FMO DATABASE

FMODB ID: N183Q

Calculation Name: 1V7M-V-Xray372

Preferred Name: Thrombopoietin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1V7M

Chain ID: V

ChEMBL ID: CHEMBL1293256

UniProt ID: P40225

Base Structure: X-ray

Registration Date: 2023-03-13

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1268593.617418
FMO2-HF: Nuclear repulsion	1213247.502158
FMO2-HF: Total energy	-55346.11526
FMO2-MP2: Total energy	-55505.774585

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(V:151:CYS)

Summations of interaction energy for fragment #1(V:151:CYS)

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.
-17.158	-7.882	11.738	-7.907	-13.108	0.012

Interaction energy analysis for fragmet #1(V:151:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.031

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	V	9	LEU	0	0.022	0.016	2.602	-10.190	-4.966	0.370	-2.650	-2.944	-0.001
4	V	10	ARG	1	0.890	0.926	4.906	2.735	2.904	-0.002	-0.006	-0.162	0.000
5	V	11	VAL	0	0.023	0.011	2.421	-3.365	-0.473	2.095	-1.335	-3.652	0.013
6	V	12	LEU	0	0.060	0.031	5.585	0.506	0.506	0.000	0.000	0.000	0.000
7	V	13	SER	0	-0.006	-0.006	7.736	0.251	0.251	0.000	0.000	0.000	0.000
8	V	14	LYS	1	0.774	0.865	8.479	-0.398	-0.398	0.000	0.000	0.000	0.000
9	V	15	LEU	0	0.057	0.041	6.530	0.136	0.136	0.000	0.000	0.000	0.000
10	V	16	LEU	0	0.022	0.005	9.651	0.005	0.005	0.000	0.000	0.000	0.000
11	V	17	ARG	1	0.888	0.969	12.710	-0.002	-0.002	0.000	0.000	0.000	0.000
12	V	18	ASP	-1	-0.801	-0.896	12.413	0.631	0.631	0.000	0.000	0.000	0.000
13	V	19	SER	0	-0.033	-0.026	13.472	0.032	0.032	0.000	0.000	0.000	0.000
14	V	20	HIS	0	0.063	0.025	15.387	-0.049	-0.049	0.000	0.000	0.000	0.000
15	V	21	VAL	0	-0.022	-0.006	18.124	0.010	0.010	0.000	0.000	0.000	0.000
16	V	22	LEU	0	-0.008	0.011	16.054	0.001	0.001	0.000	0.000	0.000	0.000
17	V	23	HIS	0	0.012	0.006	19.565	-0.019	-0.019	0.000	0.000	0.000	0.000
18	V	24	SER	0	-0.048	-0.037	21.432	-0.014	-0.014	0.000	0.000	0.000	0.000
19	V	25	ARG	1	0.913	0.953	20.318	-0.369	-0.369	0.000	0.000	0.000	0.000
20	V	26	LEU	0	-0.027	-0.003	24.264	0.017	0.017	0.000	0.000	0.000	0.000
21	V	27	SER	0	0.012	0.005	26.253	-0.014	-0.014	0.000	0.000	0.000	0.000
22	V	28	GLN	0	-0.020	-0.014	27.550	-0.015	-0.015	0.000	0.000	0.000	0.000
23	V	29	CYS	0	-0.017	0.012	27.786	0.034	0.034	0.000	0.000	0.000	0.000
24	V	30	PRO	0	0.033	0.024	30.665	-0.010	-0.010	0.000	0.000	0.000	0.000
25	V	31	GLU	-1	-0.934	-0.965	33.867	0.145	0.145	0.000	0.000	0.000	0.000
26	V	32	VAL	0	-0.026	-0.009	29.134	0.017	0.017	0.000	0.000	0.000	0.000
27	V	33	HIS	0	0.020	0.004	31.921	-0.025	-0.025	0.000	0.000	0.000	0.000
28	V	34	PRO	0	-0.065	-0.043	30.602	0.016	0.016	0.000	0.000	0.000	0.000
29	V	35	LEU	0	-0.009	0.012	25.887	-0.002	-0.002	0.000	0.000	0.000	0.000
