FMO DATABASE

FMODB ID: 175MZ

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	OptHSide
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	-664561.075615
FMO2-HF: Nuclear repulsion	627917.946115
FMO2-HF: Total energy	-36643.1295
FMO2-MP2: Total energy	-36750.501563

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.
-12.798	-1.52	6.397	-5.674	-12.004	-0.034

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 : -0.029 / q_NPA : -0.017

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

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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	-0.032	-0.004	2.076	-1.520	0.743	0.985	-1.358	-1.889	0.002
4	A	5	THR	0	0.022	0.021	2.697	-1.308	-0.023	0.659	-0.832	-1.113	-0.012
5	A	6	VAL	0	-0.044	-0.028	5.426	0.066	0.066	0.000	0.000	0.000	0.000
6	A	96	CYS	0	-0.015	-0.004	8.263	0.001	0.001	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.110	0.047	11.653	0.026	0.026	0.000	0.000	0.000	0.000
8	A	9	SER	0	-0.047	-0.019	13.232	0.014	0.014	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.069	-0.019	12.582	0.013	0.013	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.034	-0.003	9.637	0.024	0.024	0.000	0.000	0.000	0.000
11	A	12	PRO	0	-0.011	-0.005	13.744	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	PRO	0	0.021	-0.010	16.349	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.839	-0.930	17.880	0.020	0.020	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.027	-0.011	13.112	0.001	0.001	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.019	0.006	15.180	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.926	-0.963	17.258	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.032	-0.040	15.329	0.000	0.000	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.017	-0.002	12.169	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	20	ASN	0	0.008	0.019	16.320	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.038	-0.017	19.925	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.027	-0.012	14.471	0.002	0.002	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.039	-0.006	18.598	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	24	SER	0	-0.085	-0.049	20.051	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.910	-0.949	21.802	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.087	-0.004	22.730	0.007	0.007	0.000	0.000	0.000	0.000
26	A	27	PRO	0	-0.016	-0.039	24.051	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.049	0.011	19.507	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	PRO	0	-0.034	-0.002	21.926	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	TYR	0	-0.006	-0.017	21.436	0.008	0.008	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.001	0.000	22.945	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	32	GLN	0	-0.063	-0.041	19.337	0.008	0.008	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.756	-0.856	18.329	0.038	0.038	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.063	0.024	17.406	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.060	-0.008	16.910	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.018	0.005	15.191	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.051	-0.028	8.510	0.016	0.016	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.030	-0.022	12.417	-0.032	-0.032	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.076	0.039	8.445	0.044	0.044	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.782	0.887	9.811	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.890	-0.949	11.344	0.372	0.372	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.021	-0.002	7.158	0.101	0.101	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.007	-0.015	3.394	-0.798	-0.150	0.039	-0.200	-0.488	0.001
43	A	44	LEU	0	-0.040	-0.002	2.493	-3.509	-1.489	0.568	-0.907	-1.681	-0.007
44	A	45	PRO	0	0.046	0.024	2.665	-0.477	0.093	0.285	-0.176	-0.679	0.001
45	A	46	THR	0	-0.007	-0.002	5.535	0.180	0.180	0.000	0.000	0.000	0.000
46	A	47	GLN	0	0.057	0.046	9.132	0.010	0.010	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.016	-0.002	11.480	0.064	0.064	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.014	-0.024	14.563	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.030	0.014	15.357	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.091	-0.056	8.769	0.004	0.004	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.031	-0.027	6.744	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	53	HIS	0	-0.017	-0.001	11.527	0.045	0.045	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.807	-0.852	12.110	0.115	0.115	0.000	0.000	0.000	0.000
54	A	55	TYR	0	0.069	0.046	13.489	0.003	0.003	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.089	-0.083	14.453	0.021	0.021	0.000	0.000	0.000	0.000
56	A	57	VAL	0	-0.010	0.031	13.250	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	58	ILE	0	0.014	0.003	16.287	0.016	0.016	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.002	-0.012	18.415	0.003	0.003	0.000	0.000	0.000	0.000
59	A	60	PRO	0	0.011	-0.006	20.327	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.001	0.011	23.688	0.005	0.005	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.034	-0.010	22.899	0.003	0.003	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.992	0.998	24.936	-0.070	-0.070	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.050	-0.039	23.074	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.910	0.943	17.069	-0.086	-0.086	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.026	0.000	19.217	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	THR	0	-0.024	-0.016	15.104	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.894	0.971	12.983	-0.043	-0.043	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.824	0.917	11.352	-0.154	-0.154	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.014	0.005	9.836	0.013	0.013	0.000	0.000	0.000	0.000
70	A	71	ILE	0	-0.038	-0.015	7.698	0.020	0.020	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.049	0.026	8.760	-0.044	-0.044	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.017	-0.009	9.037	0.030	0.030	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.926	-0.962	9.906	-0.129	-0.129	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.053	-0.008	10.329	0.020	0.020	0.000	0.000	0.000	0.000
75	A	76	THR	0	0.002	-0.031	12.122	0.010	0.010	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.032	-0.006	11.485	-0.040	-0.040	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.745	-0.812	6.746	-0.567	-0.567	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.810	-0.917	7.665	-0.148	-0.148	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.097	-0.083	2.296	-1.466	-0.426	1.442	-0.519	-1.964	-0.004
80	A	81	TYR	0	0.030	0.005	5.675	0.057	0.057	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.022	0.030	5.983	0.015	0.015	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.017	-0.010	8.332	-0.064	-0.064	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.859	-0.906	9.534	0.592	0.592	0.000	0.000	0.000	0.000
84	A	85	HIS	0	0.002	-0.011	12.245	0.024	0.024	0.000	0.000	0.000	0.000
85	A	86	TYR	0	-0.067	-0.075	9.068	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.048	0.012	8.601	0.149	0.149	0.000	0.000	0.000	0.000
87	A	88	THR	0	-0.099	-0.083	5.411	0.377	0.377	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.073	0.013	3.127	-1.494	-0.469	0.112	-0.259	-0.879	0.000
89	A	90	SER	0	-0.018	-0.001	2.658	-2.025	-0.420	1.568	-1.454	-1.719	-0.012
90	A	91	LEU	0	-0.016	-0.005	2.571	-0.838	-0.099	0.731	0.043	-1.513	-0.003
91	A	92	ILE	0	0.004	-0.012	3.880	-0.069	0.014	0.008	-0.012	-0.079	0.000
92	A	93	ASP	-1	-0.836	-0.892	7.659	-0.329	-0.329	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.022	-0.018	10.057	0.057	0.057	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.088	-0.060	13.315	0.028	0.028	0.000	0.000	0.000	0.000

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