FMO DATABASE

FMODB ID: Z6Q1N

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	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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1172763.045985
FMO2-HF: Nuclear repulsion	1116231.165401
FMO2-HF: Total energy	-56531.880584
FMO2-MP2: Total energy	-56690.524196

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.
-6.225	-1.033	1.162	-1.96	-4.396	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 : 0.024 / q_NPA : -0.007

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	-0.023	-0.008	3.905	-0.743	0.435	0.000	-0.507	-0.672	0.000
4	C	3005	LEU	0	0.055	0.036	5.924	0.293	0.293	0.000	0.000	0.000	0.000
5	C	3006	PRO	0	0.016	0.000	9.363	0.011	0.011	0.000	0.000	0.000	0.000
6	C	3007	GLY	0	0.027	0.009	12.331	0.017	0.017	0.000	0.000	0.000	0.000
7	C	3008	TRP	0	-0.038	-0.002	9.642	-0.003	-0.003	0.000	0.000	0.000	0.000
8	C	3009	SER	0	0.024	0.011	9.363	-0.086	-0.086	0.000	0.000	0.000	0.000
9	C	3010	ALA	0	0.019	-0.003	6.810	-0.034	-0.034	0.000	0.000	0.000	0.000
10	C	3011	TYR	0	-0.051	-0.018	7.881	0.116	0.116	0.000	0.000	0.000	0.000
11	C	3012	ASP	-1	-0.850	-0.929	4.766	-2.111	-1.919	-0.001	-0.015	-0.176	0.000
12	C	3013	GLN	0	-0.046	-0.021	2.916	-2.341	-0.264	0.382	-0.643	-1.817	0.000
13	C	3014	HIS	0	-0.005	0.003	5.031	-0.013	0.047	-0.001	-0.004	-0.055	0.000
14	C	3016	TYR	0	-0.001	-0.027	8.458	0.090	0.090	0.000	0.000	0.000	0.000
15	C	3017	GLN	0	-0.013	-0.022	12.195	0.010	0.010	0.000	0.000	0.000	0.000
16	C	3018	ALA	0	-0.020	-0.016	15.009	0.009	0.009	0.000	0.000	0.000	0.000
17	C	3019	PHE	0	0.031	0.028	17.254	0.011	0.011	0.000	0.000	0.000	0.000
18	C	3020	ASN	0	-0.033	-0.036	21.155	0.004	0.004	0.000	0.000	0.000	0.000
19	C	3021	GLU	-1	-0.824	-0.900	24.441	-0.065	-0.065	0.000	0.000	0.000	0.000
20	C	3022	PRO	0	-0.052	-0.019	25.884	-0.007	-0.007	0.000	0.000	0.000	0.000
21	C	3023	LYS	1	0.835	0.913	24.168	0.084	0.084	0.000	0.000	0.000	0.000
22	C	3024	THR	0	0.038	-0.001	28.534	-0.003	-0.003	0.000	0.000	0.000	0.000
23	C	3025	TRP	0	0.023	0.021	25.271	-0.005	-0.005	0.000	0.000	0.000	0.000
24	C	3026	ASP	-1	-0.812	-0.928	26.096	-0.082	-0.082	0.000	0.000	0.000	0.000
25	C	3027	GLU	-1	-0.902	-0.933	26.684	-0.061	-0.061	0.000	0.000	0.000	0.000
26	C	3028	ALA	0	-0.014	-0.008	23.515	-0.003	-0.003	0.000	0.000	0.000	0.000
27	C	3029	GLU	-1	-0.748	-0.875	20.387	-0.155	-0.155	0.000	0.000	0.000	0.000
28	C	3030	ARG	1	0.844	0.914	20.576	0.063	0.063	0.000	0.000	0.000	0.000
29	C	3031	PHE	0	0.047	0.037	20.567	-0.001	-0.001	0.000	0.000	0.000	0.000
