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: YZL22

Calculation Name: 2PTG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PTG

Chain ID: A

ChEMBL ID:

UniProt ID: Q0VIP6

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 -2550391.030931
FMO2-HF: Nuclear repulsion 2466838.982037
FMO2-HF: Total energy -83552.048894
FMO2-MP2: Total energy -83798.366269


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:93:PRO)


Summations of interaction energy for fragment #1(A:93:PRO)
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.
-3.756-0.6020.123-1.456-1.820.004
Interaction energy analysis for fragmet #1(A:93:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.007
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].
3A95PRO0-0.0240.0002.981-2.3840.7060.124-1.450-1.7640.004
4A96VAL00.020-0.0075.594-0.963-0.899-0.001-0.006-0.0560.000
5A97ASP-1-0.819-0.8729.2590.4450.4450.0000.0000.0000.000
6A98LEU0-0.012-0.02211.542-0.095-0.0950.0000.0000.0000.000
7A99ARG10.8690.90913.480-0.531-0.5310.0000.0000.0000.000
8A100GLY0-0.0340.00217.062-0.037-0.0370.0000.0000.0000.000
9A101LYS10.8150.90216.890-0.217-0.2170.0000.0000.0000.000
10A102THR00.009-0.00319.8540.0030.0030.0000.0000.0000.000
11A103ALA00.0120.00020.962-0.003-0.0030.0000.0000.0000.000
12A104PHE00.0260.01823.078-0.005-0.0050.0000.0000.0000.000
13A105VAL0-0.003-0.00922.711-0.003-0.0030.0000.0000.0000.000
14A106ALA00.0530.03025.761-0.004-0.0040.0000.0000.0000.000
15A107GLY00.0450.03127.9010.0010.0010.0000.0000.0000.000
16A108VAL0-0.048-0.01026.166-0.001-0.0010.0000.0000.0000.000
17A109ALA00.0130.00528.802-0.002-0.0020.0000.0000.0000.000
18A110ASP-1-0.823-0.92129.2390.0560.0560.0000.0000.0000.000
19A111SER0-0.016-0.01827.1620.0040.0040.0000.0000.0000.000
20A112ASN0-0.051-0.03125.2950.0080.0080.0000.0000.0000.000
21A113GLY00.0740.05425.205-0.002-0.0020.0000.0000.0000.000
22A114TYR00.002-0.03821.5990.0130.0130.0000.0000.0000.000
23A115GLY00.0240.01321.9860.0130.0130.0000.0000.0000.000
24A116TRP00.0430.02623.1020.0150.0150.0000.0000.0000.000
25A117ALA00.013-0.00119.1620.0160.0160.0000.0000.0000.000
26A118ILE00.0270.00918.2940.0280.0280.0000.0000.0000.000
27A119CYS0-0.056-0.01518.7670.0240.0240.0000.0000.0000.000
28A120LYS10.8150.89818.190-0.128-0.1280.0000.0000.0000.000
29A121LEU0-0.013-0.00512.5720.0360.0360.0000.0000.0000.000
30A122LEU00.003-0.00314.6490.0640.0640.0000.0000.0000.000
31A123ARG10.8660.93216.877-0.162-0.1620.0000.0000.0000.000
32A124ALA0-0.045-0.01913.9520.0090.0090.0000.0000.0000.000
33A125ALA0-0.0060.00312.7030.0610.0610.0000.0000.0000.000
34A126GLY0-0.005-0.01313.6520.0260.0260.0000.0000.0000.000
35A127ALA0-0.0160.00916.827-0.037-0.0370.0000.0000.0000.000
36A128ARG10.8510.90418.935-0.140-0.1400.0000.0000.0000.000
