FMO DATABASE

FMODB ID: NNZKQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1172715.250868
FMO2-HF: Nuclear repulsion	1120415.956352
FMO2-HF: Total energy	-52299.294516
FMO2-MP2: Total energy	-52454.936329

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.
-72.152	-62.716	4.674	-6.246	-7.865	-0.066

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 : 0.949 / q_NPA : 0.973

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	-0.030	-0.030	3.703	-4.249	-2.346	-0.004	-0.925	-0.974	0.004
4	A	31	ALA	0	0.007	0.003	5.864	2.027	2.027	0.000	0.000	0.000	0.000
5	A	32	HIS	0	-0.015	0.033	9.625	-0.941	-0.941	0.000	0.000	0.000	0.000
6	A	33	LEU	0	-0.009	-0.011	12.491	0.884	0.884	0.000	0.000	0.000	0.000
7	A	34	ILE	0	0.041	0.015	15.962	0.242	0.242	0.000	0.000	0.000	0.000
8	A	35	GLY	0	0.030	0.016	19.440	0.124	0.124	0.000	0.000	0.000	0.000
9	A	36	ASP	-1	-0.890	-0.953	22.961	-10.757	-10.757	0.000	0.000	0.000	0.000
10	A	37	PRO	0	0.039	0.005	25.412	0.309	0.309	0.000	0.000	0.000	0.000
11	A	38	SER	0	-0.077	-0.032	28.452	0.455	0.455	0.000	0.000	0.000	0.000
12	A	39	LYS	1	0.940	0.963	28.571	9.825	9.825	0.000	0.000	0.000	0.000
13	A	40	GLN	0	-0.009	0.009	30.538	0.424	0.424	0.000	0.000	0.000	0.000
14	A	41	ASN	0	0.019	0.006	32.209	0.168	0.168	0.000	0.000	0.000	0.000
15	A	42	SER	0	-0.067	-0.045	29.032	0.065	0.065	0.000	0.000	0.000	0.000
16	A	43	LEU	0	0.005	0.027	23.340	0.072	0.072	0.000	0.000	0.000	0.000
17	A	44	LEU	0	-0.032	-0.017	24.202	-0.164	-0.164	0.000	0.000	0.000	0.000
18	A	45	TRP	0	0.027	0.016	18.701	-0.201	-0.201	0.000	0.000	0.000	0.000
19	A	46	ARG	1	0.864	0.931	19.517	12.306	12.306	0.000	0.000	0.000	0.000
20	A	47	ALA	0	0.055	0.003	14.689	-0.268	-0.268	0.000	0.000	0.000	0.000
21	A	48	ASN	0	-0.009	0.004	16.033	-0.383	-0.383	0.000	0.000	0.000	0.000
22	A	49	THR	0	0.008	-0.004	18.428	0.496	0.496	0.000	0.000	0.000	0.000
23	A	50	ASP	-1	-0.847	-0.915	17.670	-13.899	-13.899	0.000	0.000	0.000	0.000
24	A	51	ARG	1	0.864	0.922	16.224	16.014	16.014	0.000	0.000	0.000	0.000
25	A	52	ALA	0	0.018	0.029	15.212	-0.274	-0.274	0.000	0.000	0.000	0.000
26	A	53	PHE	0	-0.001	-0.006	7.817	0.162	0.162	0.000	0.000	0.000	0.000
27	A	54	LEU	0	-0.002	-0.003	10.604	-0.377	-0.377	0.000	0.000	0.000	0.000
28	A	55	GLN	0	-0.033	-0.019	4.006	4.861	5.145	-0.001	-0.040	-0.243	0.000
29	A	56	ASP	-1	-0.854	-0.937	2.163	-54.507	-51.570	3.098	-3.041	-2.994	-0.043
30	A	57	GLY	0	0.073	0.031	5.342	-1.297	-1.257	-0.001	-0.001	-0.038	0.000
31	A	58	PHE	0	-0.045	-0.004	6.865	1.621	1.621	0.000	0.000	0.000	0.000
32	A	59	SER	0	0.019	0.003	10.204	1.303	1.303	0.000	0.000	0.000	0.000
