FMO DATABASE

FMODB ID: 76M4K

Calculation Name: 3MER-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MER

Chain ID: A

ChEMBL ID:

UniProt ID: P74712

Base Structure: X-ray

Registration Date: 2023-09-22

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	173
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1737631.940679
FMO2-HF: Nuclear repulsion	1672285.313458
FMO2-HF: Total energy	-65346.627221
FMO2-MP2: Total energy	-65540.323781

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:16:GLU)

Summations of interaction energy for fragment #1(A:16:GLU)

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.
39.85	7.893	60.441	-18.771	-9.712	0.031

Interaction energy analysis for fragmet #1(A:16:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.995 / q_NPA : -1.020

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	18	ASN	0	0.065	0.019	3.816	1.477	2.957	-0.016	-0.612	-0.852	0.003
4	A	19	ASP	-1	-0.832	-0.928	4.982	47.151	47.387	-0.001	-0.003	-0.231	0.000
5	A	20	PHE	0	0.013	0.008	7.384	-2.512	-2.512	0.000	0.000	0.000	0.000
6	A	21	LEU	0	0.009	0.019	8.722	-1.717	-1.717	0.000	0.000	0.000	0.000
7	A	22	VAL	0	-0.034	-0.020	6.176	-1.768	-1.768	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.133	-0.082	9.266	-2.065	-2.065	0.000	0.000	0.000	0.000
9	A	24	VAL	0	0.021	0.002	12.252	-1.750	-1.750	0.000	0.000	0.000	0.000
10	A	25	ALA	0	0.025	0.013	11.898	-1.244	-1.244	0.000	0.000	0.000	0.000
11	A	26	ASN	0	-0.037	-0.020	13.982	-0.950	-0.950	0.000	0.000	0.000	0.000
12	A	27	GLN	0	-0.061	-0.028	16.941	-0.535	-0.535	0.000	0.000	0.000	0.000
13	A	28	ILE	0	-0.025	0.005	15.177	-0.721	-0.721	0.000	0.000	0.000	0.000
14	A	29	PRO	0	0.050	0.074	19.072	0.473	0.473	0.000	0.000	0.000	0.000
15	A	30	GLN	0	-0.010	-0.013	20.433	-0.152	-0.152	0.000	0.000	0.000	0.000
16	A	31	GLY	0	0.080	0.037	20.653	-0.644	-0.644	0.000	0.000	0.000	0.000
17	A	32	LYS	1	0.891	0.963	20.122	-11.825	-11.825	0.000	0.000	0.000	0.000
18	A	33	ILE	0	0.034	0.024	15.192	-0.120	-0.120	0.000	0.000	0.000	0.000
19	A	34	LEU	0	-0.012	-0.007	17.545	0.216	0.216	0.000	0.000	0.000	0.000
20	A	35	CYS	0	-0.065	-0.024	13.249	0.673	0.673	0.000	0.000	0.000	0.000
21	A	36	LEU	0	0.015	-0.005	15.302	-0.490	-0.490	0.000	0.000	0.000	0.000
22	A	37	ALA	0	0.016	-0.001	15.301	0.588	0.588	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.829	-0.927	9.801	24.225	24.225	0.000	0.000	0.000	0.000
24	A	39	GLY	0	-0.027	-0.021	10.466	1.509	1.509	0.000	0.000	0.000	0.000
25	A	40	GLU	-1	-0.974	-0.990	5.221	36.117	36.117	0.000	0.000	0.000	0.000
26	A	41	GLY	0	0.131	0.066	8.337	-0.878	-0.878	0.000	0.000	0.000	0.000
27	A	42	ARG	1	0.862	0.949	1.607	-47.877	-81.595	60.459	-18.149	-8.593	0.028
