FMO DATABASE

FMODB ID: 39J3L

Calculation Name: 5N9J-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: G

ChEMBL ID:

UniProt ID: P87310

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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1019365.312218
FMO2-HF: Nuclear repulsion	950119.175345
FMO2-HF: Total energy	-69246.136872
FMO2-MP2: Total energy	-69445.69319

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(G:2:GLU)

Summations of interaction energy for fragment #1(G:2:GLU)

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.
-60.112	-56.631	0.387	-1.162	-2.708	0.004

Interaction energy analysis for fragmet #1(G:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.925 / q_NPA : -0.969

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	G	4	GLN	0	0.020	0.000	3.786	-6.617	-4.892	-0.006	-0.648	-1.071	0.004
4	G	5	ARG	1	0.986	1.016	3.007	-48.421	-47.476	0.185	-0.255	-0.876	0.000
5	G	6	ALA	0	0.016	0.006	4.218	-3.553	-3.219	-0.001	-0.124	-0.209	0.000
6	G	7	ILE	0	0.012	-0.011	5.989	-3.170	-3.170	0.000	0.000	0.000	0.000
7	G	8	ASP	-1	-0.841	-0.920	7.765	23.776	23.776	0.000	0.000	0.000	0.000
8	G	9	SER	0	-0.040	-0.019	8.330	-2.145	-2.145	0.000	0.000	0.000	0.000
9	G	10	ILE	0	-0.086	-0.041	9.976	-1.629	-1.629	0.000	0.000	0.000	0.000
10	G	11	GLU	-1	-0.917	-0.955	12.195	15.724	15.724	0.000	0.000	0.000	0.000
11	G	12	GLU	-1	-0.885	-0.932	13.033	16.447	16.447	0.000	0.000	0.000	0.000
12	G	13	CYS	0	-0.075	-0.035	14.216	-0.768	-0.768	0.000	0.000	0.000	0.000
13	G	14	LEU	0	0.015	0.015	16.103	-1.291	-1.291	0.000	0.000	0.000	0.000
14	G	15	ASN	0	0.027	-0.002	17.150	-0.311	-0.311	0.000	0.000	0.000	0.000
15	G	16	LYS	1	0.983	0.990	18.659	-16.424	-16.424	0.000	0.000	0.000	0.000
16	G	17	GLN	0	0.013	-0.002	20.276	-1.205	-1.205	0.000	0.000	0.000	0.000
17	G	18	LEU	0	-0.026	-0.005	22.172	-0.638	-0.638	0.000	0.000	0.000	0.000
18	G	19	ARG	1	0.915	0.954	23.384	-11.477	-11.477	0.000	0.000	0.000	0.000
19	G	20	LEU	0	-0.004	-0.020	22.889	-0.350	-0.350	0.000	0.000	0.000	0.000
20	G	21	SER	0	-0.037	-0.011	26.232	-0.536	-0.536	0.000	0.000	0.000	0.000
21	G	22	SER	0	-0.055	-0.029	28.056	-0.429	-0.429	0.000	0.000	0.000	0.000
22	G	23	GLU	-1	-1.003	-0.985	29.086	9.419	9.419	0.000	0.000	0.000	0.000
23	G	24	LYS	1	0.943	0.975	30.447	-9.516	-9.516	0.000	0.000	0.000	0.000
24	G	25	VAL	0	0.019	0.023	30.218	0.330	0.330	0.000	0.000	0.000	0.000
25	G	26	ASP	-1	-0.883	-0.963	29.136	9.916	9.916	0.000	0.000	0.000	0.000
26	G	27	GLN	0	-0.009	-0.002	28.404	0.178	0.178	0.000	0.000	0.000	0.000
27	G	28	TYR	0	0.001	-0.002	23.129	0.292	0.292	0.000	0.000	0.000	0.000
