FMO DATABASE

FMODB ID: R5728

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1401964.547051
FMO2-HF: Nuclear repulsion	1338736.571857
FMO2-HF: Total energy	-63227.975194
FMO2-MP2: Total energy	-63416.132845

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.
-149.505	-139.625	6.597	-6.861	-9.617	-0.075

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 : 0.919 / q_NPA : 0.935

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	0.070	0.031	3.113	1.367	3.481	0.046	-0.893	-1.267	-0.001
4	B	18	LYS	1	0.833	0.895	2.310	55.553	57.019	2.633	-1.140	-2.960	-0.004
5	B	19	ALA	0	0.020	0.011	3.687	3.986	4.168	0.006	0.024	-0.211	0.000
6	B	20	ILE	0	0.011	0.015	5.776	2.984	2.984	0.000	0.000	0.000	0.000
7	B	21	VAL	0	0.026	0.007	6.970	2.295	2.295	0.000	0.000	0.000	0.000
8	B	22	GLU	-1	-0.896	-0.952	7.730	-22.636	-22.636	0.000	0.000	0.000	0.000
9	B	23	ALA	0	-0.014	-0.009	9.589	1.898	1.898	0.000	0.000	0.000	0.000
10	B	24	LEU	0	-0.035	-0.014	11.248	1.437	1.437	0.000	0.000	0.000	0.000
11	B	25	LEU	0	0.001	-0.013	11.357	1.093	1.093	0.000	0.000	0.000	0.000
12	B	26	PHE	0	-0.050	-0.021	13.535	1.045	1.045	0.000	0.000	0.000	0.000
13	B	27	ALA	0	-0.030	-0.014	15.404	0.860	0.860	0.000	0.000	0.000	0.000
14	B	28	ALA	0	-0.035	0.000	16.965	0.702	0.702	0.000	0.000	0.000	0.000
15	B	29	GLY	0	0.005	0.009	18.347	0.703	0.703	0.000	0.000	0.000	0.000
16	B	30	ASP	-1	-0.974	-1.006	20.032	-12.275	-12.275	0.000	0.000	0.000	0.000
17	B	31	GLU	-1	-0.969	-0.966	22.429	-11.021	-11.021	0.000	0.000	0.000	0.000
18	B	32	GLY	0	-0.038	-0.012	18.517	-0.158	-0.158	0.000	0.000	0.000	0.000
19	B	33	LEU	0	-0.021	-0.022	14.940	0.140	0.140	0.000	0.000	0.000	0.000
20	B	34	SER	0	0.019	0.004	17.832	-0.425	-0.425	0.000	0.000	0.000	0.000
21	B	35	LEU	0	-0.019	-0.018	13.729	-0.488	-0.488	0.000	0.000	0.000	0.000
22	B	36	SER	0	0.015	0.013	15.577	-0.528	-0.528	0.000	0.000	0.000	0.000
23	B	37	GLN	0	0.016	0.021	17.318	-0.313	-0.313	0.000	0.000	0.000	0.000
24	B	38	ILE	0	0.023	0.016	11.283	-0.379	-0.379	0.000	0.000	0.000	0.000
25	B	39	ALA	0	-0.008	-0.014	12.569	-0.899	-0.899	0.000	0.000	0.000	0.000
26	B	40	ALA	0	-0.008	-0.001	13.623	-0.093	-0.093	0.000	0.000	0.000	0.000
27	B	41	VAL	0	-0.057	-0.027	12.819	0.240	0.240	0.000	0.000	0.000	0.000
28	B	42	LEU	0	-0.081	-0.048	7.831	-0.600	-0.600	0.000	0.000	0.000	0.000
29	B	43	GLU	-1	-0.949	-0.951	11.390	-17.810	-17.810	0.000	0.000	0.000	0.000
30	B	44	VAL	0	-0.033	-0.005	9.466	-0.714	-0.714	0.000	0.000	0.000	0.000
31	B	45	SER	0	0.006	0.010	12.739	1.124	1.124	0.000	0.000	0.000	0.000