30	V	36	PRO	0	0.050	0.038	30.556	-0.020	-0.020	0.000	0.000	0.000	0.000
31	V	37	THR	0	0.002	-0.008	30.418	-0.011	-0.011	0.000	0.000	0.000	0.000
32	V	38	PRO	0	-0.042	-0.027	29.697	0.009	0.009	0.000	0.000	0.000	0.000
33	V	39	VAL	0	0.006	0.013	23.503	0.010	0.010	0.000	0.000	0.000	0.000
34	V	40	LEU	0	0.015	0.009	23.937	-0.024	-0.024	0.000	0.000	0.000	0.000
35	V	41	LEU	0	-0.028	-0.009	20.112	0.044	0.044	0.000	0.000	0.000	0.000
36	V	42	PRO	0	0.006	-0.004	16.531	-0.038	-0.038	0.000	0.000	0.000	0.000
37	V	43	ALA	0	0.015	0.006	19.190	-0.038	-0.038	0.000	0.000	0.000	0.000
38	V	44	VAL	0	0.005	0.013	20.427	-0.036	-0.036	0.000	0.000	0.000	0.000
39	V	45	ASP	-1	-0.893	-0.928	21.628	-0.301	-0.301	0.000	0.000	0.000	0.000
40	V	46	PHE	0	0.004	-0.024	18.868	-0.052	-0.052	0.000	0.000	0.000	0.000
41	V	47	SER	0	0.020	0.005	22.246	0.002	0.002	0.000	0.000	0.000	0.000
42	V	48	LEU	0	-0.038	-0.011	16.938	0.011	0.011	0.000	0.000	0.000	0.000
43	V	49	GLY	0	0.029	0.017	19.233	-0.080	-0.080	0.000	0.000	0.000	0.000
44	V	50	GLU	-1	-0.864	-0.946	21.032	-0.432	-0.432	0.000	0.000	0.000	0.000
45	V	51	TRP	0	-0.016	-0.016	12.247	-0.084	-0.084	0.000	0.000	0.000	0.000
46	V	52	LYS	1	0.864	0.947	13.350	1.485	1.485	0.000	0.000	0.000	0.000
47	V	53	THR	0	-0.049	-0.036	17.034	-0.073	-0.073	0.000	0.000	0.000	0.000
48	V	54	GLN	0	0.008	0.017	17.489	0.023	0.023	0.000	0.000	0.000	0.000
49	V	55	MET	0	0.043	0.013	16.290	-0.150	-0.150	0.000	0.000	0.000	0.000
50	V	56	GLU	-1	-0.862	-0.964	10.745	-1.993	-1.993	0.000	0.000	0.000	0.000
51	V	57	GLU	-1	-0.837	-0.906	10.906	-0.414	-0.414	0.000	0.000	0.000	0.000
52	V	58	THR	0	0.010	0.011	12.132	0.119	0.119	0.000	0.000	0.000	0.000
53	V	59	LYS	1	0.835	0.946	12.199	1.198	1.198	0.000	0.000	0.000	0.000
54	V	60	ALA	0	0.038	0.002	8.485	0.033	0.033	0.000	0.000	0.000	0.000
55	V	61	GLN	0	-0.037	-0.030	10.340	0.421	0.421	0.000	0.000	0.000	0.000
56	V	62	ASP	-1	-0.814	-0.898	12.937	-0.199	-0.199	0.000	0.000	0.000	0.000
57	V	63	ILE	0	-0.071	-0.033	10.135	0.064	0.064	0.000	0.000	0.000	0.000
58	V	64	LEU	0	0.005	0.026	9.665	0.145	0.145	0.000	0.000	0.000	0.000
59	V	65	GLY	0	0.080	0.049	11.635	0.080	0.080	0.000	0.000	0.000	0.000
60	V	66	ALA	0	-0.008	-0.007	14.530	-0.012	-0.012	0.000	0.000	0.000	0.000
61	V	67	VAL	0	-0.056	-0.050	9.424	-0.018	-0.018	0.000	0.000	0.000	0.000
62	V	68	THR	0	-0.013	-0.022	12.780	0.121	0.121	0.000	0.000	0.000	0.000
63	V	69	LEU	0	0.029	0.022	14.553	-0.014	-0.014	0.000	0.000	0.000	0.000
64	V	70	LEU	0	0.005	0.015	13.401	-0.014	-0.014	0.000	0.000	0.000	0.000
65	V	71	LEU	0	-0.065	-0.023	12.686	0.004	0.004	0.000	0.000	0.000	0.000
66	V	72	GLU	-1	-0.892	-0.961	15.594	0.438	0.438	0.000	0.000	0.000	0.000
67	V	73	GLY	0	0.038	0.015	18.887	-0.038	-0.038	0.000	0.000	0.000	0.000
