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: JQMJ9

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2842113.552607
FMO2-HF: Nuclear repulsion 2751762.514584
FMO2-HF: Total energy -90351.038023
FMO2-MP2: Total energy -90612.132125


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.
-3.240.5135.174-3.47-5.456-0.006
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 : -0.015 / q_NPA : -0.020
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].
3A250VAL00.008-0.0012.915-5.026-2.2140.581-1.354-2.0380.010
4A251THR00.0090.0072.020-5.889-5.5734.587-1.947-2.956-0.016
5A252ILE00.0250.0183.7030.5431.1680.006-0.169-0.4620.000
6A253LEU00.0030.0035.8200.5000.5000.0000.0000.0000.000
7A254GLN0-0.056-0.0386.089-0.252-0.2520.0000.0000.0000.000
8A255ALA0-0.021-0.0017.9450.1460.1460.0000.0000.0000.000
9A256LEU00.0300.0209.9130.1630.1630.0000.0000.0000.000
10A257ASN00.0500.02611.3260.1610.1610.0000.0000.0000.000
11A258LYS10.8680.93912.8630.6170.6170.0000.0000.0000.000
12A259ALA0-0.024-0.02614.657-0.005-0.0050.0000.0000.0000.000
13A260ALA0-0.0040.01516.0320.0200.0200.0000.0000.0000.000
14A261LEU0-0.033-0.02317.9890.0070.0070.0000.0000.0000.000
15A262PRO0-0.0280.01221.5500.0160.0160.0000.0000.0000.000
16A263VAL00.008-0.00323.5190.0110.0110.0000.0000.0000.000
17A264LEU0-0.053-0.02326.788-0.010-0.0100.0000.0000.0000.000
18A265GLU-1-0.881-0.94229.608-0.021-0.0210.0000.0000.0000.000
19A266SER0-0.101-0.09433.153-0.006-0.0060.0000.0000.0000.000
20A267HIS0-0.019-0.01534.7780.0000.0000.0000.0000.0000.000
21A268HIS00.0370.06138.432-0.002-0.0020.0000.0000.0000.000
22A269ASN00.0140.00140.5610.0020.0020.0000.0000.0000.000
23A270HIS0-0.001-0.02240.2330.0020.0020.0000.0000.0000.000
24A271GLY0-0.0180.00945.3790.0020.0020.0000.0000.0000.000
25A272GLN0-0.073-0.03447.8670.0010.0010.0000.0000.0000.000
26A273PRO00.0490.01548.1350.0010.0010.0000.0000.0000.000
27A274PRO00.0330.03345.695-0.002-0.0020.0000.0000.0000.000
28A275THR0-0.010-0.01747.0100.0020.0020.0000.0000.0000.000
29A276LYS10.9260.94745.683-0.020-0.0200.0000.0000.0000.000
30A277VAL00.023-0.00244.841-0.001-0.0010.0000.0000.0000.000
31A278HIS0-0.057-0.03244.823-0.003-0.0030.0000.0000.0000.000
32A279LEU00.0140.01341.660-0.002-0.0020.0000.0000.0000.000
33A280LEU00.0300.01240.542-0.001-0.0010.0000.0000.0000.000
34A281ASN00.0230.01840.107-0.004-0.0040.0000.0000.0000.000
35A282SER0-0.009-0.02338.571-0.006-0.0060.0000.0000.0000.000
36A283LEU0-0.006-0.00735.597-0.004-0.0040.0000.0000.0000.000
37A284VAL0-0.0020.00735.293-0.003-0.0030.0000.0000.0000.000
38A285LYS10.8020.88935.7400.0230.0230.0000.0000.0000.000
39A286LEU0-0.046-0.02731.508-0.008-0.0080.0000.0000.0000.000
