FMO DATABASE

FMODB ID: MVLVZ

Calculation Name: 4J4E-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4E

Chain ID: C

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

Total energy (hartree)

FMO2-HF: Electronic energy	-556741.218312
FMO2-HF: Nuclear repulsion	517517.204429
FMO2-HF: Total energy	-39224.013883
FMO2-MP2: Total energy	-39336.136379

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(C:1:LEU)

Summations of interaction energy for fragment #1(C: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.
-31.496	-36.493	16.947	-5.954	-5.996	0.045

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.025

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	C	3	LYS	1	0.911	0.930	1.901	-31.991	-36.988	16.947	-5.954	-5.996	0.045
4	C	4	PHE	0	0.074	0.028	6.166	0.167	0.167	0.000	0.000	0.000	0.000
5	C	5	SER	0	0.032	0.020	8.724	0.111	0.111	0.000	0.000	0.000	0.000
6	C	6	GLN	0	-0.036	0.000	7.810	0.414	0.414	0.000	0.000	0.000	0.000
7	C	7	THR	0	-0.053	-0.028	9.696	0.042	0.042	0.000	0.000	0.000	0.000
8	C	8	CYS	0	-0.097	-0.012	11.627	-0.094	-0.094	0.000	0.000	0.000	0.000
9	C	9	TYR	0	0.020	-0.013	13.947	0.046	0.046	0.000	0.000	0.000	0.000
10	C	10	ASN	0	-0.036	-0.033	17.396	-0.020	-0.020	0.000	0.000	0.000	0.000
11	C	11	SER	0	0.005	-0.003	16.098	-0.008	-0.008	0.000	0.000	0.000	0.000
12	C	12	ALA	0	-0.014	-0.003	18.325	0.025	0.025	0.000	0.000	0.000	0.000
13	C	13	ILE	0	0.014	0.002	16.382	-0.035	-0.035	0.000	0.000	0.000	0.000
14	C	14	GLN	0	-0.004	0.000	20.460	0.018	0.018	0.000	0.000	0.000	0.000
15	C	15	GLY	0	0.024	0.022	22.744	-0.014	-0.014	0.000	0.000	0.000	0.000
16	C	16	SER	0	0.003	-0.008	19.503	0.011	0.011	0.000	0.000	0.000	0.000
17	C	17	VAL	0	-0.009	0.000	18.325	-0.039	-0.039	0.000	0.000	0.000	0.000
18	C	18	LEU	0	0.014	0.024	13.039	0.028	0.028	0.000	0.000	0.000	0.000
19	C	19	THR	0	0.002	-0.022	17.241	-0.023	-0.023	0.000	0.000	0.000	0.000
20	C	20	SER	0	0.030	0.011	15.419	0.031	0.031	0.000	0.000	0.000	0.000
21	C	21	THR	0	-0.018	-0.020	17.563	-0.022	-0.022	0.000	0.000	0.000	0.000
22	C	23	GLU	-1	-0.751	-0.846	14.064	0.071	0.071	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.880	0.941	14.041	0.117	0.117	0.000	0.000	0.000	0.000
24	C	25	THR	0	0.036	0.008	12.382	0.015	0.015	0.000	0.000	0.000	0.000
25	C	26	ASN	0	-0.014	-0.006	14.991	0.018	0.018	0.000	0.000	0.000	0.000
26	C	27	GLY	0	-0.016	-0.011	18.795	-0.020	-0.020	0.000	0.000	0.000	0.000
27	C	28	GLY	0	0.032	0.029	20.476	0.016	0.016	0.000	0.000	0.000	0.000
28	C	29	TYR	0	-0.028	-0.037	17.825	-0.014	-0.014	0.000	0.000	0.000	0.000
