FMO DATABASE

FMODB ID: 2269R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1301326.918514
FMO2-HF: Nuclear repulsion	1241504.412214
FMO2-HF: Total energy	-59822.506299
FMO2-MP2: Total energy	-59989.293987

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.
-37.334	-27.401	12.306	-10.623	-11.613	-0.004

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 : -0.007 / q_NPA : -0.006

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	-0.033	-0.016	3.374	-3.206	2.195	-0.043	-2.888	-2.470	0.003
4	A	40	HIS	0	0.006	0.000	3.266	1.836	2.399	0.018	-0.119	-0.462	0.000
5	A	41	GLU	-1	-0.967	-0.970	6.225	-2.964	-2.964	0.000	0.000	0.000	0.000
6	A	42	PHE	0	-0.014	-0.019	8.216	0.656	0.656	0.000	0.000	0.000	0.000
7	A	43	LYS	1	0.834	0.927	10.646	0.336	0.336	0.000	0.000	0.000	0.000
8	A	44	LYS	1	0.869	0.931	11.171	0.905	0.905	0.000	0.000	0.000	0.000
9	A	45	SER	0	0.016	0.006	13.533	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	46	ALA	0	0.007	-0.009	16.373	0.056	0.056	0.000	0.000	0.000	0.000
11	A	47	LYS	1	0.945	0.975	17.269	0.349	0.349	0.000	0.000	0.000	0.000
12	A	48	THR	0	0.034	0.040	18.692	0.051	0.051	0.000	0.000	0.000	0.000
13	A	67	ALA	0	-0.001	-0.039	7.736	0.198	0.198	0.000	0.000	0.000	0.000
14	A	68	ASP	-1	-0.736	-0.899	2.419	-10.755	-7.003	5.173	-3.775	-5.149	-0.024
15	A	69	GLN	0	-0.023	0.003	4.694	1.636	1.930	-0.001	-0.018	-0.275	0.000
16	A	70	CYS	0	-0.076	-0.013	6.377	-0.452	-0.452	0.000	0.000	0.000	0.000
17	A	71	ALA	0	0.112	0.071	5.373	-0.238	-0.238	0.000	0.000	0.000	0.000
18	A	72	ASN	0	0.020	0.025	1.973	-15.417	-15.524	7.160	-3.823	-3.229	0.017
19	A	73	ARG	1	0.844	0.904	5.364	-3.869	-3.839	-0.001	0.000	-0.028	0.000
20	A	74	CYS	0	-0.105	-0.019	8.766	-0.495	-0.495	0.000	0.000	0.000	0.000
21	A	75	THR	0	0.028	-0.010	6.817	-0.437	-0.437	0.000	0.000	0.000	0.000
22	A	76	ARG	1	0.923	0.959	5.649	-3.539	-3.539	0.000	0.000	0.000	0.000
23	A	77	ASN	0	0.029	0.009	10.355	-0.167	-0.167	0.000	0.000	0.000	0.000
24	A	78	LYS	1	0.960	0.985	11.876	-2.056	-2.056	0.000	0.000	0.000	0.000
25	A	79	GLY	0	-0.009	-0.011	13.542	0.075	0.075	0.000	0.000	0.000	0.000
26	A	80	LEU	0	-0.033	-0.009	13.570	-0.041	-0.041	0.000	0.000	0.000	0.000
27	A	81	PRO	0	0.006	0.007	17.541	-0.039	-0.039	0.000	0.000	0.000	0.000
28	A	82	PHE	0	0.026	0.009	17.317	-0.060	-0.060	0.000	0.000	0.000	0.000
29	A	83	THR	0	0.055	0.040	16.749	0.070	0.070	0.000	0.000	0.000	0.000
30	A	85	LYS	1	0.888	0.948	14.388	-0.109	-0.109	0.000	0.000	0.000	0.000
31	A	86	ALA	0	0.002	0.002	15.012	-0.123	-0.123	0.000	0.000	0.000	0.000
32	A	87	PHE	0	0.003	-0.002	8.856	0.232	0.232	0.000	0.000	0.000	0.000
33	A	88	VAL	0	0.020	0.024	14.636	-0.144	-0.144	0.000	0.000	0.000	0.000
