FMO DATABASE

FMODB ID: 4JLNN

Calculation Name: 3RD6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD6

Chain ID: A

ChEMBL ID:

UniProt ID: Q98FZ2

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1321305.358076
FMO2-HF: Nuclear repulsion	1265006.321296
FMO2-HF: Total energy	-56299.03678
FMO2-MP2: Total energy	-56465.677997

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:HIS)

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

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.
-163.842	-161.247	21.444	-13.395	-10.644	-0.134

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.887 / q_NPA : 0.917

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	-0.013	-0.005	3.877	-5.910	-3.091	-0.020	-1.609	-1.190	0.004
4	A	6	ILE	0	0.004	0.020	6.354	2.734	2.734	0.000	0.000	0.000	0.000
5	A	7	HIS	0	0.024	0.007	8.999	1.331	1.331	0.000	0.000	0.000	0.000
6	A	8	SER	0	-0.030	-0.013	12.527	1.182	1.182	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.009	-0.028	16.076	0.009	0.009	0.000	0.000	0.000	0.000
8	A	10	PHE	0	0.000	0.028	19.153	0.205	0.205	0.000	0.000	0.000	0.000
9	A	11	THR	0	0.028	-0.007	22.332	-0.123	-0.123	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.047	-0.022	25.077	0.153	0.153	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.834	-0.891	28.569	-9.292	-9.292	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.794	0.867	32.122	8.824	8.824	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.003	0.000	34.884	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	16	TYR	0	-0.053	-0.034	33.878	-0.073	-0.073	0.000	0.000	0.000	0.000
15	A	17	PRO	0	0.008	0.004	40.067	0.056	0.056	0.000	0.000	0.000	0.000
16	A	18	GLN	0	0.018	0.008	41.305	0.064	0.064	0.000	0.000	0.000	0.000
17	A	19	SER	0	0.027	-0.018	42.201	-0.098	-0.098	0.000	0.000	0.000	0.000
18	A	20	PRO	0	-0.021	-0.017	39.697	-0.139	-0.139	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.774	-0.850	39.079	-7.525	-7.525	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.818	0.908	39.053	7.738	7.738	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.010	-0.002	35.377	-0.143	-0.143	0.000	0.000	0.000	0.000
22	A	24	PHE	0	0.024	0.011	34.213	-0.296	-0.296	0.000	0.000	0.000	0.000
23	A	25	HIS	0	-0.018	-0.013	35.349	-0.188	-0.188	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.015	-0.010	35.370	-0.110	-0.110	0.000	0.000	0.000	0.000
25	A	27	PHE	0	-0.007	-0.004	28.552	-0.363	-0.363	0.000	0.000	0.000	0.000
26	A	28	ALA	0	0.000	0.005	31.629	-0.273	-0.273	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.807	-0.875	34.057	-8.471	-8.471	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.820	0.908	30.621	10.096	10.096	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.011	-0.011	33.561	-0.184	-0.184	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.026	-0.037	35.810	0.122	0.122	0.000	0.000	0.000	0.000
31	A	33	VAL	0	0.018	0.016	29.330	-0.130	-0.130	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.780	0.882	30.146	9.892	9.892	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.815	0.904	32.798	8.467	8.467	0.000	0.000	0.000	0.000
34	A	36	TRP	0	-0.059	-0.032	29.240	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	37	ARG	1	0.811	0.887	24.167	11.843	11.843	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.038	-0.019	26.306	-0.477	-0.477	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.842	-0.907	28.858	-10.012	-10.012	0.000	0.000	0.000	0.000
38	A	40	GLY	0	-0.033	-0.042	31.385	-0.226	-0.226	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.876	-0.919	33.517	-7.933	-7.933	0.000	0.000	0.000	0.000
40	A	42	GLY	0	0.004	0.004	35.539	-0.240	-0.240	0.000	0.000	0.000	0.000
41	A	43	PHE	0	-0.071	-0.048	32.931	0.226	0.226	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.023	0.005	30.418	-0.114	-0.114	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.023	0.024	28.767	0.122	0.122	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.054	-0.029	25.393	-0.126	-0.126	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.818	-0.894	24.561	-12.309	-12.309	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.072	0.024	26.007	-0.133	-0.133	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.014	0.003	25.861	0.724	0.724	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.042	-0.042	26.818	-0.314	-0.314	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.848	-0.902	28.630	-10.022	-10.022	0.000	0.000	0.000	0.000
