FMO DATABASE

FMODB ID: JQ4N9

Calculation Name: 4MXV-A-Xray372

Preferred Name: TNF-beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4MXV

Chain ID: A

ChEMBL ID: CHEMBL2059

UniProt ID: P01374

Base Structure: X-ray

Registration Date: 2023-09-22

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1172679.197915
FMO2-HF: Nuclear repulsion	1120379.28288
FMO2-HF: Total energy	-52299.915035
FMO2-MP2: Total energy	-52455.538411

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:28:LYS)

Summations of interaction energy for fragment #1(A:28:LYS)

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.
-88.196	-80.912	12.796	-8.88	-11.202	-0.098

Interaction energy analysis for fragmet #1(A:28:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.923 / q_NPA : 0.959

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	30	ALA	0	-0.032	-0.027	3.619	-5.752	-3.713	-0.001	-1.009	-1.029	0.004
4	A	31	ALA	0	0.007	0.000	5.855	2.565	2.565	0.000	0.000	0.000	0.000
5	A	32	HIS	0	-0.005	0.030	9.628	-1.398	-1.398	0.000	0.000	0.000	0.000
6	A	33	LEU	0	-0.016	-0.014	12.517	1.037	1.037	0.000	0.000	0.000	0.000
7	A	34	ILE	0	0.030	0.011	15.973	0.232	0.232	0.000	0.000	0.000	0.000
8	A	35	GLY	0	0.049	0.027	19.467	0.150	0.150	0.000	0.000	0.000	0.000
9	A	36	ASP	-1	-0.813	-0.875	22.973	-11.000	-11.000	0.000	0.000	0.000	0.000
10	A	37	PRO	0	0.064	0.017	25.455	0.335	0.335	0.000	0.000	0.000	0.000
11	A	38	SER	0	-0.083	-0.055	28.487	0.450	0.450	0.000	0.000	0.000	0.000
12	A	39	LYS	1	0.879	0.938	28.189	10.183	10.183	0.000	0.000	0.000	0.000
13	A	40	GLN	0	-0.018	-0.008	30.528	0.464	0.464	0.000	0.000	0.000	0.000
14	A	41	ASN	0	0.007	0.007	32.181	0.172	0.172	0.000	0.000	0.000	0.000
15	A	42	SER	0	-0.047	-0.036	29.078	0.080	0.080	0.000	0.000	0.000	0.000
16	A	43	LEU	0	0.003	0.023	23.367	0.082	0.082	0.000	0.000	0.000	0.000
17	A	44	LEU	0	-0.025	-0.018	24.231	-0.190	-0.190	0.000	0.000	0.000	0.000
18	A	45	TRP	0	0.027	0.012	18.695	-0.205	-0.205	0.000	0.000	0.000	0.000
19	A	46	ARG	1	0.819	0.891	19.495	12.614	12.614	0.000	0.000	0.000	0.000
20	A	47	ALA	0	0.058	0.005	14.739	-0.318	-0.318	0.000	0.000	0.000	0.000
21	A	48	ASN	0	-0.009	0.005	16.075	-0.402	-0.402	0.000	0.000	0.000	0.000
22	A	49	THR	0	0.008	0.008	18.472	0.547	0.547	0.000	0.000	0.000	0.000
23	A	50	ASP	-1	-0.854	-0.918	17.701	-14.284	-14.284	0.000	0.000	0.000	0.000
24	A	51	ARG	1	0.864	0.911	16.391	16.200	16.200	0.000	0.000	0.000	0.000
25	A	52	ALA	0	0.000	0.017	15.260	-0.325	-0.325	0.000	0.000	0.000	0.000
26	A	53	PHE	0	0.016	0.007	8.004	0.278	0.278	0.000	0.000	0.000	0.000
27	A	54	LEU	0	-0.010	-0.007	10.604	-0.507	-0.507	0.000	0.000	0.000	0.000
28	A	55	GLN	0	-0.034	-0.020	3.673	4.771	5.169	-0.001	-0.111	-0.286	0.000