34	A	89	PHE	0	0.036	-0.005	11.621	0.207	0.207	0.000	0.000	0.000	0.000
35	A	90	ASH	0	0.022	0.001	13.753	-0.155	-0.155	0.000	0.000	0.000	0.000
36	A	91	LYS	1	0.912	0.964	14.583	0.115	0.115	0.000	0.000	0.000	0.000
37	A	92	ALA	0	0.015	0.028	18.764	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	93	ARG	1	0.945	0.961	19.373	-0.166	-0.166	0.000	0.000	0.000	0.000
39	A	94	LYS	1	0.977	1.001	18.162	-0.346	-0.346	0.000	0.000	0.000	0.000
40	A	95	GLN	0	0.043	0.023	12.828	0.133	0.133	0.000	0.000	0.000	0.000
41	A	97	LEU	0	-0.024	-0.001	14.050	0.023	0.023	0.000	0.000	0.000	0.000
42	A	98	TRP	0	-0.004	-0.019	10.922	-0.077	-0.077	0.000	0.000	0.000	0.000
43	A	99	PHE	0	0.040	0.021	15.992	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	100	PRO	0	0.004	0.036	17.538	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	101	PHE	0	0.014	-0.018	19.900	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	102	ASN	0	0.031	0.018	19.171	0.053	0.053	0.000	0.000	0.000	0.000
47	A	103	SER	0	-0.041	-0.040	20.731	0.022	0.022	0.000	0.000	0.000	0.000
48	A	104	MET	0	-0.075	-0.031	21.053	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	105	SER	0	-0.039	-0.008	24.350	0.016	0.016	0.000	0.000	0.000	0.000
50	A	117	ASP	-1	-0.886	-0.973	13.879	-0.376	-0.376	0.000	0.000	0.000	0.000
51	A	118	LEU	0	-0.003	0.004	15.159	0.115	0.115	0.000	0.000	0.000	0.000
52	A	119	TYR	0	-0.011	-0.003	9.556	-0.177	-0.177	0.000	0.000	0.000	0.000
53	A	120	GLU	-1	-0.785	-0.884	13.296	-0.128	-0.128	0.000	0.000	0.000	0.000
54	A	121	ASN	0	0.040	0.009	12.900	-0.291	-0.291	0.000	0.000	0.000	0.000
55	A	122	LYS	1	0.960	0.968	12.349	1.427	1.427	0.000	0.000	0.000	0.000
56	A	123	ASP	-1	-0.834	-0.893	14.113	-0.471	-0.471	0.000	0.000	0.000	0.000
57	A	124	TYR	0	-0.080	-0.054	16.289	0.095	0.095	0.000	0.000	0.000	0.000
58	A	125	ILE	0	-0.054	-0.026	17.518	0.031	0.031	0.000	0.000	0.000	0.000
59	A	126	ARG	1	0.868	0.942	19.927	0.171	0.171	0.000	0.000	0.000	0.000
60	A	127	ASN	0	-0.002	0.006	20.100	0.034	0.034	0.000	0.000	0.000	0.000
61	A	128	CYS	0	-0.014	-0.018	22.558	0.006	0.006	0.000	0.000	0.000	0.000
62	A	129	ILE	0	-0.008	-0.005	26.290	0.006	0.006	0.000	0.000	0.000	0.000
63	A	130	ILE	0	0.021	-0.004	29.556	0.008	0.008	0.000	0.000	0.000	0.000
64	A	131	GLY	0	0.069	0.033	33.137	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	132	LYS	1	0.875	0.942	34.869	0.145	0.145	0.000	0.000	0.000	0.000
66	A	133	GLY	0	0.027	0.014	31.151	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	134	GLY	0	0.019	0.006	30.644	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	135	SER	0	-0.054	-0.046	29.450	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	136	TYR	0	0.073	0.048	22.622	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	137	LYS	1	0.904	0.941	22.470	0.271	0.271	0.000	0.000	0.000	0.000