33	A	60	LEU	0	0.013	0.017	13.965	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	61	SER	0	-0.010	-0.002	17.181	0.620	0.620	0.000	0.000	0.000	0.000
35	A	62	ASN	0	0.004	-0.009	19.981	0.230	0.230	0.000	0.000	0.000	0.000
36	A	63	ASN	0	0.016	0.000	21.489	-0.105	-0.105	0.000	0.000	0.000	0.000
37	A	64	SER	0	-0.008	0.013	19.155	0.054	0.054	0.000	0.000	0.000	0.000
38	A	65	LEU	0	-0.041	-0.030	11.766	-0.066	-0.066	0.000	0.000	0.000	0.000
39	A	66	LEU	0	0.008	-0.006	14.182	0.290	0.290	0.000	0.000	0.000	0.000
40	A	67	VAL	0	-0.037	-0.005	9.911	-1.553	-1.553	0.000	0.000	0.000	0.000
41	A	68	PRO	0	0.008	0.031	7.051	1.172	1.172	0.000	0.000	0.000	0.000
42	A	69	THR	0	0.029	-0.008	6.788	0.243	0.243	0.000	0.000	0.000	0.000
43	A	70	SER	0	0.037	0.030	9.347	-0.499	-0.499	0.000	0.000	0.000	0.000
44	A	71	GLY	0	-0.001	0.011	7.908	-1.911	-1.911	0.000	0.000	0.000	0.000
45	A	72	ILE	0	-0.036	-0.008	7.322	2.381	2.381	0.000	0.000	0.000	0.000
46	A	73	TYR	0	0.003	-0.034	6.475	-6.019	-6.019	0.000	0.000	0.000	0.000
47	A	74	PHE	0	-0.022	0.008	8.186	2.993	2.993	0.000	0.000	0.000	0.000
48	A	75	VAL	0	0.020	0.004	10.028	-0.730	-0.730	0.000	0.000	0.000	0.000
49	A	76	TYR	0	-0.039	-0.053	10.791	0.683	0.683	0.000	0.000	0.000	0.000
50	A	77	SER	0	-0.035	-0.037	15.206	0.267	0.267	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.044	-0.011	18.099	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	79	VAL	0	0.028	0.021	21.020	0.139	0.139	0.000	0.000	0.000	0.000
53	A	80	VAL	0	0.007	-0.002	24.440	0.087	0.087	0.000	0.000	0.000	0.000
54	A	81	PHE	0	0.025	0.004	27.593	0.190	0.190	0.000	0.000	0.000	0.000
55	A	82	SER	0	0.018	-0.003	31.089	0.120	0.120	0.000	0.000	0.000	0.000
56	A	83	GLY	0	0.025	0.009	34.330	0.051	0.051	0.000	0.000	0.000	0.000
57	A	84	LYS	1	1.007	1.025	38.049	7.444	7.444	0.000	0.000	0.000	0.000
58	A	92	SER	0	-0.006	-0.014	47.969	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	93	SER	0	0.015	0.010	44.344	0.094	0.094	0.000	0.000	0.000	0.000
60	A	94	PRO	0	-0.029	-0.025	41.810	-0.051	-0.051	0.000	0.000	0.000	0.000
61	A	95	LEU	0	-0.030	0.004	37.104	0.016	0.016	0.000	0.000	0.000	0.000
62	A	96	TYR	0	-0.019	-0.023	32.753	-0.071	-0.071	0.000	0.000	0.000	0.000
63	A	97	LEU	0	-0.064	-0.023	31.640	-0.047	-0.047	0.000	0.000	0.000	0.000
64	A	98	ALA	0	0.043	0.003	29.675	0.000	0.000	0.000	0.000	0.000	0.000
65	A	99	HIS	0	0.000	-0.001	21.275	0.569	0.569	0.000	0.000	0.000	0.000
66	A	100	GLU	-1	-0.859	-0.932	23.774	-11.753	-11.753	0.000	0.000	0.000	0.000
67	A	101	VAL	0	-0.022	-0.013	16.989	-0.189	-0.189	0.000	0.000	0.000	0.000
68	A	102	GLN	0	-0.036	-0.020	20.384	-0.111	-0.111	0.000	0.000	0.000	0.000
