FMO DATABASE

FMODB ID: 223VR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-940285.163135
FMO2-HF: Nuclear repulsion	894828.173256
FMO2-HF: Total energy	-45456.989879
FMO2-MP2: Total energy	-45589.795111

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.
-0.946	0.324	-0.014	-0.526	-0.73	0.001

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 : -0.007 / 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

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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	17	ASN	0	0.035	0.036	3.892	-0.703	0.567	-0.014	-0.526	-0.730	0.001
4	A	18	ILE	0	-0.037	-0.008	6.774	0.263	0.263	0.000	0.000	0.000	0.000
5	A	19	ALA	0	0.032	0.027	9.651	-0.040	-0.040	0.000	0.000	0.000	0.000
6	A	20	THR	0	0.014	-0.022	13.007	0.068	0.068	0.000	0.000	0.000	0.000
7	A	21	TYR	0	-0.107	-0.079	16.173	-0.033	-0.033	0.000	0.000	0.000	0.000
8	A	22	THR	0	0.002	-0.007	19.524	0.028	0.028	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.015	0.009	22.602	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	24	THR	0	-0.029	-0.012	26.237	0.013	0.013	0.000	0.000	0.000	0.000
11	A	25	ILE	0	-0.026	0.001	28.417	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	26	GLN	0	0.063	0.006	30.668	0.004	0.004	0.000	0.000	0.000	0.000
13	A	27	GLY	0	0.043	0.037	33.921	0.003	0.003	0.000	0.000	0.000	0.000
14	A	28	LYS	1	0.807	0.887	35.426	-0.054	-0.054	0.000	0.000	0.000	0.000
15	A	29	GLY	0	0.022	0.035	33.338	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	30	GLU	-1	-0.910	-0.981	29.800	0.028	0.028	0.000	0.000	0.000	0.000
17	A	31	VAL	0	0.022	0.013	25.398	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	32	CYS	0	-0.035	0.016	24.676	0.009	0.009	0.000	0.000	0.000	0.000
19	A	33	ILE	0	0.019	0.018	19.378	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	34	ILE	0	-0.048	-0.032	20.292	0.011	0.011	0.000	0.000	0.000	0.000
21	A	35	GLY	0	0.045	0.023	16.179	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	36	ASN	0	-0.029	-0.039	14.344	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	37	LYS	1	0.904	0.959	16.108	0.198	0.198	0.000	0.000	0.000	0.000
24	A	38	GLU	-1	-0.922	-0.971	16.904	-0.275	-0.275	0.000	0.000	0.000	0.000
25	A	39	GLY	0	-0.019	-0.002	17.916	0.003	0.003	0.000	0.000	0.000	0.000
26	A	40	LYS	1	0.960	0.995	12.235	0.533	0.533	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.025	-0.034	13.269	0.016	0.016	0.000	0.000	0.000	0.000
28	A	42	ARG	1	0.854	0.944	6.561	0.388	0.388	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.027	0.015	9.525	0.072	0.072	0.000	0.000	0.000	0.000
30	A	44	GLY	0	-0.003	-0.011	7.736	-0.149	-0.149	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.907	-0.964	7.782	0.964	0.964	0.000	0.000	0.000	0.000
32	A	46	LEU	0	-0.074	-0.023	8.784	-0.047	-0.047	0.000	0.000	0.000	0.000
33	A	47	TYR	0	0.026	-0.007	10.474	0.091	0.091	0.000	0.000	0.000	0.000
34	A	48	ALA	0	0.012	0.002	12.344	-0.070	-0.070	0.000	0.000	0.000	0.000
35	A	49	VAL	0	-0.018	-0.002	15.238	0.025	0.025	0.000	0.000	0.000	0.000
36	A	50	LEU	0	0.005	0.011	17.642	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	51	HIS	1	0.877	0.920	17.873	-0.272	-0.272	0.000	0.000	0.000	0.000
38	A	52	SER	0	0.047	-0.018	22.630	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	53	THR	0	-0.036	-0.018	25.881	0.008	0.008	0.000	0.000	0.000	0.000
40	A	54	ASN	0	-0.044	-0.011	27.620	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	55	VAL	0	0.038	0.016	29.767	0.005	0.005	0.000	0.000	0.000	0.000
42	A	56	ASN	0	-0.014	-0.012	30.832	0.009	0.009	0.000	0.000	0.000	0.000
43	A	57	ALA	0	-0.037	-0.001	28.874	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	58	ASP	-1	-0.839	-0.912	30.353	0.097	0.097	0.000	0.000	0.000	0.000
45	A	59	MET	0	-0.055	-0.041	27.025	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	60	THR	0	-0.030	-0.002	26.603	0.008	0.008	0.000	0.000	0.000	0.000
47	A	61	LEU	0	0.015	0.015	19.062	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	62	ILE	0	-0.010	-0.017	23.478	0.010	0.010	0.000	0.000	0.000	0.000
49	A	63	LEU	0	0.001	0.025	17.055	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	64	LEU	0	-0.010	-0.010	20.924	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	65	ARG	1	0.894	0.931	15.167	0.077	0.077	0.000	0.000	0.000	0.000
52	A	66	ASN	0	0.007	-0.002	21.707	0.013	0.013	0.000	0.000	0.000	0.000
53	A	67	VAL	0	-0.004	-0.003	22.996	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.021	0.001	24.826	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	69	GLY	0	0.008	0.019	26.569	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	70	ASN	0	-0.042	-0.028	28.356	0.000	0.000	0.000	0.000	0.000	0.000
