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: JLQ89

Calculation Name: 2YMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YMO

Chain ID: A

ChEMBL ID:

UniProt ID: C6KSX0

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2654608.393654
FMO2-HF: Nuclear repulsion 2560871.129001
FMO2-HF: Total energy -93737.264653
FMO2-MP2: Total energy -94002.689139


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:29:LEU)


Summations of interaction energy for fragment #1(A:29:LEU)
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.
-12.769-3.9988.433-4.962-12.242-0.027
Interaction energy analysis for fragmet #1(A:29:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.015
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].
3A31CYS0-0.0410.0073.8620.1552.321-0.026-1.095-1.0450.000
4A32ASP-1-0.752-0.8866.7080.3600.3600.0000.0000.0000.000
5A33PHE00.0240.0049.6930.0780.0780.0000.0000.0000.000
6A34ASN0-0.036-0.01012.663-0.099-0.0990.0000.0000.0000.000
7A35ASP-1-0.892-0.97013.4240.4800.4800.0000.0000.0000.000
8A36VAL0-0.033-0.0059.2220.0220.0220.0000.0000.0000.000
9A37TYR0-0.040-0.0236.519-0.513-0.5130.0000.0000.0000.000
10A38LYS10.8330.92112.576-0.653-0.6530.0000.0000.0000.000
11A39LEU00.0250.01115.323-0.023-0.0230.0000.0000.0000.000
12A40GLU-1-0.840-0.88618.1210.4120.4120.0000.0000.0000.000
13A41PHE0-0.046-0.03821.3630.0070.0070.0000.0000.0000.000
14A42HIS00.0100.00921.753-0.035-0.0350.0000.0000.0000.000
15A43PRO00.010-0.01726.479-0.015-0.0150.0000.0000.0000.000
16A44ASN0-0.050-0.03130.2650.0080.0080.0000.0000.0000.000
17A45GLN00.011-0.00624.3550.0140.0140.0000.0000.0000.000
18A46GLN00.0360.02829.298-0.005-0.0050.0000.0000.0000.000
19A47THR0-0.013-0.00826.567-0.008-0.0080.0000.0000.0000.000
20A48SER0-0.0070.02122.9100.0040.0040.0000.0000.0000.000
21A49VAL0-0.003-0.00619.2890.0070.0070.0000.0000.0000.000
22A50THR00.008-0.00517.152-0.009-0.0090.0000.0000.0000.000
23A51LYS10.8330.91813.620-0.697-0.6970.0000.0000.0000.000
24A52LEU00.0170.01012.115-0.088-0.0880.0000.0000.0000.000
25A54ASN0-0.003-0.0177.631-0.021-0.0210.0000.0000.0000.000
26A55LEU0-0.023-0.0102.231-0.6070.3253.100-1.300-2.732-0.003
27A56THR00.009-0.0063.416-0.656-0.2000.024-0.137-0.3430.000
28A57PRO0-0.0190.0092.343-2.948-1.4812.031-0.953-2.546-0.001
29A58ASN0-0.026-0.0372.9692.8091.7210.1611.190-0.2620.000
30A59VAL00.0200.0026.357-0.100-0.1000.0000.0000.0000.000
31A60LEU0-0.042-0.0158.791-0.085-0.0850.0000.0000.0000.000
32A61GLU-1-0.821-0.8942.715-10.081-7.2861.040-1.536-2.299-0.019
33A62LYS10.8750.9545.2551.0531.208-0.001-0.022-0.1320.000
34A63VAL00.0400.0262.201-3.185-1.5512.097-1.137-2.594-0.004
35A64THR0-0.0160.0043.5600.4000.6540.0070.028-0.2890.000
36A65ILE00.009-0.0025.9800.4400.4400.0000.0000.0000.000
37A66LYS10.8820.9638.688-0.776-0.7760.0000.0000.0000.000
