FMO DATABASE

FMODB ID: 7GL3K

Calculation Name: 3FD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

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	-1315065.472031
FMO2-HF: Nuclear repulsion	1257106.425021
FMO2-HF: Total energy	-57959.04701
FMO2-MP2: Total energy	-58122.181489

3D Structure Molmil

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.
-0.105	2.076	-0.024	-1.217	-0.941	0.001

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 : -0.010 / q_NPA : -0.028

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	0.017	0.024	3.888	0.257	2.438	-0.024	-1.217	-0.941	0.001
4	A	86	HIS	0	0.066	0.022	7.250	-0.070	-0.070	0.000	0.000	0.000	0.000
5	A	87	THR	0	-0.033	-0.023	10.409	-0.142	-0.142	0.000	0.000	0.000	0.000
6	A	88	PHE	0	0.001	0.021	8.240	-0.138	-0.138	0.000	0.000	0.000	0.000
7	A	89	GLN	0	-0.027	-0.020	10.685	0.169	0.169	0.000	0.000	0.000	0.000
8	A	90	VAL	0	0.027	0.012	11.544	-0.075	-0.075	0.000	0.000	0.000	0.000
9	A	91	PRO	0	-0.011	-0.013	13.860	0.056	0.056	0.000	0.000	0.000	0.000
10	A	92	GLN	0	-0.014	0.003	12.839	0.011	0.011	0.000	0.000	0.000	0.000
11	A	93	ASN	0	0.016	0.005	16.991	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	94	TYR	0	-0.001	-0.011	19.434	0.016	0.016	0.000	0.000	0.000	0.000
13	A	95	THR	0	0.010	0.000	22.508	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	96	LYS	1	0.865	0.944	25.377	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	97	ALA	0	-0.034	-0.008	27.981	0.001	0.001	0.000	0.000	0.000	0.000
16	A	98	ASN	0	0.018	-0.006	28.874	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	99	CYS	0	-0.100	-0.027	28.627	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	100	THR	0	-0.030	-0.026	31.932	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	101	TYR	0	0.064	0.014	33.611	0.003	0.003	0.000	0.000	0.000	0.000
20	A	102	CYS	0	-0.072	-0.024	35.585	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	103	ASN	0	0.008	0.044	35.804	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	104	THR	0	-0.002	-0.039	38.011	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	105	ARG	1	0.916	0.951	40.885	-0.058	-0.058	0.000	0.000	0.000	0.000
24	A	106	GLU	-1	-0.784	-0.860	36.870	0.085	0.085	0.000	0.000	0.000	0.000
25	A	107	TYR	0	-0.041	0.003	38.821	0.000	0.000	0.000	0.000	0.000	0.000
26	A	108	THR	0	-0.007	-0.002	39.670	0.000	0.000	0.000	0.000	0.000	0.000
27	A	109	PHE	0	-0.006	-0.009	41.424	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	110	SER	0	-0.024	-0.009	41.744	0.002	0.002	0.000	0.000	0.000	0.000
29	A	111	TYR	0	0.007	-0.014	43.221	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	112	LYS	1	0.849	0.908	43.388	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	113	GLY	0	0.061	0.041	43.191	0.000	0.000	0.000	0.000	0.000	0.000
32	A	114	CYS	0	-0.033	0.003	38.979	0.002	0.002	0.000	0.000	0.000	0.000
33	A	116	PHE	0	0.068	0.041	37.283	0.002	0.002	0.000	0.000	0.000	0.000
34	A	117	TYR	0	0.003	-0.028	34.565	0.001	0.001	0.000	0.000	0.000	0.000
35	A	118	PHE	0	0.010	0.010	35.429	0.000	0.000	0.000	0.000	0.000	0.000
36	A	119	THR	0	-0.022	-0.009	30.635	0.001	0.001	0.000	0.000	0.000	0.000
37	A	120	LYS	1	0.903	0.943	33.886	-0.081	-0.081	0.000	0.000	0.000	0.000
38	A	121	LYS	1	0.976	0.995	27.007	-0.149	-0.149	0.000	0.000	0.000	0.000
39	A	122	LYS	1	0.923	0.963	31.941	-0.069	-0.069	0.000	0.000	0.000	0.000
40	A	123	HIS	0	0.055	0.014	26.940	0.015	0.015	0.000	0.000	0.000	0.000
41	A	124	THR	0	0.060	0.027	24.607	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	125	TRP	0	-0.002	-0.006	25.937	0.006	0.006	0.000	0.000	0.000	0.000
