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

tag_button

FMODB ID: 4JYMN

Calculation Name: 3LPM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LPM

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2774323.776778
FMO2-HF: Nuclear repulsion 2686936.194714
FMO2-HF: Total energy -87387.582064
FMO2-MP2: Total energy -87645.001233


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:5:LYS)


Summations of interaction energy for fragment #1(A:5:LYS)
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.
-14.922-13.148-0.014-0.761-10.002
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.996 / q_NPA : 0.990
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].
3A7LYS10.8680.9233.88130.45132.019-0.013-0.752-0.8050.002
4A8LEU00.0570.0496.3460.0950.0950.0000.0000.0000.000
5A9ILE0-0.054-0.0339.6820.2900.2900.0000.0000.0000.000
6A10GLY00.0240.00812.1970.9800.9800.0000.0000.0000.000
7A11ASP-1-0.773-0.86915.113-14.489-14.4890.0000.0000.0000.000
8A12GLU-1-0.745-0.82212.673-22.270-22.2700.0000.0000.0000.000
9A13ARG10.8320.89113.67514.99314.9930.0000.0000.0000.000
10A14LEU00.0040.0008.441-0.362-0.3620.0000.0000.0000.000
11A15ASP-1-0.732-0.81112.432-15.219-15.2190.0000.0000.0000.000
12A16TYR0-0.029-0.02714.001-1.866-1.8660.0000.0000.0000.000
13A17LEU0-0.0300.00315.8880.7470.7470.0000.0000.0000.000
14A18LEU00.0330.00817.951-0.443-0.4430.0000.0000.0000.000
15A19ALA00.0080.01920.036-0.058-0.0580.0000.0000.0000.000
16A20GLU-1-0.895-0.96918.356-14.513-14.5130.0000.0000.0000.000
17A21ASN0-0.073-0.04116.564-0.948-0.9480.0000.0000.0000.000
18A22LEU00.0140.03413.171-1.317-1.3170.0000.0000.0000.000
19A23ARG10.8000.86810.50221.87921.8790.0000.0000.0000.000
20A24ILE00.0030.01712.662-0.772-0.7720.0000.0000.0000.000
21A25ILE0-0.027-0.0078.6240.5730.5730.0000.0000.0000.000
22A26GLN0-0.017-0.01512.8870.8330.8330.0000.0000.0000.000
23A27SER0-0.019-0.04916.407-0.312-0.3120.0000.0000.0000.000
24A28PRO0-0.025-0.00518.9820.3190.3190.0000.0000.0000.000
25A29SER0-0.025-0.01221.7300.6000.6000.0000.0000.0000.000
26A30VAL0-0.052-0.01220.3450.3030.3030.0000.0000.0000.000
27A31PHE00.0350.00419.5590.2460.2460.0000.0000.0000.000
28A32SER00.015-0.01119.744-0.896-0.8960.0000.0000.0000.000
29A33PHE00.0120.02418.9180.6070.6070.0000.0000.0000.000
30A34SER00.0310.01122.6350.2210.2210.0000.0000.0000.000
31A35ILE00.0550.00726.054-0.204-0.2040.0000.0000.0000.000
32A36ASP-1-0.795-0.85828.342-9.834-9.8340.0000.0000.0000.000
33A37ALA00.0470.02724.2920.0660.0660.0000.0000.0000.000
34A38VAL00.0190.01123.552-0.171-0.1710.0000.0000.0000.000
35A39LEU0-0.009-0.00225.7520.1230.1230.0000.0000.0000.000
36A40LEU00.0110.00427.7240.1720.1720.0000.0000.0000.000
37A41ALA00.0240.02224.2140.0910.0910.0000.0000.0000.000
38A42LYS10.8000.89226.17810.71110.7110.0000.0000.0000.000
