FMO DATABASE

FMODB ID: LN4G9

Calculation Name: 3MEA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MEA

Chain ID: A

ChEMBL ID:

UniProt ID: Q96ES7

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	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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1599947.119813
FMO2-HF: Nuclear repulsion	1536039.319146
FMO2-HF: Total energy	-63907.800667
FMO2-MP2: Total energy	-64096.721835

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:124:LEU)

Summations of interaction energy for fragment #1(A:124:LEU)

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.
-8.879	-7.136	7.573	-4.449	-4.867	-0.026

Interaction energy analysis for fragmet #1(A:124:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.021

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	126	PHE	0	0.019	0.012	3.040	-3.735	-0.577	0.028	-1.589	-1.597	0.003
4	A	127	GLN	0	0.062	0.032	1.955	-4.975	-6.464	7.546	-2.846	-3.211	-0.029
5	A	128	GLY	0	0.042	0.019	4.544	0.424	0.498	-0.001	-0.014	-0.059	0.000
6	A	129	THR	0	-0.043	-0.018	6.316	0.001	0.001	0.000	0.000	0.000	0.000
7	A	130	LEU	0	-0.011	0.016	8.399	-0.033	-0.033	0.000	0.000	0.000	0.000
8	A	131	PRO	0	-0.025	0.000	11.547	0.114	0.114	0.000	0.000	0.000	0.000
9	A	132	LEU	0	0.009	0.005	12.877	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	133	TRP	0	-0.013	-0.012	16.060	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	134	ILE	0	-0.003	-0.001	18.437	0.013	0.013	0.000	0.000	0.000	0.000
12	A	135	GLY	0	0.035	0.039	21.566	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	136	LYS	1	0.805	0.872	23.901	-0.091	-0.091	0.000	0.000	0.000	0.000
14	A	137	PRO	0	0.000	-0.021	27.872	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	138	GLY	0	0.009	0.014	31.627	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	139	ASP	-1	-0.864	-0.909	26.552	0.071	0.071	0.000	0.000	0.000	0.000
17	A	140	LYS	1	0.936	0.964	29.359	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	141	PRO	0	0.048	0.022	25.060	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	142	PRO	0	-0.016	0.011	22.390	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	143	PRO	0	0.016	-0.015	24.120	0.003	0.003	0.000	0.000	0.000	0.000
21	A	144	LEU	0	-0.036	-0.004	20.126	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	145	CYS	0	-0.027	0.009	19.693	0.016	0.016	0.000	0.000	0.000	0.000
23	A	146	GLY	0	0.029	0.002	19.676	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	147	ALA	0	-0.025	-0.017	21.012	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	148	ILE	0	-0.056	-0.005	24.264	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	149	PRO	0	-0.004	0.002	24.616	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	150	ALA	0	0.035	0.008	24.653	0.002	0.002	0.000	0.000	0.000	0.000
28	A	151	SER	0	0.014	0.004	26.275	0.003	0.003	0.000	0.000	0.000	0.000
29	A	152	GLY	0	0.005	0.003	29.319	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	153	ASP	-1	-0.915	-0.959	31.391	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	154	TYR	0	-0.028	-0.011	20.978	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	155	VAL	0	-0.025	-0.011	25.744	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	156	ALA	0	-0.007	0.013	21.001	0.000	0.000	0.000	0.000	0.000	0.000
34	A	157	ARG	1	0.933	0.948	18.391	0.086	0.086	0.000	0.000	0.000	0.000