38A67CYS0-0.049-0.00711.5930.0720.0720.0000.0000.0000.000
39A68GLY00.0970.05714.501-0.070-0.0700.0000.0000.0000.000
40A69SER0-0.028-0.04817.1460.0110.0110.0000.0000.0000.000
41A70ASP-1-0.803-0.87719.8120.1780.1780.0000.0000.0000.000
42A71LYS10.8060.91022.408-0.206-0.2060.0000.0000.0000.000
43A72LEU0-0.0140.00918.037-0.001-0.0010.0000.0000.0000.000
44A73ASN00.0100.00620.656-0.012-0.0120.0000.0000.0000.000
45A74TYR0-0.034-0.02316.692-0.004-0.0040.0000.0000.0000.000
46A75ASN00.0110.00619.596-0.023-0.0230.0000.0000.0000.000
47A76LEU00.014-0.00812.9410.0510.0510.0000.0000.0000.000
48A77TYR0-0.0360.01016.728-0.049-0.0490.0000.0000.0000.000
49A78PRO00.1070.03115.6920.0390.0390.0000.0000.0000.000
50A79PRO00.021-0.00816.2670.0080.0080.0000.0000.0000.000
51A80THR00.0450.02214.0820.0030.0030.0000.0000.0000.000
52A81CYS0-0.172-0.04811.037-0.074-0.0740.0000.0000.0000.000
53A82PHE00.0350.01210.4070.0010.0010.0000.0000.0000.000
54A83GLU-1-0.969-0.98313.120-0.164-0.1640.0000.0000.0000.000
55A117ILE0-0.013-0.02216.1450.0100.0100.0000.0000.0000.000
56A118ASN0-0.044-0.02116.628-0.076-0.0760.0000.0000.0000.000
57A119GLU-1-0.908-0.97510.7810.1230.1230.0000.0000.0000.000
58A120VAL00.0040.01610.783-0.060-0.0600.0000.0000.0000.000
59A121SER0-0.075-0.0717.056-0.022-0.0220.0000.0000.0000.000
60A122PHE00.0680.0397.6360.0500.0500.0000.0000.0000.000
61A123ARG10.8780.9266.9580.8800.8800.0000.0000.0000.000
62A124ILE00.0410.0335.2060.2100.2100.0000.0000.0000.000
63A125PRO00.0530.0369.355-0.113-0.1130.0000.0000.0000.000
64A126PRO0-0.003-0.01212.814-0.020-0.0200.0000.0000.0000.000
65A127ASN0-0.009-0.01112.6030.1180.1180.0000.0000.0000.000
66A128MET0-0.025-0.02015.818-0.028-0.0280.0000.0000.0000.000
67A129MET00.0100.02817.0330.0230.0230.0000.0000.0000.000
68A130PRO0-0.006-0.01415.766-0.023-0.0230.0000.0000.0000.000
69A131GLU-1-0.897-0.92913.988-0.148-0.1480.0000.0000.0000.000
70A132LYS10.8970.94714.7140.0160.0160.0000.0000.0000.000
71A133PRO0-0.005-0.00611.047-0.035-0.0350.0000.0000.0000.000
72A134ILE00.0280.03610.8910.0250.0250.0000.0000.0000.000
73A135TYR0-0.062-0.06210.8480.0530.0530.0000.0000.0000.000
74A137PHE0-0.006-0.00413.2240.1070.1070.0000.0000.0000.000
75A139GLU-1-0.812-0.89815.3760.2510.2510.0000.0000.0000.000
76A140ASN00.002-0.01319.010-0.047-0.0470.0000.0000.0000.000
77A141LYS10.9180.95521.503-0.182-0.1820.0000.0000.0000.000
78A142LYS10.9170.94425.146-0.218-0.2180.0000.0000.0000.000
79A158ASP-1-0.902-0.91329.6850.1540.1540.0000.0000.0000.000
80A159ILE0-0.023-0.00927.1000.0080.0080.0000.0000.0000.000
81A160ILE0-0.017-0.02221.079-0.002-0.0020.0000.0000.0000.000
82A161ASN00.0010.03120.237-0.006-0.0060.0000.0000.0000.000
83A162ARG10.8570.90017.811-0.314-0.3140.0000.0000.0000.000
84A163GLY00.0340.00113.7610.0450.0450.0000.0000.0000.000
