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: K9673

Calculation Name: 2PTG-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PTG

Chain ID: B

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 -2552854.449229
FMO2-HF: Nuclear repulsion 2469302.36928
FMO2-HF: Total energy -83552.079948
FMO2-MP2: Total energy -83798.430432


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(B:93:PRO)


Summations of interaction energy for fragment #1(B: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.
-3.321-0.1570.22-1.402-1.9820.004
Interaction energy analysis for fragmet #1(B:93:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.018
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].
3B95PRO0-0.0190.0062.818-2.7350.3740.221-1.394-1.9360.004
4B96VAL00.012-0.0144.847-0.163-0.108-0.001-0.008-0.0460.000
5B97ASP-1-0.829-0.8778.5140.3060.3060.0000.0000.0000.000
6B98LEU0-0.015-0.02311.2820.0050.0050.0000.0000.0000.000
7B99ARG10.8760.91613.220-0.315-0.3150.0000.0000.0000.000
8B100GLY0-0.041-0.00216.850-0.012-0.0120.0000.0000.0000.000
9B101LYS10.8360.91016.569-0.113-0.1130.0000.0000.0000.000
10B102THR00.000-0.00419.762-0.011-0.0110.0000.0000.0000.000
11B103ALA00.0250.01020.150-0.001-0.0010.0000.0000.0000.000
12B104PHE00.0200.01222.2920.0010.0010.0000.0000.0000.000
13B105VAL00.000-0.00622.385-0.006-0.0060.0000.0000.0000.000
14B106ALA00.0570.02725.3140.0030.0030.0000.0000.0000.000
15B107GLY00.0220.01327.795-0.008-0.0080.0000.0000.0000.000
16B108VAL0-0.037-0.01526.145-0.004-0.0040.0000.0000.0000.000
17B109ALA00.0300.01628.8470.0070.0070.0000.0000.0000.000
18B110ASP-1-0.825-0.91429.107-0.081-0.0810.0000.0000.0000.000
19B111SER0-0.005-0.01727.797-0.001-0.0010.0000.0000.0000.000
20B112ASN0-0.070-0.03725.566-0.001-0.0010.0000.0000.0000.000
21B113GLY00.0680.04425.100-0.010-0.0100.0000.0000.0000.000
22B114TYR0-0.005-0.03921.212-0.006-0.0060.0000.0000.0000.000
23B115GLY00.0590.03721.736-0.008-0.0080.0000.0000.0000.000
24B116TRP00.0450.01723.0900.0030.0030.0000.0000.0000.000
25B117ALA0-0.026-0.01718.9740.0000.0000.0000.0000.0000.000
26B118ILE00.0490.02118.316-0.010-0.0100.0000.0000.0000.000
27B119CYS0-0.059-0.01318.6840.0080.0080.0000.0000.0000.000
28B120LYS10.9260.97618.9920.1470.1470.0000.0000.0000.000
29B121LEU00.0100.00512.9450.0050.0050.0000.0000.0000.000
30B122LEU0-0.009-0.00914.5170.0030.0030.0000.0000.0000.000
31B123ARG10.8270.89216.2400.0390.0390.0000.0000.0000.000
32B124ALA0-0.041-0.01114.0140.0210.0210.0000.0000.0000.000
33B125ALA0-0.0080.00012.0890.0140.0140.0000.0000.0000.000
34B126GLY00.005-0.01213.0200.0620.0620.0000.0000.0000.000
35B127ALA0-0.0190.00516.1160.0160.0160.0000.0000.0000.000
36B128ARG10.9310.96818.269-0.041-0.0410.0000.0000.0000.000
37B129VAL0-0.021-0.01320.245-0.001-0.0010.0000.0000.0000.000