28	A	43	ASN	0	0.062	0.031	5.137	4.272	4.317	-0.001	-0.007	-0.036	0.000
29	A	44	ALA	0	0.055	0.036	7.570	-0.853	-0.853	0.000	0.000	0.000	0.000
30	A	45	CYS	0	-0.018	-0.012	7.460	-1.497	-1.497	0.000	0.000	0.000	0.000
31	A	46	PHE	0	-0.037	-0.030	6.135	0.474	0.474	0.000	0.000	0.000	0.000
32	A	47	LEU	0	0.066	0.054	8.027	-1.249	-1.249	0.000	0.000	0.000	0.000
33	A	48	ALA	0	0.035	0.018	11.566	-1.218	-1.218	0.000	0.000	0.000	0.000
34	A	49	SER	0	-0.135	-0.082	10.380	-0.511	-0.511	0.000	0.000	0.000	0.000
35	A	50	LEU	0	-0.025	-0.023	11.163	-0.338	-0.338	0.000	0.000	0.000	0.000
36	A	51	GLY	0	-0.016	0.011	14.315	-1.075	-1.075	0.000	0.000	0.000	0.000
37	A	52	TYR	0	-0.092	-0.079	14.868	-0.662	-0.662	0.000	0.000	0.000	0.000
38	A	53	GLU	-1	-0.956	-0.985	16.932	13.124	13.124	0.000	0.000	0.000	0.000
39	A	54	VAL	0	-0.016	-0.033	13.312	-0.328	-0.328	0.000	0.000	0.000	0.000
40	A	55	THR	0	-0.061	-0.035	16.392	-0.576	-0.576	0.000	0.000	0.000	0.000
41	A	56	ALA	0	0.007	0.012	13.261	0.139	0.139	0.000	0.000	0.000	0.000
42	A	57	VAL	0	0.007	-0.014	15.176	-0.689	-0.689	0.000	0.000	0.000	0.000
43	A	58	ASP	-1	-0.834	-0.935	15.121	17.495	17.495	0.000	0.000	0.000	0.000
44	A	59	GLN	0	0.090	0.033	17.252	-1.098	-1.098	0.000	0.000	0.000	0.000
45	A	60	SER	0	-0.054	-0.004	16.146	-0.462	-0.462	0.000	0.000	0.000	0.000
46	A	61	SER	0	0.046	0.005	17.330	0.446	0.446	0.000	0.000	0.000	0.000
47	A	62	VAL	0	-0.016	-0.010	15.948	0.105	0.105	0.000	0.000	0.000	0.000
48	A	63	GLY	0	0.032	0.020	13.459	0.717	0.717	0.000	0.000	0.000	0.000
49	A	64	LEU	0	0.053	0.027	13.152	0.885	0.885	0.000	0.000	0.000	0.000
50	A	65	ALA	0	-0.039	-0.016	15.141	0.189	0.189	0.000	0.000	0.000	0.000
51	A	66	LYS	1	0.928	0.958	10.511	-22.038	-22.038	0.000	0.000	0.000	0.000
52	A	67	ALA	0	0.075	0.048	10.488	1.282	1.282	0.000	0.000	0.000	0.000
53	A	68	LYS	1	0.888	0.942	11.580	-14.762	-14.762	0.000	0.000	0.000	0.000
54	A	69	GLN	0	-0.003	-0.007	13.147	0.651	0.651	0.000	0.000	0.000	0.000
55	A	70	LEU	0	0.060	0.052	5.612	0.576	0.576	0.000	0.000	0.000	0.000
56	A	71	ALA	0	0.008	-0.012	10.006	0.820	0.820	0.000	0.000	0.000	0.000
57	A	72	GLN	0	-0.091	-0.055	11.969	-0.226	-0.226	0.000	0.000	0.000	0.000
58	A	73	GLU	-1	-0.971	-0.968	10.634	22.668	22.668	0.000	0.000	0.000	0.000
59	A	74	LYS	1	0.867	0.952	5.824	-35.584	-35.584	0.000	0.000	0.000	0.000
60	A	75	GLY	0	0.004	0.014	10.851	-0.297	-0.297	0.000	0.000	0.000	0.000
61	A	76	VAL	0	-0.020	0.013	11.418	-0.732	-0.732	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.887	0.930	14.472	-13.958	-13.958	0.000	0.000	0.000	0.000
63	A	78	ILE	0	0.011	0.017	14.793	-0.824	-0.824	0.000	0.000	0.000	0.000
64	A	79	THR	0	0.035	-0.002	12.805	0.727	0.727	0.000	0.000	0.000	0.000