28	G	29	VAL	0	0.063	0.024	24.034	0.494	0.494	0.000	0.000	0.000	0.000
29	G	30	LEU	0	0.040	0.035	23.045	0.667	0.667	0.000	0.000	0.000	0.000
30	G	31	ILE	0	-0.007	-0.013	22.702	0.526	0.526	0.000	0.000	0.000	0.000
31	G	32	GLU	-1	-0.944	-0.993	19.313	16.668	16.668	0.000	0.000	0.000	0.000
32	G	33	ASN	0	0.019	0.027	18.296	1.580	1.580	0.000	0.000	0.000	0.000
33	G	34	TRP	0	0.010	0.006	17.804	1.257	1.257	0.000	0.000	0.000	0.000
34	G	35	THR	0	-0.052	-0.013	17.741	1.069	1.069	0.000	0.000	0.000	0.000
35	G	36	SER	0	-0.011	-0.013	14.705	1.388	1.388	0.000	0.000	0.000	0.000
36	G	37	LEU	0	0.033	0.016	13.483	1.887	1.887	0.000	0.000	0.000	0.000
37	G	38	VAL	0	-0.014	-0.012	13.600	1.062	1.062	0.000	0.000	0.000	0.000
38	G	39	GLY	0	0.001	0.006	13.178	0.701	0.701	0.000	0.000	0.000	0.000
39	G	40	HIS	1	0.902	0.936	9.304	-24.199	-24.199	0.000	0.000	0.000	0.000
40	G	41	LEU	0	0.098	0.051	9.278	2.125	2.125	0.000	0.000	0.000	0.000
41	G	42	LYS	1	0.957	0.996	11.503	-19.237	-19.237	0.000	0.000	0.000	0.000
42	G	43	THR	0	-0.081	-0.024	6.983	1.434	1.434	0.000	0.000	0.000	0.000
43	G	44	LEU	0	0.055	0.031	6.930	2.287	2.287	0.000	0.000	0.000	0.000
44	G	45	HIS	0	0.024	0.012	7.985	-0.735	-0.735	0.000	0.000	0.000	0.000
45	G	46	SER	0	-0.056	-0.071	9.412	-0.998	-0.998	0.000	0.000	0.000	0.000
46	G	47	LEU	0	0.004	0.019	2.759	-1.083	-0.606	0.209	-0.135	-0.552	0.000
47	G	48	ILE	0	-0.005	-0.003	7.186	-0.792	-0.792	0.000	0.000	0.000	0.000
48	G	49	SER	0	-0.031	-0.012	9.380	-1.649	-1.649	0.000	0.000	0.000	0.000
49	G	50	ASN	0	0.002	-0.004	8.677	0.140	0.140	0.000	0.000	0.000	0.000
50	G	51	TYR	0	0.038	0.026	8.694	-2.213	-2.213	0.000	0.000	0.000	0.000
51	G	52	THR	0	-0.056	-0.040	10.466	-1.864	-1.864	0.000	0.000	0.000	0.000
52	G	53	ASN	0	0.031	0.026	13.676	-1.811	-1.811	0.000	0.000	0.000	0.000
53	G	54	GLY	0	0.023	0.013	13.371	-0.868	-0.868	0.000	0.000	0.000	0.000
54	G	55	ARG	1	0.893	0.941	13.959	-18.588	-18.588	0.000	0.000	0.000	0.000
55	G	56	GLU	-1	-0.931	-0.974	15.491	13.527	13.527	0.000	0.000	0.000	0.000
56	G	57	LEU	0	0.036	0.030	17.533	-0.725	-0.725	0.000	0.000	0.000	0.000
57	G	58	GLN	0	-0.020	-0.020	16.957	-0.813	-0.813	0.000	0.000	0.000	0.000
58	G	59	ASN	0	-0.030	-0.024	18.907	-1.053	-1.053	0.000	0.000	0.000	0.000
59	G	60	GLU	-1	-0.824	-0.910	21.405	11.380	11.380	0.000	0.000	0.000	0.000
60	G	61	ILE	0	-0.028	-0.004	20.306	-0.453	-0.453	0.000	0.000	0.000	0.000
61	G	62	SER	0	-0.100	-0.046	22.837	-0.656	-0.656	0.000	0.000	0.000	0.000
62	G	63	SER	0	-0.020	-0.011	24.492	-0.649	-0.649	0.000	0.000	0.000	0.000
63	G	64	LEU	0	0.031	0.009	25.974	-0.475	-0.475	0.000	0.000	0.000	0.000
64	G	65	LEU	0	-0.005	0.006	25.047	-0.337	-0.337	0.000	0.000	0.000	0.000