38B130LEU0-0.0160.00122.8750.0000.0000.0000.0000.0000.000
39B131VAL00.021-0.00225.621-0.007-0.0070.0000.0000.0000.000
40B132GLY00.0320.01227.9000.0060.0060.0000.0000.0000.000
41B133THR0-0.035-0.03330.846-0.005-0.0050.0000.0000.0000.000
42B134TRP00.0640.02232.6630.0030.0030.0000.0000.0000.000
43B135PRO00.0070.00535.9590.0000.0000.0000.0000.0000.000
44B136PRO0-0.0020.00138.7750.0010.0010.0000.0000.0000.000
45B137VAL00.0400.02134.4940.0010.0010.0000.0000.0000.000
46B138TYR00.0470.03234.5550.0010.0010.0000.0000.0000.000
47B139SER0-0.021-0.01636.1020.0030.0030.0000.0000.0000.000
48B140ILE0-0.120-0.05436.1550.0020.0020.0000.0000.0000.000
49B141PHE00.0580.02030.1390.0010.0010.0000.0000.0000.000
50B142LYS10.8380.94734.6460.0140.0140.0000.0000.0000.000
51B143LYS10.9170.96535.6510.0240.0240.0000.0000.0000.000
52B176VAL0-0.045-0.02922.2170.0020.0020.0000.0000.0000.000
53B177PHE00.0210.00022.588-0.003-0.0030.0000.0000.0000.000
54B178ASP-1-0.806-0.87123.5700.0040.0040.0000.0000.0000.000
55B179LYS10.7910.88726.8080.0020.0020.0000.0000.0000.000
56B180ILE0-0.0230.00028.814-0.004-0.0040.0000.0000.0000.000
57B181TYR0-0.026-0.05530.0920.0030.0030.0000.0000.0000.000
58B182PRO0-0.044-0.00933.840-0.004-0.0040.0000.0000.0000.000
59B183LEU00.010-0.01231.7870.0020.0020.0000.0000.0000.000
60B184ASP-1-0.845-0.91735.585-0.034-0.0340.0000.0000.0000.000
61B185ALA0-0.001-0.00633.8820.0020.0020.0000.0000.0000.000
62B186VAL0-0.0040.02335.941-0.001-0.0010.0000.0000.0000.000
63B187PHE0-0.003-0.00238.8290.0010.0010.0000.0000.0000.000
64B188ASP-1-0.718-0.82638.849-0.020-0.0200.0000.0000.0000.000
65B189THR0-0.068-0.03940.2860.0030.0030.0000.0000.0000.000
66B190PRO00.0410.01343.077-0.001-0.0010.0000.0000.0000.000
67B191GLN00.0150.00245.558-0.001-0.0010.0000.0000.0000.000
68B192ASP-1-0.831-0.88343.953-0.015-0.0150.0000.0000.0000.000
69B193VAL0-0.058-0.02244.069-0.002-0.0020.0000.0000.0000.000
70B194PRO00.0350.03646.6810.0010.0010.0000.0000.0000.000
71B195PRO00.034-0.00349.4900.0000.0000.0000.0000.0000.000
72B196GLU-1-0.951-0.98149.517-0.020-0.0200.0000.0000.0000.000
73B197VAL0-0.0120.00144.602-0.001-0.0010.0000.0000.0000.000
74B198SER00.005-0.00947.3340.0000.0000.0000.0000.0000.000
75B199SER0-0.038-0.01548.6120.0010.0010.0000.0000.0000.000
76B200ASN0-0.0070.01047.2930.0000.0000.0000.0000.0000.000
77B201LYS11.0100.99047.0280.0180.0180.0000.0000.0000.000
78B202ARG10.8130.88743.0920.0200.0200.0000.0000.0000.000
79B203TYR00.0820.04141.348-0.001-0.0010.0000.0000.0000.000
80B204ALA0-0.015-0.00244.2020.0020.0020.0000.0000.0000.000
81B205GLY0-0.014-0.01246.121-0.001-0.0010.0000.0000.0000.000
82B206VAL0-0.087-0.02540.4780.0010.0010.0000.0000.0000.000
83B207GLY00.005-0.00641.1560.0010.0010.0000.0000.0000.000
84B208GLY00.0370.01741.737-0.001-0.0010.0000.0000.0000.000