65	A	80	THR	0	-0.054	-0.016	15.440	-0.282	-0.282	0.000	0.000	0.000	0.000
66	A	81	VAL	0	0.025	0.029	16.172	0.172	0.172	0.000	0.000	0.000	0.000
67	A	82	GLN	0	-0.036	-0.013	18.302	-1.049	-1.049	0.000	0.000	0.000	0.000
68	A	83	SER	0	0.014	0.006	20.700	-0.208	-0.208	0.000	0.000	0.000	0.000
69	A	84	ASN	0	0.027	0.008	20.731	0.400	0.400	0.000	0.000	0.000	0.000
70	A	85	LEU	0	0.026	-0.007	19.247	-0.089	-0.089	0.000	0.000	0.000	0.000
71	A	86	ALA	0	-0.062	-0.019	23.426	-0.237	-0.237	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.975	-0.981	26.841	9.168	9.168	0.000	0.000	0.000	0.000
73	A	88	PHE	0	-0.014	0.007	22.631	0.121	0.121	0.000	0.000	0.000	0.000
74	A	89	ASP	-1	-0.972	-0.992	26.630	9.800	9.800	0.000	0.000	0.000	0.000
75	A	90	ILE	0	-0.023	-0.007	23.629	0.195	0.195	0.000	0.000	0.000	0.000
76	A	91	VAL	0	-0.015	-0.011	26.840	-0.271	-0.271	0.000	0.000	0.000	0.000
77	A	92	ALA	0	0.029	-0.005	28.194	0.291	0.291	0.000	0.000	0.000	0.000
78	A	93	ASP	-1	-0.892	-0.959	29.295	9.774	9.774	0.000	0.000	0.000	0.000
79	A	94	ALA	0	-0.026	-0.008	26.804	-0.115	-0.115	0.000	0.000	0.000	0.000
80	A	95	TRP	0	-0.077	-0.046	20.180	0.503	0.503	0.000	0.000	0.000	0.000
81	A	96	GLU	-1	-0.818	-0.911	21.693	11.767	11.767	0.000	0.000	0.000	0.000
82	A	97	GLY	0	0.003	0.000	19.106	0.258	0.258	0.000	0.000	0.000	0.000
83	A	98	ILE	0	-0.052	-0.012	18.850	0.029	0.029	0.000	0.000	0.000	0.000
84	A	99	VAL	0	0.026	0.003	13.015	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	100	SER	0	-0.008	-0.004	16.028	0.050	0.050	0.000	0.000	0.000	0.000
86	A	101	ILE	0	0.025	0.003	9.523	0.258	0.258	0.000	0.000	0.000	0.000
87	A	102	PHE	0	-0.026	-0.029	9.802	0.181	0.181	0.000	0.000	0.000	0.000
88	A	103	CYS	0	-0.011	0.021	14.032	-0.433	-0.433	0.000	0.000	0.000	0.000
89	A	104	HIS	0	-0.054	-0.024	16.775	0.060	0.060	0.000	0.000	0.000	0.000
90	A	105	LEU	0	0.021	-0.005	19.633	-0.228	-0.228	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.025	0.018	23.174	-0.040	-0.040	0.000	0.000	0.000	0.000
92	A	107	SER	0	0.047	-0.029	26.695	0.146	0.146	0.000	0.000	0.000	0.000
93	A	108	SER	0	-0.044	-0.019	28.758	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	109	LEU	0	0.003	0.005	24.846	-0.132	-0.132	0.000	0.000	0.000	0.000
95	A	110	ARG	1	0.804	0.906	23.622	-11.330	-11.330	0.000	0.000	0.000	0.000
96	A	111	GLN	0	0.027	-0.003	26.830	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	112	GLN	0	-0.028	-0.003	29.637	-0.411	-0.411	0.000	0.000	0.000	0.000
98	A	113	LEU	0	-0.002	-0.003	22.426	-0.057	-0.057	0.000	0.000	0.000	0.000
99	A	114	TYR	0	0.056	0.016	22.003	0.249	0.249	0.000	0.000	0.000	0.000
100	A	115	PRO	0	0.030	0.027	26.833	0.062	0.062	0.000	0.000	0.000	0.000
101	A	116	LYS	1	0.944	0.967	27.639	-10.096	-10.096	0.000	0.000	0.000	0.000
