FMO DATABASE

FMODB ID: 6NQ8Z

Calculation Name: 3GPR-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GPR

Chain ID: C

ChEMBL ID:

UniProt ID: P81397

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1170108.847058
FMO2-HF: Nuclear repulsion	1113577.955431
FMO2-HF: Total energy	-56530.891627
FMO2-MP2: Total energy	-56689.569004

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(C:3002:PHE)

Summations of interaction energy for fragment #1(C:3002:PHE)

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.
-3.764	-0.418	0.086	-1.114	-2.319	0.003

Interaction energy analysis for fragmet #1(C:3002:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.012

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	C	3004	CYS	0	-0.043	-0.002	3.810	-0.978	0.087	-0.004	-0.464	-0.597	0.001
4	C	3005	LEU	0	0.049	0.027	5.987	0.224	0.224	0.000	0.000	0.000	0.000
5	C	3006	PRO	0	0.028	-0.001	9.162	0.040	0.040	0.000	0.000	0.000	0.000
6	C	3007	GLY	0	0.020	0.012	12.225	0.039	0.039	0.000	0.000	0.000	0.000
7	C	3008	TRP	0	-0.031	-0.004	9.675	0.006	0.006	0.000	0.000	0.000	0.000
8	C	3009	SER	0	0.013	0.016	9.644	-0.073	-0.073	0.000	0.000	0.000	0.000
9	C	3010	ALA	0	0.020	-0.010	7.086	-0.052	-0.052	0.000	0.000	0.000	0.000
10	C	3011	TYR	0	-0.045	-0.011	8.435	0.078	0.078	0.000	0.000	0.000	0.000
11	C	3012	ASP	-1	-0.918	-0.956	5.510	-0.865	-0.865	0.000	0.000	0.000	0.000
12	C	3013	GLN	0	0.026	0.003	3.291	-1.509	-0.226	0.053	-0.371	-0.965	0.002
13	C	3014	HIS	0	-0.008	-0.001	5.683	-0.163	-0.163	0.000	0.000	0.000	0.000
14	C	3016	TYR	0	-0.003	-0.031	8.757	0.091	0.091	0.000	0.000	0.000	0.000
15	C	3017	GLN	0	0.000	-0.028	12.432	-0.017	-0.017	0.000	0.000	0.000	0.000
16	C	3018	ALA	0	-0.029	-0.010	15.073	0.014	0.014	0.000	0.000	0.000	0.000
17	C	3019	PHE	0	0.032	0.032	17.265	0.010	0.010	0.000	0.000	0.000	0.000
18	C	3020	ASN	0	-0.035	-0.035	21.109	0.003	0.003	0.000	0.000	0.000	0.000
19	C	3021	GLU	-1	-0.860	-0.919	24.454	-0.116	-0.116	0.000	0.000	0.000	0.000
20	C	3022	PRO	0	-0.048	-0.021	25.762	-0.008	-0.008	0.000	0.000	0.000	0.000
21	C	3023	LYS	1	0.872	0.931	24.783	0.135	0.135	0.000	0.000	0.000	0.000
22	C	3024	THR	0	0.020	0.009	28.839	0.002	0.002	0.000	0.000	0.000	0.000
23	C	3025	TRP	0	0.028	0.021	25.617	-0.009	-0.009	0.000	0.000	0.000	0.000
24	C	3026	ASP	-1	-0.878	-0.972	26.463	-0.107	-0.107	0.000	0.000	0.000	0.000
25	C	3027	GLU	-1	-0.923	-0.972	25.797	-0.104	-0.104	0.000	0.000	0.000	0.000
26	C	3028	ALA	0	0.013	0.009	23.716	-0.009	-0.009	0.000	0.000	0.000	0.000
27	C	3029	GLU	-1	-0.744	-0.886	20.719	-0.202	-0.202	0.000	0.000	0.000	0.000
