FMO DATABASE

FMODB ID: N1LQQ

Calculation Name: 3QD7-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QD7

Chain ID: X

ChEMBL ID:

UniProt ID: P76053

Base Structure: X-ray

Registration Date: 2023-03-14

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1183232.452046
FMO2-HF: Nuclear repulsion	1131488.838818
FMO2-HF: Total energy	-51743.613227
FMO2-MP2: Total energy	-51895.274232

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(X:40:ASP)

Summations of interaction energy for fragment #1(X:40:ASP)

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.
-22.035	-13.513	0.991	-4.271	-5.242	0.023

Interaction energy analysis for fragmet #1(X:40:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.884 / q_NPA : -0.944

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	X	42	LEU	0	0.000	0.013	2.560	-18.451	-11.582	0.919	-3.553	-4.235	0.026
4	X	43	GLN	0	0.029	-0.013	4.218	-3.049	-3.038	-0.001	-0.006	-0.004	0.000
5	X	44	LEU	0	-0.046	-0.009	5.406	-3.708	-3.708	0.000	0.000	0.000	0.000
6	X	45	ASP	-1	-0.843	-0.926	3.389	47.099	48.145	0.062	-0.464	-0.644	-0.003
7	X	46	ASN	0	-0.082	-0.033	5.975	-2.481	-2.481	0.000	0.000	0.000	0.000
8	X	47	PHE	0	0.012	-0.010	7.600	-2.435	-2.435	0.000	0.000	0.000	0.000
9	X	48	LEU	0	-0.049	0.008	11.097	-1.733	-1.733	0.000	0.000	0.000	0.000
10	X	49	THR	0	-0.004	-0.023	13.796	-0.566	-0.566	0.000	0.000	0.000	0.000
11	X	50	THR	0	-0.038	-0.028	17.075	-0.393	-0.393	0.000	0.000	0.000	0.000
12	X	51	GLY	0	0.020	0.016	19.711	-0.155	-0.155	0.000	0.000	0.000	0.000
13	X	52	PHE	0	-0.008	-0.031	23.341	0.080	0.080	0.000	0.000	0.000	0.000
14	X	53	LEU	0	-0.043	-0.005	23.709	0.017	0.017	0.000	0.000	0.000	0.000
15	X	54	ASP	-1	-0.785	-0.874	24.623	11.545	11.545	0.000	0.000	0.000	0.000
16	X	55	ILE	0	-0.061	-0.045	27.160	0.108	0.108	0.000	0.000	0.000	0.000
17	X	56	ILE	0	0.046	0.034	25.964	-0.319	-0.319	0.000	0.000	0.000	0.000
18	X	57	PRO	0	0.022	0.014	29.869	0.009	0.009	0.000	0.000	0.000	0.000
19	X	58	LEU	0	-0.036	-0.016	32.304	0.136	0.136	0.000	0.000	0.000	0.000
20	X	59	SER	0	-0.068	-0.026	34.149	0.037	0.037	0.000	0.000	0.000	0.000
21	X	60	GLN	0	0.020	0.017	32.245	0.050	0.050	0.000	0.000	0.000	0.000
22	X	61	PRO	0	0.016	0.023	30.500	0.199	0.199	0.000	0.000	0.000	0.000
23	X	62	LEU	0	0.006	0.002	23.550	0.106	0.106	0.000	0.000	0.000	0.000
24	X	63	GLU	-1	-0.952	-0.998	26.774	9.398	9.398	0.000	0.000	0.000	0.000
25	X	64	PHE	0	0.026	0.022	19.602	-0.032	-0.032	0.000	0.000	0.000	0.000
26	X	65	ARG	1	0.923	0.949	23.797	-9.988	-9.988	0.000	0.000	0.000	0.000
