FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: R8KL8

Calculation Name: 1VHC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VHC

Chain ID: A

ChEMBL ID:

UniProt ID: P44480

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2402511.740293
FMO2-HF: Nuclear repulsion 2322977.14806
FMO2-HF: Total energy -79534.592233
FMO2-MP2: Total energy -79768.242122


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
0.972.215-0.011-0.487-0.7470.003
Interaction energy analysis for fragmet #1(A:2:SER)
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 : -0.016
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   
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].
3A4THR00.045-0.0013.858-0.7390.385-0.010-0.478-0.6360.003
4A5THR00.0540.0016.3690.4130.4130.0000.0000.0000.000
5A6GLN00.0140.0059.2040.1530.1530.0000.0000.0000.000
6A7GLN00.0460.0396.728-0.506-0.5060.0000.0000.0000.000
7A8ILE0-0.0040.0065.8000.2800.2800.0000.0000.0000.000
8A9ILE0-0.0070.0009.2870.1600.1600.0000.0000.0000.000
9A10GLU-1-0.748-0.85012.694-0.163-0.1630.0000.0000.0000.000
10A11LYS10.9430.9858.145-0.444-0.4440.0000.0000.0000.000
11A12LEU0-0.035-0.01612.4120.0580.0580.0000.0000.0000.000
12A13ARG10.8440.90014.5500.1930.1930.0000.0000.0000.000
13A14GLU-1-0.958-0.96513.9530.1300.1300.0000.0000.0000.000
14A15LEU0-0.019-0.01313.8710.0010.0010.0000.0000.0000.000
15A16LYS10.8690.91817.957-0.007-0.0070.0000.0000.0000.000
16A17ILE0-0.041-0.01019.475-0.011-0.0110.0000.0000.0000.000
17A18VAL00.0250.01416.0020.0200.0200.0000.0000.0000.000
18A19PRO00.0010.01317.411-0.019-0.0190.0000.0000.0000.000
19A20VAL0-0.036-0.02718.4430.0240.0240.0000.0000.0000.000
20A21ILE00.0040.00118.101-0.015-0.0150.0000.0000.0000.000
21A22ALA0-0.030-0.02620.4510.0110.0110.0000.0000.0000.000
22A23LEU0-0.016-0.00520.662-0.006-0.0060.0000.0000.0000.000
23A24ASP-1-0.826-0.89624.3760.1410.1410.0000.0000.0000.000
24A25ASN0-0.023-0.02825.7640.0020.0020.0000.0000.0000.000
25A26ALA00.0320.01620.9870.0070.0070.0000.0000.0000.000
26A27ASP-1-0.866-0.94221.3340.2690.2690.0000.0000.0000.000
27A28ASP-1-0.810-0.89622.8230.1900.1900.0000.0000.0000.000
28A29ILE0-0.057-0.03117.110-0.005-0.0050.0000.0000.0000.000
29A30LEU00.0120.02018.1080.0180.0180.0000.0000.0000.000
30A31PRO00.0340.02920.3950.0030.0030.0000.0000.0000.000
31A32LEU0-0.0030.02520.720-0.012-0.0120.0000.0000.0000.000
32A33ALA00.0180.00616.764-0.009-0.0090.0000.0000.0000.000
33A34ASP-1-0.805-0.89118.7330.2950.2950.0000.0000.0000.000
34A35THR0-0.087-0.06120.833-0.022-0.0220.0000.0000.0000.000
35A36LEU0-0.028-0.01118.600-0.020-0.0200.0000.0000.0000.000
36A37ALA00.0370.02517.510-0.014-0.0140.0000.0000.0000.000
37A38LYS10.8720.93019.199-0.182-0.1820.0000.0000.0000.000
38A39ASN0-0.066-0.03322.405-0.033-0.0330.0000.0000.0000.000
39A40GLY00.0340.03120.714-0.018-0.0180.0000.0000.0000.000
40A41LEU0-0.037-0.02117.803-0.004-0.0040.0000.0000.0000.000
41A42SER00.0230.00913.576-0.014-0.0140.0000.0000.0000.000
42A43VAL0-0.020-0.01112.8150.0740.0740.0000.0000.0000.000
43A44ALA0-0.001-0.00113.365-0.041-0.0410.0000.0000.0000.000
44A45GLU-1-0.846-0.91113.5810.1530.1530.0000.0000.0000.000
