FMO DATABASE

FMODB ID: 3JRZL

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	OptHSide
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	-1597082.652443
FMO2-HF: Nuclear repulsion	1533175.09512
FMO2-HF: Total energy	-63907.557322
FMO2-MP2: Total energy	-64096.456142

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.
-8.937	-6.857	6.106	-4.005	-4.18	-0.025

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 : -0.036 / q_NPA : -0.025

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	0.010	0.012	3.265	-3.758	-0.704	-0.009	-1.537	-1.508	0.002
4	A	127	GLN	0	0.069	0.029	1.990	-4.753	-5.775	6.116	-2.462	-2.632	-0.027
5	A	128	GLY	0	0.041	0.016	4.804	0.362	0.410	-0.001	-0.006	-0.040	0.000
6	A	129	THR	0	-0.053	-0.021	6.623	0.003	0.003	0.000	0.000	0.000	0.000
7	A	130	LEU	0	0.003	0.016	8.690	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	131	PRO	0	-0.011	0.007	11.874	0.094	0.094	0.000	0.000	0.000	0.000
9	A	132	LEU	0	-0.011	-0.010	13.311	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	133	TRP	0	0.010	0.004	16.563	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	134	ILE	0	0.000	0.004	18.924	0.008	0.008	0.000	0.000	0.000	0.000
12	A	135	GLY	0	0.003	0.009	21.777	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	136	LYS	1	0.813	0.883	24.323	-0.093	-0.093	0.000	0.000	0.000	0.000
14	A	137	PRO	0	0.026	-0.013	28.091	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	138	GLY	0	-0.016	0.001	31.685	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	139	ASP	-1	-0.834	-0.877	27.118	0.072	0.072	0.000	0.000	0.000	0.000
17	A	140	LYS	1	0.913	0.944	29.099	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	141	PRO	0	0.070	0.038	25.281	0.000	0.000	0.000	0.000	0.000	0.000
19	A	142	PRO	0	-0.021	0.004	22.633	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	143	PRO	0	0.024	-0.012	24.497	0.002	0.002	0.000	0.000	0.000	0.000
21	A	144	LEU	0	-0.044	-0.010	20.489	0.000	0.000	0.000	0.000	0.000	0.000
22	A	145	CYS	0	-0.021	0.012	20.073	0.013	0.013	0.000	0.000	0.000	0.000
23	A	146	GLY	0	0.015	0.004	20.138	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	147	ALA	0	-0.010	-0.013	21.684	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	148	ILE	0	-0.053	-0.006	24.743	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	149	PRO	0	-0.012	0.001	25.192	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	150	ALA	0	0.022	0.003	25.250	0.003	0.003	0.000	0.000	0.000	0.000
28	A	151	SER	0	0.043	0.012	26.822	0.003	0.003	0.000	0.000	0.000	0.000
29	A	152	GLY	0	-0.007	-0.011	29.682	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	153	ASP	-1	-0.933	-0.967	31.509	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	154	TYR	0	-0.005	0.009	21.138	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	155	VAL	0	-0.031	-0.013	26.010	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	156	ALA	0	0.005	0.014	21.356	0.002	0.002	0.000	0.000	0.000	0.000
34	A	157	ARG	1	0.928	0.948	18.596	0.078	0.078	0.000	0.000	0.000	0.000
35	A	158	PRO	0	-0.015	-0.025	19.915	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	159	GLY	0	0.005	0.016	16.097	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	160	ASP	-1	-0.861	-0.918	15.205	-0.153	-0.153	0.000	0.000	0.000	0.000