39A43PHE0-0.030-0.00628.3870.2830.2830.0000.0000.0000.000
40A44SER00.004-0.00327.7500.3600.3600.0000.0000.0000.000
41A45TYR0-0.046-0.01429.150-0.205-0.2050.0000.0000.0000.000
42A46LEU00.0150.00125.062-0.013-0.0130.0000.0000.0000.000
43A47PRO0-0.020-0.00427.2010.3910.3910.0000.0000.0000.000
44A48ILE00.0170.00028.499-0.310-0.3100.0000.0000.0000.000
45A49ARG10.9570.96427.4759.7589.7580.0000.0000.0000.000
46A50LYS10.9360.97824.79411.86411.8640.0000.0000.0000.000
47A51GLY00.0660.03626.0560.0440.0440.0000.0000.0000.000
48A52LYS10.9070.94324.32311.80211.8020.0000.0000.0000.000
49A53ILE00.0300.01423.2730.6460.6460.0000.0000.0000.000
50A54ILE00.0160.01023.332-0.480-0.4800.0000.0000.0000.000
51A55ASP-1-0.758-0.87022.225-13.139-13.1390.0000.0000.0000.000
52A56LEU0-0.005-0.01423.579-0.347-0.3470.0000.0000.0000.000
53A57CYS0-0.092-0.05125.1160.4610.4610.0000.0000.0000.000
54A58SER00.004-0.01919.963-0.317-0.3170.0000.0000.0000.000
55A59GLY00.0310.02920.173-0.410-0.4100.0000.0000.0000.000
56A60ASN0-0.054-0.05115.867-0.008-0.0080.0000.0000.0000.000
57A61GLY00.0380.00915.539-1.277-1.2770.0000.0000.0000.000
58A62ILE0-0.012-0.00317.004-0.104-0.1040.0000.0000.0000.000
59A63ILE00.0220.01018.6920.0330.0330.0000.0000.0000.000
60A64PRO00.008-0.01517.4140.1310.1310.0000.0000.0000.000
61A65LEU00.0190.02412.963-0.149-0.1490.0000.0000.0000.000
62A66LEU00.0270.02416.9940.2330.2330.0000.0000.0000.000
63A67LEU0-0.075-0.03420.4320.8000.8000.0000.0000.0000.000
64A68SER0-0.034-0.02617.0710.1300.1300.0000.0000.0000.000
65A69THR00.0180.01217.3480.4120.4120.0000.0000.0000.000
66A70ARG10.8460.92019.70212.83912.8390.0000.0000.0000.000
67A71THR0-0.039-0.01722.2500.6410.6410.0000.0000.0000.000
68A72LYS10.9520.97120.99113.70413.7040.0000.0000.0000.000
69A73ALA0-0.046-0.01022.135-0.052-0.0520.0000.0000.0000.000
70A74LYS10.8460.92916.89617.17817.1780.0000.0000.0000.000
71A75ILE0-0.014-0.01318.7981.0211.0210.0000.0000.0000.000
72A76VAL00.0140.02018.559-0.801-0.8010.0000.0000.0000.000
73A77GLY00.0510.01319.1390.5890.5890.0000.0000.0000.000
74A78VAL0-0.062-0.02619.421-0.576-0.5760.0000.0000.0000.000
75A79GLU-1-0.818-0.90419.842-13.297-13.2970.0000.0000.0000.000
76A80ILE0-0.012-0.00220.924-0.468-0.4680.0000.0000.0000.000
77A81GLN0-0.068-0.04322.3320.2520.2520.0000.0000.0000.000
78A82GLU-1-0.796-0.90418.170-16.788-16.7880.0000.0000.0000.000
79A83ARG10.8470.93215.39917.47217.4720.0000.0000.0000.000
80A84LEU0-0.018-0.00816.474-1.019-1.0190.0000.0000.0000.000
81A85ALA00.0680.03016.436-0.936-0.9360.0000.0000.0000.000
82A86ASP-1-0.796-0.87812.133-26.475-26.4750.0000.0000.0000.000
83A87MET0-0.063-0.01911.943-1.969-1.9690.0000.0000.0000.000
84A88ALA00.0190.03612.176-1.502-1.5020.0000.0000.0000.000
85A89LYS10.8460.91510.55919.43219.4320.0000.0000.0000.000
