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: VR9L1

Calculation Name: 3KEY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KEY

Chain ID: A

ChEMBL ID:

UniProt ID: P38960

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1824903.321116
FMO2-HF: Nuclear repulsion 1754637.585947
FMO2-HF: Total energy -70265.735168
FMO2-MP2: Total energy -70471.28361


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:312:ARG)


Summations of interaction energy for fragment #1(A:312:ARG)
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.
44.09143.3615.464-7.405-7.328-0.073
Interaction energy analysis for fragmet #1(A:312:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.978 / q_NPA : 0.969
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].
3A314SER00.0550.0342.888-11.556-8.5540.383-1.609-1.776-0.005
4A315ALA00.0740.0404.962-3.224-3.2240.0000.0000.0000.000
5A316LYS10.8740.9175.86325.28225.2820.0000.0000.0000.000
6A317SER00.014-0.0026.5161.5571.5570.0000.0000.0000.000
7A318ASN0-0.074-0.0331.920-33.704-37.73115.082-5.756-5.299-0.068
8A319LEU00.0580.0355.1312.3652.425-0.001-0.005-0.0540.000
9A320MET0-0.013-0.0028.6392.6642.6640.0000.0000.0000.000
10A321LEU0-0.029-0.0154.8871.1151.1150.0000.0000.0000.000
11A322ILE00.0040.0076.7842.4032.4030.0000.0000.0000.000
12A323LEU0-0.014-0.0189.2692.3482.3480.0000.0000.0000.000
13A324LEU0-0.025-0.00311.5681.7061.7060.0000.0000.0000.000
14A325GLY00.0210.01611.6311.3271.3270.0000.0000.0000.000
15A326LEU00.0090.01012.8201.3581.3580.0000.0000.0000.000
16A327GLN0-0.027-0.00915.2941.3311.3310.0000.0000.0000.000
17A328MET0-0.011-0.00118.2190.7690.7690.0000.0000.0000.000
18A329LYS10.9840.98619.74110.79710.7970.0000.0000.0000.000
19A330GLU-1-0.850-0.91321.068-12.007-12.0070.0000.0000.0000.000
20A331ILE00.0070.00217.081-0.158-0.1580.0000.0000.0000.000
21A332SER00.0650.02620.784-0.102-0.1020.0000.0000.0000.000
22A333ASN00.0450.00019.176-1.384-1.3840.0000.0000.0000.000
23A334SER0-0.003-0.01519.496-0.467-0.4670.0000.0000.0000.000
24A335ASP-1-0.833-0.88020.411-13.193-13.1930.0000.0000.0000.000
25A336LEU00.0010.00413.702-0.721-0.7210.0000.0000.0000.000
26A337TYR0-0.019-0.01215.252-0.950-0.9500.0000.0000.0000.000
27A338LYS10.8470.91116.82913.00813.0080.0000.0000.0000.000
28A339LEU0-0.0050.01513.424-0.153-0.1530.0000.0000.0000.000
29A340LYS11.0221.00012.19319.59019.5900.0000.0000.0000.000
30A341GLU-1-0.908-0.9428.054-30.398-30.3980.0000.0000.0000.000
31A342VAL00.0280.0108.629-2.906-2.9060.0000.0000.0000.000
32A343ARG10.8710.91910.47117.19917.1990.0000.0000.0000.000
33A344SER0-0.020-0.0148.3730.3160.3160.0000.0000.0000.000
34A345VAL0-0.050-0.0215.063-1.736-1.7360.0000.0000.0000.000
35A346VAL0-0.021-0.0057.5220.8360.8360.0000.0000.0000.000
36A347THR00.004-0.02111.1410.8390.8390.0000.0000.0000.000