71	A	138	GLY	0	0.058	0.046	20.167	-0.026	-0.026	0.000	0.000	0.000	0.000
72	A	139	THR	0	0.023	-0.006	15.491	0.010	0.010	0.000	0.000	0.000	0.000
73	A	140	VAL	0	-0.005	0.016	18.270	-0.080	-0.080	0.000	0.000	0.000	0.000
74	A	141	SER	0	0.027	0.012	18.457	0.040	0.040	0.000	0.000	0.000	0.000
75	A	142	ILE	0	-0.021	-0.012	20.447	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	143	THR	0	-0.026	-0.037	23.668	0.017	0.017	0.000	0.000	0.000	0.000
77	A	144	LYS	1	0.890	0.938	27.104	0.266	0.266	0.000	0.000	0.000	0.000
78	A	145	SER	0	-0.032	-0.012	29.553	0.008	0.008	0.000	0.000	0.000	0.000
79	A	146	GLY	0	-0.020	-0.007	25.979	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	147	ILE	0	-0.032	-0.017	25.776	-0.035	-0.035	0.000	0.000	0.000	0.000
81	A	148	LYS	1	0.969	0.989	18.937	0.815	0.815	0.000	0.000	0.000	0.000
82	A	149	CYS	0	-0.013	-0.006	23.285	0.019	0.019	0.000	0.000	0.000	0.000
83	A	150	GLN	0	0.001	0.001	23.646	-0.044	-0.044	0.000	0.000	0.000	0.000
84	A	151	PRO	0	-0.049	-0.042	22.455	0.011	0.011	0.000	0.000	0.000	0.000
85	A	152	TRP	0	-0.006	-0.001	24.319	0.047	0.047	0.000	0.000	0.000	0.000
86	A	153	SER	0	-0.028	-0.022	23.822	0.025	0.025	0.000	0.000	0.000	0.000
87	A	154	SER	0	-0.032	-0.003	26.248	0.026	0.026	0.000	0.000	0.000	0.000
88	A	155	MET	0	-0.002	0.003	27.996	0.006	0.006	0.000	0.000	0.000	0.000
89	A	156	ILE	0	0.011	0.036	29.770	0.014	0.014	0.000	0.000	0.000	0.000
90	A	157	PRO	0	0.012	-0.024	28.906	-0.029	-0.029	0.000	0.000	0.000	0.000
91	A	158	HIS	1	0.793	0.923	30.968	0.351	0.351	0.000	0.000	0.000	0.000
92	A	159	GLU	-1	-0.821	-0.894	32.451	-0.229	-0.229	0.000	0.000	0.000	0.000
93	A	160	HIS	0	-0.003	-0.010	30.136	0.027	0.027	0.000	0.000	0.000	0.000
94	A	161	SER	0	0.031	0.023	34.749	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	162	PHE	0	-0.017	-0.027	31.492	0.011	0.011	0.000	0.000	0.000	0.000
96	A	163	LEU	0	0.049	0.038	30.397	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	164	PRO	0	0.083	0.018	27.009	0.016	0.016	0.000	0.000	0.000	0.000
98	A	165	SER	0	-0.041	-0.016	29.707	0.011	0.011	0.000	0.000	0.000	0.000
99	A	166	SER	0	-0.019	-0.008	32.651	0.016	0.016	0.000	0.000	0.000	0.000
100	A	167	TYR	0	-0.018	0.011	31.364	0.013	0.013	0.000	0.000	0.000	0.000
101	A	168	ARG	1	1.003	1.009	30.071	0.131	0.131	0.000	0.000	0.000	0.000
102	A	169	GLY	0	0.011	0.006	28.095	0.009	0.009	0.000	0.000	0.000	0.000
103	A	170	LYS	1	0.887	0.936	28.168	0.187	0.187	0.000	0.000	0.000	0.000
104	A	171	ASP	-1	-0.846	-0.894	22.403	-0.412	-0.412	0.000	0.000	0.000	0.000