86A90ARG10.7190.7997.58923.20823.2080.0000.0000.0000.000
87A91SER00.002-0.0077.284-3.498-3.4980.0000.0000.0000.000
88A92VAL0-0.029-0.0049.156-1.131-1.1310.0000.0000.0000.000
89A93ALA00.0260.0154.932-0.371-0.3710.0000.0000.0000.000
90A94TYR0-0.069-0.0324.757-5.639-5.433-0.001-0.009-0.1950.000
91A95ASN0-0.055-0.0625.7841.0371.0370.0000.0000.0000.000
92A96GLN0-0.049-0.0045.6862.8382.8380.0000.0000.0000.000
93A97LEU00.0200.0118.1153.1793.1790.0000.0000.0000.000
94A98GLU-1-0.856-0.9506.041-39.784-39.7840.0000.0000.0000.000
95A99ASP-1-0.913-0.94810.650-18.776-18.7760.0000.0000.0000.000
96A100GLN0-0.112-0.05713.3221.3931.3930.0000.0000.0000.000
97A101ILE0-0.008-0.00713.8671.5991.5990.0000.0000.0000.000
98A102GLU-1-0.916-0.95413.967-17.835-17.8350.0000.0000.0000.000
99A103ILE0-0.027-0.01114.2571.1671.1670.0000.0000.0000.000
100A104ILE0-0.038-0.02816.351-0.383-0.3830.0000.0000.0000.000
101A105GLU-1-0.812-0.89817.142-17.820-17.8200.0000.0000.0000.000
102A106TYR0-0.073-0.08120.9050.3590.3590.0000.0000.0000.000
103A107ASP-1-0.788-0.88224.582-10.276-10.2760.0000.0000.0000.000
104A108LEU00.0700.02827.5120.2090.2090.0000.0000.0000.000
105A109LYS10.8050.88728.72610.06710.0670.0000.0000.0000.000
106A110LYS10.8470.91230.62510.63710.6370.0000.0000.0000.000
107A111ILE00.0580.04124.414-0.116-0.1160.0000.0000.0000.000
108A112THR00.010-0.00427.987-0.192-0.1920.0000.0000.0000.000
109A113ASP-1-0.853-0.88928.843-10.151-10.1510.0000.0000.0000.000
110A114LEU0-0.027-0.00823.181-0.207-0.2070.0000.0000.0000.000
111A115ILE0-0.030-0.00424.226-0.333-0.3330.0000.0000.0000.000
112A116PRO0-0.020-0.01527.4050.4400.4400.0000.0000.0000.000
113A117LYS10.9370.96530.7748.2648.2640.0000.0000.0000.000
114A118GLU-1-0.840-0.91233.395-8.159-8.1590.0000.0000.0000.000
115A119ARG10.9000.95130.1639.7719.7710.0000.0000.0000.000
116A120ALA00.0020.01628.452-0.184-0.1840.0000.0000.0000.000
117A121ASP-1-0.841-0.92028.686-10.258-10.2580.0000.0000.0000.000
118A122ILE0-0.013-0.00527.7480.3660.3660.0000.0000.0000.000
119A123VAL0-0.0090.01327.864-0.319-0.3190.0000.0000.0000.000
120A124THR0-0.001-0.00226.0050.2450.2450.0000.0000.0000.000
121A125CYS00.0000.00727.511-0.307-0.3070.0000.0000.0000.000
122A126ASN00.0780.01726.4680.4960.4960.0000.0000.0000.000
123A127PRO00.0110.00927.602-0.343-0.3430.0000.0000.0000.000
124A128PRO00.0050.02026.7710.2490.2490.0000.0000.0000.000
125A152MET00.0570.01938.9830.0940.0940.0000.0000.0000.000
126A153CYS00.0460.01139.181-0.143-0.1430.0000.0000.0000.000
127A154THR00.0610.02834.060-0.108-0.1080.0000.0000.0000.000
128A155LEU0-0.0090.01335.098-0.268-0.2680.0000.0000.0000.000
129A156GLU-1-0.729-0.83336.587-7.638-7.6380.0000.0000.0000.000
130A157ASP-1-0.829-0.90534.756-8.792-8.7920.0000.0000.0000.000
131A158THR0-0.018-0.02431.214-0.172-0.1720.0000.0000.0000.000
