FMO DATABASE

FMODB ID: 3JKLL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1174036.212661
FMO2-HF: Nuclear repulsion	1121735.863984
FMO2-HF: Total energy	-52300.348677
FMO2-MP2: Total energy	-52456.015505

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.
-115.371	-113.409	27.391	-14.407	-14.947	-0.165

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 : 0.886 / q_NPA : 0.925

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	-0.017	-0.021	3.917	-6.017	-4.511	-0.008	-0.698	-0.801	0.003
4	A	31	ALA	0	0.007	0.002	6.183	3.206	3.206	0.000	0.000	0.000	0.000
5	A	32	HIS	0	0.010	0.036	9.918	-1.699	-1.699	0.000	0.000	0.000	0.000
6	A	33	LEU	0	0.006	0.014	12.867	0.974	0.974	0.000	0.000	0.000	0.000
7	A	34	ILE	0	0.007	0.000	16.433	0.183	0.183	0.000	0.000	0.000	0.000
8	A	35	GLY	0	0.042	0.020	19.892	0.137	0.137	0.000	0.000	0.000	0.000
9	A	36	ASP	-1	-0.789	-0.867	23.270	-11.027	-11.027	0.000	0.000	0.000	0.000
10	A	37	PRO	0	0.042	0.013	25.252	0.386	0.386	0.000	0.000	0.000	0.000
11	A	38	SER	0	-0.091	-0.047	28.387	0.482	0.482	0.000	0.000	0.000	0.000
12	A	39	LYS	1	0.860	0.912	28.266	10.646	10.646	0.000	0.000	0.000	0.000
13	A	40	GLN	0	-0.016	-0.012	30.611	0.498	0.498	0.000	0.000	0.000	0.000
14	A	41	ASN	0	0.005	-0.001	32.354	0.104	0.104	0.000	0.000	0.000	0.000
15	A	42	SER	0	-0.021	-0.030	29.610	0.090	0.090	0.000	0.000	0.000	0.000
16	A	43	LEU	0	-0.012	0.019	23.766	0.100	0.100	0.000	0.000	0.000	0.000
17	A	44	LEU	0	-0.011	0.000	24.756	-0.303	-0.303	0.000	0.000	0.000	0.000
18	A	45	TRP	0	0.019	0.006	19.219	-0.115	-0.115	0.000	0.000	0.000	0.000
19	A	46	ARG	1	0.827	0.898	19.395	12.940	12.940	0.000	0.000	0.000	0.000
20	A	47	ALA	0	0.055	0.012	14.322	-0.375	-0.375	0.000	0.000	0.000	0.000
21	A	48	ASN	0	-0.001	0.011	15.305	-0.528	-0.528	0.000	0.000	0.000	0.000
22	A	49	THR	0	0.021	0.008	17.714	0.882	0.882	0.000	0.000	0.000	0.000
23	A	50	ASP	-1	-0.869	-0.933	17.498	-14.505	-14.505	0.000	0.000	0.000	0.000
24	A	51	ARG	1	0.876	0.920	16.084	16.155	16.155	0.000	0.000	0.000	0.000
25	A	52	ALA	0	-0.006	0.017	15.070	-0.534	-0.534	0.000	0.000	0.000	0.000
26	A	53	PHE	0	-0.010	-0.006	7.914	0.516	0.516	0.000	0.000	0.000	0.000
27	A	54	LEU	0	0.000	-0.003	10.127	-0.387	-0.387	0.000	0.000	0.000	0.000
28	A	55	GLN	0	-0.047	-0.033	3.167	5.169	5.993	0.012	-0.276	-0.560	-0.001
29	A	56	ASP	-1	-0.847	-0.933	1.894	-53.906	-54.216	9.631	-5.045	-4.277	-0.062
30	A	57	GLY	0	0.070	0.031	4.777	-1.643	-1.610	-0.001	-0.008	-0.024	0.000
31	A	58	PHE	0	-0.033	-0.007	6.496	1.967	1.967	0.000	0.000	0.000	0.000
32	A	59	SER	0	0.007	0.008	9.876	1.597	1.597	0.000	0.000	0.000	0.000
