FMO DATABASE

FMODB ID: 4JKLN

Calculation Name: 1PM3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PM3

Chain ID: A

ChEMBL ID:

UniProt ID: O27887

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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-377162.221899
FMO2-HF: Nuclear repulsion	350600.200113
FMO2-HF: Total energy	-26562.021785
FMO2-MP2: Total energy	-26638.377249

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
2.226	3.586	-0.021	-0.63	-0.709	0

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.030

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].
3	A	2	ARG	1	0.836	0.904	3.866	-0.186	1.174	-0.021	-0.630	-0.709
4	A	3	ILE	0	0.064	0.022	6.733	-0.258	-0.258	0.000	0.000	0.000
5	A	4	VAL	0	0.030	0.001	9.012	-0.275	-0.275	0.000	0.000	0.000
6	A	5	GLU	-1	-0.861	-0.922	10.416	0.804	0.804	0.000	0.000	0.000
7	A	6	GLU	-1	-0.863	-0.924	6.733	-0.141	-0.141	0.000	0.000	0.000
8	A	7	MET	0	-0.037	-0.019	6.924	-0.234	-0.234	0.000	0.000	0.000
9	A	8	VAL	0	0.045	0.031	10.582	-0.096	-0.096	0.000	0.000	0.000
10	A	9	GLY	0	-0.012	0.002	14.023	-0.087	-0.087	0.000	0.000	0.000
11	A	10	LYS	1	0.819	0.921	10.607	-0.726	-0.726	0.000	0.000	0.000
12	A	11	GLU	-1	-0.826	-0.889	15.845	0.373	0.373	0.000	0.000	0.000
13	A	12	VAL	0	0.036	0.022	15.655	0.039	0.039	0.000	0.000	0.000
14	A	13	LEU	0	-0.039	-0.014	17.707	-0.053	-0.053	0.000	0.000	0.000
15	A	14	ASP	-1	-0.731	-0.864	19.112	0.299	0.299	0.000	0.000	0.000
16	A	15	SER	0	0.016	0.002	21.792	-0.013	-0.013	0.000	0.000	0.000
17	A	16	SER	0	-0.046	-0.017	22.964	-0.033	-0.033	0.000	0.000	0.000
18	A	17	ALA	0	-0.034	-0.016	22.578	-0.016	-0.016	0.000	0.000	0.000
19	A	18	LYS	1	0.845	0.919	23.666	-0.276	-0.276	0.000	0.000	0.000
20	A	19	VAL	0	0.007	-0.012	21.766	0.026	0.026	0.000	0.000	0.000
21	A	20	ILE	0	-0.055	-0.022	20.162	-0.026	-0.026	0.000	0.000	0.000
22	A	21	GLY	0	0.028	0.011	21.563	-0.016	-0.016	0.000	0.000	0.000
23	A	22	LYS	1	0.792	0.887	18.969	-0.376	-0.376	0.000	0.000	0.000
24	A	23	VAL	0	0.038	0.023	13.539	-0.031	-0.031	0.000	0.000	0.000
25	A	24	LYS	1	0.771	0.876	16.837	-0.564	-0.564	0.000	0.000	0.000
26	A	25	ASP	-1	-0.859	-0.935	15.220	1.034	1.034	0.000	0.000	0.000
27	A	26	VAL	0	-0.082	-0.057	10.791	0.013	0.013	0.000	0.000	0.000
28	A	27	GLU	-1	-0.829	-0.872	14.114	0.757	0.757	0.000	0.000	0.000
29	A	28	VAL	0	-0.016	-0.030	12.142	0.185	0.185	0.000	0.000	0.000
30	A	29	ASP	-1	-0.716	-0.804	14.931	0.558	0.558	0.000	0.000	0.000
31	A	30	ILE	0	-0.073	-0.047	16.062	0.081	0.081	0.000	0.000	0.000