40A287ALA00.0390.02331.360-0.006-0.0060.0000.0000.0000.000
41A288GLU-1-0.758-0.88130.716-0.043-0.0430.0000.0000.0000.000
42A289ARG10.8240.90030.6630.0360.0360.0000.0000.0000.000
43A290GLU-1-0.785-0.87427.097-0.025-0.0250.0000.0000.0000.000
44A291LEU00.0310.01826.085-0.012-0.0120.0000.0000.0000.000
45A292VAL0-0.007-0.00326.197-0.014-0.0140.0000.0000.0000.000
46A293HIS0-0.010-0.00923.236-0.028-0.0280.0000.0000.0000.000
47A294LEU00.0120.01621.821-0.026-0.0260.0000.0000.0000.000
48A295ILE00.0170.00821.342-0.025-0.0250.0000.0000.0000.000
49A296ASN0-0.104-0.05420.934-0.040-0.0400.0000.0000.0000.000
50A297TRP0-0.011-0.00715.314-0.026-0.0260.0000.0000.0000.000
51A298ALA00.0580.02616.809-0.055-0.0550.0000.0000.0000.000
52A299LYS10.9190.96216.6000.1940.1940.0000.0000.0000.000
53A300ASN0-0.0200.00013.703-0.105-0.1050.0000.0000.0000.000
54A301VAL0-0.0090.00212.150-0.137-0.1370.0000.0000.0000.000
55A302PRO0-0.002-0.0047.9040.0160.0160.0000.0000.0000.000
56A303GLY00.0670.02710.5330.1090.1090.0000.0000.0000.000
57A304TYR00.012-0.01612.7070.0800.0800.0000.0000.0000.000
58A305THR0-0.029-0.01915.6990.0370.0370.0000.0000.0000.000
59A306ASP-1-0.954-0.97514.086-0.545-0.5450.0000.0000.0000.000
60A307LEU0-0.060-0.00716.7300.0540.0540.0000.0000.0000.000
61A308SER0-0.001-0.02119.424-0.018-0.0180.0000.0000.0000.000
62A309LEU00.032-0.00223.1080.0050.0050.0000.0000.0000.000
63A310SER00.0450.01324.9790.0060.0060.0000.0000.0000.000
64A311ASP-1-0.772-0.83722.422-0.045-0.0450.0000.0000.0000.000
65A312GLN0-0.071-0.02720.2700.0070.0070.0000.0000.0000.000
66A313VAL0-0.0100.00322.6640.0040.0040.0000.0000.0000.000
67A314HIS00.0350.01425.1200.0030.0030.0000.0000.0000.000
68A315LEU0-0.015-0.01519.2780.0130.0130.0000.0000.0000.000
69A316ILE00.0240.01321.6490.0140.0140.0000.0000.0000.000
70A317GLU-1-0.885-0.96424.634-0.031-0.0310.0000.0000.0000.000
71A318CYS0-0.072-0.02625.2450.0130.0130.0000.0000.0000.000
72A319CYS0-0.036-0.00622.6850.0040.0040.0000.0000.0000.000
73A320TRP00.0250.00924.8960.0020.0020.0000.0000.0000.000
74A321MET0-0.0090.01126.3350.0010.0010.0000.0000.0000.000
75A322GLU-1-0.781-0.88324.5440.0970.0970.0000.0000.0000.000
76A323LEU0-0.033-0.01820.1620.0070.0070.0000.0000.0000.000
77A324LEU0-0.0030.00523.9540.0030.0030.0000.0000.0000.000
78A325LEU0-0.014-0.00326.9210.0050.0050.0000.0000.0000.000
79A326LEU00.0210.02520.0220.0100.0100.0000.0000.0000.000
80A327ASN00.0320.00421.8160.0170.0170.0000.0000.0000.000
81A328CYS0-0.0150.01124.3530.0040.0040.0000.0000.0000.000
82A329ALA00.0270.02226.0040.0050.0050.0000.0000.0000.000
83A330PHE00.005-0.00820.4980.0050.0050.0000.0000.0000.000
