FMO DATABASE

FMODB ID: K3453

Calculation Name: 3W6J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W6J

Chain ID: B

ChEMBL ID:

UniProt ID: A0A0E0

Base Structure: X-ray

Registration Date: 2023-06-20

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	168
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1407844.795547
FMO2-HF: Nuclear repulsion	1344615.044158
FMO2-HF: Total energy	-63229.75139
FMO2-MP2: Total energy	-63417.820105

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(B:15:LYS)

Summations of interaction energy for fragment #1(B:15:LYS)

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.
-197.161	-200.419	32.1	-15.268	-13.576	-0.161

Interaction energy analysis for fragmet #1(B:15:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.911

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	B	17	ALA	0	0.081	0.035	3.796	1.539	3.290	-0.007	-0.789	-0.955	0.002
4	B	18	LYS	1	0.822	0.890	2.328	63.858	65.557	2.422	-1.240	-2.882	-0.003
5	B	19	ALA	0	0.021	0.011	3.995	4.126	4.358	0.003	-0.044	-0.191	0.000
6	B	20	ILE	0	0.009	0.012	6.192	3.190	3.190	0.000	0.000	0.000	0.000
7	B	21	VAL	0	0.028	0.010	7.251	2.422	2.422	0.000	0.000	0.000	0.000
8	B	22	GLU	-1	-0.822	-0.901	8.145	-24.261	-24.261	0.000	0.000	0.000	0.000
9	B	23	ALA	0	-0.018	-0.015	9.910	2.078	2.078	0.000	0.000	0.000	0.000
10	B	24	LEU	0	-0.003	-0.001	11.439	1.589	1.589	0.000	0.000	0.000	0.000
11	B	25	LEU	0	-0.006	-0.014	11.890	1.163	1.163	0.000	0.000	0.000	0.000
12	B	26	PHE	0	-0.056	-0.025	14.004	1.081	1.081	0.000	0.000	0.000	0.000
13	B	27	ALA	0	-0.038	-0.020	15.819	0.935	0.935	0.000	0.000	0.000	0.000
14	B	28	ALA	0	-0.023	0.002	17.279	0.759	0.759	0.000	0.000	0.000	0.000
15	B	29	GLY	0	0.006	0.010	18.635	0.712	0.712	0.000	0.000	0.000	0.000
16	B	30	ASP	-1	-0.973	-1.006	20.291	-12.809	-12.809	0.000	0.000	0.000	0.000
17	B	31	GLU	-1	-0.951	-0.963	22.769	-11.284	-11.284	0.000	0.000	0.000	0.000
18	B	32	GLY	0	-0.050	-0.019	18.760	-0.098	-0.098	0.000	0.000	0.000	0.000
19	B	33	LEU	0	-0.014	-0.012	15.157	0.230	0.230	0.000	0.000	0.000	0.000
20	B	34	SER	0	0.012	-0.001	17.864	-0.627	-0.627	0.000	0.000	0.000	0.000
21	B	35	LEU	0	-0.003	-0.004	13.456	-0.625	-0.625	0.000	0.000	0.000	0.000
22	B	36	SER	0	-0.013	-0.034	15.436	-0.633	-0.633	0.000	0.000	0.000	0.000
23	B	37	GLN	0	0.001	0.011	17.408	-0.144	-0.144	0.000	0.000	0.000	0.000
24	B	38	ILE	0	0.001	0.006	11.208	-0.396	-0.396	0.000	0.000	0.000	0.000
25	B	39	ALA	0	-0.004	-0.013	12.670	-1.017	-1.017	0.000	0.000	0.000	0.000
26	B	40	ALA	0	0.004	0.007	13.722	-0.147	-0.147	0.000	0.000	0.000	0.000
