0.1180.0000.0000.0000.000
72A75LEU0-0.0370.00022.1770.3360.3360.0000.0000.0000.000
73A76VAL00.0340.01324.823-0.504-0.5040.0000.0000.0000.000
74A77ASP-1-0.808-0.90123.46714.31714.3170.0000.0000.0000.000
75A78ASP-1-0.927-0.94724.55811.31111.3110.0000.0000.0000.000
76A79LEU00.0470.03224.905-0.349-0.3490.0000.0000.0000.000
77A80SER0-0.023-0.05224.8360.6310.6310.0000.0000.0000.000
78A81GLU-1-0.829-0.92023.93813.67913.6790.0000.0000.0000.000
79A82PHE0-0.0230.00525.825-0.028-0.0280.0000.0000.0000.000
80A83ASP-1-0.710-0.81828.56710.57810.5780.0000.0000.0000.000
81A84LEU0-0.064-0.03122.8030.0760.0760.0000.0000.0000.000
82A85ASP-1-0.892-0.94527.10811.74511.7450.0000.0000.0000.000
83A86ASP-1-0.840-0.91629.3809.2169.2160.0000.0000.0000.000
84A87MET0-0.042-0.01627.156-0.028-0.0280.0000.0000.0000.000
85A88LYS10.7040.83924.114-12.695-12.6950.0000.0000.0000.000
86A89ALA0-0.019-0.00129.932-0.188-0.1880.0000.0000.0000.000
87A90GLU-1-0.864-0.88933.5098.4798.4790.0000.0000.0000.000
88A91GLY0-0.034-0.01132.243-0.144-0.1440.0000.0000.0000.000
89A92ARG10.7790.85930.508-8.959-8.9590.0000.0000.0000.000
90A93GLU-1-0.720-0.83327.01710.84910.8490.0000.0000.0000.000
91A94PRO0-0.015-0.00223.0850.1260.1260.0000.0000.0000.000
92A95ALA0-0.0310.00622.1570.1440.1440.0000.0000.0000.000
93A96LEU0-0.055-0.04816.8510.9270.9270.0000.0000.0000.000
94A97VAL00.0340.03118.603-0.556-0.5560.0000.0000.0000.000
95A98VAL0-0.048-0.03514.7271.3801.3800.0000.0000.0000.000
96A99GLU-1-0.828-0.90815.82617.06817.0680.0000.0000.0000.000
97A100THR00.009-0.01515.6321.4031.4030.0000.0000.0000.000
98A101SER0-0.012-0.03416.9830.9370.9370.0000.0000.0000.000
99A102PRO0-0.029-0.01117.800-0.197-0.1970.0000.0000.0000.000
100A103LYS10.9170.96019.433-14.159-14.1590.0000.0000.0000.000
101A104ASN0-0.0040.01420.771-1.095-1.0950.0000.0000.0000.000
102A105TYR0-0.079-0.07019.3571.5211.5210.0000.0000.0000.000
103A106GLN00.0410.04219.6690.1900.1900.0000.0000.0000.000
104A107ALA0-0.006-0.01820.7890.7700.7700.0000.0000.0000.000
105A108TRP00.0370.01819.185-0.435-0.4350.0000.0000.0000.000
106A109VAL00.0640.02123.0960.1960.1960.0000.0000.0000.000
107A110LYS10.8290.91024.531-11.844-11.8440.0000.0000.0000.000
108A111VAL00.0230.02426.749-0.225-0.2250.0000.0000.0000.000
109A112ALA00.018-0.00329.784-0.361-0.3610.0000.0000.0000.000
110A113ASP-1-0.863-0.92427.62911.31511.3150.0000.0000.0000.000
111A114ALA00.0290.01128.3820.2940.2940.0000.0000.0000.000
112A115ALA00.0130.01131.047-0.322-0.3220.0000.0000.0000.000
113A116GLY00.0160.01432.5560.1760.1760.0000.0000.0000.000
114A117GLY00.0460.01432.6990.1010.1010.0000.0000.0000.000
115A118GLU-1-0.887-0.92733.7408.0308.0300.0000.0000.0000.000
116A119LEU00.0140.00835.8040.0170.0170.0000.0000.0000.000
117A120ARG10.8610.92429.139-10.746-10.7460.0000.0000.0000.000
118A121GLY00.0490.03432.0400.2240.2240.0000.0000.0000.000
119A122GLN00.0060.00033.6840.0670.0670.0000.0000.0000.000
120A123ILE00.0100.00431.886-0.055-0.0550.0000.0000.0000.000
121A124ALA00.0150.01230.4730.0750.0750.0000.0000.0000.000
122A125ARG10.9000.94631.768-8.664-8.6640.0000.0000.0000.000
123A126THR0-0.050-0.02434.867-0.183-0.1830.0000.0000.0000.000
124A127LEU0-0.017-0.02529.5180.0140.0140.0000.0000.0000.000
125A128ALA0-0.0040.00031.6040.1320.1320.0000.0000.0000.000
126A129SER0-0.023-0.01532.503-0.116-0.1160.0000.0000.0000.000
127A130GLU-1-0.844-0.89934.3328.8678.8670.0000.0000.0000.000
128A131TYR0-0.072-0.07931.3790.0720.0720.0000.0000.0000.000
129A132ASP-1-0.937-0.95532.0689.0869.0860.0000.0000.0000.000
130A133ALA00.0120.01928.9520.1820.1820.0000.0000.0000.000
