FMO DATABASE

FMODB ID: MNY6Z

Calculation Name: 3DWV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DWV

Chain ID: A

ChEMBL ID:

UniProt ID: Q869A5

Base Structure: X-ray

Registration Date: 2023-09-23

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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1654735.439943
FMO2-HF: Nuclear repulsion	1591126.370685
FMO2-HF: Total energy	-63609.069258
FMO2-MP2: Total energy	-63795.687801

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:9:MET)

Summations of interaction energy for fragment #1(A:9:MET)

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.
-26.289	-25.784	24.093	-9.445	-15.149	0.013

Interaction energy analysis for fragmet #1(A:9:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.031

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	11	ALA	0	0.035	0.014	2.945	-1.986	0.550	0.014	-1.034	-1.516	0.002
4	A	12	ALA	0	-0.069	-0.016	2.830	-0.413	1.015	0.707	-0.656	-1.478	-0.003
5	A	13	SER	0	-0.047	-0.027	4.434	0.366	0.435	0.000	-0.019	-0.049	0.000
6	A	14	SER	0	0.009	0.011	7.747	-0.079	-0.079	0.000	0.000	0.000	0.000
7	A	15	ILE	0	0.003	-0.023	7.780	0.107	0.107	0.000	0.000	0.000	0.000
8	A	16	PHE	0	-0.057	-0.022	8.948	-0.244	-0.244	0.000	0.000	0.000	0.000
9	A	17	ASP	-1	-0.840	-0.914	6.138	-0.054	-0.054	0.000	0.000	0.000	0.000
10	A	18	PHE	0	-0.083	-0.046	2.481	-2.206	-1.120	1.624	-0.701	-2.008	-0.007
11	A	19	GLU	-1	-0.902	-0.932	7.667	-0.675	-0.675	0.000	0.000	0.000	0.000
12	A	20	VAL	0	-0.038	-0.041	9.866	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	21	LEU	0	0.038	0.038	12.428	0.057	0.057	0.000	0.000	0.000	0.000
14	A	22	ASP	-1	-0.760	-0.891	15.664	-0.212	-0.212	0.000	0.000	0.000	0.000
15	A	23	ALA	0	-0.026	-0.016	18.493	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	24	ASP	-1	-0.931	-0.952	20.798	-0.165	-0.165	0.000	0.000	0.000	0.000
17	A	25	HIS	0	-0.054	-0.039	18.275	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	26	LYS	1	0.841	0.921	19.867	0.176	0.176	0.000	0.000	0.000	0.000
19	A	27	PRO	0	0.013	-0.011	16.921	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	28	TYR	0	-0.015	-0.038	15.675	0.046	0.046	0.000	0.000	0.000	0.000
21	A	29	ASN	0	0.021	0.003	15.933	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	30	LEU	0	0.061	0.021	11.220	0.039	0.039	0.000	0.000	0.000	0.000
23	A	31	VAL	0	0.021	0.006	15.489	0.053	0.053	0.000	0.000	0.000	0.000
24	A	32	GLN	0	-0.083	-0.037	16.566	0.040	0.040	0.000	0.000	0.000	0.000
25	A	33	HIS	0	0.034	0.035	17.002	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	34	LYS	1	0.971	0.995	14.642	-0.026	-0.026	0.000	0.000	0.000	0.000
27	A	35	GLY	0	-0.006	-0.001	18.242	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	36	SER	0	-0.056	-0.032	20.227	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	37	PRO	0	-0.013	0.012	18.853	0.009	0.009	0.000	0.000	0.000	0.000
30	A	38	LEU	0	-0.002	-0.009	14.782	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	39	LEU	0	-0.005	0.000	17.115	0.047	0.047	0.000	0.000	0.000	0.000
32	A	40	ILE	0	-0.025	-0.012	11.642	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	41	TYR	0	0.054	0.023	14.780	0.043	0.043	0.000	0.000	0.000	0.000
