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: 3JNYL

Calculation Name: 4N1Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N1Y

Chain ID: A

ChEMBL ID:

UniProt ID: K1QUU5

Base Structure: X-ray

Registration Date: 2023-09-20

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2849939.735317
FMO2-HF: Nuclear repulsion 2759588.304925
FMO2-HF: Total energy -90351.430391
FMO2-MP2: Total energy -90612.451854


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:248:GLN)


Summations of interaction energy for fragment #1(A:248: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.
0.1114.142.919-2.57-4.379-0.009
Interaction energy analysis for fragmet #1(A:248:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.006
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].
3A250VAL0-0.0130.0013.319-3.349-0.9760.081-1.090-1.3640.005
4A251THR00.006-0.0102.331-3.621-2.5372.838-1.342-2.580-0.014
5A252ILE0-0.0010.0134.0360.4330.9290.001-0.137-0.3610.000
6A253LEU00.0150.0136.3080.4820.4820.0000.0000.0000.000
7A254GLN0-0.047-0.0376.057-0.184-0.1840.0000.0000.0000.000
8A255ALA0-0.024-0.0068.1810.1620.1620.0000.0000.0000.000
9A256LEU00.0380.01510.1330.1810.1810.0000.0000.0000.000
10A257ASN00.0520.02811.6760.1860.1860.0000.0000.0000.000
11A258LYS10.8680.94113.2140.7080.7080.0000.0000.0000.000
12A259ALA0-0.007-0.01315.022-0.004-0.0040.0000.0000.0000.000
13A260ALA0-0.0110.00816.3720.0240.0240.0000.0000.0000.000
14A261LEU0-0.034-0.01418.3590.0150.0150.0000.0000.0000.000
15A262PRO0-0.0200.00822.1000.0210.0210.0000.0000.0000.000
16A263VAL00.016-0.01024.0470.0070.0070.0000.0000.0000.000
17A264LEU0-0.064-0.02227.292-0.002-0.0020.0000.0000.0000.000
18A265GLU-1-0.856-0.91329.655-0.033-0.0330.0000.0000.0000.000
19A266SER0-0.099-0.08833.253-0.008-0.0080.0000.0000.0000.000
20A267HIS0-0.049-0.03635.232-0.002-0.0020.0000.0000.0000.000
21A268HIS00.0360.05638.668-0.003-0.0030.0000.0000.0000.000
22A269ASN00.0260.00340.9820.0040.0040.0000.0000.0000.000
23A270HIS00.004-0.01640.4620.0030.0030.0000.0000.0000.000
24A271GLY0-0.0250.01445.5760.0030.0030.0000.0000.0000.000
25A272GLN0-0.071-0.04548.300-0.001-0.0010.0000.0000.0000.000
26A273PRO00.0480.01748.5420.0010.0010.0000.0000.0000.000
27A274PRO00.0240.03045.895-0.002-0.0020.0000.0000.0000.000
28A275THR0-0.006-0.02047.2750.0020.0020.0000.0000.0000.000
29A276LYS10.9210.95545.689-0.005-0.0050.0000.0000.0000.000
30A277VAL00.0290.00645.225-0.002-0.0020.0000.0000.0000.000
31A278HIS0-0.052-0.02045.289-0.005-0.0050.0000.0000.0000.000
32A279LEU00.0270.00841.824-0.003-0.0030.0000.0000.0000.000
33A280LEU00.0250.01340.735-0.002-0.0020.0000.0000.0000.000
34A281ASN00.005-0.00440.513-0.007-0.0070.0000.0000.0000.000