30	C	3032	CYS	0	-0.082	0.007	15.374	0.006	0.006	0.000	0.000	0.000	0.000
31	C	3033	THR	0	-0.062	-0.050	16.228	-0.008	-0.008	0.000	0.000	0.000	0.000
32	C	3034	GLU	-1	-0.891	-0.920	17.281	-0.068	-0.068	0.000	0.000	0.000	0.000
33	C	3035	GLN	0	-0.044	-0.030	14.232	-0.014	-0.014	0.000	0.000	0.000	0.000
34	C	3036	ALA	0	-0.008	-0.006	11.865	0.008	0.008	0.000	0.000	0.000	0.000
35	C	3037	LYS	1	0.887	0.947	7.003	0.322	0.322	0.000	0.000	0.000	0.000
36	C	3038	ARG	1	0.918	0.948	10.722	0.118	0.118	0.000	0.000	0.000	0.000
37	C	3039	GLY	0	-0.014	-0.019	12.108	-0.028	-0.028	0.000	0.000	0.000	0.000
38	C	3040	HIS	0	0.014	0.005	13.797	0.030	0.030	0.000	0.000	0.000	0.000
39	C	3041	LEU	0	0.034	0.002	16.225	-0.022	-0.022	0.000	0.000	0.000	0.000
40	C	3042	VAL	0	-0.068	-0.023	16.535	-0.018	-0.018	0.000	0.000	0.000	0.000
41	C	3043	SER	0	0.043	0.018	16.598	0.012	0.012	0.000	0.000	0.000	0.000
42	C	3044	ILE	0	-0.064	-0.019	16.789	-0.026	-0.026	0.000	0.000	0.000	0.000
43	C	3045	GLY	0	0.040	0.022	16.799	0.019	0.019	0.000	0.000	0.000	0.000
44	C	3046	SER	0	-0.019	-0.019	15.543	0.007	0.007	0.000	0.000	0.000	0.000
45	C	3047	ASP	-1	-0.867	-0.932	17.570	-0.168	-0.168	0.000	0.000	0.000	0.000
46	C	3048	GLY	0	0.018	0.000	16.539	0.007	0.007	0.000	0.000	0.000	0.000
47	C	3049	GLU	-1	-0.835	-0.906	13.100	-0.389	-0.389	0.000	0.000	0.000	0.000
48	C	3050	ALA	0	-0.010	-0.009	16.005	0.007	0.007	0.000	0.000	0.000	0.000
49	C	3051	ASP	-1	-0.834	-0.930	19.706	-0.136	-0.136	0.000	0.000	0.000	0.000
50	C	3052	PHE	0	0.017	0.027	11.959	0.007	0.007	0.000	0.000	0.000	0.000
51	C	3053	VAL	0	0.060	0.023	15.459	0.007	0.007	0.000	0.000	0.000	0.000
52	C	3054	ALA	0	-0.027	-0.008	17.787	0.017	0.017	0.000	0.000	0.000	0.000
53	C	3055	GLN	0	-0.004	-0.011	19.164	0.011	0.011	0.000	0.000	0.000	0.000
54	C	3056	LEU	0	0.034	0.042	13.472	0.018	0.018	0.000	0.000	0.000	0.000
55	C	3057	VAL	0	0.014	0.006	18.035	0.014	0.014	0.000	0.000	0.000	0.000
56	C	3058	THR	0	-0.125	-0.063	20.633	0.016	0.016	0.000	0.000	0.000	0.000
57	C	3059	ASN	0	-0.053	-0.035	19.084	0.004	0.004	0.000	0.000	0.000	0.000
58	C	3060	ASN	0	0.004	0.008	18.077	0.015	0.015	0.000	0.000	0.000	0.000
59	C	3061	ILE	0	-0.052	-0.034	22.024	0.011	0.011	0.000	0.000	0.000	0.000
60	C	3062	LYS	1	0.942	0.966	25.092	0.073	0.073	0.000	0.000	0.000	0.000
61	C	3063	ARG	1	0.968	0.973	25.876	0.084	0.084	0.000	0.000	0.000	0.000
62	C	3064	PRO	0	-0.012	0.024	27.463	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	3065	GLU	-1	-0.844	-0.915	28.834	-0.072	-0.072	0.000	0.000	0.000	0.000