37A348SER0-0.0320.0038.0490.1140.1140.0000.0000.0000.000
38A349LEU00.0010.0069.5701.1971.1970.0000.0000.0000.000
39A350ALA00.0400.01310.9271.3961.3960.0000.0000.0000.000
40A351SER0-0.044-0.03412.3511.2771.2770.0000.0000.0000.000
41A352PHE00.0010.01512.2730.6720.6720.0000.0000.0000.000
42A353LEU0-0.010-0.02114.2201.0921.0920.0000.0000.0000.000
43A354PHE00.003-0.00616.8480.9680.9680.0000.0000.0000.000
44A355GLN0-0.034-0.02615.2851.1081.1080.0000.0000.0000.000
45A356GLN0-0.051-0.01217.0570.1500.1500.0000.0000.0000.000
46A357GLN0-0.0300.00019.8380.7530.7530.0000.0000.0000.000
47A358ASN00.0180.01123.0080.2230.2230.0000.0000.0000.000
48A359VAL00.0440.01226.1580.0450.0450.0000.0000.0000.000
49A360GLY00.0210.01328.9270.2920.2920.0000.0000.0000.000
50A361VAL0-0.084-0.03325.4510.1380.1380.0000.0000.0000.000
51A362MET00.017-0.00125.794-0.469-0.4690.0000.0000.0000.000
52A363LYS10.8550.93022.35813.43213.4320.0000.0000.0000.000
53A364SER00.0460.02024.201-0.278-0.2780.0000.0000.0000.000
54A365PHE00.0530.00715.234-0.211-0.2110.0000.0000.0000.000
55A366ASP-1-0.797-0.88219.146-13.799-13.7990.0000.0000.0000.000
56A367SER0-0.0120.00220.369-0.294-0.2940.0000.0000.0000.000
57A368LEU00.0370.01517.946-0.312-0.3120.0000.0000.0000.000
58A369GLU-1-0.804-0.87415.077-19.475-19.4750.0000.0000.0000.000
59A370LYS10.8120.89216.10812.55812.5580.0000.0000.0000.000
60A371GLU-1-0.821-0.87718.376-14.152-14.1520.0000.0000.0000.000
61A372ALA00.0210.00013.043-0.266-0.2660.0000.0000.0000.000
62A373PHE0-0.020-0.01313.658-1.229-1.2290.0000.0000.0000.000
63A374ARG10.8960.92114.80314.47314.4730.0000.0000.0000.000
64A375ASP-1-0.802-0.88414.906-16.790-16.7900.0000.0000.0000.000
65A376LEU0-0.079-0.0309.172-0.559-0.5590.0000.0000.0000.000
66A377VAL00.0160.01112.937-0.426-0.4260.0000.0000.0000.000
67A378ASN00.0290.01415.5650.5510.5510.0000.0000.0000.000
68A379ARG10.8290.89912.57820.63320.6330.0000.0000.0000.000
69A380LEU0-0.020-0.00411.518-0.063-0.0630.0000.0000.0000.000
70A381VAL00.0260.01315.3210.5130.5130.0000.0000.0000.000
71A382SER0-0.020-0.01218.6890.7140.7140.0000.0000.0000.000
72A383GLN0-0.049-0.00914.534-1.154-1.1540.0000.0000.0000.000
73A384GLY00.0820.03018.7530.1040.1040.0000.0000.0000.000
74A385LEU0-0.081-0.03013.7420.0140.0140.0000.0000.0000.000
75A386ILE0-0.028-0.01215.697-0.306-0.3060.0000.0000.0000.000
76A387GLY00.0350.02118.8060.3930.3930.0000.0000.0000.000
77A388LEU0-0.030-0.02321.514-0.519-0.5190.0000.0000.0000.000
78A389LYS10.7970.90023.86812.34812.3480.0000.0000.0000.000
79A390ASP-1-0.745-0.84526.412-9.857-9.8570.0000.0000.0000.000
80A391LYS10.7950.89125.55411.31311.3130.0000.0000.0000.000
81A392THR0-0.026-0.02628.4290.0100.0100.0000.0000.0000.000
82A393SER0-0.056-0.04127.968-0.062-0.0620.0000.0000.0000.000
83A394GLU-1-0.827-0.89623.356-12.674-12.6740.0000.0000.0000.000
