FMO DATABASE

FMODB ID: 858NY

Calculation Name: 3PM2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PM2

Chain ID: A

ChEMBL ID:

UniProt ID: Q7PF80

Base Structure: X-ray

Registration Date: 2023-06-21

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1704850.885235
FMO2-HF: Nuclear repulsion	1633720.219247
FMO2-HF: Total energy	-71130.665987
FMO2-MP2: Total energy	-71320.998888

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-1.569	1.993	0.448	-1.557	-2.453	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.004

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	3	ASN	0	0.011	-0.002	3.123	-0.344	2.347	0.149	-1.319	-1.521	-0.002
4	A	4	PRO	0	-0.007	-0.018	2.594	0.382	1.253	0.299	-0.238	-0.932	0.000
5	A	5	CYS	0	-0.008	0.007	5.548	0.103	0.103	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.047	0.019	7.640	0.305	0.305	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.896	0.958	7.181	0.141	0.141	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.007	0.018	11.507	0.112	0.112	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.021	-0.011	12.596	0.043	0.043	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.012	-0.014	13.243	0.002	0.002	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.015	-0.005	15.627	0.026	0.026	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.003	-0.005	19.031	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.844	0.920	21.371	0.034	0.034	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.045	0.019	21.622	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.045	0.015	20.123	0.018	0.018	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.047	0.021	22.044	0.018	0.018	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.843	-0.902	25.466	-0.061	-0.061	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.112	-0.021	19.784	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.010	0.016	21.161	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.002	0.013	24.708	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.006	0.007	21.715	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.006	0.000	24.691	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.076	-0.045	24.863	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.054	0.019	24.411	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.003	-0.005	26.041	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.865	-0.926	27.344	-0.125	-0.125	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.051	0.008	26.858	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	28	SER	0	0.033	0.020	27.516	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.003	0.014	29.163	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.015	0.009	19.663	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	31	MET	0	0.016	-0.003	23.932	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.030	-0.012	25.695	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.077	-0.021	22.688	0.031	0.031	0.000	0.000	0.000	0.000
34	A	34	HIS	0	-0.018	-0.022	18.834	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.031	-0.017	22.095	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.922	0.982	24.463	0.291	0.291	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.065	0.019	20.805	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.019	0.009	16.534	-0.080	-0.080	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.015	0.008	17.895	-0.072	-0.072	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.014	-0.029	18.567	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.013	-0.007	14.239	-0.087	-0.087	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.938	0.954	13.678	0.510	0.510	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.939	0.989	13.193	0.587	0.587	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.028	-0.010	13.022	-0.150	-0.150	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.089	-0.029	9.589	-0.146	-0.146	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.019	-0.007	8.396	-0.666	-0.666	0.000	0.000	0.000	0.000
47	A	47	MET	0	-0.065	-0.010	9.809	0.165	0.165	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.928	-0.951	7.117	-1.804	-1.804	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.013	-0.007	7.971	0.424	0.424	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.011	-0.004	9.238	-0.197	-0.197	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.011	0.004	9.368	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.863	0.917	11.797	1.093	1.093	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.011	0.011	14.473	-0.042	-0.042	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.051	-0.015	14.983	0.040	0.040	0.000	0.000	0.000	0.000
