FMO DATABASE

FMODB ID: 669KZ

Calculation Name: 4D3C-A-Xray372

Preferred Name: Hepatocyte growth factor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4D3C

Chain ID: A

ChEMBL ID: CHEMBL5479

UniProt ID: P14210

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	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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1305384.606292
FMO2-HF: Nuclear repulsion	1245561.373988
FMO2-HF: Total energy	-59823.232304
FMO2-MP2: Total energy	-59989.968134

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:37:ASN)

Summations of interaction energy for fragment #1(A:37:ASN)

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.
-43.038	-33.775	14.103	-11.015	-12.348	-0.026

Interaction energy analysis for fragmet #1(A:37:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.012

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	39	ILE	0	-0.036	-0.022	3.820	-0.338	2.896	-0.025	-1.672	-1.537	0.004
4	A	40	HIS	0	0.009	0.012	3.076	2.524	3.050	0.022	-0.124	-0.423	0.000
5	A	41	GLU	-1	-0.925	-0.967	6.143	-3.605	-3.605	0.000	0.000	0.000	0.000
6	A	42	PHE	0	-0.028	-0.032	7.315	0.721	0.721	0.000	0.000	0.000	0.000
7	A	43	LYS	1	0.831	0.929	11.039	0.491	0.491	0.000	0.000	0.000	0.000
8	A	44	LYS	1	0.836	0.918	11.697	1.565	1.565	0.000	0.000	0.000	0.000
9	A	45	SER	0	0.032	0.019	13.841	0.052	0.052	0.000	0.000	0.000	0.000
10	A	46	ALA	0	0.008	-0.011	16.591	0.042	0.042	0.000	0.000	0.000	0.000
11	A	47	LYS	1	0.935	0.967	17.433	0.618	0.618	0.000	0.000	0.000	0.000
12	A	48	THR	0	0.011	0.018	19.232	0.109	0.109	0.000	0.000	0.000	0.000
13	A	67	ALA	0	0.042	0.001	6.690	0.148	0.148	0.000	0.000	0.000	0.000
14	A	68	ASP	-1	-0.741	-0.896	2.383	-19.889	-16.135	6.539	-4.352	-5.942	-0.042
15	A	69	GLN	0	-0.006	0.011	4.262	1.981	2.318	-0.001	-0.040	-0.296	0.000
16	A	70	CYS	0	-0.084	-0.037	6.292	-0.272	-0.272	0.000	0.000	0.000	0.000
17	A	71	ALA	0	0.094	0.068	4.684	0.005	0.001	-0.001	-0.004	0.010	0.000
18	A	72	ASN	0	0.019	0.018	2.050	-17.305	-15.970	7.571	-4.819	-4.087	0.012
19	A	73	ARG	1	0.857	0.914	5.132	-3.083	-3.048	-0.001	-0.004	-0.029	0.000
20	A	74	CYS	0	-0.094	-0.026	8.756	-0.395	-0.395	0.000	0.000	0.000	0.000
21	A	75	THR	0	0.059	0.007	6.568	-0.226	-0.226	0.000	0.000	0.000	0.000
22	A	76	ARG	1	0.918	0.958	4.668	-5.066	-5.020	-0.001	0.000	-0.044	0.000
23	A	77	ASN	0	0.035	0.021	9.487	-0.108	-0.108	0.000	0.000	0.000	0.000
24	A	78	LYS	1	0.945	0.973	11.463	-2.152	-2.152	0.000	0.000	0.000	0.000
25	A	79	GLY	0	0.002	-0.002	13.238	0.070	0.070	0.000	0.000	0.000	0.000
26	A	80	LEU	0	-0.030	0.004	13.300	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	81	PRO	0	-0.003	-0.006	17.333	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	82	PHE	0	0.007	-0.001	17.114	-0.054	-0.054	0.000	0.000	0.000	0.000