27	X	66	ARG	1	0.884	0.942	16.344	-15.693	-15.693	0.000	0.000	0.000	0.000
28	X	67	GLU	-1	-0.880	-0.951	23.219	11.184	11.184	0.000	0.000	0.000	0.000
29	X	68	GLY	0	-0.024	-0.016	24.221	0.352	0.352	0.000	0.000	0.000	0.000
30	X	69	LEU	0	-0.051	-0.010	21.320	0.177	0.177	0.000	0.000	0.000	0.000
31	X	70	GLN	0	0.007	0.002	24.836	-0.221	-0.221	0.000	0.000	0.000	0.000
32	X	71	HIS	0	0.049	0.011	26.817	0.235	0.235	0.000	0.000	0.000	0.000
33	X	72	GLY	0	0.013	0.009	28.550	-0.092	-0.092	0.000	0.000	0.000	0.000
34	X	73	VAL	0	-0.057	-0.027	22.637	0.128	0.128	0.000	0.000	0.000	0.000
35	X	74	LEU	0	0.034	0.013	24.875	0.260	0.260	0.000	0.000	0.000	0.000
36	X	75	ASP	-1	-0.806	-0.902	27.313	9.450	9.450	0.000	0.000	0.000	0.000
37	X	76	LYS	1	0.794	0.907	19.797	-13.824	-13.824	0.000	0.000	0.000	0.000
38	X	77	LEU	0	-0.014	-0.005	22.670	0.245	0.245	0.000	0.000	0.000	0.000
39	X	78	ARG	1	0.894	0.953	25.509	-8.886	-8.886	0.000	0.000	0.000	0.000
40	X	79	SER	0	-0.019	-0.012	28.580	-0.325	-0.325	0.000	0.000	0.000	0.000
41	X	80	GLY	0	0.008	0.026	24.985	-0.006	-0.006	0.000	0.000	0.000	0.000
42	X	81	LYS	1	0.915	0.957	24.639	-11.626	-11.626	0.000	0.000	0.000	0.000
43	X	82	TYR	0	0.002	-0.007	21.807	0.779	0.779	0.000	0.000	0.000	0.000
44	X	83	PRO	0	-0.030	-0.007	21.866	-0.454	-0.454	0.000	0.000	0.000	0.000
45	X	84	GLN	0	0.055	0.022	21.950	0.104	0.104	0.000	0.000	0.000	0.000
46	X	85	GLN	0	0.070	0.034	17.812	-0.191	-0.191	0.000	0.000	0.000	0.000
47	X	86	ALA	0	-0.011	0.002	17.335	0.909	0.909	0.000	0.000	0.000	0.000
48	X	87	SER	0	-0.082	-0.056	19.078	-0.530	-0.530	0.000	0.000	0.000	0.000
49	X	88	LEU	0	0.066	0.049	15.375	0.344	0.344	0.000	0.000	0.000	0.000
50	X	89	ASN	0	-0.031	-0.029	18.901	-0.832	-0.832	0.000	0.000	0.000	0.000
51	X	90	LEU	0	0.072	0.025	17.845	0.352	0.352	0.000	0.000	0.000	0.000
52	X	91	LEU	0	-0.030	-0.001	21.678	-0.441	-0.441	0.000	0.000	0.000	0.000
53	X	92	ARG	1	0.890	0.934	25.199	-10.836	-10.836	0.000	0.000	0.000	0.000
54	X	93	GLN	0	0.074	0.060	20.040	-0.324	-0.324	0.000	0.000	0.000	0.000
55	X	94	PRO	0	0.034	0.017	20.744	-0.315	-0.315	0.000	0.000	0.000	0.000
56	X	95	VAL	0	0.059	0.015	20.236	0.609	0.609	0.000	0.000	0.000	0.000
57	X	96	GLU	-1	-0.748	-0.847	14.478	18.885	18.885	0.000	0.000	0.000	0.000
58	X	97	GLU	-1	-0.841	-0.897	15.495	19.336	19.336	0.000	0.000	0.000	0.000
59	X	98	CYS	0	-0.068	-0.033	16.055	0.552	0.552	0.000	0.000	0.000	0.000
60	X	99	ARG	1	0.816	0.875	12.219	-19.575	-19.575	0.000	0.000	0.000	0.000
61	X	100	LYS	1	0.801	0.888	11.582	-18.091	-18.091	0.000	0.000	0.000	0.000
62	X	101	MET	0	-0.034	-0.017	11.276	1.400	1.400	0.000	0.000	0.000	0.000