38	A	161	LYS	1	0.857	0.928	12.567	0.383	0.383	0.000	0.000	0.000	0.000
39	A	162	VAL	0	-0.033	-0.026	16.782	0.033	0.033	0.000	0.000	0.000	0.000
40	A	163	ALA	0	0.051	0.041	20.076	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	164	ALA	0	-0.008	-0.018	22.436	0.010	0.010	0.000	0.000	0.000	0.000
42	A	165	ARG	1	0.829	0.917	25.065	0.050	0.050	0.000	0.000	0.000	0.000
43	A	166	VAL	0	0.041	0.018	26.933	0.004	0.004	0.000	0.000	0.000	0.000
44	A	167	LYS	1	0.783	0.879	29.636	0.065	0.065	0.000	0.000	0.000	0.000
45	A	168	ALA	0	0.027	-0.001	31.003	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	169	VAL	0	0.025	0.006	32.310	0.001	0.001	0.000	0.000	0.000	0.000
47	A	170	ASP	-1	-0.905	-0.965	35.042	-0.046	-0.046	0.000	0.000	0.000	0.000
48	A	171	GLY	0	0.091	0.071	38.821	0.000	0.000	0.000	0.000	0.000	0.000
49	A	172	ASP	-1	-0.957	-0.963	34.737	-0.050	-0.050	0.000	0.000	0.000	0.000
50	A	173	GLU	-1	-0.795	-0.862	32.223	-0.061	-0.061	0.000	0.000	0.000	0.000
51	A	174	GLN	0	0.006	0.003	26.279	0.008	0.008	0.000	0.000	0.000	0.000
52	A	175	TRP	0	-0.023	-0.012	25.315	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	176	ILE	0	0.051	0.030	22.768	0.003	0.003	0.000	0.000	0.000	0.000
54	A	177	LEU	0	0.003	0.001	15.094	0.008	0.008	0.000	0.000	0.000	0.000
55	A	178	ALA	0	0.010	0.003	19.565	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	179	GLU	-1	-0.884	-0.945	14.898	-0.387	-0.387	0.000	0.000	0.000	0.000
57	A	180	VAL	0	-0.039	-0.014	18.396	0.015	0.015	0.000	0.000	0.000	0.000
58	A	181	VAL	0	0.012	0.019	19.866	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	182	SER	0	-0.040	-0.034	22.350	0.008	0.008	0.000	0.000	0.000	0.000
60	A	183	TYR	0	0.050	0.000	25.221	0.003	0.003	0.000	0.000	0.000	0.000
61	A	184	SER	0	-0.011	0.012	27.875	0.004	0.004	0.000	0.000	0.000	0.000
62	A	185	HIS	0	0.083	0.015	29.499	0.005	0.005	0.000	0.000	0.000	0.000
63	A	186	ALA	0	-0.038	0.000	33.475	0.004	0.004	0.000	0.000	0.000	0.000
64	A	187	THR	0	-0.018	-0.019	34.374	0.002	0.002	0.000	0.000	0.000	0.000
65	A	188	ASN	0	-0.007	0.013	32.763	0.001	0.001	0.000	0.000	0.000	0.000
66	A	189	LYS	1	0.927	0.964	31.408	0.061	0.061	0.000	0.000	0.000	0.000
67	A	190	TYR	0	0.055	0.029	24.884	0.001	0.001	0.000	0.000	0.000	0.000
68	A	191	GLU	-1	-0.853	-0.878	26.201	-0.107	-0.107	0.000	0.000	0.000	0.000
69	A	192	VAL	0	-0.016	-0.024	22.493	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	193	ASP	-1	-0.740	-0.857	20.401	-0.185	-0.185	0.000	0.000	0.000	0.000
71	A	194	ASP	-1	-0.807	-0.907	20.254	-0.207	-0.207	0.000	0.000	0.000	0.000
72	A	195	ILE	0	-0.036	-0.036	15.280	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	196	ASP	-1	-0.893	-0.938	16.648	-0.285	-0.285	0.000	0.000	0.000	0.000
74	A	197	GLU	-1	-0.931	-0.964	14.316	-0.476	-0.476	0.000	0.000	0.000	0.000
75	A	198	GLU	-1	-1.007	-0.987	17.210	-0.183	-0.183	0.000	0.000	0.000	0.000
76	A	199	GLY	0	-0.009	0.005	18.922	0.005	0.005	0.000	0.000	0.000	0.000
77	A	200	LYS	1	0.667	0.817	16.894	0.304	0.304	0.000	0.000	0.000	0.000
78	A	201	GLU	-1	-0.810	-0.890	21.184	-0.119	-0.119	0.000	0.000	0.000	0.000
79	A	202	ARG	1	0.744	0.853	23.608	0.153	0.153	0.000	0.000	0.000	0.000
80	A	203	HIS	0	-0.043	-0.031	25.920	0.020	0.020	0.000	0.000	0.000	0.000