69	A	103	LEU	0	0.014	0.008	16.558	-0.745	-0.745	0.000	0.000	0.000	0.000
70	A	104	PHE	0	-0.016	-0.009	19.708	0.705	0.705	0.000	0.000	0.000	0.000
71	A	105	SER	0	-0.007	-0.008	21.211	-0.324	-0.324	0.000	0.000	0.000	0.000
72	A	106	SER	0	0.034	0.005	23.894	0.175	0.175	0.000	0.000	0.000	0.000
73	A	107	GLN	0	-0.055	-0.022	26.424	0.612	0.612	0.000	0.000	0.000	0.000
74	A	108	TYR	0	0.001	-0.003	28.807	0.177	0.177	0.000	0.000	0.000	0.000
75	A	109	PRO	0	-0.002	-0.009	28.615	-0.033	-0.033	0.000	0.000	0.000	0.000
76	A	110	PHE	0	0.001	0.001	27.184	0.042	0.042	0.000	0.000	0.000	0.000
77	A	111	HIS	0	0.031	0.029	24.306	-0.798	-0.798	0.000	0.000	0.000	0.000
78	A	112	VAL	0	-0.027	-0.007	21.547	0.477	0.477	0.000	0.000	0.000	0.000
79	A	113	PRO	0	0.003	-0.005	22.190	-0.619	-0.619	0.000	0.000	0.000	0.000
80	A	114	LEU	0	-0.040	0.003	16.519	-0.175	-0.175	0.000	0.000	0.000	0.000
81	A	115	LEU	0	-0.062	-0.024	16.836	-0.196	-0.196	0.000	0.000	0.000	0.000
82	A	116	SER	0	0.085	0.050	21.419	0.176	0.176	0.000	0.000	0.000	0.000
83	A	117	SER	0	-0.063	-0.033	24.967	-0.073	-0.073	0.000	0.000	0.000	0.000
84	A	118	GLN	0	0.062	0.033	27.177	0.099	0.099	0.000	0.000	0.000	0.000
85	A	119	LYS	1	0.910	0.946	30.843	9.181	9.181	0.000	0.000	0.000	0.000
86	A	120	MET	0	-0.011	0.000	33.475	0.033	0.033	0.000	0.000	0.000	0.000
87	A	121	VAL	0	-0.001	0.019	36.415	0.202	0.202	0.000	0.000	0.000	0.000
88	A	122	TYR	0	0.071	0.017	38.811	0.033	0.033	0.000	0.000	0.000	0.000
89	A	123	PRO	0	0.012	-0.008	42.664	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	124	GLY	0	0.005	0.028	45.575	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	125	LEU	0	-0.050	-0.032	41.042	0.011	0.011	0.000	0.000	0.000	0.000
92	A	126	GLN	0	-0.035	-0.027	45.474	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	127	GLU	-1	-0.868	-0.916	43.028	-6.922	-6.922	0.000	0.000	0.000	0.000
94	A	128	PRO	0	-0.050	-0.018	39.432	-0.089	-0.089	0.000	0.000	0.000	0.000
95	A	129	TRP	0	0.016	0.022	34.034	-0.172	-0.172	0.000	0.000	0.000	0.000
96	A	130	LEU	0	-0.012	-0.038	31.374	-0.061	-0.061	0.000	0.000	0.000	0.000
97	A	131	HIS	0	-0.032	-0.004	31.712	-0.169	-0.169	0.000	0.000	0.000	0.000
98	A	132	SER	0	0.007	0.004	26.226	-0.189	-0.189	0.000	0.000	0.000	0.000
99	A	133	MET	0	-0.044	-0.010	25.487	0.267	0.267	0.000	0.000	0.000	0.000
100	A	134	TYR	0	0.040	0.022	15.770	-0.473	-0.473	0.000	0.000	0.000	0.000
101	A	135	HIS	0	-0.009	-0.017	19.616	0.202	0.202	0.000	0.000	0.000	0.000
102	A	136	GLY	0	0.034	0.007	15.377	-0.392	-0.392	0.000	0.000	0.000	0.000
103	A	137	ALA	0	-0.032	0.006	14.746	0.482	0.482	0.000	0.000	0.000	0.000
