FMO DATABASE

FMODB ID: G6LY1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1700887.557182
FMO2-HF: Nuclear repulsion	1629757.292525
FMO2-HF: Total energy	-71130.264657
FMO2-MP2: Total energy	-71320.61727

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.
-4.194	-0.148	0.764	-2.017	-2.792	-0.005

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 : -0.001

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	-0.005	2.809	-1.564	1.608	0.402	-1.766	-1.808	-0.005
4	A	4	PRO	0	0.010	-0.011	2.543	0.297	1.171	0.362	-0.251	-0.984	0.000
5	A	5	CYS	0	-0.044	-0.017	5.530	0.073	0.073	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.040	0.017	7.458	0.227	0.227	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.893	0.956	7.343	-0.273	-0.273	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.000	0.022	11.304	0.086	0.086	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.026	-0.022	12.935	0.068	0.068	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.013	-0.010	13.492	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.017	-0.005	15.964	0.010	0.010	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.008	-0.002	19.128	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.845	0.920	21.365	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.065	0.030	21.363	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.057	0.017	19.994	0.019	0.019	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.022	0.016	21.896	0.019	0.019	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.864	-0.918	25.260	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.127	-0.032	19.981	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.002	0.027	21.224	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.008	0.022	24.553	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.003	-0.004	21.759	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.007	0.000	24.505	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.053	-0.030	24.646	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.053	0.016	24.182	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.022	-0.018	25.927	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.872	-0.924	27.342	-0.101	-0.101	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.047	0.001	26.836	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.014	0.004	27.428	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.060	0.021	29.098	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.020	0.013	19.358	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	31	MET	0	-0.005	-0.009	24.348	-0.031	-0.031	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.022	0.004	25.766	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.081	-0.023	22.606	0.028	0.028	0.000	0.000	0.000	0.000
34	A	34	HIS	0	-0.025	-0.021	19.082	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.014	-0.017	22.126	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.923	0.983	24.543	0.280	0.280	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.050	0.012	20.608	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.017	0.011	16.580	-0.072	-0.072	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.018	0.010	17.794	-0.068	-0.068	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.016	-0.013	18.308	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.008	-0.006	14.175	-0.078	-0.078	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.948	0.956	13.553	0.450	0.450	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.932	0.980	13.207	0.599	0.599	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.027	-0.019	13.515	-0.124	-0.124	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.101	-0.021	9.167	-0.149	-0.149	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.026	-0.012	8.377	-0.644	-0.644	0.000	0.000	0.000	0.000
47	A	47	MET	0	-0.073	-0.011	9.975	0.222	0.222	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.918	-0.946	7.411	-2.206	-2.206	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.018	-0.010	7.954	0.450	0.450	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.013	-0.011	9.438	-0.187	-0.187	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.013	0.013	8.870	-0.080	-0.080	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.900	0.938	11.264	1.144	1.144	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.003	0.008	13.942	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	54	CYS	0	-0.048	-0.007	14.800	0.013	0.013	0.000	0.000	0.000	0.000
