FMO DATABASE

FMODB ID: NNG5Q

Calculation Name: 3B79-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3B79

Chain ID: A

ChEMBL ID:
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UniProt ID: Q87FE3

Base Structure: X-ray

Registration Date: 2023-09-23

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1040656.949549
FMO2-HF: Nuclear repulsion	992850.488516
FMO2-HF: Total energy	-47806.461032
FMO2-MP2: Total energy	-47946.185755

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
0.195	1.679	-0.004	-0.639	-0.84	0.003

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.003

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	2	LYS	1	0.974	0.968	3.818	0.280	1.764	-0.004	-0.639	-0.840	0.003
4	A	3	ASP	-1	-0.775	-0.872	5.952	0.074	0.074	0.000	0.000	0.000	0.000
5	A	4	PRO	0	0.079	0.046	9.458	0.116	0.116	0.000	0.000	0.000	0.000
6	A	5	LEU	0	0.032	0.019	10.994	0.102	0.102	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.024	-0.017	9.685	0.084	0.084	0.000	0.000	0.000	0.000
8	A	7	ASN	0	-0.026	-0.022	7.584	0.269	0.269	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.012	0.000	9.877	0.096	0.096	0.000	0.000	0.000	0.000
10	A	9	LEU	0	-0.014	-0.009	13.377	0.029	0.029	0.000	0.000	0.000	0.000
11	A	10	ILE	0	-0.040	-0.021	10.228	0.028	0.028	0.000	0.000	0.000	0.000
12	A	11	TYR	0	0.060	0.030	12.545	0.008	0.008	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.043	0.014	13.765	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.031	-0.015	15.970	0.003	0.003	0.000	0.000	0.000	0.000
15	A	14	ARG	1	0.855	0.921	12.988	-0.526	-0.526	0.000	0.000	0.000	0.000
16	A	15	TYR	0	0.031	0.029	16.741	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	16	TYR	0	-0.043	-0.023	19.072	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	17	GLY	0	-0.031	-0.012	20.111	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.091	-0.036	19.756	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	19	ALA	0	-0.014	0.000	17.269	0.043	0.043	0.000	0.000	0.000	0.000
21	A	20	ASN	0	0.014	-0.004	15.922	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	21	SER	0	0.065	0.031	12.566	0.064	0.064	0.000	0.000	0.000	0.000
23	A	22	PRO	0	0.064	-0.002	8.567	-0.103	-0.103	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.939	-0.964	11.314	0.263	0.263	0.000	0.000	0.000	0.000
25	A	24	ALA	0	-0.002	-0.004	13.195	-0.075	-0.075	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.021	-0.004	14.258	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.022	0.005	13.082	-0.047	-0.047	0.000	0.000	0.000	0.000
28	A	27	ASN	0	-0.011	0.009	16.019	-0.051	-0.051	0.000	0.000	0.000	0.000
29	A	28	GLY	0	0.046	0.019	18.251	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.068	-0.022	18.307	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.020	-0.009	19.067	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.000	-0.003	13.698	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.039	-0.023	17.330	0.005	0.005	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.854	-0.914	14.239	-0.421	-0.421	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.013	-0.009	12.732	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.854	0.927	10.720	0.465	0.465	0.000	0.000	0.000	0.000
37	A	36	LEU	0	0.002	-0.015	13.644	0.048	0.048	0.000	0.000	0.000	0.000
38	A	37	THR	0	0.019	0.005	15.747	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	38	PRO	0	0.068	0.015	18.644	0.020	0.020	0.000	0.000	0.000	0.000
40	A	39	PHE	0	0.017	0.010	21.172	0.016	0.016	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.026	-0.010	19.083	0.013	0.013	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.020	0.032	17.169	0.017	0.017	0.000	0.000	0.000	0.000
43	A	42	PRO	0	0.003	0.002	20.102	0.021	0.021	0.000	0.000	0.000	0.000
44	A	43	ARG	1	0.915	0.950	22.662	0.012	0.012	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.050	0.031	17.343	0.011	0.011	0.000	0.000	0.000	0.000
46	A	45	ALA	0	-0.012	-0.023	19.458	0.029	0.029	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.908	-0.947	20.723	0.098	0.098	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.835	0.922	19.446	-0.071	-0.071	0.000	0.000	0.000	0.000
49	A	48	ALA	0	-0.022	-0.006	18.577	0.024	0.024	0.000	0.000	0.000	0.000
50	A	49	GLY	0	-0.015	0.002	20.118	0.014	0.014	0.000	0.000	0.000	0.000
51	A	50	LEU	0	-0.073	-0.040	19.420	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	51	VAL	0	-0.002	-0.006	23.496	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.019	0.011	22.037	0.003	0.003	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.895	0.940	24.119	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.874	-0.927	24.752	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	55	ASN	0	-0.063	-0.036	26.371	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	56	ARG	1	0.991	0.987	27.706	0.023	0.023	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.002	0.005	29.265	0.004	0.004	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.820	-0.891	29.057	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	59	LEU	0	0.060	0.030	24.362	0.005	0.005	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.790	-0.908	28.175	0.001	0.001	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.808	0.891	30.898	0.005	0.005	0.000	0.000	0.000	0.000