35	A	158	PRO	0	-0.030	-0.030	19.901	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	159	GLY	0	0.008	0.019	15.966	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	160	ASP	-1	-0.849	-0.914	15.068	-0.149	-0.149	0.000	0.000	0.000	0.000
38	A	161	LYS	1	0.836	0.907	12.215	0.386	0.386	0.000	0.000	0.000	0.000
39	A	162	VAL	0	-0.037	-0.025	16.435	0.034	0.034	0.000	0.000	0.000	0.000
40	A	163	ALA	0	0.065	0.051	19.790	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	164	ALA	0	-0.015	-0.028	22.050	0.007	0.007	0.000	0.000	0.000	0.000
42	A	165	ARG	1	0.815	0.916	24.738	0.039	0.039	0.000	0.000	0.000	0.000
43	A	166	VAL	0	0.045	0.031	26.484	0.004	0.004	0.000	0.000	0.000	0.000
44	A	167	LYS	1	0.778	0.872	29.161	0.056	0.056	0.000	0.000	0.000	0.000
45	A	168	ALA	0	0.018	0.004	30.964	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	169	VAL	0	0.021	0.000	32.303	0.001	0.001	0.000	0.000	0.000	0.000
47	A	170	ASP	-1	-0.884	-0.945	34.917	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	171	GLY	0	0.052	0.052	38.609	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	172	ASP	-1	-0.931	-0.956	34.330	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	173	GLU	-1	-0.823	-0.891	31.973	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	174	GLN	0	0.022	0.013	25.823	0.007	0.007	0.000	0.000	0.000	0.000
52	A	175	TRP	0	-0.013	-0.013	25.045	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	176	ILE	0	0.057	0.047	22.478	0.005	0.005	0.000	0.000	0.000	0.000
54	A	177	LEU	0	-0.016	-0.004	14.999	0.011	0.011	0.000	0.000	0.000	0.000
55	A	178	ALA	0	0.009	0.002	19.411	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	179	GLU	-1	-0.843	-0.916	15.047	-0.371	-0.371	0.000	0.000	0.000	0.000
57	A	180	VAL	0	-0.024	-0.005	18.339	0.012	0.012	0.000	0.000	0.000	0.000
58	A	181	VAL	0	-0.005	0.006	19.790	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	182	SER	0	-0.033	-0.027	22.219	0.007	0.007	0.000	0.000	0.000	0.000
60	A	183	TYR	0	0.060	0.009	25.149	0.004	0.004	0.000	0.000	0.000	0.000
61	A	184	SER	0	-0.012	0.015	27.856	0.005	0.005	0.000	0.000	0.000	0.000
62	A	185	HIS	0	0.097	0.015	29.282	0.007	0.007	0.000	0.000	0.000	0.000
63	A	186	ALA	0	-0.032	-0.006	33.263	0.004	0.004	0.000	0.000	0.000	0.000
64	A	187	THR	0	-0.053	-0.034	34.498	0.001	0.001	0.000	0.000	0.000	0.000
65	A	188	ASN	0	-0.011	0.006	32.733	0.000	0.000	0.000	0.000	0.000	0.000
66	A	189	LYS	1	0.934	0.975	31.100	0.058	0.058	0.000	0.000	0.000	0.000
67	A	190	TYR	0	0.048	0.033	24.657	0.000	0.000	0.000	0.000	0.000	0.000
68	A	191	GLU	-1	-0.839	-0.875	25.988	-0.103	-0.103	0.000	0.000	0.000	0.000
69	A	192	VAL	0	-0.021	-0.026	22.344	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	193	ASP	-1	-0.728	-0.834	20.394	-0.172	-0.172	0.000	0.000	0.000	0.000
71	A	194	ASP	-1	-0.819	-0.913	20.141	-0.182	-0.182	0.000	0.000	0.000	0.000
72	A	195	ILE	0	-0.022	-0.029	14.812	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	196	ASP	-1	-0.919	-0.951	16.382	-0.254	-0.254	0.000	0.000	0.000	0.000
74	A	197	GLU	-1	-0.941	-0.967	14.092	-0.432	-0.432	0.000	0.000	0.000	0.000
75	A	198	GLU	-1	-1.009	-0.991	17.035	-0.166	-0.166	0.000	0.000	0.000	0.000
76	A	199	GLY	0	0.006	0.004	19.630	0.004	0.004	0.000	0.000	0.000	0.000
77	A	200	LYS	1	0.696	0.843	16.808	0.270	0.270	0.000	0.000	0.000	0.000