55	A	55	CYS	0	0.025	0.010	16.887	0.121	0.121	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.011	0.001	18.682	0.045	0.045	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.031	0.013	18.220	0.046	0.046	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.775	-0.885	20.261	-0.314	-0.314	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.019	0.007	22.562	0.029	0.029	0.000	0.000	0.000	0.000
60	A	61	MET	0	0.025	0.024	22.185	0.034	0.034	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.032	-0.031	25.776	0.035	0.035	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.114	-0.061	27.805	0.020	0.020	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.004	-0.004	28.090	0.013	0.013	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.062	-0.034	30.726	0.013	0.013	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.019	0.025	27.104	0.006	0.006	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.058	-0.032	24.075	0.005	0.005	0.000	0.000	0.000	0.000
67	A	68	SER	0	0.030	0.013	27.602	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	ASN	0	-0.034	-0.017	28.348	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.085	0.029	24.117	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.765	0.882	24.107	0.227	0.227	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.019	-0.012	23.028	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.836	-0.905	26.367	-0.110	-0.110	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.894	0.919	26.248	0.075	0.075	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.880	-0.923	28.331	-0.089	-0.089	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.007	-0.006	31.813	0.006	0.006	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.002	0.001	24.042	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.022	-0.040	28.604	0.004	0.004	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.877	0.945	29.584	0.091	0.091	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.004	-0.006	29.864	0.006	0.006	0.000	0.000	0.000	0.000
80	A	81	TYR	0	0.048	0.017	22.496	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.007	0.007	28.665	0.008	0.008	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.841	-0.893	31.508	-0.073	-0.073	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.035	-0.006	29.336	0.006	0.006	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.035	-0.051	29.496	0.008	0.008	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.819	0.897	32.071	0.079	0.079	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.039	-0.022	34.975	0.003	0.003	0.000	0.000	0.000	0.000
87	A	88	MET	0	-0.029	0.017	27.933	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.000	0.001	31.370	0.004	0.004	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.049	0.014	32.037	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.804	-0.903	29.172	0.009	0.009	0.000	0.000	0.000	0.000
91	A	92	TRP	0	0.066	0.013	23.657	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.019	0.019	28.275	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.828	0.884	28.322	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.060	0.027	23.447	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.016	-0.025	24.442	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.027	-0.012	25.342	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.795	-0.867	23.959	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.000	0.005	20.936	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.012	-0.007	21.000	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.853	-0.902	22.809	-0.058	-0.058	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.035	0.018	20.133	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	103	CYS	0	-0.013	-0.010	14.556	0.035	0.035	0.000	0.000	0.000	0.000