34	A	42	ASN	0	0.007	0.022	14.058	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	43	VAL	0	-0.026	-0.016	15.896	0.031	0.031	0.000	0.000	0.000	0.000
36	A	44	ALA	0	0.074	0.029	18.800	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	45	SER	0	-0.047	-0.027	21.482	0.005	0.005	0.000	0.000	0.000	0.000
38	A	46	LYS	1	0.929	0.966	25.069	0.054	0.054	0.000	0.000	0.000	0.000
39	A	47	CYS	0	0.078	0.057	27.857	0.001	0.001	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.040	0.031	29.680	0.002	0.002	0.000	0.000	0.000	0.000
41	A	49	TYR	0	-0.004	0.002	29.576	0.006	0.006	0.000	0.000	0.000	0.000
42	A	50	THR	0	0.021	0.013	24.963	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	51	LYS	1	0.912	0.942	24.557	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	52	GLY	0	0.119	0.082	27.418	0.010	0.010	0.000	0.000	0.000	0.000
45	A	53	GLY	0	0.023	0.015	23.945	0.003	0.003	0.000	0.000	0.000	0.000
46	A	54	TYR	0	-0.019	-0.023	24.579	0.002	0.002	0.000	0.000	0.000	0.000
47	A	55	GLU	-1	-0.902	-0.961	26.080	0.021	0.021	0.000	0.000	0.000	0.000
48	A	56	THR	0	-0.007	0.013	24.613	0.002	0.002	0.000	0.000	0.000	0.000
49	A	57	ALA	0	0.022	0.013	22.586	0.004	0.004	0.000	0.000	0.000	0.000
50	A	58	THR	0	-0.017	-0.021	24.129	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	59	THR	0	-0.024	-0.016	27.093	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	60	LEU	0	-0.022	-0.007	23.654	0.000	0.000	0.000	0.000	0.000	0.000
53	A	61	TYR	0	0.002	-0.006	23.738	0.001	0.001	0.000	0.000	0.000	0.000
54	A	62	ASN	0	-0.032	-0.039	25.824	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	63	LYS	1	0.789	0.908	29.192	-0.062	-0.062	0.000	0.000	0.000	0.000
56	A	64	TYR	0	0.004	-0.034	26.302	0.002	0.002	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.927	0.989	26.112	0.008	0.008	0.000	0.000	0.000	0.000
58	A	66	SER	0	-0.041	-0.019	27.118	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	67	GLN	0	-0.052	-0.038	28.109	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	68	GLY	0	0.037	0.028	25.533	0.007	0.007	0.000	0.000	0.000	0.000
61	A	69	PHE	0	-0.042	-0.008	20.939	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	70	THR	0	0.019	-0.008	19.109	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	71	VAL	0	0.005	0.010	19.464	0.025	0.025	0.000	0.000	0.000	0.000
64	A	72	LEU	0	-0.001	0.002	14.709	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	73	ALA	0	-0.010	-0.014	16.786	0.021	0.021	0.000	0.000	0.000	0.000
66	A	74	PHE	0	0.063	0.021	11.832	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	75	PRO	0	-0.055	-0.032	15.375	0.024	0.024	0.000	0.000	0.000	0.000
68	A	76	SER	0	0.054	0.007	15.775	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	77	ASN	0	-0.053	-0.045	15.511	0.056	0.056	0.000	0.000	0.000	0.000
70	A	78	GLN	0	-0.052	-0.037	18.170	0.015	0.015	0.000	0.000	0.000	0.000
71	A	79	PHE	0	0.022	0.022	17.184	0.029	0.029	0.000	0.000	0.000	0.000
72	A	80	GLY	0	0.057	0.019	17.554	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	81	GLY	0	0.034	0.030	19.229	0.010	0.010	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.063	-0.038	14.948	0.037	0.037	0.000	0.000	0.000	0.000
75	A	83	GLU	-1	-0.736	-0.829	14.520	-0.320	-0.320	0.000	0.000	0.000	0.000
76	A	84	PRO	0	-0.067	-0.034	15.424	0.030	0.030	0.000	0.000	0.000	0.000
