FMO DATABASE

FMODB ID: 2267R

Calculation Name: 3FD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FD4

Chain ID: A

ChEMBL ID:

UniProt ID: P03205

Base Structure: X-ray

Registration Date: 2023-06-20

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1318111.397183
FMO2-HF: Nuclear repulsion	1260151.791195
FMO2-HF: Total energy	-57959.605987
FMO2-MP2: Total energy	-58122.646861

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:83:PRO)

Summations of interaction energy for fragment #1(A:83: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.
0.55	2.441	-0.022	-1.015	-0.855	0.002

Interaction energy analysis for fragmet #1(A:83:PRO)

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 : -0.026

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	85	LEU	0	0.008	0.013	3.873	0.967	2.858	-0.022	-1.015	-0.855	0.002
4	A	86	HIS	0	0.072	0.035	7.301	-0.154	-0.154	0.000	0.000	0.000	0.000
5	A	87	THR	0	-0.018	-0.020	10.198	-0.125	-0.125	0.000	0.000	0.000	0.000
6	A	88	PHE	0	-0.009	0.004	7.667	-0.132	-0.132	0.000	0.000	0.000	0.000
7	A	89	GLN	0	-0.022	-0.012	10.510	0.164	0.164	0.000	0.000	0.000	0.000
8	A	90	VAL	0	0.016	0.008	11.447	-0.071	-0.071	0.000	0.000	0.000	0.000
9	A	91	PRO	0	-0.002	-0.009	13.819	0.050	0.050	0.000	0.000	0.000	0.000
10	A	92	GLN	0	-0.017	0.004	12.744	0.003	0.003	0.000	0.000	0.000	0.000
11	A	93	ASN	0	0.009	0.002	16.927	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	94	TYR	0	0.007	-0.008	19.215	0.014	0.014	0.000	0.000	0.000	0.000
13	A	95	THR	0	0.005	-0.003	22.387	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	96	LYS	1	0.849	0.933	25.555	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	97	ALA	0	-0.003	0.013	27.925	0.000	0.000	0.000	0.000	0.000	0.000
16	A	98	ASN	0	-0.009	-0.003	28.752	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	99	CYS	0	-0.079	-0.046	29.191	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	100	THR	0	-0.055	-0.040	32.328	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	101	TYR	0	0.089	0.026	33.719	0.004	0.004	0.000	0.000	0.000	0.000
20	A	102	CYS	0	-0.090	-0.014	35.681	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	103	ASN	0	0.053	0.054	35.870	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	104	THR	0	-0.006	-0.024	38.072	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	105	ARG	1	0.876	0.932	40.853	-0.047	-0.047	0.000	0.000	0.000	0.000
24	A	106	GLU	-1	-0.781	-0.844	36.585	0.073	0.073	0.000	0.000	0.000	0.000
25	A	107	TYR	0	-0.018	0.000	38.820	0.001	0.001	0.000	0.000	0.000	0.000
26	A	108	THR	0	-0.017	0.000	39.456	0.000	0.000	0.000	0.000	0.000	0.000
27	A	109	PHE	0	0.000	-0.008	41.158	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	110	SER	0	-0.042	-0.030	41.578	0.002	0.002	0.000	0.000	0.000	0.000
29	A	111	TYR	0	0.010	-0.015	43.213	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	112	LYS	1	0.839	0.902	43.277	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	113	GLY	0	0.065	0.049	43.034	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	114	CYS	0	-0.018	0.003	38.775	0.002	0.002	0.000	0.000	0.000	0.000
33	A	116	PHE	0	0.048	0.029	37.339	0.001	0.001	0.000	0.000	0.000	0.000
34	A	117	TYR	0	0.017	-0.020	34.622	0.002	0.002	0.000	0.000	0.000	0.000
35	A	118	PHE	0	0.009	0.015	35.615	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	119	THR	0	-0.024	-0.014	30.311	0.000	0.000	0.000	0.000	0.000	0.000
37	A	120	LYS	1	0.875	0.921	33.480	-0.067	-0.067	0.000	0.000	0.000	0.000
38	A	121	LYS	1	0.909	0.974	25.791	-0.138	-0.138	0.000	0.000	0.000	0.000
39	A	122	LYS	1	0.943	0.968	31.575	-0.061	-0.061	0.000	0.000	0.000	0.000
40	A	123	HIS	0	0.043	0.009	26.820	0.013	0.013	0.000	0.000	0.000	0.000
