FMO DATABASE

FMODB ID: 3JMYL

Calculation Name: 3HD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HD4

Chain ID: A

ChEMBL ID:

UniProt ID: P03416

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1129182.866456
FMO2-HF: Nuclear repulsion	1078529.568283
FMO2-HF: Total energy	-50653.298173
FMO2-MP2: Total energy	-50805.522939

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:64:PRO)

Summations of interaction energy for fragment #1(A:64:PRO)

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.
-2.162	0.954	0.035	-1.369	-1.782	0

Interaction energy analysis for fragmet #1(A:64:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.007

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].
3	A	66	TYR	0	0.003	0.011	3.369	-1.484	1.632	0.035	-1.369	-1.782
4	A	67	SER	0	0.013	0.004	5.534	0.340	0.340	0.000	0.000	0.000
5	A	68	TRP	0	0.040	0.004	8.717	0.111	0.111	0.000	0.000	0.000
6	A	69	PHE	0	0.012	0.013	11.626	0.103	0.103	0.000	0.000	0.000
7	A	70	SER	0	-0.011	-0.005	11.563	-0.051	-0.051	0.000	0.000	0.000
8	A	71	GLY	0	0.018	0.009	12.502	-0.034	-0.034	0.000	0.000	0.000
9	A	72	ILE	0	-0.016	0.003	13.127	0.048	0.048	0.000	0.000	0.000
10	A	73	THR	0	-0.046	-0.052	15.143	-0.014	-0.014	0.000	0.000	0.000
11	A	74	GLN	0	-0.018	0.006	16.685	-0.005	-0.005	0.000	0.000	0.000
12	A	75	PHE	0	-0.031	-0.030	19.013	0.019	0.019	0.000	0.000	0.000
13	A	76	GLN	0	-0.022	-0.002	21.904	0.004	0.004	0.000	0.000	0.000
14	A	77	LYS	1	0.942	0.952	22.505	-0.014	-0.014	0.000	0.000	0.000
15	A	78	GLY	0	0.025	0.006	23.631	0.002	0.002	0.000	0.000	0.000
16	A	79	LYS	1	0.862	0.959	23.974	0.048	0.048	0.000	0.000	0.000
17	A	80	GLU	-1	-0.874	-0.942	21.665	-0.114	-0.114	0.000	0.000	0.000
18	A	81	PHE	0	-0.050	-0.025	17.333	0.001	0.001	0.000	0.000	0.000
19	A	82	GLN	0	-0.012	-0.015	20.691	-0.011	-0.011	0.000	0.000	0.000
20	A	83	PHE	0	-0.005	0.000	19.323	0.007	0.007	0.000	0.000	0.000
21	A	84	ALA	0	0.039	0.023	24.268	-0.001	-0.001	0.000	0.000	0.000
22	A	85	GLU	-1	-0.888	-0.951	26.359	-0.144	-0.144	0.000	0.000	0.000
23	A	86	GLY	0	0.006	0.013	26.462	0.011	0.011	0.000	0.000	0.000
24	A	87	GLN	0	-0.057	-0.039	25.728	0.000	0.000	0.000	0.000	0.000
25	A	88	GLY	0	0.069	0.015	21.909	-0.009	-0.009	0.000	0.000	0.000
26	A	89	VAL	0	-0.043	0.008	19.112	-0.024	-0.024	0.000	0.000	0.000
27	A	90	PRO	0	-0.017	-0.003	16.378	0.031	0.031	0.000	0.000	0.000