84A331ARG10.7340.82124.572-0.001-0.0010.0000.0000.0000.000
85A332SER0-0.036-0.02826.580-0.006-0.0060.0000.0000.0000.000
86A333ILE00.0070.02724.1430.0030.0030.0000.0000.0000.000
87A334GLU-1-0.864-0.93027.9590.0680.0680.0000.0000.0000.000
88A335HIS0-0.104-0.05030.153-0.001-0.0010.0000.0000.0000.000
89A336GLY00.0600.01531.691-0.002-0.0020.0000.0000.0000.000
90A337GLY00.0210.02532.6590.0000.0000.0000.0000.0000.000
91A338LYS10.7900.90334.156-0.071-0.0710.0000.0000.0000.000
92A339SER0-0.008-0.03435.380-0.005-0.0050.0000.0000.0000.000
93A340LEU0-0.011-0.00231.4550.0060.0060.0000.0000.0000.000
94A341ALA0-0.0030.00230.780-0.007-0.0070.0000.0000.0000.000
95A342PHE00.0200.00230.590-0.002-0.0020.0000.0000.0000.000
96A343ALA00.0560.02830.947-0.008-0.0080.0000.0000.0000.000
97A344PRO00.0170.01030.7170.0060.0060.0000.0000.0000.000
98A345ASP-1-0.731-0.82333.350-0.007-0.0070.0000.0000.0000.000
99A346LEU0-0.032-0.01035.5470.0000.0000.0000.0000.0000.000
100A347VAL00.0090.00634.4750.0030.0030.0000.0000.0000.000
101A348LEU0-0.017-0.00336.458-0.001-0.0010.0000.0000.0000.000
102A349ASP-1-0.749-0.85537.6120.0460.0460.0000.0000.0000.000
103A350ARG10.8750.91637.500-0.079-0.0790.0000.0000.0000.000
104A351SER0-0.038-0.03641.686-0.001-0.0010.0000.0000.0000.000
105A352SER0-0.020-0.02541.330-0.004-0.0040.0000.0000.0000.000
106A353TRP0-0.027-0.02536.523-0.001-0.0010.0000.0000.0000.000
107A354SER00.0290.01841.5690.0000.0000.0000.0000.0000.000
108A355THR0-0.069-0.01345.056-0.002-0.0020.0000.0000.0000.000
109A356VAL0-0.052-0.03740.489-0.003-0.0030.0000.0000.0000.000
110A357GLU-1-0.843-0.90243.0220.0230.0230.0000.0000.0000.000
111A358MET0-0.0150.00238.3220.0010.0010.0000.0000.0000.000
112A359THR00.0170.00038.7010.0020.0020.0000.0000.0000.000
113A360GLU-1-0.836-0.91037.8680.0690.0690.0000.0000.0000.000
114A361ILE00.0150.00833.8280.0060.0060.0000.0000.0000.000
115A362PHE00.025-0.00834.2050.0060.0060.0000.0000.0000.000
116A363GLU-1-0.810-0.88034.9190.0780.0780.0000.0000.0000.000
117A364GLN0-0.041-0.01531.3760.0000.0000.0000.0000.0000.000
118A365VAL0-0.009-0.01429.3460.0110.0110.0000.0000.0000.000
119A366ALA0-0.011-0.00430.3010.0080.0080.0000.0000.0000.000
120A367ALA00.0340.01732.1010.0070.0070.0000.0000.0000.000
121A368VAL00.0080.00226.0610.0140.0140.0000.0000.0000.000
122A369SER0-0.041-0.03727.4030.0140.0140.0000.0000.0000.000
123A370GLU-1-0.928-0.96328.1680.1370.1370.0000.0000.0000.000
124A371GLN00.005-0.00326.6220.0180.0180.0000.0000.0000.000
125A372MET0-0.0430.00523.3110.0250.0250.0000.0000.0000.000
126A373MET00.0210.01624.6190.0150.0150.0000.0000.0000.000
127A374GLN0-0.023-0.01126.7500.0110.0110.0000.0000.0000.000