27	B	41	VAL	0	-0.036	-0.020	13.599	0.254	0.254	0.000	0.000	0.000	0.000
28	B	42	LEU	0	-0.079	-0.040	8.206	-0.840	-0.840	0.000	0.000	0.000	0.000
29	B	43	GLU	-1	-0.969	-0.966	11.625	-17.425	-17.425	0.000	0.000	0.000	0.000
30	B	44	VAL	0	-0.063	-0.014	9.708	-0.380	-0.380	0.000	0.000	0.000	0.000
31	B	45	SER	0	-0.031	-0.040	12.920	1.353	1.353	0.000	0.000	0.000	0.000
32	B	46	GLU	-1	-0.786	-0.906	12.757	-18.124	-18.124	0.000	0.000	0.000	0.000
33	B	47	LEU	0	-0.036	-0.013	12.614	-0.866	-0.866	0.000	0.000	0.000	0.000
34	B	48	GLU	-1	-0.845	-0.909	8.941	-27.449	-27.449	0.000	0.000	0.000	0.000
35	B	49	ALA	0	0.035	0.011	8.328	-3.832	-3.832	0.000	0.000	0.000	0.000
36	B	50	LYS	1	0.810	0.897	9.401	18.623	18.623	0.000	0.000	0.000	0.000
37	B	51	ALA	0	0.030	0.026	6.712	-1.147	-1.147	0.000	0.000	0.000	0.000
38	B	52	VAL	0	-0.021	-0.003	4.107	-6.283	-6.082	-0.001	-0.019	-0.182	0.000
39	B	53	ILE	0	0.020	0.013	6.212	-1.157	-1.157	0.000	0.000	0.000	0.000
40	B	54	GLU	-1	-0.907	-0.960	8.813	-25.403	-25.403	0.000	0.000	0.000	0.000
41	B	55	GLU	-1	-0.808	-0.873	1.751	-153.756	-160.897	29.683	-13.176	-9.366	-0.160
42	B	56	LEU	0	0.021	0.014	6.149	1.590	1.590	0.000	0.000	0.000	0.000
43	B	57	GLN	0	-0.022	-0.013	7.933	2.848	2.848	0.000	0.000	0.000	0.000
44	B	58	GLN	0	0.000	0.011	7.988	3.621	3.621	0.000	0.000	0.000	0.000
45	B	59	ASP	-1	-0.834	-0.910	6.275	-44.103	-44.103	0.000	0.000	0.000	0.000
46	B	60	CYS	0	-0.103	-0.055	9.404	3.244	3.244	0.000	0.000	0.000	0.000
47	B	61	ARG	1	0.828	0.906	11.938	25.739	25.739	0.000	0.000	0.000	0.000
48	B	62	ARG	1	0.806	0.882	11.188	23.803	23.803	0.000	0.000	0.000	0.000
49	B	63	GLU	-1	-0.927	-0.965	14.578	-15.269	-15.269	0.000	0.000	0.000	0.000
50	B	64	GLU	-1	-0.811	-0.872	13.575	-20.924	-20.924	0.000	0.000	0.000	0.000
51	B	65	ARG	1	0.800	0.897	10.226	23.753	23.753	0.000	0.000	0.000	0.000
52	B	66	GLY	0	0.037	0.004	15.751	0.541	0.541	0.000	0.000	0.000	0.000
53	B	67	ILE	0	-0.034	-0.024	13.631	0.895	0.895	0.000	0.000	0.000	0.000
54	B	68	GLN	0	0.014	-0.001	15.621	-0.276	-0.276	0.000	0.000	0.000	0.000
55	B	69	LEU	0	0.030	0.027	11.163	0.623	0.623	0.000	0.000	0.000	0.000
56	B	70	VAL	0	-0.057	-0.029	15.168	-0.082	-0.082	0.000	0.000	0.000	0.000
57	B	71	GLU	-1	-0.771	-0.880	16.661	-19.025	-19.025	0.000	0.000	0.000	0.000
58	B	72	LEU	0	-0.063	-0.041	18.954	0.633	0.633	0.000	0.000	0.000	0.000
59	B	73	GLY	0	0.020	0.013	22.640	0.366	0.366	0.000	0.000	0.000	0.000
60	B	74	GLY	0	-0.003	0.000	20.514	0.324	0.324	0.000	0.000	0.000	0.000
61	B	75	VAL	0	0.011	0.016	19.712	-0.589	-0.589	0.000	0.000	0.000	0.000
62	B	76	PHE	0	-0.027	-0.021	14.995	-0.372	-0.372	0.000	0.000	0.000	0.000