102	A	117	VAL	0	0.005	0.021	23.142	0.102	0.102	0.000	0.000	0.000	0.000
103	A	118	TYR	0	0.016	-0.003	25.679	0.071	0.071	0.000	0.000	0.000	0.000
104	A	119	GLN	0	-0.048	-0.027	27.840	-0.183	-0.183	0.000	0.000	0.000	0.000
105	A	120	GLY	0	0.027	0.034	26.521	-0.184	-0.184	0.000	0.000	0.000	0.000
106	A	121	LEU	0	-0.035	-0.014	22.369	0.125	0.125	0.000	0.000	0.000	0.000
107	A	122	LYS	1	0.908	0.961	26.195	-11.086	-11.086	0.000	0.000	0.000	0.000
108	A	123	PRO	0	-0.075	-0.027	27.352	0.301	0.301	0.000	0.000	0.000	0.000
109	A	124	GLY	0	0.090	0.057	27.148	0.054	0.054	0.000	0.000	0.000	0.000
110	A	125	GLY	0	-0.033	-0.013	23.682	0.526	0.526	0.000	0.000	0.000	0.000
111	A	126	VAL	0	-0.059	-0.047	18.974	-0.188	-0.188	0.000	0.000	0.000	0.000
112	A	127	PHE	0	-0.005	-0.007	20.099	0.307	0.307	0.000	0.000	0.000	0.000
113	A	128	ILE	0	0.001	0.011	13.067	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	129	LEU	0	-0.028	-0.014	16.325	0.075	0.075	0.000	0.000	0.000	0.000
115	A	130	GLU	-1	-0.850	-0.947	11.596	22.797	22.797	0.000	0.000	0.000	0.000
116	A	131	GLY	0	0.042	0.042	14.384	0.135	0.135	0.000	0.000	0.000	0.000
117	A	132	PHE	0	-0.014	-0.011	13.608	-0.051	-0.051	0.000	0.000	0.000	0.000
118	A	133	ALA	0	0.024	0.015	17.442	-0.543	-0.543	0.000	0.000	0.000	0.000
119	A	134	PRO	0	0.025	0.000	20.745	0.065	0.065	0.000	0.000	0.000	0.000
120	A	135	GLU	-1	-0.849	-0.940	22.531	12.066	12.066	0.000	0.000	0.000	0.000
121	A	136	GLN	0	-0.031	-0.017	17.038	0.040	0.040	0.000	0.000	0.000	0.000
122	A	137	LEU	0	-0.013	0.001	20.864	0.138	0.138	0.000	0.000	0.000	0.000
123	A	138	GLN	0	-0.063	-0.018	23.615	-0.560	-0.560	0.000	0.000	0.000	0.000
124	A	139	TYR	0	-0.120	-0.053	19.305	0.140	0.140	0.000	0.000	0.000	0.000
125	A	140	ASN	0	0.003	-0.026	20.175	-0.091	-0.091	0.000	0.000	0.000	0.000
126	A	141	THR	0	-0.040	-0.041	14.740	-0.207	-0.207	0.000	0.000	0.000	0.000
127	A	142	GLY	0	0.031	0.031	14.706	1.146	1.146	0.000	0.000	0.000	0.000
128	A	143	GLY	0	0.061	0.034	16.541	-0.265	-0.265	0.000	0.000	0.000	0.000
129	A	144	PRO	0	-0.053	-0.018	17.749	-0.405	-0.405	0.000	0.000	0.000	0.000
130	A	145	LYS	1	1.017	0.986	21.211	-10.710	-10.710	0.000	0.000	0.000	0.000
131	A	146	ASP	-1	-0.929	-0.976	24.405	10.082	10.082	0.000	0.000	0.000	0.000
132	A	147	LEU	0	0.071	0.027	25.230	0.341	0.341	0.000	0.000	0.000	0.000
133	A	148	ASP	-1	-0.815	-0.857	26.730	10.355	10.355	0.000	0.000	0.000	0.000
134	A	149	LEU	0	-0.051	-0.029	22.315	0.113	0.113	0.000	0.000	0.000	0.000
135	A	150	LEU	0	-0.101	-0.040	20.324	0.667	0.667	0.000	0.000	0.000	0.000
136	A	151	PRO	0	0.035	0.025	22.885	-0.314	-0.314	0.000	0.000	0.000	0.000
137	A	152	LYS	1	0.997	0.983	23.749	-10.397	-10.397	0.000	0.000	0.000	0.000
