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: N92KQ

Calculation Name: 4FHR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FHR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WY63

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 OptH
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 -2074051.920413
FMO2-HF: Nuclear repulsion 2000363.809923
FMO2-HF: Total energy -73688.110489
FMO2-MP2: Total energy -73902.00633


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:45:THR)


Summations of interaction energy for fragment #1(A:45:THR)
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.
-7.493-1.0957.271-5.319-8.348-0.037
Interaction energy analysis for fragmet #1(A:45:THR)
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 : -0.003
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].
3A47PHE00.0760.0433.632-0.7681.742-0.029-1.315-1.1670.005
4A48SER0-0.023-0.0176.506-0.415-0.4150.0000.0000.0000.000
5A49LYS10.9670.9649.0320.1030.1030.0000.0000.0000.000
6A50GLU-1-0.910-0.96012.3410.1680.1680.0000.0000.0000.000
7A51GLN00.0690.0467.7950.1290.1290.0000.0000.0000.000
8A52LEU00.0700.0338.9690.0170.0170.0000.0000.0000.000
9A53ARG10.8610.95911.935-0.201-0.2010.0000.0000.0000.000
10A54THR00.0390.00714.076-0.029-0.0290.0000.0000.0000.000
11A55PHE00.0460.0248.948-0.018-0.0180.0000.0000.0000.000
12A56GLN0-0.027-0.00214.3390.0090.0090.0000.0000.0000.000
13A57MET0-0.055-0.02516.839-0.033-0.0330.0000.0000.0000.000
14A58ILE00.0240.02315.741-0.020-0.0200.0000.0000.0000.000
15A59HIS00.043-0.00114.558-0.025-0.0250.0000.0000.0000.000
16A60GLU-1-0.831-0.92119.2110.1460.1460.0000.0000.0000.000
17A61ASN0-0.0140.00921.919-0.031-0.0310.0000.0000.0000.000
18A62PHE00.0120.01420.908-0.011-0.0110.0000.0000.0000.000
19A63GLY00.0390.01222.827-0.012-0.0120.0000.0000.0000.000
20A64ARG10.9010.93724.461-0.147-0.1470.0000.0000.0000.000
21A65ALA00.0080.00226.513-0.011-0.0110.0000.0000.0000.000
22A66LEU0-0.015-0.00324.528-0.009-0.0090.0000.0000.0000.000
23A67SER0-0.009-0.02727.694-0.010-0.0100.0000.0000.0000.000
24A68THR0-0.0150.00430.194-0.010-0.0100.0000.0000.0000.000
25A69TYR0-0.046-0.04930.227-0.007-0.0070.0000.0000.0000.000
26A70LEU00.015-0.01028.511-0.006-0.0060.0000.0000.0000.000
27A71SER00.0140.00132.574-0.007-0.0070.0000.0000.0000.000
28A72GLY0-0.032-0.00635.335-0.006-0.0060.0000.0000.0000.000
29A73ARG10.7500.83033.736-0.084-0.0840.0000.0000.0000.000
30A74LEU00.009-0.00633.319-0.003-0.0030.0000.0000.0000.000
31A75ARG10.8760.95537.439-0.061-0.0610.0000.0000.0000.000
32A76THR00.0070.00337.458-0.004-0.0040.0000.0000.0000.000
33A77PHE0-0.040-0.01334.0400.0020.0020.0000.0000.0000.000
34A78VAL0-0.018-0.00431.0670.0000.0000.0000.0000.0000.000
35A79ASP-1-0.872-0.90530.5760.1000.1000.0000.0000.0000.000
36A80VAL0-0.036-0.03425.2420.0060.0060.0000.0000.0000.000
37A81GLU-1-0.951-0.95225.2310.1160.1160.0000.0000.0000.000