132A159ILE00.0030.01033.321-0.171-0.1710.0000.0000.0000.000
133A160ARG10.8440.92135.5328.7608.7600.0000.0000.0000.000
134A161VAL0-0.0130.00130.4080.0250.0250.0000.0000.0000.000
135A162ALA00.0450.02031.800-0.128-0.1280.0000.0000.0000.000
136A163ALA00.0280.01332.813-0.049-0.0490.0000.0000.0000.000
137A164SER0-0.095-0.04333.5670.0390.0390.0000.0000.0000.000
138A165LEU00.0770.03728.355-0.044-0.0440.0000.0000.0000.000
139A166LEU0-0.0520.00131.329-0.124-0.1240.0000.0000.0000.000
140A167LYS10.8280.92631.03910.36110.3610.0000.0000.0000.000
141A168GLN0-0.019-0.03735.1160.0920.0920.0000.0000.0000.000
142A169GLY0-0.023-0.01437.534-0.086-0.0860.0000.0000.0000.000
143A170GLY0-0.0090.00134.082-0.106-0.1060.0000.0000.0000.000
144A171LYS10.7860.87732.7049.5989.5980.0000.0000.0000.000
145A172ALA00.0490.02731.987-0.388-0.3880.0000.0000.0000.000
146A173ASN0-0.033-0.02730.1820.4280.4280.0000.0000.0000.000
147A174PHE00.019-0.00930.953-0.331-0.3310.0000.0000.0000.000
148A175VAL00.0150.02330.2470.2040.2040.0000.0000.0000.000
149A176HIS0-0.004-0.01132.760-0.040-0.0400.0000.0000.0000.000
150A177ARG10.8770.91433.3159.0939.0930.0000.0000.0000.000
151A178PRO0-0.022-0.02438.2710.0690.0690.0000.0000.0000.000
152A179GLU-1-0.825-0.91441.355-7.659-7.6590.0000.0000.0000.000
153A180ARG10.7930.87740.4667.6667.6660.0000.0000.0000.000
154A181LEU0-0.0030.00240.489-0.045-0.0450.0000.0000.0000.000
155A182LEU00.0190.00342.559-0.028-0.0280.0000.0000.0000.000
156A183ASP-1-0.742-0.85843.518-7.099-7.0990.0000.0000.0000.000
157A184ILE0-0.042-0.01538.199-0.085-0.0850.0000.0000.0000.000
158A185ILE0-0.009-0.00341.554-0.091-0.0910.0000.0000.0000.000
159A186ASP-1-0.882-0.93743.566-6.700-6.7000.0000.0000.0000.000
160A187ILE0-0.056-0.03440.392-0.009-0.0090.0000.0000.0000.000
161A188MET0-0.049-0.03038.403-0.118-0.1180.0000.0000.0000.000
162A189ARG10.8400.89041.1386.8416.8410.0000.0000.0000.000
163A190LYS10.8100.90743.7167.3267.3260.0000.0000.0000.000
164A191TYR0-0.072-0.05639.7560.0020.0020.0000.0000.0000.000
165A192ARG10.7870.85640.3207.5667.5660.0000.0000.0000.000
166A193LEU0-0.0060.00236.356-0.132-0.1320.0000.0000.0000.000
167A194GLU-1-0.746-0.83740.511-6.903-6.9030.0000.0000.0000.000
168A195PRO00.0100.00040.733-0.196-0.1960.0000.0000.0000.000
169A196LYS10.7520.85840.0817.4307.4300.0000.0000.0000.000
170A197ARG10.7720.88433.7149.2549.2540.0000.0000.0000.000
171A198ILE00.0230.01838.990-0.116-0.1160.0000.0000.0000.000
172A199GLN0-0.016-0.01235.414-0.065-0.0650.0000.0000.0000.000
173A200PHE00.0330.02537.669-0.162-0.1620.0000.0000.0000.000
174A201VAL00.0060.00534.470-0.069-0.0690.0000.0000.0000.000
175A202HIS00.012-0.00837.7220.0340.0340.0000.0000.0000.000
176A203PRO00.0080.01137.538-0.131-0.1310.0000.0000.0000.000
