FMO DATABASE

FMODB ID: 6YNZZ

Calculation Name: 2P38-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P38

Chain ID: A

ChEMBL ID:

UniProt ID: Q9V219

Base Structure: X-ray

Registration Date: 2023-09-21

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1557951.615736
FMO2-HF: Nuclear repulsion	1496092.488011
FMO2-HF: Total energy	-61859.127725
FMO2-MP2: Total energy	-62044.316272

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:5:LEU)

Summations of interaction energy for fragment #1(A:5: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.
-12.459	-8.907	10.83	-3.827	-10.553	-0.02

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.008

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	7	VAL	0	-0.031	-0.025	3.146	-2.013	0.781	0.081	-1.202	-1.673	0.004
4	A	8	ARG	1	0.712	0.823	5.194	1.211	1.259	-0.001	-0.003	-0.043	0.000
5	A	9	ARG	1	0.942	0.970	8.726	0.950	0.950	0.000	0.000	0.000	0.000
6	A	10	ALA	0	-0.061	-0.026	11.659	-0.108	-0.108	0.000	0.000	0.000	0.000
7	A	11	SER	0	-0.004	-0.030	12.960	0.047	0.047	0.000	0.000	0.000	0.000
8	A	12	SER	0	0.086	0.027	15.318	0.044	0.044	0.000	0.000	0.000	0.000
9	A	13	TRP	0	-0.021	-0.016	16.349	0.038	0.038	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.734	-0.816	11.931	-0.583	-0.583	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.039	0.011	15.879	0.043	0.043	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.832	-0.902	18.007	-0.136	-0.136	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.107	-0.047	16.147	0.035	0.035	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.051	-0.029	14.064	0.032	0.032	0.000	0.000	0.000	0.000
15	A	19	LEU	0	0.058	0.020	18.293	0.029	0.029	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.957	0.992	21.843	0.067	0.067	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.839	-0.907	19.739	0.044	0.044	0.000	0.000	0.000	0.000
18	A	22	ALA	0	0.013	-0.001	21.823	0.015	0.015	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.884	-0.937	23.291	-0.048	-0.048	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.641	0.799	23.083	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	25	TYR	0	-0.099	-0.077	23.972	0.009	0.009	0.000	0.000	0.000	0.000
22	A	26	GLY	0	-0.022	-0.005	27.562	0.005	0.005	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.873	-0.920	27.661	-0.031	-0.031	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.048	-0.023	19.980	0.012	0.012	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.005	-0.006	23.978	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	30	HIS	0	-0.088	-0.037	16.913	0.013	0.013	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.893	-0.953	20.636	-0.142	-0.142	0.000	0.000	0.000	0.000
28	A	32	PHE	0	0.001	0.016	16.638	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	33	PHE	0	0.057	0.001	13.427	0.045	0.045	0.000	0.000	0.000	0.000
30	A	34	CYS	0	-0.040	-0.010	8.796	-0.085	-0.085	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.026	-0.016	7.523	0.166	0.166	0.000	0.000	0.000	0.000
32	A	36	VAL	0	-0.010	0.002	2.209	-1.036	-1.244	3.523	-0.827	-2.488	-0.006
33	A	37	GLU	-1	-0.785	-0.866	3.997	-1.671	-1.205	0.002	-0.116	-0.352	0.000
34	A	38	GLY	0	0.050	0.012	2.250	-3.971	-2.086	4.723	-3.315	-3.293	-0.019
35	A	39	LYS	1	0.877	0.942	3.028	0.849	-1.449	0.164	2.365	-0.231	-0.001
36	A	40	TYR	0	0.004	-0.007	6.072	-0.290	-0.290	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.864	0.920	5.630	0.415	0.415	0.000	0.000	0.000	0.000
38	A	42	ASP	-1	-0.851	-0.902	5.588	0.898	0.898	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.019	-0.006	7.375	-0.226	-0.226	0.000	0.000	0.000	0.000
40	A	44	TYR	0	-0.005	-0.021	5.740	0.235	0.235	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.039	0.031	10.592	-0.093	-0.093	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.026	-0.013	11.389	0.051	0.051	0.000	0.000	0.000	0.000
43	A	47	ASN	0	0.079	0.032	14.311	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.771	-0.891	16.679	-0.179	-0.179	0.000	0.000	0.000	0.000
45	A	49	GLU	-1	-0.933	-0.967	18.304	-0.128	-0.128	0.000	0.000	0.000	0.000
46	A	50	VAL	0	0.019	0.000	12.307	-0.042	-0.042	0.000	0.000	0.000	0.000