85A164ILE0-0.040-0.01313.258-0.054-0.0540.0000.0000.0000.000
86A165VAL00.023-0.0067.4540.1850.1850.0000.0000.0000.000
87A166GLU-1-0.816-0.8788.8210.2750.2750.0000.0000.0000.000
88A167ILE0-0.019-0.0125.3490.2390.2390.0000.0000.0000.000
89A168ILE00.0230.0047.074-0.116-0.1160.0000.0000.0000.000
90A169ILE00.0130.0087.372-0.218-0.2180.0000.0000.0000.000
91A170PRO0-0.0450.0067.2140.0840.0840.0000.0000.0000.000
92A171SER00.009-0.0179.5500.0490.0490.0000.0000.0000.000
93A172LEU0-0.061-0.02713.131-0.055-0.0550.0000.0000.0000.000
94A173ASN00.004-0.01115.1760.0700.0700.0000.0000.0000.000
95A174GLU-1-0.899-0.94218.018-0.331-0.3310.0000.0000.0000.000
96A175LYS10.9020.93518.6070.2290.2290.0000.0000.0000.000
97A176VAL0-0.0070.00216.273-0.021-0.0210.0000.0000.0000.000
98A177LYS10.8090.89318.8580.4290.4290.0000.0000.0000.000
99A178GLY00.037-0.00421.314-0.019-0.0190.0000.0000.0000.000
100A179CYS0-0.120-0.04123.0220.0200.0200.0000.0000.0000.000
101A180ASP-1-0.675-0.78824.813-0.247-0.2470.0000.0000.0000.000
102A181PHE0-0.028-0.02526.1440.0170.0170.0000.0000.0000.000
103A182THR0-0.083-0.05827.0350.0090.0090.0000.0000.0000.000
104A183THR00.003-0.01926.7540.0130.0130.0000.0000.0000.000
105A184SER0-0.021-0.02228.691-0.011-0.0110.0000.0000.0000.000
106A185GLU-1-0.875-0.90629.290-0.161-0.1610.0000.0000.0000.000
107A186SER0-0.054-0.04924.169-0.016-0.0160.0000.0000.0000.000
108A187THR00.020-0.00221.231-0.001-0.0010.0000.0000.0000.000
109A188ILE0-0.0370.00218.101-0.016-0.0160.0000.0000.0000.000
110A189PHE00.0140.01019.715-0.026-0.0260.0000.0000.0000.000
111A190SER0-0.015-0.00922.4220.0160.0160.0000.0000.0000.000
112A191LYS10.8770.93424.5400.2290.2290.0000.0000.0000.000
113A192GLY00.0320.01726.414-0.019-0.0190.0000.0000.0000.000
114A193TYR0-0.022-0.00328.8040.0060.0060.0000.0000.0000.000
115A194SER00.003-0.03431.7640.0000.0000.0000.0000.0000.000
116A195ILE00.0500.00534.3210.0000.0000.0000.0000.0000.000
117A196ASN00.0280.00335.9250.0000.0000.0000.0000.0000.000
118A197GLU-1-0.843-0.87735.472-0.137-0.1370.0000.0000.0000.000
119A198ILE00.0470.02032.8380.0020.0020.0000.0000.0000.000
120A199SER0-0.042-0.01136.2920.0050.0050.0000.0000.0000.000
121A200ASN00.020-0.02339.5780.0010.0010.0000.0000.0000.000
122A201LYS10.8140.94939.2740.1170.1170.0000.0000.0000.000
123A202SER0-0.044-0.04044.0360.0030.0030.0000.0000.0000.000
124A203SER00.0550.00347.100-0.002-0.0020.0000.0000.0000.000
125A204ASN00.0100.00848.4660.0010.0010.0000.0000.0000.000
126A205ASN00.0140.04543.251-0.006-0.0060.0000.0000.0000.000
127A206GLN00.033-0.00843.173-0.001-0.0010.0000.0000.0000.000
128A207GLN0-0.043-0.01541.316-0.002-0.0020.0000.0000.0000.000
129A208ASP-1-0.842-0.92636.169-0.132-0.1320.0000.0000.0000.000
130A209ILE0-0.053-0.01932.9950.0020.0020.0000.0000.0000.000