33	A	60	LEU	0	0.017	0.005	13.511	-0.274	-0.274	0.000	0.000	0.000	0.000
34	A	61	SER	0	0.005	0.000	17.054	0.786	0.786	0.000	0.000	0.000	0.000
35	A	62	ASN	0	0.013	0.001	20.350	-0.098	-0.098	0.000	0.000	0.000	0.000
36	A	63	ASN	0	-0.002	-0.008	21.860	-0.177	-0.177	0.000	0.000	0.000	0.000
37	A	64	SER	0	0.000	0.025	18.862	-0.113	-0.113	0.000	0.000	0.000	0.000
38	A	65	LEU	0	-0.034	-0.022	11.911	0.124	0.124	0.000	0.000	0.000	0.000
39	A	66	LEU	0	-0.018	-0.012	14.428	0.048	0.048	0.000	0.000	0.000	0.000
40	A	67	VAL	0	0.004	0.003	9.727	-1.587	-1.587	0.000	0.000	0.000	0.000
41	A	68	PRO	0	-0.006	0.017	7.208	1.511	1.511	0.000	0.000	0.000	0.000
42	A	69	THR	0	0.029	0.005	7.461	0.689	0.689	0.000	0.000	0.000	0.000
43	A	70	SER	0	0.038	0.027	9.457	-1.028	-1.028	0.000	0.000	0.000	0.000
44	A	71	GLY	0	-0.019	-0.003	7.524	-1.963	-1.963	0.000	0.000	0.000	0.000
45	A	72	ILE	0	-0.013	0.002	6.753	2.883	2.883	0.000	0.000	0.000	0.000
46	A	73	TYR	0	-0.007	-0.022	5.930	-10.289	-10.289	0.000	0.000	0.000	0.000
47	A	74	PHE	0	-0.010	0.011	6.544	4.598	4.598	0.000	0.000	0.000	0.000
48	A	75	VAL	0	0.020	0.002	8.363	-1.112	-1.112	0.000	0.000	0.000	0.000
49	A	76	TYR	0	-0.026	-0.037	10.352	0.693	0.693	0.000	0.000	0.000	0.000
50	A	77	SER	0	-0.027	-0.026	14.214	0.374	0.374	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.057	-0.018	17.616	-0.169	-0.169	0.000	0.000	0.000	0.000
52	A	79	VAL	0	0.034	0.026	20.656	0.165	0.165	0.000	0.000	0.000	0.000
53	A	80	VAL	0	0.006	-0.005	24.326	0.085	0.085	0.000	0.000	0.000	0.000
54	A	81	PHE	0	0.025	0.017	27.443	0.214	0.214	0.000	0.000	0.000	0.000
55	A	82	SER	0	-0.004	-0.006	30.902	0.139	0.139	0.000	0.000	0.000	0.000
56	A	83	GLY	0	0.032	0.005	34.214	0.059	0.059	0.000	0.000	0.000	0.000
57	A	84	LYS	1	1.020	1.033	37.995	7.654	7.654	0.000	0.000	0.000	0.000
58	A	92	SER	0	0.004	-0.011	46.669	0.019	0.019	0.000	0.000	0.000	0.000
59	A	93	SER	0	0.009	0.004	43.354	0.128	0.128	0.000	0.000	0.000	0.000
60	A	94	PRO	0	-0.023	-0.021	40.617	-0.059	-0.059	0.000	0.000	0.000	0.000
61	A	95	LEU	0	-0.045	-0.006	36.670	0.043	0.043	0.000	0.000	0.000	0.000
62	A	96	TYR	0	0.001	-0.022	31.256	-0.102	-0.102	0.000	0.000	0.000	0.000
63	A	97	LEU	0	-0.081	-0.026	31.399	0.011	0.011	0.000	0.000	0.000	0.000
64	A	98	ALA	0	0.010	-0.008	28.650	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	99	HIS	0	0.004	0.002	20.962	0.739	0.739	0.000	0.000	0.000	0.000
66	A	100	GLU	-1	-0.784	-0.862	22.799	-12.711	-12.711	0.000	0.000	0.000	0.000
67	A	101	VAL	0	0.010	0.018	16.326	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	102	GLN	0	-0.060	-0.048	19.810	0.205	0.205	0.000	0.000	0.000	0.000