57	A	71	GLY	0	0.011	0.017	28.565	0.005	0.005	0.000	0.000	0.000	0.000
58	A	72	TRP	0	-0.012	-0.001	21.849	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	73	GLY	0	0.023	0.005	25.447	0.004	0.004	0.000	0.000	0.000	0.000
60	A	74	GLU	-1	-0.840	-0.902	24.366	0.065	0.065	0.000	0.000	0.000	0.000
61	A	75	ILE	0	-0.032	0.001	18.792	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	76	LYS	1	0.874	0.930	18.104	-0.193	-0.193	0.000	0.000	0.000	0.000
63	A	77	ARG	1	0.854	0.900	22.639	-0.082	-0.082	0.000	0.000	0.000	0.000
64	A	78	ASN	0	-0.031	-0.013	20.923	0.011	0.011	0.000	0.000	0.000	0.000
65	A	79	ASP	-1	-0.902	-0.945	23.675	0.124	0.124	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.016	-0.001	23.471	0.020	0.020	0.000	0.000	0.000	0.000
67	A	81	ASP	-1	-0.846	-0.918	21.519	0.211	0.211	0.000	0.000	0.000	0.000
68	A	82	LYS	1	0.849	0.932	20.862	-0.175	-0.175	0.000	0.000	0.000	0.000
69	A	83	PRO	0	-0.018	-0.014	15.659	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	84	LEU	0	-0.014	0.023	16.813	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	85	LYS	1	0.943	0.960	11.593	-0.793	-0.793	0.000	0.000	0.000	0.000
72	A	86	TYR	0	-0.053	-0.049	13.471	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	87	GLU	-1	-0.852	-0.886	11.913	0.246	0.246	0.000	0.000	0.000	0.000
74	A	88	ASP	-1	-0.797	-0.898	12.508	-0.098	-0.098	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.030	-0.049	9.570	-0.064	-0.064	0.000	0.000	0.000	0.000
76	A	90	TYR	0	-0.041	-0.010	14.004	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	91	THR	0	0.026	0.010	15.521	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	92	SER	0	0.001	0.013	17.070	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	93	GLY	0	0.033	0.025	16.330	0.002	0.002	0.000	0.000	0.000	0.000
80	A	94	LEU	0	-0.011	-0.010	16.780	0.027	0.027	0.000	0.000	0.000	0.000
81	A	95	SER	0	0.010	0.036	16.981	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	96	TRP	0	-0.057	-0.034	12.176	0.021	0.021	0.000	0.000	0.000	0.000
83	A	97	ILE	0	-0.013	-0.014	18.924	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	98	TRP	0	0.065	0.037	14.381	0.032	0.032	0.000	0.000	0.000	0.000
85	A	99	LYS	1	0.924	0.951	20.859	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	100	ILE	0	0.020	0.016	22.405	0.016	0.016	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.859	0.917	25.803	-0.053	-0.053	0.000	0.000	0.000	0.000
88	A	102	ASN	0	0.013	-0.002	29.303	0.016	0.016	0.000	0.000	0.000	0.000
89	A	103	ASN	0	-0.022	-0.023	30.513	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	104	SER	0	0.093	0.074	33.659	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	105	SER	0	-0.043	-0.050	35.640	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.901	-0.938	35.405	0.062	0.062	0.000	0.000	0.000	0.000
93	A	107	THR	0	-0.019	-0.005	33.995	0.003	0.003	0.000	0.000	0.000	0.000
94	A	108	SER	0	0.006	0.001	30.540	0.004	0.004	0.000	0.000	0.000	0.000
95	A	109	ASN	0	0.041	0.033	25.368	0.007	0.007	0.000	0.000	0.000	0.000
96	A	110	TYR	0	0.010	0.028	22.813	0.005	0.005	0.000	0.000	0.000	0.000
97	A	111	SER	0	0.035	-0.003	20.246	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	112	LEU	0	-0.016	-0.003	17.743	0.017	0.017	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.836	-0.892	13.878	0.285	0.285	0.000	0.000	0.000	0.000
100	A	114	ALA	0	-0.002	-0.024	13.689	0.038	0.038	0.000	0.000	0.000	0.000
101	A	115	THR	0	-0.027	-0.009	8.285	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	116	VAL	0	-0.017	-0.005	10.115	0.018	0.018	0.000	0.000	0.000	0.000
103	A	117	HIS	0	-0.003	-0.032	8.643	-0.090	-0.090	0.000	0.000	0.000	0.000
104	A	118	ASP	-1	-0.925	-0.942	10.100	-0.599	-0.599	0.000	0.000	0.000	0.000
105	A	119	ASP	-1	-0.910	-0.957	10.878	-0.621	-0.621	0.000	0.000	0.000	0.000
106	A	120	LYS	1	0.831	0.905	13.388	0.080	0.080	0.000	0.000	0.000	0.000
107	A	121	GLU	-1	-0.895	-0.952	16.101	-0.222	-0.222	0.000	0.000	0.000	0.000
108	A	122	ASP	-1	-0.894	-0.952	19.483	-0.060	-0.060	0.000	0.000	0.000	0.000
109	A	123	SER	0	-0.078	-0.039	22.189	0.012	0.012	0.000	0.000	0.000	0.000
110	A	124	ASP	-1	-0.738	-0.838	17.824	-0.162	-0.162	0.000	0.000	0.000	0.000
111	A	125	VAL	0	-0.036	-0.008	21.265	0.016	0.016	0.000	0.000	0.000	0.000
112	A	126	LEU	0	-0.008	0.002	24.186	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	127	THR	0	-0.019	-0.016	26.572	0.008	0.008	0.000	0.000	0.000	0.000
114	A	128	LYS	1	0.920	0.957	29.504	0.024	0.024	0.000	0.000	0.000	0.000
115	A	130	PRO	0	0.001	-0.014	26.937	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	131	VAL	0	0.003	0.010	30.056	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)