FMO DATABASE

FMODB ID: M3G6Z

Calculation Name: 3FD4-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3FD4

Chain ID: A

ChEMBL ID:
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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	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1313411.505499
FMO2-HF: Nuclear repulsion	1255453.437979
FMO2-HF: Total energy	-57958.06752
FMO2-MP2: Total energy	-58121.283886

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.
0.49	2.429	-0.02	-1.07	-0.849	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 : 0.004 / 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	0.009	0.016	3.888	0.817	2.756	-0.020	-1.070	-0.849	0.001
4	A	86	HIS	0	0.069	0.026	7.299	-0.195	-0.195	0.000	0.000	0.000	0.000
5	A	87	THR	0	-0.027	-0.018	10.080	-0.113	-0.113	0.000	0.000	0.000	0.000
6	A	88	PHE	0	0.022	0.029	8.387	-0.124	-0.124	0.000	0.000	0.000	0.000
7	A	89	GLN	0	-0.043	-0.030	10.407	0.138	0.138	0.000	0.000	0.000	0.000
8	A	90	VAL	0	0.014	0.009	11.280	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	91	PRO	0	-0.020	-0.019	13.690	0.059	0.059	0.000	0.000	0.000	0.000
10	A	92	GLN	0	-0.004	0.007	12.573	0.006	0.006	0.000	0.000	0.000	0.000
11	A	93	ASN	0	0.015	0.004	16.846	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	94	TYR	0	0.009	-0.002	19.383	0.026	0.026	0.000	0.000	0.000	0.000
13	A	95	THR	0	-0.009	-0.012	22.400	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	96	LYS	1	0.929	0.984	25.297	0.004	0.004	0.000	0.000	0.000	0.000
15	A	97	ALA	0	-0.018	0.003	27.833	0.000	0.000	0.000	0.000	0.000	0.000
16	A	98	ASN	0	0.026	-0.002	28.568	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	99	CYS	0	-0.103	-0.020	28.500	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	100	THR	0	-0.006	-0.003	31.681	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	101	TYR	0	0.038	0.000	33.422	0.004	0.004	0.000	0.000	0.000	0.000
20	A	102	CYS	0	-0.058	-0.022	35.418	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	103	ASN	0	0.015	0.043	35.412	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	104	THR	0	-0.021	-0.050	37.850	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	105	ARG	1	0.938	0.965	40.706	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	106	GLU	-1	-0.876	-0.931	37.221	0.063	0.063	0.000	0.000	0.000	0.000
25	A	107	TYR	0	-0.123	-0.020	38.624	0.000	0.000	0.000	0.000	0.000	0.000
26	A	108	THR	0	-0.003	0.003	39.484	0.000	0.000	0.000	0.000	0.000	0.000
27	A	109	PHE	0	-0.008	-0.019	41.234	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	110	SER	0	-0.014	0.008	41.569	0.001	0.001	0.000	0.000	0.000	0.000
29	A	111	TYR	0	0.015	-0.012	43.062	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	112	LYS	1	0.866	0.909	43.251	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	113	GLY	0	0.058	0.038	43.086	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	114	CYS	0	-0.030	0.002	38.870	0.001	0.001	0.000	0.000	0.000	0.000
33	A	116	PHE	0	0.072	0.039	37.124	0.001	0.001	0.000	0.000	0.000	0.000
34	A	117	TYR	0	0.002	-0.016	34.348	0.003	0.003	0.000	0.000	0.000	0.000
35	A	118	PHE	0	0.019	0.012	35.222	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	119	THR	0	-0.024	-0.004	30.449	0.002	0.002	0.000	0.000	0.000	0.000
37	A	120	LYS	1	1.002	0.997	33.648	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	121	LYS	1	0.975	0.993	28.129	-0.109	-0.109	0.000	0.000	0.000	0.000
39	A	122	LYS	1	0.922	0.960	31.665	-0.047	-0.047	0.000	0.000	0.000	0.000
40	A	123	HIS	0	0.051	0.019	26.447	0.010	0.010	0.000	0.000	0.000	0.000
41	A	124	THR	0	0.056	0.027	24.360	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	125	TRP	0	0.004	-0.004	25.651	0.003	0.003	0.000	0.000	0.000	0.000