69	A	103	LEU	0	0.018	0.012	16.883	-1.030	-1.030	0.000	0.000	0.000	0.000
70	A	104	PHE	0	0.028	0.013	19.756	0.827	0.827	0.000	0.000	0.000	0.000
71	A	105	SER	0	-0.017	-0.017	21.454	-0.264	-0.264	0.000	0.000	0.000	0.000
72	A	106	SER	0	0.016	-0.012	24.103	0.196	0.196	0.000	0.000	0.000	0.000
73	A	107	GLN	0	-0.009	0.023	25.782	0.664	0.664	0.000	0.000	0.000	0.000
74	A	108	TYR	0	0.036	0.029	28.498	-0.202	-0.202	0.000	0.000	0.000	0.000
75	A	109	PRO	0	-0.042	-0.020	28.705	-0.039	-0.039	0.000	0.000	0.000	0.000
76	A	110	PHE	0	-0.016	-0.037	27.354	0.136	0.136	0.000	0.000	0.000	0.000
77	A	111	HIS	0	0.019	0.015	24.108	-0.854	-0.854	0.000	0.000	0.000	0.000
78	A	112	VAL	0	-0.024	-0.005	21.307	0.581	0.581	0.000	0.000	0.000	0.000
79	A	113	PRO	0	-0.005	-0.002	21.926	-0.688	-0.688	0.000	0.000	0.000	0.000
80	A	114	LEU	0	-0.043	-0.004	15.765	-0.302	-0.302	0.000	0.000	0.000	0.000
81	A	115	LEU	0	-0.053	-0.020	15.387	-0.342	-0.342	0.000	0.000	0.000	0.000
82	A	116	SER	0	0.046	0.001	19.910	0.050	0.050	0.000	0.000	0.000	0.000
83	A	117	SER	0	-0.074	-0.037	23.581	-0.153	-0.153	0.000	0.000	0.000	0.000
84	A	118	GLN	0	0.022	0.004	25.748	0.126	0.126	0.000	0.000	0.000	0.000
85	A	119	LYS	1	0.867	0.918	29.471	10.118	10.118	0.000	0.000	0.000	0.000
86	A	120	MET	0	0.013	0.013	32.396	0.088	0.088	0.000	0.000	0.000	0.000
87	A	121	VAL	0	0.003	0.026	36.173	0.199	0.199	0.000	0.000	0.000	0.000
88	A	122	TYR	0	0.047	0.005	37.944	0.081	0.081	0.000	0.000	0.000	0.000
89	A	123	PRO	0	0.006	-0.011	41.786	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	124	GLY	0	-0.015	0.007	44.806	0.057	0.057	0.000	0.000	0.000	0.000
91	A	125	LEU	0	-0.042	-0.014	40.009	0.029	0.029	0.000	0.000	0.000	0.000
92	A	126	GLN	0	-0.024	-0.019	44.395	0.040	0.040	0.000	0.000	0.000	0.000
93	A	127	GLU	-1	-0.857	-0.918	42.524	-7.240	-7.240	0.000	0.000	0.000	0.000
94	A	128	PRO	0	-0.074	-0.033	39.242	-0.107	-0.107	0.000	0.000	0.000	0.000
95	A	129	TRP	0	0.012	0.006	34.190	-0.200	-0.200	0.000	0.000	0.000	0.000
96	A	130	LEU	0	-0.003	-0.020	30.898	-0.090	-0.090	0.000	0.000	0.000	0.000
97	A	131	HIS	0	0.022	0.018	30.764	-0.183	-0.183	0.000	0.000	0.000	0.000
98	A	132	SER	0	0.004	0.010	25.118	-0.252	-0.252	0.000	0.000	0.000	0.000
99	A	133	MET	0	-0.032	-0.011	24.533	0.425	0.425	0.000	0.000	0.000	0.000
100	A	134	TYR	0	0.033	0.025	14.398	-0.313	-0.313	0.000	0.000	0.000	0.000
101	A	135	HIS	0	-0.034	-0.028	18.351	0.152	0.152	0.000	0.000	0.000	0.000
102	A	136	GLY	0	0.042	0.003	14.221	-0.519	-0.519	0.000	0.000	0.000	0.000
103	A	137	ALA	0	-0.034	0.003	13.191	0.810	0.810	0.000	0.000	0.000	0.000