32	B	46	GLU	-1	-0.788	-0.934	12.908	-17.415	-17.415	0.000	0.000	0.000	0.000
33	B	47	LEU	0	-0.047	-0.019	13.458	-0.668	-0.668	0.000	0.000	0.000	0.000
34	B	48	GLU	-1	-0.923	-0.977	8.748	-30.184	-30.184	0.000	0.000	0.000	0.000
35	B	49	ALA	0	0.023	0.006	9.061	-3.194	-3.194	0.000	0.000	0.000	0.000
36	B	50	LYS	1	0.911	0.955	9.466	17.289	17.289	0.000	0.000	0.000	0.000
37	B	51	ALA	0	0.038	0.035	7.343	-0.546	-0.546	0.000	0.000	0.000	0.000
38	B	52	VAL	0	-0.006	0.001	4.763	-3.181	-3.046	-0.001	-0.004	-0.130	0.000
39	B	53	ILE	0	-0.004	-0.005	6.494	-0.605	-0.605	0.000	0.000	0.000	0.000
40	B	54	GLU	-1	-0.919	-0.956	9.315	-25.037	-25.037	0.000	0.000	0.000	0.000
41	B	55	GLU	-1	-0.868	-0.935	2.248	-101.091	-95.108	3.913	-4.848	-5.049	-0.070
42	B	56	LEU	0	0.013	0.003	6.680	1.134	1.134	0.000	0.000	0.000	0.000
43	B	57	GLN	0	-0.065	-0.039	7.539	1.850	1.850	0.000	0.000	0.000	0.000
44	B	58	GLN	0	-0.010	0.019	8.895	2.971	2.971	0.000	0.000	0.000	0.000
45	B	59	ASP	-1	-0.779	-0.884	6.227	-38.778	-38.778	0.000	0.000	0.000	0.000
46	B	60	CYS	0	-0.136	-0.054	9.738	2.357	2.357	0.000	0.000	0.000	0.000
47	B	61	ARG	1	0.870	0.896	12.750	22.683	22.683	0.000	0.000	0.000	0.000
48	B	62	ARG	1	0.932	0.979	11.957	23.008	23.008	0.000	0.000	0.000	0.000
49	B	63	GLU	-1	-0.920	-0.973	15.336	-14.273	-14.273	0.000	0.000	0.000	0.000
50	B	64	GLU	-1	-0.961	-0.969	13.732	-19.367	-19.367	0.000	0.000	0.000	0.000
51	B	65	ARG	1	0.859	0.948	10.363	22.363	22.363	0.000	0.000	0.000	0.000
52	B	66	GLY	0	0.056	0.025	16.462	0.488	0.488	0.000	0.000	0.000	0.000
53	B	67	ILE	0	-0.017	-0.012	14.544	0.757	0.757	0.000	0.000	0.000	0.000
54	B	68	GLN	0	-0.014	-0.021	15.495	-0.226	-0.226	0.000	0.000	0.000	0.000
55	B	69	LEU	0	0.048	0.030	11.041	0.515	0.515	0.000	0.000	0.000	0.000
56	B	70	VAL	0	-0.054	-0.023	14.980	-0.105	-0.105	0.000	0.000	0.000	0.000
57	B	71	GLU	-1	-0.865	-0.938	17.433	-17.125	-17.125	0.000	0.000	0.000	0.000
58	B	72	LEU	0	-0.083	-0.059	19.042	0.624	0.624	0.000	0.000	0.000	0.000
59	B	73	GLY	0	0.021	0.016	22.714	0.406	0.406	0.000	0.000	0.000	0.000
60	B	74	GLY	0	0.003	0.005	21.006	0.261	0.261	0.000	0.000	0.000	0.000
61	B	75	VAL	0	-0.010	0.008	20.067	-0.388	-0.388	0.000	0.000	0.000	0.000
62	B	76	PHE	0	-0.002	-0.011	15.095	-0.389	-0.389	0.000	0.000	0.000	0.000
63	B	77	LEU	0	0.054	0.026	17.040	0.236	0.236	0.000	0.000	0.000	0.000
64	B	78	LEU	0	0.003	-0.003	12.620	-0.759	-0.759	0.000	0.000	0.000	0.000
65	B	79	ALA	0	0.045	0.029	16.652	0.865	0.865	0.000	0.000	0.000	0.000
66	B	80	THR	0	0.001	-0.003	19.078	-0.621	-0.621	0.000	0.000	0.000	0.000