68	V	74	VAL	0	-0.080	-0.063	16.647	-0.027	-0.027	0.000	0.000	0.000	0.000
69	V	75	MET	0	-0.039	-0.024	18.444	0.003	0.003	0.000	0.000	0.000	0.000
70	V	76	ALA	0	0.066	0.041	21.080	-0.021	-0.021	0.000	0.000	0.000	0.000
71	V	77	ALA	0	-0.005	0.008	23.618	-0.032	-0.032	0.000	0.000	0.000	0.000
72	V	78	ARG	1	0.846	0.910	21.512	-0.528	-0.528	0.000	0.000	0.000	0.000
73	V	79	GLY	0	0.006	0.014	24.578	0.007	0.007	0.000	0.000	0.000	0.000
74	V	80	GLN	0	-0.004	0.011	26.753	-0.034	-0.034	0.000	0.000	0.000	0.000
75	V	81	LEU	0	-0.060	-0.027	26.851	-0.022	-0.022	0.000	0.000	0.000	0.000
76	V	82	GLY	0	0.054	0.034	28.785	0.022	0.022	0.000	0.000	0.000	0.000
77	V	83	PRO	0	-0.012	-0.036	29.015	0.009	0.009	0.000	0.000	0.000	0.000
78	V	84	THR	0	-0.019	-0.007	28.433	0.013	0.013	0.000	0.000	0.000	0.000
79	V	86	LEU	0	0.092	0.033	24.875	0.025	0.025	0.000	0.000	0.000	0.000
80	V	87	SER	0	0.033	0.028	24.325	0.041	0.041	0.000	0.000	0.000	0.000
81	V	88	SER	0	-0.014	0.006	23.141	0.057	0.057	0.000	0.000	0.000	0.000
82	V	89	LEU	0	0.003	0.000	21.440	0.060	0.060	0.000	0.000	0.000	0.000
83	V	90	LEU	0	0.015	-0.002	19.960	0.052	0.052	0.000	0.000	0.000	0.000
84	V	91	GLY	0	-0.025	-0.023	18.993	0.009	0.009	0.000	0.000	0.000	0.000
85	V	92	GLN	0	0.031	0.016	16.545	0.080	0.080	0.000	0.000	0.000	0.000
86	V	93	LEU	0	-0.014	0.004	14.858	0.092	0.092	0.000	0.000	0.000	0.000
87	V	94	SER	0	0.059	0.016	13.746	0.046	0.046	0.000	0.000	0.000	0.000
88	V	95	GLY	0	-0.007	0.005	12.810	0.134	0.134	0.000	0.000	0.000	0.000
89	V	96	GLN	0	-0.001	-0.008	10.309	0.228	0.228	0.000	0.000	0.000	0.000
90	V	97	VAL	0	0.002	-0.015	9.024	0.156	0.156	0.000	0.000	0.000	0.000
91	V	98	ARG	1	0.962	0.982	9.129	-1.052	-1.052	0.000	0.000	0.000	0.000
92	V	99	LEU	0	0.000	0.019	5.487	0.401	0.401	0.000	0.000	0.000	0.000
93	V	100	LEU	0	-0.030	-0.007	4.494	-0.103	-0.013	-0.001	-0.010	-0.079	0.000
94	V	101	LEU	0	0.015	0.008	5.495	0.526	0.526	0.000	0.000	0.000	0.000
95	V	102	GLY	0	0.020	0.013	6.053	0.117	0.117	0.000	0.000	0.000	0.000
96	V	103	ALA	0	-0.030	-0.014	1.778	0.478	-3.498	9.232	-2.293	-2.963	0.002
97	V	104	LEU	0	0.019	0.004	3.092	3.223	3.336	0.041	0.409	-0.563	-0.001
98	V	105	GLN	0	0.056	0.017	5.985	-0.899	-0.899	0.000	0.000	0.000	0.000
99	V	106	SER	0	-0.031	-0.010	5.153	-0.663	-0.542	-0.002	-0.001	-0.119	0.000
100	V	107	LEU	0	-0.080	-0.033	3.683	-2.135	-1.428	0.013	-0.143	-0.577	0.001
101	V	108	LEU	0	-0.004	-0.005	5.582	-1.222	-1.217	-0.002	0.000	-0.003	0.000
102	V	109	GLY	0	-0.008	0.017	8.971	-0.380	-0.380	0.000	0.000	0.000	0.000
103	V	110	THR	0	-0.030	-0.023	11.029	-0.200	-0.200	0.000	0.000	0.000	0.000
104	V	111	GLN	0	-0.062	-0.031	11.645	0.153	0.153	0.000	0.000	0.000	0.000
105	V	112	LEU	0	0.008	0.001	13.031	-0.138	-0.138	0.000	0.000	0.000	0.000
106	V	113	PRO	0	0.014	-0.005	15.831	0.060	0.060	0.000	0.000	0.000	0.000