29	A	83	THR	0	0.042	0.028	16.493	0.078	0.078	0.000	0.000	0.000	0.000
30	A	85	LYS	1	0.887	0.949	14.625	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	86	ALA	0	0.011	0.012	14.396	-0.142	-0.142	0.000	0.000	0.000	0.000
32	A	87	PHE	0	-0.024	-0.004	8.540	0.250	0.250	0.000	0.000	0.000	0.000
33	A	88	VAL	0	0.017	0.018	13.899	-0.158	-0.158	0.000	0.000	0.000	0.000
34	A	89	PHE	0	0.012	-0.017	10.926	0.161	0.161	0.000	0.000	0.000	0.000
35	A	90	ASH	0	0.028	0.018	13.863	-0.160	-0.160	0.000	0.000	0.000	0.000
36	A	91	LYS	1	0.893	0.949	14.359	0.651	0.651	0.000	0.000	0.000	0.000
37	A	92	ALA	0	0.019	0.030	18.449	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	93	ARG	1	0.953	0.966	19.193	0.090	0.090	0.000	0.000	0.000	0.000
39	A	94	LYS	1	0.980	1.003	17.768	-0.174	-0.174	0.000	0.000	0.000	0.000
40	A	95	GLN	0	0.037	0.012	12.652	0.040	0.040	0.000	0.000	0.000	0.000
41	A	97	LEU	0	-0.027	0.009	14.299	0.096	0.096	0.000	0.000	0.000	0.000
42	A	98	TRP	0	0.004	-0.025	10.454	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	99	PHE	0	0.031	0.017	15.580	0.018	0.018	0.000	0.000	0.000	0.000
44	A	100	PRO	0	0.041	0.044	17.409	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	101	PHE	0	-0.012	-0.018	19.596	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	102	ASN	0	0.035	0.006	18.677	0.036	0.036	0.000	0.000	0.000	0.000
47	A	103	SER	0	-0.041	-0.041	20.267	0.043	0.043	0.000	0.000	0.000	0.000
48	A	104	MET	0	-0.052	-0.014	21.373	0.002	0.002	0.000	0.000	0.000	0.000
49	A	105	SER	0	-0.046	-0.018	23.851	0.034	0.034	0.000	0.000	0.000	0.000
50	A	117	ASP	-1	-0.841	-0.940	14.065	-0.892	-0.892	0.000	0.000	0.000	0.000
51	A	118	LEU	0	0.006	0.012	15.475	0.087	0.087	0.000	0.000	0.000	0.000
52	A	119	TYR	0	0.001	-0.005	10.022	-0.286	-0.286	0.000	0.000	0.000	0.000
53	A	120	GLU	-1	-0.719	-0.859	13.276	-0.387	-0.387	0.000	0.000	0.000	0.000
54	A	121	ASN	0	-0.012	-0.019	12.446	-0.344	-0.344	0.000	0.000	0.000	0.000
55	A	122	LYS	1	0.920	0.960	11.658	2.011	2.011	0.000	0.000	0.000	0.000
56	A	123	ASP	-1	-0.835	-0.892	13.603	-0.568	-0.568	0.000	0.000	0.000	0.000
57	A	124	TYR	0	-0.043	-0.035	16.038	0.116	0.116	0.000	0.000	0.000	0.000
58	A	125	ILE	0	-0.077	-0.027	17.405	0.040	0.040	0.000	0.000	0.000	0.000
59	A	126	ARG	1	0.883	0.923	19.689	0.247	0.247	0.000	0.000	0.000	0.000
60	A	127	ASN	0	0.008	0.009	20.330	0.042	0.042	0.000	0.000	0.000	0.000
61	A	128	CYS	0	-0.019	-0.007	22.402	0.012	0.012	0.000	0.000	0.000	0.000
62	A	129	ILE	0	-0.005	0.004	26.105	0.015	0.015	0.000	0.000	0.000	0.000
63	A	130	ILE	0	0.038	-0.003	29.470	0.016	0.016	0.000	0.000	0.000	0.000
64	A	131	GLY	0	0.043	0.030	33.255	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	132	LYS	1	0.848	0.910	34.432	0.191	0.191	0.000	0.000	0.000	0.000
