FMO DATABASE

FMODB ID: 82QMY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1181036.099103
FMO2-HF: Nuclear repulsion	1129292.762287
FMO2-HF: Total energy	-51743.336816
FMO2-MP2: Total energy	-51895.030979

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.
-10.163	-2.371	1.622	-3.833	-5.583	0.012

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 : -0.904 / q_NPA : -0.953

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	X	42	LEU	0	-0.003	0.006	2.498	-16.415	-10.401	0.904	-2.798	-4.121	0.023
4	X	43	GLN	0	0.051	0.002	3.973	-2.972	-2.941	-0.001	0.004	-0.034	0.000
5	X	44	LEU	0	-0.045	-0.014	5.029	-3.522	-3.522	0.000	0.000	0.000	0.000
6	X	45	ASP	-1	-0.847	-0.928	2.778	50.263	52.010	0.719	-1.039	-1.428	-0.011
7	X	46	ASN	0	-0.113	-0.060	5.719	-2.706	-2.706	0.000	0.000	0.000	0.000
8	X	47	PHE	0	0.032	0.006	7.948	-1.877	-1.877	0.000	0.000	0.000	0.000
9	X	48	LEU	0	-0.064	-0.003	10.802	-1.762	-1.762	0.000	0.000	0.000	0.000
10	X	49	THR	0	-0.010	-0.013	13.553	-0.392	-0.392	0.000	0.000	0.000	0.000
11	X	50	THR	0	-0.028	-0.028	16.747	-0.475	-0.475	0.000	0.000	0.000	0.000
12	X	51	GLY	0	0.006	0.011	19.791	-0.085	-0.085	0.000	0.000	0.000	0.000
13	X	52	PHE	0	0.019	-0.016	23.228	0.064	0.064	0.000	0.000	0.000	0.000
14	X	53	LEU	0	-0.051	-0.007	23.589	0.024	0.024	0.000	0.000	0.000	0.000
15	X	54	ASP	-1	-0.821	-0.891	24.885	11.370	11.370	0.000	0.000	0.000	0.000
16	X	55	ILE	0	-0.059	-0.046	27.344	0.116	0.116	0.000	0.000	0.000	0.000
17	X	56	ILE	0	0.041	0.024	26.215	-0.272	-0.272	0.000	0.000	0.000	0.000
18	X	57	PRO	0	0.032	0.027	30.247	-0.033	-0.033	0.000	0.000	0.000	0.000
19	X	58	LEU	0	-0.033	-0.012	32.549	0.139	0.139	0.000	0.000	0.000	0.000
20	X	59	SER	0	-0.062	-0.027	34.381	0.071	0.071	0.000	0.000	0.000	0.000
21	X	60	GLN	0	0.009	0.012	32.197	0.082	0.082	0.000	0.000	0.000	0.000
22	X	61	PRO	0	0.021	0.027	31.054	0.235	0.235	0.000	0.000	0.000	0.000
23	X	62	LEU	0	0.021	0.000	23.886	0.082	0.082	0.000	0.000	0.000	0.000
24	X	63	GLU	-1	-0.974	-0.995	27.047	9.367	9.367	0.000	0.000	0.000	0.000
25	X	64	PHE	0	0.023	0.021	20.158	0.018	0.018	0.000	0.000	0.000	0.000
26	X	65	ARG	1	0.927	0.952	24.473	-9.850	-9.850	0.000	0.000	0.000	0.000
27	X	66	ARG	1	0.895	0.948	16.835	-15.444	-15.444	0.000	0.000	0.000	0.000
28	X	67	GLU	-1	-0.905	-0.964	23.812	11.067	11.067	0.000	0.000	0.000	0.000
29	X	68	GLY	0	-0.008	-0.007	24.773	0.365	0.365	0.000	0.000	0.000	0.000
30	X	69	LEU	0	-0.055	-0.013	22.027	0.244	0.244	0.000	0.000	0.000	0.000
