FMO DATABASE

FMODB ID: 493KN

Calculation Name: 3GGN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GGN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RZE3

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptH
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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1128259.206207
FMO2-HF: Nuclear repulsion	1077838.371341
FMO2-HF: Total energy	-50420.834866
FMO2-MP2: Total energy	-50570.530802

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:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-19.952	-21.262	22.927	-10.737	-10.881	-0.064

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.026

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	A	5	VAL	0	0.046	0.039	3.807	-1.624	0.623	-0.025	-1.062	-1.160	0.002
4	A	6	ARG	1	0.913	0.943	6.205	-0.488	-0.488	0.000	0.000	0.000	0.000
5	A	7	ASP	-1	-0.794	-0.892	9.743	0.253	0.253	0.000	0.000	0.000	0.000
6	A	8	ALA	0	-0.046	-0.032	12.981	-0.016	-0.016	0.000	0.000	0.000	0.000
7	A	9	VAL	0	0.017	0.016	16.686	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.023	0.002	19.994	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	11	ILE	0	0.003	-0.009	22.413	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	12	GLY	0	0.013	0.027	25.970	0.000	0.000	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.912	0.948	28.126	-0.038	-0.038	0.000	0.000	0.000	0.000
12	A	14	PRO	0	0.004	-0.001	28.813	0.006	0.006	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.069	0.032	26.420	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.868	-0.951	26.554	0.031	0.031	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.062	-0.024	28.419	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.016	-0.009	23.675	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	19	TYR	0	-0.025	-0.030	23.395	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	20	ALA	0	0.012	-0.007	23.903	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.044	-0.010	22.778	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	22	TRP	0	0.032	-0.004	15.304	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.837	0.915	20.684	0.025	0.025	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.884	-0.922	22.942	-0.050	-0.050	0.000	0.000	0.000	0.000
23	A	25	LEU	0	-0.012	-0.024	18.866	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	26	PRO	0	0.005	0.004	20.109	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.049	0.034	22.078	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	28	LEU	0	0.005	-0.004	16.068	0.011	0.011	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.069	-0.020	16.767	0.018	0.018	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.013	0.003	17.848	0.010	0.010	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.062	-0.026	17.661	0.015	0.015	0.000	0.000	0.000	0.000
30	A	32	MET	0	-0.058	-0.031	11.425	0.018	0.018	0.000	0.000	0.000	0.000
31	A	33	THR	0	0.031	0.001	14.535	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	34	HIS	0	-0.033	0.000	9.403	0.043	0.043	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.068	-0.034	12.100	-0.083	-0.083	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.869	0.925	14.323	0.165	0.165	0.000	0.000	0.000	0.000
35	A	37	SER	0	-0.030	-0.041	17.239	0.013	0.013	0.000	0.000	0.000	0.000
36	A	38	VAL	0	0.024	0.020	16.567	-0.033	-0.033	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.927	-0.959	19.179	-0.109	-0.109	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.007	0.001	21.755	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.075	-0.037	21.813	0.002	0.002	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.842	-0.916	24.709	-0.092	-0.092	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.900	-0.952	25.058	-0.053	-0.053	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.859	0.930	19.908	0.087	0.087	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.915	0.970	20.686	0.113	0.113	0.000	0.000	0.000	0.000
44	A	46	SER	0	0.026	0.023	18.729	0.010	0.010	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.917	0.964	18.513	0.149	0.149	0.000	0.000	0.000	0.000
46	A	48	TRP	0	-0.015	-0.018	12.655	0.009	0.009	0.000	0.000	0.000	0.000
47	A	49	THR	0	0.002	-0.009	15.709	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	50	VAL	0	0.015	0.017	11.196	0.029	0.029	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.796	-0.904	14.377	-0.188	-0.188	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.054	-0.026	14.029	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	53	PRO	0	0.027	0.013	14.656	0.034	0.034	0.000	0.000	0.000	0.000
52	A	54	ALA	0	0.012	0.038	17.705	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	55	PRO	0	-0.027	-0.043	19.556	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.000	-0.014	15.317	0.009	0.009	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.024	0.044	19.274	0.011	0.011	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.035	-0.024	17.055	0.009	0.009	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.035	-0.023	12.525	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.008	-0.001	14.990	0.013	0.013	0.000	0.000	0.000	0.000
59	A	61	TRP	0	-0.040	-0.025	10.727	-0.099	-0.099	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.837	-0.922	15.713	-0.167	-0.167	0.000	0.000	0.000	0.000