37A129VAL0-0.023-0.01020.665-0.010-0.0100.0000.0000.0000.000
38A130LEU00.0170.01523.418-0.010-0.0100.0000.0000.0000.000
39A131VAL00.003-0.01025.9730.0040.0040.0000.0000.0000.000
40A132GLY00.0350.01728.320-0.005-0.0050.0000.0000.0000.000
41A133THR0-0.043-0.03930.9830.0010.0010.0000.0000.0000.000
42A134TRP00.0440.01832.771-0.002-0.0020.0000.0000.0000.000
43A135PRO00.0160.01135.9860.0010.0010.0000.0000.0000.000
44A136PRO00.000-0.00538.9400.0010.0010.0000.0000.0000.000
45A137VAL00.0210.01134.1690.0000.0000.0000.0000.0000.000
46A138TYR00.0210.02134.9550.0030.0030.0000.0000.0000.000
47A139SER00.002-0.00536.2230.0010.0010.0000.0000.0000.000
48A140ILE0-0.091-0.04937.177-0.001-0.0010.0000.0000.0000.000
49A141PHE00.0520.02630.1410.0010.0010.0000.0000.0000.000
50A142LYS10.8840.95835.062-0.054-0.0540.0000.0000.0000.000
51A143LYS10.8770.95637.120-0.047-0.0470.0000.0000.0000.000
52A176VAL00.0070.00122.3780.0040.0040.0000.0000.0000.000
53A177PHE00.0330.02122.9260.0140.0140.0000.0000.0000.000
54A178ASP-1-0.887-0.91825.5810.1310.1310.0000.0000.0000.000
55A179LYS10.8420.91127.326-0.087-0.0870.0000.0000.0000.000
56A180ILE0-0.036-0.01229.3650.0030.0030.0000.0000.0000.000
57A181TYR0-0.008-0.04930.840-0.002-0.0020.0000.0000.0000.000
58A182PRO0-0.043-0.00934.1950.0010.0010.0000.0000.0000.000
59A183LEU00.008-0.01432.2230.0010.0010.0000.0000.0000.000
60A184ASP-1-0.829-0.91435.7660.0360.0360.0000.0000.0000.000
61A185ALA00.001-0.00534.110-0.002-0.0020.0000.0000.0000.000
62A186VAL0-0.0050.02436.128-0.002-0.0020.0000.0000.0000.000
63A187PHE0-0.007-0.00238.970-0.003-0.0030.0000.0000.0000.000
64A188ASP-1-0.732-0.83539.0650.0340.0340.0000.0000.0000.000
65A189THR0-0.065-0.03940.6650.0020.0020.0000.0000.0000.000
66A190PRO00.0400.01243.602-0.001-0.0010.0000.0000.0000.000
67A191GLN00.008-0.00146.1880.0000.0000.0000.0000.0000.000
68A192ASP-1-0.837-0.88544.2730.0250.0250.0000.0000.0000.000
69A193VAL0-0.071-0.02644.3840.0000.0000.0000.0000.0000.000
70A194PRO0-0.0120.01346.916-0.001-0.0010.0000.0000.0000.000
71A195PRO00.021-0.00449.8210.0010.0010.0000.0000.0000.000
72A196GLU-1-0.836-0.93750.8220.0220.0220.0000.0000.0000.000
73A197VAL0-0.0190.00445.2420.0010.0010.0000.0000.0000.000
74A198SER0-0.0100.00547.1700.0020.0020.0000.0000.0000.000
75A199SER0-0.030-0.01348.3430.0010.0010.0000.0000.0000.000
76A200ASN00.000-0.00447.214-0.001-0.0010.0000.0000.0000.000
77A201LYS10.9370.95046.709-0.025-0.0250.0000.0000.0000.000
78A202ARG10.8870.94442.772-0.035-0.0350.0000.0000.0000.000
79A203TYR00.0290.00841.6350.0020.0020.0000.0000.0000.000
80A204ALA00.006-0.00244.7480.0010.0010.0000.0000.0000.000
81A205GLY0-0.032-0.01846.3020.0010.0010.0000.0000.0000.000
82A206VAL0-0.061-0.02141.0880.0020.0020.0000.0000.0000.000
83A207GLY00.0130.00541.3170.0030.0030.0000.0000.0000.000