31	X	70	GLN	0	0.015	0.002	25.348	-0.119	-0.119	0.000	0.000	0.000	0.000
32	X	71	HIS	0	0.043	0.004	27.339	0.175	0.175	0.000	0.000	0.000	0.000
33	X	72	GLY	0	0.022	0.012	29.076	-0.117	-0.117	0.000	0.000	0.000	0.000
34	X	73	VAL	0	-0.046	-0.019	23.214	0.061	0.061	0.000	0.000	0.000	0.000
35	X	74	LEU	0	0.038	0.003	25.463	0.252	0.252	0.000	0.000	0.000	0.000
36	X	75	ASP	-1	-0.860	-0.930	27.604	9.322	9.322	0.000	0.000	0.000	0.000
37	X	76	LYS	1	0.770	0.900	19.857	-13.806	-13.806	0.000	0.000	0.000	0.000
38	X	77	LEU	0	-0.015	-0.006	23.072	0.241	0.241	0.000	0.000	0.000	0.000
39	X	78	ARG	1	0.954	0.996	25.942	-8.739	-8.739	0.000	0.000	0.000	0.000
40	X	79	SER	0	-0.025	-0.017	29.318	-0.223	-0.223	0.000	0.000	0.000	0.000
41	X	80	GLY	0	0.030	0.039	25.463	0.036	0.036	0.000	0.000	0.000	0.000
42	X	81	LYS	1	0.917	0.958	24.826	-11.671	-11.671	0.000	0.000	0.000	0.000
43	X	82	TYR	0	-0.009	-0.023	22.242	0.709	0.709	0.000	0.000	0.000	0.000
44	X	83	PRO	0	-0.026	-0.003	21.812	-0.355	-0.355	0.000	0.000	0.000	0.000
45	X	84	GLN	0	0.067	0.024	22.514	0.022	0.022	0.000	0.000	0.000	0.000
46	X	85	GLN	0	0.058	0.031	18.217	-0.219	-0.219	0.000	0.000	0.000	0.000
47	X	86	ALA	0	-0.022	0.002	17.572	0.912	0.912	0.000	0.000	0.000	0.000
48	X	87	SER	0	-0.057	-0.039	19.067	-0.432	-0.432	0.000	0.000	0.000	0.000
49	X	88	LEU	0	0.059	0.044	15.570	0.253	0.253	0.000	0.000	0.000	0.000
50	X	89	ASN	0	-0.022	-0.029	18.942	-0.687	-0.687	0.000	0.000	0.000	0.000
51	X	90	LEU	0	0.054	0.018	17.509	0.301	0.301	0.000	0.000	0.000	0.000
52	X	91	LEU	0	-0.046	-0.017	21.415	-0.423	-0.423	0.000	0.000	0.000	0.000
53	X	92	ARG	1	0.902	0.938	24.420	-10.483	-10.483	0.000	0.000	0.000	0.000
54	X	93	GLN	0	0.076	0.062	20.262	-0.068	-0.068	0.000	0.000	0.000	0.000
55	X	94	PRO	0	0.042	0.023	20.897	-0.269	-0.269	0.000	0.000	0.000	0.000
56	X	95	VAL	0	0.064	0.023	20.077	0.520	0.520	0.000	0.000	0.000	0.000
57	X	96	GLU	-1	-0.780	-0.866	14.489	18.773	18.773	0.000	0.000	0.000	0.000
58	X	97	GLU	-1	-0.835	-0.898	15.682	18.882	18.882	0.000	0.000	0.000	0.000
59	X	98	CYS	0	-0.058	-0.027	15.941	0.598	0.598	0.000	0.000	0.000	0.000
60	X	99	ARG	1	0.831	0.888	12.039	-19.557	-19.557	0.000	0.000	0.000	0.000
61	X	100	LYS	1	0.815	0.895	11.543	-17.754	-17.754	0.000	0.000	0.000	0.000
62	X	101	MET	0	-0.024	-0.011	11.149	1.279	1.279	0.000	0.000	0.000	0.000
63	X	102	VAL	0	0.023	0.008	12.716	0.580	0.580	0.000	0.000	0.000	0.000
64	X	103	PHE	0	0.024	0.029	5.352	-0.257	-0.257	0.000	0.000	0.000	0.000