29	C	30	ASN	0	-0.050	-0.026	17.669	0.010	0.010	0.000	0.000	0.000	0.000
30	C	31	THR	0	0.011	0.011	17.960	-0.014	-0.014	0.000	0.000	0.000	0.000
31	C	32	SER	0	-0.064	-0.016	15.912	-0.025	-0.025	0.000	0.000	0.000	0.000
32	C	33	SER	0	0.030	0.001	17.134	0.012	0.012	0.000	0.000	0.000	0.000
33	C	34	ILE	0	0.002	0.007	12.204	-0.024	-0.024	0.000	0.000	0.000	0.000
34	C	35	ASP	-1	-0.742	-0.836	16.266	-0.269	-0.269	0.000	0.000	0.000	0.000
35	C	36	LEU	0	0.020	0.010	12.643	-0.057	-0.057	0.000	0.000	0.000	0.000
36	C	37	ASN	0	0.022	-0.004	15.766	0.000	0.000	0.000	0.000	0.000	0.000
37	C	38	SER	0	-0.068	-0.060	17.400	-0.009	-0.009	0.000	0.000	0.000	0.000
38	C	39	VAL	0	-0.061	-0.022	11.289	-0.026	-0.026	0.000	0.000	0.000	0.000
39	C	40	ILE	0	0.004	0.006	12.567	-0.044	-0.044	0.000	0.000	0.000	0.000
40	C	41	GLU	-1	-0.823	-0.888	14.879	-0.165	-0.165	0.000	0.000	0.000	0.000
41	C	42	ASN	0	-0.008	-0.036	16.820	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	43	VAL	0	-0.024	-0.026	17.160	0.010	0.010	0.000	0.000	0.000	0.000
43	C	44	ASP	-1	-0.864	-0.943	19.965	-0.070	-0.070	0.000	0.000	0.000	0.000
44	C	45	GLY	0	0.042	0.037	22.312	0.012	0.012	0.000	0.000	0.000	0.000
45	C	46	SER	0	-0.088	-0.038	16.815	0.008	0.008	0.000	0.000	0.000	0.000
46	C	47	LEU	0	0.047	0.023	15.178	-0.017	-0.017	0.000	0.000	0.000	0.000
47	C	48	LYS	1	0.878	0.934	12.821	0.159	0.159	0.000	0.000	0.000	0.000
48	C	49	TRP	0	0.037	0.026	8.033	-0.065	-0.065	0.000	0.000	0.000	0.000
49	C	50	GLN	0	-0.038	-0.033	9.961	-0.020	-0.020	0.000	0.000	0.000	0.000
50	C	51	GLY	0	0.055	0.035	12.760	0.044	0.044	0.000	0.000	0.000	0.000
51	C	52	SER	0	-0.083	-0.036	15.532	-0.027	-0.027	0.000	0.000	0.000	0.000
52	C	53	ASN	0	-0.011	-0.024	18.122	0.017	0.017	0.000	0.000	0.000	0.000
53	C	54	PHE	0	0.040	0.020	17.560	0.026	0.026	0.000	0.000	0.000	0.000
54	C	55	ILE	0	0.031	0.031	20.552	0.021	0.021	0.000	0.000	0.000	0.000
55	C	56	GLU	-1	-0.850	-0.905	22.973	-0.128	-0.128	0.000	0.000	0.000	0.000
56	C	57	THR	0	-0.136	-0.090	23.044	0.015	0.015	0.000	0.000	0.000	0.000
57	C	58	CYS	0	-0.067	-0.012	21.017	-0.004	-0.004	0.000	0.000	0.000	0.000
58	C	59	ARG	1	0.880	0.926	24.105	0.051	0.051	0.000	0.000	0.000	0.000
59	C	60	ASN	0	-0.041	-0.038	24.548	-0.004	-0.004	0.000	0.000	0.000	0.000
60	C	61	THR	0	-0.015	-0.010	20.818	0.011	0.011	0.000	0.000	0.000	0.000
61	C	62	GLN	0	-0.038	-0.022	20.849	0.012	0.012	0.000	0.000	0.000	0.000
62	C	63	LEU	0	-0.017	0.001	15.917	-0.017	-0.017	0.000	0.000	0.000	0.000
63	C	64	ALA	0	0.009	0.004	17.377	0.018	0.018	0.000	0.000	0.000	0.000
64	C	65	GLY	0	0.067	0.018	16.663	0.001	0.001	0.000	0.000	0.000	0.000
