FMO DATABASE

FMODB ID: 98QL2

Calculation Name: 4IT7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IT7

Chain ID: A

ChEMBL ID:

UniProt ID: E9N3T6

Base Structure: X-ray

Registration Date: 2023-09-23

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742111.259423
FMO2-HF: Nuclear repulsion	701449.463217
FMO2-HF: Total energy	-40661.796206
FMO2-MP2: Total energy	-40779.164352

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:6:GLY)

Summations of interaction energy for fragment #1(A:6:GLY)

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.
-0.696	0.672	3.356	-2.13	-2.593	0.003

Interaction energy analysis for fragmet #1(A:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.002

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	8	PHE	0	-0.049	-0.027	3.855	2.081	3.349	-0.014	-0.763	-0.492	0.002
4	A	9	SER	0	0.027	0.023	7.346	-0.163	-0.163	0.000	0.000	0.000	0.000
5	A	10	THR	0	0.004	-0.017	9.703	-0.028	-0.028	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.846	0.931	13.423	-0.418	-0.418	0.000	0.000	0.000	0.000
7	A	12	ASP	-1	-0.748	-0.875	15.166	0.149	0.149	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.007	-0.008	18.720	0.018	0.018	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.058	-0.034	21.041	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.823	-0.902	18.191	0.328	0.328	0.000	0.000	0.000	0.000
11	A	16	PRO	0	0.055	0.017	21.492	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	17	LYS	1	0.806	0.911	16.494	-0.324	-0.324	0.000	0.000	0.000	0.000
13	A	18	ILE	0	-0.012	-0.010	15.401	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	19	GLN	0	-0.006	-0.013	19.281	-0.031	-0.031	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.000	0.005	22.169	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	21	LEU	0	-0.055	-0.031	16.337	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	22	ALA	0	0.030	0.018	20.425	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.024	0.016	22.206	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.779	0.865	20.748	-0.164	-0.164	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.054	0.024	20.799	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	26	LEU	0	0.013	0.010	22.760	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	27	GLN	0	-0.003	-0.007	26.357	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	28	ARG	1	0.874	0.939	23.149	-0.070	-0.070	0.000	0.000	0.000	0.000
24	A	29	ILE	0	0.004	-0.001	23.738	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	30	ASN	0	-0.026	-0.032	26.931	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.034	-0.013	28.816	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	32	ALA	0	0.002	0.009	27.435	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	33	SER	0	-0.042	-0.007	29.470	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	34	ASN	0	0.020	-0.012	31.131	0.003	0.003	0.000	0.000	0.000	0.000
30	A	35	ASP	-1	-0.836	-0.901	34.009	0.006	0.006	0.000	0.000	0.000	0.000
31	A	36	LEU	0	0.033	0.011	35.916	0.002	0.002	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.047	-0.015	37.504	0.002	0.002	0.000	0.000	0.000	0.000
33	A	38	GLN	0	0.005	0.009	34.079	0.000	0.000	0.000	0.000	0.000	0.000
34	A	39	GLN	0	-0.046	-0.022	30.621	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	40	THR	0	0.011	0.010	31.216	0.006	0.006	0.000	0.000	0.000	0.000
36	A	41	ILE	0	0.005	-0.001	25.237	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	42	VAL	0	-0.023	0.000	28.959	0.001	0.001	0.000	0.000	0.000	0.000
38	A	43	LYS	1	0.946	0.957	26.133	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	44	VAL	0	0.037	0.023	20.487	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.071	-0.037	22.095	0.002	0.002	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.057	-0.053	17.390	0.016	0.016	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.049	0.020	16.104	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.869	0.940	11.299	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	49	THR	0	0.011	0.001	9.836	-0.156	-0.156	0.000	0.000	0.000	0.000
45	A	50	GLN	0	0.007	0.024	4.204	-0.273	-0.107	0.000	-0.054	-0.111	0.000
46	A	51	VAL	0	0.024	-0.002	4.676	-0.925	-0.833	-0.001	-0.016	-0.075	0.000
47	A	52	VAL	0	-0.017	-0.001	1.933	-0.612	-0.909	3.357	-1.261	-1.799	0.001
48	A	53	ALA	0	0.025	0.017	3.653	-0.610	-0.471	0.014	-0.036	-0.116	0.000