78	A	201	GLU	-1	-0.826	-0.898	21.366	-0.104	-0.104	0.000	0.000	0.000	0.000
79	A	202	ARG	1	0.735	0.826	23.426	0.146	0.146	0.000	0.000	0.000	0.000
80	A	203	HIS	0	-0.030	-0.033	26.079	0.018	0.018	0.000	0.000	0.000	0.000
81	A	204	THR	0	-0.029	-0.033	27.224	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	205	LEU	0	-0.035	-0.008	26.297	0.009	0.009	0.000	0.000	0.000	0.000
83	A	206	SER	0	-0.021	-0.020	29.732	0.000	0.000	0.000	0.000	0.000	0.000
84	A	207	ARG	1	0.868	0.895	29.226	0.037	0.037	0.000	0.000	0.000	0.000
85	A	208	ARG	1	0.882	0.951	29.857	0.026	0.026	0.000	0.000	0.000	0.000
86	A	209	ARG	1	0.761	0.847	29.510	0.057	0.057	0.000	0.000	0.000	0.000
87	A	210	VAL	0	0.018	0.022	23.865	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	211	ILE	0	-0.008	0.005	23.396	0.007	0.007	0.000	0.000	0.000	0.000
89	A	212	PRO	0	-0.007	-0.012	20.818	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	213	LEU	0	0.006	0.019	15.687	0.012	0.012	0.000	0.000	0.000	0.000
91	A	214	PRO	0	-0.017	-0.005	17.421	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	215	GLN	0	-0.016	-0.015	15.687	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	216	TRP	0	-0.017	-0.018	15.223	0.003	0.003	0.000	0.000	0.000	0.000
94	A	217	LYS	1	0.812	0.922	14.117	-0.374	-0.374	0.000	0.000	0.000	0.000
95	A	218	ALA	0	0.070	0.029	17.144	0.014	0.014	0.000	0.000	0.000	0.000
96	A	219	ASN	0	0.070	0.017	20.399	0.030	0.030	0.000	0.000	0.000	0.000
97	A	220	PRO	0	-0.016	0.000	21.404	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	221	GLU	-1	-0.923	-0.973	24.021	0.198	0.198	0.000	0.000	0.000	0.000
99	A	222	THR	0	-0.108	-0.078	24.262	0.001	0.001	0.000	0.000	0.000	0.000
100	A	223	ASP	-1	-0.852	-0.897	24.080	0.116	0.116	0.000	0.000	0.000	0.000
101	A	224	PRO	0	0.029	0.011	25.618	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	225	GLU	-1	-0.888	-0.957	27.327	0.075	0.075	0.000	0.000	0.000	0.000
103	A	226	ALA	0	-0.052	-0.019	24.099	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	227	LEU	0	-0.019	-0.006	22.255	0.007	0.007	0.000	0.000	0.000	0.000
105	A	228	PHE	0	-0.007	0.001	23.465	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	229	GLN	0	0.016	-0.009	27.137	0.008	0.008	0.000	0.000	0.000	0.000
107	A	230	LYS	1	0.865	0.903	29.954	-0.049	-0.049	0.000	0.000	0.000	0.000
108	A	231	GLU	-1	-0.885	-0.935	31.469	0.031	0.031	0.000	0.000	0.000	0.000
109	A	232	GLN	0	-0.011	0.012	29.958	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	233	LEU	0	0.019	0.012	30.242	0.002	0.002	0.000	0.000	0.000	0.000
111	A	234	VAL	0	-0.052	-0.032	25.712	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	235	LEU	0	-0.020	-0.009	25.112	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	236	ALA	0	0.016	-0.001	22.102	0.005	0.005	0.000	0.000	0.000	0.000
114	A	237	LEU	0	-0.010	0.002	16.514	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	238	TYR	0	0.013	0.021	20.546	0.018	0.018	0.000	0.000	0.000	0.000
116	A	239	PRO	0	-0.010	-0.010	19.403	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	240	GLN	0	-0.020	-0.017	16.177	-0.026	-0.026	0.000	0.000	0.000	0.000
118	A	241	THR	0	0.014	0.016	19.539	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	242	THR	0	0.048	0.027	17.609	0.003	0.003	0.000	0.000	0.000	0.000
120	A	243	CYS	0	-0.025	-0.012	19.508	0.001	0.001	0.000	0.000	0.000	0.000