32	A	31	GLU	-1	-0.968	-0.973	18.171	0.396	0.396	0.000	0.000	0.000
33	A	32	SER	0	-0.118	-0.107	15.428	0.023	0.023	0.000	0.000	0.000
34	A	33	GLN	0	-0.074	-0.037	9.154	-0.061	-0.061	0.000	0.000	0.000
35	A	34	ALA	0	-0.002	0.016	11.086	0.402	0.402	0.000	0.000	0.000
36	A	35	ILE	0	-0.041	-0.031	7.872	-0.042	-0.042	0.000	0.000	0.000
37	A	36	GLU	-1	-0.922	-0.954	11.803	0.636	0.636	0.000	0.000	0.000
38	A	37	SER	0	-0.088	-0.078	14.900	-0.112	-0.112	0.000	0.000	0.000
39	A	38	LEU	0	-0.015	-0.001	11.717	0.160	0.160	0.000	0.000	0.000
40	A	39	VAL	0	0.024	0.034	15.544	-0.130	-0.130	0.000	0.000	0.000
41	A	40	LEU	0	-0.003	-0.007	17.140	0.028	0.028	0.000	0.000	0.000
42	A	41	GLY	0	0.016	0.000	20.179	-0.042	-0.042	0.000	0.000	0.000
43	A	42	LYS	1	0.911	0.948	23.076	-0.259	-0.259	0.000	0.000	0.000
44	A	43	GLY	0	0.020	0.001	26.228	-0.020	-0.020	0.000	0.000	0.000
45	A	44	GLY	0	-0.020	0.003	27.090	-0.014	-0.014	0.000	0.000	0.000
46	A	54	GLY	0	-0.005	-0.016	28.580	-0.002	-0.002	0.000	0.000	0.000
47	A	55	GLU	-1	-0.823	-0.898	22.356	0.538	0.538	0.000	0.000	0.000
48	A	56	THR	0	-0.068	-0.038	22.711	-0.046	-0.046	0.000	0.000	0.000
49	A	57	ILE	0	0.068	0.044	20.530	0.034	0.034	0.000	0.000	0.000
50	A	58	VAL	0	-0.040	-0.017	17.586	-0.068	-0.068	0.000	0.000	0.000
51	A	59	PRO	0	0.067	0.039	17.146	0.107	0.107	0.000	0.000	0.000
52	A	60	TYR	0	0.041	0.019	7.946	0.188	0.188	0.000	0.000	0.000
53	A	61	GLU	-1	-0.859	-0.938	13.945	0.713	0.713	0.000	0.000	0.000
54	A	62	MET	0	-0.020	0.003	16.059	-0.101	-0.101	0.000	0.000	0.000
55	A	63	VAL	0	0.008	0.001	11.130	-0.100	-0.100	0.000	0.000	0.000
56	A	64	LYS	1	0.739	0.863	13.857	-0.245	-0.245	0.000	0.000	0.000
57	A	65	LYS	1	0.918	0.938	10.403	-0.044	-0.044	0.000	0.000	0.000
58	A	66	ILE	0	0.056	0.030	7.307	0.016	0.016	0.000	0.000	0.000
59	A	67	GLY	0	0.019	0.015	9.126	-0.172	-0.172	0.000	0.000	0.000
60	A	68	ASP	-1	-0.890	-0.944	11.044	0.154	0.154	0.000	0.000	0.000
61	A	69	LYS	1	0.807	0.884	14.037	-0.256	-0.256	0.000	0.000	0.000
62	A	70	ILE	0	0.012	0.014	11.398	0.005	0.005	0.000	0.000	0.000
63	A	71	LEU	0	-0.022	-0.004	13.807	-0.085	-0.085	0.000	0.000	0.000
64	A	72	LEU	0	0.047	0.027	15.061	0.063	0.063	0.000	0.000	0.000
65	A	73	LYS	1	0.759	0.863	15.029	-0.572	-0.572	0.000	0.000	0.000
66	A	74	GLY	0	0.011	0.002	19.506	0.017	0.017	0.000	0.000	0.000
67	A	75	PRO	0	-0.037	-0.020	23.143	0.013	0.013	0.000	0.000	0.000
68	A	76	GLU	-1	-0.889	-0.951	25.455	0.152	0.152	0.000	0.000	0.000
69	A	77	GLU	-1	-0.827	-0.878	20.631	0.190	0.190	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)