FMO DATABASE

FMODB ID: MV2VZ

Calculation Name: 4M9O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M9O

Chain ID: A

ChEMBL ID:

UniProt ID: Q04475

Base Structure: X-ray

Registration Date: 2023-06-26

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-713773.032727
FMO2-HF: Nuclear repulsion	674149.318365
FMO2-HF: Total energy	-39623.714362
FMO2-MP2: Total energy	-39737.709663

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:LYS)

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

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.
22.239	23.752	-0.016	-0.623	-0.873	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.980 / q_NPA : 0.974

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	3	SER	0	-0.023	-0.009	3.875	3.379	4.722	-0.015	-0.608	-0.720
4	A	4	THR	0	0.007	0.002	6.281	0.871	0.871	0.000	0.000	0.000
5	A	5	PRO	0	-0.004	-0.005	9.947	0.691	0.691	0.000	0.000	0.000
6	A	6	LYS	1	0.851	0.939	9.700	20.897	20.897	0.000	0.000	0.000
7	A	7	VAL	0	-0.007	-0.006	15.033	-0.007	-0.007	0.000	0.000	0.000
8	A	8	HIS	0	0.014	0.019	18.330	0.659	0.659	0.000	0.000	0.000
9	A	9	VAL	0	0.014	-0.010	21.960	-0.081	-0.081	0.000	0.000	0.000
10	A	10	TYR	0	-0.012	-0.010	24.054	0.123	0.123	0.000	0.000	0.000
11	A	11	SER	0	0.020	-0.006	28.368	-0.064	-0.064	0.000	0.000	0.000
12	A	12	HIS	0	-0.026	-0.011	31.571	-0.186	-0.186	0.000	0.000	0.000
13	A	13	PHE	0	0.006	0.013	32.627	0.126	0.126	0.000	0.000	0.000
14	A	14	PRO	0	0.044	0.021	35.137	-0.176	-0.176	0.000	0.000	0.000
15	A	15	GLY	0	0.010	0.002	36.367	0.047	0.047	0.000	0.000	0.000
16	A	16	GLU	-1	-0.903	-0.968	37.338	-6.754	-6.754	0.000	0.000	0.000
17	A	17	TYR	0	0.005	-0.008	40.035	-0.002	-0.002	0.000	0.000	0.000
18	A	18	GLY	0	0.045	0.042	42.822	0.135	0.135	0.000	0.000	0.000
19	A	19	LYS	1	0.834	0.918	39.513	7.450	7.450	0.000	0.000	0.000
20	A	20	PRO	0	-0.025	-0.006	40.567	-0.198	-0.198	0.000	0.000	0.000
21	A	21	ASN	0	-0.035	-0.025	35.562	-0.069	-0.069	0.000	0.000	0.000
22	A	22	THR	0	0.007	-0.003	31.694	0.069	0.069	0.000	0.000	0.000
23	A	23	LEU	0	0.017	0.032	29.457	-0.092	-0.092	0.000	0.000	0.000
24	A	24	ILE	0	-0.024	-0.029	25.603	-0.106	-0.106	0.000	0.000	0.000
25	A	25	CYS	0	-0.052	0.005	22.604	-0.350	-0.350	0.000	0.000	0.000
26	A	26	TYR	0	-0.013	-0.004	18.505	-0.278	-0.278	0.000	0.000	0.000
27	A	27	VAL	0	0.028	0.009	15.577	-0.245	-0.245	0.000	0.000	0.000
28	A	28	SER	0	0.054	0.023	14.891	-0.529	-0.529	0.000	0.000	0.000
29	A	29	SER	0	-0.042	-0.025	10.948	-0.263	-0.263	0.000	0.000	0.000
30	A	30	PHE	0	-0.001	0.005	8.946	-0.274	-0.274	0.000	0.000	0.000
31	A	31	HIS	0	-0.004	0.014	4.769	-2.140	-1.970	-0.001	-0.015	-0.153
32	A	32	PRO	0	0.042	0.002	4.962	-2.448	-2.448	0.000	0.000	0.000
33	A	33	PRO	0	0.040	0.013	6.611	1.527	1.527	0.000	0.000	0.000
34	A	34	ASP	-1	-0.897	-0.941	9.859	-23.603	-23.603	0.000	0.000	0.000
35	A	35	ILE	0	-0.051	-0.023	11.596	-0.797	-0.797	0.000	0.000	0.000
36	A	36	SER	0	-0.035	-0.007	14.118	0.985	0.985	0.000	0.000	0.000
37	A	37	ILE	0	0.031	0.001	17.838	-0.322	-0.322	0.000	0.000	0.000
38	A	38	GLU	-1	-0.848	-0.921	20.628	-11.636	-11.636	0.000	0.000	0.000
39	A	39	LEU	0	0.003	0.007	24.304	-0.181	-0.181	0.000	0.000	0.000
40	A	40	LEU	0	-0.021	-0.012	26.206	0.075	0.075	0.000	0.000	0.000
41	A	41	LYS	1	0.904	0.941	29.898	8.076	8.076	0.000	0.000	0.000
42	A	42	ASN	0	-0.028	-0.028	33.535	-0.103	-0.103	0.000	0.000	0.000
43	A	43	GLY	0	0.038	0.027	31.928	0.153	0.153	0.000	0.000	0.000
44	A	44	GLN	0	-0.052	-0.024	31.928	-0.146	-0.146	0.000	0.000	0.000