63	B	77	LEU	0	0.048	0.027	16.807	0.251	0.251	0.000	0.000	0.000	0.000
64	B	78	LEU	0	-0.006	-0.005	12.323	-0.795	-0.795	0.000	0.000	0.000	0.000
65	B	79	ALA	0	0.039	0.024	16.552	0.970	0.970	0.000	0.000	0.000	0.000
66	B	80	THR	0	0.015	0.002	18.926	-0.534	-0.534	0.000	0.000	0.000	0.000
67	B	81	LYS	1	0.838	0.942	17.382	17.657	17.657	0.000	0.000	0.000	0.000
68	B	82	LYS	1	0.963	0.968	21.618	12.807	12.807	0.000	0.000	0.000	0.000
69	B	83	GLU	-1	-0.857	-0.923	21.241	-14.038	-14.038	0.000	0.000	0.000	0.000
70	B	84	HIS	0	0.001	-0.008	20.700	0.406	0.406	0.000	0.000	0.000	0.000
71	B	85	ALA	0	0.046	0.037	25.642	0.346	0.346	0.000	0.000	0.000	0.000
72	B	86	PRO	0	-0.031	-0.027	28.222	0.381	0.381	0.000	0.000	0.000	0.000
73	B	87	TYR	0	-0.007	-0.023	27.479	0.531	0.531	0.000	0.000	0.000	0.000
74	B	88	LEU	0	0.046	0.021	25.050	0.217	0.217	0.000	0.000	0.000	0.000
75	B	89	LYS	1	0.916	0.976	29.057	9.041	9.041	0.000	0.000	0.000	0.000
76	B	90	LYS	1	0.961	0.990	31.781	9.834	9.834	0.000	0.000	0.000	0.000
77	B	91	LEU	0	-0.032	-0.002	28.003	0.219	0.219	0.000	0.000	0.000	0.000
78	B	92	VAL	0	-0.031	-0.034	32.020	0.102	0.102	0.000	0.000	0.000	0.000
79	B	93	GLU	-1	-0.941	-0.981	34.698	-8.304	-8.304	0.000	0.000	0.000	0.000
80	B	94	ALA	0	-0.025	-0.004	35.606	0.264	0.264	0.000	0.000	0.000	0.000
81	B	95	PRO	0	-0.029	-0.014	37.342	-0.076	-0.076	0.000	0.000	0.000	0.000
82	B	96	GLY	0	0.047	0.015	37.224	0.064	0.064	0.000	0.000	0.000	0.000
83	B	97	ALA	0	-0.023	0.004	34.845	0.044	0.044	0.000	0.000	0.000	0.000
84	B	98	SER	0	0.029	0.029	33.055	-0.274	-0.274	0.000	0.000	0.000	0.000
85	B	99	PRO	0	0.065	0.022	29.453	0.194	0.194	0.000	0.000	0.000	0.000
86	B	100	LEU	0	0.003	0.005	31.885	0.084	0.084	0.000	0.000	0.000	0.000
87	B	101	SER	0	-0.030	-0.023	35.109	0.200	0.200	0.000	0.000	0.000	0.000
88	B	102	GLN	0	0.019	0.004	32.649	0.173	0.173	0.000	0.000	0.000	0.000
89	B	103	ALA	0	0.069	0.039	33.558	0.109	0.109	0.000	0.000	0.000	0.000
90	B	104	ALA	0	-0.032	-0.006	35.212	0.159	0.159	0.000	0.000	0.000	0.000
91	B	105	LEU	0	0.016	0.000	37.859	0.191	0.191	0.000	0.000	0.000	0.000
92	B	106	GLU	-1	-0.781	-0.853	33.413	-8.935	-8.935	0.000	0.000	0.000	0.000
93	B	107	THR	0	-0.022	-0.031	37.461	0.101	0.101	0.000	0.000	0.000	0.000
94	B	108	LEU	0	-0.027	-0.015	39.617	0.149	0.149	0.000	0.000	0.000	0.000
95	B	109	ALA	0	0.008	0.011	39.910	0.182	0.182	0.000	0.000	0.000	0.000
96	B	110	ILE	0	0.005	0.000	36.862	0.133	0.133	0.000	0.000	0.000	0.000
97	B	111	ILE	0	-0.019	-0.013	41.427	0.140	0.140	0.000	0.000	0.000	0.000
98	B	112	ALA	0	-0.018	-0.013	44.796	0.147	0.147	0.000	0.000	0.000	0.000