67	B	81	LYS	1	0.884	0.965	16.626	17.164	17.164	0.000	0.000	0.000	0.000
68	B	82	LYS	1	0.970	0.962	22.152	12.206	12.206	0.000	0.000	0.000	0.000
69	B	83	GLU	-1	-0.886	-0.944	22.069	-13.046	-13.046	0.000	0.000	0.000	0.000
70	B	84	HIS	0	0.011	0.007	21.591	0.364	0.364	0.000	0.000	0.000	0.000
71	B	85	ALA	0	0.019	0.005	26.295	0.281	0.281	0.000	0.000	0.000	0.000
72	B	86	PRO	0	-0.046	-0.028	28.831	0.348	0.348	0.000	0.000	0.000	0.000
73	B	87	TYR	0	0.035	0.003	28.018	0.474	0.474	0.000	0.000	0.000	0.000
74	B	88	LEU	0	0.053	0.032	25.984	0.153	0.153	0.000	0.000	0.000	0.000
75	B	89	LYS	1	0.943	0.980	29.865	9.181	9.181	0.000	0.000	0.000	0.000
76	B	90	LYS	1	0.938	0.965	32.796	9.342	9.342	0.000	0.000	0.000	0.000
77	B	91	LEU	0	-0.023	0.004	28.733	0.192	0.192	0.000	0.000	0.000	0.000
78	B	92	VAL	0	-0.023	-0.032	32.403	0.158	0.158	0.000	0.000	0.000	0.000
79	B	93	GLU	-1	-0.981	-0.984	34.772	-7.801	-7.801	0.000	0.000	0.000	0.000
80	B	94	ALA	0	-0.030	-0.017	36.227	0.245	0.245	0.000	0.000	0.000	0.000
81	B	95	PRO	0	-0.014	0.003	37.482	-0.094	-0.094	0.000	0.000	0.000	0.000
82	B	96	GLY	0	0.031	0.003	37.698	0.021	0.021	0.000	0.000	0.000	0.000
83	B	97	ALA	0	-0.027	0.000	34.914	0.096	0.096	0.000	0.000	0.000	0.000
84	B	98	SER	0	0.024	0.026	33.077	-0.224	-0.224	0.000	0.000	0.000	0.000
85	B	99	PRO	0	0.061	0.012	29.306	0.173	0.173	0.000	0.000	0.000	0.000
86	B	100	LEU	0	-0.001	0.009	31.716	0.063	0.063	0.000	0.000	0.000	0.000
87	B	101	SER	0	-0.023	-0.018	34.966	0.148	0.148	0.000	0.000	0.000	0.000
88	B	102	GLN	0	0.051	0.006	32.902	0.167	0.167	0.000	0.000	0.000	0.000
89	B	103	ALA	0	0.075	0.056	33.859	0.013	0.013	0.000	0.000	0.000	0.000
90	B	104	ALA	0	-0.024	0.035	35.357	0.153	0.153	0.000	0.000	0.000	0.000
91	B	105	LEU	0	0.008	0.004	37.281	0.157	0.157	0.000	0.000	0.000	0.000
92	B	106	GLU	-1	-0.868	-0.919	32.810	-8.765	-8.765	0.000	0.000	0.000	0.000
93	B	107	THR	0	-0.054	-0.092	37.109	0.056	0.056	0.000	0.000	0.000	0.000
94	B	108	LEU	0	-0.025	-0.022	39.412	0.128	0.128	0.000	0.000	0.000	0.000
95	B	109	ALA	0	0.002	0.007	39.611	0.179	0.179	0.000	0.000	0.000	0.000
96	B	110	ILE	0	0.012	0.002	36.853	0.103	0.103	0.000	0.000	0.000	0.000
97	B	111	ILE	0	-0.027	-0.008	41.344	0.133	0.133	0.000	0.000	0.000	0.000
98	B	112	ALA	0	-0.003	-0.001	44.687	0.114	0.114	0.000	0.000	0.000	0.000
99	B	113	TYR	0	-0.032	-0.026	43.554	0.106	0.106	0.000	0.000	0.000	0.000
100	B	114	ARG	1	0.881	0.939	41.696	6.996	6.996	0.000	0.000	0.000	0.000
101	B	115	GLN	0	-0.019	0.027	45.849	0.043	0.043	0.000	0.000	0.000	0.000
