FMO DATABASE

FMODB ID: YZRZ2

Calculation Name: 4J4G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4G

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-509439.585554
FMO2-HF: Nuclear repulsion	470215.230532
FMO2-HF: Total energy	-39224.355023
FMO2-MP2: Total energy	-39336.325833

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:1:LEU)

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

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.
-3.843	-1.419	0.091	-1.044	-1.471	0.006

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.006

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	3	LYS	1	0.929	0.953	2.870	-3.977	-1.553	0.091	-1.044	-1.471	0.006
4	A	4	PHE	0	0.088	0.039	6.401	0.067	0.067	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.016	-0.005	9.043	0.045	0.045	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.030	-0.018	8.207	0.138	0.138	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.047	0.036	11.277	0.033	0.033	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.141	-0.067	12.754	-0.044	-0.044	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.003	-0.018	14.759	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.019	-0.022	18.230	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.036	-0.024	16.034	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.001	0.004	18.212	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.019	0.009	15.941	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.009	0.010	19.940	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.012	-0.006	22.217	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.028	-0.030	19.280	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.009	0.009	17.959	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.025	0.000	12.649	0.012	0.012	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.037	0.015	16.777	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.022	0.019	15.141	0.008	0.008	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.008	-0.001	17.481	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.802	-0.884	14.840	0.445	0.445	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.888	0.936	14.701	-0.158	-0.158	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.013	-0.005	14.191	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.039	-0.031	16.108	0.026	0.026	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.046	0.035	18.934	-0.029	-0.029	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.013	0.011	20.694	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	29	TYR	0	0.016	0.010	18.696	0.019	0.019	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.029	-0.024	17.728	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.016	0.027	18.153	0.026	0.026	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.068	-0.011	16.200	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.032	-0.020	17.433	0.013	0.013	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.015	-0.006	11.296	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.787	-0.880	15.535	-0.096	-0.096	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.007	-0.016	12.610	-0.028	-0.028	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.012	0.002	15.154	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.048	-0.011	15.336	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.006	-0.011	10.662	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.031	-0.006	11.566	-0.069	-0.069	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.832	-0.897	13.835	-0.263	-0.263	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.006	-0.008	16.676	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.004	-0.010	17.829	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.930	-0.968	20.155	-0.115	-0.115	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.003	0.010	22.838	0.007	0.007	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.041	-0.012	17.525	0.008	0.008	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.031	-0.009	15.713	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.800	0.878	12.886	0.348	0.348	0.000	0.000	0.000	0.000
48	A	49	TRP	0	0.012	0.002	8.552	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.027	0.000	10.699	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.010	-0.008	9.840	-0.095	-0.095	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.028	-0.008	10.899	0.079	0.079	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.035	0.004	11.505	-0.041	-0.041	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.046	0.044	13.443	0.015	0.015	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.021	-0.008	15.946	0.011	0.011	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.871	-0.925	11.236	-0.485	-0.485	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.085	-0.059	13.985	0.022	0.022	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.049	-0.029	16.560	0.008	0.008	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.871	0.920	20.141	0.151	0.151	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.059	-0.054	23.213	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.013	0.022	24.149	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.039	-0.026	27.060	0.007	0.007	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.003	0.011	30.259	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.016	-0.007	32.483	0.005	0.005	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.015	-0.004	34.973	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.004	-0.012	36.835	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.033	-0.035	33.392	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.927	-0.930	31.561	-0.106	-0.106	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.027	0.006	24.503	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.025	0.013	28.466	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.007	-0.016	24.386	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.811	-0.856	25.070	-0.131	-0.131	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.867	0.943	14.206	0.370	0.370	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.044	0.024	18.208	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.931	0.946	15.427	0.202	0.202	0.000	0.000	0.000	0.000
75	A	77	ALA	0	0.021	0.019	13.874	0.020	0.020	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.009	0.011	15.740	0.006	0.006	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.012	-0.006	15.365	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.002	0.002	18.437	0.008	0.008	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.004	-0.008	19.732	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	82	SER	0	-0.006	-0.001	21.703	0.004	0.004	0.000	0.000	0.000	0.000
81	A	83	THR	0	0.009	0.002	24.225	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.947	0.967	27.017	0.015	0.015	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.042	0.020	30.527	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.032	-0.021	33.703	0.005	0.005	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.027	-0.002	36.904	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.860	-0.933	39.774	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.937	-0.940	37.872	-0.024	-0.024	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.834	0.903	40.343	0.027	0.027	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.040	0.000	42.379	0.000	0.000	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.069	0.052	45.050	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.002	-0.013	48.523	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.036	-0.034	51.226	0.000	0.000	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.938	-0.974	54.203	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.020	0.019	55.070	0.000	0.000	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.048	-0.015	52.526	0.000	0.000	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.019	0.004	46.275	0.000	0.000	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.947	0.964	49.096	0.016	0.016	0.000	0.000	0.000	0.000
98	A	100	TYR	0	-0.003	0.006	41.857	0.000	0.000	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.961	-0.986	45.770	-0.018	-0.018	0.000	0.000	0.000	0.000

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