85B209PHE0-0.049-0.03838.488-0.001-0.0010.0000.0000.0000.000
86B210THR0-0.035-0.03338.252-0.003-0.0030.0000.0000.0000.000
87B211ILE0-0.003-0.01134.3420.0010.0010.0000.0000.0000.000
88B212SER0-0.014-0.03335.9430.0020.0020.0000.0000.0000.000
89B213GLU-1-0.814-0.88237.947-0.008-0.0080.0000.0000.0000.000
90B214VAL0-0.008-0.00932.8800.0020.0020.0000.0000.0000.000
91B215ALA00.0290.02533.3430.0020.0020.0000.0000.0000.000
92B216GLU-1-0.822-0.87634.3330.0120.0120.0000.0000.0000.000
93B217ALA0-0.043-0.01735.5370.0030.0030.0000.0000.0000.000
94B218VAL0-0.001-0.00329.4010.0030.0030.0000.0000.0000.000
95B219ARG10.8280.87531.660-0.008-0.0080.0000.0000.0000.000
96B220ALA0-0.018-0.00233.4400.0050.0050.0000.0000.0000.000
97B221ASP-1-0.788-0.84631.2930.0090.0090.0000.0000.0000.000
98B222VAL0-0.075-0.05327.4550.0040.0040.0000.0000.0000.000
99B223GLY00.0070.03529.0730.0070.0070.0000.0000.0000.000
100B224GLN0-0.023-0.03627.193-0.003-0.0030.0000.0000.0000.000
101B225ILE0-0.0130.01524.5870.0060.0060.0000.0000.0000.000
102B226ASP-1-0.823-0.90020.0700.0820.0820.0000.0000.0000.000
103B227ILE00.0060.00416.616-0.003-0.0030.0000.0000.0000.000
104B228LEU00.0160.01821.1890.0030.0030.0000.0000.0000.000
105B229VAL00.005-0.00220.903-0.011-0.0110.0000.0000.0000.000
106B230HIS00.0170.00824.0210.0040.0040.0000.0000.0000.000
107B231SER0-0.0140.00025.949-0.012-0.0120.0000.0000.0000.000
108B232LEU0-0.034-0.01127.1060.0060.0060.0000.0000.0000.000
109B233ALA00.0360.02729.548-0.005-0.0050.0000.0000.0000.000
110B234ASN0-0.029-0.04831.0610.0080.0080.0000.0000.0000.000
111B235GLY00.0460.05533.663-0.003-0.0030.0000.0000.0000.000
112B236PRO00.0190.02035.6700.0000.0000.0000.0000.0000.000
113B237GLU-1-0.786-0.90139.071-0.037-0.0370.0000.0000.0000.000
114B238VAL0-0.018-0.01335.548-0.002-0.0020.0000.0000.0000.000
115B239THR0-0.009-0.00634.8820.0000.0000.0000.0000.0000.000
116B240LYS10.7660.89437.8200.0390.0390.0000.0000.0000.000
117B241PRO00.0290.01741.5840.0010.0010.0000.0000.0000.000
118B242LEU00.0490.00542.2720.0020.0020.0000.0000.0000.000
119B243LEU0-0.019-0.01345.3990.0020.0020.0000.0000.0000.000
120B244GLN00.0000.01946.5070.0000.0000.0000.0000.0000.000
121B245THR0-0.019-0.01944.4840.0000.0000.0000.0000.0000.000
122B246SER00.0190.01847.2560.0020.0020.0000.0000.0000.000
123B247ARG10.9950.98747.1870.0210.0210.0000.0000.0000.000
124B248LYS11.0010.99446.8970.0240.0240.0000.0000.0000.000
125B249GLY00.0210.01845.0650.0000.0000.0000.0000.0000.000
126B250TYR00.0470.01640.808-0.001-0.0010.0000.0000.0000.000
127B251LEU00.0160.00141.723-0.001-0.0010.0000.0000.0000.000
128B252ALA00.0110.01541.6380.0000.0000.0000.0000.0000.000
129B253ALA00.0420.03138.804-0.001-0.0010.0000.0000.0000.000
130B254VAL00.0330.03937.323-0.003-0.0030.0000.0000.0000.000
