FMO DATABASE

FMODB ID: V5V91

Calculation Name: 1BOX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BOX

Chain ID: A

ChEMBL ID:

UniProt ID: P05798

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptH
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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-664593.592538
FMO2-HF: Nuclear repulsion	627951.168998
FMO2-HF: Total energy	-36642.423541
FMO2-MP2: Total energy	-36749.877847

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-13.004	-1.722	6.934	-5.769	-12.444	-0.035

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / 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 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	4	GLY	0	-0.052	-0.009	2.156	-2.176	0.317	0.973	-1.447	-2.019	0.002
4	A	5	THR	0	0.027	0.028	2.836	-0.895	0.208	0.471	-0.631	-0.943	-0.008
5	A	6	VAL	0	-0.047	-0.028	5.488	0.072	0.072	0.000	0.000	0.000	0.000
6	A	96	CYS	0	-0.014	-0.020	8.505	0.003	0.003	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.102	0.047	11.871	0.030	0.030	0.000	0.000	0.000	0.000
8	A	9	SER	0	-0.043	-0.010	13.214	0.015	0.015	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.062	-0.016	12.669	0.013	0.013	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.038	0.000	9.555	0.027	0.027	0.000	0.000	0.000	0.000
11	A	12	PRO	0	-0.027	-0.015	13.665	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	13	PRO	0	0.053	0.006	16.375	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.895	-0.949	18.017	0.028	0.028	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.043	-0.015	13.264	0.003	0.003	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.019	0.005	15.312	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.924	-0.961	17.361	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.033	-0.041	15.499	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.019	0.000	12.408	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	20	ASN	0	0.002	0.020	16.423	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.041	-0.025	20.074	0.000	0.000	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.016	-0.002	14.510	0.002	0.002	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.049	-0.010	18.678	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.080	-0.047	20.149	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.904	-0.938	21.790	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.102	-0.015	22.707	0.007	0.007	0.000	0.000	0.000	0.000
26	A	27	PRO	0	-0.012	-0.042	24.012	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.054	0.014	19.561	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	PRO	0	-0.030	-0.005	21.962	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	TYR	0	-0.007	-0.010	21.276	0.008	0.008	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.013	-0.015	22.674	0.000	0.000	0.000	0.000	0.000	0.000
31	A	32	GLN	0	-0.041	-0.031	18.989	0.010	0.010	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.759	-0.864	18.079	0.070	0.070	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.047	0.011	17.219	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.062	-0.005	16.885	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.023	0.009	15.214	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.036	-0.021	8.243	0.022	0.022	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.042	-0.030	12.515	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.084	0.040	8.376	0.042	0.042	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.771	0.883	9.437	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.888	-0.944	11.231	0.494	0.494	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.021	0.000	6.976	0.123	0.123	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.007	-0.018	3.318	-0.869	-0.195	0.049	-0.207	-0.515	0.001
43	A	44	LEU	0	-0.049	-0.002	2.492	-3.358	-1.362	1.009	-1.032	-1.973	-0.008
44	A	45	PRO	0	0.047	0.022	2.792	-0.358	0.122	0.194	-0.107	-0.567	0.001
45	A	46	THR	0	0.017	0.014	5.738	0.234	0.234	0.000	0.000	0.000	0.000
46	A	47	GLN	0	0.029	0.031	8.855	0.000	0.000	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.019	-0.006	11.524	0.073	0.073	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.020	-0.026	14.413	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.033	0.014	15.340	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.084	-0.051	8.709	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.015	-0.021	6.553	-0.046	-0.046	0.000	0.000	0.000	0.000
52	A	53	HIS	0	-0.017	-0.001	11.364	0.041	0.041	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.879	-0.909	12.012	0.178	0.178	0.000	0.000	0.000	0.000
54	A	55	TYR	0	0.072	0.056	13.234	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.097	-0.087	14.286	0.028	0.028	0.000	0.000	0.000	0.000
56	A	57	VAL	0	-0.013	0.022	13.377	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	58	ILE	0	0.020	0.005	16.531	0.018	0.018	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.023	-0.023	18.556	0.004	0.004	0.000	0.000	0.000	0.000
59	A	60	PRO	0	0.043	0.017	20.480	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.002	0.005	23.811	0.005	0.005	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.035	-0.011	23.040	0.002	0.002	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.991	1.002	25.111	-0.090	-0.090	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.041	-0.028	22.715	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.978	0.986	17.261	-0.126	-0.126	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.035	-0.012	19.191	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	THR	0	-0.015	-0.015	14.988	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.926	0.983	13.189	-0.076	-0.076	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.819	0.915	11.053	-0.209	-0.209	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.024	0.010	10.006	0.022	0.022	0.000	0.000	0.000	0.000
70	A	71	ILE	0	-0.050	-0.021	7.365	0.017	0.017	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.059	0.028	8.592	-0.043	-0.043	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.008	-0.013	8.959	0.040	0.040	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.922	-0.956	9.790	-0.120	-0.120	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.051	-0.011	10.546	0.019	0.019	0.000	0.000	0.000	0.000
75	A	76	THR	0	0.006	-0.023	12.199	0.015	0.015	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.040	-0.008	11.484	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.777	-0.819	6.754	-0.627	-0.627	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.835	-0.927	7.792	-0.130	-0.130	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.072	-0.075	2.338	-1.610	-0.484	1.442	-0.575	-1.992	-0.005
80	A	81	TYR	0	0.028	0.001	5.858	0.057	0.057	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.022	0.015	6.158	0.031	0.031	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.019	-0.004	8.543	-0.085	-0.085	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.856	-0.898	9.527	0.703	0.703	0.000	0.000	0.000	0.000
84	A	85	HIS	0	0.012	-0.005	12.233	0.023	0.023	0.000	0.000	0.000	0.000
85	A	86	TYR	0	-0.064	-0.065	8.677	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.041	0.013	8.606	0.184	0.184	0.000	0.000	0.000	0.000
87	A	88	THR	0	-0.076	-0.075	5.391	0.400	0.400	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.060	0.009	2.522	-1.689	-0.580	0.484	-0.350	-1.243	0.000
89	A	90	SER	0	-0.026	-0.007	2.431	-2.372	-0.726	1.737	-1.622	-1.761	-0.015
90	A	91	LEU	0	-0.021	-0.001	2.643	-0.558	0.017	0.569	0.218	-1.361	-0.003
91	A	92	ILE	0	0.005	-0.009	3.948	-0.064	0.016	0.006	-0.016	-0.070	0.000
92	A	93	ASP	-1	-0.841	-0.902	7.724	-0.358	-0.358	0.000	0.000	0.000	0.000
93	A	94	GLN	0	0.017	-0.001	10.096	0.064	0.064	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.100	-0.059	13.357	0.031	0.031	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)