65	G	66	LYS	1	0.889	0.929	28.119	-10.401	-10.401	0.000	0.000	0.000	0.000
66	G	67	GLN	0	0.010	0.010	30.448	-0.435	-0.435	0.000	0.000	0.000	0.000
67	G	68	ASP	-1	-0.898	-0.948	31.016	9.487	9.487	0.000	0.000	0.000	0.000
68	G	69	LYS	1	0.932	0.965	29.105	-10.494	-10.494	0.000	0.000	0.000	0.000
69	G	70	GLU	-1	-0.871	-0.930	33.733	7.770	7.770	0.000	0.000	0.000	0.000
70	G	71	LEU	0	-0.018	-0.012	35.289	-0.286	-0.286	0.000	0.000	0.000	0.000
71	G	72	ASP	-1	-0.881	-0.943	35.034	8.673	8.673	0.000	0.000	0.000	0.000
72	G	73	LEU	0	-0.051	-0.054	36.901	-0.244	-0.244	0.000	0.000	0.000	0.000
73	G	74	GLN	0	-0.021	0.011	39.889	-0.333	-0.333	0.000	0.000	0.000	0.000
74	G	75	ILE	0	-0.033	-0.006	40.450	-0.249	-0.249	0.000	0.000	0.000	0.000
75	G	76	GLN	0	-0.074	-0.038	40.649	-0.270	-0.270	0.000	0.000	0.000	0.000
76	G	77	ASP	-1	-0.917	-0.958	43.562	6.918	6.918	0.000	0.000	0.000	0.000
77	G	78	CYS	0	-0.002	0.003	46.018	-0.211	-0.211	0.000	0.000	0.000	0.000
78	G	79	MET	0	0.005	0.000	46.818	-0.202	-0.202	0.000	0.000	0.000	0.000
79	G	80	ARG	1	0.934	0.959	45.353	-6.957	-6.957	0.000	0.000	0.000	0.000
80	G	81	GLU	-1	-0.928	-0.953	49.240	5.996	5.996	0.000	0.000	0.000	0.000
81	G	82	MET	0	-0.036	-0.021	51.677	-0.129	-0.129	0.000	0.000	0.000	0.000
82	G	83	THR	0	-0.075	-0.043	50.697	-0.107	-0.107	0.000	0.000	0.000	0.000
83	G	84	SER	0	-0.061	-0.029	52.583	-0.075	-0.075	0.000	0.000	0.000	0.000
84	G	85	ILE	0	-0.057	-0.016	55.055	-0.134	-0.134	0.000	0.000	0.000	0.000
85	G	86	TYR	0	-0.094	-0.046	57.169	-0.141	-0.141	0.000	0.000	0.000	0.000
86	G	87	ASP	-1	-0.880	-0.931	57.569	5.477	5.477	0.000	0.000	0.000	0.000
87	G	88	THR	0	-0.047	-0.011	56.066	-0.112	-0.112	0.000	0.000	0.000	0.000
88	G	89	HIS	0	0.004	-0.005	59.288	-0.019	-0.019	0.000	0.000	0.000	0.000
89	G	90	LEU	0	-0.003	-0.002	59.914	-0.009	-0.009	0.000	0.000	0.000	0.000
90	G	91	PRO	0	-0.009	0.003	63.215	-0.077	-0.077	0.000	0.000	0.000	0.000
91	G	92	LYS	1	0.989	0.973	66.706	-4.534	-4.534	0.000	0.000	0.000	0.000
92	G	93	THR	0	0.035	0.008	68.078	-0.033	-0.033	0.000	0.000	0.000	0.000
93	G	94	VAL	0	0.023	0.016	70.390	-0.075	-0.075	0.000	0.000	0.000	0.000
94	G	95	SER	0	0.024	0.015	73.249	-0.038	-0.038	0.000	0.000	0.000	0.000
95	G	96	GLY	0	0.030	0.010	76.198	-0.037	-0.037	0.000	0.000	0.000	0.000
96	G	97	ARG	1	1.002	0.982	78.933	-3.856	-3.856	0.000	0.000	0.000	0.000
97	G	98	LYS	1	0.884	0.978	74.825	-4.341	-4.341	0.000	0.000	0.000	0.000
98	G	99	ARG	1	0.904	0.929	76.945	-4.078	-4.078	0.000	0.000	0.000	0.000
99	G	100	GLN	0	0.040	0.020	82.876	-0.038	-0.038	0.000	0.000	0.000	0.000