131A134ASP-1-0.865-0.93628.50010.36810.3680.0000.0000.0000.000
132A135PRO0-0.032-0.03330.3340.1050.1050.0000.0000.0000.000
133A136ALA0-0.077-0.03130.045-0.121-0.1210.0000.0000.0000.000
134A137SER0-0.028-0.04625.622-0.021-0.0210.0000.0000.0000.000
135A138ALA0-0.0150.01228.0920.2440.2440.0000.0000.0000.000
136A139ASP-1-0.849-0.94129.34710.49410.4940.0000.0000.0000.000
137A140SER0-0.061-0.06028.9980.3360.3360.0000.0000.0000.000
138A141ARG10.6950.84226.062-11.338-11.3380.0000.0000.0000.000
139A142HIS00.0620.06724.6030.2180.2180.0000.0000.0000.000
140A143TYR0-0.087-0.06919.9750.6610.6610.0000.0000.0000.000
141A144GLY00.0640.04519.998-0.356-0.3560.0000.0000.0000.000
142A145ARG10.7870.86515.653-17.661-17.6610.0000.0000.0000.000
143A146LEU0-0.0250.00311.083-0.125-0.1250.0000.0000.0000.000
144A147ALA00.015-0.00311.0671.0961.0960.0000.0000.0000.000
145A148GLY0-0.035-0.0237.1071.8681.8680.0000.0000.0000.000
146A149PHE0-0.003-0.0116.5237.8287.8280.0000.0000.0000.000
147A150THR0-0.019-0.0079.241-2.132-2.1320.0000.0000.0000.000
148A151ASN00.007-0.01311.746-1.171-1.1710.0000.0000.0000.000
149A152ARG10.8220.89813.929-21.373-21.3730.0000.0000.0000.000
150A153LYS10.8300.94117.819-15.038-15.0380.0000.0000.0000.000
151A154ASP-1-0.778-0.82419.03314.42714.4270.0000.0000.0000.000
152A155LYS10.8880.92619.827-11.258-11.2580.0000.0000.0000.000
153A163GLN0-0.079-0.05614.529-0.882-0.8820.0000.0000.0000.000
154A164PRO00.0210.02414.0121.5751.5750.0000.0000.0000.000
155A165TRP0-0.016-0.0127.0802.2892.2890.0000.0000.0000.000
156A166VAL00.0340.03411.513-1.364-1.3640.0000.0000.0000.000
157A167LEU0-0.046-0.01610.6293.6743.6740.0000.0000.0000.000
158A168LEU0-0.013-0.00712.296-1.283-1.2830.0000.0000.0000.000
159A169ARG10.8850.94113.778-14.074-14.0740.0000.0000.0000.000
160A170GLU-1-0.820-0.90416.73113.64313.6430.0000.0000.0000.000
161A171SER0-0.027-0.02714.9170.7230.7230.0000.0000.0000.000
162A172LYS10.9060.94517.029-13.106-13.1060.0000.0000.0000.000
163A173GLY00.0160.01319.855-0.296-0.2960.0000.0000.0000.000
164A174LYS10.6990.85921.224-11.218-11.2180.0000.0000.0000.000
165A175THR00.0050.00324.6860.2670.2670.0000.0000.0000.000
166A176ALA00.0220.02127.822-0.174-0.1740.0000.0000.0000.000
167A177THR0-0.034-0.06229.469-0.266-0.2660.0000.0000.0000.000
168A178ALA0-0.0020.00532.635-0.316-0.3160.0000.0000.0000.000
169A179GLY0-0.017-0.00432.313-0.113-0.1130.0000.0000.0000.000
170A180PRO00.020-0.00733.177-0.137-0.1370.0000.0000.0000.000
171A181ALA00.0320.02236.059-0.175-0.1750.0000.0000.0000.000
172A182LEU00.0600.02933.468-0.177-0.1770.0000.0000.0000.000
173A183VAL0-0.028-0.01434.622-0.091-0.0910.0000.0000.0000.000
174A184GLN0-0.044-0.02637.347-0.059-0.0590.0000.0000.0000.000
175A185GLN00.0020.00640.048-0.052-0.0520.0000.0000.0000.000
176A186ALA00.0210.00937.848-0.146-0.1460.0000.0000.0000.000
177A187GLY00.0160.00139.905-0.091-0.0910.0000.0000.0000.000
178A188GLN0-0.065-0.04041.984-0.260-0.2600.0000.0000.0000.000
179A189GLN00.0090.00740.762-0.026-0.0260.0000.0000.0000.000
180A190ILE00.0060.00939.191-0.103-0.1030.0000.0000.0000.000
181A191GLU-1-0.825-0.88243.7866.4436.4430.0000.0000.0000.000
182A192GLN00.0190.01247.024-0.265-0.2650.0000.0000.0000.000
183A193ALA00.001-0.00445.782-0.134-0.1340.0000.0000.0000.000
184A194GLN0-0.028-0.01346.544-0.156-0.1560.0000.0000.0000.000
185A195ARG10.7930.86848.622-6.377-6.3770.0000.0000.0000.000
186A196GLN0-0.085-0.03451.003-0.217-0.2170.0000.0000.0000.000
187A197GLN0-0.066-0.03651.9900.1260.1260.0000.0000.0000.000
188A198GLU-1-0.946-0.95053.1545.6105.6100.0000.0000.0000.000