28	C	3030	ARG	1	0.871	0.938	20.902	0.100	0.100	0.000	0.000	0.000	0.000
29	C	3031	PHE	0	0.024	0.025	20.577	-0.001	-0.001	0.000	0.000	0.000	0.000
30	C	3032	CYS	0	-0.052	0.002	15.197	0.005	0.005	0.000	0.000	0.000	0.000
31	C	3033	THR	0	0.029	-0.003	16.152	-0.024	-0.024	0.000	0.000	0.000	0.000
32	C	3034	GLU	-1	-1.025	-0.987	17.068	-0.144	-0.144	0.000	0.000	0.000	0.000
33	C	3035	GLN	0	-0.045	-0.022	14.309	-0.020	-0.020	0.000	0.000	0.000	0.000
34	C	3036	ALA	0	-0.008	0.000	10.723	0.003	0.003	0.000	0.000	0.000	0.000
35	C	3037	LYS	1	0.953	0.988	7.276	0.533	0.533	0.000	0.000	0.000	0.000
36	C	3038	ARG	1	0.931	0.953	10.379	0.256	0.256	0.000	0.000	0.000	0.000
37	C	3039	GLY	0	-0.020	-0.017	13.007	-0.002	-0.002	0.000	0.000	0.000	0.000
38	C	3040	HIS	0	-0.019	-0.019	13.961	0.020	0.020	0.000	0.000	0.000	0.000
39	C	3041	LEU	0	0.004	0.003	16.148	-0.028	-0.028	0.000	0.000	0.000	0.000
40	C	3042	VAL	0	-0.055	-0.012	16.444	-0.010	-0.010	0.000	0.000	0.000	0.000
41	C	3043	SER	0	0.041	0.013	16.598	0.018	0.018	0.000	0.000	0.000	0.000
42	C	3044	ILE	0	-0.054	-0.023	17.183	-0.014	-0.014	0.000	0.000	0.000	0.000
43	C	3045	GLY	0	0.039	0.021	17.927	0.015	0.015	0.000	0.000	0.000	0.000
44	C	3046	SER	0	0.001	-0.010	15.742	0.010	0.010	0.000	0.000	0.000	0.000
45	C	3047	ASP	-1	-0.862	-0.930	18.271	-0.123	-0.123	0.000	0.000	0.000	0.000
46	C	3048	GLY	0	0.003	0.003	17.017	0.002	0.002	0.000	0.000	0.000	0.000
47	C	3049	GLU	-1	-0.866	-0.932	13.340	-0.293	-0.293	0.000	0.000	0.000	0.000
48	C	3050	ALA	0	-0.003	-0.004	16.494	-0.007	-0.007	0.000	0.000	0.000	0.000
49	C	3051	ASP	-1	-0.862	-0.944	20.057	-0.128	-0.128	0.000	0.000	0.000	0.000
50	C	3052	PHE	0	0.002	0.017	12.220	0.001	0.001	0.000	0.000	0.000	0.000
51	C	3053	VAL	0	0.067	0.030	16.131	-0.008	-0.008	0.000	0.000	0.000	0.000
52	C	3054	ALA	0	-0.045	-0.013	18.196	0.006	0.006	0.000	0.000	0.000	0.000
53	C	3055	GLN	0	0.005	-0.005	19.262	0.005	0.005	0.000	0.000	0.000	0.000
54	C	3056	LEU	0	0.041	0.041	13.772	0.007	0.007	0.000	0.000	0.000	0.000
55	C	3057	VAL	0	0.010	-0.002	18.281	0.007	0.007	0.000	0.000	0.000	0.000
56	C	3058	THR	0	-0.044	-0.007	20.766	0.010	0.010	0.000	0.000	0.000	0.000
57	C	3059	ASN	0	-0.067	-0.037	19.516	0.000	0.000	0.000	0.000	0.000	0.000
58	C	3060	ASN	0	0.002	-0.011	18.333	0.003	0.003	0.000	0.000	0.000	0.000
59	C	3061	ILE	0	-0.090	-0.043	22.092	0.009	0.009	0.000	0.000	0.000	0.000
60	C	3062	LYS	1	0.939	0.953	25.062	0.101	0.101	0.000	0.000	0.000	0.000
61	C	3063	ARG	1	0.951	0.962	25.637	0.088	0.088	0.000	0.000	0.000	0.000
62	C	3064	PRO	0	-0.026	0.028	27.359	0.003	0.003	0.000	0.000	0.000	0.000