61	A	63	ALA	0	-0.027	-0.031	14.344	-0.065	-0.065	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.893	-0.954	16.181	-0.095	-0.095	0.000	0.000	0.000	0.000
63	A	65	LEU	0	0.009	0.007	16.616	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.078	-0.059	15.225	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.023	-0.024	18.157	0.021	0.021	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.779	-0.870	19.868	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.920	-0.940	22.553	0.057	0.057	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.061	0.018	24.778	0.007	0.007	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.045	0.020	26.296	0.004	0.004	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.863	0.931	24.334	-0.042	-0.042	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.842	0.906	18.276	-0.077	-0.077	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.041	0.058	18.098	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.010	-0.006	15.005	0.015	0.015	0.000	0.000	0.000	0.000
74	A	76	TRP	0	0.039	0.034	11.315	0.036	0.036	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.933	0.956	10.336	0.111	0.111	0.000	0.000	0.000	0.000
76	A	78	SER	0	0.028	0.032	10.749	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	79	LEU	0	0.027	0.014	12.853	0.033	0.033	0.000	0.000	0.000	0.000
78	A	80	PRO	0	-0.022	-0.027	14.470	-0.071	-0.071	0.000	0.000	0.000	0.000
79	A	81	GLY	0	0.027	0.019	14.582	0.036	0.036	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.050	-0.007	12.790	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.950	0.967	13.031	0.365	0.365	0.000	0.000	0.000	0.000
82	A	84	ILE	0	0.056	0.036	7.136	-0.085	-0.085	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.814	-0.874	7.199	-1.200	-1.200	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.066	-0.063	6.192	-0.822	-0.822	0.000	0.000	0.000	0.000
85	A	87	SER	0	-0.065	-0.058	7.364	0.461	0.461	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.044	0.009	8.476	-0.069	-0.069	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.948	-0.968	10.925	0.136	0.136	0.000	0.000	0.000	0.000
88	A	90	VAL	0	-0.001	0.011	13.905	0.041	0.041	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.031	-0.017	16.453	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	92	PHE	0	0.014	0.014	19.238	0.007	0.007	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.841	0.883	19.015	-0.158	-0.158	0.000	0.000	0.000	0.000
92	A	94	PRO	0	-0.046	-0.005	24.010	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.024	0.006	25.934	0.008	0.008	0.000	0.000	0.000	0.000
94	A	96	PRO	0	-0.001	-0.012	25.827	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	97	GLY	0	-0.010	0.002	28.613	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.072	0.036	30.594	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.909	0.957	29.746	-0.055	-0.055	0.000	0.000	0.000	0.000
98	A	100	GLY	0	0.018	0.011	28.847	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	101	THR	0	-0.058	-0.038	24.044	0.002	0.002	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.843	-0.895	20.410	0.149	0.149	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.014	-0.001	18.111	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.051	-0.024	14.853	0.019	0.019	0.000	0.000	0.000	0.000
103	A	105	VAL	0	0.066	0.034	11.418	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	106	ARG	1	0.926	0.960	7.168	-0.551	-0.551	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.028	0.020	6.895	-0.097	-0.097	0.000	0.000	0.000	0.000
106	A	108	THR	0	-0.002	0.019	4.224	0.384	0.650	-0.001	-0.098	-0.167	0.000
107	A	109	TYR	0	0.009	0.004	2.520	-2.804	0.651	3.573	-2.127	-4.901	-0.002
108	A	110	ARG	1	0.858	0.930	1.770	-13.331	-20.609	19.380	-7.450	-4.653	-0.064
109	A	127	GLU	-1	-0.839	-0.896	7.104	0.443	0.443	0.000	0.000	0.000	0.000
110	A	128	PRO	0	0.015	-0.001	5.660	0.016	0.016	0.000	0.000	0.000	0.000
111	A	129	SER	0	-0.039	-0.049	7.595	-0.114	-0.114	0.000	0.000	0.000	0.000
112	A	130	GLN	0	-0.009	-0.008	9.004	-0.045	-0.045	0.000	0.000	0.000	0.000
113	A	131	GLN	0	-0.013	-0.005	11.316	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	132	LEU	0	0.019	0.006	9.948	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	133	ARG	1	0.898	0.961	12.483	-0.237	-0.237	0.000	0.000	0.000	0.000
116	A	134	ASP	-1	-0.885	-0.954	14.677	0.089	0.089	0.000	0.000	0.000	0.000
117	A	135	ASP	-1	-0.806	-0.881	14.547	0.082	0.082	0.000	0.000	0.000	0.000
118	A	136	LEU	0	-0.009	-0.010	14.460	-0.024	-0.024	0.000	0.000	0.000	0.000
119	A	137	MET	0	-0.041	-0.021	17.989	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	138	ARG	1	0.894	0.964	18.266	-0.072	-0.072	0.000	0.000	0.000	0.000
121	A	139	PHE	0	0.066	0.022	20.402	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	140	LYS	1	0.788	0.894	22.040	-0.081	-0.081	0.000	0.000	0.000	0.000
123	A	141	ARG	1	0.972	0.974	23.926	-0.040	-0.040	0.000	0.000	0.000	0.000
124	A	142	GLU	-1	-0.893	-0.952	24.494	0.019	0.019	0.000	0.000	0.000	0.000
125	A	143	GLN	0	0.033	0.019	25.447	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	144	GLU	-1	-0.867	-0.941	27.360	0.059	0.059	0.000	0.000	0.000	0.000
127	A	145	LEU	0	-0.068	-0.018	29.966	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	146	GLY	0	-0.039	-0.007	31.061	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	147	LEU	0	-0.064	-0.030	27.894	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)