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

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FMODB ID: 2L25R

Calculation Name: 3HD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W2Q0

Base Structure: X-ray

Registration Date: 2023-09-26

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1798146.439469
FMO2-HF: Nuclear repulsion 1727375.484509
FMO2-HF: Total energy -70770.95496
FMO2-MP2: Total energy -70976.554352


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:28:GLN)


Summations of interaction energy for fragment #1(A:28:GLN)
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.
-4.921-0.0670.641-2.238-3.2550.01
Interaction energy analysis for fragmet #1(A:28:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.008
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].
3A30ALA0-0.017-0.0032.731-5.384-2.0880.605-1.720-2.1810.012
4A31GLN00.0300.0024.4181.2111.395-0.001-0.019-0.1630.000
5A32GLN0-0.0030.0075.0010.5620.672-0.001-0.002-0.1070.000
6A33TYR0-0.080-0.0348.009-0.556-0.5560.0000.0000.0000.000
7A34VAL00.0230.02411.7000.1280.1280.0000.0000.0000.000
8A35ASN0-0.001-0.01914.5590.0070.0070.0000.0000.0000.000
9A36ILE0-0.0080.01517.838-0.046-0.0460.0000.0000.0000.000
10A37ASN0-0.085-0.02121.0360.0340.0340.0000.0000.0000.000
11A38PRO00.033-0.01424.139-0.020-0.0200.0000.0000.0000.000
12A39PRO00.0050.00624.4820.0050.0050.0000.0000.0000.000
13A40MET0-0.019-0.00424.661-0.027-0.0270.0000.0000.0000.000
14A41PRO0-0.034-0.01426.9170.0240.0240.0000.0000.0000.000
15A42SER0-0.012-0.02928.373-0.013-0.0130.0000.0000.0000.000
16A43ASP-1-0.881-0.91829.6090.2420.2420.0000.0000.0000.000
17A44THR0-0.038-0.03731.033-0.028-0.0280.0000.0000.0000.000
18A45PRO00.011-0.00532.0100.0170.0170.0000.0000.0000.000
19A46GLY0-0.025-0.01732.820-0.007-0.0070.0000.0000.0000.000
20A47LYS10.8550.93229.248-0.274-0.2740.0000.0000.0000.000
21A48ILE00.0070.01923.0370.0050.0050.0000.0000.0000.000
22A49GLU-1-0.721-0.84525.7180.3000.3000.0000.0000.0000.000
23A50VAL0-0.010-0.00120.2220.0480.0480.0000.0000.0000.000
24A51LEU0-0.026-0.01622.350-0.048-0.0480.0000.0000.0000.000
25A52GLU-1-0.793-0.90220.8260.3110.3110.0000.0000.0000.000
26A53PHE0-0.012-0.01321.353-0.045-0.0450.0000.0000.0000.000
27A54PHE00.039-0.01321.833-0.002-0.0020.0000.0000.0000.000
28A55ALA00.0580.01424.102-0.007-0.0070.0000.0000.0000.000
29A56TYR00.020-0.01626.079-0.009-0.0090.0000.0000.0000.000
30A57THR0-0.003-0.00528.428-0.007-0.0070.0000.0000.0000.000
31A58CYS0-0.0560.00621.675-0.026-0.0260.0000.0000.0000.000
32A59PRO00.0360.00922.3680.0100.0100.0000.0000.0000.000
33A60HIS00.0560.01918.184-0.001-0.0010.0000.0000.0000.000
34A61CYS0-0.052-0.01520.2150.0330.0330.0000.0000.0000.000
35A62ALA00.0210.00922.1080.0090.0090.0000.0000.0000.000
36A63ALA0-0.044-0.02520.4280.0020.0020.0000.0000.0000.000
37A64ILE0-0.0040.00316.3040.0010.0010.0000.0000.0000.000