50	A	52	PHE	0	0.027	0.025	29.538	-0.254	-0.254	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.823	0.901	29.113	10.929	10.929	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.031	0.015	28.466	-0.395	-0.395	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.014	-0.004	26.641	0.246	0.246	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.003	0.010	27.671	0.080	0.080	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.029	-0.007	24.628	-0.407	-0.407	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.826	-0.858	23.517	-12.154	-12.154	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.024	-0.010	21.104	-0.743	-0.743	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.010	-0.017	21.919	0.892	0.892	0.000	0.000	0.000	0.000
59	A	61	ARG	1	0.717	0.823	20.494	12.542	12.542	0.000	0.000	0.000	0.000
60	A	62	PHE	0	0.049	0.026	21.674	0.678	0.678	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.033	0.021	21.815	-0.643	-0.643	0.000	0.000	0.000	0.000
62	A	64	TYR	0	0.047	0.022	23.458	0.539	0.539	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.015	0.007	25.155	-0.259	-0.259	0.000	0.000	0.000	0.000
64	A	66	GLY	0	-0.013	-0.007	25.862	0.019	0.019	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.030	-0.004	22.219	-0.332	-0.332	0.000	0.000	0.000	0.000
66	A	68	PRO	0	-0.014	-0.032	17.005	0.134	0.134	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.830	-0.896	18.582	-14.655	-14.655	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.004	0.003	17.261	-1.336	-1.336	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.859	0.907	16.334	17.202	17.202	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.003	0.002	16.626	-1.224	-1.224	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.774	-0.848	16.872	-16.670	-16.670	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.020	-0.012	18.170	-0.834	-0.834	0.000	0.000	0.000	0.000
73	A	75	GLN	0	-0.041	-0.030	20.736	0.683	0.683	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.031	0.018	22.955	-0.293	-0.293	0.000	0.000	0.000	0.000
75	A	77	GLN	0	-0.044	-0.014	22.176	-0.468	-0.468	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.793	-0.882	25.935	-9.929	-9.929	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.012	0.002	29.159	-0.173	-0.173	0.000	0.000	0.000	0.000
78	A	80	VAL	0	-0.028	-0.003	32.092	0.238	0.238	0.000	0.000	0.000	0.000
79	A	81	PRO	0	0.009	-0.007	35.188	-0.059	-0.059	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.850	-0.936	37.806	-7.818	-7.818	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.070	-0.035	36.587	0.123	0.123	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.814	0.880	29.765	9.846	9.846	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.003	0.011	28.110	0.093	0.093	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.011	0.012	24.423	-0.276	-0.276	0.000	0.000	0.000	0.000
85	A	87	PHE	0	0.006	-0.004	21.839	0.187	0.187	0.000	0.000	0.000	0.000
86	A	88	SER	0	-0.010	0.009	18.330	-0.581	-0.581	0.000	0.000	0.000	0.000
87	A	89	TYR	0	-0.050	-0.060	17.336	0.213	0.213	0.000	0.000	0.000	0.000
88	A	90	ARG	1	0.864	0.926	12.904	18.141	18.141	0.000	0.000	0.000	0.000
89	A	91	MET	0	0.021	0.039	13.167	1.366	1.366	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.005	0.001	12.127	-2.489	-2.489	0.000	0.000	0.000	0.000
91	A	93	ILE	0	0.030	0.025	12.483	1.871	1.871	0.000	0.000	0.000	0.000
92	A	94	GLY	0	0.016	0.008	12.853	-1.197	-1.197	0.000	0.000	0.000	0.000
93	A	95	PRO	0	-0.055	-0.031	10.284	-0.091	-0.091	0.000	0.000	0.000	0.000
94	A	96	GLN	0	0.002	0.007	7.097	-5.949	-5.949	0.000	0.000	0.000	0.000
95	A	97	PRO	0	0.000	0.003	6.608	2.687	2.687	0.000	0.000	0.000	0.000
96	A	98	MET	0	0.011	-0.004	7.592	-3.316	-3.316	0.000	0.000	0.000	0.000