29	A	56	ASP	-1	-0.861	-0.942	1.981	-54.958	-54.163	6.003	-3.478	-3.320	-0.048
30	A	57	GLY	0	0.078	0.031	5.298	-1.404	-1.363	-0.001	-0.002	-0.038	0.000
31	A	58	PHE	0	-0.039	-0.003	6.657	1.660	1.660	0.000	0.000	0.000	0.000
32	A	59	SER	0	0.022	0.005	10.204	1.388	1.388	0.000	0.000	0.000	0.000
33	A	60	LEU	0	0.004	0.012	13.965	-0.081	-0.081	0.000	0.000	0.000	0.000
34	A	61	SER	0	0.007	0.000	17.181	0.680	0.680	0.000	0.000	0.000	0.000
35	A	62	ASN	0	0.000	-0.008	19.985	0.079	0.079	0.000	0.000	0.000	0.000
36	A	63	ASN	0	-0.001	-0.005	21.407	-0.182	-0.182	0.000	0.000	0.000	0.000
37	A	64	SER	0	0.005	0.020	19.114	0.006	0.006	0.000	0.000	0.000	0.000
38	A	65	LEU	0	-0.042	-0.031	11.469	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	66	LEU	0	-0.007	-0.007	14.353	0.272	0.272	0.000	0.000	0.000	0.000
40	A	67	VAL	0	-0.031	-0.004	10.296	-1.598	-1.598	0.000	0.000	0.000	0.000
41	A	68	PRO	0	0.023	0.033	7.000	1.306	1.306	0.000	0.000	0.000	0.000
42	A	69	THR	0	0.033	0.003	7.222	0.841	0.841	0.000	0.000	0.000	0.000
43	A	70	SER	0	0.039	0.030	9.367	-0.806	-0.806	0.000	0.000	0.000	0.000
44	A	71	GLY	0	-0.014	0.002	7.613	-1.792	-1.792	0.000	0.000	0.000	0.000
45	A	72	ILE	0	-0.033	-0.012	7.120	2.387	2.387	0.000	0.000	0.000	0.000
46	A	73	TYR	0	-0.003	-0.027	6.403	-7.742	-7.742	0.000	0.000	0.000	0.000
47	A	74	PHE	0	-0.027	0.007	7.784	3.605	3.605	0.000	0.000	0.000	0.000
48	A	75	VAL	0	0.018	0.003	9.445	-0.742	-0.742	0.000	0.000	0.000	0.000
49	A	76	TYR	0	-0.030	-0.039	10.540	0.739	0.739	0.000	0.000	0.000	0.000
50	A	77	SER	0	-0.029	-0.028	14.965	0.366	0.366	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.064	-0.027	18.053	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	79	VAL	0	0.040	0.028	20.999	0.172	0.172	0.000	0.000	0.000	0.000
53	A	80	VAL	0	0.015	0.000	24.422	0.100	0.100	0.000	0.000	0.000	0.000
54	A	81	PHE	0	0.024	0.002	27.590	0.215	0.215	0.000	0.000	0.000	0.000
55	A	82	SER	0	0.003	-0.007	31.079	0.130	0.130	0.000	0.000	0.000	0.000
56	A	83	GLY	0	0.020	0.009	34.333	0.051	0.051	0.000	0.000	0.000	0.000
57	A	84	LYS	1	1.012	1.026	38.050	7.568	7.568	0.000	0.000	0.000	0.000
58	A	92	SER	0	-0.016	-0.015	47.132	0.044	0.044	0.000	0.000	0.000	0.000
59	A	93	SER	0	0.025	0.010	43.991	0.094	0.094	0.000	0.000	0.000	0.000
60	A	94	PRO	0	-0.020	-0.022	41.587	-0.052	-0.052	0.000	0.000	0.000	0.000
61	A	95	LEU	0	-0.045	-0.004	37.059	0.016	0.016	0.000	0.000	0.000	0.000
62	A	96	TYR	0	0.001	-0.007	32.275	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	97	LEU	0	-0.067	-0.022	31.652	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	98	ALA	0	0.028	-0.004	29.488	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	99	HIS	0	0.011	0.010	21.127	0.699	0.699	0.000	0.000	0.000	0.000