38A65GLU-1-0.758-0.84520.3520.1940.1940.0000.0000.0000.000
39A66PRO00.0080.00323.4960.0160.0160.0000.0000.0000.000
40A67MET0-0.025-0.01417.2280.0180.0180.0000.0000.0000.000
41A68VAL0-0.015-0.00519.7480.0380.0380.0000.0000.0000.000
42A69GLU-1-0.918-0.97021.8160.1560.1560.0000.0000.0000.000
43A70ASP-1-0.905-0.94823.3030.1830.1830.0000.0000.0000.000
44A71TRP00.0010.00218.6870.0120.0120.0000.0000.0000.000
45A72ALA0-0.006-0.01622.2370.0200.0200.0000.0000.0000.000
46A73LYS10.7750.89024.938-0.165-0.1650.0000.0000.0000.000
47A74THR0-0.067-0.03223.6470.0010.0010.0000.0000.0000.000
48A75ALA00.0030.02923.2070.0290.0290.0000.0000.0000.000
49A76PRO00.021-0.00322.318-0.023-0.0230.0000.0000.0000.000
50A77GLN00.0490.02525.254-0.026-0.0260.0000.0000.0000.000
51A78ASP-1-0.949-0.96026.1540.4020.4020.0000.0000.0000.000
52A79VAL0-0.023-0.01522.9230.0190.0190.0000.0000.0000.000
53A80VAL0-0.0210.00026.225-0.027-0.0270.0000.0000.0000.000
54A81LEU00.0140.00722.6450.0270.0270.0000.0000.0000.000
55A82LYS10.8220.90525.554-0.310-0.3100.0000.0000.0000.000
56A83GLN0-0.066-0.03724.8300.0100.0100.0000.0000.0000.000
57A84VAL0-0.037-0.02725.907-0.018-0.0180.0000.0000.0000.000
58A85PRO0-0.0140.02526.3810.0060.0060.0000.0000.0000.000
59A86ILE00.0170.01124.309-0.001-0.0010.0000.0000.0000.000
60A87ALA0-0.017-0.03427.714-0.019-0.0190.0000.0000.0000.000
61A88PHE00.0250.00122.474-0.005-0.0050.0000.0000.0000.000
62A89ASN00.008-0.00228.420-0.011-0.0110.0000.0000.0000.000
63A90ALA00.0620.01731.9700.0040.0040.0000.0000.0000.000
64A91GLY00.0240.01834.9820.0020.0020.0000.0000.0000.000
65A92MET0-0.0160.02626.759-0.006-0.0060.0000.0000.0000.000
66A93LYS10.9730.99432.522-0.087-0.0870.0000.0000.0000.000
67A94PRO0-0.021-0.00734.7320.0060.0060.0000.0000.0000.000
68A95LEU00.0130.00131.7040.0010.0010.0000.0000.0000.000
69A96GLN0-0.016-0.02130.613-0.005-0.0050.0000.0000.0000.000
70A97GLN0-0.016-0.02333.1370.0040.0040.0000.0000.0000.000
71A98LEU0-0.0050.01434.5640.0000.0000.0000.0000.0000.000
72A99TYR00.0190.02330.2400.0000.0000.0000.0000.0000.000
73A100TYR00.050-0.00331.3440.0020.0020.0000.0000.0000.000
74A101THR0-0.006-0.01436.251-0.003-0.0030.0000.0000.0000.000
75A102LEU0-0.017-0.01235.282-0.004-0.0040.0000.0000.0000.000
76A103GLN00.0080.00833.095-0.003-0.0030.0000.0000.0000.000
77A104ALA0-0.0010.01037.603-0.001-0.0010.0000.0000.0000.000
78A105LEU0-0.133-0.07040.909-0.005-0.0050.0000.0000.0000.000
79A106GLU-1-0.936-0.95740.2510.0980.0980.0000.0000.0000.000
80A107ARG10.7640.84439.632-0.073-0.0730.0000.0000.0000.000
81A108PRO00.0470.03134.827-0.003-0.0030.0000.0000.0000.000
82A109ASP-1-0.779-0.87134.4870.0770.0770.0000.0000.0000.000
83A110LEU0-0.036-0.03535.484-0.006-0.0060.0000.0000.0000.000
84A111HIS00.0230.01928.080-0.020-0.0200.0000.0000.0000.000
85A112PRO00.0660.03529.652-0.006-0.0060.0000.0000.0000.000
86A113LYS10.9180.96030.845-0.071-0.0710.0000.0000.0000.000