84A208GLY00.0350.00942.280-0.001-0.0010.0000.0000.0000.000
85A209PHE0-0.019-0.01838.9590.0030.0030.0000.0000.0000.000
86A210THR0-0.044-0.03938.7770.0010.0010.0000.0000.0000.000
87A211ILE0-0.007-0.01534.8170.0040.0040.0000.0000.0000.000
88A212SER0-0.016-0.03636.5680.0030.0030.0000.0000.0000.000
89A213GLU-1-0.822-0.88338.6390.0410.0410.0000.0000.0000.000
90A214VAL00.001-0.00633.6060.0030.0030.0000.0000.0000.000
91A215ALA00.0160.02033.9750.0050.0050.0000.0000.0000.000
92A216GLU-1-0.824-0.90534.8580.0520.0520.0000.0000.0000.000
93A217ALA0-0.051-0.01636.2210.0020.0020.0000.0000.0000.000
94A218VAL0-0.007-0.00530.0290.0040.0040.0000.0000.0000.000
95A219ARG10.8200.89232.407-0.049-0.0490.0000.0000.0000.000
96A220ALA0-0.027-0.01134.2230.0010.0010.0000.0000.0000.000
97A221ASP-1-0.807-0.86032.1670.0790.0790.0000.0000.0000.000
98A222VAL0-0.073-0.05328.1640.0070.0070.0000.0000.0000.000
99A223GLY00.0010.03229.6740.0050.0050.0000.0000.0000.000
100A224GLN0-0.024-0.03227.6280.0000.0000.0000.0000.0000.000
101A225ILE00.0150.03025.5160.0110.0110.0000.0000.0000.000
102A226ASP-1-0.819-0.89520.7510.1550.1550.0000.0000.0000.000
103A227ILE0-0.005-0.00417.387-0.001-0.0010.0000.0000.0000.000
104A228LEU00.0120.01621.955-0.003-0.0030.0000.0000.0000.000
105A229VAL0-0.005-0.01021.321-0.001-0.0010.0000.0000.0000.000
106A230HIS00.0150.00924.3060.0010.0010.0000.0000.0000.000
107A231SER0-0.039-0.01325.650-0.005-0.0050.0000.0000.0000.000
108A232LEU0-0.019-0.00626.925-0.002-0.0020.0000.0000.0000.000
109A233ALA00.0190.01529.563-0.005-0.0050.0000.0000.0000.000
110A234ASN0-0.015-0.00830.922-0.002-0.0020.0000.0000.0000.000
111A235GLY00.0860.06933.231-0.002-0.0020.0000.0000.0000.000
112A236PRO0-0.030-0.00835.471-0.002-0.0020.0000.0000.0000.000
113A237GLU-1-0.828-0.88338.6300.0070.0070.0000.0000.0000.000
114A238VAL0-0.015-0.01435.9340.0010.0010.0000.0000.0000.000
115A239THR00.0090.00235.264-0.002-0.0020.0000.0000.0000.000
116A240LYS10.8280.91837.909-0.010-0.0100.0000.0000.0000.000
117A241PRO00.0410.02541.7390.0000.0000.0000.0000.0000.000
118A242LEU00.054-0.00142.5400.0010.0010.0000.0000.0000.000
119A243LEU0-0.013-0.00745.6790.0010.0010.0000.0000.0000.000
120A244GLN0-0.018-0.00146.8270.0000.0000.0000.0000.0000.000
121A245THR0-0.034-0.02444.6350.0010.0010.0000.0000.0000.000
122A246SER0-0.002-0.00847.0760.0000.0000.0000.0000.0000.000
123A247ARG10.9830.98747.367-0.006-0.0060.0000.0000.0000.000
124A248LYS11.0050.99747.214-0.013-0.0130.0000.0000.0000.000
125A249GLY0-0.0100.00245.3120.0010.0010.0000.0000.0000.000
126A250TYR00.0790.03040.9530.0010.0010.0000.0000.0000.000
127A251LEU00.0180.00441.9720.0000.0000.0000.0000.0000.000
128A252ALA00.0040.01341.9440.0010.0010.0000.0000.0000.000
129A253ALA00.0390.02039.2110.0020.0020.0000.0000.0000.000
130A254VAL00.0350.03737.6830.0010.0010.0000.0000.0000.000