66	A	100	GLU	-1	-0.791	-0.880	23.720	-12.369	-12.369	0.000	0.000	0.000	0.000
67	A	101	VAL	0	-0.015	-0.005	17.101	-0.168	-0.168	0.000	0.000	0.000	0.000
68	A	102	GLN	0	-0.062	-0.045	20.518	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	103	LEU	0	0.012	0.008	17.160	-0.804	-0.804	0.000	0.000	0.000	0.000
70	A	104	PHE	0	-0.010	-0.004	20.207	0.780	0.780	0.000	0.000	0.000	0.000
71	A	105	SER	0	-0.004	-0.018	21.613	-0.334	-0.334	0.000	0.000	0.000	0.000
72	A	106	SER	0	0.018	-0.010	24.281	0.163	0.163	0.000	0.000	0.000	0.000
73	A	107	GLN	0	-0.036	-0.004	26.190	0.532	0.532	0.000	0.000	0.000	0.000
74	A	108	TYR	0	0.005	0.000	29.160	0.188	0.188	0.000	0.000	0.000	0.000
75	A	109	PRO	0	-0.025	-0.009	29.220	-0.052	-0.052	0.000	0.000	0.000	0.000
76	A	110	PHE	0	0.020	0.003	27.598	0.054	0.054	0.000	0.000	0.000	0.000
77	A	111	HIS	0	0.023	0.028	24.787	-0.830	-0.830	0.000	0.000	0.000	0.000
78	A	112	VAL	0	-0.022	-0.004	21.694	0.505	0.505	0.000	0.000	0.000	0.000
79	A	113	PRO	0	0.007	-0.001	22.521	-0.674	-0.674	0.000	0.000	0.000	0.000
80	A	114	LEU	0	-0.037	0.002	16.625	-0.198	-0.198	0.000	0.000	0.000	0.000
81	A	115	LEU	0	-0.061	-0.023	16.343	-0.264	-0.264	0.000	0.000	0.000	0.000
82	A	116	SER	0	0.043	0.012	20.923	0.087	0.087	0.000	0.000	0.000	0.000
83	A	117	SER	0	-0.072	-0.034	24.466	-0.114	-0.114	0.000	0.000	0.000	0.000
84	A	118	GLN	0	0.045	0.022	26.650	0.047	0.047	0.000	0.000	0.000	0.000
85	A	119	LYS	1	0.855	0.914	30.367	9.775	9.775	0.000	0.000	0.000	0.000
86	A	120	MET	0	-0.001	0.001	33.000	0.042	0.042	0.000	0.000	0.000	0.000
87	A	121	VAL	0	-0.013	0.007	36.330	0.225	0.225	0.000	0.000	0.000	0.000
88	A	122	TYR	0	0.081	0.027	38.516	0.037	0.037	0.000	0.000	0.000	0.000
89	A	123	PRO	0	0.016	-0.004	42.346	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	124	GLY	0	-0.001	0.026	45.501	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	125	LEU	0	-0.041	-0.028	41.038	0.009	0.009	0.000	0.000	0.000	0.000
92	A	126	GLN	0	-0.034	-0.026	45.292	0.003	0.003	0.000	0.000	0.000	0.000
93	A	127	GLU	-1	-0.860	-0.918	42.895	-7.162	-7.162	0.000	0.000	0.000	0.000
94	A	128	PRO	0	-0.063	-0.023	39.465	-0.102	-0.102	0.000	0.000	0.000	0.000
95	A	129	TRP	0	0.012	0.011	34.217	-0.207	-0.207	0.000	0.000	0.000	0.000
96	A	130	LEU	0	-0.005	-0.028	31.270	-0.065	-0.065	0.000	0.000	0.000	0.000
97	A	131	HIS	0	0.008	0.020	31.408	-0.243	-0.243	0.000	0.000	0.000	0.000
98	A	132	SER	0	0.008	0.007	25.917	-0.207	-0.207	0.000	0.000	0.000	0.000
99	A	133	MET	0	-0.038	-0.006	25.090	0.303	0.303	0.000	0.000	0.000	0.000
100	A	134	TYR	0	0.031	0.017	15.250	-0.432	-0.432	0.000	0.000	0.000	0.000
101	A	135	HIS	0	-0.018	-0.014	18.982	0.148	0.148	0.000	0.000	0.000	0.000