64	C	3066	LEU	0	0.001	-0.024	25.244	0.000	0.000	0.000	0.000	0.000	0.000
65	C	3067	TYR	0	-0.051	-0.014	27.829	-0.007	-0.007	0.000	0.000	0.000	0.000
66	C	3068	VAL	0	-0.010	0.000	21.738	0.000	0.000	0.000	0.000	0.000	0.000
67	C	3069	TRP	0	0.039	0.013	24.331	-0.003	-0.003	0.000	0.000	0.000	0.000
68	C	3070	ILE	0	-0.022	-0.018	21.731	-0.009	-0.009	0.000	0.000	0.000	0.000
69	C	3071	GLY	0	0.056	0.030	21.780	-0.006	-0.006	0.000	0.000	0.000	0.000
70	C	3072	LEU	0	-0.053	-0.010	22.770	0.003	0.003	0.000	0.000	0.000	0.000
71	C	3073	ARG	1	0.843	0.922	25.892	0.085	0.085	0.000	0.000	0.000	0.000
72	C	3074	ASP	-1	-0.783	-0.852	29.036	-0.076	-0.076	0.000	0.000	0.000	0.000
73	C	3075	ARG	1	0.877	0.924	31.996	0.065	0.065	0.000	0.000	0.000	0.000
74	C	3076	ARG	1	0.886	0.938	35.355	0.064	0.064	0.000	0.000	0.000	0.000
75	C	3077	LYS	1	0.826	0.898	37.115	0.044	0.044	0.000	0.000	0.000	0.000
76	C	3078	GLU	-1	-0.854	-0.908	34.137	-0.051	-0.051	0.000	0.000	0.000	0.000
77	C	3079	GLN	0	0.049	0.013	32.859	-0.001	-0.001	0.000	0.000	0.000	0.000
78	C	3080	GLN	0	-0.084	-0.051	28.131	-0.002	-0.002	0.000	0.000	0.000	0.000
79	C	3081	CYS	0	0.033	0.027	30.390	-0.007	-0.007	0.000	0.000	0.000	0.000
80	C	3082	SER	0	-0.039	-0.041	31.944	0.004	0.004	0.000	0.000	0.000	0.000
81	C	3083	SER	0	-0.073	-0.040	33.560	0.002	0.002	0.000	0.000	0.000	0.000
82	C	3084	GLU	-1	-0.905	-0.960	33.457	-0.071	-0.071	0.000	0.000	0.000	0.000
83	C	3085	TRP	0	-0.005	0.013	37.448	0.001	0.001	0.000	0.000	0.000	0.000
84	C	3086	SER	0	-0.009	-0.013	39.123	-0.001	-0.001	0.000	0.000	0.000	0.000
85	C	3087	MET	0	-0.035	-0.028	40.714	0.001	0.001	0.000	0.000	0.000	0.000
86	C	3088	SER	0	0.012	0.005	36.054	0.000	0.000	0.000	0.000	0.000	0.000
87	C	3089	ALA	0	-0.030	0.002	37.580	0.000	0.000	0.000	0.000	0.000	0.000
88	C	3090	SER	0	0.034	0.017	36.601	-0.001	-0.001	0.000	0.000	0.000	0.000
89	C	3091	ILE	0	-0.014	-0.014	37.149	0.003	0.003	0.000	0.000	0.000	0.000
90	C	3092	ILE	0	0.002	-0.003	38.837	0.000	0.000	0.000	0.000	0.000	0.000
91	C	3093	TYR	0	-0.024	-0.013	41.650	0.002	0.002	0.000	0.000	0.000	0.000
92	C	3094	VAL	0	-0.002	0.002	41.597	-0.001	-0.001	0.000	0.000	0.000	0.000
93	C	3095	ASN	0	-0.026	-0.015	44.706	0.002	0.002	0.000	0.000	0.000	0.000
94	C	3096	TRP	0	0.012	0.009	39.876	0.000	0.000	0.000	0.000	0.000	0.000
95	C	3097	ASN	0	0.015	0.000	46.132	0.002	0.002	0.000	0.000	0.000	0.000
96	C	3098	THR	0	-0.018	0.001	43.687	0.000	0.000	0.000	0.000	0.000	0.000
97	C	3099	GLY	0	0.048	0.020	45.258	0.000	0.000	0.000	0.000	0.000	0.000
98	C	3100	GLU	-1	-0.816	-0.889	42.104	-0.042	-0.042	0.000	0.000	0.000	0.000