43	A	126	ASN	0	0.034	0.006	20.367	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	127	GLY	0	0.031	0.010	22.954	0.005	0.005	0.000	0.000	0.000	0.000
45	A	128	CYS	0	-0.006	0.005	24.008	0.008	0.008	0.000	0.000	0.000	0.000
46	A	129	PHE	0	-0.013	0.006	23.005	0.000	0.000	0.000	0.000	0.000	0.000
47	A	130	GLN	0	0.009	0.022	18.209	0.009	0.009	0.000	0.000	0.000	0.000
48	A	131	ALA	0	0.029	0.012	22.548	0.007	0.007	0.000	0.000	0.000	0.000
49	A	132	CYS	0	-0.123	-0.070	25.506	0.000	0.000	0.000	0.000	0.000	0.000
50	A	133	ALA	0	-0.026	0.002	23.254	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	134	GLU	-1	-0.917	-0.965	20.872	0.184	0.184	0.000	0.000	0.000	0.000
52	A	135	LEU	0	-0.145	-0.044	25.250	0.003	0.003	0.000	0.000	0.000	0.000
53	A	136	TYR	0	0.000	-0.020	28.996	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	137	PRO	0	0.072	0.036	28.425	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	139	THR	0	-0.014	-0.007	28.875	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	140	TYR	0	-0.008	-0.023	27.960	0.005	0.005	0.000	0.000	0.000	0.000
57	A	141	PHE	0	-0.014	-0.003	27.370	0.000	0.000	0.000	0.000	0.000	0.000
58	A	142	TYR	0	0.059	0.014	29.622	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	143	GLY	0	0.037	0.015	33.064	0.000	0.000	0.000	0.000	0.000	0.000
60	A	144	PRO	0	-0.029	-0.012	34.899	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	145	THR	0	0.055	0.023	38.696	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	146	PRO	0	0.012	-0.015	41.104	0.002	0.002	0.000	0.000	0.000	0.000
63	A	147	ASP	-1	-0.830	-0.885	44.654	0.006	0.006	0.000	0.000	0.000	0.000
64	A	148	ILE	0	-0.011	0.006	40.691	0.002	0.002	0.000	0.000	0.000	0.000
65	A	149	LEU	0	-0.011	-0.009	40.946	0.002	0.002	0.000	0.000	0.000	0.000
66	A	150	PRO	0	0.039	0.013	43.110	0.002	0.002	0.000	0.000	0.000	0.000
67	A	151	VAL	0	-0.032	-0.013	45.101	0.001	0.001	0.000	0.000	0.000	0.000
68	A	152	VAL	0	-0.011	-0.010	39.827	0.002	0.002	0.000	0.000	0.000	0.000
69	A	153	THR	0	0.005	-0.012	42.909	0.003	0.003	0.000	0.000	0.000	0.000
70	A	154	ARG	1	0.957	0.977	44.435	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	155	ASN	0	-0.083	-0.028	43.709	0.002	0.002	0.000	0.000	0.000	0.000
72	A	156	LEU	0	-0.029	0.021	40.518	0.002	0.002	0.000	0.000	0.000	0.000
73	A	157	ASN	0	0.051	0.010	44.830	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	158	ALA	0	-0.034	-0.050	45.904	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	159	ILE	0	-0.009	0.006	43.340	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	160	GLU	-1	-0.906	-0.923	41.523	0.029	0.029	0.000	0.000	0.000	0.000
77	A	161	SER	0	-0.036	-0.028	38.323	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	162	LEU	0	0.003	0.011	36.063	0.004	0.004	0.000	0.000	0.000	0.000
79	A	163	TRP	0	-0.011	-0.015	30.747	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	164	VAL	0	-0.021	-0.010	33.381	0.004	0.004	0.000	0.000	0.000	0.000
81	A	165	GLY	0	0.059	0.028	30.370	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	166	VAL	0	-0.043	-0.015	31.100	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	167	TYR	0	-0.008	-0.011	27.647	0.004	0.004	0.000	0.000	0.000	0.000
84	A	168	ARG	1	0.909	0.972	29.754	0.042	0.042	0.000	0.000	0.000	0.000
85	A	169	VAL	0	-0.004	-0.020	26.100	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	170	GLY	0	0.012	0.014	28.525	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	171	GLU	-1	-0.924	-0.955	29.597	-0.066	-0.066	0.000	0.000	0.000	0.000
88	A	172	GLY	0	-0.034	-0.010	31.800	0.005	0.005	0.000	0.000	0.000	0.000
89	A	173	ASN	0	-0.016	-0.009	33.246	0.003	0.003	0.000	0.000	0.000	0.000