131A255SER00.0010.00337.1250.0010.0010.0000.0000.0000.000
132A256SER0-0.027-0.02936.3090.0030.0030.0000.0000.0000.000
133A257SER0-0.067-0.05733.5140.0020.0020.0000.0000.0000.000
134A258SER0-0.019-0.02232.532-0.001-0.0010.0000.0000.0000.000
135A259TYR00.0030.00933.3080.0020.0020.0000.0000.0000.000
136A260SER00.043-0.00534.1900.0010.0010.0000.0000.0000.000
137A261PHE0-0.045-0.02426.0860.0040.0040.0000.0000.0000.000
138A262VAL00.0050.00831.3900.0030.0030.0000.0000.0000.000
139A263SER00.001-0.02733.3130.0030.0030.0000.0000.0000.000
140A264LEU0-0.0030.00129.0510.0020.0020.0000.0000.0000.000
141A265LEU00.011-0.00927.4710.0040.0040.0000.0000.0000.000
142A266GLN0-0.026-0.01230.7510.0020.0020.0000.0000.0000.000
143A267HIS00.001-0.01234.1090.0000.0000.0000.0000.0000.000
144A268PHE00.014-0.00929.4920.0030.0030.0000.0000.0000.000
145A269LEU00.0290.02928.7200.0050.0050.0000.0000.0000.000
146A270PRO0-0.045-0.02430.5380.0030.0030.0000.0000.0000.000
147A271LEU0-0.047-0.01430.4190.0000.0000.0000.0000.0000.000
148A272MET0-0.0330.00524.0990.0060.0060.0000.0000.0000.000
149A273LYS10.8120.90423.337-0.136-0.1360.0000.0000.0000.000
150A274GLU-1-0.751-0.84724.6920.0670.0670.0000.0000.0000.000
151A275GLY0-0.055-0.01921.2600.0100.0100.0000.0000.0000.000
152A276GLY0-0.037-0.01019.9450.0160.0160.0000.0000.0000.000
153A277SER0-0.035-0.02118.909-0.017-0.0170.0000.0000.0000.000
154A278ALA00.0160.00220.9270.0120.0120.0000.0000.0000.000
155A279LEU0-0.051-0.02418.817-0.007-0.0070.0000.0000.0000.000
156A280ALA00.0390.02822.5340.0050.0050.0000.0000.0000.000
157A281LEU00.002-0.00222.046-0.002-0.0020.0000.0000.0000.000
158A282SER00.0240.02824.5740.0000.0000.0000.0000.0000.000
159A283TYR00.015-0.01725.817-0.002-0.0020.0000.0000.0000.000
160A284ILE0-0.017-0.00727.8050.0000.0000.0000.0000.0000.000
161A303ALA00.0680.03831.1210.0000.0000.0000.0000.0000.000
162A304LEU00.014-0.01028.421-0.001-0.0010.0000.0000.0000.000
163A305GLU-1-0.826-0.88326.723-0.017-0.0170.0000.0000.0000.000
164A306SER0-0.0330.00328.466-0.004-0.0040.0000.0000.0000.000
165A307ASP-1-0.826-0.92330.4750.0100.0100.0000.0000.0000.000
166A308CYS0-0.0380.00124.0900.0040.0040.0000.0000.0000.000
167A309ARG10.9220.94326.1890.0180.0180.0000.0000.0000.000
168A310THR0-0.043-0.01527.836-0.001-0.0010.0000.0000.0000.000
169A311LEU00.0410.01028.6600.0010.0010.0000.0000.0000.000
170A312ALA0-0.0130.00625.1350.0040.0040.0000.0000.0000.000
171A313PHE0-0.002-0.00226.7290.0000.0000.0000.0000.0000.000
172A314GLU-1-0.924-0.96929.3840.0190.0190.0000.0000.0000.000
173A315ALA00.0340.00527.3310.0020.0020.0000.0000.0000.000
174A316GLY00.0210.02626.4150.0040.0040.0000.0000.0000.000
175A317ARG10.8120.89627.320-0.001-0.0010.0000.0000.0000.000
176A318ALA0-0.0080.01430.7780.0010.0010.0000.0000.0000.000
