FMO DATABASE

FMODB ID: ZY54N

Calculation Name: 1PM4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PM4

Chain ID: A

ChEMBL ID:

UniProt ID: Q57221

Base Structure: X-ray

Registration Date: 2023-06-20

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-941265.079345
FMO2-HF: Nuclear repulsion	895806.886844
FMO2-HF: Total energy	-45458.192501
FMO2-MP2: Total energy	-45590.980192

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:15:ILE)

Summations of interaction energy for fragment #1(A:15:ILE)

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.
-0.486	0.711	-0.011	-0.468	-0.719	0.002

Interaction energy analysis for fragmet #1(A:15:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / 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

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	17	ASN	0	0.020	0.006	3.933	-0.092	1.105	-0.011	-0.468	-0.719	0.002
4	A	18	ILE	0	-0.048	-0.026	6.618	0.311	0.311	0.000	0.000	0.000	0.000
5	A	19	ALA	0	0.041	0.025	9.106	0.004	0.004	0.000	0.000	0.000	0.000
6	A	20	THR	0	-0.005	-0.017	12.372	0.030	0.030	0.000	0.000	0.000	0.000
7	A	21	TYR	0	-0.041	-0.044	15.404	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	22	THR	0	-0.054	-0.057	18.783	0.034	0.034	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.038	0.033	22.050	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	24	THR	0	-0.035	-0.023	25.794	0.013	0.013	0.000	0.000	0.000	0.000
11	A	25	ILE	0	-0.019	0.008	27.944	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	26	GLN	0	0.053	0.009	30.376	0.003	0.003	0.000	0.000	0.000	0.000
13	A	27	GLY	0	0.043	0.036	33.698	0.003	0.003	0.000	0.000	0.000	0.000
14	A	28	LYS	1	0.820	0.894	35.280	-0.052	-0.052	0.000	0.000	0.000	0.000
15	A	29	GLY	0	0.021	0.021	33.392	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	30	GLU	-1	-0.821	-0.919	29.711	0.025	0.025	0.000	0.000	0.000	0.000
17	A	31	VAL	0	0.027	0.021	25.043	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	32	CYS	0	-0.028	0.019	24.485	0.008	0.008	0.000	0.000	0.000	0.000
19	A	33	ILE	0	0.021	0.019	19.049	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	34	ILE	0	-0.042	-0.017	19.495	0.009	0.009	0.000	0.000	0.000	0.000
21	A	35	GLY	0	0.050	0.022	15.532	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	36	ASN	0	-0.025	-0.035	13.583	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	37	LYS	1	0.823	0.893	15.250	0.227	0.227	0.000	0.000	0.000	0.000
24	A	38	GLU	-1	-0.823	-0.901	16.798	-0.292	-0.292	0.000	0.000	0.000	0.000
25	A	39	GLY	0	-0.030	-0.001	17.396	0.011	0.011	0.000	0.000	0.000	0.000
26	A	40	LYS	1	0.775	0.859	12.606	0.456	0.456	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.025	-0.033	13.415	0.005	0.005	0.000	0.000	0.000	0.000
28	A	42	ARG	1	0.821	0.899	6.796	0.403	0.403	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.008	0.018	9.684	0.082	0.082	0.000	0.000	0.000	0.000
30	A	44	GLY	0	0.031	0.006	7.795	-0.162	-0.162	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.807	-0.893	8.206	0.857	0.857	0.000	0.000	0.000	0.000
32	A	46	LEU	0	-0.056	0.001	9.013	-0.106	-0.106	0.000	0.000	0.000	0.000
33	A	47	TYR	0	0.015	-0.006	10.605	0.101	0.101	0.000	0.000	0.000	0.000