84A395THR0-0.004-0.00323.008-0.811-0.8110.0000.0000.0000.000
85A396PHE00.001-0.01618.8840.1010.1010.0000.0000.0000.000
86A397ASP-1-0.827-0.93821.413-12.639-12.6390.0000.0000.0000.000
87A398LEU0-0.005-0.01516.351-0.605-0.6050.0000.0000.0000.000
88A399LEU00.0150.00918.922-0.476-0.4760.0000.0000.0000.000
89A400PRO0-0.0060.00620.119-0.146-0.1460.0000.0000.0000.000
90A401LEU00.0240.01613.139-0.157-0.1570.0000.0000.0000.000
91A402LYS10.8700.92516.58916.39916.3990.0000.0000.0000.000
92A403ASN00.0260.01518.567-0.075-0.0750.0000.0000.0000.000
93A404LEU0-0.008-0.00218.2310.1850.1850.0000.0000.0000.000
94A405PHE00.007-0.01711.655-0.554-0.5540.0000.0000.0000.000
95A406GLU-1-0.845-0.90317.402-13.267-13.2670.0000.0000.0000.000
96A407TYR0-0.039-0.02020.6410.6980.6980.0000.0000.0000.000
97A408ALA00.0150.00117.2670.3900.3900.0000.0000.0000.000
98A409GLU-1-0.842-0.93315.327-19.033-19.0330.0000.0000.0000.000
99A410LYS10.8370.91318.78013.36513.3650.0000.0000.0000.000
100A411ARG10.8900.95621.20212.72812.7280.0000.0000.0000.000
101A412ILE00.0290.00315.9710.3820.3820.0000.0000.0000.000
102A413SER00.0280.01920.1770.6970.6970.0000.0000.0000.000
103A414VAL0-0.043-0.02722.3110.4070.4070.0000.0000.0000.000
104A415LEU00.0140.00421.3360.3640.3640.0000.0000.0000.000
105A416MET00.0160.01619.3360.0080.0080.0000.0000.0000.000
106A417LYS10.8910.95223.38612.26612.2660.0000.0000.0000.000
107A418LEU0-0.027-0.00126.6480.4090.4090.0000.0000.0000.000
108A419GLN0-0.042-0.01325.2820.3190.3190.0000.0000.0000.000
109A420CYS0-0.018-0.00824.4150.2500.2500.0000.0000.0000.000
110A421TYR00.0430.02722.774-0.605-0.6050.0000.0000.0000.000
111A422THR00.001-0.00821.652-0.413-0.4130.0000.0000.0000.000
112A423GLY0-0.001-0.00222.1640.5290.5290.0000.0000.0000.000
113A424THR0-0.026-0.01222.073-0.456-0.4560.0000.0000.0000.000
114A425VAL0-0.101-0.05220.7900.2710.2710.0000.0000.0000.000
115A426GLN00.0270.00622.782-0.192-0.1920.0000.0000.0000.000
116A427LEU0-0.001-0.01322.687-0.191-0.1910.0000.0000.0000.000
117A428SER00.0420.00624.827-0.145-0.1450.0000.0000.0000.000
118A429HIS00.0130.01927.1330.0050.0050.0000.0000.0000.000
119A430VAL0-0.029-0.01222.150-0.021-0.0210.0000.0000.0000.000
120A431GLN0-0.050-0.02725.4690.3260.3260.0000.0000.0000.000
121A432GLU-1-0.876-0.93127.315-9.518-9.5180.0000.0000.0000.000
122A433LYS10.8930.95027.80810.45010.4500.0000.0000.0000.000
123A434LEU0-0.058-0.04122.909-0.041-0.0410.0000.0000.0000.000
124A435HIS00.0200.02626.857-0.157-0.1570.0000.0000.0000.000
125A436LEU0-0.038-0.01122.139-0.221-0.2210.0000.0000.0000.000
126A437PRO00.038-0.00725.667-0.385-0.3850.0000.0000.0000.000
127A438TYR00.0030.00624.2350.0020.0020.0000.0000.0000.000
128A439ILE0-0.0550.00019.465-0.498-0.4980.0000.0000.0000.000
129A440THR00.0480.02619.2490.2140.2140.0000.0000.0000.000