102	A	136	GLY	0	0.042	0.010	14.711	-0.413	-0.413	0.000	0.000	0.000	0.000
103	A	137	ALA	0	-0.030	0.003	13.851	0.538	0.538	0.000	0.000	0.000	0.000
104	A	138	ALA	0	-0.007	-0.002	10.437	-1.566	-1.566	0.000	0.000	0.000	0.000
105	A	139	PHE	0	0.047	0.013	11.355	2.000	2.000	0.000	0.000	0.000	0.000
106	A	140	GLN	0	-0.051	-0.029	11.144	-1.757	-1.757	0.000	0.000	0.000	0.000
107	A	141	LEU	0	0.013	0.025	11.467	1.444	1.444	0.000	0.000	0.000	0.000
108	A	142	THR	0	-0.064	-0.062	12.165	-1.167	-1.167	0.000	0.000	0.000	0.000
109	A	143	GLN	0	-0.046	-0.032	11.396	0.638	0.638	0.000	0.000	0.000	0.000
110	A	144	GLY	0	-0.003	0.002	13.269	1.170	1.170	0.000	0.000	0.000	0.000
111	A	145	ASP	-1	-0.805	-0.886	14.782	-17.907	-17.907	0.000	0.000	0.000	0.000
112	A	146	GLN	0	-0.034	-0.032	15.674	-0.276	-0.276	0.000	0.000	0.000	0.000
113	A	147	LEU	0	0.019	0.012	13.187	0.355	0.355	0.000	0.000	0.000	0.000
114	A	148	SER	0	0.035	0.020	17.252	0.108	0.108	0.000	0.000	0.000	0.000
115	A	149	THR	0	0.027	0.002	19.587	-0.481	-0.481	0.000	0.000	0.000	0.000
116	A	150	HIS	0	-0.017	0.016	22.152	0.163	0.163	0.000	0.000	0.000	0.000
117	A	151	THR	0	-0.038	-0.051	25.384	-0.255	-0.255	0.000	0.000	0.000	0.000
118	A	152	ASP	-1	-0.850	-0.912	27.687	-9.790	-9.790	0.000	0.000	0.000	0.000
119	A	153	GLY	0	0.038	-0.006	31.337	-0.024	-0.024	0.000	0.000	0.000	0.000
120	A	154	ILE	0	-0.007	-0.016	29.039	0.009	0.009	0.000	0.000	0.000	0.000
121	A	155	PRO	0	0.040	0.014	31.290	-0.111	-0.111	0.000	0.000	0.000	0.000
122	A	156	HIS	1	0.774	0.890	33.424	8.813	8.813	0.000	0.000	0.000	0.000
123	A	157	LEU	0	0.048	0.042	26.788	-0.101	-0.101	0.000	0.000	0.000	0.000
124	A	158	VAL	0	-0.018	-0.012	28.351	0.254	0.254	0.000	0.000	0.000	0.000
125	A	159	LEU	0	-0.022	-0.008	25.932	-0.438	-0.438	0.000	0.000	0.000	0.000
126	A	160	SER	0	0.016	0.006	25.469	0.189	0.189	0.000	0.000	0.000	0.000
127	A	161	PRO	0	0.058	0.015	20.659	-0.263	-0.263	0.000	0.000	0.000	0.000
128	A	162	SER	0	-0.017	0.000	20.266	-0.607	-0.607	0.000	0.000	0.000	0.000
129	A	163	THR	0	-0.030	-0.032	22.013	-0.067	-0.067	0.000	0.000	0.000	0.000
130	A	164	VAL	0	0.009	0.020	22.434	-0.018	-0.018	0.000	0.000	0.000	0.000
131	A	165	PHE	0	-0.024	-0.013	16.668	-0.154	-0.154	0.000	0.000	0.000	0.000
132	A	166	PHE	0	0.013	0.024	16.258	0.059	0.059	0.000	0.000	0.000	0.000
133	A	167	GLY	0	0.036	0.025	12.574	0.113	0.113	0.000	0.000	0.000	0.000
134	A	168	ALA	0	0.005	0.013	10.017	0.518	0.518	0.000	0.000	0.000	0.000
135	A	169	PHE	0	-0.019	-0.008	4.920	0.111	0.111	0.000	0.000	0.000	0.000
136	A	170	ALA	0	0.047	0.039	2.853	1.157	1.912	0.140	-0.183	-0.713	-0.001
137	A	171	LEU	0	-0.043	-0.024	2.057	-27.745	-24.489	6.656	-4.097	-5.816	-0.053

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:LYS)