99	B	113	TYR	0	-0.022	-0.029	43.848	0.130	0.130	0.000	0.000	0.000	0.000
100	B	114	ARG	1	0.828	0.912	41.939	7.159	7.159	0.000	0.000	0.000	0.000
101	B	115	GLN	0	-0.026	0.021	46.291	0.092	0.092	0.000	0.000	0.000	0.000
102	B	116	PRO	0	-0.028	-0.021	48.979	0.078	0.078	0.000	0.000	0.000	0.000
103	B	117	ILE	0	0.044	0.032	42.721	-0.037	-0.037	0.000	0.000	0.000	0.000
104	B	118	THR	0	-0.056	-0.056	44.876	-0.007	-0.007	0.000	0.000	0.000	0.000
105	B	119	ARG	1	0.870	0.914	39.536	7.567	7.567	0.000	0.000	0.000	0.000
106	B	120	ALA	0	-0.013	-0.007	40.735	-0.182	-0.182	0.000	0.000	0.000	0.000
107	B	121	GLU	-1	-0.780	-0.889	39.861	-7.010	-7.010	0.000	0.000	0.000	0.000
108	B	122	ILE	0	-0.011	-0.009	39.015	-0.148	-0.148	0.000	0.000	0.000	0.000
109	B	123	GLU	-1	-0.826	-0.921	36.460	-8.372	-8.372	0.000	0.000	0.000	0.000
110	B	124	GLU	-1	-0.947	-0.954	35.203	-8.647	-8.647	0.000	0.000	0.000	0.000
111	B	125	ILE	0	-0.063	-0.033	34.914	-0.198	-0.198	0.000	0.000	0.000	0.000
112	B	126	ARG	1	0.766	0.835	33.104	8.736	8.736	0.000	0.000	0.000	0.000
113	B	127	GLY	0	0.039	0.046	31.056	-0.276	-0.276	0.000	0.000	0.000	0.000
114	B	128	VAL	0	-0.018	-0.011	30.402	-0.270	-0.270	0.000	0.000	0.000	0.000
115	B	129	LYS	1	0.949	0.978	31.204	10.073	10.073	0.000	0.000	0.000	0.000
116	B	130	SER	0	0.005	-0.014	35.137	-0.120	-0.120	0.000	0.000	0.000	0.000
117	B	131	ASP	-1	-0.935	-0.963	37.778	-7.454	-7.454	0.000	0.000	0.000	0.000
118	B	132	LYS	1	0.924	0.963	37.961	7.823	7.823	0.000	0.000	0.000	0.000
119	B	133	PRO	0	0.011	-0.007	36.945	0.163	0.163	0.000	0.000	0.000	0.000
120	B	134	LEU	0	0.071	0.039	39.841	0.162	0.162	0.000	0.000	0.000	0.000
121	B	135	GLN	0	0.006	0.011	42.914	0.107	0.107	0.000	0.000	0.000	0.000
122	B	136	THR	0	-0.037	-0.034	40.991	0.137	0.137	0.000	0.000	0.000	0.000
123	B	137	LEU	0	-0.020	0.005	42.207	0.124	0.124	0.000	0.000	0.000	0.000
124	B	138	MET	0	-0.034	-0.003	45.435	0.170	0.170	0.000	0.000	0.000	0.000
125	B	139	ALA	0	-0.032	-0.014	46.993	0.138	0.138	0.000	0.000	0.000	0.000
126	B	140	ARG	1	0.905	0.954	45.572	6.819	6.819	0.000	0.000	0.000	0.000
127	B	141	ALA	0	0.036	0.026	48.710	0.049	0.049	0.000	0.000	0.000	0.000
128	B	142	LEU	0	0.004	0.026	45.904	0.062	0.062	0.000	0.000	0.000	0.000
129	B	143	ILE	0	-0.003	-0.006	46.407	-0.019	-0.019	0.000	0.000	0.000	0.000
130	B	144	LYS	1	0.967	0.969	49.271	5.776	5.776	0.000	0.000	0.000	0.000
131	B	145	GLU	-1	-0.831	-0.871	51.086	-5.965	-5.965	0.000	0.000	0.000	0.000
132	B	146	VAL	0	-0.024	-0.012	52.707	0.102	0.102	0.000	0.000	0.000	0.000
133	B	147	GLY	0	0.029	0.018	53.848	0.121	0.121	0.000	0.000	0.000	0.000