90	A	174	TRP	0	-0.032	-0.021	32.059	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	175	THR	0	0.014	-0.008	30.575	0.002	0.002	0.000	0.000	0.000	0.000
92	A	176	SER	0	0.010	0.003	31.338	0.003	0.003	0.000	0.000	0.000	0.000
93	A	177	LEU	0	0.032	0.008	26.266	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	178	ASP	-1	-0.882	-0.925	29.969	0.008	0.008	0.000	0.000	0.000	0.000
95	A	179	GLY	0	-0.003	0.013	32.573	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	180	GLY	0	0.021	-0.005	33.966	0.003	0.003	0.000	0.000	0.000	0.000
97	A	181	THR	0	-0.027	-0.021	35.916	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	182	PHE	0	-0.045	-0.014	35.629	0.003	0.003	0.000	0.000	0.000	0.000
99	A	183	LYS	1	0.973	0.980	38.952	0.011	0.011	0.000	0.000	0.000	0.000
100	A	184	VAL	0	0.004	-0.001	36.473	0.003	0.003	0.000	0.000	0.000	0.000
101	A	185	TYR	0	0.017	0.007	39.770	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	186	GLN	0	-0.002	-0.017	37.262	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	187	ILE	0	0.017	0.024	39.555	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	188	PHE	0	0.048	0.024	36.082	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	189	GLY	0	0.023	0.045	35.337	0.001	0.001	0.000	0.000	0.000	0.000
106	A	190	SER	0	-0.025	-0.024	31.597	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	191	HIS	0	0.058	0.009	25.990	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	192	CYS	0	-0.061	-0.010	28.225	0.006	0.006	0.000	0.000	0.000	0.000
109	A	193	THR	0	0.039	-0.010	31.073	0.001	0.001	0.000	0.000	0.000	0.000
110	A	194	TYR	0	-0.058	-0.035	33.688	0.005	0.005	0.000	0.000	0.000	0.000
111	A	195	VAL	0	0.010	0.018	36.332	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	196	SER	0	0.044	-0.009	39.748	0.003	0.003	0.000	0.000	0.000	0.000
113	A	197	LYS	1	0.965	0.991	42.660	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	198	PHE	0	-0.002	-0.017	46.045	0.000	0.000	0.000	0.000	0.000	0.000
115	A	199	SER	0	-0.010	0.024	43.025	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	200	THR	0	0.026	-0.003	45.180	0.001	0.001	0.000	0.000	0.000	0.000
117	A	201	VAL	0	-0.025	-0.003	42.040	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	202	PRO	0	0.015	0.010	37.113	0.001	0.001	0.000	0.000	0.000	0.000
119	A	203	VAL	0	0.000	0.008	38.506	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	204	SER	0	0.000	-0.023	35.243	0.003	0.003	0.000	0.000	0.000	0.000
121	A	205	HIS	0	-0.009	-0.008	34.023	0.001	0.001	0.000	0.000	0.000	0.000
122	A	206	HIS	0	0.023	0.026	34.113	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	207	GLU	-1	-0.823	-0.901	30.253	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	209	SER	0	-0.066	-0.046	26.940	0.008	0.008	0.000	0.000	0.000	0.000
125	A	210	PHE	0	0.044	0.023	28.282	0.009	0.009	0.000	0.000	0.000	0.000
126	A	211	LEU	0	-0.015	-0.006	28.052	0.000	0.000	0.000	0.000	0.000	0.000
127	A	212	LYS	1	0.900	0.942	31.546	-0.019	-0.019	0.000	0.000	0.000	0.000
128	A	213	PRO	0	-0.013	0.005	31.959	0.005	0.005	0.000	0.000	0.000	0.000
129	A	215	LEU	0	0.029	0.023	32.295	0.003	0.003	0.000	0.000	0.000	0.000
130	A	217	VAL	0	-0.010	-0.002	32.520	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	218	SER	0	0.050	0.008	32.671	0.003	0.003	0.000	0.000	0.000	0.000
132	A	219	GLN	0	0.038	0.017	33.999	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	220	ARG	1	0.927	0.945	36.839	-0.028	-0.028	0.000	0.000	0.000	0.000
134	A	221	SER	0	0.044	0.007	38.745	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	222	ASN	0	-0.003	0.016	40.374	-0.001	-0.001	0.000	0.000	0.000	0.000

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