FMO DATABASE

FMODB ID: MNVKZ

Calculation Name: 3LUA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LUA

Chain ID: A

ChEMBL ID:

UniProt ID: A3DK02

Base Structure: X-ray

Registration Date: 2023-09-21

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1155688.457238
FMO2-HF: Nuclear repulsion	1106154.188045
FMO2-HF: Total energy	-49534.269193
FMO2-MP2: Total energy	-49682.663009

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.
-22.011	-16.604	19.39	-11.18	-13.617	-0.088

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 : -0.042 / q_NPA : -0.031

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	3	GLY	0	0.007	0.000	2.050	-0.916	1.546	1.673	-1.852	-2.284	-0.005
4	A	4	THR	0	-0.008	-0.017	2.722	-1.568	-0.383	1.288	-0.652	-1.821	-0.011
5	A	5	VAL	0	-0.068	-0.035	4.305	0.123	0.182	0.000	-0.013	-0.046	0.000
6	A	6	LEU	0	-0.016	-0.004	7.946	0.031	0.031	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.006	-0.003	11.036	0.010	0.010	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.034	-0.017	13.829	0.024	0.024	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.751	-0.893	17.302	-0.180	-0.180	0.000	0.000	0.000	0.000
10	A	10	TYR	0	0.045	0.019	19.865	0.000	0.000	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.073	-0.025	22.152	0.007	0.007	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.793	-0.888	19.689	-0.185	-0.185	0.000	0.000	0.000	0.000
13	A	13	TYR	0	0.041	0.014	19.121	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.853	-0.906	20.255	-0.207	-0.207	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.777	0.882	15.556	0.192	0.192	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.812	-0.910	14.754	-0.372	-0.372	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.775	0.872	15.765	0.174	0.174	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.067	-0.060	13.722	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.813	0.889	10.962	0.327	0.327	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.031	0.025	11.915	-0.071	-0.071	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.091	-0.045	13.773	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.016	-0.021	8.560	0.063	0.063	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.838	-0.893	9.659	-0.870	-0.870	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.123	-0.069	11.048	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.148	-0.068	9.911	0.108	0.108	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.033	0.008	6.964	0.131	0.131	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.916	-0.937	1.848	-14.218	-15.441	12.028	-5.581	-5.224	-0.052
28	A	28	TYR	0	-0.075	-0.051	2.418	-3.334	-1.778	2.453	-2.137	-1.871	-0.020
29	A	29	ASP	-1	-0.804	-0.886	2.370	-2.157	-0.916	1.947	-0.920	-2.268	0.000
30	A	30	PHE	0	-0.021	-0.026	4.160	0.012	0.139	0.001	-0.025	-0.103	0.000
31	A	31	ILE	0	0.017	0.022	7.388	0.107	0.107	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.769	-0.855	9.917	-0.315	-0.315	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.050	-0.034	13.488	0.039	0.039	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.743	-0.855	16.703	-0.128	-0.128	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.003	-0.005	19.792	0.018	0.018	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.051	0.022	21.344	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.885	0.955	23.031	0.047	0.047	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.892	0.917	15.895	0.134	0.134	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.086	0.037	17.818	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.058	-0.051	19.353	0.005	0.005	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.085	-0.038	20.360	0.011	0.011	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.028	0.031	13.719	0.004	0.004	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.066	-0.037	16.271	0.008	0.008	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.892	0.939	17.533	0.025	0.025	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.860	-0.918	15.270	0.015	0.015	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.045	-0.016	12.104	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.839	-0.936	11.304	0.052	0.052	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.093	-0.044	8.491	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.017	0.020	8.306	-0.051	-0.051	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.033	0.017	6.432	0.035	0.035	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.043	-0.027	9.244	0.020	0.020	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.008	0.013	10.611	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.010	0.001	12.664	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	MET	0	0.012	0.009	15.412	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.709	-0.804	18.594	-0.138	-0.138	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.007	-0.016	21.976	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.006	-0.003	24.387	0.011	0.011	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.036	0.009	20.463	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.011	-0.007	25.103	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.009	