131B255SER00.0010.00436.871-0.001-0.0010.0000.0000.0000.000
132B256SER0-0.030-0.01836.184-0.002-0.0020.0000.0000.0000.000
133B257SER0-0.070-0.05033.118-0.003-0.0030.0000.0000.0000.000
134B258SER0-0.042-0.03032.008-0.004-0.0040.0000.0000.0000.000
135B259TYR00.0060.01033.0570.0000.0000.0000.0000.0000.000
136B260SER00.035-0.01233.9390.0020.0020.0000.0000.0000.000
137B261PHE0-0.043-0.02625.8120.0000.0000.0000.0000.0000.000
138B262VAL00.0230.01931.2260.0030.0030.0000.0000.0000.000
139B263SER0-0.006-0.03033.2280.0050.0050.0000.0000.0000.000
140B264LEU0-0.008-0.00228.7780.0030.0030.0000.0000.0000.000
141B265LEU00.023-0.00427.3980.0050.0050.0000.0000.0000.000
142B266GLN0-0.030-0.01030.4390.0070.0070.0000.0000.0000.000
143B267HIS00.000-0.01233.8090.0060.0060.0000.0000.0000.000
144B268PHE00.004-0.01428.7240.0040.0040.0000.0000.0000.000
145B269LEU00.0240.02828.5400.0050.0050.0000.0000.0000.000
146B270PRO0-0.006-0.01130.0230.0060.0060.0000.0000.0000.000
147B271LEU0-0.057-0.02629.5690.0050.0050.0000.0000.0000.000
148B272MET0-0.079-0.02323.6230.0030.0030.0000.0000.0000.000
149B273LYS10.8110.89723.240-0.059-0.0590.0000.0000.0000.000
150B274GLU-1-0.786-0.89124.4540.0420.0420.0000.0000.0000.000
151B275GLY0-0.060-0.01221.4740.0140.0140.0000.0000.0000.000
152B276GLY0-0.035-0.00819.9870.0040.0040.0000.0000.0000.000
153B277SER0-0.067-0.03118.084-0.007-0.0070.0000.0000.0000.000
154B278ALA00.0450.01220.642-0.001-0.0010.0000.0000.0000.000
155B279LEU0-0.040-0.01918.740-0.010-0.0100.0000.0000.0000.000
156B280ALA00.0400.03022.4980.0030.0030.0000.0000.0000.000
157B281LEU0-0.0030.00021.847-0.012-0.0120.0000.0000.0000.000
158B282SER00.0240.01724.3520.0070.0070.0000.0000.0000.000
159B283TYR00.006-0.01325.574-0.011-0.0110.0000.0000.0000.000
160B284ILE0-0.034-0.01227.4620.0090.0090.0000.0000.0000.000
161B303ALA00.0840.04830.6720.0000.0000.0000.0000.0000.000
162B304LEU0-0.017-0.02929.6260.0030.0030.0000.0000.0000.000
163B305GLU-1-0.807-0.87326.992-0.088-0.0880.0000.0000.0000.000
164B306SER0-0.013-0.01928.5090.0000.0000.0000.0000.0000.000
165B307ASP-1-0.893-0.90931.010-0.038-0.0380.0000.0000.0000.000
166B308CYS0-0.0200.00224.3860.0050.0050.0000.0000.0000.000
167B309ARG10.9230.93726.4570.0610.0610.0000.0000.0000.000
168B310THR0-0.025-0.01028.1200.0060.0060.0000.0000.0000.000
169B311LEU00.0450.01828.7280.0050.0050.0000.0000.0000.000
170B312ALA0-0.022-0.00425.1360.0050.0050.0000.0000.0000.000
171B313PHE0-0.033-0.01326.7390.0080.0080.0000.0000.0000.000
172B314GLU-1-0.921-0.96929.313-0.009-0.0090.0000.0000.0000.000
173B315ALA00.0240.00427.2370.0060.0060.0000.0000.0000.000
174B316GLY00.0230.02626.2250.0070.0070.0000.0000.0000.000
175B317ARG10.8160.89327.088-0.006-0.0060.0000.0000.0000.000
176B318ALA0-0.0150.00630.5580.0040.0040.0000.0000.0000.000