87A114VAL0-0.0070.01032.154-0.013-0.0130.0000.0000.0000.000
88A115PHE0-0.0020.00926.113-0.016-0.0160.0000.0000.0000.000
89A116THR00.0110.00529.865-0.011-0.0110.0000.0000.0000.000
90A117ALA00.0240.01331.548-0.013-0.0130.0000.0000.0000.000
91A118ILE0-0.027-0.00830.591-0.010-0.0100.0000.0000.0000.000
92A119HIS0-0.043-0.03526.943-0.028-0.0280.0000.0000.0000.000
93A120THR0-0.022-0.00930.032-0.015-0.0150.0000.0000.0000.000
94A121GLU-1-0.845-0.90631.9410.0010.0010.0000.0000.0000.000
95A122ARG10.8340.92729.1100.0400.0400.0000.0000.0000.000
96A123LYS10.8500.91934.867-0.010-0.0100.0000.0000.0000.000
97A124ARG10.9370.95435.6170.0290.0290.0000.0000.0000.000
98A125LEU00.0030.01435.7240.0010.0010.0000.0000.0000.000
99A126PHE00.013-0.01732.7930.0040.0040.0000.0000.0000.000
100A127ASP-1-0.842-0.90736.6500.0280.0280.0000.0000.0000.000
101A128LYS10.8410.90439.952-0.057-0.0570.0000.0000.0000.000
102A129LYS10.8550.93942.136-0.017-0.0170.0000.0000.0000.000
103A130ALA00.004-0.00640.505-0.001-0.0010.0000.0000.0000.000
104A131MET0-0.049-0.01536.2760.0020.0020.0000.0000.0000.000
105A132GLY00.0650.02740.5720.0020.0020.0000.0000.0000.000
106A133GLU-1-0.869-0.91543.9880.0190.0190.0000.0000.0000.000
107A134TRP00.0070.00636.3720.0000.0000.0000.0000.0000.000
108A135ALA00.0430.03341.6750.0000.0000.0000.0000.0000.000
109A136ALA00.0260.00342.5410.0010.0010.0000.0000.0000.000
110A137SER0-0.127-0.07242.803-0.002-0.0020.0000.0000.0000.000
111A138GLN0-0.043-0.02039.9470.0020.0020.0000.0000.0000.000
112A139GLY00.0210.01643.3030.0040.0040.0000.0000.0000.000
113A140VAL0-0.060-0.01842.4540.0040.0040.0000.0000.0000.000
114A141ASP-1-0.820-0.91445.8840.0420.0420.0000.0000.0000.000
115A142ARG10.8650.90947.176-0.031-0.0310.0000.0000.0000.000
116A143ALA00.0310.02548.4340.0020.0020.0000.0000.0000.000
117A144LYS10.9440.96646.475-0.070-0.0700.0000.0000.0000.000
118A145PHE00.003-0.00240.3750.0040.0040.0000.0000.0000.000
119A146ASP-1-0.825-0.92544.9420.0480.0480.0000.0000.0000.000
120A147SER0-0.0320.01046.7900.0030.0030.0000.0000.0000.000
121A148VAL00.039-0.00142.5600.0030.0030.0000.0000.0000.000
122A149PHE00.0200.02538.8820.0050.0050.0000.0000.0000.000
123A150ASP-1-0.858-0.91742.1580.0650.0650.0000.0000.0000.000
124A151SER0-0.053-0.02943.3410.0030.0030.0000.0000.0000.000
125A152PHE00.0580.00943.3460.0040.0040.0000.0000.0000.000
126A153SER00.0000.01540.8240.0070.0070.0000.0000.0000.000
127A154VAL00.0310.02538.3680.0090.0090.0000.0000.0000.000
128A155GLN0-0.033-0.02138.3750.0020.0020.0000.0000.0000.000
129A156THR0-0.027-0.03038.7840.0060.0060.0000.0000.0000.000
130A157GLN00.015-0.00235.4720.0020.0020.0000.0000.0000.000
131A158VAL00.0080.01034.2800.0100.0100.0000.0000.0000.000
132A159GLN0-0.029-0.01133.7950.0000.0000.0000.0000.0000.000
133A160ARG10.8540.90332.407-0.229-0.2290.0000.0000.0000.000
134A161ALA00.0240.01630.1750.0180.0180.0000.0000.0000.000
