FMO DATABASE

FMODB ID: 4L5NN

Calculation Name: 4YVQ-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YVQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q940U6

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-578909.172036
FMO2-HF: Nuclear repulsion	541520.032734
FMO2-HF: Total energy	-37389.139302
FMO2-MP2: Total energy	-37492.248542

3D Structure Molmil

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:439:MET)

Summations of interaction energy for fragment #1(A:439: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.
-30.499	-33.99	10.284	-1.571	-5.221	0.037

Interaction energy analysis for fragmet #1(A:439:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.098 / q_NPA : 0.002

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].
4	A	440	LEU	0	-0.022	0.132	2.948	-0.190	0.257	0.184	-0.238	-0.392	0.000
5	A	441	GLU	0	0.050	-0.132	3.879	1.372	2.415	-0.008	-0.532	-0.503	0.001
6	A	441	GLU	-1	-0.868	-0.796	3.151	-9.009	-11.417	0.000	2.756	-0.348	-0.002
7	A	442	THR	0	0.022	-0.108	4.732	0.777	0.865	-0.002	-0.009	-0.077	0.000
8	A	442	THR	0	-0.056	0.059	3.964	0.020	0.102	-0.001	-0.025	-0.056	0.000
9	A	443	VAL	0	0.048	-0.092	6.201	0.626	0.626	0.000	0.000	0.000	0.000
10	A	443	VAL	0	-0.072	0.124	5.497	0.087	0.087	0.000	0.000	0.000	0.000
11	A	444	PRO	0	0.017	-0.133	7.773	0.142	0.142	0.000	0.000	0.000	0.000
12	A	445	THR	0	-0.002	0.010	9.769	0.153	0.153	0.000	0.000	0.000	0.000
13	A	445	THR	0	0.015	0.081	9.218	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	446	ILE	0	0.152	-0.059	9.509	-0.086	-0.086	0.000	0.000	0.000	0.000
15	A	446	ILE	0	-0.098	0.096	6.727	0.070	0.070	0.000	0.000	0.000	0.000
16	A	447	LYS	0	0.087	-0.091	10.852	0.020	0.020	0.000	0.000	0.000	0.000
17	A	447	LYS	1	0.867	1.069	12.947	-0.187	-0.187	0.000	0.000	0.000	0.000
18	A	448	LYS	0	-0.009	-0.130	13.639	0.029	0.029	0.000	0.000	0.000	0.000
19	A	448	LYS	1	0.772	1.002	14.092	0.371	0.371	0.000	0.000	0.000	0.000
20	A	449	LEU	0	0.149	-0.099	14.157	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	449	LEU	0	-0.066	0.135	13.544	0.001	0.001	0.000	0.000	0.000	0.000
22	A	450	ARG	0	0.085	-0.090	15.009	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	450	ARG	1	0.860	1.058	14.054	-0.553	-0.553	0.000	0.000	0.000	0.000
24	A	451	ALA	0	0.093	-0.078	16.798	0.005	0.005	0.000	0.000	0.000	0.000
25	A	451	ALA	0	-0.094	0.091	18.772	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	452	TYR	0	0.054	-0.092	18.828	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	452	TYR	0	-0.093	0.084	18.866	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	453	ALA	0	0.095	-0.103	19.455	-0.030	-0.030	0.000	0.000	0.000	0.000
29	A	453	ALA	0	-0.068	0.109	19.364	0.009	0.009	0.000	0.000	0.000	0.000
30	A	454	GLU	0	0.115	-0.094	20.857	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	454	GLU	-1	-0.909	-0.782	21.440	0.258	0.258	0.000	0.000	0.000	0.000
32	A	455	ARG	0	0.098	-0.086	22.813	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	455	ARG	1	0.858	1.057	24.057	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	456	ILE	0	0.046	-0.094	24.395	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	456	ILE	0	-0.083	0.088	23.327	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	457	ARG	0	0.105	-0.097	25.052	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	457	ARG	1	0.654	0.918	24.406	-0.211	-0.211	0.000	0.000	0.000	0.000