134	B	148	ARG	1	0.774	0.851	52.420	5.856	5.856	0.000	0.000	0.000	0.000
135	B	149	ALA	0	0.005	0.005	51.073	0.083	0.083	0.000	0.000	0.000	0.000
136	B	150	GLU	-1	-0.876	-0.924	53.217	-5.487	-5.487	0.000	0.000	0.000	0.000
137	B	151	GLY	0	0.084	0.042	53.614	0.069	0.069	0.000	0.000	0.000	0.000
138	B	152	THR	0	-0.024	-0.026	48.323	0.049	0.049	0.000	0.000	0.000	0.000
139	B	153	GLY	0	0.017	0.014	49.405	-0.108	-0.108	0.000	0.000	0.000	0.000
140	B	154	ARG	1	0.782	0.897	50.493	5.521	5.521	0.000	0.000	0.000	0.000
141	B	155	PRO	0	0.015	0.017	47.863	0.035	0.035	0.000	0.000	0.000	0.000
142	B	156	ILE	0	0.016	-0.004	47.967	0.109	0.109	0.000	0.000	0.000	0.000
143	B	157	LEU	0	0.011	0.032	48.400	-0.161	-0.161	0.000	0.000	0.000	0.000
144	B	158	TYR	0	-0.008	-0.028	46.460	0.103	0.103	0.000	0.000	0.000	0.000
145	B	159	GLY	0	0.068	0.011	49.331	-0.020	-0.020	0.000	0.000	0.000	0.000
146	B	160	THR	0	-0.014	0.004	48.314	-0.044	-0.044	0.000	0.000	0.000	0.000
147	B	161	THR	0	-0.060	-0.034	50.706	0.090	0.090	0.000	0.000	0.000	0.000
148	B	162	PRO	0	0.032	0.000	53.592	-0.038	-0.038	0.000	0.000	0.000	0.000
149	B	163	GLU	-1	-0.877	-0.949	54.044	-5.598	-5.598	0.000	0.000	0.000	0.000
150	B	164	PHE	0	0.001	-0.010	46.567	-0.064	-0.064	0.000	0.000	0.000	0.000
151	B	165	LEU	0	-0.013	-0.002	51.177	-0.065	-0.065	0.000	0.000	0.000	0.000
152	B	166	ASP	-1	-0.865	-0.925	53.198	-5.463	-5.463	0.000	0.000	0.000	0.000
153	B	167	TYR	0	-0.069	-0.023	46.237	-0.025	-0.025	0.000	0.000	0.000	0.000
154	B	168	PHE	0	-0.059	-0.037	44.708	-0.135	-0.135	0.000	0.000	0.000	0.000
155	B	169	GLY	0	-0.019	-0.003	50.058	-0.029	-0.029	0.000	0.000	0.000	0.000
156	B	170	LEU	0	-0.027	-0.002	49.648	0.096	0.096	0.000	0.000	0.000	0.000
157	B	171	LYS	1	0.750	0.856	53.956	5.570	5.570	0.000	0.000	0.000	0.000
158	B	172	THR	0	-0.073	-0.050	56.208	0.068	0.068	0.000	0.000	0.000	0.000
159	B	173	LEU	0	0.030	0.005	51.779	-0.098	-0.098	0.000	0.000	0.000	0.000
160	B	174	GLU	-1	-0.874	-0.953	52.115	-5.644	-5.644	0.000	0.000	0.000	0.000
161	B	175	GLU	-1	-0.828	-0.878	53.184	-5.566	-5.566	0.000	0.000	0.000	0.000
162	B	176	LEU	0	-0.040	-0.008	47.292	-0.104	-0.104	0.000	0.000	0.000	0.000
163	B	177	PRO	0	-0.015	-0.002	45.828	0.024	0.024	0.000	0.000	0.000	0.000
164	B	178	PRO	0	0.032	0.026	46.381	-0.115	-0.115	0.000	0.000	0.000	0.000
165	B	179	LEU	0	0.001	-0.004	41.557	-0.102	-0.102	0.000	0.000	0.000	0.000
166	B	180	PRO	0	-0.034	-0.017	43.223	0.005	0.005	0.000	0.000	0.000	0.000
167	B	181	GLU	-1	-0.925	-0.954	38.650	-7.539	-7.539	0.000	0.000	0.000	0.000
168	B	182	TRP	0	-0.011	0.004	38.516	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:15:LYS)