63	C	3065	GLU	-1	-0.915	-0.952	29.218	-0.075	-0.075	0.000	0.000	0.000	0.000
64	C	3066	LEU	0	0.005	-0.032	25.227	-0.002	-0.002	0.000	0.000	0.000	0.000
65	C	3067	TYR	0	-0.018	-0.015	28.063	-0.003	-0.003	0.000	0.000	0.000	0.000
66	C	3068	VAL	0	-0.019	-0.001	21.816	-0.004	-0.004	0.000	0.000	0.000	0.000
67	C	3069	TRP	0	0.042	0.014	24.392	0.003	0.003	0.000	0.000	0.000	0.000
68	C	3070	ILE	0	-0.032	-0.017	21.922	-0.013	-0.013	0.000	0.000	0.000	0.000
69	C	3071	GLY	0	0.063	0.029	22.227	-0.004	-0.004	0.000	0.000	0.000	0.000
70	C	3072	LEU	0	-0.055	-0.019	23.291	0.001	0.001	0.000	0.000	0.000	0.000
71	C	3073	ARG	1	0.867	0.941	26.136	0.106	0.106	0.000	0.000	0.000	0.000
72	C	3074	ASP	-1	-0.870	-0.903	28.863	-0.078	-0.078	0.000	0.000	0.000	0.000
73	C	3075	ARG	1	0.870	0.928	31.719	0.076	0.076	0.000	0.000	0.000	0.000
74	C	3076	ARG	1	0.970	0.992	35.322	0.060	0.060	0.000	0.000	0.000	0.000
75	C	3077	LYS	1	0.833	0.897	37.219	0.051	0.051	0.000	0.000	0.000	0.000
76	C	3078	GLU	-1	-0.873	-0.919	34.505	-0.063	-0.063	0.000	0.000	0.000	0.000
77	C	3079	GLN	0	0.027	0.016	33.064	0.000	0.000	0.000	0.000	0.000	0.000
78	C	3080	GLN	0	-0.077	-0.045	28.470	-0.005	-0.005	0.000	0.000	0.000	0.000
79	C	3081	CYS	0	0.026	0.007	31.108	-0.004	-0.004	0.000	0.000	0.000	0.000
80	C	3082	SER	0	-0.041	-0.039	32.289	0.004	0.004	0.000	0.000	0.000	0.000
81	C	3083	SER	0	-0.055	-0.041	33.736	0.003	0.003	0.000	0.000	0.000	0.000
82	C	3084	GLU	-1	-0.926	-0.956	33.821	-0.061	-0.061	0.000	0.000	0.000	0.000
83	C	3085	TRP	0	-0.009	-0.003	37.719	0.003	0.003	0.000	0.000	0.000	0.000
84	C	3086	SER	0	-0.007	-0.009	39.386	-0.001	-0.001	0.000	0.000	0.000	0.000
85	C	3087	MET	0	-0.008	-0.018	41.057	0.001	0.001	0.000	0.000	0.000	0.000
86	C	3088	SER	0	0.002	0.003	36.744	0.000	0.000	0.000	0.000	0.000	0.000
87	C	3089	ALA	0	-0.023	0.002	38.306	-0.001	-0.001	0.000	0.000	0.000	0.000
88	C	3090	SER	0	0.024	0.016	37.384	-0.001	-0.001	0.000	0.000	0.000	0.000
89	C	3091	ILE	0	-0.001	-0.003	37.956	0.003	0.003	0.000	0.000	0.000	0.000
90	C	3092	ILE	0	-0.005	-0.007	39.589	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	3093	TYR	0	-0.025	-0.017	42.340	0.002	0.002	0.000	0.000	0.000	0.000
92	C	3094	VAL	0	-0.002	0.005	42.143	0.000	0.000	0.000	0.000	0.000	0.000
93	C	3095	ASN	0	-0.006	-0.004	45.357	0.000	0.000	0.000	0.000	0.000	0.000
94	C	3096	TRP	0	0.020	0.012	39.873	0.001	0.001	0.000	0.000	0.000	0.000
95	C	3097	ASN	0	0.017	0.006	46.374	0.002	0.002	0.000	0.000	0.000	0.000
96	C	3098	THR	0	-0.012	-0.008	43.934	0.000	0.000	0.000	0.000	0.000	0.000
97	C	3099	GLY	0	0.040	0.022	44.956	0.000	0.000	0.000	0.000	0.000	0.000