177A204ARG10.9380.95138.4047.5517.5510.0000.0000.0000.000
178A205SER0-0.007-0.01041.1880.0100.0100.0000.0000.0000.000
179A206ASP-1-0.818-0.88943.986-6.856-6.8560.0000.0000.0000.000
180A207ARG10.8360.91242.9417.1167.1160.0000.0000.0000.000
181A208GLU-1-0.907-0.93944.122-6.939-6.9390.0000.0000.0000.000
182A209ALA0-0.039-0.01940.677-0.159-0.1590.0000.0000.0000.000
183A210ASN00.0430.01235.3550.1640.1640.0000.0000.0000.000
184A211THR0-0.064-0.04933.219-0.073-0.0730.0000.0000.0000.000
185A212VAL0-0.025-0.00636.5160.2160.2160.0000.0000.0000.000
186A213LEU0-0.0010.01832.084-0.238-0.2380.0000.0000.0000.000
187A214VAL00.012-0.00334.9300.3260.3260.0000.0000.0000.000
188A215GLU-1-0.746-0.86134.449-9.414-9.4140.0000.0000.0000.000
189A216GLY00.0300.01036.4300.3430.3430.0000.0000.0000.000
190A217ILE0-0.061-0.01436.782-0.240-0.2400.0000.0000.0000.000
191A218LYS10.7880.88136.8718.8278.8270.0000.0000.0000.000
192A219ASP-1-0.765-0.85638.927-7.676-7.6760.0000.0000.0000.000
193A220GLY0-0.0070.00842.0010.1540.1540.0000.0000.0000.000
194A221LYS10.8860.93043.1617.1277.1270.0000.0000.0000.000
195A222PRO00.0980.04545.881-0.122-0.1220.0000.0000.0000.000
196A223GLY00.0020.01047.3980.0360.0360.0000.0000.0000.000
197A224VAL00.0070.01642.943-0.147-0.1470.0000.0000.0000.000
198A225LYS10.9280.96042.2457.3217.3210.0000.0000.0000.000
199A226TYR00.0490.00942.036-0.228-0.2280.0000.0000.0000.000
200A227VAL0-0.034-0.01537.4940.1050.1050.0000.0000.0000.000
201A228PRO00.0280.00240.4220.0330.0330.0000.0000.0000.000
202A229PRO00.0230.02839.396-0.240-0.2400.0000.0000.0000.000
203A230VAL0-0.011-0.00734.0500.0050.0050.0000.0000.0000.000
204A231ILE00.0230.01637.4510.0350.0350.0000.0000.0000.000
205A232VAL0-0.0140.00032.888-0.146-0.1460.0000.0000.0000.000
206A233TYR0-0.031-0.01331.654-0.258-0.2580.0000.0000.0000.000
207A234ASP-1-0.784-0.89636.818-7.866-7.8660.0000.0000.0000.000
208A235GLU-1-0.939-0.98739.551-6.928-6.9280.0000.0000.0000.000
209A236LEU0-0.0150.01239.8150.0950.0950.0000.0000.0000.000
210A237GLY0-0.106-0.06238.0760.0450.0450.0000.0000.0000.000
211A238GLU-1-0.800-0.86732.012-9.798-9.7980.0000.0000.0000.000
212A239TYR0-0.035-0.02028.8500.0740.0740.0000.0000.0000.000
213A240THR00.022-0.00933.4610.0930.0930.0000.0000.0000.000
214A241PRO00.019-0.00333.826-0.287-0.2870.0000.0000.0000.000
215A242VAL00.0260.01533.118-0.225-0.2250.0000.0000.0000.000
216A243ILE00.0060.00529.866-0.271-0.2710.0000.0000.0000.000
217A244LYS10.8210.89629.2438.9838.9830.0000.0000.0000.000
218A245GLU-1-0.830-0.88628.346-10.784-10.7840.0000.0000.0000.000
219A246ILE0-0.019-0.02127.422-0.399-0.3990.0000.0000.0000.000
220A247LEU0-0.028-0.00324.834-0.462-0.4620.0000.0000.0000.000
221A248TYR0-0.046-0.03323.563-0.363-0.3630.0000.0000.0000.000
222A249GLY0-0.0140.01224.558-0.050-0.0500.0000.0000.0000.000