47	A	51	TRP	0	-0.016	-0.014	13.782	-0.089	-0.089	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.815	0.893	14.928	0.112	0.112	0.000	0.000	0.000	0.000
49	A	53	ILE	0	0.038	0.022	13.425	-0.042	-0.042	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.043	-0.023	8.163	-0.075	-0.075	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.887	-0.933	11.616	-0.786	-0.786	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.953	-0.954	14.370	-0.514	-0.514	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.077	-0.043	11.598	-0.046	-0.046	0.000	0.000	0.000	0.000
54	A	58	ASN	0	0.020	0.007	4.436	-0.188	-0.141	-0.001	-0.012	-0.034	0.000
55	A	59	MET	0	0.021	0.016	7.144	0.274	0.274	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.955	0.968	2.826	-3.932	-2.994	0.123	-0.302	-0.758	0.003
57	A	61	PRO	0	0.094	0.023	2.355	-0.492	-0.653	2.217	-0.412	-1.644	-0.001
58	A	62	TYR	0	-0.067	-0.037	5.322	-0.280	-0.239	-0.001	-0.003	-0.037	0.000
59	A	63	SER	0	-0.018	-0.005	8.083	-0.095	-0.095	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.038	0.008	6.449	-0.116	-0.116	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.065	0.029	10.085	-0.091	-0.091	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.025	-0.011	11.306	0.110	0.110	0.000	0.000	0.000	0.000
63	A	67	PHE	0	0.007	0.021	8.814	-0.043	-0.043	0.000	0.000	0.000	0.000
64	A	68	VAL	0	0.015	0.011	10.711	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.047	0.021	11.600	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	70	THR	0	-0.056	-0.029	8.909	0.000	0.000	0.000	0.000	0.000	0.000
67	A	71	ILE	0	-0.007	0.005	10.506	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	72	ARG	1	0.825	0.916	11.187	-0.219	-0.219	0.000	0.000	0.000	0.000
69	A	73	VAL	0	0.019	0.026	13.612	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	74	ASP	-1	-0.859	-0.923	16.786	0.055	0.055	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.909	-0.959	19.487	0.082	0.082	0.000	0.000	0.000	0.000
72	A	76	ASN	0	-0.141	-0.076	22.612	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.020	-0.015	20.957	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.005	0.002	21.377	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	79	GLU	-1	-0.839	-0.889	15.857	-0.199	-0.199	0.000	0.000	0.000	0.000
76	A	80	LYN	0	0.031	0.015	16.856	0.002	0.002	0.000	0.000	0.000	0.000
77	A	81	PHE	0	0.065	0.025	13.245	0.000	0.000	0.000	0.000	0.000	0.000
78	A	82	TYR	0	-0.066	-0.043	14.644	0.031	0.031	0.000	0.000	0.000	0.000
79	A	83	PRO	0	0.051	0.054	14.818	0.034	0.034	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.049	-0.052	13.137	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	85	LEU	0	0.017	-0.014	16.718	-0.026	-0.026	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.856	-0.920	15.947	0.167	0.167	0.000	0.000	0.000	0.000
83	A	87	PHE	0	0.013	0.012	16.867	-0.021	-0.021	0.000	0.000	0.000	0.000
84	A	88	PHE	0	-0.026	-0.033	18.085	-0.022	-0.022	0.000	0.000	0.000	0.000
85	A	89	SER	0	-0.039	-0.012	19.738	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.018	-0.017	17.110	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.031	0.002	21.738	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	92	LYS	1	0.998	1.014	24.738	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	93	LEU	0	-0.039	-0.023	27.856	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	94	GLU	-1	-0.827	-0.913	29.491	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	95	LYS	1	0.785	0.880	30.136	0.008	0.008	0.000	0.000	0.000	0.000
92	A	96	ASN	0	-0.051	-0.033	29.892	0.005	0.005	0.000	0.000	0.000	0.000
93	A	97	TYR	0	0.004	-0.013	30.025	0.006	0.006	0.000	0.000	0.000	0.000
94	A	98	VAL	0	-0.031	-0.028	31.928	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	99	ILE	0	0.038	0.040	33.209	0.005	0.005	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.013	-0.001	33.370	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	101	GLY	0	0.043	0.013	36.613	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	102	PRO	0	0.033	0.051	37.298	0.005	0.005	0.000	0.000	0.000	0.000
99	A	103	LYS	1	0.937	0.961	37.135	-0.056	-0.056	0.000	0.000	0.000	0.000
100	A	104	ALA	0	0.038	0.009	37.054	0.004	0.004	0.000	0.000	0.000	0.000
101	A	105	SER	0	0.014	-0.005	33.527	0.005	0.005	0.000	0.000	0.000	0.000