65	X	104	SER	0	-0.020	-0.020	7.700	0.854	0.854	0.000	0.000	0.000	0.000
66	X	105	PHE	0	-0.018	-0.012	8.921	0.643	0.643	0.000	0.000	0.000	0.000
67	X	106	ILE	0	-0.024	-0.013	10.431	-0.325	-0.325	0.000	0.000	0.000	0.000
68	X	107	GLN	0	0.018	0.008	5.293	0.468	0.468	0.000	0.000	0.000	0.000
69	X	108	GLN	0	-0.071	-0.029	7.469	0.364	0.364	0.000	0.000	0.000	0.000
70	X	109	ALA	0	0.017	-0.002	9.438	-1.007	-1.007	0.000	0.000	0.000	0.000
71	X	110	LEU	0	-0.027	-0.016	9.034	-1.419	-1.419	0.000	0.000	0.000	0.000
72	X	111	ALA	0	-0.008	0.008	7.465	-1.041	-1.041	0.000	0.000	0.000	0.000
73	X	112	ASP	-1	-0.869	-0.917	9.473	21.160	21.160	0.000	0.000	0.000	0.000
74	X	113	GLY	0	-0.071	-0.035	12.838	-1.888	-1.888	0.000	0.000	0.000	0.000
75	X	114	LEU	0	0.004	0.008	14.468	-1.827	-1.827	0.000	0.000	0.000	0.000
76	X	115	ARG	1	0.946	0.976	15.905	-12.791	-12.791	0.000	0.000	0.000	0.000
77	X	116	ASN	0	-0.040	-0.030	18.624	-0.385	-0.385	0.000	0.000	0.000	0.000
78	X	117	VAL	0	0.043	0.037	15.791	0.072	0.072	0.000	0.000	0.000	0.000
79	X	118	LEU	0	-0.063	-0.030	19.096	-0.531	-0.531	0.000	0.000	0.000	0.000
80	X	119	ILE	0	0.042	0.020	16.850	0.444	0.444	0.000	0.000	0.000	0.000
81	X	120	ILE	0	-0.012	-0.011	20.866	-0.705	-0.705	0.000	0.000	0.000	0.000
82	X	121	HIS	0	0.053	0.014	23.086	0.392	0.392	0.000	0.000	0.000	0.000
83	X	122	GLY	0	-0.010	-0.009	24.525	-0.204	-0.204	0.000	0.000	0.000	0.000
84	X	123	LYS	1	0.908	0.962	28.220	-9.074	-9.074	0.000	0.000	0.000	0.000
85	X	124	GLY	0	0.041	0.025	31.547	-0.025	-0.025	0.000	0.000	0.000	0.000
86	X	125	ARG	1	0.848	0.907	32.915	-8.711	-8.711	0.000	0.000	0.000	0.000
87	X	126	ASP	-1	-0.764	-0.890	35.389	8.423	8.423	0.000	0.000	0.000	0.000
88	X	127	ASP	-1	-0.789	-0.891	33.587	8.943	8.943	0.000	0.000	0.000	0.000
89	X	128	LYS	1	0.906	0.966	31.961	-8.563	-8.563	0.000	0.000	0.000	0.000
90	X	129	SER	0	-0.031	-0.007	32.030	0.186	0.186	0.000	0.000	0.000	0.000
91	X	130	HIS	0	0.012	-0.014	24.436	-0.129	-0.129	0.000	0.000	0.000	0.000
92	X	131	ALA	0	0.006	-0.002	27.015	0.355	0.355	0.000	0.000	0.000	0.000
93	X	132	ASN	0	0.000	-0.011	27.053	0.394	0.394	0.000	0.000	0.000	0.000
94	X	133	ILE	0	0.015	0.032	25.021	0.192	0.192	0.000	0.000	0.000	0.000
95	X	134	VAL	0	0.028	0.000	21.770	0.427	0.427	0.000	0.000	0.000	0.000
96	X	135	ARG	1	0.764	0.872	22.728	-9.618	-9.618	0.000	0.000	0.000	0.000
97	X	136	SER	0	0.001	-0.012	23.962	0.092	0.092	0.000	0.000	0.000	0.000
98	X	137	TYR	0	0.065	0.028	20.219	0.113	0.113	0.000	0.000	0.000	0.000