77	A	85	GLY	0	-0.023	-0.014	18.170	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	86	ASN	0	0.023	0.018	21.877	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	87	GLU	-1	-0.888	-0.944	23.112	-0.087	-0.087	0.000	0.000	0.000	0.000
80	A	88	GLU	-1	-0.885	-0.976	24.704	-0.048	-0.048	0.000	0.000	0.000	0.000
81	A	89	GLU	-1	-0.944	-0.972	26.460	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	90	ILE	0	-0.041	-0.054	25.084	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	91	LYS	1	0.885	0.973	28.213	0.047	0.047	0.000	0.000	0.000	0.000
84	A	92	GLU	-1	-1.013	-0.992	30.430	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	93	PHE	0	-0.020	-0.002	31.630	0.003	0.003	0.000	0.000	0.000	0.000
86	A	94	VAL	0	0.000	-0.001	31.833	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	96	THR	0	-0.055	-0.034	29.987	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	97	LYS	1	0.973	0.983	25.664	0.122	0.122	0.000	0.000	0.000	0.000
89	A	98	PHE	0	0.010	-0.001	22.431	0.010	0.010	0.000	0.000	0.000	0.000
90	A	99	LYS	1	0.929	0.954	25.707	0.048	0.048	0.000	0.000	0.000	0.000
91	A	100	ALA	0	0.011	-0.002	24.426	0.008	0.008	0.000	0.000	0.000	0.000
92	A	101	GLU	-1	-0.848	-0.915	26.572	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	102	PHE	0	-0.031	0.011	21.606	0.001	0.001	0.000	0.000	0.000	0.000
94	A	103	PRO	0	0.011	-0.007	19.775	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	104	ILE	0	-0.045	-0.017	19.434	0.007	0.007	0.000	0.000	0.000	0.000
96	A	105	MET	0	-0.038	-0.007	14.939	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	106	ALA	0	0.027	0.018	16.335	0.023	0.023	0.000	0.000	0.000	0.000
98	A	107	LYS	1	0.845	0.920	15.524	0.170	0.170	0.000	0.000	0.000	0.000
99	A	108	ILE	0	-0.012	0.007	10.322	-0.052	-0.052	0.000	0.000	0.000	0.000
100	A	109	ASN	0	-0.007	0.010	11.948	0.061	0.061	0.000	0.000	0.000	0.000
101	A	110	VAL	0	-0.037	-0.025	10.229	-0.124	-0.124	0.000	0.000	0.000	0.000
102	A	111	ASN	0	-0.078	-0.046	10.141	0.059	0.059	0.000	0.000	0.000	0.000
103	A	112	GLY	0	0.065	0.020	11.613	-0.047	-0.047	0.000	0.000	0.000	0.000
104	A	113	GLU	-1	-0.930	-0.958	9.963	-0.507	-0.507	0.000	0.000	0.000	0.000
105	A	114	ASN	0	0.028	0.015	9.819	-0.215	-0.215	0.000	0.000	0.000	0.000
106	A	115	ALA	0	-0.080	-0.021	7.418	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	116	HIS	0	0.047	0.034	7.015	-0.691	-0.691	0.000	0.000	0.000	0.000
108	A	117	PRO	0	0.075	0.024	2.884	-0.624	-0.085	0.224	-0.112	-0.650	0.000
109	A	118	LEU	0	0.054	0.021	2.527	-4.365	-2.444	0.925	-1.287	-1.559	-0.021
110	A	119	TYR	0	0.029	0.000	5.020	0.967	1.040	-0.001	-0.001	-0.070	0.000
111	A	120	GLU	-1	-0.888	-0.937	2.918	-0.431	0.041	0.282	-0.151	-0.603	-0.001
112	A	121	TYR	0	-0.016	-0.020	2.740	1.338	3.294	1.821	-1.137	-2.641	-0.003
113	A	122	MET	0	0.014	0.020	3.923	-0.191	-0.356	0.029	0.308	-0.172	0.000
114	A	123	LYS	1	0.780	0.884	7.134	0.097	0.097	0.000	0.000	0.000	0.000
115	A	124	LYS	1	0.864	0.915	2.190	-14.424	-23.834	18.468	-4.655	-4.403	0.046
116	A	125	THR	0	-0.012	0.001	6.753	-0.263	-0.263	0.000	0.000	0.000	0.000
117	A	126	LYS	1	0.876	0.951	8.959	-1.027	-1.027	0.000	0.000	0.000	0.000
118	A	127	PRO	0	0.031	0.022	11.927	-0.111	-0.111	0.000	0.000	0.000	0.000
119	A	128	GLY	0	0.001	-0.008	12.728	-0.115	-0.115	0.000	0.000	0.000	0.000