121	A	244	PHE	0	-0.017	-0.022	18.415	0.011	0.011	0.000	0.000	0.000	0.000
122	A	245	TYR	0	-0.004	-0.018	23.591	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	246	ARG	1	0.824	0.873	26.440	0.017	0.017	0.000	0.000	0.000	0.000
124	A	247	ALA	0	0.019	0.019	26.805	0.000	0.000	0.000	0.000	0.000	0.000
125	A	248	LEU	0	0.014	0.021	28.867	0.000	0.000	0.000	0.000	0.000	0.000
126	A	249	ILE	0	-0.029	-0.005	25.596	0.004	0.004	0.000	0.000	0.000	0.000
127	A	250	HIS	0	0.045	0.027	28.018	0.003	0.003	0.000	0.000	0.000	0.000
128	A	251	ALA	0	-0.009	-0.023	27.117	0.000	0.000	0.000	0.000	0.000	0.000
129	A	252	PRO	0	0.004	0.015	25.128	0.004	0.004	0.000	0.000	0.000	0.000
130	A	253	PRO	0	-0.006	0.014	21.025	0.001	0.001	0.000	0.000	0.000	0.000
131	A	254	GLN	0	-0.023	-0.039	23.421	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	255	ARG	1	0.841	0.896	21.920	-0.234	-0.234	0.000	0.000	0.000	0.000
133	A	256	PRO	0	0.020	0.017	18.169	0.006	0.006	0.000	0.000	0.000	0.000
134	A	257	GLN	0	-0.017	-0.022	16.269	0.022	0.022	0.000	0.000	0.000	0.000
135	A	258	ASP	-1	-0.820	-0.856	16.846	0.252	0.252	0.000	0.000	0.000	0.000
136	A	259	ASP	-1	-0.841	-0.939	15.900	0.300	0.300	0.000	0.000	0.000	0.000
137	A	260	TYR	0	0.035	0.027	19.292	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	261	SER	0	-0.003	0.010	21.791	0.003	0.003	0.000	0.000	0.000	0.000
139	A	262	VAL	0	-0.044	-0.030	23.941	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	263	LEU	0	0.031	0.026	26.533	0.002	0.002	0.000	0.000	0.000	0.000
141	A	264	PHE	0	0.019	-0.011	22.755	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	265	GLU	-1	-0.799	-0.869	28.958	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	266	ASP	-1	-0.820	-0.890	31.047	-0.013	-0.013	0.000	0.000	0.000	0.000
144	A	267	THR	0	-0.004	-0.013	32.973	0.002	0.002	0.000	0.000	0.000	0.000
145	A	268	SER	0	-0.099	-0.053	33.868	0.000	0.000	0.000	0.000	0.000	0.000
146	A	269	TYR	0	-0.055	-0.034	31.291	0.002	0.002	0.000	0.000	0.000	0.000
147	A	270	ALA	0	-0.036	-0.030	37.584	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	271	ASP	-1	-0.909	-0.959	37.269	0.015	0.015	0.000	0.000	0.000	0.000
149	A	272	GLY	0	-0.018	-0.001	37.068	0.001	0.001	0.000	0.000	0.000	0.000
150	A	273	TYR	0	-0.034	-0.022	32.308	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	274	SER	0	-0.007	0.004	28.781	0.000	0.000	0.000	0.000	0.000	0.000
152	A	275	PRO	0	0.015	-0.006	29.487	0.004	0.004	0.000	0.000	0.000	0.000
153	A	276	PRO	0	-0.023	-0.011	28.204	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	277	LEU	0	0.005	0.018	23.629	0.002	0.002	0.000	0.000	0.000	0.000
155	A	278	ASN	0	-0.028	-0.015	19.698	-0.013	-0.013	0.000	0.000	0.000	0.000
156	A	279	VAL	0	0.006	0.007	18.784	-0.010	-0.010	0.000	0.000	0.000	0.000
157	A	280	ALA	0	0.006	0.002	14.472	0.015	0.015	0.000	0.000	0.000	0.000
158	A	281	GLN	0	0.027	-0.025	16.526	-0.051	-0.051	0.000	0.000	0.000	0.000
159	A	282	ARG	1	0.815	0.918	7.946	0.131	0.131	0.000	0.000	0.000	0.000
160	A	283	TYR	0	-0.015	-0.014	12.035	-0.047	-0.047	0.000	0.000	0.000	0.000
161	A	284	VAL	0	0.047	0.022	17.622	-0.007	-0.007	0.000	0.000	0.000	0.000
162	A	285	VAL	0	0.002	0.009	21.089	0.006	0.006	0.000	0.000	0.000	0.000
163	A	286	ALA	0	0.055	0.034	23.571	0.001	0.001	0.000	0.000	0.000	0.000
164	A	287	CYS	0	-0.071	-0.022	27.381	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:124:LEU)