81	A	204	THR	0	-0.030	-0.037	27.474	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	205	LEU	0	-0.043	-0.016	26.657	0.008	0.008	0.000	0.000	0.000	0.000
83	A	206	SER	0	-0.030	-0.028	30.191	0.000	0.000	0.000	0.000	0.000	0.000
84	A	207	ARG	1	0.914	0.931	29.251	0.041	0.041	0.000	0.000	0.000	0.000
85	A	208	ARG	1	0.875	0.939	29.644	0.032	0.032	0.000	0.000	0.000	0.000
86	A	209	ARG	1	0.714	0.834	29.735	0.067	0.067	0.000	0.000	0.000	0.000
87	A	210	VAL	0	0.038	0.031	24.113	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	211	ILE	0	-0.010	0.003	23.878	0.008	0.008	0.000	0.000	0.000	0.000
89	A	212	PRO	0	-0.015	-0.017	21.472	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	213	LEU	0	0.002	0.020	16.208	0.011	0.011	0.000	0.000	0.000	0.000
91	A	214	PRO	0	-0.012	-0.001	17.970	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	215	GLN	0	-0.030	-0.024	15.848	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	216	TRP	0	-0.020	-0.020	15.425	0.011	0.011	0.000	0.000	0.000	0.000
94	A	217	LYS	1	0.868	0.941	13.803	-0.385	-0.385	0.000	0.000	0.000	0.000
95	A	218	ALA	0	0.091	0.034	17.652	0.015	0.015	0.000	0.000	0.000	0.000
96	A	219	ASN	0	0.068	0.009	20.891	0.023	0.023	0.000	0.000	0.000	0.000
97	A	220	PRO	0	-0.009	0.004	21.732	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	221	GLU	-1	-0.938	-0.979	24.294	0.185	0.185	0.000	0.000	0.000	0.000
99	A	222	THR	0	-0.096	-0.069	24.697	0.002	0.002	0.000	0.000	0.000	0.000
100	A	223	ASP	-1	-0.866	-0.909	24.780	0.108	0.108	0.000	0.000	0.000	0.000
101	A	224	PRO	0	0.023	0.011	26.180	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	225	GLU	-1	-0.916	-0.967	27.835	0.068	0.068	0.000	0.000	0.000	0.000
103	A	226	ALA	0	-0.054	-0.024	24.833	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	227	LEU	0	-0.019	0.006	22.541	0.001	0.001	0.000	0.000	0.000	0.000
105	A	228	PHE	0	-0.015	-0.010	23.880	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	229	GLN	0	0.012	-0.019	27.661	0.007	0.007	0.000	0.000	0.000	0.000
107	A	230	LYS	1	0.877	0.915	30.538	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	231	GLU	-1	-0.875	-0.937	32.026	0.020	0.020	0.000	0.000	0.000	0.000
109	A	232	GLN	0	-0.018	0.017	30.384	0.000	0.000	0.000	0.000	0.000	0.000
110	A	233	LEU	0	0.002	0.002	30.689	0.000	0.000	0.000	0.000	0.000	0.000
111	A	234	VAL	0	-0.049	-0.025	26.092	0.001	0.001	0.000	0.000	0.000	0.000
112	A	235	LEU	0	-0.039	-0.020	25.442	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	236	ALA	0	0.017	-0.003	22.460	0.005	0.005	0.000	0.000	0.000	0.000
114	A	237	LEU	0	-0.013	0.000	16.697	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	238	TYR	0	0.012	0.026	20.779	0.016	0.016	0.000	0.000	0.000	0.000
116	A	239	PRO	0	0.017	0.001	19.564	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	240	GLN	0	-0.029	-0.020	16.146	-0.021	-0.021	0.000	0.000	0.000	0.000
118	A	241	THR	0	0.016	0.018	19.604	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	242	THR	0	0.031	0.017	17.400	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	243	CYS	0	-0.007	0.000	19.641	0.004	0.004	0.000	0.000	0.000	0.000
121	A	244	PHE	0	-0.026	-0.024	18.742	0.007	0.007	0.000	0.000	0.000	0.000
122	A	245	TYR	0	0.010	-0.006	23.869	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	246	ARG	1	0.817	0.867	26.793	0.032	0.032	0.000	0.000	0.000	0.000