120	A	129	ILE	0	0.056	0.020	16.264	0.016	0.016	0.000	0.000	0.000	0.000
121	A	130	LEU	0	-0.013	0.004	19.016	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	131	ALA	0	-0.002	-0.010	18.311	0.004	0.004	0.000	0.000	0.000	0.000
123	A	132	THR	0	0.037	0.023	14.454	0.039	0.039	0.000	0.000	0.000	0.000
124	A	133	LYS	1	1.012	1.005	8.063	-0.624	-0.624	0.000	0.000	0.000	0.000
125	A	134	ALA	0	0.009	0.011	11.849	0.011	0.011	0.000	0.000	0.000	0.000
126	A	135	ILE	0	0.002	0.003	11.581	0.065	0.065	0.000	0.000	0.000	0.000
127	A	136	LYS	1	0.895	0.959	14.511	-0.229	-0.229	0.000	0.000	0.000	0.000
128	A	137	TRP	0	0.048	0.021	18.201	-0.028	-0.028	0.000	0.000	0.000	0.000
129	A	138	ASN	0	0.094	0.039	18.335	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	139	PHE	0	-0.011	-0.021	19.172	0.014	0.014	0.000	0.000	0.000	0.000
131	A	140	THR	0	-0.041	-0.010	15.172	0.031	0.031	0.000	0.000	0.000	0.000
132	A	141	SER	0	-0.012	-0.006	15.815	-0.022	-0.022	0.000	0.000	0.000	0.000
133	A	142	PHE	0	-0.015	-0.005	11.398	0.057	0.057	0.000	0.000	0.000	0.000
134	A	143	LEU	0	0.014	0.014	14.458	-0.057	-0.057	0.000	0.000	0.000	0.000
135	A	144	ILE	0	-0.037	-0.003	11.871	0.104	0.104	0.000	0.000	0.000	0.000
136	A	145	ASP	-1	-0.785	-0.909	15.138	0.347	0.347	0.000	0.000	0.000	0.000
137	A	146	ARG	1	0.978	0.973	16.633	-0.159	-0.159	0.000	0.000	0.000	0.000
138	A	147	ASP	-1	-0.899	-0.928	15.159	0.207	0.207	0.000	0.000	0.000	0.000
139	A	148	GLY	0	-0.035	-0.033	12.926	0.011	0.011	0.000	0.000	0.000	0.000
140	A	149	VAL	0	0.035	0.017	10.884	0.201	0.201	0.000	0.000	0.000	0.000
141	A	150	PRO	0	-0.043	-0.027	8.850	-0.161	-0.161	0.000	0.000	0.000	0.000
142	A	151	VAL	0	0.022	0.011	12.120	0.096	0.096	0.000	0.000	0.000	0.000
143	A	152	GLU	-1	-0.943	-0.981	15.269	0.313	0.313	0.000	0.000	0.000	0.000
144	A	153	ARG	1	0.767	0.883	11.834	-0.430	-0.430	0.000	0.000	0.000	0.000
145	A	154	PHE	0	0.009	0.006	16.100	-0.015	-0.015	0.000	0.000	0.000	0.000
146	A	155	SER	0	-0.019	-0.021	18.615	-0.013	-0.013	0.000	0.000	0.000	0.000
147	A	156	PRO	0	0.020	-0.004	20.434	0.001	0.001	0.000	0.000	0.000	0.000
148	A	157	GLY	0	0.016	0.013	22.514	-0.010	-0.010	0.000	0.000	0.000	0.000
149	A	158	ALA	0	-0.081	-0.030	23.152	0.001	0.001	0.000	0.000	0.000	0.000
150	A	159	SER	0	0.031	0.022	25.087	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	160	VAL	0	0.066	0.008	26.627	0.009	0.009	0.000	0.000	0.000	0.000
152	A	161	LYS	1	0.928	0.976	27.767	-0.081	-0.081	0.000	0.000	0.000	0.000
153	A	162	ASP	-1	-0.842	-0.921	25.636	0.133	0.133	0.000	0.000	0.000	0.000
154	A	163	ILE	0	-0.061	-0.032	21.712	0.016	0.016	0.000	0.000	0.000	0.000
155	A	164	GLU	-1	-0.787	-0.874	24.337	0.090	0.090	0.000	0.000	0.000	0.000
156	A	165	GLU	-1	-0.930	-0.959	26.535	0.121	0.121	0.000	0.000	0.000	0.000
157	A	166	LYS	1	0.907	0.963	21.690	-0.217	-0.217	0.000	0.000	0.000	0.000
158	A	167	LEU	0	-0.003	-0.004	21.982	0.010	0.010	0.000	0.000	0.000	0.000
159	A	168	ILE	0	0.016	0.003	23.797	-0.004	-0.004	0.000	0.000	0.000	0.000
160	A	169	PRO	0	-0.025	-0.011	24.969	-0.007	-0.007	0.000	0.000	0.000	0.000
161	A	170	LEU	0	-0.079	-0.035	19.587	0.002	0.002	0.000	0.000	0.000	0.000
162	A	171	LEU	0	-0.060	-0.010	23.447	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:MET)