38A82ILE0-0.036-0.02419.2360.0100.0100.0000.0000.0000.000
39A83SER0-0.025-0.01318.893-0.010-0.0100.0000.0000.0000.000
40A84ILE0-0.021-0.01312.7360.0280.0280.0000.0000.0000.000
41A85ASP-1-0.881-0.93313.0280.3420.3420.0000.0000.0000.000
42A86GLN0-0.065-0.0375.5000.6430.570-0.001-0.0050.0790.000
43A87LEU00.0310.0248.902-0.187-0.1870.0000.0000.0000.000
44A88THR0-0.027-0.0117.3010.3920.3920.0000.0000.0000.000
45A89TYR00.030-0.0188.833-0.127-0.1270.0000.0000.0000.000
46A90GLU-1-0.949-0.98711.0430.0410.0410.0000.0000.0000.000
47A91GLU-1-0.902-0.95610.8990.3300.3300.0000.0000.0000.000
48A92PHE00.0620.03513.111-0.038-0.0380.0000.0000.0000.000
49A93ILE00.0300.06114.895-0.064-0.0640.0000.0000.0000.000
50A94ARG10.8820.93516.860-0.168-0.1680.0000.0000.0000.000
51A95SER0-0.114-0.08417.893-0.023-0.0230.0000.0000.0000.000
52A96VAL0-0.0160.00218.823-0.018-0.0180.0000.0000.0000.000
53A97MET0-0.016-0.00421.502-0.020-0.0200.0000.0000.0000.000
54A98ILE0-0.0360.03025.3410.0030.0030.0000.0000.0000.000
55A99PRO0-0.048-0.04427.502-0.008-0.0080.0000.0000.0000.000
56A100SER0-0.002-0.04224.7150.0030.0030.0000.0000.0000.000
57A101PHE0-0.019-0.01926.254-0.010-0.0100.0000.0000.0000.000
58A102ILE00.0180.01320.6330.0140.0140.0000.0000.0000.000
59A103VAL00.0020.00022.315-0.017-0.0170.0000.0000.0000.000
60A104ILE00.0020.00918.1960.0260.0260.0000.0000.0000.000
61A105PHE0-0.037-0.02017.464-0.025-0.0250.0000.0000.0000.000
62A106THR00.1100.05917.6920.0240.0240.0000.0000.0000.000
63A107GLY00.018-0.02118.8810.0000.0000.0000.0000.0000.000
64A108ASP-1-0.851-0.92220.0660.1160.1160.0000.0000.0000.000
65A109VAL0-0.065-0.02617.056-0.011-0.0110.0000.0000.0000.000
66A110PHE0-0.086-0.03214.3760.0140.0140.0000.0000.0000.000
67A111GLU-1-0.903-0.94014.0170.0440.0440.0000.0000.0000.000
68A112GLY00.000-0.01113.261-0.011-0.0110.0000.0000.0000.000
69A113SER0-0.103-0.11214.257-0.002-0.0020.0000.0000.0000.000
70A114ALA00.006-0.00113.5330.0590.0590.0000.0000.0000.000
71A115ILE0-0.029-0.01115.103-0.051-0.0510.0000.0000.0000.000
72A116PHE00.0100.00317.3240.0280.0280.0000.0000.0000.000
73A117GLU-1-0.918-0.97520.1980.2010.2010.0000.0000.0000.000
74A118MET0-0.0010.01921.7640.0010.0010.0000.0000.0000.000
75A119ARG10.9941.00223.716-0.156-0.1560.0000.0000.0000.000
76A120LEU00.041-0.00427.159-0.004-0.0040.0000.0000.0000.000
77A121ASP-1-0.785-0.86630.3210.1000.1000.0000.0000.0000.000
78A122LEU00.0330.03027.924-0.006-0.0060.0000.0000.0000.000
79A123PHE0-0.006-0.01229.766-0.005-0.0050.0000.0000.0000.000
80A124TYR0-0.030-0.04931.748-0.006-0.0060.0000.0000.0000.000
81A125THR0-0.011-0.00634.779-0.006-0.0060.0000.0000.0000.000
82A126MET0-0.016-0.01031.697-0.001-0.0010.0000.0000.0000.000
83A127LEU0-0.008-0.00735.349-0.004-0.0040.0000.0000.0000.000
84A128ASP-1-0.848-0.93636.9370.0520.0520.0000.0000.0000.000
85A129ILE00.0310.03438.097-0.002-0.0020.0000.0000.0000.000
86A130ILE0-0.107-0.05235.302-0.003-0.0030.0000.0000.0000.000