41	A	124	THR	0	0.057	0.027	24.326	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	125	TRP	0	0.007	-0.001	25.868	0.004	0.004	0.000	0.000	0.000	0.000
43	A	126	ASN	0	0.006	-0.018	21.419	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	127	GLY	0	0.028	0.024	23.038	0.006	0.006	0.000	0.000	0.000	0.000
45	A	128	CYS	0	-0.052	-0.011	24.101	0.004	0.004	0.000	0.000	0.000	0.000
46	A	129	PHE	0	-0.026	0.001	23.182	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	130	GLN	0	-0.013	-0.002	18.743	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	131	ALA	0	0.001	0.001	22.814	0.003	0.003	0.000	0.000	0.000	0.000
49	A	132	CYS	0	-0.082	-0.042	25.778	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	133	ALA	0	0.009	0.006	23.779	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	134	GLU	-1	-0.863	-0.927	22.099	0.173	0.173	0.000	0.000	0.000	0.000
52	A	135	LEU	0	-0.112	-0.027	25.526	0.000	0.000	0.000	0.000	0.000	0.000
53	A	136	TYR	0	0.010	-0.032	29.340	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	137	PRO	0	0.067	0.029	28.908	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	139	THR	0	-0.022	-0.004	29.480	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	140	TYR	0	-0.018	-0.045	28.137	0.006	0.006	0.000	0.000	0.000	0.000
57	A	141	PHE	0	0.000	-0.005	27.533	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	142	TYR	0	0.063	0.017	29.695	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	143	GLY	0	0.067	0.031	33.053	0.001	0.001	0.000	0.000	0.000	0.000
60	A	144	PRO	0	-0.044	-0.020	34.994	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	145	THR	0	0.057	0.022	38.726	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	146	PRO	0	0.020	-0.014	41.074	0.002	0.002	0.000	0.000	0.000	0.000
63	A	147	ASP	-1	-0.785	-0.851	44.560	0.012	0.012	0.000	0.000	0.000	0.000
64	A	148	ILE	0	0.010	-0.001	40.525	0.001	0.001	0.000	0.000	0.000	0.000
65	A	149	LEU	0	-0.026	0.003	41.034	0.002	0.002	0.000	0.000	0.000	0.000
66	A	150	PRO	0	0.043	0.012	43.131	0.002	0.002	0.000	0.000	0.000	0.000
67	A	151	VAL	0	-0.035	-0.010	45.008	0.001	0.001	0.000	0.000	0.000	0.000
68	A	152	VAL	0	-0.015	-0.003	39.788	0.002	0.002	0.000	0.000	0.000	0.000
69	A	153	THR	0	0.034	0.010	42.613	0.002	0.002	0.000	0.000	0.000	0.000
70	A	154	ARG	1	0.973	0.990	44.356	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	155	ASN	0	-0.089	-0.057	43.859	0.000	0.000	0.000	0.000	0.000	0.000
72	A	156	LEU	0	0.003	0.035	40.981	0.002	0.002	0.000	0.000	0.000	0.000
73	A	157	ASN	0	0.001	-0.032	44.693	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	158	ALA	0	-0.004	-0.014	45.985	0.000	0.000	0.000	0.000	0.000	0.000
75	A	159	ILE	0	0.005	0.006	43.822	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	160	GLU	-1	-0.855	-0.899	41.136	0.038	0.038	0.000	0.000	0.000	0.000
77	A	161	SER	0	-0.029	-0.029	38.528	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	162	LEU	0	-0.016	0.008	36.173	0.004	0.004	0.000	0.000	0.000	0.000
79	A	163	TRP	0	-0.007	-0.014	30.779	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	164	VAL	0	-0.019	-0.025	33.265	0.003	0.003	0.000	0.000	0.000	0.000
81	A	165	GLY	0	0.048	0.042	30.342	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	166	VAL	0	-0.056	-0.031	31.281	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	167	TYR	0	0.008	0.012	28.036	0.004	0.004	0.000	0.000	0.000	0.000
84	A	168	ARG	1	0.895	0.950	29.863	0.016	0.016	0.000	0.000	0.000	0.000
85	A	169	VAL	0	0.003	-0.003	26.297	0.000	0.000	0.000	0.000	0.000	0.000
86	A	170	GLY	0	0.009	0.006	28.436	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	171	GLU	-1	-0.937	-0.969	29.663	-0.043	-0.043	0.000	0.000	0.000	0.000
88	A	172	GLY	0	-0.010	0.010	32.038	0.003	0.003	0.000	0.000	0.000	0.000