28	A	91	ILE	0	-0.047	-0.015	19.678	-0.009	-0.009	0.000	0.000	0.000
29	A	92	ALA	0	0.019	0.001	19.400	0.003	0.003	0.000	0.000	0.000
30	A	93	ASN	0	-0.009	-0.016	21.533	0.003	0.003	0.000	0.000	0.000
31	A	94	GLY	0	0.018	0.008	22.405	-0.010	-0.010	0.000	0.000	0.000
32	A	95	ILE	0	-0.023	0.005	19.390	-0.008	-0.008	0.000	0.000	0.000
33	A	96	PRO	0	0.016	0.019	22.982	0.011	0.011	0.000	0.000	0.000
34	A	97	ALA	0	0.062	0.009	24.603	-0.015	-0.015	0.000	0.000	0.000
35	A	98	SER	0	0.025	0.015	25.711	-0.005	-0.005	0.000	0.000	0.000
36	A	99	GLU	-1	-0.761	-0.871	20.805	-0.293	-0.293	0.000	0.000	0.000
37	A	100	GLN	0	-0.072	-0.034	20.819	-0.017	-0.017	0.000	0.000	0.000
38	A	101	LYS	1	0.887	0.952	20.317	0.276	0.276	0.000	0.000	0.000
39	A	102	GLY	0	0.017	0.002	16.867	-0.039	-0.039	0.000	0.000	0.000
40	A	103	TYR	0	-0.031	-0.023	10.520	0.017	0.017	0.000	0.000	0.000
41	A	104	TRP	0	-0.049	-0.028	13.680	-0.071	-0.071	0.000	0.000	0.000
42	A	105	TYR	0	0.039	0.009	6.314	0.035	0.035	0.000	0.000	0.000
43	A	106	ARG	1	0.788	0.891	10.658	0.193	0.193	0.000	0.000	0.000
44	A	107	HIS	0	0.034	0.018	5.539	-0.065	-0.065	0.000	0.000	0.000
45	A	108	ASN	0	0.032	-0.015	9.293	0.084	0.084	0.000	0.000	0.000
46	A	109	ARG	1	0.875	0.919	10.982	0.005	0.005	0.000	0.000	0.000
47	A	110	ARG	1	0.917	0.982	10.620	-0.026	-0.026	0.000	0.000	0.000
48	A	111	SER	0	-0.030	-0.037	12.110	-0.035	-0.035	0.000	0.000	0.000
49	A	112	PHE	0	-0.009	0.008	12.782	0.044	0.044	0.000	0.000	0.000
50	A	113	LYS	1	0.898	0.960	15.135	-0.235	-0.235	0.000	0.000	0.000
51	A	114	THR	0	-0.039	-0.039	17.072	0.016	0.016	0.000	0.000	0.000
52	A	115	PRO	0	0.016	-0.009	20.305	0.005	0.005	0.000	0.000	0.000
53	A	116	ASP	-1	-0.784	-0.848	22.296	0.139	0.139	0.000	0.000	0.000
54	A	117	GLY	0	0.037	0.007	21.729	0.005	0.005	0.000	0.000	0.000
55	A	118	GLN	0	-0.038	-0.021	22.426	-0.010	-0.010	0.000	0.000	0.000
56	A	119	GLN	0	-0.051	-0.021	15.812	0.028	0.028	0.000	0.000	0.000
57	A	120	LYS	1	0.986	0.998	18.395	-0.147	-0.147	0.000	0.000	0.000
58	A	121	GLN	0	0.053	0.018	17.097	0.009	0.009	0.000	0.000	0.000
59	A	122	LEU	0	-0.047	-0.023	13.615	-0.006	-0.006	0.000	0.000	0.000
60	A	123	LEU	0	0.009	0.015	16.212	-0.009	-0.009	0.000	0.000	0.000
61	A	124	PRO	0	0.037	0.021	13.747	0.021	0.021	0.000	0.000	0.000
62	A	125	ARG	1	0.805	0.900	11.178	0.001	0.001	0.000	0.000	0.000