38	A	458	VAL	0	0.061	-0.097	26.603	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	458	VAL	0	-0.093	0.104	26.639	0.002	0.002	0.000	0.000	0.000	0.000
40	A	459	ALA	0	0.197	-0.059	28.801	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	459	ALA	0	-0.087	0.104	29.780	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	460	GLU	0	0.017	-0.126	29.936	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	460	GLU	-1	-0.889	-0.787	29.702	0.063	0.063	0.000	0.000	0.000	0.000
44	A	461	LEU	0	0.124	-0.085	30.756	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	461	LEU	0	-0.107	0.098	30.388	0.003	0.003	0.000	0.000	0.000	0.000
46	A	462	GLU	0	0.053	-0.141	32.350	0.000	0.000	0.000	0.000	0.000	0.000
47	A	462	GLU	-1	-0.973	-0.826	32.870	0.096	0.096	0.000	0.000	0.000	0.000
48	A	463	LYS	0	0.102	-0.074	34.459	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	463	LYS	1	0.727	0.972	33.392	-0.055	-0.055	0.000	0.000	0.000	0.000
50	A	464	CYS	0	0.078	-0.120	35.175	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	464	CYS	0	-0.152	0.100	34.877	0.002	0.002	0.000	0.000	0.000	0.000
52	A	465	MET	0	0.056	-0.123	36.453	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	465	MET	0	-0.070	0.108	35.744	0.002	0.002	0.000	0.000	0.000	0.000
54	A	466	SER	0	0.054	-0.093	38.367	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	466	SER	0	-0.065	0.054	38.493	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	467	LYS	0	-0.008	-0.084	40.214	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	467	LYS	1	0.830	1.033	37.620	-0.066	-0.066	0.000	0.000	0.000	0.000
58	A	468	MET	0	0.070	-0.093	41.598	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	468	MET	0	-0.127	0.081	39.686	0.005	0.005	0.000	0.000	0.000	0.000
60	A	469	GLY	0	0.003	-0.109	42.845	0.000	0.000	0.000	0.000	0.000	0.000
61	A	470	ASP	0	0.028	-0.029	45.208	0.004	0.004	0.000	0.000	0.000	0.000
62	A	470	ASP	-1	-0.936	-0.826	48.496	0.064	0.064	0.000	0.000	0.000	0.000
63	A	471	ASP	0	0.080	-0.105	45.086	0.002	0.002	0.000	0.000	0.000	0.000
64	A	471	ASP	-1	-0.976	-0.840	43.934	0.087	0.087	0.000	0.000	0.000	0.000
65	A	472	ILE	0	0.059	-0.119	41.554	0.007	0.007	0.000	0.000	0.000	0.000
66	A	472	ILE	0	-0.073	0.129	39.405	0.001	0.001	0.000	0.000	0.000	0.000
67	A	473	ASN	0	0.075	-0.059	42.261	0.000	0.000	0.000	0.000	0.000	0.000
68	A	473	ASN	0	-0.025	0.100	42.533	0.007	0.007	0.000	0.000	0.000	0.000
69	A	474	LYS	0	0.093	-0.074	40.037	0.005	0.005	0.000	0.000	0.000	0.000
70	A	474	LYS	1	0.881	1.044	40.406	-0.124	-0.124	0.000	0.000	0.000	0.000
71	A	475	LYS	0	0.123	-0.055	38.332	0.008	0.008	0.000	0.000	0.000	0.000
72	A	475	LYS	1	0.893	1.063	39.376	-0.126	-0.126	0.000	0.000	0.000	0.000
73	A	476	THR	0	0.028	-0.115	37.475	0.012	0.012	0.000	0.000	0.000	0.000
74	A	476	THR	0	-0.039	0.084	39.511	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	477	THR	0	0.044	-0.079	37.011	0.003	0.003	0.000	0.000	0.000	0.000
76	A	477	THR	0	-0.034	0.055	35.805	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	478	ARG	0	0.097	-0.064	33.762	0.005	0.005	0.000	0.000	0.000	0.000
78	A	478	ARG	1	0.716	0.954	28.827	-0.245	-0.245	0.000	0.000	0.000	0.000
79	A	479	ALA	0	0.099	-0.104	32.665	0.017	0.017	0.000	0.000	0.000	0.000
80	A	479	ALA	0	-0.078	0.108	35.409	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	480	VAL	0	0.058	-0.105	32.790	0.010	0.010	0.000	0.000	0.000	0.000