35A282SER0-0.003-0.01939.392-0.007-0.0070.0000.0000.0000.000
36A283LEU0-0.009-0.00536.156-0.004-0.0040.0000.0000.0000.000
37A284VAL0-0.0190.00335.683-0.004-0.0040.0000.0000.0000.000
38A285LYS10.7960.87535.7780.0450.0450.0000.0000.0000.000
39A286LEU0-0.022-0.01031.481-0.009-0.0090.0000.0000.0000.000
40A287ALA00.0440.03031.559-0.009-0.0090.0000.0000.0000.000
41A288GLU-1-0.737-0.87230.947-0.073-0.0730.0000.0000.0000.000
42A289ARG10.8100.90531.1650.0550.0550.0000.0000.0000.000
43A290GLU-1-0.784-0.87527.121-0.061-0.0610.0000.0000.0000.000
44A291LEU00.0240.02026.420-0.017-0.0170.0000.0000.0000.000
45A292VAL0-0.002-0.00226.626-0.019-0.0190.0000.0000.0000.000
46A293HIS0-0.019-0.01323.701-0.031-0.0310.0000.0000.0000.000
47A294LEU0-0.010-0.00522.185-0.032-0.0320.0000.0000.0000.000
48A295ILE00.0200.01121.769-0.030-0.0300.0000.0000.0000.000
49A296ASN0-0.092-0.04120.841-0.052-0.0520.0000.0000.0000.000
50A297TRP00.005-0.01215.700-0.032-0.0320.0000.0000.0000.000
51A298ALA00.0630.03217.066-0.062-0.0620.0000.0000.0000.000
52A299LYS10.8920.94716.9030.2690.2690.0000.0000.0000.000
53A300ASN0-0.037-0.01114.200-0.103-0.1030.0000.0000.0000.000
54A301VAL00.0320.02412.419-0.148-0.1480.0000.0000.0000.000
55A302PRO0-0.035-0.0148.1850.0190.0190.0000.0000.0000.000
56A303GLY00.0550.02410.8730.0720.0720.0000.0000.0000.000
57A304TYR0-0.002-0.04012.9500.1080.1080.0000.0000.0000.000
58A305THR0-0.057-0.04715.5470.0540.0540.0000.0000.0000.000
59A306ASP-1-0.904-0.94014.854-0.764-0.7640.0000.0000.0000.000
60A307LEU0-0.0410.00216.5010.0540.0540.0000.0000.0000.000
61A308SER0-0.016-0.03219.410-0.001-0.0010.0000.0000.0000.000
62A309LEU00.036-0.00323.1970.0080.0080.0000.0000.0000.000
63A310SER00.0340.01925.1180.0130.0130.0000.0000.0000.000
64A311ASP-1-0.765-0.83522.324-0.164-0.1640.0000.0000.0000.000
65A312GLN0-0.054-0.02820.4370.0210.0210.0000.0000.0000.000
66A313VAL0-0.0080.01922.6140.0060.0060.0000.0000.0000.000
67A314HIS00.0360.01425.6190.0050.0050.0000.0000.0000.000
68A315LEU0-0.030-0.01819.4480.0170.0170.0000.0000.0000.000
69A316ILE00.0290.01522.2420.0170.0170.0000.0000.0000.000
70A317GLU-1-0.891-0.97824.628-0.087-0.0870.0000.0000.0000.000
71A318CYS0-0.063-0.01925.3790.0170.0170.0000.0000.0000.000
72A319CYS0-0.059-0.01922.7560.0080.0080.0000.0000.0000.000
73A320TRP00.007-0.00725.0280.0060.0060.0000.0000.0000.000
74A321MET0-0.0070.01226.5650.0020.0020.0000.0000.0000.000
75A322GLU-1-0.787-0.87724.2780.0420.0420.0000.0000.0000.000
76A323LEU0-0.026-0.01120.1270.0100.0100.0000.0000.0000.000
77A324LEU0-0.0030.00423.8190.0050.0050.0000.0000.0000.000
78A325LEU0-0.002-0.00327.1120.0090.0090.0000.0000.0000.000
79A326LEU00.0230.01419.9480.0140.0140.0000.0000.0000.000
80A327ASN00.0170.00022.1280.0220.0220.0000.0000.0000.000