100	G	101	LYS	1	0.961	0.994	86.207	-3.673	-3.673	0.000	0.000	0.000	0.000
101	G	102	VAL	0	0.058	0.025	87.566	-0.018	-0.018	0.000	0.000	0.000	0.000
102	G	103	ASN	0	-0.001	0.006	90.333	-0.026	-0.026	0.000	0.000	0.000	0.000
103	G	104	ALA	0	0.077	0.013	92.942	0.007	0.007	0.000	0.000	0.000	0.000
104	G	105	GLU	-1	-0.887	-0.921	93.930	3.222	3.222	0.000	0.000	0.000	0.000
105	G	106	THR	0	0.010	0.003	93.865	0.012	0.012	0.000	0.000	0.000	0.000
106	G	107	LEU	0	-0.042	-0.009	88.783	0.017	0.017	0.000	0.000	0.000	0.000
107	G	108	LEU	0	0.018	-0.006	92.884	0.019	0.019	0.000	0.000	0.000	0.000
108	G	109	ASP	-1	-0.905	-0.952	94.519	3.275	3.275	0.000	0.000	0.000	0.000
109	G	110	TYR	0	-0.028	-0.015	89.858	-0.014	-0.014	0.000	0.000	0.000	0.000
110	G	111	GLY	0	0.028	0.008	91.238	0.016	0.016	0.000	0.000	0.000	0.000
111	G	112	ARG	1	0.976	0.978	92.080	-3.226	-3.226	0.000	0.000	0.000	0.000
112	G	113	LYS	1	0.885	0.943	94.998	-3.304	-3.304	0.000	0.000	0.000	0.000
113	G	114	LEU	0	-0.014	-0.008	88.079	-0.004	-0.004	0.000	0.000	0.000	0.000
114	G	115	SER	0	-0.002	0.013	91.197	0.038	0.038	0.000	0.000	0.000	0.000
115	G	116	LYS	1	0.967	0.977	91.964	-3.261	-3.261	0.000	0.000	0.000	0.000
116	G	117	PHE	0	-0.057	-0.037	91.840	-0.010	-0.010	0.000	0.000	0.000	0.000
117	G	118	SER	0	0.006	0.016	86.154	0.033	0.033	0.000	0.000	0.000	0.000
118	G	119	SER	0	-0.050	-0.012	87.409	0.049	0.049	0.000	0.000	0.000	0.000
119	G	120	ALA	0	0.013	0.015	87.995	-0.033	-0.033	0.000	0.000	0.000	0.000
120	G	139	PRO	0	0.039	0.021	86.497	-0.001	-0.001	0.000	0.000	0.000	0.000
121	G	140	TRP	0	-0.011	-0.023	83.927	0.046	0.046	0.000	0.000	0.000	0.000
122	G	141	PRO	0	-0.071	-0.016	89.501	-0.032	-0.032	0.000	0.000	0.000	0.000
123	G	142	SER	0	0.039	-0.002	92.532	0.008	0.008	0.000	0.000	0.000	0.000
124	G	143	GLU	-1	-0.811	-0.906	93.691	3.362	3.362	0.000	0.000	0.000	0.000
125	G	144	ASP	-1	-0.784	-0.888	95.123	3.232	3.232	0.000	0.000	0.000	0.000
126	G	145	GLN	0	-0.092	-0.067	97.271	-0.068	-0.068	0.000	0.000	0.000	0.000
127	G	146	MET	0	-0.016	-0.009	92.071	-0.006	-0.006	0.000	0.000	0.000	0.000
128	G	147	ARG	1	0.861	0.933	97.372	-3.144	-3.144	0.000	0.000	0.000	0.000
129	G	148	LYS	1	0.875	0.934	100.109	-3.212	-3.212	0.000	0.000	0.000	0.000
130	G	149	THR	0	-0.045	0.012	98.288	-0.034	-0.034	0.000	0.000	0.000	0.000
131	G	150	LEU	0	0.070	0.004	101.077	-0.013	-0.013	0.000	0.000	0.000	0.000
132	G	151	LEU	0	0.003	0.012	96.912	-0.019	-0.019	0.000	0.000	0.000	0.000
133	G	152	PHE	0	0.054	0.035	99.342	-0.007	-0.007	0.000	0.000	0.000	0.000
134	G	153	GLN	0	0.012	0.019	101.320	-0.013	-0.013	0.000	0.000	0.000	0.000
135	G	154	PHE	0	0.007	0.000	103.568	-0.026	-0.026	0.000	0.000	0.000	0.000