89	A	173	ASN	0	-0.024	-0.032	33.563	0.002	0.002	0.000	0.000	0.000	0.000
90	A	174	TRP	0	-0.027	-0.012	32.212	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	175	THR	0	-0.005	-0.030	30.981	0.001	0.001	0.000	0.000	0.000	0.000
92	A	176	SER	0	-0.002	-0.010	31.415	0.004	0.004	0.000	0.000	0.000	0.000
93	A	177	LEU	0	0.031	0.017	26.361	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	178	ASP	-1	-0.826	-0.881	30.028	0.017	0.017	0.000	0.000	0.000	0.000
95	A	179	GLY	0	0.009	0.027	32.411	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	180	GLY	0	0.039	0.011	33.734	0.003	0.003	0.000	0.000	0.000	0.000
97	A	181	THR	0	-0.031	-0.015	36.045	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	182	PHE	0	-0.043	-0.007	35.579	0.002	0.002	0.000	0.000	0.000	0.000
99	A	183	LYS	1	0.971	0.987	39.091	0.001	0.001	0.000	0.000	0.000	0.000
100	A	184	VAL	0	0.026	0.006	36.630	0.002	0.002	0.000	0.000	0.000	0.000
101	A	185	TYR	0	0.002	-0.004	39.906	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	186	GLN	0	0.021	0.006	37.315	0.000	0.000	0.000	0.000	0.000	0.000
103	A	187	ILE	0	0.013	0.020	39.725	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	188	PHE	0	0.030	0.014	36.392	0.000	0.000	0.000	0.000	0.000	0.000
105	A	189	GLY	0	0.019	0.033	35.680	0.000	0.000	0.000	0.000	0.000	0.000
106	A	190	SER	0	-0.027	-0.026	31.679	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	191	HIS	0	0.067	0.016	25.800	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	192	CYS	0	-0.045	-0.013	28.265	0.004	0.004	0.000	0.000	0.000	0.000
109	A	193	THR	0	0.025	-0.027	30.877	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	194	TYR	0	-0.068	-0.036	33.618	0.006	0.006	0.000	0.000	0.000	0.000
111	A	195	VAL	0	0.011	0.018	36.333	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	196	SER	0	0.066	0.002	39.737	0.003	0.003	0.000	0.000	0.000	0.000
113	A	197	LYS	1	0.850	0.939	42.616	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	198	PHE	0	0.013	0.000	46.086	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	199	SER	0	-0.022	0.016	42.897	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	200	THR	0	0.031	0.002	44.956	0.001	0.001	0.000	0.000	0.000	0.000
117	A	201	VAL	0	-0.033	-0.009	42.274	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	202	PRO	0	0.022	0.008	37.276	0.002	0.002	0.000	0.000	0.000	0.000
119	A	203	VAL	0	-0.014	0.002	38.500	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	204	SER	0	0.011	-0.002	35.237	0.003	0.003	0.000	0.000	0.000	0.000
121	A	205	HIS	0	-0.011	-0.016	34.156	0.001	0.001	0.000	0.000	0.000	0.000
122	A	206	HIS	0	0.034	0.027	34.291	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	207	GLU	-1	-0.789	-0.855	29.977	0.031	0.031	0.000	0.000	0.000	0.000
124	A	209	SER	0	-0.056	-0.060	27.085	0.008	0.008	0.000	0.000	0.000	0.000
125	A	210	PHE	0	0.026	0.007	28.503	0.007	0.007	0.000	0.000	0.000	0.000
126	A	211	LEU	0	0.020	0.007	28.433	0.000	0.000	0.000	0.000	0.000	0.000
127	A	212	LYS	1	0.850	0.938	31.875	-0.038	-0.038	0.000	0.000	0.000	0.000
128	A	213	PRO	0	0.001	0.004	32.201	0.006	0.006	0.000	0.000	0.000	0.000
129	A	215	LEU	0	0.017	0.011	32.385	0.002	0.002	0.000	0.000	0.000	0.000
130	A	217	VAL	0	-0.015	-0.003	32.839	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	218	SER	0	0.041	0.013	32.913	0.004	0.004	0.000	0.000	0.000	0.000
132	A	219	GLN	0	0.044	0.026	34.364	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	220	ARG	1	0.917	0.949	37.046	-0.030	-0.030	0.000	0.000	0.000	0.000
134	A	221	SER	0	0.040	0.017	39.971	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	222	ASN	0	-0.024	0.003	41.018	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:83:PRO)