81A328CYS00.0050.01824.5770.0070.0070.0000.0000.0000.000
82A329ALA00.0170.02525.9910.0080.0080.0000.0000.0000.000
83A330PHE0-0.011-0.00620.8740.0070.0070.0000.0000.0000.000
84A331ARG10.7520.83425.0140.0290.0290.0000.0000.0000.000
85A332SER0-0.033-0.02727.055-0.003-0.0030.0000.0000.0000.000
86A333ILE0-0.0010.02124.2160.0050.0050.0000.0000.0000.000
87A334GLU-1-0.884-0.94128.0860.0700.0700.0000.0000.0000.000
88A335HIS0-0.071-0.04030.3620.0010.0010.0000.0000.0000.000
89A336GLY00.0500.01331.822-0.003-0.0030.0000.0000.0000.000
90A337GLY00.0170.02632.5300.0000.0000.0000.0000.0000.000
91A338LYS10.8010.91034.086-0.075-0.0750.0000.0000.0000.000
92A339SER0-0.016-0.02935.762-0.004-0.0040.0000.0000.0000.000
93A340LEU0-0.002-0.00131.4620.0070.0070.0000.0000.0000.000
94A341ALA00.0060.00630.988-0.007-0.0070.0000.0000.0000.000
95A342PHE00.0270.00530.965-0.004-0.0040.0000.0000.0000.000
96A343ALA00.0450.02731.192-0.010-0.0100.0000.0000.0000.000
97A344PRO00.006-0.00130.8100.0070.0070.0000.0000.0000.000
98A345ASP-1-0.724-0.82233.430-0.017-0.0170.0000.0000.0000.000
99A346LEU0-0.045-0.02135.7090.0010.0010.0000.0000.0000.000
100A347VAL00.0230.01434.5680.0020.0020.0000.0000.0000.000
101A348LEU0-0.025-0.00536.691-0.001-0.0010.0000.0000.0000.000
102A349ASP-1-0.744-0.84737.9530.0400.0400.0000.0000.0000.000
103A350ARG10.8580.90637.235-0.073-0.0730.0000.0000.0000.000
104A351SER0-0.024-0.02941.800-0.002-0.0020.0000.0000.0000.000
105A352SER0-0.015-0.02941.571-0.005-0.0050.0000.0000.0000.000
106A353TRP0-0.023-0.02736.372-0.002-0.0020.0000.0000.0000.000
107A354SER00.0110.01041.297-0.001-0.0010.0000.0000.0000.000
108A355THR0-0.085-0.03644.612-0.003-0.0030.0000.0000.0000.000
109A356VAL0-0.057-0.03440.420-0.004-0.0040.0000.0000.0000.000
110A357GLU-1-0.852-0.91642.6610.0060.0060.0000.0000.0000.000
111A358MET00.0060.01638.0760.0000.0000.0000.0000.0000.000
112A359THR00.013-0.00338.3370.0020.0020.0000.0000.0000.000
113A360GLU-1-0.831-0.89137.9250.0510.0510.0000.0000.0000.000
114A361ILE0-0.0010.01033.4280.0060.0060.0000.0000.0000.000
115A362PHE00.013-0.01333.8240.0050.0050.0000.0000.0000.000
116A363GLU-1-0.794-0.88634.5600.0710.0710.0000.0000.0000.000
117A364GLN0-0.033-0.00931.1400.0000.0000.0000.0000.0000.000
118A365VAL00.005-0.00429.1520.0110.0110.0000.0000.0000.000
119A366ALA0-0.0050.00629.8620.0080.0080.0000.0000.0000.000
120A367ALA00.0270.01431.4990.0100.0100.0000.0000.0000.000
121A368VAL00.0240.00325.5090.0170.0170.0000.0000.0000.000
122A369SER0-0.049-0.04026.8090.0170.0170.0000.0000.0000.000
123A370GLU-1-0.872-0.93527.6560.1440.1440.0000.0000.0000.000
124A371GLN0-0.036-0.02226.7220.0270.0270.0000.0000.0000.000
125A372MET0-0.038-0.00322.8050.0300.0300.0000.0000.0000.000