107	V	114	PRO	0	0.023	0.023	17.791	-0.003	-0.003	0.000	0.000	0.000	0.000
108	V	115	GLN	0	-0.043	-0.023	18.737	-0.070	-0.070	0.000	0.000	0.000	0.000
109	V	116	GLY	0	0.066	0.040	19.368	-0.007	-0.007	0.000	0.000	0.000	0.000
110	V	117	ARG	1	0.805	0.895	21.214	0.248	0.248	0.000	0.000	0.000	0.000
111	V	118	THR	0	0.013	-0.003	22.090	0.001	0.001	0.000	0.000	0.000	0.000
112	V	119	THR	0	-0.014	-0.005	24.312	-0.022	-0.022	0.000	0.000	0.000	0.000
113	V	120	ALA	0	0.011	0.000	25.292	0.029	0.029	0.000	0.000	0.000	0.000
114	V	121	HIS	0	0.001	0.003	25.107	-0.033	-0.033	0.000	0.000	0.000	0.000
115	V	122	LYS	1	0.915	0.947	27.367	-0.099	-0.099	0.000	0.000	0.000	0.000
116	V	123	ASP	-1	-0.770	-0.893	27.422	0.090	0.090	0.000	0.000	0.000	0.000
117	V	124	PRO	0	0.034	0.015	25.280	0.005	0.005	0.000	0.000	0.000	0.000
118	V	125	ASN	0	-0.019	-0.021	23.562	0.021	0.021	0.000	0.000	0.000	0.000
119	V	126	ALA	0	0.024	0.010	22.871	-0.004	-0.004	0.000	0.000	0.000	0.000
120	V	127	ILE	0	0.019	0.007	19.762	-0.006	-0.006	0.000	0.000	0.000	0.000
121	V	128	PHE	0	-0.047	-0.029	18.792	0.037	0.037	0.000	0.000	0.000	0.000
122	V	129	LEU	0	0.000	0.021	18.631	-0.022	-0.022	0.000	0.000	0.000	0.000
123	V	130	SER	0	0.059	0.026	18.459	-0.036	-0.036	0.000	0.000	0.000	0.000
124	V	131	PHE	0	0.030	0.020	10.450	-0.046	-0.046	0.000	0.000	0.000	0.000
125	V	132	GLN	0	-0.024	-0.025	14.077	-0.113	-0.113	0.000	0.000	0.000	0.000
126	V	133	HIS	0	-0.028	-0.016	15.493	-0.101	-0.101	0.000	0.000	0.000	0.000
127	V	134	LEU	0	0.042	0.017	12.996	-0.130	-0.130	0.000	0.000	0.000	0.000
128	V	135	LEU	0	-0.039	-0.018	9.228	-0.193	-0.193	0.000	0.000	0.000	0.000
129	V	136	ARG	1	0.878	0.939	12.113	0.174	0.174	0.000	0.000	0.000	0.000
130	V	137	GLY	0	0.010	0.010	14.536	-0.110	-0.110	0.000	0.000	0.000	0.000
131	V	138	LYS	1	0.943	0.979	12.936	0.160	0.160	0.000	0.000	0.000	0.000
132	V	139	VAL	0	0.070	0.034	7.626	-0.189	-0.189	0.000	0.000	0.000	0.000
133	V	140	ARG	1	0.977	0.999	8.683	1.135	1.135	0.000	0.000	0.000	0.000
134	V	141	PHE	0	-0.035	-0.036	10.539	-0.371	-0.371	0.000	0.000	0.000	0.000
135	V	142	LEU	0	-0.016	-0.003	6.960	0.189	0.189	0.000	0.000	0.000	0.000
136	V	143	MET	0	-0.028	-0.010	4.458	-1.693	-1.572	-0.001	-0.015	-0.104	0.000
137	V	144	LEU	0	-0.030	-0.005	7.136	-0.444	-0.444	0.000	0.000	0.000	0.000
138	V	145	VAL	0	-0.026	-0.002	9.553	0.240	0.240	0.000	0.000	0.000	0.000
139	V	146	GLY	0	0.012	0.011	9.603	0.045	0.045	0.000	0.000	0.000	0.000
140	V	147	GLY	0	0.008	0.011	5.875	-1.246	-1.246	0.000	0.000	0.000	0.000
141	V	148	SER	0	0.030	0.022	6.536	0.142	0.142	0.000	0.000	0.000	0.000
142	V	149	THR	0	-0.077	-0.053	3.604	-3.502	0.308	-0.005	-1.863	-1.942	-0.002

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Interactive mode: IFIE and PIEDA for fragment #1(V:151:CYS)