104	A	138	ALA	0	-0.003	-0.004	9.645	-1.963	-1.963	0.000	0.000	0.000	0.000
105	A	139	PHE	0	0.036	0.013	10.467	2.287	2.287	0.000	0.000	0.000	0.000
106	A	140	GLN	0	-0.039	-0.019	10.639	-2.189	-2.189	0.000	0.000	0.000	0.000
107	A	141	LEU	0	0.003	0.010	11.064	1.328	1.328	0.000	0.000	0.000	0.000
108	A	142	THR	0	-0.064	-0.074	11.951	-1.114	-1.114	0.000	0.000	0.000	0.000
109	A	143	GLN	0	-0.051	-0.039	11.469	0.310	0.310	0.000	0.000	0.000	0.000
110	A	144	GLY	0	0.020	0.017	13.566	1.331	1.331	0.000	0.000	0.000	0.000
111	A	145	ASP	-1	-0.816	-0.876	14.179	-18.716	-18.716	0.000	0.000	0.000	0.000
112	A	146	GLN	0	-0.036	-0.030	15.105	-0.631	-0.631	0.000	0.000	0.000	0.000
113	A	147	LEU	0	0.036	0.026	12.515	0.582	0.582	0.000	0.000	0.000	0.000
114	A	148	SER	0	-0.004	-0.009	16.814	0.155	0.155	0.000	0.000	0.000	0.000
115	A	149	THR	0	0.019	0.006	19.803	-0.572	-0.572	0.000	0.000	0.000	0.000
116	A	150	HIS	0	-0.007	0.010	22.190	0.239	0.239	0.000	0.000	0.000	0.000
117	A	151	THR	0	-0.023	-0.047	25.360	-0.328	-0.328	0.000	0.000	0.000	0.000
118	A	152	ASP	-1	-0.830	-0.874	27.760	-10.008	-10.008	0.000	0.000	0.000	0.000
119	A	153	GLY	0	0.054	0.003	31.146	-0.062	-0.062	0.000	0.000	0.000	0.000
120	A	154	ILE	0	-0.011	-0.009	29.232	0.104	0.104	0.000	0.000	0.000	0.000
121	A	155	PRO	0	0.021	0.004	31.640	-0.131	-0.131	0.000	0.000	0.000	0.000
122	A	156	HIS	1	0.792	0.902	33.432	9.122	9.122	0.000	0.000	0.000	0.000
123	A	157	LEU	0	0.012	0.021	26.906	-0.065	-0.065	0.000	0.000	0.000	0.000
124	A	158	VAL	0	0.004	-0.001	28.310	0.237	0.237	0.000	0.000	0.000	0.000
125	A	159	LEU	0	-0.022	-0.007	26.380	-0.467	-0.467	0.000	0.000	0.000	0.000
126	A	160	SER	0	-0.011	-0.006	25.426	0.238	0.238	0.000	0.000	0.000	0.000
127	A	161	PRO	0	0.063	0.007	20.643	-0.315	-0.315	0.000	0.000	0.000	0.000
128	A	162	SER	0	-0.011	0.007	20.335	-0.659	-0.659	0.000	0.000	0.000	0.000
129	A	163	THR	0	-0.018	-0.021	22.192	0.019	0.019	0.000	0.000	0.000	0.000
130	A	164	VAL	0	0.015	0.012	22.917	0.027	0.027	0.000	0.000	0.000	0.000
131	A	165	PHE	0	-0.020	-0.008	16.802	-0.148	-0.148	0.000	0.000	0.000	0.000
132	A	166	PHE	0	0.019	0.018	16.013	0.092	0.092	0.000	0.000	0.000	0.000
133	A	167	GLY	0	0.035	0.016	12.760	0.177	0.177	0.000	0.000	0.000	0.000
134	A	168	ALA	0	0.007	0.010	9.649	0.664	0.664	0.000	0.000	0.000	0.000
135	A	169	PHE	0	-0.014	-0.010	4.132	0.144	0.340	-0.001	-0.013	-0.182	0.000
136	A	170	ALA	0	0.068	0.052	2.296	-0.041	1.145	0.840	-0.685	-1.340	-0.003
137	A	171	LEU	0	-0.060	-0.024	1.843	-53.223	-54.696	16.918	-7.682	-7.763	-0.102

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