131A210VAL0-0.0020.00433.065-0.011-0.0110.0000.0000.0000.000
132A212THR00.0270.00728.723-0.013-0.0130.0000.0000.0000.000
133A213VAL0-0.0140.00423.4390.0060.0060.0000.0000.0000.000
134A214LYS10.8280.91926.3050.2190.2190.0000.0000.0000.000
135A215ALA00.0160.01221.313-0.013-0.0130.0000.0000.0000.000
136A216HIS10.8540.92819.0490.4060.4060.0000.0000.0000.000
137A217ALA00.0530.01918.277-0.035-0.0350.0000.0000.0000.000
138A218ASN00.0090.00213.800-0.026-0.0260.0000.0000.0000.000
139A219ASP-1-0.783-0.87214.851-0.459-0.4590.0000.0000.0000.000
140A220LEU0-0.033-0.01212.526-0.048-0.0480.0000.0000.0000.000
141A221ILE0-0.015-0.01315.7930.0630.0630.0000.0000.0000.000
142A222GLY00.038-0.00417.409-0.054-0.0540.0000.0000.0000.000
143A223PHE0-0.047-0.02419.7180.0310.0310.0000.0000.0000.000
144A224LYS10.9510.98121.6200.2160.2160.0000.0000.0000.000
145A225CYS0-0.0330.00823.9470.0060.0060.0000.0000.0000.000
146A226PRO00.0650.02726.903-0.005-0.0050.0000.0000.0000.000
147A227SER00.0030.00627.4520.0000.0000.0000.0000.0000.000
148A228ASN0-0.021-0.01428.6710.0060.0060.0000.0000.0000.000
149A229TYR0-0.0030.00730.6700.0100.0100.0000.0000.0000.000
150A230SER00.0210.01730.147-0.011-0.0110.0000.0000.0000.000
151A231VAL00.008-0.01925.451-0.004-0.0040.0000.0000.0000.000
152A232GLU-1-0.856-0.88728.724-0.146-0.1460.0000.0000.0000.000
153A233PRO00.024-0.00426.2150.0010.0010.0000.0000.0000.000
154A234HIS00.0650.01825.123-0.010-0.0100.0000.0000.0000.000
155A235ASP-1-0.813-0.89422.809-0.265-0.2650.0000.0000.0000.000
156A236CYS0-0.063-0.00422.411-0.028-0.0280.0000.0000.0000.000
157A237PHE00.019-0.00918.847-0.033-0.0330.0000.0000.0000.000
158A238VAL0-0.0060.01319.018-0.024-0.0240.0000.0000.0000.000
159A239SER0-0.040-0.03921.2310.0240.0240.0000.0000.0000.000
160A240ALA00.0230.00424.502-0.016-0.0160.0000.0000.0000.000
161A241PHE00.0100.02126.7680.0130.0130.0000.0000.0000.000
162A242ASN0-0.008-0.00629.780-0.004-0.0040.0000.0000.0000.000
163A243LEU0-0.003-0.01131.8080.0090.0090.0000.0000.0000.000
164A244SER0-0.041-0.02734.1270.0070.0070.0000.0000.0000.000
165A245GLY00.0110.00735.5650.0060.0060.0000.0000.0000.000
166A246LYS10.8960.96232.6610.1560.1560.0000.0000.0000.000
167A247ASN00.0440.01128.251-0.013-0.0130.0000.0000.0000.000
168A248GLU-1-0.896-0.93628.295-0.157-0.1570.0000.0000.0000.000
169A249ASN00.0240.00522.511-0.016-0.0160.0000.0000.0000.000
170A250LEU0-0.012-0.01221.7960.0130.0130.0000.0000.0000.000
171A251GLU-1-0.811-0.92818.575-0.333-0.3330.0000.0000.0000.000
172A252ASN0-0.052-0.01520.7720.0010.0010.0000.0000.0000.000
173A253LYS10.8280.89923.2410.2100.2100.0000.0000.0000.000
174A254LEU00.0370.01020.1540.0040.0040.0000.0000.0000.000
175A255LYS10.8740.97316.8940.2990.2990.0000.0000.0000.000
176A256LEU0-0.023-0.00716.266-0.045-0.0450.0000.0000.0000.000
177A257THR0-0.012-0.00711.086-0.060-0.0600.0000.0000.0000.000