128A375ASN0-0.107-0.04822.5840.0330.0330.0000.0000.0000.000
129A376HIS0-0.096-0.05522.2760.0250.0250.0000.0000.0000.000
130A377LEU0-0.034-0.00718.5030.0290.0290.0000.0000.0000.000
131A378HIS00.0610.03514.786-0.024-0.0240.0000.0000.0000.000
132A379LYS10.9690.96615.8960.0250.0250.0000.0000.0000.000
133A380ASP-1-0.804-0.89911.5500.3910.3910.0000.0000.0000.000
134A381GLU-1-0.723-0.84913.0060.4480.4480.0000.0000.0000.000
135A382LEU00.0080.02614.939-0.013-0.0130.0000.0000.0000.000
136A383LEU0-0.060-0.02912.646-0.029-0.0290.0000.0000.0000.000
137A384LEU0-0.002-0.0078.994-0.073-0.0730.0000.0000.0000.000
138A385LEU00.0060.00213.040-0.001-0.0010.0000.0000.0000.000
139A386GLN00.0000.00416.362-0.004-0.0040.0000.0000.0000.000
140A387ALA00.001-0.00513.088-0.014-0.0140.0000.0000.0000.000
141A388MET0-0.009-0.00112.803-0.012-0.0120.0000.0000.0000.000
142A389VAL0-0.022-0.01815.4470.0070.0070.0000.0000.0000.000
143A390LEU0-0.012-0.01716.993-0.003-0.0030.0000.0000.0000.000
144A391VAL0-0.049-0.03113.892-0.006-0.0060.0000.0000.0000.000
145A392ASN0-0.025-0.00717.1200.0480.0480.0000.0000.0000.000
146A393ALA0-0.0340.00119.2740.0080.0080.0000.0000.0000.000
147A394GLU-1-0.768-0.85122.0760.0640.0640.0000.0000.0000.000
148A395VAL00.0210.01222.4240.0110.0110.0000.0000.0000.000
149A396ARG10.8030.87324.092-0.041-0.0410.0000.0000.0000.000
150A397ARG10.8650.93023.158-0.136-0.1360.0000.0000.0000.000
151A398LEU00.0630.04722.561-0.010-0.0100.0000.0000.0000.000
152A399ALA00.0200.00223.8860.0100.0100.0000.0000.0000.000
153A400SER0-0.011-0.03319.513-0.011-0.0110.0000.0000.0000.000
154A401TYR00.0150.01019.1210.0060.0060.0000.0000.0000.000
155A402ASN00.0260.00017.1880.0710.0710.0000.0000.0000.000
156A403GLN0-0.012-0.00315.0470.0840.0840.0000.0000.0000.000
157A404ILE00.0730.02814.2360.0000.0000.0000.0000.0000.000
158A405PHE0-0.0150.00314.6440.0510.0510.0000.0000.0000.000
159A406ASN0-0.043-0.04111.1030.1870.1870.0000.0000.0000.000
160A407MET0-0.0360.00110.0620.1340.1340.0000.0000.0000.000
161A408GLN0-0.011-0.00210.436-0.019-0.0190.0000.0000.0000.000
162A409GLN00.0230.0079.725-0.068-0.0680.0000.0000.0000.000
163A410SER00.0330.0275.7680.1910.1910.0000.0000.0000.000
164A411LEU0-0.016-0.0176.3560.0120.0120.0000.0000.0000.000
165A412LEU0-0.025-0.0158.8710.0560.0560.0000.0000.0000.000
166A413ASP-1-0.910-0.9475.5733.6123.6120.0000.0000.0000.000
167A414ALA00.0070.0015.662-0.030-0.0300.0000.0000.0000.000
168A415ILE0-0.025-0.0096.8510.0160.0160.0000.0000.0000.000
169A416VAL0-0.0010.0009.961-0.110-0.1100.0000.0000.0000.000
170A417ASP-1-0.829-0.8825.3243.3273.3270.0000.0000.0000.000
171A418THR0-0.092-0.0748.880-0.161-0.1610.0000.0000.0000.000