138	A	153	LEU	0	0.056	0.028	22.009	-0.018	-0.018	0.000	0.000	0.000	0.000
139	A	154	GLU	-1	-0.898	-0.955	24.413	10.252	10.252	0.000	0.000	0.000	0.000
140	A	155	THR	0	-0.067	-0.026	27.456	-0.233	-0.233	0.000	0.000	0.000	0.000
141	A	156	LEU	0	0.018	0.017	21.474	-0.104	-0.104	0.000	0.000	0.000	0.000
142	A	157	GLN	0	0.040	0.016	25.364	-0.407	-0.407	0.000	0.000	0.000	0.000
143	A	158	SER	0	-0.078	-0.032	27.075	-0.302	-0.302	0.000	0.000	0.000	0.000
144	A	159	GLU	-1	-0.823	-0.920	26.722	10.777	10.777	0.000	0.000	0.000	0.000
145	A	160	LEU	0	-0.066	-0.037	24.440	0.022	0.022	0.000	0.000	0.000	0.000
146	A	161	PRO	0	0.000	-0.002	28.634	0.141	0.141	0.000	0.000	0.000	0.000
147	A	162	SER	0	-0.042	-0.021	31.412	-0.126	-0.126	0.000	0.000	0.000	0.000
148	A	163	LEU	0	-0.045	0.002	24.585	-0.062	-0.062	0.000	0.000	0.000	0.000
149	A	164	ASN	0	-0.020	0.006	27.768	-0.200	-0.200	0.000	0.000	0.000	0.000
150	A	165	TRP	0	0.013	-0.004	22.792	0.759	0.759	0.000	0.000	0.000	0.000
151	A	166	LEU	0	-0.001	0.008	22.318	-0.137	-0.137	0.000	0.000	0.000	0.000
152	A	167	ILE	0	-0.012	-0.004	18.067	0.218	0.218	0.000	0.000	0.000	0.000
153	A	168	ALA	0	0.015	0.001	21.712	0.015	0.015	0.000	0.000	0.000	0.000
154	A	169	ASN	0	-0.041	-0.005	17.618	-1.082	-1.082	0.000	0.000	0.000	0.000
155	A	170	ASN	0	0.053	0.012	20.059	0.000	0.000	0.000	0.000	0.000	0.000
156	A	171	LEU	0	-0.056	-0.026	15.546	-0.099	-0.099	0.000	0.000	0.000	0.000
157	A	172	GLU	-1	-0.835	-0.922	19.062	13.178	13.178	0.000	0.000	0.000	0.000
158	A	173	ARG	1	0.919	0.986	11.310	-22.724	-22.724	0.000	0.000	0.000	0.000
159	A	174	ASN	0	0.025	0.006	18.452	0.099	0.099	0.000	0.000	0.000	0.000
160	A	184	LYS	1	0.829	0.921	15.301	-14.274	-14.274	0.000	0.000	0.000	0.000
161	A	185	ALA	0	-0.004	-0.002	14.665	0.390	0.390	0.000	0.000	0.000	0.000
162	A	186	ALA	0	0.056	0.045	16.734	-0.050	-0.050	0.000	0.000	0.000	0.000
163	A	187	LEU	0	-0.045	-0.024	13.038	0.225	0.225	0.000	0.000	0.000	0.000
164	A	188	ILE	0	-0.002	0.005	17.041	-0.769	-0.769	0.000	0.000	0.000	0.000
165	A	189	GLN	0	-0.006	-0.007	13.105	0.017	0.017	0.000	0.000	0.000	0.000
166	A	190	LEU	0	-0.016	-0.004	17.376	-0.912	-0.912	0.000	0.000	0.000	0.000
167	A	191	LEU	0	0.027	0.014	18.192	0.772	0.772	0.000	0.000	0.000	0.000
168	A	192	GLY	0	-0.003	-0.004	20.017	-0.583	-0.583	0.000	0.000	0.000	0.000
169	A	193	GLN	0	0.027	-0.006	22.936	-0.074	-0.074	0.000	0.000	0.000	0.000
170	A	194	LYS	1	0.835	0.919	24.948	-10.682	-10.682	0.000	0.000	0.000	0.000
171	A	195	LEU	0	-0.008	-0.002	27.923	0.043	0.043	0.000	0.000	0.000	0.000
172	A	196	GLU	-1	-0.846	-0.921	29.314	10.375	10.375	0.000	0.000	0.000	0.000
173	A	197	HIS	0	-0.053	-0.027	32.747	-0.286	-0.286	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:GLU)