99	X	138	VAL	0	-0.026	-0.005	19.112	0.610	0.610	0.000	0.000	0.000	0.000
100	X	139	ALA	0	-0.004	-0.002	19.604	0.427	0.427	0.000	0.000	0.000	0.000
101	X	140	ARG	1	0.857	0.942	19.206	-13.143	-13.143	0.000	0.000	0.000	0.000
102	X	141	TRP	0	-0.038	-0.031	15.558	0.427	0.427	0.000	0.000	0.000	0.000
103	X	142	LEU	0	-0.010	-0.003	15.474	0.865	0.865	0.000	0.000	0.000	0.000
104	X	143	THR	0	-0.051	-0.033	16.529	0.230	0.230	0.000	0.000	0.000	0.000
105	X	144	GLU	-1	-0.745	-0.867	14.532	16.773	16.773	0.000	0.000	0.000	0.000
106	X	145	PHE	0	-0.001	0.012	9.419	1.038	1.038	0.000	0.000	0.000	0.000
107	X	146	ASP	-1	-0.783	-0.877	12.583	16.857	16.857	0.000	0.000	0.000	0.000
108	X	147	ASP	-1	-0.848	-0.908	11.113	20.686	20.686	0.000	0.000	0.000	0.000
109	X	148	VAL	0	-0.025	0.005	14.097	-0.737	-0.737	0.000	0.000	0.000	0.000
110	X	149	GLN	0	-0.012	-0.012	16.524	-0.558	-0.558	0.000	0.000	0.000	0.000
111	X	150	ALA	0	0.031	-0.003	20.000	-0.600	-0.600	0.000	0.000	0.000	0.000
112	X	151	TYR	0	-0.018	-0.012	20.408	0.327	0.327	0.000	0.000	0.000	0.000
113	X	152	CYS	0	-0.024	-0.010	23.114	-0.381	-0.381	0.000	0.000	0.000	0.000
114	X	153	THR	0	-0.003	0.012	26.017	0.257	0.257	0.000	0.000	0.000	0.000
115	X	154	ALA	0	0.014	0.022	26.768	-0.108	-0.108	0.000	0.000	0.000	0.000
116	X	155	LEU	0	0.061	0.022	28.528	-0.380	-0.380	0.000	0.000	0.000	0.000
117	X	156	PRO	0	0.014	-0.017	31.123	0.228	0.228	0.000	0.000	0.000	0.000
118	X	157	HIS	0	-0.014	0.006	30.669	-0.155	-0.155	0.000	0.000	0.000	0.000
119	X	158	HIS	0	0.025	0.027	27.398	0.080	0.080	0.000	0.000	0.000	0.000
120	X	159	GLY	0	0.053	0.027	27.901	0.365	0.365	0.000	0.000	0.000	0.000
121	X	160	GLY	0	-0.039	-0.015	30.086	-0.164	-0.164	0.000	0.000	0.000	0.000
122	X	161	SER	0	0.051	0.003	29.651	0.290	0.290	0.000	0.000	0.000	0.000
123	X	162	GLY	0	-0.071	-0.033	29.111	0.067	0.067	0.000	0.000	0.000	0.000
124	X	163	ALA	0	-0.003	0.008	25.235	0.372	0.372	0.000	0.000	0.000	0.000
125	X	164	CYS	0	-0.016	0.005	22.626	-0.226	-0.226	0.000	0.000	0.000	0.000
126	X	165	TYR	0	0.025	0.000	22.612	0.330	0.330	0.000	0.000	0.000	0.000
127	X	166	VAL	0	0.064	0.020	17.420	-0.162	-0.162	0.000	0.000	0.000	0.000
128	X	167	ALA	0	-0.063	-0.030	19.957	0.128	0.128	0.000	0.000	0.000	0.000
129	X	168	LEU	0	0.034	0.008	13.985	0.084	0.084	0.000	0.000	0.000	0.000
130	X	169	ARG	1	0.756	0.833	13.920	-18.936	-18.936	0.000	0.000	0.000	0.000
131	X	170	LYS	1	0.866	0.933	14.591	-15.772	-15.772	0.000	0.000	0.000	0.000

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