172A419ALA0-0.018-0.02010.585-0.135-0.1350.0000.0000.0000.000
173A420GLN00.0060.00011.522-0.114-0.1140.0000.0000.0000.000
174A421LYS10.8210.92910.038-0.938-0.9380.0000.0000.0000.000
175A422TYR0-0.079-0.07912.920-0.087-0.0870.0000.0000.0000.000
176A423HIS10.7530.87416.005-0.535-0.5350.0000.0000.0000.000
177A424PRO00.0360.03216.5270.0170.0170.0000.0000.0000.000
178A425ASP-1-0.879-0.93317.0980.5630.5630.0000.0000.0000.000
179A426ASN0-0.0190.00018.929-0.053-0.0530.0000.0000.0000.000
180A427VAL00.015-0.01019.1830.0290.0290.0000.0000.0000.000
181A428ARG10.9240.95520.419-0.304-0.3040.0000.0000.0000.000
182A429HIS0-0.038-0.00817.157-0.034-0.0340.0000.0000.0000.000
183A430VAL00.0840.03114.613-0.035-0.0350.0000.0000.0000.000
184A431PRO0-0.015-0.00517.800-0.043-0.0430.0000.0000.0000.000
185A432ALA00.0220.01120.522-0.034-0.0340.0000.0000.0000.000
186A433VAL00.0470.01618.677-0.037-0.0370.0000.0000.0000.000
187A434LEU0-0.001-0.00416.099-0.036-0.0360.0000.0000.0000.000
188A435LEU0-0.029-0.00720.144-0.034-0.0340.0000.0000.0000.000
189A436LEU0-0.0050.00723.053-0.031-0.0310.0000.0000.0000.000
190A437LEU00.0170.00218.607-0.027-0.0270.0000.0000.0000.000
191A438THR0-0.050-0.02323.322-0.024-0.0240.0000.0000.0000.000
192A439HIS00.0220.01326.341-0.027-0.0270.0000.0000.0000.000
193A440ILE00.0050.00424.394-0.015-0.0150.0000.0000.0000.000
194A441ARG10.8500.92123.434-0.118-0.1180.0000.0000.0000.000
195A442GLN0-0.027-0.00427.515-0.010-0.0100.0000.0000.0000.000
196A443ALA00.0330.00530.259-0.010-0.0100.0000.0000.0000.000
197A444GLY00.0080.00429.181-0.011-0.0110.0000.0000.0000.000
198A445GLU-1-0.906-0.95030.1820.0450.0450.0000.0000.0000.000
199A446ARG10.8010.89232.405-0.086-0.0860.0000.0000.0000.000
200A447GLY00.008-0.00233.628-0.006-0.0060.0000.0000.0000.000
201A448ILE00.0220.01330.206-0.007-0.0070.0000.0000.0000.000
202A449ALA0-0.013-0.00734.607-0.006-0.0060.0000.0000.0000.000
203A450PHE0-0.062-0.04037.665-0.004-0.0040.0000.0000.0000.000
204A451PHE00.048-0.00435.185-0.004-0.0040.0000.0000.0000.000
205A452GLN00.0440.04537.189-0.007-0.0070.0000.0000.0000.000
206A453ARG10.9170.98140.000-0.029-0.0290.0000.0000.0000.000
207A454LEU00.0350.01140.527-0.002-0.0020.0000.0000.0000.000
208A455LYS10.7480.86839.3440.0100.0100.0000.0000.0000.000
209A456SER0-0.068-0.03842.827-0.001-0.0010.0000.0000.0000.000
210A457GLU-1-0.959-0.98345.7430.0140.0140.0000.0000.0000.000
211A458GLY0-0.016-0.00746.8220.0000.0000.0000.0000.0000.000
212A459VAL0-0.040-0.01147.964-0.002-0.0020.0000.0000.0000.000
213A460VAL0-0.037-0.01142.224-0.002-0.0020.0000.0000.0000.000
214A461THR00.0160.00143.650-0.001-0.0010.0000.0000.0000.000
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