99	C	3101	SER	0	-0.041	-0.025	39.204	0.000	0.000	0.000	0.000	0.000	0.000
100	C	3102	GLN	0	0.007	-0.003	33.732	-0.001	-0.001	0.000	0.000	0.000	0.000
101	C	3103	MET	0	-0.017	-0.002	34.357	0.002	0.002	0.000	0.000	0.000	0.000
102	C	3104	CYS	0	-0.074	-0.025	29.989	-0.007	-0.007	0.000	0.000	0.000	0.000
103	C	3105	GLN	0	0.040	0.014	27.881	-0.003	-0.003	0.000	0.000	0.000	0.000
104	C	3106	GLY	0	0.018	-0.002	26.907	-0.003	-0.003	0.000	0.000	0.000	0.000
105	C	3107	LEU	0	-0.018	-0.006	22.577	-0.002	-0.002	0.000	0.000	0.000	0.000
106	C	3108	ALA	0	0.045	0.023	26.614	-0.002	-0.002	0.000	0.000	0.000	0.000
107	C	3109	ARG	1	0.790	0.882	23.587	0.110	0.110	0.000	0.000	0.000	0.000
108	C	3110	TRP	0	0.057	0.039	28.949	0.005	0.005	0.000	0.000	0.000	0.000
109	C	3111	THR	0	0.018	-0.006	31.904	0.004	0.004	0.000	0.000	0.000	0.000
110	C	3112	GLY	0	-0.038	-0.011	28.578	0.000	0.000	0.000	0.000	0.000	0.000
111	C	3113	PHE	0	0.096	0.044	25.838	0.000	0.000	0.000	0.000	0.000	0.000
112	C	3114	ARG	1	0.831	0.922	22.467	0.137	0.137	0.000	0.000	0.000	0.000
113	C	3115	LYS	1	0.845	0.932	27.017	0.091	0.091	0.000	0.000	0.000	0.000
114	C	3116	TRP	0	0.004	-0.002	22.912	0.000	0.000	0.000	0.000	0.000	0.000
115	C	3117	ASP	-1	-0.900	-0.942	28.956	-0.071	-0.071	0.000	0.000	0.000	0.000
116	C	3118	TYR	0	-0.032	-0.025	30.642	-0.005	-0.005	0.000	0.000	0.000	0.000
117	C	3119	SER	0	0.003	0.005	32.843	0.003	0.003	0.000	0.000	0.000	0.000
118	C	3120	ASP	-1	-0.847	-0.939	34.299	-0.057	-0.057	0.000	0.000	0.000	0.000
119	C	3122	GLN	0	-0.014	-0.014	32.191	-0.004	-0.004	0.000	0.000	0.000	0.000
120	C	3123	ALA	0	0.022	0.034	32.924	0.002	0.002	0.000	0.000	0.000	0.000
121	C	3124	LYS	1	0.867	0.925	30.913	0.056	0.056	0.000	0.000	0.000	0.000
122	C	3125	ASN	0	0.002	0.007	28.647	0.005	0.005	0.000	0.000	0.000	0.000
123	C	3126	PRO	0	0.004	0.005	25.122	-0.002	-0.002	0.000	0.000	0.000	0.000
124	C	3127	PHE	0	0.003	-0.002	20.580	-0.001	-0.001	0.000	0.000	0.000	0.000
125	C	3128	VAL	0	0.012	-0.006	16.259	0.000	0.000	0.000	0.000	0.000	0.000
126	C	3130	LYS	1	0.818	0.900	12.215	0.320	0.320	0.000	0.000	0.000	0.000
127	C	3131	PHE	0	-0.023	0.010	9.400	0.024	0.024	0.000	0.000	0.000	0.000
128	C	3132	SER	0	0.046	0.022	7.004	-0.042	-0.042	0.000	0.000	0.000	0.000
129	C	3133	SER	0	0.015	0.016	2.577	-0.952	0.081	0.763	-0.674	-1.122	0.003
130	C	3134	GLU	-1	-0.974	-0.986	4.401	-0.008	0.119	-0.001	-0.030	-0.095	0.000
131	C	3135	CYS	0	-0.007	0.004	4.296	-0.682	-0.157	0.020	-0.087	-0.459	0.000

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