63	X	102	VAL	0	0.010	-0.001	12.538	0.770	0.770	0.000	0.000	0.000	0.000
64	X	103	PHE	0	0.029	0.021	5.302	-0.376	-0.376	0.000	0.000	0.000	0.000
65	X	104	SER	0	-0.033	-0.017	7.725	1.039	1.039	0.000	0.000	0.000	0.000
66	X	105	PHE	0	0.005	-0.006	8.805	1.025	1.025	0.000	0.000	0.000	0.000
67	X	106	ILE	0	-0.023	-0.003	9.906	-0.221	-0.221	0.000	0.000	0.000	0.000
68	X	107	GLN	0	0.006	0.002	3.422	-3.452	-2.856	0.011	-0.248	-0.359	0.000
69	X	108	GLN	0	-0.067	-0.040	7.027	0.748	0.748	0.000	0.000	0.000	0.000
70	X	109	ALA	0	0.007	-0.003	9.052	-0.933	-0.933	0.000	0.000	0.000	0.000
71	X	110	LEU	0	-0.017	-0.014	8.606	-1.868	-1.868	0.000	0.000	0.000	0.000
72	X	111	ALA	0	-0.019	0.005	7.064	-0.921	-0.921	0.000	0.000	0.000	0.000
73	X	112	ASP	-1	-0.871	-0.922	9.090	21.195	21.195	0.000	0.000	0.000	0.000
74	X	113	GLY	0	-0.039	-0.014	12.183	-1.922	-1.922	0.000	0.000	0.000	0.000
75	X	114	LEU	0	-0.025	-0.006	14.049	-1.905	-1.905	0.000	0.000	0.000	0.000
76	X	115	ARG	1	0.965	0.980	15.836	-12.841	-12.841	0.000	0.000	0.000	0.000
77	X	116	ASN	0	-0.056	-0.036	18.525	-0.422	-0.422	0.000	0.000	0.000	0.000
78	X	117	VAL	0	0.034	0.027	15.675	0.203	0.203	0.000	0.000	0.000	0.000
79	X	118	LEU	0	-0.059	-0.022	18.947	-0.597	-0.597	0.000	0.000	0.000	0.000
80	X	119	ILE	0	0.044	0.018	16.632	0.448	0.448	0.000	0.000	0.000	0.000
81	X	120	ILE	0	-0.007	-0.015	20.785	-0.638	-0.638	0.000	0.000	0.000	0.000
82	X	121	HIS	0	0.043	0.014	23.180	0.321	0.321	0.000	0.000	0.000	0.000
83	X	122	GLY	0	0.002	-0.005	24.336	-0.224	-0.224	0.000	0.000	0.000	0.000
84	X	123	LYS	1	0.877	0.956	28.044	-9.207	-9.207	0.000	0.000	0.000	0.000
85	X	124	GLY	0	0.050	0.028	31.398	-0.061	-0.061	0.000	0.000	0.000	0.000
86	X	125	ARG	1	0.797	0.885	32.821	-8.803	-8.803	0.000	0.000	0.000	0.000
87	X	126	ASP	-1	-0.755	-0.886	35.523	8.449	8.449	0.000	0.000	0.000	0.000
88	X	127	ASP	-1	-0.808	-0.893	33.269	8.969	8.969	0.000	0.000	0.000	0.000
89	X	128	LYS	1	0.929	0.964	31.811	-8.546	-8.546	0.000	0.000	0.000	0.000
90	X	129	SER	0	0.007	0.007	31.560	0.243	0.243	0.000	0.000	0.000	0.000
91	X	130	HIS	0	0.012	-0.008	24.475	-0.113	-0.113	0.000	0.000	0.000	0.000
92	X	131	ALA	0	0.019	0.008	27.210	0.335	0.335	0.000	0.000	0.000	0.000
93	X	132	ASN	0	-0.007	-0.008	27.237	0.325	0.325	0.000	0.000	0.000	0.000
94	X	133	ILE	0	-0.003	0.025	25.087	0.199	0.199	0.000	0.000	0.000	0.000
95	X	134	VAL	0	0.015	-0.001	21.789	0.432	0.432	0.000	0.000	0.000	0.000
96	X	135	ARG	1	0.776	0.874	22.784	-9.648	-9.648	0.000	0.000	0.000	0.000
97	X	136	SER	0	0.008	-0.006	23.895	0.101	0.101	0.000	0.000	0.000	0.000