130A441THR00.0780.03219.537-0.729-0.7290.0000.0000.0000.000
131A442ASN00.0220.00115.466-0.542-0.5420.0000.0000.0000.000
132A443GLY0-0.0090.00014.696-1.473-1.4730.0000.0000.0000.000
133A444ILE00.0240.01115.637-1.058-1.0580.0000.0000.0000.000
134A445VAL00.0240.01012.248-0.757-0.7570.0000.0000.0000.000
135A446ASP-1-0.784-0.87310.578-28.607-28.6070.0000.0000.0000.000
136A447VAL00.0170.01411.344-1.860-1.8600.0000.0000.0000.000
137A448PHE00.0860.03113.282-0.425-0.4250.0000.0000.0000.000
138A449LYS10.8650.9377.97425.46425.4640.0000.0000.0000.000
139A450GLU-1-0.807-0.8986.947-38.647-38.6470.0000.0000.0000.000
140A451CYS0-0.0220.0029.8900.2490.2490.0000.0000.0000.000
141A452LEU00.0460.03912.0280.5970.5970.0000.0000.0000.000
142A453LYS10.8190.9133.88446.99547.2290.000-0.035-0.1990.000
143A454ARG10.7700.8839.58225.55725.5570.0000.0000.0000.000
144A455THR00.012-0.01611.4591.1201.1200.0000.0000.0000.000
145A456LYS10.8950.93111.45120.03720.0370.0000.0000.0000.000
146A457LYS10.8990.9457.45230.90830.9080.0000.0000.0000.000
147A458GLN0-0.027-0.00112.8831.0471.0470.0000.0000.0000.000
148A459TYR00.0110.01516.0961.0841.0840.0000.0000.0000.000
149A460PRO00.0130.01915.9160.2100.2100.0000.0000.0000.000
150A461GLU-1-0.889-0.95217.634-13.737-13.7370.0000.0000.0000.000
151A462VAL0-0.026-0.02420.3080.5700.5700.0000.0000.0000.000
152A463LEU0-0.020-0.01315.0730.1900.1900.0000.0000.0000.000
153A464LYS10.8590.92916.45112.44612.4460.0000.0000.0000.000
154A465ASN0-0.096-0.06513.756-2.115-2.1150.0000.0000.0000.000
155A466TRP00.0230.0248.5960.2650.2650.0000.0000.0000.000
156A467TRP00.0010.00112.843-0.800-0.8000.0000.0000.0000.000
157A468ILE0-0.057-0.03612.6580.2000.2000.0000.0000.0000.000
158A469ASP-1-0.804-0.87115.005-14.882-14.8820.0000.0000.0000.000
159A470LEU0-0.047-0.04517.073-0.245-0.2450.0000.0000.0000.000
160A471ASP-1-0.847-0.90920.103-11.180-11.1800.0000.0000.0000.000
161A480ASN0-0.004-0.02022.638-0.516-0.5160.0000.0000.0000.000
162A481SER00.0490.02723.720-0.081-0.0810.0000.0000.0000.000
163A482GLY00.0230.00223.0950.2060.2060.0000.0000.0000.000
164A483ILE0-0.073-0.01416.896-0.275-0.2750.0000.0000.0000.000
165A484LEU00.0220.02419.4820.3510.3510.0000.0000.0000.000
166A485LEU0-0.032-0.01316.654-0.768-0.7680.0000.0000.0000.000
167A486HIS00.0380.01617.2980.9730.9730.0000.0000.0000.000
168A487LEU0-0.050-0.03916.935-1.136-1.1360.0000.0000.0000.000
169A488GLU-1-0.768-0.86217.939-13.115-13.1150.0000.0000.0000.000
170A489TYR00.014-0.01718.868-0.694-0.6940.0000.0000.0000.000
171A490ALA0-0.050-0.02019.8100.0770.0770.0000.0000.0000.000
172A491ALA00.026-0.00321.7780.3360.3360.0000.0000.0000.000
173A492ALA0-0.0180.00324.2280.3820.3820.0000.0000.0000.000
174A493TYR0-0.003-0.00124.4920.3470.3470.0000.0000.0000.000
175A494SER0-0.064-0.02226.3010.2260.2260.0000.0000.0000.000