63	A	126	TRP	0	0.045	0.020	11.288	-0.030	-0.030	0.000	0.000	0.000
64	A	127	TYR	0	0.029	-0.007	8.174	0.083	0.083	0.000	0.000	0.000
65	A	128	PHE	0	0.064	0.045	11.071	-0.037	-0.037	0.000	0.000	0.000
66	A	129	TYR	0	-0.035	-0.021	5.764	0.085	0.085	0.000	0.000	0.000
67	A	130	TYR	0	0.102	0.051	12.475	0.079	0.079	0.000	0.000	0.000
68	A	131	LEU	0	0.040	0.024	14.068	-0.083	-0.083	0.000	0.000	0.000
69	A	132	GLY	0	0.045	0.036	14.854	0.024	0.024	0.000	0.000	0.000
70	A	133	THR	0	-0.063	-0.031	11.125	-0.038	-0.038	0.000	0.000	0.000
71	A	134	GLY	0	0.029	0.008	7.502	0.074	0.074	0.000	0.000	0.000
72	A	135	PRO	0	-0.072	-0.043	5.538	0.072	0.072	0.000	0.000	0.000
73	A	136	HIS	0	-0.014	-0.015	7.070	0.146	0.146	0.000	0.000	0.000
74	A	137	ALA	0	-0.018	0.014	9.908	0.123	0.123	0.000	0.000	0.000
75	A	138	GLY	0	-0.025	-0.021	11.718	0.078	0.078	0.000	0.000	0.000
76	A	139	ALA	0	-0.053	-0.010	14.108	0.055	0.055	0.000	0.000	0.000
77	A	140	SER	0	0.014	0.003	16.029	-0.010	-0.010	0.000	0.000	0.000
78	A	141	TYR	0	0.007	-0.018	19.365	-0.007	-0.007	0.000	0.000	0.000
79	A	142	GLY	0	-0.001	-0.008	20.207	0.022	0.022	0.000	0.000	0.000
80	A	143	ASP	-1	-0.840	-0.897	18.405	-0.254	-0.254	0.000	0.000	0.000
81	A	144	SER	0	-0.031	-0.015	19.257	-0.011	-0.011	0.000	0.000	0.000
82	A	145	ILE	0	-0.013	-0.008	14.101	0.003	0.003	0.000	0.000	0.000
83	A	146	GLU	-1	-0.804	-0.889	16.519	-0.138	-0.138	0.000	0.000	0.000
84	A	147	GLY	0	-0.082	-0.046	13.843	-0.026	-0.026	0.000	0.000	0.000
85	A	148	VAL	0	0.020	0.015	13.089	-0.064	-0.064	0.000	0.000	0.000
86	A	149	PHE	0	-0.004	0.006	15.296	0.039	0.039	0.000	0.000	0.000
87	A	150	TRP	0	-0.006	0.000	15.920	-0.038	-0.038	0.000	0.000	0.000
88	A	151	VAL	0	-0.035	-0.013	18.507	0.025	0.025	0.000	0.000	0.000
89	A	152	ALA	0	0.045	0.001	20.852	-0.026	-0.026	0.000	0.000	0.000
90	A	153	ASN	0	-0.020	-0.002	23.422	0.025	0.025	0.000	0.000	0.000
91	A	154	SER	0	0.045	0.002	26.360	-0.005	-0.005	0.000	0.000	0.000
92	A	155	GLN	0	-0.063	-0.024	29.159	0.005	0.005	0.000	0.000	0.000
93	A	156	ALA	0	-0.027	0.001	24.310	-0.001	-0.001	0.000	0.000	0.000
94	A	157	ASP	-1	-0.764	-0.853	26.000	-0.176	-0.176	0.000	0.000	0.000
95	A	158	THR	0	-0.047	-0.039	22.943	-0.014	-0.014	0.000	0.000	0.000
96	A	159	ASN	0	-0.046	-0.031	22.816	-0.015	-0.015	0.000	0.000	0.000
97	A	160	THR	0	-0.027	-0.023	22.920	-0.008	-0.008	0.000	0.000	0.000