126A373MET00.0160.02124.1800.0170.0170.0000.0000.0000.000
127A374GLN0-0.045-0.02226.5260.0180.0180.0000.0000.0000.000
128A375ASN0-0.089-0.04922.0500.0430.0430.0000.0000.0000.000
129A376HIS0-0.093-0.05422.0370.0300.0300.0000.0000.0000.000
130A377LEU0-0.038-0.00818.0920.0300.0300.0000.0000.0000.000
131A378HIS00.0640.03915.027-0.041-0.0410.0000.0000.0000.000
132A379LYS10.9560.96016.3050.0580.0580.0000.0000.0000.000
133A380ASP-1-0.793-0.90011.8770.3760.3760.0000.0000.0000.000
134A381GLU-1-0.726-0.85013.0600.4470.4470.0000.0000.0000.000
135A382LEU00.0100.02014.832-0.026-0.0260.0000.0000.0000.000
136A383LEU0-0.052-0.01912.913-0.034-0.0340.0000.0000.0000.000
137A384LEU00.0110.0028.852-0.095-0.0950.0000.0000.0000.000
138A385LEU0-0.0050.00512.9400.0000.0000.0000.0000.0000.000
139A386GLN0-0.0020.00116.393-0.004-0.0040.0000.0000.0000.000
140A387ALA0-0.001-0.00512.919-0.023-0.0230.0000.0000.0000.000
141A388MET0-0.024-0.01012.776-0.016-0.0160.0000.0000.0000.000
142A389VAL0-0.020-0.01715.4760.0040.0040.0000.0000.0000.000
143A390LEU0-0.002-0.00516.983-0.006-0.0060.0000.0000.0000.000
144A391VAL0-0.043-0.02914.151-0.013-0.0130.0000.0000.0000.000
145A392ASN0-0.033-0.01017.3390.0450.0450.0000.0000.0000.000
146A393ALA00.0200.02819.5870.0200.0200.0000.0000.0000.000
147A394GLU-1-0.745-0.82922.227-0.003-0.0030.0000.0000.0000.000
148A395VAL0-0.003-0.00922.3140.0090.0090.0000.0000.0000.000
149A396ARG10.8130.88524.2380.0250.0250.0000.0000.0000.000
150A397ARG10.8500.91523.134-0.028-0.0280.0000.0000.0000.000
151A398LEU00.0540.04122.696-0.006-0.0060.0000.0000.0000.000
152A399ALA0-0.0070.00123.9110.0050.0050.0000.0000.0000.000
153A400SER0-0.005-0.03219.370-0.015-0.0150.0000.0000.0000.000
154A401TYR00.0400.02318.926-0.018-0.0180.0000.0000.0000.000
155A402ASN00.0170.00117.0290.0540.0540.0000.0000.0000.000
156A403GLN0-0.014-0.00214.7330.0640.0640.0000.0000.0000.000
157A404ILE00.0630.03114.128-0.030-0.0300.0000.0000.0000.000
158A405PHE0-0.0090.00414.8030.0340.0340.0000.0000.0000.000
159A406ASN0-0.033-0.03511.0580.0830.0830.0000.0000.0000.000
160A407MET0-0.0290.01310.0350.0480.0480.0000.0000.0000.000
161A408GLN0-0.015-0.00810.561-0.001-0.0010.0000.0000.0000.000
162A409GLN00.0110.0029.851-0.039-0.0390.0000.0000.0000.000
163A410SER00.0300.0055.8990.1710.1710.0000.0000.0000.000
164A411LEU0-0.012-0.0126.209-0.063-0.0630.0000.0000.0000.000
165A412LEU0-0.016-0.0128.9070.1040.1040.0000.0000.0000.000
166A413ASP-1-0.909-0.9535.7422.6892.6890.0000.0000.0000.000
167A414ALA00.0100.0015.5150.1880.1880.0000.0000.0000.000
168A415ILE0-0.020-0.0046.6310.0060.0060.0000.0000.0000.000
169A416VAL0-0.0090.0019.558-0.095-0.0950.0000.0000.0000.000
170A417ASP-1-0.828-0.8795.0384.0284.104-0.001-0.001-0.0740.000