105	A	172	LEU	0	0.031	0.026	24.989	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	173	GLN	0	0.002	-0.005	20.944	0.040	0.040	0.000	0.000	0.000	0.000
107	A	174	GLU	-1	-0.898	-0.958	17.373	-0.659	-0.659	0.000	0.000	0.000	0.000
108	A	175	ASN	0	-0.044	-0.029	19.771	0.004	0.004	0.000	0.000	0.000	0.000
109	A	176	TYR	0	0.019	0.008	16.637	-0.045	-0.045	0.000	0.000	0.000	0.000
110	A	177	CYS	0	-0.016	-0.005	22.074	0.022	0.022	0.000	0.000	0.000	0.000
111	A	178	ARG	1	0.729	0.834	21.334	0.432	0.432	0.000	0.000	0.000	0.000
112	A	179	ASN	0	0.042	0.048	27.666	0.009	0.009	0.000	0.000	0.000	0.000
113	A	180	PRO	0	-0.010	-0.019	30.436	0.019	0.019	0.000	0.000	0.000	0.000
114	A	181	ARG	1	0.920	0.942	32.517	0.185	0.185	0.000	0.000	0.000	0.000
115	A	182	GLY	0	-0.024	0.009	34.772	0.010	0.010	0.000	0.000	0.000	0.000
116	A	183	GLU	-1	-0.864	-0.941	35.668	-0.200	-0.200	0.000	0.000	0.000	0.000
117	A	184	GLU	-1	-0.785	-0.900	36.432	-0.157	-0.157	0.000	0.000	0.000	0.000
118	A	185	GLY	0	-0.016	0.008	36.117	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	186	GLY	0	0.029	0.028	32.836	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	187	PRO	0	-0.119	-0.075	28.081	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	188	TRP	0	-0.001	0.009	29.893	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	190	PHE	0	0.026	0.015	28.488	0.023	0.023	0.000	0.000	0.000	0.000
123	A	191	THR	0	0.026	0.009	27.785	-0.041	-0.041	0.000	0.000	0.000	0.000
124	A	192	SER	0	-0.039	-0.049	25.628	0.009	0.009	0.000	0.000	0.000	0.000
125	A	193	ASN	0	0.052	0.022	27.737	0.006	0.006	0.000	0.000	0.000	0.000
126	A	194	PRO	0	0.020	-0.020	30.853	0.012	0.012	0.000	0.000	0.000	0.000
127	A	195	GLU	-1	-0.916	-0.939	33.757	-0.258	-0.258	0.000	0.000	0.000	0.000
128	A	196	VAL	0	-0.001	0.017	33.025	0.014	0.014	0.000	0.000	0.000	0.000
129	A	197	ARG	1	0.883	0.934	33.132	0.222	0.222	0.000	0.000	0.000	0.000
130	A	198	TYR	0	-0.031	-0.034	32.138	-0.019	-0.019	0.000	0.000	0.000	0.000
131	A	199	GLU	-1	-0.737	-0.847	30.910	-0.335	-0.335	0.000	0.000	0.000	0.000
132	A	200	VAL	0	0.030	0.010	30.653	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	202	ASP	-1	-0.812	-0.888	27.685	-0.293	-0.293	0.000	0.000	0.000	0.000
134	A	203	ILE	0	-0.080	-0.044	24.613	-0.040	-0.040	0.000	0.000	0.000	0.000
135	A	204	PRO	0	0.065	0.042	25.715	0.022	0.022	0.000	0.000	0.000	0.000
136	A	205	GLN	0	-0.073	-0.054	28.006	0.001	0.001	0.000	0.000	0.000	0.000
137	A	207	SER	0	0.018	0.013	30.185	0.003	0.003	0.000	0.000	0.000	0.000
138	A	208	GLU	-1	-0.872	-0.910	31.123	-0.226	-0.226	0.000	0.000	0.000	0.000

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