FMO DATABASE

FMODB ID: 22Z9R

Calculation Name: 2FDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FDQ

Chain ID: A

ChEMBL ID:

UniProt ID: P82934

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-595003.160878
FMO2-HF: Nuclear repulsion	560204.465812
FMO2-HF: Total energy	-34798.695065
FMO2-MP2: Total energy	-34900.010862

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:SER)

Summations of interaction energy for fragment #1(A:1:SER)

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.
-44.743	-44.116	25.028	-14.951	-10.703	-0.111

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.029

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 ES EX CT+mix DI(MP2)

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].
3	A	3	ALA	0	0.047	0.017	3.868	-4.375	-2.692	-0.003	-0.800	-0.879	0.004
4	A	4	GLU	-1	-0.906	-0.957	2.328	-11.105	-6.664	3.672	-4.191	-3.922	-0.040
5	A	5	PHE	0	-0.008	0.000	3.974	-0.879	-0.440	0.000	-0.226	-0.213	0.001
6	A	6	ASP	-1	-0.856	-0.923	5.840	2.024	2.024	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.842	0.924	7.612	-0.542	-0.542	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.021	0.010	7.896	-0.136	-0.136	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.036	-0.026	9.552	-0.063	-0.063	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.806	-0.889	11.736	0.325	0.325	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.797	-0.894	11.515	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.003	-0.004	13.640	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.753	0.864	15.460	-0.287	-0.287	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.071	-0.029	17.085	0.015	0.015	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.025	-0.004	17.471	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.915	0.964	20.499	0.051	0.051	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.002	0.008	23.706	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.826	0.913	23.719	0.125	0.125	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.008	0.028	20.635	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.042	0.007	23.527	0.020	0.020	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.857	-0.949	23.087	-0.166	-0.166	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.871	-0.940	22.459	-0.292	-0.292	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.693	-0.812	19.166	-0.308	-0.308	0.000	0.000	0.000	0.000
24	A	24	MET	0	-0.031	0.004	18.208	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.001	-0.011	18.828	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	PHE	0	-0.001	0.021	12.727	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.034	0.018	13.572	-0.078	-0.078	0.000	0.000	0.000	0.000
28	A	28	TYR	0	0.004	-0.006	14.096	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.019	-0.031	15.326	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	30	HIS	1	0.904	0.942	10.671	0.852	0.852	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.060	0.039	10.744	-0.110	-0.110	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.857	0.958	11.717	0.181	0.181	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.019	-0.026	11.746	0.138	0.138	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.023	0.009	7.538	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.018	-0.026	9.157	0.177	0.177	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.061	-0.022	11.259	0.099	0.099	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.016	0.010	12.723	0.028	0.028	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.785	-0.878	13.642	-0.495	-0.495	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.068	-0.029	16.691	0.054	0.054	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.022	0.004	18.656	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.001	0.003	21.804	0.028	0.028	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.844	-0.923	24.492	-0.108	-0.108	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.779	0.881	27.019	0.152	0.152	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.029	-0.015	26.819	0.011	0.011	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.075	0.036	29.864	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.009	-0.022	33.657	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.062	0.037	35.881	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.781	-0.861	29.868	-0.074	-0.074	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.041	-0.006	30.292	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.890	0.942	27.092	0.050	0.050	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.032	0.018	26.070	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.827	0.909	25.591	0.079	0.079	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.065	0.042	25.716	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.860	0.937	21.713	0.116	0.116	0.000	0.000	0.000	0.000
55	A	55	TRP	0	0.008	-0.015	21.156	-0.035	-0.035	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.787	-0.875	22.323	-0.206	-0.206	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.003	-0.011	19.736	-0.027	-0.027	0.000	0.000	0.000	0.000
58	A	58	TRP	0	0.009	-0.010	16.043	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.004	0.016	18.518	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.031	-0.025	20.477	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.024	0.003	13.606	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.849	0.931	15.722	0.239	0.239	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.030	0.013	16.222	0.010	0.010	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.097	-0.049	10.938	-0.081	-0.081	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.005	-0.017	8.417	-0.118	-0.118	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.891	0.924	6.842	0.036	0.036	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.800	-0.863	1.594	-30.982	-38.501	20.578	-8.953	-4.105	-0.079
68	A	68	ASP	-1	-0.832	-0.887	4.823	-2.317	-2.225	-0.001	-0.002	-0.089	0.000
69	A	69	ALA	0	-0.033	0.006	7.830	0.267	0.267	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.001	-0.001	2.591	-0.608	0.710	0.780	-0.735	-1.363	0.003
71	A	71	LYS	1	0.899	0.957	4.814	2.781	2.781	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.005	-0.030	5.502	0.670	0.670	0.000	0.000	0.000	0.000
73	A	73	TYR	0	-0.040	-0.027	7.908	0.368	0.368	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.021	0.010	3.928	0.194	0.367	0.002	-0.044	-0.132	0.000
75	A	75	ASP	-1	-0.879	-0.938	8.239	-1.501	-1.501	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.801	0.884	10.577	0.748	0.748	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.013	0.001	10.863	0.143	0.143	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.807	-0.893	10.489	-0.217	-0.217	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.865	-0.891	13.075	-0.414	-0.414	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.002	-0.006	16.025	0.077	0.077	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.803	0.861	12.255	0.222	0.222	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.776	0.888	14.425	0.467	0.467	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.829	0.912	19.464	0.287	0.287	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.071	-0.062	20.774	0.022	0.022	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.015	0.021	20.497	0.026	0.026	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.025	-0.016	17.042	0.009	0.009	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:1:SER)