171A418THR0-0.073-0.0638.706-0.201-0.2010.0000.0000.0000.000
172A419ALA0-0.019-0.00810.774-0.140-0.1400.0000.0000.0000.000
173A420GLN00.015-0.00711.595-0.146-0.1460.0000.0000.0000.000
174A421LYS10.8040.9059.983-0.964-0.9640.0000.0000.0000.000
175A422TYR0-0.079-0.06712.793-0.078-0.0780.0000.0000.0000.000
176A423HIS10.7580.87316.109-0.590-0.5900.0000.0000.0000.000
177A424PRO00.0420.03616.3620.0150.0150.0000.0000.0000.000
178A425ASP-1-0.869-0.93217.0600.7020.7020.0000.0000.0000.000
179A426ASN0-0.0160.00218.977-0.064-0.0640.0000.0000.0000.000
180A427VAL0-0.001-0.01718.8780.0100.0100.0000.0000.0000.000
181A428ARG10.9220.96020.052-0.353-0.3530.0000.0000.0000.000
182A429HIS0-0.031-0.00716.832-0.038-0.0380.0000.0000.0000.000
183A430VAL00.0580.02514.314-0.044-0.0440.0000.0000.0000.000
184A431PRO0-0.009-0.01417.450-0.051-0.0510.0000.0000.0000.000
185A432ALA0-0.0040.00320.513-0.042-0.0420.0000.0000.0000.000
186A433VAL00.0390.01418.229-0.042-0.0420.0000.0000.0000.000
187A434LEU0-0.001-0.00415.753-0.043-0.0430.0000.0000.0000.000
188A435LEU0-0.012-0.00119.812-0.041-0.0410.0000.0000.0000.000
189A436LEU0-0.0130.01022.987-0.032-0.0320.0000.0000.0000.000
190A437LEU00.0390.01218.542-0.028-0.0280.0000.0000.0000.000
191A438THR0-0.062-0.03423.236-0.026-0.0260.0000.0000.0000.000
192A439HIS00.0210.01726.319-0.027-0.0270.0000.0000.0000.000
193A440ILE00.0020.00924.163-0.013-0.0130.0000.0000.0000.000
194A441ARG10.8100.88023.364-0.049-0.0490.0000.0000.0000.000
195A442GLN0-0.019-0.00127.474-0.009-0.0090.0000.0000.0000.000
196A443ALA00.0200.00330.043-0.009-0.0090.0000.0000.0000.000
197A444GLY00.011-0.00129.195-0.009-0.0090.0000.0000.0000.000
198A445GLU-1-0.895-0.94230.1840.0030.0030.0000.0000.0000.000
199A446ARG10.7730.86732.609-0.063-0.0630.0000.0000.0000.000
200A447GLY00.0170.00233.724-0.004-0.0040.0000.0000.0000.000
201A448ILE00.0400.01830.131-0.006-0.0060.0000.0000.0000.000
202A449ALA0-0.013-0.00134.575-0.005-0.0050.0000.0000.0000.000
203A450PHE0-0.017-0.01737.747-0.003-0.0030.0000.0000.0000.000
204A451PHE00.028-0.01435.356-0.003-0.0030.0000.0000.0000.000
205A452GLN00.0360.02437.112-0.008-0.0080.0000.0000.0000.000
206A453ARG10.8420.93739.791-0.005-0.0050.0000.0000.0000.000
207A454LEU00.0230.02140.339-0.002-0.0020.0000.0000.0000.000
208A455LYS10.7550.87239.3470.0420.0420.0000.0000.0000.000
209A456SER0-0.099-0.05343.143-0.001-0.0010.0000.0000.0000.000
210A457GLU-1-0.878-0.94445.719-0.003-0.0030.0000.0000.0000.000
211A458GLY0-0.0130.00746.7020.0010.0010.0000.0000.0000.000
212A459VAL0-0.049-0.03348.080-0.002-0.0020.0000.0000.0000.000
213A460VAL0-0.043-0.01542.3330.0000.0000.0000.0000.0000.000
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