43	A	126	ASN	0	0.043	0.009	20.994	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	127	GLY	0	0.036	0.013	23.200	0.008	0.008	0.000	0.000	0.000	0.000
45	A	128	CYS	0	-0.034	-0.006	24.254	0.007	0.007	0.000	0.000	0.000	0.000
46	A	129	PHE	0	-0.009	0.011	23.150	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	130	GLN	0	-0.044	-0.018	18.360	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	131	ALA	0	0.025	0.014	22.754	0.003	0.003	0.000	0.000	0.000	0.000
49	A	132	CYS	0	-0.126	-0.077	25.731	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	133	ALA	0	-0.020	0.002	23.485	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	134	GLU	-1	-0.880	-0.932	21.163	0.233	0.233	0.000	0.000	0.000	0.000
52	A	135	LEU	0	-0.128	-0.034	25.442	0.000	0.000	0.000	0.000	0.000	0.000
53	A	136	TYR	0	-0.034	-0.049	29.196	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	137	PRO	0	0.074	0.034	28.554	0.002	0.002	0.000	0.000	0.000	0.000
55	A	139	THR	0	-0.010	-0.002	29.013	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	140	TYR	0	-0.014	-0.035	28.105	0.009	0.009	0.000	0.000	0.000	0.000
57	A	141	PHE	0	-0.004	0.001	27.615	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	142	TYR	0	0.046	0.005	29.795	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	143	GLY	0	0.055	0.018	33.225	0.000	0.000	0.000	0.000	0.000	0.000
60	A	144	PRO	0	-0.040	-0.015	35.055	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	145	THR	0	0.065	0.025	38.856	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	146	PRO	0	0.017	-0.008	41.245	0.002	0.002	0.000	0.000	0.000	0.000
63	A	147	ASP	-1	-0.811	-0.877	44.789	0.022	0.022	0.000	0.000	0.000	0.000
64	A	148	ILE	0	-0.005	-0.001	40.725	0.001	0.001	0.000	0.000	0.000	0.000
65	A	149	LEU	0	-0.018	-0.007	41.228	0.002	0.002	0.000	0.000	0.000	0.000
66	A	150	PRO	0	0.045	0.016	43.285	0.002	0.002	0.000	0.000	0.000	0.000
67	A	151	VAL	0	-0.034	-0.013	45.173	0.001	0.001	0.000	0.000	0.000	0.000
68	A	152	VAL	0	-0.025	-0.014	39.960	0.002	0.002	0.000	0.000	0.000	0.000
69	A	153	THR	0	0.040	0.011	42.884	0.002	0.002	0.000	0.000	0.000	0.000
70	A	154	ARG	1	0.963	0.982	44.646	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	155	ASN	0	-0.095	-0.035	43.821	0.000	0.000	0.000	0.000	0.000	0.000
72	A	156	LEU	0	-0.018	0.017	41.097	0.002	0.002	0.000	0.000	0.000	0.000
73	A	157	ASN	0	0.023	-0.015	45.069	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	158	ALA	0	-0.008	-0.024	46.155	0.000	0.000	0.000	0.000	0.000	0.000
75	A	159	ILE	0	0.002	0.004	43.757	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	160	GLU	-1	-0.889	-0.920	41.582	0.047	0.047	0.000	0.000	0.000	0.000
77	A	161	SER	0	-0.030	-0.026	38.596	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	162	LEU	0	-0.002	0.013	36.312	0.004	0.004	0.000	0.000	0.000	0.000
79	A	163	TRP	0	-0.017	-0.017	30.972	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	164	VAL	0	-0.015	-0.015	33.594	0.003	0.003	0.000	0.000	0.000	0.000
81	A	165	GLY	0	0.058	0.033	30.553	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	166	VAL	0	-0.052	-0.018	31.274	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	167	TYR	0	-0.011	-0.005	27.997	0.005	0.005	0.000	0.000	0.000	0.000
84	A	168	ARG	1	0.899	0.960	29.906	0.002	0.002	0.000	0.000	0.000	0.000
85	A	169	VAL	0	0.002	-0.014	26.233	0.002	0.002	0.000	0.000	0.000	0.000
86	A	170	GLY	0	0.012	0.013	28.638	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	171	GLU	-1	-0.932	-0.960	29.692	-0.035	-0.035	0.000	0.000	0.000	0.000
88	A	172	GLY	0	-0.031	-0.007	31.881	0.003	0.003	0.000	0.000	0.000	0.000
89	A	173	ASN	0	-0.022	-0.011	33.327	0.001	0.001	0.000	0.000	0.000	0.000