104	A	138	ALA	0	0.001	0.000	11.195	-1.304	-1.304	0.000	0.000	0.000	0.000
105	A	139	PHE	0	0.041	0.011	11.848	1.664	1.664	0.000	0.000	0.000	0.000
106	A	140	GLN	0	-0.023	-0.023	11.563	-1.472	-1.472	0.000	0.000	0.000	0.000
107	A	141	LEU	0	-0.010	0.018	11.087	1.328	1.328	0.000	0.000	0.000	0.000
108	A	142	THR	0	-0.050	-0.052	12.101	-1.213	-1.213	0.000	0.000	0.000	0.000
109	A	143	GLN	0	-0.037	-0.030	11.391	0.766	0.766	0.000	0.000	0.000	0.000
110	A	144	GLY	0	-0.010	0.002	13.267	1.078	1.078	0.000	0.000	0.000	0.000
111	A	145	ASP	-1	-0.805	-0.883	14.451	-16.977	-16.977	0.000	0.000	0.000	0.000
112	A	146	GLN	0	-0.045	-0.039	15.603	-0.363	-0.363	0.000	0.000	0.000	0.000
113	A	147	LEU	0	0.013	0.013	12.733	0.379	0.379	0.000	0.000	0.000	0.000
114	A	148	SER	0	0.038	0.021	16.998	0.073	0.073	0.000	0.000	0.000	0.000
115	A	149	THR	0	0.036	-0.006	19.752	-0.398	-0.398	0.000	0.000	0.000	0.000
116	A	150	HIS	0	0.009	0.045	22.240	0.119	0.119	0.000	0.000	0.000	0.000
117	A	151	THR	0	-0.025	-0.038	25.394	-0.235	-0.235	0.000	0.000	0.000	0.000
118	A	152	ASP	-1	-0.882	-0.934	27.756	-9.347	-9.347	0.000	0.000	0.000	0.000
119	A	153	GLY	0	0.029	-0.010	31.405	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	154	ILE	0	-0.009	-0.014	29.144	0.010	0.010	0.000	0.000	0.000	0.000
121	A	155	PRO	0	0.035	0.013	31.310	-0.110	-0.110	0.000	0.000	0.000	0.000
122	A	156	HIS	1	0.761	0.878	33.431	8.538	8.538	0.000	0.000	0.000	0.000
123	A	157	LEU	0	0.054	0.038	26.859	-0.088	-0.088	0.000	0.000	0.000	0.000
124	A	158	VAL	0	-0.025	-0.013	28.163	0.237	0.237	0.000	0.000	0.000	0.000
125	A	159	LEU	0	-0.011	-0.002	25.559	-0.408	-0.408	0.000	0.000	0.000	0.000
126	A	160	SER	0	0.001	0.007	25.417	0.139	0.139	0.000	0.000	0.000	0.000
127	A	161	PRO	0	0.066	0.013	20.585	-0.231	-0.231	0.000	0.000	0.000	0.000
128	A	162	SER	0	-0.023	0.000	20.208	-0.546	-0.546	0.000	0.000	0.000	0.000
129	A	163	THR	0	-0.046	-0.041	21.951	-0.034	-0.034	0.000	0.000	0.000	0.000
130	A	164	VAL	0	0.033	0.027	22.379	0.004	0.004	0.000	0.000	0.000	0.000
131	A	165	PHE	0	-0.029	-0.011	16.589	-0.202	-0.202	0.000	0.000	0.000	0.000
132	A	166	PHE	0	0.018	0.028	16.112	0.088	0.088	0.000	0.000	0.000	0.000
133	A	167	GLY	0	0.040	0.024	12.605	0.016	0.016	0.000	0.000	0.000	0.000
134	A	168	ALA	0	0.000	0.009	10.096	0.547	0.547	0.000	0.000	0.000	0.000
135	A	169	PHE	0	-0.032	-0.012	4.953	-0.126	-0.126	0.000	0.000	0.000	0.000
136	A	170	ALA	0	0.046	0.034	2.338	1.344	1.928	0.717	-0.337	-0.965	-0.003
137	A	171	LEU	0	-0.052	-0.025	2.707	-15.348	-11.660	0.865	-1.902	-2.651	-0.024

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