-0.009	27.513	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.797	-0.885	28.323	-0.083	-0.083	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.774	0.877	28.602	0.054	0.054	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.816	-0.899	27.391	-0.061	-0.061	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.026	0.026	24.237	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.030	-0.026	24.108	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.878	-0.919	26.086	-0.054	-0.054	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.001	0.002	20.570	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.018	-0.011	21.391	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.006	-0.006	22.359	0.003	0.003	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.021	-0.005	22.549	0.005	0.005	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.000	-0.003	17.327	0.005	0.005	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.777	0.889	17.894	0.122	0.122	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.069	-0.034	21.848	0.012	0.012	0.000	0.000	0.000	0.000
74	A	74	ASN	0	0.035	0.011	17.634	0.021	0.021	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.011	-0.006	19.318	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.872	0.942	14.910	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.005	0.004	13.946	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.039	0.001	16.145	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.034	-0.031	17.917	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.017	0.032	12.537	0.007	0.007	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.011	0.014	13.193	0.017	0.017	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.039	0.009	14.829	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.000	0.004	14.763	0.021	0.021	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.015	0.006	18.024	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.006	-0.010	19.572	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.041	-0.044	21.456	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.835	0.917	24.551	0.114	0.114	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.032	-0.034	27.684	0.008	0.008	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.851	-0.940	29.115	-0.102	-0.102	0.000	0.000	0.000	0.000
90	A	90	ASN	0	0.013	0.019	31.586	0.006	0.006	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.034	0.003	32.696	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.018	0.019	34.097	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.026	0.001	30.542	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.908	0.973	27.349	0.109	0.109	0.000	0.000	0.000	0.000
95	A	95	HIS	0	0.030	0.014	29.676	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.011	-0.006	31.474	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.019	0.007	25.947	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.013	-0.018	26.426	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.810	0.917	27.873	0.065	0.065	0.000	0.000	0.000	0.000
100	A	100	PHE	0	-0.010	0.008	24.388	0.005	0.005	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.976	0.982	23.188	0.057	0.057	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.036	0.024	21.000	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.022	-0.016	18.140	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.742	-0.812	19.878	-0.188	-0.188	0.000	0.000	0.000	0.000
105	A	105	TYR	0	-0.015	-0.012	21.629	0.005	0.005	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.029	-0.009	19.701	0.012	0.012	0.000	0.000	0.000	0.000
107	A	107	LEU	0	0.018	0.010	23.852	0.003	0.003	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.782	0.880	21.522	0.170	0.170	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.011	-0.024	26.240	0.010	0.010	0.000	0.000	0.000	0.000
110	A	110	TYR	0	0.036	0.025	19.599	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	PRO	0	-0.010	0.005	24.344	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	112	THR	0	0.072	0.016	19.567	0.005	0.005	0.000	0.000	0.000	0.000
113	A	113	LYS	1	1.021	1.006	19.623	0.188	0.188	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.802	0.880	20.800	0.178	0.178	0.000	0.000	0.000	0.000
115	A	115	LEU	0	0.039	0.013	15.636	0.010	0.010	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.763	-0.849	15.389	-0.383	-0.383	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.033	-0.028	16.246	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.075	-0.035	18.009	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.055	0.020	11.544	0.024	0.024	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.840	0.901	13.985	0.427	0.427	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.037	-0.012	15.198	0.032	0.032	0.000	0.000	0.000	0.000
122	A	122	VAL	0	-0.050	-0.031	14.530	0.027	0.027	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.000	-0.008	9.159	0.051	0.051	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.798	0.913	13.129	0.231	0.231	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.034	0.022	11.660	-0.028	-0.028	0.000	0.000	0.000	0.000

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