82	A	480	VAL	0	-0.028	0.123	33.343	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	481	ASP	0	0.101	-0.078	30.525	0.000	0.000	0.000	0.000	0.000	0.000
84	A	481	ASP	-1	-0.861	-0.775	29.309	0.222	0.222	0.000	0.000	0.000	0.000
85	A	482	ASP	0	0.116	-0.103	28.393	0.014	0.014	0.000	0.000	0.000	0.000
86	A	482	ASP	-1	-0.884	-0.760	28.851	0.250	0.250	0.000	0.000	0.000	0.000
87	A	483	LEU	0	0.107	-0.096	27.908	0.023	0.023	0.000	0.000	0.000	0.000
88	A	483	LEU	0	-0.091	0.115	30.040	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	484	SER	0	-0.002	-0.096	27.931	0.007	0.007	0.000	0.000	0.000	0.000
90	A	484	SER	0	-0.030	0.084	28.395	0.000	0.000	0.000	0.000	0.000	0.000
91	A	485	ARG	0	0.030	-0.105	24.381	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	485	ARG	1	0.773	1.010	23.920	-0.271	-0.271	0.000	0.000	0.000	0.000
93	A	486	GLY	0	0.011	-0.114	23.260	0.037	0.037	0.000	0.000	0.000	0.000
94	A	487	ILE	0	0.066	-0.007	23.700	0.028	0.028	0.000	0.000	0.000	0.000
95	A	487	ILE	0	-0.071	0.109	25.014	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	488	VAL	0	0.076	-0.102	22.117	0.005	0.005	0.000	0.000	0.000	0.000
97	A	488	VAL	0	-0.059	0.121	20.711	0.000	0.000	0.000	0.000	0.000	0.000
98	A	489	ASN	0	0.133	-0.079	19.036	0.009	0.009	0.000	0.000	0.000	0.000
99	A	489	ASN	0	-0.128	0.049	19.753	0.022	0.022	0.000	0.000	0.000	0.000
100	A	490	ARG	0	0.091	-0.074	18.368	0.068	0.068	0.000	0.000	0.000	0.000
101	A	490	ARG	1	0.857	1.059	21.819	-0.257	-0.257	0.000	0.000	0.000	0.000
102	A	491	PHE	0	0.088	-0.087	19.263	0.017	0.017	0.000	0.000	0.000	0.000
103	A	491	PHE	0	-0.123	0.080	20.088	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	492	LEU	0	0.070	-0.109	16.142	-0.041	-0.041	0.000	0.000	0.000	0.000
105	A	492	LEU	0	-0.089	0.082	15.584	0.007	0.007	0.000	0.000	0.000	0.000
106	A	493	HIS	0	0.080	-0.084	14.266	0.067	0.067	0.000	0.000	0.000	0.000
107	A	493	HIS	0	-0.076	0.098	14.926	0.005	0.005	0.000	0.000	0.000	0.000
108	A	494	GLY	0	0.007	-0.092	13.220	0.111	0.111	0.000	0.000	0.000	0.000
109	A	495	PRO	0	0.061	0.009	12.396	0.040	0.040	0.000	0.000	0.000	0.000
110	A	496	MET	0	0.110	0.017	9.909	-0.063	-0.063	0.000	0.000	0.000	0.000
111	A	496	MET	0	-0.130	0.082	10.715	0.010	0.010	0.000	0.000	0.000	0.000
112	A	497	GLN	0	0.127	-0.095	8.454	0.512	0.512	0.000	0.000	0.000	0.000
113	A	497	GLN	0	-0.066	0.121	10.678	-0.147	-0.147	0.000	0.000	0.000	0.000
114	A	498	HIS	0	0.029	-0.096	8.200	0.408	0.408	0.000	0.000	0.000	0.000
115	A	498	HIS	0	-0.143	0.071	10.227	-0.048	-0.048	0.000	0.000	0.000	0.000
116	A	499	LEU	0	0.119	-0.082	6.419	-0.595	-0.595	0.000	0.000	0.000	0.000
117	A	499	LEU	0	-0.104	0.092	6.633	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	500	ARG	0	0.059	-0.094	3.633	-0.268	-0.084	0.005	-0.101	-0.088	0.000
119	A	500	ARG	1	0.793	1.009	2.041	-21.155	-24.580	10.007	-3.469	-3.113	0.036
120	A	501	CYS	0	0.137	-0.046	3.506	-2.528	-1.877	0.026	-0.322	-0.355	0.002
121	A	501	CYS	0	-0.180	0.081	5.709	-0.052	-0.052	0.000	0.000	0.000	0.000
122	A	502	ASP	0	0.090	-0.113	4.444	-1.614	-1.556	-0.002	-0.016	-0.041	0.000
123	A	502	ASP	-1	-0.806	-0.770	6.485	0.602	0.602	0.000	0.000	0.000	0.000
124	A	503	GLY	0	-0.110	-0.182	7.366	0.291	0.291	0.000	0.000	0.000	0.000
125	A	504	SER	0	-0.020	0.009	10.220	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	504	SER	0	-0.051	0.034	13.289	0.026	0.026	0.000	0.000	0.000	0.000