65	C	66	SER	0	-0.024	-0.020	14.706	0.004	0.004	0.000	0.000	0.000	0.000
66	C	67	SER	0	-0.054	-0.033	11.121	0.018	0.018	0.000	0.000	0.000	0.000
67	C	68	GLU	-1	-0.976	-0.957	12.219	0.013	0.013	0.000	0.000	0.000	0.000
68	C	69	LEU	0	-0.010	-0.004	14.003	-0.007	-0.007	0.000	0.000	0.000	0.000
69	C	70	ALA	0	0.019	0.013	15.832	0.004	0.004	0.000	0.000	0.000	0.000
70	C	71	ALA	0	0.025	-0.008	18.984	-0.012	-0.012	0.000	0.000	0.000	0.000
71	C	72	GLU	-1	-0.828	-0.881	21.527	-0.042	-0.042	0.000	0.000	0.000	0.000
72	C	74	LYS	1	0.861	0.938	23.722	0.104	0.104	0.000	0.000	0.000	0.000
73	C	75	THR	0	0.054	0.039	24.903	-0.008	-0.008	0.000	0.000	0.000	0.000
74	C	76	ARG	1	0.790	0.876	21.569	0.133	0.133	0.000	0.000	0.000	0.000
75	C	77	ALA	0	-0.021	-0.004	27.547	0.006	0.006	0.000	0.000	0.000	0.000
76	C	78	GLN	0	0.023	0.020	31.158	0.001	0.001	0.000	0.000	0.000	0.000
77	C	79	GLN	0	0.005	-0.014	34.168	-0.002	-0.002	0.000	0.000	0.000	0.000
78	C	80	PHE	0	-0.009	0.002	36.762	0.002	0.002	0.000	0.000	0.000	0.000
79	C	81	VAL	0	0.010	0.000	35.975	-0.003	-0.003	0.000	0.000	0.000	0.000
80	C	82	SER	0	-0.028	-0.014	39.464	0.003	0.003	0.000	0.000	0.000	0.000
81	C	83	THR	0	0.020	0.010	40.528	-0.001	-0.001	0.000	0.000	0.000	0.000
82	C	84	LYS	1	0.914	0.943	42.495	0.031	0.031	0.000	0.000	0.000	0.000
83	C	85	ILE	0	0.032	0.026	43.744	-0.001	-0.001	0.000	0.000	0.000	0.000
84	C	86	ASN	0	-0.036	-0.032	46.041	-0.001	-0.001	0.000	0.000	0.000	0.000
85	C	87	LEU	0	0.005	-0.001	49.079	0.001	0.001	0.000	0.000	0.000	0.000
86	C	88	ASP	-1	-0.877	-0.944	51.767	-0.013	-0.013	0.000	0.000	0.000	0.000
87	C	89	ASP	-1	-0.908	-0.930	47.192	-0.015	-0.015	0.000	0.000	0.000	0.000
88	C	90	HIS	0	-0.081	-0.057	47.283	0.001	0.001	0.000	0.000	0.000	0.000
89	C	91	ILE	0	-0.063	-0.014	51.575	0.001	0.001	0.000	0.000	0.000	0.000
90	C	92	ALA	0	0.063	0.044	54.870	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	93	ASN	0	-0.029	-0.032	58.227	0.000	0.000	0.000	0.000	0.000	0.000
92	C	94	ILE	0	-0.025	-0.007	59.966	0.000	0.000	0.000	0.000	0.000	0.000
93	C	95	ASP	-1	-0.885	-0.958	63.119	-0.004	-0.004	0.000	0.000	0.000	0.000
94	C	96	GLY	0	0.010	0.014	66.900	0.000	0.000	0.000	0.000	0.000	0.000
95	C	97	THR	0	-0.084	-0.042	62.876	0.000	0.000	0.000	0.000	0.000	0.000
96	C	98	LEU	0	-0.013	-0.002	58.835	0.000	0.000	0.000	0.000	0.000	0.000
97	C	99	LYS	1	0.879	0.946	58.292	0.005	0.005	0.000	0.000	0.000	0.000
98	C	100	TYR	0	0.017	0.013	48.113	0.000	0.000	0.000	0.000	0.000	0.000
99	C	101	GLU	-1	-0.925	-0.957	51.742	-0.004	-0.004	0.000	0.000	0.000	0.000

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