97	A	99	SER	0	0.022	-0.001	9.521	-0.551	-0.551	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.053	-0.016	10.733	0.889	0.889	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.001	-0.006	12.730	-0.828	-0.828	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.042	-0.016	16.027	0.257	0.257	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.004	-0.015	19.273	-0.185	-0.185	0.000	0.000	0.000	0.000
102	A	104	THR	0	-0.018	-0.010	22.451	0.337	0.337	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.015	-0.005	25.846	-0.044	-0.044	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.921	-0.965	28.972	-9.910	-9.910	0.000	0.000	0.000	0.000
105	A	107	LEU	0	-0.009	-0.011	32.237	0.000	0.000	0.000	0.000	0.000	0.000
106	A	108	THR	0	0.018	0.019	35.767	0.214	0.214	0.000	0.000	0.000	0.000
107	A	109	PRO	0	0.022	-0.004	38.069	0.012	0.012	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.050	-0.031	40.996	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	111	GLY	0	-0.049	-0.012	42.860	0.091	0.091	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.920	-0.957	46.428	-6.641	-6.641	0.000	0.000	0.000	0.000
111	A	113	GLY	0	0.019	0.025	43.619	-0.025	-0.025	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.052	-0.035	38.142	-0.051	-0.051	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.837	0.903	35.426	8.627	8.627	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.018	0.016	30.840	-0.103	-0.103	0.000	0.000	0.000	0.000
115	A	117	THR	0	-0.016	-0.010	30.231	-0.152	-0.152	0.000	0.000	0.000	0.000
116	A	118	TYR	0	0.014	-0.011	22.713	0.148	0.148	0.000	0.000	0.000	0.000
117	A	119	THR	0	0.015	0.007	23.617	-0.122	-0.122	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.756	-0.832	19.164	-15.289	-15.289	0.000	0.000	0.000	0.000
119	A	121	GLN	0	0.004	0.006	17.893	-0.092	-0.092	0.000	0.000	0.000	0.000
120	A	122	GLY	0	0.000	-0.015	14.917	-0.084	-0.084	0.000	0.000	0.000	0.000
121	A	123	ALA	0	-0.008	0.001	9.803	-0.074	-0.074	0.000	0.000	0.000	0.000
122	A	124	PHE	0	0.009	-0.001	9.944	-0.465	-0.465	0.000	0.000	0.000	0.000
123	A	125	PHE	0	-0.026	-0.010	4.733	-1.640	-1.547	-0.001	-0.001	-0.090	0.000
124	A	126	ASP	-1	-0.787	-0.885	1.760	-128.025	-128.553	21.466	-11.717	-9.222	-0.138
125	A	127	GLY	0	0.018	0.016	4.627	3.528	3.739	-0.001	-0.068	-0.142	0.000
126	A	128	VAL	0	-0.010	0.003	7.603	4.425	4.425	0.000	0.000	0.000	0.000
127	A	129	ASP	-1	-0.801	-0.890	10.077	-19.647	-19.647	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.028	-0.035	12.512	1.866	1.866	0.000	0.000	0.000	0.000
129	A	131	ALA	0	-0.016	0.002	14.859	1.171	1.171	0.000	0.000	0.000	0.000
130	A	132	LYS	1	0.851	0.907	16.321	18.999	18.999	0.000	0.000	0.000	0.000
131	A	133	GLY	0	0.090	0.046	18.838	0.670	0.670	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.840	0.899	14.237	19.378	19.378	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.841	-0.887	19.428	-11.821	-11.821	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.938	-0.968	22.387	-12.388	-12.388	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.022	0.006	22.981	0.543	0.543	0.000	0.000	0.000	0.000
136	A	138	THR	0	-0.016	-0.020	22.367	0.474	0.474	0.000	0.000	0.000	0.000
137	A	139	ARG	1	0.827	0.892	25.043	11.863	11.863	0.000	0.000	0.000	0.000
138	A	140	GLY	0	0.010	0.015	27.441	0.465	0.465	0.000	0.000	0.000	0.000
139	A	141	LEU	0	-0.009	-0.011	25.251	0.382	0.382	0.000	0.000	0.000	0.000
140	A	142	LEU	0	0.003	-0.002	28.256	0.359	0.359	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.812	-0.871	31.076	-8.517	-8.517	0.000	0.000	0.000	0.000
142	A	144	ALA	0	-0.014	-0.003	31.787	0.314	0.314	0.000	0.000	0.000	0.000
143	A	145	LEU	0	0.000	0.000	32.405	0.284	0.284	0.000	0.000	0.000	0.000
144	A	146	ALA	0	-0.014	-0.004	34.414	0.280	0.280	0.000	0.000	0.000	0.000
145	A	147	ALA	0	-0.037	-0.012	37.036	0.276	0.276	0.000	0.000	0.000	0.000
146	A	148	GLU	-1	-0.787	-0.865	36.285	-8.008	-8.008	0.000	0.000	0.000	0.000
147	A	149	LEU	0	-0.113	-0.056	37.255	0.475	0.475	0.000	0.000	0.000	0.000

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