177B319ARG10.8050.89827.906-0.032-0.0320.0000.0000.0000.000
178B320ALA0-0.009-0.01024.1530.0070.0070.0000.0000.0000.000
179B321VAL0-0.051-0.00923.3400.0020.0020.0000.0000.0000.000
180B322ARG10.8200.91015.9160.0420.0420.0000.0000.0000.000
181B323VAL00.0050.00122.133-0.002-0.0020.0000.0000.0000.000
182B324ASN0-0.017-0.01919.319-0.007-0.0070.0000.0000.0000.000
183B325CYS0-0.043-0.02921.7900.0070.0070.0000.0000.0000.000
184B326ILE0-0.0110.00817.618-0.017-0.0170.0000.0000.0000.000
185B327SER00.001-0.00321.6660.0170.0170.0000.0000.0000.000
186B328ALA0-0.0060.00522.174-0.010-0.0100.0000.0000.0000.000
187B329GLY00.0620.02123.7830.0130.0130.0000.0000.0000.000
188B330PRO0-0.034-0.01725.745-0.001-0.0010.0000.0000.0000.000
189B331LEU0-0.0060.01823.477-0.006-0.0060.0000.0000.0000.000
190B363LYS10.7820.86716.8290.2580.2580.0000.0000.0000.000
191B364GLU-1-0.856-0.92219.978-0.202-0.2020.0000.0000.0000.000
192B365LEU00.0150.01620.139-0.019-0.0190.0000.0000.0000.000
193B366GLU-1-0.802-0.88319.141-0.167-0.1670.0000.0000.0000.000
194B367SER0-0.061-0.05219.809-0.011-0.0110.0000.0000.0000.000
195B368ASP-1-0.806-0.91215.203-0.330-0.3300.0000.0000.0000.000
196B369ASP-1-0.805-0.86315.077-0.331-0.3310.0000.0000.0000.000
197B370VAL00.0320.01115.232-0.027-0.0270.0000.0000.0000.000
198B371GLY00.0020.00416.4900.0010.0010.0000.0000.0000.000
199B372ARG10.7880.85510.4950.4040.4040.0000.0000.0000.000
200B373ALA0-0.0030.00912.271-0.032-0.0320.0000.0000.0000.000
201B374ALA00.028-0.00114.0720.0120.0120.0000.0000.0000.000
202B375LEU00.0030.00511.1860.0250.0250.0000.0000.0000.000
203B376PHE00.0120.0039.2490.0300.0300.0000.0000.0000.000
204B377LEU00.0350.02511.6480.0600.0600.0000.0000.0000.000
205B378LEU0-0.013-0.00215.0600.0480.0480.0000.0000.0000.000
206B379SER0-0.050-0.02810.7940.0450.0450.0000.0000.0000.000
207B380PRO00.013-0.02111.326-0.011-0.0110.0000.0000.0000.000
208B381LEU0-0.0150.0036.6220.0200.0200.0000.0000.0000.000
209B382ALA0-0.0080.01710.101-0.005-0.0050.0000.0000.0000.000
210B383ARG10.9520.97012.623-0.226-0.2260.0000.0000.0000.000
211B384ALA0-0.027-0.01014.7610.0130.0130.0000.0000.0000.000
212B385VAL0-0.021-0.00315.006-0.011-0.0110.0000.0000.0000.000
213B386THR00.0530.02717.8070.0040.0040.0000.0000.0000.000
214B387GLY00.0140.00321.3320.0010.0010.0000.0000.0000.000
215B388ALA0-0.024-0.00819.632-0.001-0.0010.0000.0000.0000.000
216B389THR00.026-0.00421.6430.0040.0040.0000.0000.0000.000
217B390LEU0-0.026-0.00815.455-0.005-0.0050.0000.0000.0000.000
218B391TYR0-0.009-0.04619.9670.0020.0020.0000.0000.0000.000
219B392VAL0-0.047-0.03317.896-0.021-0.0210.0000.0000.0000.000
220B393ASP-1-0.761-0.90320.337-0.138-0.1380.0000.0000.0000.000
221B394ASN0-0.092-0.05820.6980.0020.0020.0000.0000.0000.000
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