34	A	48	ALA	0	0.025	0.005	12.460	-0.079	-0.079	0.000	0.000	0.000	0.000
35	A	49	VAL	0	-0.030	-0.008	15.235	0.028	0.028	0.000	0.000	0.000	0.000
36	A	50	LEU	0	0.017	0.015	17.529	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	51	HIS	1	0.816	0.873	17.218	-0.268	-0.268	0.000	0.000	0.000	0.000
38	A	52	SER	0	0.012	-0.027	22.594	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	53	THR	0	-0.032	-0.024	25.343	0.007	0.007	0.000	0.000	0.000	0.000
40	A	54	ASN	0	-0.082	-0.043	27.242	0.000	0.000	0.000	0.000	0.000	0.000
41	A	55	VAL	0	0.035	0.000	29.594	0.005	0.005	0.000	0.000	0.000	0.000
42	A	56	ASN	0	-0.039	-0.012	30.720	0.008	0.008	0.000	0.000	0.000	0.000
43	A	57	ALA	0	-0.028	-0.008	28.820	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	58	ASP	-1	-0.860	-0.922	29.456	0.093	0.093	0.000	0.000	0.000	0.000
45	A	59	MET	0	-0.040	-0.024	27.245	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	60	THR	0	-0.026	-0.002	26.477	0.008	0.008	0.000	0.000	0.000	0.000
47	A	61	LEU	0	-0.008	0.008	19.059	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	62	ILE	0	-0.014	-0.021	23.599	0.008	0.008	0.000	0.000	0.000	0.000
49	A	63	LEU	0	-0.007	0.022	17.047	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	64	LEU	0	-0.002	-0.006	20.955	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	65	ARG	1	0.831	0.859	15.500	0.108	0.108	0.000	0.000	0.000	0.000
52	A	66	ASN	0	0.011	0.010	21.710	0.009	0.009	0.000	0.000	0.000	0.000
53	A	67	VAL	0	-0.006	-0.017	22.926	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.018	0.016	25.137	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	69	GLY	0	-0.015	-0.002	26.041	0.001	0.001	0.000	0.000	0.000	0.000
56	A	70	ASN	0	-0.043	-0.033	28.207	0.003	0.003	0.000	0.000	0.000	0.000
57	A	71	GLY	0	0.034	0.028	28.658	0.006	0.006	0.000	0.000	0.000	0.000
58	A	72	TRP	0	-0.025	-0.011	21.587	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	73	GLY	0	0.015	0.008	25.605	0.005	0.005	0.000	0.000	0.000	0.000
60	A	74	GLU	-1	-0.814	-0.874	24.603	0.059	0.059	0.000	0.000	0.000	0.000
61	A	75	ILE	0	-0.028	-0.001	18.757	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	76	LYS	1	0.870	0.917	18.231	-0.175	-0.175	0.000	0.000	0.000	0.000
63	A	77	ARG	1	0.829	0.879	22.880	-0.074	-0.074	0.000	0.000	0.000	0.000
64	A	78	ASN	0	-0.037	-0.021	20.288	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	79	ASP	-1	-0.807	-0.894	23.703	0.140	0.140	0.000	0.000	0.000	0.000
66	A	80	ILE	0	-0.003	0.002	23.650	0.019	0.019	0.000	0.000	0.000	0.000
67	A	81	ASP	-1	-0.819	-0.904	21.367	0.231	0.231	0.000	0.000	0.000	0.000
68	A	82	LYS	1	0.807	0.909	21.092	-0.158	-0.158	0.000	0.000	0.000	0.000
69	A	83	PRO	0	-0.026	-0.018	15.512	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	84	LEU	0	-0.022	0.014	17.145	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	85	LYS	1	0.840	0.895	10.429	-0.916	-0.916	0.000	0.000	0.000	0.000
72	A	86	TYR	0	-0.047	-0.054	13.846	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	87	GLU	-1	-0.867	-0.901	11.360	0.261	0.261	0.000	0.000	0.000	0.000
74	A	88	ASP	-1	-0.766	-0.831	12.512	-0.117	-0.117	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.008	-0.044	9.546	-0.076	-0.076	0.000	0.000	0.000	0.000