45	A	45	VAL	0	-0.011	-0.011	27.612	-0.038	-0.038	0.000	0.000	0.000
46	A	46	MET	0	-0.033	0.001	30.252	0.240	0.240	0.000	0.000	0.000
47	A	47	SER	0	0.008	-0.015	31.093	-0.265	-0.265	0.000	0.000	0.000
48	A	48	ASP	-1	-0.877	-0.932	33.300	-8.586	-8.586	0.000	0.000	0.000
49	A	49	THR	0	-0.014	0.008	28.455	0.015	0.015	0.000	0.000	0.000
50	A	50	LYS	1	0.838	0.915	29.068	9.484	9.484	0.000	0.000	0.000
51	A	51	GLN	0	0.024	-0.004	21.331	-0.113	-0.113	0.000	0.000	0.000
52	A	52	THR	0	-0.016	-0.002	21.415	0.274	0.274	0.000	0.000	0.000
53	A	53	ASP	-1	-0.853	-0.928	21.619	-12.711	-12.711	0.000	0.000	0.000
54	A	54	LEU	0	-0.071	-0.035	13.679	-0.166	-0.166	0.000	0.000	0.000
55	A	55	ALA	0	0.042	0.039	18.058	0.065	0.065	0.000	0.000	0.000
56	A	56	PHE	0	-0.019	-0.029	10.450	-1.019	-1.019	0.000	0.000	0.000
57	A	57	GLU	-1	-0.774	-0.860	14.542	-12.952	-12.952	0.000	0.000	0.000
58	A	58	LYS	1	0.823	0.883	14.046	13.551	13.551	0.000	0.000	0.000
59	A	59	GLY	0	0.038	0.031	12.970	-0.137	-0.137	0.000	0.000	0.000
60	A	60	TRP	0	-0.011	-0.012	8.833	-1.840	-1.840	0.000	0.000	0.000
61	A	61	GLN	0	-0.003	0.002	9.660	-0.895	-0.895	0.000	0.000	0.000
62	A	62	PHE	0	0.041	0.019	8.534	0.887	0.887	0.000	0.000	0.000
63	A	63	HIS	0	-0.092	-0.050	12.869	-0.039	-0.039	0.000	0.000	0.000
64	A	64	LEU	0	-0.002	0.011	16.072	0.137	0.137	0.000	0.000	0.000
65	A	65	THR	0	0.024	0.010	18.872	0.066	0.066	0.000	0.000	0.000
66	A	66	LYS	1	0.813	0.904	22.426	12.409	12.409	0.000	0.000	0.000
67	A	67	SER	0	0.000	-0.001	25.012	0.049	0.049	0.000	0.000	0.000
68	A	68	VAL	0	0.033	0.004	28.729	-0.041	-0.041	0.000	0.000	0.000
69	A	69	ALA	0	0.010	0.019	32.185	0.039	0.039	0.000	0.000	0.000
70	A	70	PHE	0	-0.029	-0.026	34.204	-0.069	-0.069	0.000	0.000	0.000
71	A	71	THR	0	0.051	0.020	37.139	0.060	0.060	0.000	0.000	0.000
72	A	72	PRO	0	-0.048	0.009	37.010	-0.048	-0.048	0.000	0.000	0.000
73	A	73	GLU	-1	-0.817	-0.944	38.889	-6.810	-6.810	0.000	0.000	0.000
74	A	74	LYS	1	0.902	0.945	40.475	6.475	6.475	0.000	0.000	0.000
75	A	75	GLY	0	0.013	0.005	40.657	0.161	0.161	0.000	0.000	0.000
76	A	76	ASP	-1	-0.785	-0.853	37.057	-7.993	-7.993	0.000	0.000	0.000
77	A	77	GLU	-1	-0.910	-0.937	31.315	-9.942	-9.942	0.000	0.000	0.000
78	A	78	TYR	0	-0.009	-0.026	31.430	0.051	0.051	0.000	0.000	0.000
79	A	79	THR	0	-0.018	-0.012	27.078	-0.248	-0.248	0.000	0.000	0.000
80	A	81	SER	0	0.002	0.003	22.150	-0.039	-0.039	0.000	0.000	0.000
81	A	82	VAL	0	0.012	0.010	16.295	-0.050	-0.050	0.000	0.000	0.000
82	A	83	ARG	1	0.846	0.920	16.423	17.351	17.351	0.000	0.000	0.000
83	A	84	HIS	0	0.053	0.010	8.425	0.573	0.573	0.000	0.000	0.000
84	A	85	MET	0	0.008	0.003	5.455	-0.555	-0.555	0.000	0.000	0.000
85	A	86	LYS	1	0.931	0.970	9.676	27.473	27.473	0.000	0.000	0.000
86	A	87	GLU	-1	-0.832	-0.879	13.355	-17.626	-17.626	0.000	0.000	0.000
87	A	88	THR	0	-0.001	-0.028	15.203	-0.327	-0.327	0.000	0.000	0.000
88	A	89	LYS	1	0.872	0.943	14.996	18.751	18.751	0.000	0.000	0.000
89	A	90	LYS	1	0.919	0.943	19.983	12.402	12.402	0.000	0.000	0.000
90	A	91	PHE	0	0.021	-0.002	17.876	-0.305	-0.305	0.000	0.000	0.000
91	A	92	SER	0	0.042	0.001	24.028	0.012	0.012	0.000	0.000	0.000
92	A	93	TRP	0	-0.031	-0.012	27.076	-0.060	-0.060	0.000	0.000	0.000
93	A	94	GLU	-1	-0.880	-0.935	28.922	-9.964	-9.964	0.000	0.000	0.000
94	A	95	PRO	0	-0.037	0.002	30.916	0.016	0.016	0.000	0.000	0.000
95	A	96	ASN	0	-0.001	-0.013	33.529	0.187	0.187	0.000	0.000	0.000
96	A	97	MET	0	-0.050	0.003	36.703	0.136	0.136	0.000	0.000	0.000

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