135A162SER00.0310.00329.1180.0140.0140.0000.0000.0000.000
136A163GLN00.0000.02029.4930.0140.0140.0000.0000.0000.000
137A164LEU0-0.030-0.02027.3900.0160.0160.0000.0000.0000.000
138A165ALA00.004-0.00425.0770.0270.0270.0000.0000.0000.000
139A166GLU-1-0.932-0.97324.8110.2380.2380.0000.0000.0000.000
140A167ALA0-0.046-0.01125.9750.0180.0180.0000.0000.0000.000
141A168ALA0-0.043-0.03121.8690.0300.0300.0000.0000.0000.000
142A169HIS0-0.039-0.01321.1980.0350.0350.0000.0000.0000.000
143A170ILE0-0.056-0.01920.0690.0300.0300.0000.0000.0000.000
144A171ASP-1-0.891-0.94618.0910.3160.3160.0000.0000.0000.000
145A172GLY0-0.012-0.01318.771-0.050-0.0500.0000.0000.0000.000
146A173THR0-0.0920.00619.4380.0290.0290.0000.0000.0000.000
147A174PRO00.052-0.03117.011-0.045-0.0450.0000.0000.0000.000
148A175ALA0-0.004-0.01217.0380.0320.0320.0000.0000.0000.000
149A176PHE0-0.0010.00315.843-0.042-0.0420.0000.0000.0000.000
150A177ALA00.0360.03217.6320.0760.0760.0000.0000.0000.000
151A178VAL0-0.012-0.01917.292-0.041-0.0410.0000.0000.0000.000
152A179GLY00.0400.00920.1370.0360.0360.0000.0000.0000.000
153A180GLY0-0.026-0.00722.861-0.008-0.0080.0000.0000.0000.000
154A181ARG10.9170.97020.380-0.671-0.6710.0000.0000.0000.000
155A182TYR00.0060.00315.8920.0230.0230.0000.0000.0000.000
156A183MET00.0660.05316.250-0.060-0.0600.0000.0000.0000.000
157A184THR00.006-0.02011.2710.1000.1000.0000.0000.0000.000
158A185SER00.0670.02812.192-0.138-0.1380.0000.0000.0000.000
159A186PRO00.0650.02611.1990.1530.1530.0000.0000.0000.000
160A187VAL00.0270.0069.6800.0450.0450.0000.0000.0000.000
161A188LEU00.0070.0178.8730.0060.0060.0000.0000.0000.000
162A189ALA0-0.023-0.0047.1010.7730.7730.0000.0000.0000.000
163A190GLY00.0240.0215.0490.1140.1140.0000.0000.0000.000
164A191ASN0-0.023-0.0186.011-0.539-0.5390.0000.0000.0000.000
165A192ASP-1-0.881-0.9559.203-0.525-0.5250.0000.0000.0000.000
166A193TYR0-0.049-0.0313.256-1.0130.2510.038-0.497-0.804-0.002
167A194ALA0-0.061-0.0277.927-0.037-0.0370.0000.0000.0000.000
168A195GLY00.0400.02111.0860.1100.1100.0000.0000.0000.000
169A196ALA00.0560.02213.242-0.101-0.1010.0000.0000.0000.000
170A197LEU00.0390.0187.499-0.009-0.0090.0000.0000.0000.000
171A198LYS10.9060.97210.8850.6630.6630.0000.0000.0000.000
172A199VAL0-0.004-0.01511.7850.0440.0440.0000.0000.0000.000
173A200VAL0-0.008-0.00312.9280.0690.0690.0000.0000.0000.000
174A201ASP-1-0.892-0.9409.761-2.249-2.2490.0000.0000.0000.000
175A202GLN0-0.072-0.05013.3650.0940.0940.0000.0000.0000.000
176A203LEU00.0000.00016.5280.0860.0860.0000.0000.0000.000
177A204ILE0-0.0240.00113.9620.0700.0700.0000.0000.0000.000
178A205VAL0-0.062-0.03016.3020.0440.0440.0000.0000.0000.000
179A206GLN00.0470.02618.9080.0390.0390.0000.0000.0000.000
180A207SER0-0.071-0.03620.7320.0400.0400.0000.0000.0000.000
181A208ARG10.9000.96216.4990.9820.9820.0000.0000.0000.000
182A209GLU-1-1.009-0.99722.861-0.482-0.4820.0000.0000.0000.000