66	A	133	GLY	0	0.027	0.018	31.194	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	134	GLY	0	-0.021	-0.010	30.455	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	135	SER	0	-0.010	-0.010	29.842	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	136	TYR	0	0.035	0.026	22.509	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	137	LYS	1	0.887	0.936	22.889	0.406	0.406	0.000	0.000	0.000	0.000
71	A	138	GLY	0	0.063	0.047	20.074	-0.042	-0.042	0.000	0.000	0.000	0.000
72	A	139	THR	0	0.011	-0.010	15.486	0.010	0.010	0.000	0.000	0.000	0.000
73	A	140	VAL	0	-0.002	0.018	18.406	-0.086	-0.086	0.000	0.000	0.000	0.000
74	A	141	SER	0	0.032	0.008	18.687	0.049	0.049	0.000	0.000	0.000	0.000
75	A	142	ILE	0	-0.020	-0.005	20.400	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	143	THR	0	-0.025	-0.044	23.758	0.010	0.010	0.000	0.000	0.000	0.000
77	A	144	LYS	1	0.838	0.900	27.360	0.319	0.319	0.000	0.000	0.000	0.000
78	A	145	SER	0	-0.035	-0.020	29.844	0.013	0.013	0.000	0.000	0.000	0.000
79	A	146	GLY	0	-0.010	-0.001	26.298	0.002	0.002	0.000	0.000	0.000	0.000
80	A	147	ILE	0	-0.014	0.000	25.668	-0.044	-0.044	0.000	0.000	0.000	0.000
81	A	148	LYS	1	0.956	0.987	18.817	0.959	0.959	0.000	0.000	0.000	0.000
82	A	149	CYS	0	0.024	0.015	23.440	0.020	0.020	0.000	0.000	0.000	0.000
83	A	150	GLN	0	-0.020	-0.025	23.745	-0.051	-0.051	0.000	0.000	0.000	0.000
84	A	151	PRO	0	-0.027	-0.035	22.424	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	152	TRP	0	-0.014	-0.015	24.368	0.069	0.069	0.000	0.000	0.000	0.000
86	A	153	SER	0	-0.039	-0.027	23.498	0.038	0.038	0.000	0.000	0.000	0.000
87	A	154	SER	0	-0.035	-0.008	26.442	0.027	0.027	0.000	0.000	0.000	0.000
88	A	155	MET	0	-0.021	-0.005	28.149	0.004	0.004	0.000	0.000	0.000	0.000
89	A	156	ILE	0	0.043	0.032	29.921	0.022	0.022	0.000	0.000	0.000	0.000
90	A	157	PRO	0	0.001	-0.013	28.668	-0.037	-0.037	0.000	0.000	0.000	0.000
91	A	158	HIS	1	0.785	0.908	31.341	0.418	0.418	0.000	0.000	0.000	0.000
92	A	159	GLU	-1	-0.831	-0.894	32.832	-0.291	-0.291	0.000	0.000	0.000	0.000
93	A	160	HIS	0	0.011	0.001	30.128	0.032	0.032	0.000	0.000	0.000	0.000
94	A	161	SER	0	0.040	0.024	35.336	0.004	0.004	0.000	0.000	0.000	0.000
95	A	162	PHE	0	-0.014	-0.030	31.592	0.014	0.014	0.000	0.000	0.000	0.000
96	A	163	LEU	0	0.054	0.041	30.150	-0.027	-0.027	0.000	0.000	0.000	0.000
97	A	164	PRO	0	0.087	0.025	26.969	0.027	0.027	0.000	0.000	0.000	0.000
98	A	165	SER	0	-0.033	-0.016	29.888	0.012	0.012	0.000	0.000	0.000	0.000
99	A	166	SER	0	-0.012	-0.006	32.873	0.023	0.023	0.000	0.000	0.000	0.000
100	A	167	TYR	0	-0.005	0.017	31.444	0.017	0.017	0.000	0.000	0.000	0.000
101	A	168	ARG	1	0.972	0.986	30.132	0.228	0.228	0.000	0.000	0.000	0.000
102	A	169	GLY	0	0.033	0.025	28.454	0.012	0.012	0.000	0.000	0.000	0.000
