FMO DATABASE

FMODB ID: K3NN3

Calculation Name: 4JPN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JPN

Chain ID: A

ChEMBL ID:

UniProt ID: P03646

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-325809.971833
FMO2-HF: Nuclear repulsion	294951.523905
FMO2-HF: Total energy	-30858.447928
FMO2-MP2: Total energy	-30945.557434

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:144:VAL)

Summations of interaction energy for fragment #1(A:144: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.
1.393	2.877	-0.013	-0.526	-0.945	0.001

Interaction energy analysis for fragmet #1(A:144:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.020

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	146	ALA	0	0.034	0.007	3.869	0.936	2.221	-0.012	-0.517	-0.756	0.001
4	A	147	GLY	0	0.018	0.019	6.030	0.260	0.260	0.000	0.000	0.000	0.000
5	A	148	PHE	0	-0.002	-0.014	5.686	-0.131	-0.131	0.000	0.000	0.000	0.000
6	A	149	GLU	-1	-0.800	-0.892	4.760	3.225	3.424	-0.001	-0.009	-0.189	0.000
7	A	150	ASN	0	0.002	0.000	7.636	-0.367	-0.367	0.000	0.000	0.000	0.000
8	A	151	GLN	0	-0.002	0.000	10.866	-0.098	-0.098	0.000	0.000	0.000	0.000
9	A	152	LYS	1	0.773	0.891	7.061	-2.438	-2.438	0.000	0.000	0.000	0.000
10	A	153	GLU	-1	-0.943	-0.965	11.568	0.391	0.391	0.000	0.000	0.000	0.000
11	A	154	LEU	0	0.008	-0.010	13.369	-0.093	-0.093	0.000	0.000	0.000	0.000
12	A	155	THR	0	-0.029	-0.030	14.998	-0.073	-0.073	0.000	0.000	0.000	0.000
13	A	156	LYS	1	0.832	0.893	15.356	-0.437	-0.437	0.000	0.000	0.000	0.000
14	A	157	MET	0	0.007	0.003	17.031	-0.046	-0.046	0.000	0.000	0.000	0.000
15	A	158	GLN	0	-0.017	-0.003	19.541	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	159	LEU	0	-0.013	-0.005	18.141	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	160	ASP	-1	-0.842	-0.897	19.902	0.303	0.303	0.000	0.000	0.000	0.000
18	A	161	ASN	0	-0.014	-0.012	22.654	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	162	GLN	0	-0.007	-0.011	24.617	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	163	LYS	1	0.804	0.905	24.323	-0.204	-0.204	0.000	0.000	0.000	0.000
21	A	164	GLU	-1	-0.866	-0.929	25.797	0.165	0.165	0.000	0.000	0.000	0.000
22	A	165	ILE	0	-0.018	-0.007	28.802	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	166	ALA	0	0.008	0.005	30.027	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	167	GLU	-1	-0.840	-0.912	28.478	0.154	0.154	0.000	0.000	0.000	0.000
25	A	168	MET	0	0.059	0.027	31.421	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	169	GLN	0	-0.048	-0.001	34.559	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	170	ASN	0	-0.073	-0.066	34.320	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	171	GLU	-1	-0.947	-0.964	36.621	0.088	0.088	0.000	0.000	0.000	0.000
29	A	172	THR	0	0.043	0.004	38.422	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	173	GLN	0	-0.036	-0.015	38.585	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	174	LYS	1	0.914	0.958	40.016	-0.078	-0.078	0.000	0.000	0.000	0.000
32	A	175	GLU	-1	-0.911	-0.944	42.442	0.063	0.063	0.000	0.000	0.000	0.000
33	A	176	ILE	0	-0.014	-0.005	44.058	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	177	ALA	0	0.005	0.003	45.813	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	178	GLY	0	0.004	0.003	46.973	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	179	ILE	0	0.027	0.010	48.172	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	180	GLN	0	-0.002	0.008	49.604	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	181	SER	0	-0.025	-0.003	51.259	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	182	ALA	0	0.011	-0.001	52.813	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	183	THR	0	0.002	-0.009	54.615	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	184	SER	0	-0.007	0.008	56.137	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	185	ARG	1	0.923	0.961	56.282	-0.039	-0.039	0.000	0.000	0.000	0.000
43	A	186	GLN	0	-0.017	-0.014	58.828	0.000	0.000	0.000	0.000	0.000	0.000
44	A	187	ASN	0	0.011	-0.013	60.020	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	188	THR	0	-0.038	-0.031	61.206	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	189	LYS	1	0.856	0.925	60.283	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	190	ASP	-1	-0.822	-0.902	64.880	0.029	0.029	0.000	0.000	0.000	0.000
48	A	191	GLN	0	-0.045	-0.013	64.375	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	192	VAL	0	-0.031	-0.014	67.278	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	193	TYR	0	-0.065	-0.038	69.670	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	194	ALA	0	0.057	0.018	71.273	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	195	GLN	0	-0.038	-0.023	70.709	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	196	ASN	0	-0.010	-0.018	69.574	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	197	GLU	-1	-0.847	-0.892	74.016	0.022	0.022	0.000	0.000	0.000	0.000
55	A	198	MET	0	-0.032	-0.024	76.553	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	199	LEU	0	0.005	0.023	75.236	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	200	ALA	0	0.056	0.024	78.716	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	201	TYR	0	-0.029	-0.014	80.705	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	202	GLN	0	0.023	0.008	80.166	0.000	0.000	0.000	0.000	0.000	0.000
60	A	203	GLN	0	0.011	0.006	78.387	0.000	0.000	0.000	0.000	0.000	0.000
61	A	204	LYS	1	0.974	1.004	83.529	-0.017	-0.017	0.000	0.000	0.000	0.000
62	A	205	GLU	-1	-0.848	-0.900	86.471	0.016	0.016	0.000	0.000	0.000	0.000
63	A	206	SER	0	0.019	-0.006	85.868	0.000	0.000	0.000	0.000	0.000	0.000
64	A	207	THR	0	-0.047	-0.037	86.532	0.000	0.000	0.000	0.000	0.000	0.000
65	A	208	ALA	0	-0.013	-0.006	88.978	0.000	0.000	0.000	0.000	0.000	0.000
66	A	209	ARG	1	0.831	0.897	86.349	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	210	VAL	0	0.003	0.003	89.050	0.000	0.000	0.000	0.000	0.000	0.000
68	A	211	ALA	0	0.004	0.002	92.300	0.000	0.000	0.000	0.000	0.000	0.000
69	A	212	SER	0	0.006	0.006	94.697	0.000	0.000	0.000	0.000	0.000	0.000
70	A	213	ILE	0	-0.004	-0.001	93.127	0.000	0.000	0.000	0.000	0.000	0.000
71	A	214	MET	0	-0.054	-0.025	93.923	0.000	0.000	0.000	0.000	0.000	0.000
72	A	215	GLU	-1	-0.903	-0.938	97.369	0.013	0.013	0.000	0.000	0.000	0.000
73	A	216	ASN	0	-0.084	-0.043	100.146	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	217	THR	0	-0.075	-0.035	98.617	0.000	0.000	0.000	0.000	0.000	0.000
75	A	218	ASN	0	-0.038	-0.017	101.168	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:144:VAL)