63	A	62	ILE	0	-0.046	-0.005	25.781	0.003	0.003	0.000	0.000	0.000	0.000
64	A	63	SER	0	0.000	0.001	29.536	0.002	0.002	0.000	0.000	0.000	0.000
65	A	64	SER	0	0.097	0.027	28.071	0.003	0.003	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.013	-0.007	27.950	0.007	0.007	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.080	-0.040	26.755	0.004	0.004	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.077	0.011	23.600	0.003	0.003	0.000	0.000	0.000	0.000
69	A	68	PRO	0	0.004	0.001	19.581	0.005	0.005	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.036	-0.009	21.503	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	ILE	0	-0.015	-0.005	16.773	0.004	0.004	0.000	0.000	0.000	0.000
72	A	71	LEU	0	-0.006	-0.002	18.915	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	72	VAL	0	-0.019	-0.021	18.649	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	73	LEU	0	0.008	0.014	16.299	0.014	0.014	0.000	0.000	0.000	0.000
75	A	74	LYS	1	0.814	0.907	19.299	0.070	0.070	0.000	0.000	0.000	0.000
76	A	75	GLY	0	-0.001	0.002	18.200	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	76	GLY	0	-0.076	-0.034	16.590	-0.027	-0.027	0.000	0.000	0.000	0.000
78	A	77	ASP	-1	-0.797	-0.895	12.883	-0.255	-0.255	0.000	0.000	0.000	0.000
79	A	78	SER	0	-0.117	-0.067	13.936	0.050	0.050	0.000	0.000	0.000	0.000
80	A	79	CYS	0	0.042	0.028	14.017	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.008	0.005	14.456	0.009	0.009	0.000	0.000	0.000	0.000
82	A	81	LEU	0	0.006	0.015	16.951	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.019	-0.017	17.231	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.031	-0.021	21.045	0.000	0.000	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.036	0.013	23.817	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	85	ASN	0	-0.004	0.011	26.567	0.000	0.000	0.000	0.000	0.000	0.000
87	A	86	MET	0	-0.001	-0.017	29.143	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.961	-0.956	31.963	0.011	0.011	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.028	-0.039	28.494	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	89	ARG	1	0.847	0.931	29.646	0.003	0.003	0.000	0.000	0.000	0.000
91	A	90	GLU	-1	-0.852	-0.913	24.209	0.003	0.003	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.061	-0.034	22.636	0.005	0.005	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.827	-0.890	19.476	0.078	0.078	0.000	0.000	0.000	0.000
94	A	93	VAL	0	0.035	-0.005	16.523	0.000	0.000	0.000	0.000	0.000	0.000
95	A	94	THR	0	-0.030	-0.016	11.972	0.029	0.029	0.000	0.000	0.000	0.000
96	A	95	THR	0	0.018	-0.023	11.680	0.006	0.006	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.023	-0.014	6.325	0.051	0.051	0.000	0.000	0.000	0.000
98	A	97	GLU	-1	-0.884	-0.924	6.986	-0.213	-0.213	0.000	0.000	0.000	0.000
99	A	98	SER	0	-0.027	-0.012	8.430	0.074	0.074	0.000	0.000	0.000	0.000
100	A	99	GLY	0	0.026	0.024	7.248	0.131	0.131	0.000	0.000	0.000	0.000
101	A	100	MET	0	-0.079	-0.049	7.990	-0.032	-0.032	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.010	-0.004	10.825	-0.027	-0.027	0.000	0.000	0.000	0.000
103	A	102	PRO	0	-0.060	-0.009	13.259	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	103	ILE	0	0.012	0.005	14.345	0.005	0.005	0.000	0.000	0.000	0.000
105	A	104	SER	0	-0.017	-0.016	17.302	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	105	ILE	0	-0.056	-0.019	18.195	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	106	PRO	0	0.128	0.072	21.356	0.007	0.007	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.046	-0.036	23.805	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	108	GLU	-1	-0.975	-0.998	25.666	-0.031	-0.031	0.000	0.000	0.000	0.000
110	A	109	ASP	-1	-0.840	-0.923	21.312	-0.058	-0.058	0.000	0.000	0.000	0.000
111	A	110	LEU	0	-0.042	-0.016	20.060	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	111	LEU	0	-0.092	-0.063	22.507	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	112	GLU	-1	-0.869	-0.936	24.036	-0.076	-0.076	0.000	0.000	0.000	0.000
114	A	113	GLN	0	0.038	0.022	19.248	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	114	TYR	0	-0.027	-0.017	21.526	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	115	THR	0	-0.073	-0.053	22.152	0.003	0.003	0.000	0.000	0.000	0.000
117	A	116	GLY	0	0.001	0.004	24.757	0.002	0.002	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.839	0.928	23.461	0.064	0.064	0.000	0.000	0.000	0.000
119	A	118	TYR	0	0.067	0.031	22.978	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	119	PHE	0	-0.002	-0.009	21.393	0.001	0.001	0.000	0.000	0.000	0.000
121	A	120	LEU	0	0.011	0.010	23.050	0.007	0.007	0.000	0.000	0.000	0.000
122	A	121	VAL	0	0.024	-0.005	20.416	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	122	LYS	1	0.964	0.996	23.691	-0.056	-0.056	0.000	0.000	0.000	0.000
124	A	123	LYS	1	1.001	1.001	25.044	-0.144	-0.144	0.000	0.000	0.000	0.000
125	A	124	GLN	0	-0.032	-0.009	25.678	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)