103	A	170	LYS	1	0.805	0.882	28.095	0.275	0.275	0.000	0.000	0.000	0.000
104	A	171	ASP	-1	-0.833	-0.901	22.451	-0.613	-0.613	0.000	0.000	0.000	0.000
105	A	172	LEU	0	0.000	0.021	24.496	-0.035	-0.035	0.000	0.000	0.000	0.000
106	A	173	GLN	0	-0.014	-0.012	21.065	0.053	0.053	0.000	0.000	0.000	0.000
107	A	174	GLU	-1	-0.881	-0.960	17.557	-0.862	-0.862	0.000	0.000	0.000	0.000
108	A	175	ASN	0	-0.068	-0.032	19.846	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	176	TYR	0	0.013	0.016	16.857	-0.050	-0.050	0.000	0.000	0.000	0.000
110	A	177	CYS	0	-0.008	0.013	22.226	0.023	0.023	0.000	0.000	0.000	0.000
111	A	178	ARG	1	0.727	0.839	21.440	0.589	0.589	0.000	0.000	0.000	0.000
112	A	179	ASN	0	0.083	0.045	27.799	0.017	0.017	0.000	0.000	0.000	0.000
113	A	180	PRO	0	0.003	-0.010	30.920	0.019	0.019	0.000	0.000	0.000	0.000
114	A	181	ARG	1	0.902	0.930	32.784	0.255	0.255	0.000	0.000	0.000	0.000
115	A	182	GLY	0	-0.009	0.022	35.125	0.014	0.014	0.000	0.000	0.000	0.000
116	A	183	GLU	-1	-0.859	-0.926	36.079	-0.265	-0.265	0.000	0.000	0.000	0.000
117	A	184	GLU	-1	-0.786	-0.896	36.574	-0.214	-0.214	0.000	0.000	0.000	0.000
118	A	185	GLY	0	-0.016	0.009	36.279	0.001	0.001	0.000	0.000	0.000	0.000
119	A	186	GLY	0	0.020	0.024	32.954	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	187	PRO	0	-0.104	-0.068	28.028	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	188	TRP	0	0.003	0.012	29.951	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	190	PHE	0	0.052	0.022	28.736	0.028	0.028	0.000	0.000	0.000	0.000
123	A	191	THR	0	-0.019	-0.008	27.991	-0.049	-0.049	0.000	0.000	0.000	0.000
124	A	192	SER	0	-0.050	-0.061	25.567	0.015	0.015	0.000	0.000	0.000	0.000
125	A	193	ASN	0	0.016	0.005	27.712	0.006	0.006	0.000	0.000	0.000	0.000
126	A	194	PRO	0	0.017	-0.018	30.912	0.011	0.011	0.000	0.000	0.000	0.000
127	A	195	GLU	-1	-0.852	-0.890	33.816	-0.304	-0.304	0.000	0.000	0.000	0.000
128	A	196	VAL	0	0.007	0.020	32.761	0.014	0.014	0.000	0.000	0.000	0.000
129	A	197	ARG	1	0.888	0.937	32.884	0.277	0.277	0.000	0.000	0.000	0.000
130	A	198	TYR	0	-0.046	-0.042	32.060	-0.021	-0.021	0.000	0.000	0.000	0.000
131	A	199	GLU	-1	-0.743	-0.847	30.999	-0.383	-0.383	0.000	0.000	0.000	0.000
132	A	200	VAL	0	0.031	0.014	30.801	-0.023	-0.023	0.000	0.000	0.000	0.000
133	A	202	ASP	-1	-0.758	-0.852	27.958	-0.346	-0.346	0.000	0.000	0.000	0.000
134	A	203	ILE	0	-0.090	-0.052	24.640	-0.049	-0.049	0.000	0.000	0.000	0.000
135	A	204	PRO	0	0.063	0.037	25.955	0.026	0.026	0.000	0.000	0.000	0.000
136	A	205	GLN	0	-0.024	-0.029	28.421	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	207	SER	0	0.005	0.008	30.052	0.008	0.008	0.000	0.000	0.000	0.000
138	A	208	GLU	-1	-0.879	-0.907	30.841	-0.265	-0.265	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:37:ASN)