55	A	55	CYS	0	0.013	-0.004	16.603	0.117	0.117	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.003	0.001	18.426	0.047	0.047	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.024	0.006	18.146	0.046	0.046	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.811	-0.912	20.153	-0.321	-0.321	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.029	0.011	22.497	0.028	0.028	0.000	0.000	0.000	0.000
60	A	61	MET	0	0.008	0.023	22.003	0.033	0.033	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.016	-0.015	25.628	0.034	0.034	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.121	-0.065	27.767	0.020	0.020	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.002	-0.005	27.932	0.013	0.013	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.056	-0.024	30.500	0.011	0.011	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.014	0.009	26.843	0.007	0.007	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.016	-0.004	24.167	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	SER	0	0.010	0.002	27.449	0.005	0.005	0.000	0.000	0.000	0.000
68	A	69	ASN	0	-0.017	-0.005	28.038	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.072	0.035	24.061	0.009	0.009	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.774	0.887	24.158	0.227	0.227	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.033	0.004	22.673	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.858	-0.913	25.941	-0.105	-0.105	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.899	0.921	25.923	0.067	0.067	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.895	-0.932	28.162	-0.081	-0.081	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.009	-0.010	31.378	0.006	0.006	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.003	-0.001	23.694	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.020	-0.037	28.369	0.006	0.006	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.940	0.979	29.278	0.082	0.082	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.016	-0.007	29.468	0.006	0.006	0.000	0.000	0.000	0.000
80	A	81	TYR	0	0.053	0.021	22.288	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	82	LEU	0	0.000	0.003	28.505	0.009	0.009	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.879	-0.915	31.428	-0.058	-0.058	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.008	0.002	29.143	0.006	0.006	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.046	-0.052	29.095	0.008	0.008	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.808	0.905	31.705	0.064	0.064	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.023	-0.012	35.016	0.003	0.003	0.000	0.000	0.000	0.000
87	A	88	MET	0	-0.067	-0.006	27.680	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.001	0.002	31.252	0.003	0.003	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.047	0.012	32.126	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.825	-0.907	29.159	0.031	0.031	0.000	0.000	0.000	0.000
91	A	92	TRP	0	0.046	0.005	23.635	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.010	0.026	28.206	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.863	0.897	28.299	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.052	0.043	23.345	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.008	-0.023	24.170	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.036	-0.024	24.927	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.792	-0.875	23.851	0.020	0.020	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.007	0.002	20.725	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.001	-0.018	20.729	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.853	-0.906	22.542	-0.042	-0.042	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.024	0.010	19.762	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	103	CYS	0	-0.017	-0.011	14.319	0.043	0.043	0.000	0.000	0.000	0.000
103	A	104	PHE	0	0.028	0.000	18.540	-0.033	-0.033	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.961	0.992	20.270	-0.027	-0.027	0.000	0.000	0.000	0.000