102	A	106	PHE	0	0.025	0.011	32.617	0.006	0.006	0.000	0.000	0.000	0.000
103	A	107	LEU	0	-0.010	0.002	32.725	0.008	0.008	0.000	0.000	0.000	0.000
104	A	108	PHE	0	0.027	0.020	27.666	0.005	0.005	0.000	0.000	0.000	0.000
105	A	109	THR	0	-0.024	-0.019	28.402	0.008	0.008	0.000	0.000	0.000	0.000
106	A	110	THR	0	-0.059	-0.023	28.217	0.008	0.008	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.073	0.047	28.361	0.004	0.004	0.000	0.000	0.000	0.000
108	A	112	LYS	1	0.730	0.862	29.133	-0.134	-0.134	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.802	-0.905	31.938	0.103	0.103	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.006	-0.001	33.449	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	115	PRO	0	-0.049	-0.021	35.775	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.916	0.923	39.260	-0.043	-0.043	0.000	0.000	0.000	0.000
113	A	117	GLU	-1	-0.836	-0.868	40.700	0.053	0.053	0.000	0.000	0.000	0.000
114	A	118	ALA	0	-0.043	-0.022	38.834	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.039	-0.028	37.041	0.002	0.002	0.000	0.000	0.000	0.000
116	A	120	ARG	1	0.863	0.927	39.039	-0.054	-0.054	0.000	0.000	0.000	0.000
117	A	121	GLU	-1	-0.840	-0.895	38.112	0.028	0.028	0.000	0.000	0.000	0.000
118	A	122	ILE	0	-0.022	-0.009	36.133	0.005	0.005	0.000	0.000	0.000	0.000
119	A	123	LYS	1	0.896	0.979	35.517	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	124	TRP	0	-0.056	-0.045	32.611	0.000	0.000	0.000	0.000	0.000	0.000
121	A	125	GLN	0	0.033	-0.007	33.722	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	126	GLY	0	0.062	0.027	33.318	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	127	SER	0	-0.044	-0.002	27.124	0.003	0.003	0.000	0.000	0.000	0.000
124	A	128	LYS	1	0.880	0.939	27.853	-0.046	-0.046	0.000	0.000	0.000	0.000
125	A	129	ARG	1	0.972	0.987	22.729	-0.097	-0.097	0.000	0.000	0.000	0.000
126	A	130	VAL	0	0.024	0.030	27.198	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	131	VAL	0	0.060	0.030	25.793	0.011	0.011	0.000	0.000	0.000	0.000
128	A	132	VAL	0	-0.037	-0.016	27.908	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	133	LEU	0	0.019	0.014	29.072	0.007	0.007	0.000	0.000	0.000	0.000
130	A	134	ASN	0	0.026	0.002	31.473	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	135	ASP	-1	-0.847	-0.948	33.579	0.058	0.058	0.000	0.000	0.000	0.000
132	A	136	LEU	0	-0.057	-0.028	34.252	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.002	0.012	33.618	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	138	ASP	-1	-0.826	-0.906	29.189	0.077	0.077	0.000	0.000	0.000	0.000
135	A	139	ILE	0	-0.023	-0.026	24.536	0.001	0.001	0.000	0.000	0.000	0.000
136	A	140	ILE	0	-0.042	-0.017	26.696	0.008	0.008	0.000	0.000	0.000	0.000
137	A	141	GLY	0	0.050	0.005	24.664	0.013	0.013	0.000	0.000	0.000	0.000
138	A	142	ILE	0	-0.102	-0.028	22.659	-0.012	-0.012	0.000	0.000	0.000	0.000
139	A	143	GLY	0	0.058	0.021	25.751	0.009	0.009	0.000	0.000	0.000	0.000
140	A	144	LEU	0	-0.074	-0.041	26.734	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	145	ILE	0	0.071	0.054	29.506	0.001	0.001	0.000	0.000	0.000	0.000
142	A	146	ASN	0	-0.091	-0.062	32.900	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	147	PRO	0	-0.013	-0.013	34.963	0.000	0.000	0.000	0.000	0.000	0.000
144	A	148	LYS	1	1.018	1.008	38.010	-0.050	-0.050	0.000	0.000	0.000	0.000
145	A	149	SER	0	-0.040	-0.009	38.083	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	150	ASP	-1	-0.763	-0.882	40.127	0.045	0.045	0.000	0.000	0.000	0.000
147	A	151	ARG	1	0.834	0.871	40.561	-0.056	-0.056	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.961	0.990	35.200	-0.083	-0.083	0.000	0.000	0.000	0.000
149	A	153	PHE	0	0.012	0.023	35.653	0.002	0.002	0.000	0.000	0.000	0.000
150	A	154	ILE	0	0.003	0.007	31.536	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	155	LYS	1	0.882	0.943	30.565	-0.078	-0.078	0.000	0.000	0.000	0.000
152	A	156	ASN	0	0.005	-0.003	27.262	0.005	0.005	0.000	0.000	0.000	0.000
153	A	157	LEU	0	-0.088	-0.037	23.939	0.002	0.002	0.000	0.000	0.000	0.000
154	A	158	LYS	1	0.861	0.929	19.121	-0.145	-0.145	0.000	0.000	0.000	0.000
155	A	159	ASP	-1	-0.776	-0.881	23.169	0.167	0.167	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)