98	A	161	ARG	1	0.841	0.915	14.686	0.449	0.449	0.000	0.000	0.000
99	A	162	SER	0	-0.059	-0.045	16.864	0.015	0.015	0.000	0.000	0.000
100	A	163	ASP	-1	-0.891	-0.956	18.496	-0.261	-0.261	0.000	0.000	0.000
101	A	164	ILE	0	-0.122	-0.053	15.751	0.013	0.013	0.000	0.000	0.000
102	A	165	VAL	0	-0.009	-0.003	13.394	-0.059	-0.059	0.000	0.000	0.000
103	A	166	GLU	-1	-0.804	-0.906	8.810	-1.422	-1.422	0.000	0.000	0.000
104	A	167	ARG	1	0.804	0.895	8.038	0.541	0.541	0.000	0.000	0.000
105	A	168	ASP	-1	-0.739	-0.824	8.706	-0.382	-0.382	0.000	0.000	0.000
106	A	169	PRO	0	-0.073	-0.048	6.668	0.089	0.089	0.000	0.000	0.000
107	A	170	SER	0	-0.099	-0.056	9.781	0.097	0.097	0.000	0.000	0.000
108	A	171	SER	0	-0.039	-0.047	12.344	0.003	0.003	0.000	0.000	0.000
109	A	172	HIS	0	-0.009	-0.001	13.142	-0.022	-0.022	0.000	0.000	0.000
110	A	173	GLU	-1	-0.908	-0.939	12.038	0.004	0.004	0.000	0.000	0.000
111	A	174	ALA	0	-0.066	-0.032	10.581	-0.050	-0.050	0.000	0.000	0.000
112	A	175	ILE	0	0.008	0.002	12.570	0.070	0.070	0.000	0.000	0.000
113	A	176	PRO	0	-0.027	-0.034	15.455	-0.025	-0.025	0.000	0.000	0.000
114	A	177	THR	0	0.027	0.019	15.565	-0.022	-0.022	0.000	0.000	0.000
115	A	178	ARG	1	0.844	0.919	18.083	0.117	0.117	0.000	0.000	0.000
116	A	179	PHE	0	0.040	0.017	19.343	-0.015	-0.015	0.000	0.000	0.000
117	A	180	ALA	0	0.052	0.035	23.846	0.011	0.011	0.000	0.000	0.000
118	A	181	PRO	0	0.026	0.004	27.224	0.001	0.001	0.000	0.000	0.000
119	A	182	GLY	0	0.027	0.016	30.018	-0.001	-0.001	0.000	0.000	0.000
120	A	183	THR	0	-0.055	-0.029	24.527	-0.004	-0.004	0.000	0.000	0.000
121	A	184	VAL	0	-0.032	-0.011	27.557	0.005	0.005	0.000	0.000	0.000
122	A	185	LEU	0	-0.001	0.001	22.854	-0.009	-0.009	0.000	0.000	0.000
123	A	186	PRO	0	-0.005	0.027	21.444	0.013	0.013	0.000	0.000	0.000
124	A	187	GLN	0	0.068	0.014	24.180	0.007	0.007	0.000	0.000	0.000
125	A	188	GLY	0	0.016	-0.003	24.521	-0.002	-0.002	0.000	0.000	0.000
126	A	189	PHE	0	0.000	-0.003	18.293	0.004	0.004	0.000	0.000	0.000
127	A	190	TYR	0	-0.043	-0.024	18.206	0.004	0.004	0.000	0.000	0.000
128	A	191	VAL	0	0.028	0.017	18.134	-0.007	-0.007	0.000	0.000	0.000
129	A	192	GLU	-1	-0.762	-0.837	14.506	0.032	0.032	0.000	0.000	0.000
130	A	193	GLY	0	0.025	0.021	17.329	-0.020	-0.020	0.000	0.000	0.000
131	A	194	SER	0	-0.017	-0.002	18.899	-0.008	-0.008	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:PRO)