178A258ASN0-0.021-0.0336.9010.0800.0800.0000.0000.0000.000
179A259ILE00.0070.01710.8740.0230.0230.0000.0000.0000.000
180A260ILE0-0.057-0.02511.512-0.048-0.0480.0000.0000.0000.000
181A261MET0-0.0030.00215.3730.0270.0270.0000.0000.0000.000
182A262ASP-1-0.819-0.89517.303-0.351-0.3510.0000.0000.0000.000
183A263HIS00.008-0.02019.1610.0210.0210.0000.0000.0000.000
184A264TYR0-0.0340.00719.2420.0360.0360.0000.0000.0000.000
185A265ASN0-0.075-0.05419.5360.0360.0360.0000.0000.0000.000
186A266ASN0-0.036-0.01323.515-0.016-0.0160.0000.0000.0000.000
187A267THR0-0.053-0.02718.7960.0040.0040.0000.0000.0000.000
188A268PHE00.0090.01018.758-0.022-0.0220.0000.0000.0000.000
189A269TYR00.011-0.01514.7350.0060.0060.0000.0000.0000.000
190A270SER00.0290.01514.495-0.003-0.0030.0000.0000.0000.000
191A271ARG10.9080.95810.3631.0101.0100.0000.0000.0000.000
192A272LEU0-0.0120.00114.6160.0110.0110.0000.0000.0000.000
193A273PRO00.0270.01915.195-0.067-0.0670.0000.0000.0000.000
194A274SER00.0380.01114.1660.0290.0290.0000.0000.0000.000
195A275LEU0-0.026-0.01316.0400.0430.0430.0000.0000.0000.000
196A276ILE0-0.049-0.01119.749-0.016-0.0160.0000.0000.0000.000
197A277SER00.0440.00722.5300.0110.0110.0000.0000.0000.000
198A278ASP-1-0.881-0.93225.664-0.176-0.1760.0000.0000.0000.000
199A279ASN0-0.046-0.02526.614-0.026-0.0260.0000.0000.0000.000
200A280TRP00.0100.00425.5400.0140.0140.0000.0000.0000.000
201A281LYS10.8400.90227.5890.1610.1610.0000.0000.0000.000
202A282PHE0-0.0100.00022.0860.0110.0110.0000.0000.0000.000
203A283PHE00.016-0.00927.718-0.005-0.0050.0000.0000.0000.000
204A285VAL00.0080.00128.0230.0040.0040.0000.0000.0000.000
205A287SER0-0.040-0.04230.6170.0110.0110.0000.0000.0000.000
206A288LYS10.9040.94233.9170.1110.1110.0000.0000.0000.000
207A289ASP-1-0.876-0.93436.518-0.105-0.1050.0000.0000.0000.000
208A290ASN0-0.062-0.04840.2760.0030.0030.0000.0000.0000.000
209A291GLU-1-0.831-0.87337.685-0.105-0.1050.0000.0000.0000.000
210A292LYS10.8180.91937.5260.1150.1150.0000.0000.0000.000
211A293LYS10.8300.92434.9500.1340.1340.0000.0000.0000.000
212A294LEU0-0.016-0.00631.0660.0020.0020.0000.0000.0000.000
213A295VAL00.0120.00230.985-0.008-0.0080.0000.0000.0000.000
214A296PHE00.0380.02522.210-0.001-0.0010.0000.0000.0000.000
215A297THR00.030-0.00427.757-0.003-0.0030.0000.0000.0000.000
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217A299GLU-1-0.824-0.91626.171-0.171-0.1710.0000.0000.0000.000
218A300ALA00.0350.02723.734-0.006-0.0060.0000.0000.0000.000
219A301SER0-0.013-0.02724.6260.0300.0300.0000.0000.0000.000
220A302ILE00.0200.02524.697-0.020-0.0200.0000.0000.0000.000
221A303SER0-0.048-0.03222.815-0.005-0.0050.0000.0000.0000.000
222A304SER00.0140.00020.494-0.019-0.0190.0000.0000.0000.000
223A305ALA00.0050.01315.7610.0060.0060.0000.0000.0000.000