49	A	54	GLY	0	0.074	0.054	7.314	-0.067	-0.067	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.031	-0.019	7.754	0.265	0.265	0.000	0.000	0.000	0.000
51	A	56	ASN	0	-0.016	-0.012	7.623	-0.218	-0.218	0.000	0.000	0.000	0.000
52	A	57	THR	0	0.018	0.001	9.134	0.233	0.233	0.000	0.000	0.000	0.000
53	A	58	VAL	0	-0.034	-0.016	11.116	-0.097	-0.097	0.000	0.000	0.000	0.000
54	A	59	LEU	0	0.008	-0.001	13.496	0.033	0.033	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.857	-0.893	17.094	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	61	LEU	0	0.003	0.001	19.984	0.013	0.013	0.000	0.000	0.000	0.000
57	A	62	LEU	0	0.010	0.016	23.386	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	63	ILE	0	0.006	-0.004	26.602	0.008	0.008	0.000	0.000	0.000	0.000
59	A	64	ALA	0	0.019	0.001	29.302	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	65	PRO	0	0.046	0.045	33.033	0.004	0.004	0.000	0.000	0.000	0.000
61	A	66	THR	0	-0.007	-0.022	35.336	0.002	0.002	0.000	0.000	0.000	0.000
62	A	67	SER	0	0.041	0.010	38.046	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	68	CYS	0	-0.067	-0.021	35.949	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	69	ARG	1	0.848	0.908	38.799	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	70	LYS	1	0.860	0.926	33.307	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	71	ASN	0	-0.042	-0.010	38.804	0.001	0.001	0.000	0.000	0.000	0.000
67	A	72	GLU	-1	-0.822	-0.898	41.517	0.015	0.015	0.000	0.000	0.000	0.000
68	A	73	THR	0	-0.038	-0.027	41.389	0.001	0.001	0.000	0.000	0.000	0.000
69	A	74	SER	0	0.025	0.022	39.544	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	75	ALA	0	0.005	-0.001	41.460	0.002	0.002	0.000	0.000	0.000	0.000
71	A	76	GLY	0	-0.007	-0.010	41.049	0.001	0.001	0.000	0.000	0.000	0.000
72	A	77	ASN	0	-0.057	-0.029	37.210	0.001	0.001	0.000	0.000	0.000	0.000
73	A	79	GLU	-1	-0.821	-0.908	35.988	0.045	0.045	0.000	0.000	0.000	0.000
74	A	80	ALA	0	-0.016	-0.013	34.872	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	81	VAL	0	-0.001	0.007	36.889	0.000	0.000	0.000	0.000	0.000	0.000
76	A	82	SER	0	0.016	-0.007	38.736	0.000	0.000	0.000	0.000	0.000	0.000
77	A	83	ASN	0	-0.057	-0.016	39.314	0.000	0.000	0.000	0.000	0.000	0.000
78	A	84	GLY	0	0.067	0.037	37.427	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	85	THR	0	-0.005	-0.023	34.787	0.002	0.002	0.000	0.000	0.000	0.000
80	A	86	LYS	1	0.877	0.949	31.603	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	87	GLN	0	0.002	0.001	28.754	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	88	ILE	0	-0.007	-0.003	23.251	0.008	0.008	0.000	0.000	0.000	0.000
83	A	89	CYS	0	-0.024	-0.002	22.313	0.005	0.005	0.000	0.000	0.000	0.000
84	A	90	THR	0	0.024	0.014	17.138	0.010	0.010	0.000	0.000	0.000	0.000
85	A	91	VAL	0	-0.043	-0.027	18.059	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	92	ALA	0	0.014	0.011	13.316	0.019	0.019	0.000	0.000	0.000	0.000
87	A	93	ILE	0	0.005	-0.003	13.864	-0.020	-0.020	0.000	0.000	0.000	0.000
88	A	94	TRP	0	-0.047	-0.014	10.038	0.036	0.036	0.000	0.000	0.000	0.000
89	A	95	GLU	-1	-0.792	-0.896	12.281	0.320	0.320	0.000	0.000	0.000	0.000
90	A	96	LYS	1	0.845	0.914	12.239	0.029	0.029	0.000	0.000	0.000	0.000
91	A	97	PRO	0	0.010	-0.003	14.483	-0.038	-0.038	0.000	0.000	0.000	0.000
92	A	98	TRP	0	-0.001	-0.003	11.054	0.008	0.008	0.000	0.000	0.000	0.000
93	A	99	GLU	-1	-0.842	-0.904	15.911	0.018	0.018	0.000	0.000	0.000	0.000
94	A	100	ASN	0	-0.073	-0.041	19.324	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	101	PHE	0	-0.029	0.009	14.960	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.766	-0.878	17.096	0.200	0.200	0.000	0.000	0.000	0.000
97	A	103	GLU	-1	-0.877	-0.910	16.218	-0.030	-0.030	0.000	0.000	0.000	0.000
98	A	104	ILE	0	-0.025	-0.031	16.984	0.023	0.023	0.000	0.000	0.000	0.000
99	A	105	THR	0	0.001	-0.009	16.716	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	106	ILE	0	-0.008	-0.015	18.136	0.003	0.003	0.000	0.000	0.000	0.000
101	A	107	LYS	1	0.878	0.940	15.584	0.089	0.089	0.000	0.000	0.000	0.000
102	A	108	GLU	-1	-0.830	-0.901	19.180	-0.092	-0.092	0.000	0.000	0.000	0.000
103	A	110	LYS	1	0.891	0.942	21.736	0.043	0.043	0.000	0.000	0.000	0.000
104	A	111	SER	0	0.049	0.013	27.606	0.007	0.007	0.000	0.000	0.000	0.000
105	A	112	ALA	0	-0.030	-0.004	28.771	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLY)