FMO DATABASE

FMODB ID: 22ZRR

Calculation Name: 1T4A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T4A

Chain ID: A

ChEMBL ID:

UniProt ID: P12049

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-493840.51151
FMO2-HF: Nuclear repulsion	460268.945488
FMO2-HF: Total energy	-33571.566022
FMO2-MP2: Total energy	-33666.739382

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:MET)

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

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.
-24.988	-20.179	18.851	-10.209	-13.453	-0.075

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.021

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	LYS	1	0.836	0.913	3.232	-0.516	2.055	0.076	-1.313	-1.335	0.001
4	A	4	VAL	0	-0.003	-0.005	5.655	0.326	0.326	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.819	0.926	8.906	1.053	1.053	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.000	-0.020	11.940	0.005	0.005	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.037	-0.040	14.893	0.075	0.075	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.018	-0.016	18.481	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.033	0.017	21.307	0.010	0.010	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.008	0.009	25.052	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.847	0.928	28.071	0.172	0.172	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.920	-0.953	30.176	-0.137	-0.137	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.044	-0.019	32.793	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.040	-0.010	32.367	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.028	0.014	33.990	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.743	-0.880	31.153	-0.133	-0.133	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.006	-0.005	34.002	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.015	-0.003	28.608	0.010	0.010	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.042	0.010	32.898	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.034	0.007	33.475	0.005	0.005	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.040	-0.015	36.473	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.006	-0.002	32.490	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.036	-0.019	35.783	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.022	0.021	37.702	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.017	-0.001	37.933	0.004	0.004	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.009	-0.006	34.429	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	HIS	0	-0.023	-0.020	39.045	0.006	0.006	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.051	-0.034	42.393	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.095	-0.038	37.884	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.063	-0.031	42.565	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.017	0.023	38.854	0.000	0.000	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.030	-0.038	40.320	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.899	-0.944	38.749	-0.082	-0.082	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.024	-0.003	35.592	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.030	-0.017	38.126	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.882	-0.939	33.940	-0.128	-0.128	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.057	-0.023	31.948	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.816	0.913	29.579	0.148	0.148	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.030	-0.017	27.084	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.001	-0.005	24.489	0.001	0.001	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.738	0.857	19.996	0.236	0.236	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.042	-0.041	13.604	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.030	-0.010	13.987	0.051	0.051	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.797	-0.872	9.609	-0.796	-0.796	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.001	-0.002	8.540	0.196	0.196	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.013	-0.014	2.600	-1.122	-1.486	2.573	-0.560	-1.649	0.001
47	A	47	ILE	0	-0.022	-0.008	3.502	0.108	0.904	0.013	-0.172	-0.637	0.000
48	A	48	GLU	-1	-0.929	-0.964	2.433	-8.534	-5.213	3.514	-2.635	-4.200	-0.030
49	A	49	LYS	1	0.778	0.868	2.331	-1.279	0.319	0.943	-0.685	-1.856	0.008
50	A	50	SER	0	-0.034	-0.025	5.147	-0.123	-0.069	-0.001	-0.002	-0.051	0.000
51	A	51	ASP	-1	-0.909	-0.959	8.869	0.123	0.123	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.829	0.909	11.702	0.189	0.189	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.863	-0.925	10.831	-0.144	-0.144	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.009	-0.013	7.216	-0.062	-0.062	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.824	-0.912	10.420	-0.451	-0.451	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.018	0.017	13.766	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.002	0.001	8.662	0.017	0.017	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.006	-0.005	10.645	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.901	0.948	13.086	0.385	0.385	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.783	-0.852	15.740	-0.192	-0.192	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.025	-0.008	9.653	0.038	0.038	0.000	0.000	0.000	0.000
62	A	62	CYS	0	-0.045	-0.024	15.302	0.027	0.027	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.886	-0.939	17.614	-0.242	-0.242	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.807	0.891	18.834	0.245	0.245	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.048	-0.011	15.762	0.021	0.021	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.010	0.005	14.139	0.017	0.017	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.013	0.006	18.543	0.010	0.010	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.032	0.021	21.775	0.008	0.008	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.038	0.014	23.078	0.014	0.014	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.016	0.011	25.715	0.005	0.005	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.010	-0.011	28.706	0.005	0.005	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.804	-0.886	24.435	-0.207	-0.207	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.835	-0.921	25.065	-0.205	-0.205	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.077	-0.091	17.993	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.848	0.917	18.233	0.472	0.472	0.000	0.000	0.000	0.000
76	A	76	TYR	0	0.029	0.005	13.376	0.019	0.019	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.794	-0.854	13.627	-0.566	-0.566	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.021	-0.015	7.378	-0.060	-0.060	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.798	-0.875	8.302	-0.917	-0.917	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.805	-0.900	1.834	-13.068	-16.235	11.733	-4.842	-3.725	-0.055

Top

Graph

Manual

About

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