90	A	174	TRP	0	-0.036	-0.030	32.304	0.001	0.001	0.000	0.000	0.000	0.000
91	A	175	THR	0	0.012	-0.020	30.848	0.000	0.000	0.000	0.000	0.000	0.000
92	A	176	SER	0	0.003	0.003	31.436	0.005	0.005	0.000	0.000	0.000	0.000
93	A	177	LEU	0	0.043	0.017	26.350	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	178	ASP	-1	-0.844	-0.893	30.073	0.036	0.036	0.000	0.000	0.000	0.000
95	A	179	GLY	0	0.008	0.023	32.652	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	180	GLY	0	0.026	-0.003	34.042	0.003	0.003	0.000	0.000	0.000	0.000
97	A	181	THR	0	-0.021	-0.013	36.004	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	182	PHE	0	-0.047	-0.015	35.587	0.001	0.001	0.000	0.000	0.000	0.000
99	A	183	LYS	1	0.968	0.982	39.078	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	184	VAL	0	0.013	0.000	36.609	0.003	0.003	0.000	0.000	0.000	0.000
101	A	185	TYR	0	0.020	0.009	39.932	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	186	GLN	0	0.008	-0.003	37.247	0.001	0.001	0.000	0.000	0.000	0.000
103	A	187	ILE	0	0.015	0.024	39.737	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	188	PHE	0	0.041	0.015	36.437	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	189	GLY	0	0.020	0.042	35.522	0.001	0.001	0.000	0.000	0.000	0.000
106	A	190	SER	0	-0.022	-0.034	31.820	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	191	HIS	0	0.059	0.009	26.152	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	192	CYS	0	-0.060	-0.007	28.473	0.005	0.005	0.000	0.000	0.000	0.000
109	A	193	THR	0	0.038	-0.013	31.281	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	194	TYR	0	-0.062	-0.031	33.900	0.006	0.006	0.000	0.000	0.000	0.000
111	A	195	VAL	0	0.007	0.012	36.549	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	196	SER	0	0.039	-0.011	39.963	0.003	0.003	0.000	0.000	0.000	0.000
113	A	197	LYS	1	0.928	0.975	42.889	-0.031	-0.031	0.000	0.000	0.000	0.000
114	A	198	PHE	0	0.004	-0.008	46.275	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	199	SER	0	-0.010	0.025	43.230	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	200	THR	0	0.025	-0.001	45.389	0.001	0.001	0.000	0.000	0.000	0.000
117	A	201	VAL	0	-0.024	-0.003	42.209	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	202	PRO	0	0.015	0.005	37.318	0.001	0.001	0.000	0.000	0.000	0.000
119	A	203	VAL	0	-0.009	0.001	38.692	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	204	SER	0	0.016	-0.006	35.485	0.004	0.004	0.000	0.000	0.000	0.000
121	A	205	HIS	0	-0.008	-0.008	34.307	0.000	0.000	0.000	0.000	0.000	0.000
122	A	206	HIS	0	0.020	0.030	34.342	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	207	GLU	-1	-0.793	-0.866	30.321	0.040	0.040	0.000	0.000	0.000	0.000
124	A	209	SER	0	-0.069	-0.062	27.200	0.010	0.010	0.000	0.000	0.000	0.000
125	A	210	PHE	0	0.033	0.014	28.556	0.007	0.007	0.000	0.000	0.000	0.000
126	A	211	LEU	0	0.003	-0.005	28.319	0.002	0.002	0.000	0.000	0.000	0.000
127	A	212	LYS	1	0.873	0.936	31.829	-0.051	-0.051	0.000	0.000	0.000	0.000
128	A	213	PRO	0	-0.021	0.004	32.221	0.007	0.007	0.000	0.000	0.000	0.000
129	A	215	LEU	0	0.032	0.027	32.524	0.001	0.001	0.000	0.000	0.000	0.000
130	A	217	VAL	0	-0.008	0.003	32.682	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	218	SER	0	0.051	0.021	32.818	0.005	0.005	0.000	0.000	0.000	0.000
132	A	219	GLN	0	0.058	0.034	34.641	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	220	ARG	1	0.920	0.945	36.992	-0.041	-0.041	0.000	0.000	0.000	0.000
134	A	221	SER	0	0.045	0.009	39.758	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	222	ASN	0	-0.011	0.015	40.587	-0.004	-0.004	0.000	0.000	0.000	0.000

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