76	A	90	TYR	0	-0.030	0.007	13.932	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	91	THR	0	0.033	0.011	15.557	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	92	SER	0	-0.011	0.005	17.375	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	93	GLY	0	0.027	0.020	16.085	0.002	0.002	0.000	0.000	0.000	0.000
80	A	94	LEU	0	-0.004	-0.004	16.552	0.031	0.031	0.000	0.000	0.000	0.000
81	A	95	SER	0	0.045	0.053	16.714	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	96	TRP	0	-0.055	-0.038	11.405	0.018	0.018	0.000	0.000	0.000	0.000
83	A	97	ILE	0	-0.027	-0.019	18.682	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	98	TRP	0	0.064	0.037	14.205	0.037	0.037	0.000	0.000	0.000	0.000
85	A	99	LYS	1	0.865	0.910	20.743	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	100	ILE	0	0.011	0.006	22.163	0.017	0.017	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.809	0.888	25.544	-0.047	-0.047	0.000	0.000	0.000	0.000
88	A	102	ASN	0	-0.006	-0.014	29.129	0.016	0.016	0.000	0.000	0.000	0.000
89	A	103	ASN	0	-0.036	-0.023	30.437	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	104	SER	0	0.124	0.072	33.393	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	105	SER	0	-0.067	-0.044	35.386	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.826	-0.904	35.169	0.064	0.064	0.000	0.000	0.000	0.000
93	A	107	THR	0	-0.016	-0.001	34.022	0.003	0.003	0.000	0.000	0.000	0.000
94	A	108	SER	0	0.028	0.020	30.426	0.003	0.003	0.000	0.000	0.000	0.000
95	A	109	ASN	0	0.039	0.030	25.054	0.007	0.007	0.000	0.000	0.000	0.000
96	A	110	TYR	0	0.009	0.030	22.746	0.005	0.005	0.000	0.000	0.000	0.000
97	A	111	SER	0	0.011	-0.008	19.886	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	112	LEU	0	0.014	0.003	17.539	0.012	0.012	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.790	-0.842	13.385	0.281	0.281	0.000	0.000	0.000	0.000
100	A	114	ALA	0	-0.001	-0.019	13.504	0.047	0.047	0.000	0.000	0.000	0.000
101	A	115	THR	0	0.003	0.003	8.568	0.006	0.006	0.000	0.000	0.000	0.000
102	A	116	VAL	0	-0.026	-0.004	10.029	0.023	0.023	0.000	0.000	0.000	0.000
103	A	117	HIS	0	0.010	-0.030	7.567	-0.076	-0.076	0.000	0.000	0.000	0.000
104	A	118	ASP	-1	-0.832	-0.880	10.497	-0.555	-0.555	0.000	0.000	0.000	0.000
105	A	119	ASP	-1	-0.872	-0.934	10.693	-0.681	-0.681	0.000	0.000	0.000	0.000
106	A	120	LYS	1	0.835	0.915	13.101	0.078	0.078	0.000	0.000	0.000	0.000
107	A	121	GLU	-1	-0.817	-0.874	15.856	-0.205	-0.205	0.000	0.000	0.000	0.000
108	A	122	ASP	-1	-0.904	-0.965	19.413	-0.066	-0.066	0.000	0.000	0.000	0.000
109	A	123	SER	0	-0.105	-0.074	21.386	0.016	0.016	0.000	0.000	0.000	0.000
110	A	124	ASP	-1	-0.721	-0.818	17.649	-0.183	-0.183	0.000	0.000	0.000	0.000
111	A	125	VAL	0	-0.050	-0.024	20.767	0.018	0.018	0.000	0.000	0.000	0.000
112	A	126	LEU	0	0.001	0.009	23.709	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	127	THR	0	-0.011	-0.014	26.075	0.010	0.010	0.000	0.000	0.000	0.000
114	A	128	LYS	1	0.876	0.934	29.122	0.029	0.029	0.000	0.000	0.000	0.000
115	A	130	PRO	0	0.040	0.015	26.584	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	131	VAL	0	-0.008	0.009	29.635	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ILE)