87A131MET0-0.116-0.06039.803-0.002-0.0020.0000.0000.0000.000
88A132GLY0-0.076-0.03342.534-0.003-0.0030.0000.0000.0000.000
89A133GLY0-0.0130.01143.540-0.003-0.0030.0000.0000.0000.000
90A134PRO0-0.016-0.02643.4330.0020.0020.0000.0000.0000.000
91A135GLY0-0.0160.00039.9630.0020.0020.0000.0000.0000.000
92A136GLU-1-0.988-0.98339.6780.0480.0480.0000.0000.0000.000
93A137ASN0-0.082-0.05940.254-0.002-0.0020.0000.0000.0000.000
94A138PRO00.0710.04936.053-0.002-0.0020.0000.0000.0000.000
95A139PRO0-0.020-0.00437.334-0.001-0.0010.0000.0000.0000.000
96A140ASN00.010-0.00532.7560.0090.0090.0000.0000.0000.000
97A141ARG10.7700.85234.838-0.064-0.0640.0000.0000.0000.000
98A142PRO00.0520.02732.2490.0040.0040.0000.0000.0000.000
99A143PRO00.0340.03231.520-0.005-0.0050.0000.0000.0000.000
100A144THR0-0.020-0.01334.548-0.002-0.0020.0000.0000.0000.000
101A145GLU-1-0.871-0.94735.8180.0560.0560.0000.0000.0000.000
102A146ILE0-0.001-0.00136.6570.0030.0030.0000.0000.0000.000
103A147GLU-1-0.727-0.83235.9390.0660.0660.0000.0000.0000.000
104A148THR00.0320.01631.1650.0070.0070.0000.0000.0000.000
105A149SER0-0.047-0.03032.8570.0040.0040.0000.0000.0000.000
106A150ILE0-0.060-0.02934.8130.0020.0020.0000.0000.0000.000
107A151MET00.0550.02531.2860.0010.0010.0000.0000.0000.000
108A152ARG10.9790.99728.604-0.086-0.0860.0000.0000.0000.000
109A153LYS10.9110.96629.890-0.062-0.0620.0000.0000.0000.000
110A154GLU-1-0.724-0.79131.2610.0900.0900.0000.0000.0000.000
111A155VAL00.0140.00025.0840.0050.0050.0000.0000.0000.000
112A156THR00.0000.00126.4040.0090.0090.0000.0000.0000.000
113A157ASN0-0.034-0.03027.4430.0040.0040.0000.0000.0000.000
114A158MET0-0.0150.00025.6310.0050.0050.0000.0000.0000.000
115A159LEU00.0350.01521.2670.0110.0110.0000.0000.0000.000
116A160THR0-0.030-0.00623.3840.0060.0060.0000.0000.0000.000
117A161LEU0-0.046-0.02425.5280.0000.0000.0000.0000.0000.000
118A162LEU0-0.035-0.00718.1540.0020.0020.0000.0000.0000.000
119A163ALA00.0320.01021.0460.0120.0120.0000.0000.0000.000
120A164GLN0-0.031-0.02522.179-0.002-0.0020.0000.0000.0000.000
121A165ALA0-0.052-0.00621.047-0.005-0.0050.0000.0000.0000.000
122A166TRP0-0.012-0.01712.6970.0110.0110.0000.0000.0000.000
123A167SER0-0.086-0.03519.849-0.002-0.0020.0000.0000.0000.000
124A168ASP-1-0.915-0.94621.9020.1230.1230.0000.0000.0000.000
125A169PHE0-0.077-0.04416.7610.0010.0010.0000.0000.0000.000
126A170GLN0-0.002-0.01916.3510.0030.0030.0000.0000.0000.000
127A171TYR00.0020.00918.6470.0050.0050.0000.0000.0000.000
128A172PHE00.0320.00618.4920.0050.0050.0000.0000.0000.000
129A173ILE0-0.028-0.01021.687-0.002-0.0020.0000.0000.0000.000
130A174PRO0-0.0160.00522.0230.0010.0010.0000.0000.0000.000
131A175SER0-0.052-0.02522.593-0.018-0.0180.0000.0000.0000.000
132A176ILE0-0.010-0.02222.7770.0100.0100.0000.0000.0000.000
133A177GLU-1-0.841-0.86519.4560.1280.1280.0000.0000.0000.000
134A178ASN0-0.051-0.04822.922-0.019-0.0190.0000.0000.0000.000