102	B	116	PRO	0	-0.049	-0.037	48.480	0.065	0.065	0.000	0.000	0.000	0.000
103	B	117	ILE	0	0.073	0.039	42.332	-0.055	-0.055	0.000	0.000	0.000	0.000
104	B	118	THR	0	-0.039	-0.026	44.824	0.010	0.010	0.000	0.000	0.000	0.000
105	B	119	ARG	1	0.940	0.956	40.390	7.179	7.179	0.000	0.000	0.000	0.000
106	B	120	ALA	0	-0.029	-0.007	40.531	-0.173	-0.173	0.000	0.000	0.000	0.000
107	B	121	GLU	-1	-0.798	-0.910	39.981	-6.766	-6.766	0.000	0.000	0.000	0.000
108	B	122	ILE	0	-0.005	-0.004	38.450	-0.134	-0.134	0.000	0.000	0.000	0.000
109	B	123	GLU	-1	-0.930	-0.973	36.086	-8.131	-8.131	0.000	0.000	0.000	0.000
110	B	124	GLU	-1	-0.934	-0.950	35.009	-8.478	-8.478	0.000	0.000	0.000	0.000
111	B	125	ILE	0	-0.042	-0.011	34.807	-0.149	-0.149	0.000	0.000	0.000	0.000
112	B	126	ARG	1	0.830	0.889	32.996	8.392	8.392	0.000	0.000	0.000	0.000
113	B	127	GLY	0	0.066	0.060	30.979	-0.252	-0.252	0.000	0.000	0.000	0.000
114	B	128	VAL	0	-0.006	-0.020	29.661	-0.276	-0.276	0.000	0.000	0.000	0.000
115	B	129	LYS	1	0.952	0.977	31.905	9.458	9.458	0.000	0.000	0.000	0.000
116	B	130	SER	0	-0.015	-0.003	35.178	-0.090	-0.090	0.000	0.000	0.000	0.000
117	B	131	ASP	-1	-0.936	-0.978	37.540	-7.351	-7.351	0.000	0.000	0.000	0.000
118	B	132	LYS	1	0.982	0.997	37.805	7.887	7.887	0.000	0.000	0.000	0.000
119	B	133	PRO	0	-0.032	-0.025	37.181	0.161	0.161	0.000	0.000	0.000	0.000
120	B	134	LEU	0	0.099	0.046	39.935	0.153	0.153	0.000	0.000	0.000	0.000
121	B	135	GLN	0	0.024	0.021	42.922	0.037	0.037	0.000	0.000	0.000	0.000
122	B	136	THR	0	-0.070	-0.044	41.513	0.199	0.199	0.000	0.000	0.000	0.000
123	B	137	LEU	0	-0.025	-0.002	42.230	0.089	0.089	0.000	0.000	0.000	0.000
124	B	138	MET	0	-0.019	0.004	45.485	0.115	0.115	0.000	0.000	0.000	0.000
125	B	139	ALA	0	-0.023	-0.003	47.342	0.123	0.123	0.000	0.000	0.000	0.000
126	B	140	ARG	1	0.926	0.961	44.559	6.707	6.707	0.000	0.000	0.000	0.000
127	B	141	ALA	0	0.001	0.012	49.044	0.053	0.053	0.000	0.000	0.000	0.000
128	B	142	LEU	0	-0.007	0.005	46.323	0.026	0.026	0.000	0.000	0.000	0.000
129	B	143	ILE	0	-0.002	-0.009	46.421	-0.022	-0.022	0.000	0.000	0.000	0.000
130	B	144	LYS	1	0.942	0.949	49.318	5.617	5.617	0.000	0.000	0.000	0.000
131	B	145	GLU	-1	-0.967	-0.974	50.813	-5.720	-5.720	0.000	0.000	0.000	0.000
132	B	146	VAL	0	-0.035	-0.006	52.561	0.079	0.079	0.000	0.000	0.000	0.000
133	B	147	GLY	0	0.025	0.017	53.565	0.116	0.116	0.000	0.000	0.000	0.000
134	B	148	ARG	1	0.871	0.914	51.892	5.717	5.717	0.000	0.000	0.000	0.000
135	B	149	ALA	0	0.015	0.009	50.718	0.067	0.067	0.000	0.000	0.000	0.000