103	A	104	PHE	0	0.025	0.000	18.859	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.960	0.984	21.000	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	106	MET	0	-0.047	-0.007	14.424	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.048	0.018	16.802	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.902	-0.938	17.925	-0.121	-0.121	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.070	-0.055	16.633	0.014	0.014	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.029	0.017	13.142	0.010	0.010	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.838	0.912	16.435	0.077	0.077	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.886	-0.944	18.548	-0.200	-0.200	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.913	-0.954	11.293	-0.714	-0.714	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.004	-0.004	15.872	-0.067	-0.067	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.821	-0.923	17.293	-0.292	-0.292	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.003	0.012	17.505	0.013	0.013	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.056	0.013	16.569	-0.027	-0.027	0.000	0.000	0.000	0.000
117	A	118	ALA	0	-0.084	-0.052	17.274	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.797	0.899	20.252	0.330	0.330	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.027	0.016	14.870	0.012	0.012	0.000	0.000	0.000	0.000
120	A	121	THR	0	0.037	0.016	19.160	0.022	0.022	0.000	0.000	0.000	0.000
121	A	122	PRO	0	-0.014	-0.008	19.204	-0.074	-0.074	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.008	-0.008	16.776	0.025	0.025	0.000	0.000	0.000	0.000
123	A	124	PHE	0	-0.052	-0.032	16.694	-0.025	-0.025	0.000	0.000	0.000	0.000
124	A	125	GLU	-1	-0.894	-0.951	20.147	-0.379	-0.379	0.000	0.000	0.000	0.000
125	A	126	GLY	0	-0.015	-0.012	23.480	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	127	GLU	-1	-0.791	-0.861	17.369	-0.805	-0.805	0.000	0.000	0.000	0.000
127	A	128	GLN	0	0.027	0.003	21.719	0.046	0.046	0.000	0.000	0.000	0.000
128	A	129	ILE	0	0.009	0.009	18.905	-0.059	-0.059	0.000	0.000	0.000	0.000
129	A	131	HIS	0	0.046	0.029	19.821	-0.071	-0.071	0.000	0.000	0.000	0.000
130	A	132	PRO	0	0.030	0.002	15.500	0.006	0.006	0.000	0.000	0.000	0.000
131	A	133	ILE	0	-0.026	0.023	17.135	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	134	SER	0	0.045	0.016	19.261	0.022	0.022	0.000	0.000	0.000	0.000
133	A	135	GLY	0	-0.016	-0.011	16.333	0.010	0.010	0.000	0.000	0.000	0.000
134	A	136	THR	0	-0.008	-0.014	14.586	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	137	ILE	0	0.004	0.006	15.791	0.025	0.025	0.000	0.000	0.000	0.000
136	A	138	LEU	0	0.013	0.012	18.414	0.023	0.023	0.000	0.000	0.000	0.000
137	A	139	ALA	0	-0.027	-0.016	13.012	0.018	0.018	0.000	0.000	0.000	0.000
138	A	141	MET	0	0.029	0.037	15.479	0.052	0.052	0.000	0.000	0.000	0.000
139	A	142	GLY	0	-0.002	0.005	17.810	0.030	0.030	0.000	0.000	0.000	0.000
140	A	143	MET	0	-0.066	-0.038	10.740	0.014	0.014	0.000	0.000	0.000	0.000
141	A	144	THR	0	-0.005	-0.014	15.189	0.056	0.056	0.000	0.000	0.000	0.000
142	A	145	LEU	0	-0.011	-0.005	17.338	0.032	0.032	0.000	0.000	0.000	0.000
143	A	146	PHE	0	-0.026	-0.025	17.129	0.017	0.017	0.000	0.000	0.000	0.000
144	A	147	ALA	0	-0.062	-0.025	15.825	0.024	0.024	0.000	0.000	0.000	0.000
145	A	148	GLU	-1	-0.913	-0.959	17.910	0.078	0.078	0.000	0.000	0.000	0.000
146	A	150	PRO	0	0.009	0.006	23.338	0.016	0.016	0.000	0.000	0.000	0.000
147	A	151	ALA	0	0.054	0.014	25.865	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	152	LYS	1	0.794	0.887	26.736	-0.018	-0.018	0.000	0.000	0.000	0.000
149	A	153	LEU	0	-0.054	-0.022	27.637	-0.006	-0.006	0.000	0.000	0.000	0.000
150	A	154	PHE	0	0.011	0.008	20.118	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	155	THR	0	-0.048	-0.046	25.662	0.012	0.012	0.000	0.000	0.000	0.000
152	A	156	VAL	0	-0.004	-0.016	24.659	0.004	0.004	0.000	0.000	0.000	0.000
153	A	157	ASN	0	0.021	0.007	24.185	-0.004	-0.004	0.000	0.000	0.000	0.000
154	A	158	ASP	-1	-0.854	-0.932	22.069	0.110	0.110	0.000	0.000	0.000	0.000
155	A	159	ASP	-1	-0.803	-0.902	20.470	0.012	0.012	0.000	0.000	0.000	0.000
156	A	161	ASN	0	0.051	0.026	18.447	0.003	0.003	0.000	0.000	0.000	0.000
157	A	162	LYS	1	0.865	0.938	16.116	-0.025	-0.025	0.000	0.000	0.000	0.000
158	A	163	LEU	0	0.010	0.001	14.937	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	164	LYS	1	0.957	0.988	14.993	-0.215	-0.215	0.000	0.000	0.000	0.000
160	A	165	SER	0	-0.031	-0.027	12.653	0.032	0.032	0.000	0.000	0.000	0.000
161	A	166	TYR	0	-0.045	-0.020	9.921	0.124	0.124	0.000	0.000	0.000	0.000
162	A	167	HIS	1	0.847	0.907	10.287	0.198	0.198	0.000	0.000	0.000	0.000
163	A	168	SER	0	-0.003	0.005	11.135	0.003	0.003	0.000	0.000	0.000	0.000
164	A	169	LYS	1	0.838	0.917	5.417	-0.382	-0.382	0.000	0.000	0.000	0.000
165	A	171	PRO	0	0.109	0.045	9.469	0.133	0.133	0.000	0.000	0.000	0.000
166	A	172	PHE	0	-0.061	-0.030	12.792	-0.002	-0.002	0.000	0.000	0.000	0.000
167	A	173	LEU	0	0.024	0.025	12.613	0.027	0.027	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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