98	C	3100	GLU	-1	-0.834	-0.900	42.349	-0.047	-0.047	0.000	0.000	0.000	0.000
99	C	3101	SER	0	-0.050	-0.030	39.586	-0.001	-0.001	0.000	0.000	0.000	0.000
100	C	3102	GLN	0	0.026	0.001	34.220	0.000	0.000	0.000	0.000	0.000	0.000
101	C	3103	MET	0	0.009	0.005	34.813	-0.001	-0.001	0.000	0.000	0.000	0.000
102	C	3104	CYS	0	-0.011	0.007	30.221	-0.006	-0.006	0.000	0.000	0.000	0.000
103	C	3105	GLN	0	0.021	0.003	28.242	-0.002	-0.002	0.000	0.000	0.000	0.000
104	C	3106	GLY	0	0.064	0.032	27.568	-0.004	-0.004	0.000	0.000	0.000	0.000
105	C	3107	LEU	0	-0.024	-0.007	22.816	-0.001	-0.001	0.000	0.000	0.000	0.000
106	C	3108	ALA	0	0.042	0.041	26.985	-0.003	-0.003	0.000	0.000	0.000	0.000
107	C	3109	ARG	1	0.843	0.922	23.465	0.119	0.119	0.000	0.000	0.000	0.000
108	C	3110	TRP	0	0.029	0.027	29.058	0.003	0.003	0.000	0.000	0.000	0.000
109	C	3111	THR	0	0.030	0.000	31.970	0.002	0.002	0.000	0.000	0.000	0.000
110	C	3112	GLY	0	-0.018	0.005	28.632	0.003	0.003	0.000	0.000	0.000	0.000
111	C	3113	PHE	0	0.094	0.033	26.153	-0.004	-0.004	0.000	0.000	0.000	0.000
112	C	3114	ARG	1	0.857	0.926	22.663	0.139	0.139	0.000	0.000	0.000	0.000
113	C	3115	LYS	1	0.845	0.938	27.368	0.080	0.080	0.000	0.000	0.000	0.000
114	C	3116	TRP	0	0.020	-0.005	23.716	-0.006	-0.006	0.000	0.000	0.000	0.000
115	C	3117	ASP	-1	-0.951	-0.963	29.325	-0.070	-0.070	0.000	0.000	0.000	0.000
116	C	3118	TYR	0	-0.009	-0.009	31.265	-0.005	-0.005	0.000	0.000	0.000	0.000
117	C	3119	SER	0	0.045	0.027	32.868	0.003	0.003	0.000	0.000	0.000	0.000
118	C	3120	ASP	-1	-0.887	-0.960	34.221	-0.069	-0.069	0.000	0.000	0.000	0.000
119	C	3122	GLN	0	-0.052	-0.023	32.326	-0.007	-0.007	0.000	0.000	0.000	0.000
120	C	3123	ALA	0	-0.008	0.013	32.698	0.003	0.003	0.000	0.000	0.000	0.000
121	C	3124	LYS	1	0.959	0.966	31.237	0.072	0.072	0.000	0.000	0.000	0.000
122	C	3125	ASN	0	-0.013	-0.006	29.032	0.006	0.006	0.000	0.000	0.000	0.000
123	C	3126	PRO	0	0.024	0.013	25.055	-0.005	-0.005	0.000	0.000	0.000	0.000
124	C	3127	PHE	0	-0.010	-0.007	20.404	0.005	0.005	0.000	0.000	0.000	0.000
125	C	3128	VAL	0	-0.005	-0.018	16.504	-0.002	-0.002	0.000	0.000	0.000	0.000
126	C	3130	LYS	1	0.878	0.932	12.465	0.276	0.276	0.000	0.000	0.000	0.000
127	C	3131	PHE	0	-0.065	-0.003	9.653	0.006	0.006	0.000	0.000	0.000	0.000
128	C	3132	SER	0	0.027	0.011	7.278	0.003	0.003	0.000	0.000	0.000	0.000
129	C	3133	SER	0	-0.010	-0.011	3.423	-0.667	-0.055	0.025	-0.212	-0.425	0.000
130	C	3134	GLU	-1	-0.975	-0.978	5.411	0.159	0.159	0.000	0.000	0.000	0.000
131	C	3135	CYS	0	0.007	0.008	4.423	-0.573	-0.187	0.012	-0.067	-0.332	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:3002:PHE)