136	B	150	GLU	-1	-0.994	-0.978	52.843	-5.315	-5.315	0.000	0.000	0.000	0.000
137	B	151	GLY	0	0.109	0.036	53.670	0.043	0.043	0.000	0.000	0.000	0.000
138	B	152	THR	0	0.003	-0.005	48.148	0.039	0.039	0.000	0.000	0.000	0.000
139	B	153	GLY	0	0.044	0.034	49.231	-0.127	-0.127	0.000	0.000	0.000	0.000
140	B	154	ARG	1	0.869	0.943	50.568	5.545	5.545	0.000	0.000	0.000	0.000
141	B	155	PRO	0	0.000	0.037	47.831	0.022	0.022	0.000	0.000	0.000	0.000
142	B	156	ILE	0	0.010	-0.018	47.700	0.062	0.062	0.000	0.000	0.000	0.000
143	B	157	LEU	0	0.040	0.016	48.313	-0.141	-0.141	0.000	0.000	0.000	0.000
144	B	158	TYR	0	-0.017	-0.031	46.534	0.090	0.090	0.000	0.000	0.000	0.000
145	B	159	GLY	0	0.063	0.010	48.911	-0.004	-0.004	0.000	0.000	0.000	0.000
146	B	160	THR	0	0.000	0.031	48.280	-0.052	-0.052	0.000	0.000	0.000	0.000
147	B	161	THR	0	-0.030	-0.007	50.702	0.105	0.105	0.000	0.000	0.000	0.000
148	B	162	PRO	0	0.054	0.000	53.469	-0.051	-0.051	0.000	0.000	0.000	0.000
149	B	163	GLU	-1	-0.913	-0.953	53.963	-5.359	-5.359	0.000	0.000	0.000	0.000
150	B	164	PHE	0	-0.031	-0.028	46.790	-0.083	-0.083	0.000	0.000	0.000	0.000
151	B	165	LEU	0	-0.025	-0.012	51.149	-0.069	-0.069	0.000	0.000	0.000	0.000
152	B	166	ASP	-1	-0.876	-0.927	53.397	-5.325	-5.325	0.000	0.000	0.000	0.000
153	B	167	TYR	0	-0.093	-0.030	45.838	-0.027	-0.027	0.000	0.000	0.000	0.000
154	B	168	PHE	0	-0.031	-0.021	45.017	-0.118	-0.118	0.000	0.000	0.000	0.000
155	B	169	GLY	0	-0.028	-0.006	50.087	-0.021	-0.021	0.000	0.000	0.000	0.000
156	B	170	LEU	0	-0.062	-0.028	49.616	0.034	0.034	0.000	0.000	0.000	0.000
157	B	171	LYS	1	0.899	0.956	53.891	5.403	5.403	0.000	0.000	0.000	0.000
158	B	172	THR	0	-0.059	-0.059	56.241	0.061	0.061	0.000	0.000	0.000	0.000
159	B	173	LEU	0	0.013	-0.016	52.352	-0.078	-0.078	0.000	0.000	0.000	0.000
160	B	174	GLU	-1	-0.911	-0.958	52.067	-5.472	-5.472	0.000	0.000	0.000	0.000
161	B	175	GLU	-1	-0.898	-0.916	53.022	-5.452	-5.452	0.000	0.000	0.000	0.000
162	B	176	LEU	0	0.005	0.015	47.074	-0.090	-0.090	0.000	0.000	0.000	0.000
163	B	177	PRO	0	-0.033	-0.019	45.310	0.041	0.041	0.000	0.000	0.000	0.000
164	B	178	PRO	0	0.059	0.035	45.960	-0.116	-0.116	0.000	0.000	0.000	0.000
165	B	179	LEU	0	0.001	-0.008	41.570	-0.098	-0.098	0.000	0.000	0.000	0.000
166	B	180	PRO	0	-0.049	-0.025	42.753	0.018	0.018	0.000	0.000	0.000	0.000
167	B	181	GLU	-1	-0.940	-0.970	37.969	-7.588	-7.588	0.000	0.000	0.000	0.000
168	B	182	TRP	0	-0.048	-0.005	38.153	-0.005	-0.005	0.000	0.000	0.000	0.000

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