136	G	155	SER	0	-0.033	-0.022	100.134	-0.021	-0.021	0.000	0.000	0.000	0.000
137	G	156	THR	0	-0.055	-0.052	102.824	-0.023	-0.023	0.000	0.000	0.000	0.000
138	G	157	SER	0	-0.039	0.004	104.952	-0.032	-0.032	0.000	0.000	0.000	0.000
139	G	158	MET	0	-0.021	-0.011	105.068	-0.014	-0.014	0.000	0.000	0.000	0.000
140	G	159	VAL	0	-0.083	-0.036	102.015	0.000	0.000	0.000	0.000	0.000	0.000
141	G	160	PRO	0	0.040	0.016	105.327	-0.021	-0.021	0.000	0.000	0.000	0.000
142	G	161	ASN	0	0.002	-0.010	105.697	0.036	0.036	0.000	0.000	0.000	0.000
143	G	162	LEU	0	0.028	0.010	105.966	0.014	0.014	0.000	0.000	0.000	0.000
144	G	163	SER	0	0.000	0.022	100.368	0.036	0.036	0.000	0.000	0.000	0.000
145	G	164	ALA	0	0.080	0.083	98.177	-0.009	-0.009	0.000	0.000	0.000	0.000
146	G	165	THR	0	0.025	-0.001	94.107	0.010	0.010	0.000	0.000	0.000	0.000
147	G	166	ALA	0	-0.012	-0.007	97.235	0.003	0.003	0.000	0.000	0.000	0.000
148	G	167	SER	0	-0.009	-0.065	100.142	-0.028	-0.028	0.000	0.000	0.000	0.000
149	G	168	GLN	0	-0.037	-0.017	95.835	-0.014	-0.014	0.000	0.000	0.000	0.000
150	G	169	LEU	0	0.075	0.053	97.561	-0.009	-0.009	0.000	0.000	0.000	0.000
151	G	170	PHE	0	-0.065	-0.054	99.142	-0.023	-0.023	0.000	0.000	0.000	0.000
152	G	171	SER	0	-0.032	-0.019	101.291	-0.027	-0.027	0.000	0.000	0.000	0.000
153	G	172	GLU	-1	-0.973	-0.961	96.200	3.315	3.315	0.000	0.000	0.000	0.000
154	G	173	GLN	0	-0.022	0.007	100.438	-0.013	-0.013	0.000	0.000	0.000	0.000
155	G	197	THR	0	0.042	0.021	118.572	-0.001	-0.001	0.000	0.000	0.000	0.000
156	G	198	LYS	1	0.923	0.938	120.142	-2.595	-2.595	0.000	0.000	0.000	0.000
157	G	199	MET	0	0.011	0.018	120.872	-0.011	-0.011	0.000	0.000	0.000	0.000
158	G	200	ASN	0	0.052	0.011	125.293	0.008	0.008	0.000	0.000	0.000	0.000
159	G	201	TYR	0	-0.068	-0.019	125.783	-0.012	-0.012	0.000	0.000	0.000	0.000
160	G	202	PRO	0	0.020	0.009	126.459	0.010	0.010	0.000	0.000	0.000	0.000
161	G	203	ALA	0	0.028	0.018	122.314	0.015	0.015	0.000	0.000	0.000	0.000
162	G	204	SER	0	0.010	-0.001	119.780	-0.008	-0.008	0.000	0.000	0.000	0.000
163	G	205	PRO	0	-0.006	0.001	121.543	0.006	0.006	0.000	0.000	0.000	0.000
164	G	206	THR	0	-0.019	-0.006	116.017	-0.001	-0.001	0.000	0.000	0.000	0.000
165	G	207	PHE	0	0.016	0.009	113.684	-0.004	-0.004	0.000	0.000	0.000	0.000
166	G	208	THR	0	-0.001	-0.010	113.798	0.026	0.026	0.000	0.000	0.000	0.000
167	G	209	THR	0	-0.040	-0.012	110.488	-0.018	-0.018	0.000	0.000	0.000	0.000
168	G	210	GLN	0	-0.027	-0.017	111.556	0.035	0.035	0.000	0.000	0.000	0.000
169	G	211	GLU	-1	-0.942	-0.961	104.724	3.064	3.064	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:2:GLU)