124	A	247	ALA	0	0.025	0.021	27.137	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	248	LEU	0	0.018	0.025	29.193	0.001	0.001	0.000	0.000	0.000	0.000
126	A	249	ILE	0	-0.027	-0.009	26.053	0.003	0.003	0.000	0.000	0.000	0.000
127	A	250	HIS	0	0.021	0.022	28.313	0.003	0.003	0.000	0.000	0.000	0.000
128	A	251	ALA	0	-0.013	-0.029	27.793	0.001	0.001	0.000	0.000	0.000	0.000
129	A	252	PRO	0	0.000	0.015	25.479	0.002	0.002	0.000	0.000	0.000	0.000
130	A	253	PRO	0	-0.005	0.003	21.320	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	254	GLN	0	-0.021	-0.025	24.066	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	255	ARG	1	0.842	0.882	22.094	-0.203	-0.203	0.000	0.000	0.000	0.000
133	A	256	PRO	0	0.040	0.031	18.529	0.002	0.002	0.000	0.000	0.000	0.000
134	A	257	GLN	0	-0.068	-0.036	16.782	0.022	0.022	0.000	0.000	0.000	0.000
135	A	258	ASP	-1	-0.805	-0.846	17.435	0.216	0.216	0.000	0.000	0.000	0.000
136	A	259	ASP	-1	-0.887	-0.960	16.726	0.202	0.202	0.000	0.000	0.000	0.000
137	A	260	TYR	0	-0.010	-0.005	19.733	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	261	SER	0	0.014	0.021	22.388	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	262	VAL	0	-0.027	-0.025	24.347	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	263	LEU	0	0.023	0.022	26.889	0.001	0.001	0.000	0.000	0.000	0.000
141	A	264	PHE	0	0.018	-0.010	23.257	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	265	GLU	-1	-0.796	-0.867	29.340	-0.018	-0.018	0.000	0.000	0.000	0.000
143	A	266	ASP	-1	-0.829	-0.902	31.468	-0.035	-0.035	0.000	0.000	0.000	0.000
144	A	267	THR	0	0.002	-0.009	33.558	0.002	0.002	0.000	0.000	0.000	0.000
145	A	268	SER	0	-0.126	-0.069	34.502	0.001	0.001	0.000	0.000	0.000	0.000
146	A	269	TYR	0	-0.037	-0.020	31.820	0.002	0.002	0.000	0.000	0.000	0.000
147	A	270	ALA	0	-0.025	-0.019	37.949	0.000	0.000	0.000	0.000	0.000	0.000
148	A	271	ASP	-1	-0.942	-0.984	37.722	0.001	0.001	0.000	0.000	0.000	0.000
149	A	272	GLY	0	-0.002	0.010	37.447	0.001	0.001	0.000	0.000	0.000	0.000
150	A	273	TYR	0	-0.027	-0.016	32.545	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	274	SER	0	-0.009	0.004	29.121	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	275	PRO	0	0.000	-0.011	29.689	0.005	0.005	0.000	0.000	0.000	0.000
153	A	276	PRO	0	-0.005	0.000	28.278	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	277	LEU	0	-0.008	0.011	23.815	0.002	0.002	0.000	0.000	0.000	0.000
155	A	278	ASN	0	-0.002	-0.006	20.173	-0.008	-0.008	0.000	0.000	0.000	0.000
156	A	279	VAL	0	-0.012	-0.003	19.064	-0.015	-0.015	0.000	0.000	0.000	0.000
157	A	280	ALA	0	0.029	0.023	15.129	0.014	0.014	0.000	0.000	0.000	0.000
158	A	281	GLN	0	0.033	-0.015	17.122	-0.039	-0.039	0.000	0.000	0.000	0.000
159	A	282	ARG	1	0.846	0.935	8.487	0.199	0.199	0.000	0.000	0.000	0.000
160	A	283	TYR	0	-0.019	-0.016	12.443	-0.040	-0.040	0.000	0.000	0.000	0.000
161	A	284	VAL	0	0.051	0.029	18.137	-0.007	-0.007	0.000	0.000	0.000	0.000
162	A	285	VAL	0	0.001	0.008	21.343	0.006	0.006	0.000	0.000	0.000	0.000
163	A	286	ALA	0	0.027	0.017	23.873	0.001	0.001	0.000	0.000	0.000	0.000
164	A	287	CYS	0	0.003	0.008	27.504	-0.009	-0.009	0.000	0.000	0.000	0.000

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