98	X	137	TYR	0	0.053	0.023	20.444	0.126	0.126	0.000	0.000	0.000	0.000
99	X	138	VAL	0	-0.024	-0.012	18.966	0.574	0.574	0.000	0.000	0.000	0.000
100	X	139	ALA	0	0.009	0.009	19.393	0.438	0.438	0.000	0.000	0.000	0.000
101	X	140	ARG	1	0.843	0.927	19.511	-13.063	-13.063	0.000	0.000	0.000	0.000
102	X	141	TRP	0	-0.028	-0.019	15.465	0.350	0.350	0.000	0.000	0.000	0.000
103	X	142	LEU	0	-0.009	-0.010	15.370	0.867	0.867	0.000	0.000	0.000	0.000
104	X	143	THR	0	-0.070	-0.041	16.639	0.128	0.128	0.000	0.000	0.000	0.000
105	X	144	GLU	-1	-0.750	-0.849	14.488	16.657	16.657	0.000	0.000	0.000	0.000
106	X	145	PHE	0	0.025	0.014	9.209	0.859	0.859	0.000	0.000	0.000	0.000
107	X	146	ASP	-1	-0.804	-0.881	12.356	16.931	16.931	0.000	0.000	0.000	0.000
108	X	147	ASP	-1	-0.856	-0.918	10.825	20.833	20.833	0.000	0.000	0.000	0.000
109	X	148	VAL	0	-0.026	-0.003	13.674	-0.738	-0.738	0.000	0.000	0.000	0.000
110	X	149	GLN	0	0.011	0.008	15.997	-0.681	-0.681	0.000	0.000	0.000	0.000
111	X	150	ALA	0	0.029	-0.002	19.356	-0.608	-0.608	0.000	0.000	0.000	0.000
112	X	151	TYR	0	-0.023	-0.021	20.151	0.351	0.351	0.000	0.000	0.000	0.000
113	X	152	CYS	0	-0.039	-0.007	22.719	-0.417	-0.417	0.000	0.000	0.000	0.000
114	X	153	THR	0	0.014	0.015	25.443	0.284	0.284	0.000	0.000	0.000	0.000
115	X	154	ALA	0	0.006	0.016	26.437	-0.112	-0.112	0.000	0.000	0.000	0.000
116	X	155	LEU	0	0.061	0.023	28.104	-0.395	-0.395	0.000	0.000	0.000	0.000
117	X	156	PRO	0	0.000	-0.021	30.934	0.219	0.219	0.000	0.000	0.000	0.000
118	X	157	HIS	0	-0.001	0.009	30.351	-0.172	-0.172	0.000	0.000	0.000	0.000
119	X	158	HIS	0	0.033	0.037	27.074	0.035	0.035	0.000	0.000	0.000	0.000
120	X	159	GLY	0	0.053	0.028	27.660	0.399	0.399	0.000	0.000	0.000	0.000
121	X	160	GLY	0	-0.031	-0.013	29.986	-0.291	-0.291	0.000	0.000	0.000	0.000
122	X	161	SER	0	0.058	0.007	29.620	0.322	0.322	0.000	0.000	0.000	0.000
123	X	162	GLY	0	-0.059	-0.043	29.158	0.014	0.014	0.000	0.000	0.000	0.000
124	X	163	ALA	0	-0.043	-0.011	24.877	0.339	0.339	0.000	0.000	0.000	0.000
125	X	164	CYS	0	-0.012	0.021	22.214	-0.237	-0.237	0.000	0.000	0.000	0.000
126	X	165	TYR	0	0.033	-0.007	22.435	0.311	0.311	0.000	0.000	0.000	0.000
127	X	166	VAL	0	0.056	0.017	17.151	-0.190	-0.190	0.000	0.000	0.000	0.000
128	X	167	ALA	0	-0.050	-0.023	19.906	0.098	0.098	0.000	0.000	0.000	0.000
129	X	168	LEU	0	0.036	0.011	13.680	0.056	0.056	0.000	0.000	0.000	0.000
130	X	169	ARG	1	0.775	0.852	13.171	-19.358	-19.358	0.000	0.000	0.000	0.000
131	X	170	LYS	1	0.863	0.930	13.788	-16.581	-16.581	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:40:ASP)