105	A	106	MET	0	-0.032	-0.003	13.978	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.033	0.015	16.480	-0.026	-0.026	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.939	-0.978	17.844	-0.126	-0.126	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.073	-0.054	16.232	0.009	0.009	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.028	0.016	12.624	0.009	0.009	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.933	0.975	15.912	0.097	0.097	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.911	-0.951	18.092	-0.220	-0.220	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.936	-0.967	11.173	-0.807	-0.807	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.025	-0.015	15.547	-0.062	-0.062	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.833	-0.933	17.025	-0.306	-0.306	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.044	-0.012	17.055	0.003	0.003	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.040	0.009	16.510	-0.028	-0.028	0.000	0.000	0.000	0.000
117	A	118	ALA	0	-0.050	-0.034	17.185	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.895	0.951	20.590	0.314	0.314	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.039	0.013	15.353	0.004	0.004	0.000	0.000	0.000	0.000
120	A	121	THR	0	0.055	0.020	19.634	0.038	0.038	0.000	0.000	0.000	0.000
121	A	122	PRO	0	-0.035	-0.026	19.731	-0.067	-0.067	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.016	-0.007	16.916	0.019	0.019	0.000	0.000	0.000	0.000
123	A	124	PHE	0	-0.049	-0.033	16.976	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	125	GLU	-1	-0.908	-0.962	20.471	-0.389	-0.389	0.000	0.000	0.000	0.000
125	A	126	GLY	0	-0.009	-0.004	23.773	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	127	GLU	-1	-0.811	-0.862	17.759	-0.833	-0.833	0.000	0.000	0.000	0.000
127	A	128	GLN	0	0.036	0.000	22.037	0.047	0.047	0.000	0.000	0.000	0.000
128	A	129	ILE	0	-0.015	-0.004	19.453	-0.047	-0.047	0.000	0.000	0.000	0.000
129	A	131	HIS	0	0.044	0.015	19.743	-0.065	-0.065	0.000	0.000	0.000	0.000
130	A	132	PRO	0	0.027	-0.003	15.493	0.001	0.001	0.000	0.000	0.000	0.000
131	A	133	ILE	0	-0.023	0.017	17.174	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	134	SER	0	0.041	0.012	19.209	0.027	0.027	0.000	0.000	0.000	0.000
133	A	135	GLY	0	0.010	-0.010	16.183	0.021	0.021	0.000	0.000	0.000	0.000
134	A	136	THR	0	-0.012	-0.001	14.517	-0.017	-0.017	0.000	0.000	0.000	0.000
135	A	137	ILE	0	0.004	0.003	15.696	0.032	0.032	0.000	0.000	0.000	0.000
136	A	138	LEU	0	0.019	0.009	18.269	0.027	0.027	0.000	0.000	0.000	0.000
137	A	139	ALA	0	-0.025	-0.014	12.914	0.026	0.026	0.000	0.000	0.000	0.000
138	A	141	MET	0	0.014	0.026	15.219	0.057	0.057	0.000	0.000	0.000	0.000
139	A	142	GLY	0	-0.001	0.006	17.795	0.033	0.033	0.000	0.000	0.000	0.000
140	A	143	MET	0	-0.070	-0.037	10.495	0.027	0.027	0.000	0.000	0.000	0.000
141	A	144	THR	0	0.001	-0.011	15.175	0.058	0.058	0.000	0.000	0.000	0.000
142	A	145	LEU	0	-0.009	-0.007	17.202	0.030	0.030	0.000	0.000	0.000	0.000
143	A	146	PHE	0	-0.025	-0.022	17.049	0.020	0.020	0.000	0.000	0.000	0.000
144	A	147	ALA	0	-0.063	-0.032	15.850	0.023	0.023	0.000	0.000	0.000	0.000
145	A	148	GLU	-1	-0.907	-0.951	17.968	0.123	0.123	0.000	0.000	0.000	0.000
146	A	150	PRO	0	0.018	0.008	23.492	0.017	0.017	0.000	0.000	0.000	0.000
147	A	151	ALA	0	0.047	0.012	25.768	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	152	LYS	1	0.821	0.892	26.652	-0.047	-0.047	0.000	0.000	0.000	0.000
149	A	153	LEU	0	-0.055	-0.027	27.596	-0.008	-0.008	0.000	0.000	0.000	0.000
150	A	154	PHE	0	0.021	0.009	20.122	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	155	THR	0	-0.053	-0.045	25.512	0.008	0.008	0.000	0.000	0.000	0.000
152	A	156	VAL	0	-0.014	-0.013	24.567	0.010	0.010	0.000	0.000	0.000	0.000
153	A	157	ASN	0	0.023	0.008	24.339	0.001	0.001	0.000	0.000	0.000	0.000
154	A	158	ASP	-1	-0.839	-0.929	22.465	0.167	0.167	0.000	0.000	0.000	0.000
155	A	159	ASP	-1	-0.838	-0.925	20.812	0.071	0.071	0.000	0.000	0.000	0.000
156	A	161	ASN	0	0.022	0.019	18.656	0.014	0.014	0.000	0.000	0.000	0.000
157	A	162	LYS	1	0.864	0.929	16.286	-0.077	-0.077	0.000	0.000	0.000	0.000
158	A	163	LEU	0	0.010	0.001	15.022	0.015	0.015	0.000	0.000	0.000	0.000
159	A	164	LYS	1	0.993	1.006	15.100	-0.287	-0.287	0.000	0.000	0.000	0.000
160	A	165	SER	0	-0.029	-0.022	12.515	0.043	0.043	0.000	0.000	0.000	0.000
161	A	166	TYR	0	-0.036	-0.013	10.116	0.106	0.106	0.000	0.000	0.000	0.000
162	A	167	HIS	1	0.861	0.914	10.264	0.108	0.108	0.000	0.000	0.000	0.000
163	A	168	SER	0	-0.017	0.010	10.524	0.019	0.019	0.000	0.000	0.000	0.000
164	A	169	LYS	1	0.875	0.932	5.232	-0.742	-0.742	0.000	0.000	0.000	0.000
165	A	171	PRO	0	0.111	0.058	9.503	0.121	0.121	0.000	0.000	0.000	0.000
166	A	172	PHE	0	-0.067	-0.037	12.681	-0.026	-0.026	0.000	0.000	0.000	0.000
167	A	173	LEU	0	0.023	0.022	12.334	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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