177A319ARG10.7680.84028.170-0.056-0.0560.0000.0000.0000.000
178A320ALA00.0000.00124.5780.0060.0060.0000.0000.0000.000
179A321VAL0-0.050-0.01023.6030.0060.0060.0000.0000.0000.000
180A322ARG10.8130.90416.210-0.094-0.0940.0000.0000.0000.000
181A323VAL00.0100.00222.1600.0110.0110.0000.0000.0000.000
182A324ASN0-0.015-0.01919.105-0.024-0.0240.0000.0000.0000.000
183A325CYS0-0.051-0.03021.6530.0070.0070.0000.0000.0000.000
184A326ILE0-0.0020.01117.516-0.008-0.0080.0000.0000.0000.000
185A327SER0-0.012-0.01021.6280.0040.0040.0000.0000.0000.000
186A328ALA0-0.015-0.00522.345-0.006-0.0060.0000.0000.0000.000
187A329GLY00.0470.02324.0030.0000.0000.0000.0000.0000.000
188A330PRO0-0.024-0.01425.9530.0070.0070.0000.0000.0000.000
189A331LEU0-0.0030.01923.673-0.002-0.0020.0000.0000.0000.000
190A363LYS10.8550.91722.4010.0390.0390.0000.0000.0000.000
191A364GLU-1-0.957-0.97621.1700.0030.0030.0000.0000.0000.000
192A365LEU0-0.0040.00320.597-0.006-0.0060.0000.0000.0000.000
193A366GLU-1-0.796-0.86916.2620.0930.0930.0000.0000.0000.000
194A367SER00.005-0.04120.207-0.002-0.0020.0000.0000.0000.000
195A368ASP-1-0.808-0.88815.7550.1540.1540.0000.0000.0000.000
196A369ASP-1-0.828-0.89115.4050.0380.0380.0000.0000.0000.000
197A370VAL00.0120.00115.4700.0010.0010.0000.0000.0000.000
198A371GLY00.0040.00616.6690.0080.0080.0000.0000.0000.000
199A372ARG10.8200.88411.450-0.110-0.1100.0000.0000.0000.000
200A373ALA00.0170.01512.2090.0170.0170.0000.0000.0000.000
201A374ALA00.019-0.00113.958-0.005-0.0050.0000.0000.0000.000
202A375LEU00.0020.00211.1770.0050.0050.0000.0000.0000.000
203A376PHE00.0080.0018.3100.0350.0350.0000.0000.0000.000
204A377LEU00.0280.01011.606-0.005-0.0050.0000.0000.0000.000
205A378LEU0-0.0140.00614.946-0.012-0.0120.0000.0000.0000.000
206A379SER0-0.049-0.02311.1760.0290.0290.0000.0000.0000.000
207A380PRO00.016-0.01911.306-0.063-0.0630.0000.0000.0000.000
208A381LEU0-0.027-0.0036.540-0.131-0.1310.0000.0000.0000.000
209A382ALA00.0010.02310.072-0.101-0.1010.0000.0000.0000.000
210A383ARG10.9500.96912.096-0.002-0.0020.0000.0000.0000.000
211A384ALA0-0.032-0.01314.823-0.001-0.0010.0000.0000.0000.000
212A385VAL0-0.022-0.00514.840-0.014-0.0140.0000.0000.0000.000
213A386THR00.0520.02717.7970.0260.0260.0000.0000.0000.000
214A387GLY00.006-0.00121.299-0.011-0.0110.0000.0000.0000.000
215A388ALA0-0.013-0.00619.397-0.006-0.0060.0000.0000.0000.000
216A389THR00.017-0.00421.3920.0120.0120.0000.0000.0000.000
217A390LEU0-0.018-0.00315.618-0.010-0.0100.0000.0000.0000.000
218A391TYR0-0.026-0.05120.1000.0130.0130.0000.0000.0000.000
219A392VAL0-0.030-0.02117.856-0.009-0.0090.0000.0000.0000.000
220A393ASP-1-0.726-0.88020.362-0.017-0.0170.0000.0000.0000.000
221A394ASN0-0.035-0.02320.0950.0030.0030.0000.0000.0000.000
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