135A179VAL0-0.066-0.02623.8710.0130.0130.0000.0000.0000.000
136A180GLU-1-0.838-0.89623.1690.0880.0880.0000.0000.0000.000
137A181THR0-0.021-0.02125.6670.0050.0050.0000.0000.0000.000
138A182ASN00.005-0.00525.5410.0080.0080.0000.0000.0000.000
139A183PRO00.0980.04820.878-0.003-0.0030.0000.0000.0000.000
140A184GLN0-0.028-0.01320.6870.0050.0050.0000.0000.0000.000
141A185PHE0-0.039-0.01822.176-0.009-0.0090.0000.0000.0000.000
142A186VAL00.0240.02617.598-0.002-0.0020.0000.0000.0000.000
143A187GLN0-0.059-0.01416.1600.0160.0160.0000.0000.0000.000
144A188ILE0-0.0010.00413.043-0.027-0.0270.0000.0000.0000.000
145A189VAL00.0130.0249.327-0.026-0.0260.0000.0000.0000.000
146A190PRO0-0.030-0.0269.8660.0090.0090.0000.0000.0000.000
147A191PRO00.0420.02610.0400.0990.0990.0000.0000.0000.000
148A192ASN0-0.004-0.0218.0540.0810.0810.0000.0000.0000.000
149A193GLU-1-0.808-0.8354.9670.3740.3740.0000.0000.0000.000
150A194ILE0-0.025-0.0153.046-1.426-0.2580.275-0.521-0.9220.004
151A195VAL00.000-0.0035.336-0.188-0.127-0.001-0.002-0.0570.000
152A196LEU0-0.043-0.0207.7800.0440.0440.0000.0000.0000.000
153A197LEU0-0.017-0.0069.592-0.130-0.1300.0000.0000.0000.000
154A198VAL0-0.015-0.00813.045-0.039-0.0390.0000.0000.0000.000
155A199THR00.018-0.00716.035-0.016-0.0160.0000.0000.0000.000
156A200ALA0-0.002-0.00519.130-0.013-0.0130.0000.0000.0000.000
157A201SER0-0.015-0.01222.567-0.008-0.0080.0000.0000.0000.000
158A202VAL00.0060.00125.311-0.006-0.0060.0000.0000.0000.000
159A203SER00.0280.01028.391-0.007-0.0070.0000.0000.0000.000
160A204TRP00.0500.01031.1680.0000.0000.0000.0000.0000.000
161A205GLY0-0.0160.00335.274-0.001-0.0010.0000.0000.0000.000
162A206GLU-1-0.927-0.97237.4020.0560.0560.0000.0000.0000.000
163A207PHE0-0.079-0.02034.3810.0010.0010.0000.0000.0000.000
164A208THR00.006-0.02128.7150.0020.0020.0000.0000.0000.000
165A209SER0-0.068-0.03528.4670.0040.0040.0000.0000.0000.000
166A210PHE0-0.011-0.01323.1310.0030.0030.0000.0000.0000.000
167A211ILE0-0.0080.00221.981-0.009-0.0090.0000.0000.0000.000
168A212ASN0-0.0050.00417.9080.0330.0330.0000.0000.0000.000
169A213VAL00.0090.00615.647-0.028-0.0280.0000.0000.0000.000
170A214CYS0-0.039-0.00812.6200.0880.0880.0000.0000.0000.000
171A215TRP00.0400.00510.745-0.070-0.0700.0000.0000.0000.000
172A216PRO00.0400.0228.2710.3440.3440.0000.0000.0000.000
173A217PHE00.0300.0012.522-6.238-3.6887.029-3.469-6.109-0.046
174A218SER0-0.080-0.0975.340-0.601-0.574-0.001-0.002-0.0230.000
175A219LEU0-0.0270.0106.898-0.045-0.0450.0000.0000.0000.000
176A220LEU0-0.015-0.0207.075-0.045-0.0450.0000.0000.0000.000
177A221GLU-1-0.955-0.9744.977-0.587-0.432-0.001-0.005-0.1490.000
178A222PRO0-0.001-0.0057.1540.0720.0720.0000.0000.0000.000
179A223LEU0-0.031-0.02210.300-0.017-0.0170.0000.0000.0000.000
180A224LEU0-0.075-0.0215.4750.0330.0330.0000.0000.0000.000
181A225GLU-1-0.983-0.98410.0880.1580.1580.0000.0000.0000.000
182A226LYS10.8630.94213.181-0.199-0.1990.0000.0000.0000.000