127	A	505	ASP	0	0.000	-0.095	11.818	0.013	0.013	0.000	0.000	0.000	0.000
128	A	505	ASP	-1	-0.911	-0.818	14.473	0.316	0.316	0.000	0.000	0.000	0.000
129	A	506	SER	0	0.046	-0.058	10.958	-0.112	-0.112	0.000	0.000	0.000	0.000
130	A	506	SER	0	-0.086	0.034	11.728	0.028	0.028	0.000	0.000	0.000	0.000
131	A	507	ARG	0	0.114	-0.070	9.117	-0.138	-0.138	0.000	0.000	0.000	0.000
132	A	507	ARG	1	0.728	0.995	5.925	-0.420	-0.420	0.000	0.000	0.000	0.000
133	A	508	THR	0	0.063	-0.089	8.028	-0.186	-0.186	0.000	0.000	0.000	0.000
134	A	508	THR	0	-0.099	0.024	10.384	-0.110	-0.110	0.000	0.000	0.000	0.000
135	A	509	LEU	0	0.175	-0.072	5.916	0.159	0.159	0.000	0.000	0.000	0.000
136	A	509	LEU	0	-0.076	0.112	3.298	0.223	-0.099	0.074	0.415	-0.167	0.000
137	A	510	SER	0	0.038	-0.083	6.578	-0.288	-0.288	0.000	0.000	0.000	0.000
138	A	510	SER	0	0.016	0.085	10.957	0.079	0.079	0.000	0.000	0.000	0.000
139	A	511	GLU	0	0.021	-0.146	9.828	-0.017	-0.017	0.000	0.000	0.000	0.000
140	A	511	GLU	-1	-0.827	-0.747	9.843	-0.646	-0.646	0.000	0.000	0.000	0.000
141	A	512	THR	0	0.005	-0.068	5.651	0.446	0.446	0.000	0.000	0.000	0.000
142	A	512	THR	0	-0.074	0.071	3.699	0.067	0.178	0.001	-0.030	-0.081	0.000
143	A	513	LEU	0	0.095	-0.104	6.992	0.176	0.176	0.000	0.000	0.000	0.000
144	A	513	LEU	0	-0.091	0.102	5.704	-0.007	-0.007	0.000	0.000	0.000	0.000
145	A	514	GLU	0	0.076	-0.097	8.293	0.223	0.223	0.000	0.000	0.000	0.000
146	A	514	GLU	-1	-0.837	-0.744	12.281	-0.766	-0.766	0.000	0.000	0.000	0.000
147	A	515	ASN	0	0.096	-0.089	10.149	0.165	0.165	0.000	0.000	0.000	0.000
148	A	515	ASN	0	-0.121	0.063	8.951	0.066	0.066	0.000	0.000	0.000	0.000
149	A	516	MET	0	0.082	-0.070	9.159	0.327	0.327	0.000	0.000	0.000	0.000
150	A	516	MET	0	-0.099	0.093	8.343	-0.161	-0.161	0.000	0.000	0.000	0.000
151	A	517	HIS	0	0.082	-0.110	10.232	0.183	0.183	0.000	0.000	0.000	0.000
152	A	517	HIS	0	-0.064	0.110	11.690	0.094	0.094	0.000	0.000	0.000	0.000
153	A	518	ALA	0	0.042	-0.126	13.419	0.095	0.095	0.000	0.000	0.000	0.000
154	A	518	ALA	0	-0.038	0.129	14.183	0.008	0.008	0.000	0.000	0.000	0.000
155	A	519	LEU	0	0.118	-0.088	13.650	0.057	0.057	0.000	0.000	0.000	0.000
156	A	519	LEU	0	-0.078	0.097	11.370	0.029	0.029	0.000	0.000	0.000	0.000
157	A	520	ASN	0	0.063	-0.099	14.085	0.098	0.098	0.000	0.000	0.000	0.000
158	A	520	ASN	0	-0.081	0.069	12.854	0.088	0.088	0.000	0.000	0.000	0.000
159	A	521	ARG	0	0.051	-0.069	15.674	0.041	0.041	0.000	0.000	0.000	0.000
160	A	521	ARG	1	0.724	0.938	15.745	0.598	0.598	0.000	0.000	0.000	0.000
161	A	522	MET	0	0.072	-0.106	18.140	0.022	0.022	0.000	0.000	0.000	0.000
162	A	522	MET	0	-0.099	0.093	18.239	0.011	0.011	0.000	0.000	0.000	0.000
163	A	523	TYR	0	0.044	-0.094	18.702	0.026	0.026	0.000	0.000	0.000	0.000
164	A	523	TYR	0	-0.084	0.092	17.074	0.017	0.017	0.000	0.000	0.000	0.000
165	A	524	GLY	0	0.053	-0.091	20.091	0.027	0.027	0.000	0.000	0.000	0.000
166	A	525	LEU	0	0.000	-0.011	16.459	0.028	0.028	0.000	0.000	0.000	0.000
167	A	525	LEU	0	-0.061	0.092	14.363	0.013	0.013	0.000	0.000	0.000	0.000
168	A	526	GLU	0	0.033	-0.112	17.570	0.052	0.052	0.000	0.000	0.000	0.000
169	A	526	GLU	-1	-0.868	-0.757	14.231	-0.509	-0.509	0.000	0.000	0.000	0.000
170	A	527	LYS	0	-0.051	-0.141	18.256	-0.003	-0.003	0.000	0.000	0.000	0.000
171	A	527	LYS	1	0.889	0.958	21.186	0.140	0.140	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:439:MET)