45A46ILE00.0200.02014.638-0.036-0.0360.0000.0000.0000.000
46A47THR0-0.043-0.03816.8200.0060.0060.0000.0000.0000.000
47A48PHE00.0580.00215.0410.0000.0000.0000.0000.0000.000
48A49ARG10.8890.95320.218-0.143-0.1430.0000.0000.0000.000
49A50SER0-0.024-0.01422.353-0.018-0.0180.0000.0000.0000.000
50A51GLU-1-0.897-0.95322.0380.2100.2100.0000.0000.0000.000
51A52ALA00.0140.00922.0950.0190.0190.0000.0000.0000.000
52A53ALA0-0.015-0.00117.9240.0280.0280.0000.0000.0000.000
53A54ALA00.0410.01416.1810.0470.0470.0000.0000.0000.000
54A55ASP-1-0.805-0.89216.1100.3960.3960.0000.0000.0000.000
55A56ALA00.0100.00917.5710.0260.0260.0000.0000.0000.000
56A57ILE0-0.020-0.01711.4180.0290.0290.0000.0000.0000.000
57A58ARG10.8660.92112.858-0.363-0.3630.0000.0000.0000.000
58A59LEU0-0.041-0.01514.2050.0330.0330.0000.0000.0000.000
59A60LEU0-0.0030.00212.917-0.002-0.0020.0000.0000.0000.000
60A61ARG10.7780.8546.628-1.631-1.6310.0000.0000.0000.000
61A62ALA0-0.033-0.01611.2380.0380.0380.0000.0000.0000.000
62A63ASN0-0.050-0.02113.595-0.043-0.0430.0000.0000.0000.000
63A64ARG10.8420.90713.369-0.445-0.4450.0000.0000.0000.000
64A65PRO00.0240.0078.7640.1030.1030.0000.0000.0000.000
65A66ASP-1-0.935-0.9667.9451.0701.0700.0000.0000.0000.000
66A67PHE0-0.0070.0039.423-0.006-0.0060.0000.0000.0000.000
67A68LEU0-0.0210.0028.0350.2100.2100.0000.0000.0000.000
68A69ILE0-0.001-0.0118.584-0.172-0.1720.0000.0000.0000.000
69A70ALA00.0000.0069.3900.0570.0570.0000.0000.0000.000
70A71ALA00.0220.00611.6980.0080.0080.0000.0000.0000.000
71A72GLY00.0420.00513.686-0.061-0.0610.0000.0000.0000.000
72A73THR0-0.085-0.04017.0180.0080.0080.0000.0000.0000.000
73A74VAL00.0340.03415.0460.0000.0000.0000.0000.0000.000
74A75LEU0-0.016-0.02618.323-0.031-0.0310.0000.0000.0000.000
75A76THR0-0.054-0.04119.608-0.012-0.0120.0000.0000.0000.000
76A77ALA00.0460.00117.7520.0160.0160.0000.0000.0000.000
77A78GLU-1-0.858-0.92616.9480.2300.2300.0000.0000.0000.000
78A79GLN00.0540.03717.2090.0280.0280.0000.0000.0000.000
79A80VAL00.0100.01012.3160.0520.0520.0000.0000.0000.000
80A81VAL00.0180.00312.3810.1030.1030.0000.0000.0000.000
81A82LEU00.0290.02312.9290.1130.1130.0000.0000.0000.000
82A83ALA00.0100.01411.9050.0730.0730.0000.0000.0000.000
83A84LYS10.8390.9315.426-0.969-0.9690.0000.0000.0000.000
84A85SER0-0.017-0.0188.8790.3020.3020.0000.0000.0000.000
85A86SER0-0.075-0.04311.317-0.042-0.0420.0000.0000.0000.000
86A87GLY00.0210.0237.887-0.029-0.0290.0000.0000.0000.000
87A88ALA00.0050.0027.5470.1700.1700.0000.0000.0000.000
88A89ASP-1-0.825-0.8954.6451.7271.848-0.001-0.009-0.1110.000
89A90PHE0-0.048-0.0375.985-0.517-0.5170.0000.0000.0000.000
90A91VAL00.0190.0168.7950.1310.1310.0000.0000.0000.000
91A92VAL0-0.022-0.00612.112-0.087-0.0870.0000.0000.0000.000
92A93THR0-0.033-0.02715.5540.0220.0220.0000.0000.0000.000
93A94PRO0-0.0080.00018.868-0.013-0.0130.0000.0000.0000.000
94A95GLY00.0270.00622.074-0.010-0.0100.0000.0000.0000.000
95A96LEU00.0090.03820.0380.0120.0120.0000.0000.0000.000
96A97ASN00.0180.00720.826-0.003-0.0030.0000.0000.0000.000
97A98PRO00.0970.02620.2270.0050.0050.0000.0000.0000.000
98A99LYS10.9800.99419.623-0.063-0.0630.0000.0000.0000.000
99A100ILE0-0.0180.00216.5320.0080.0080.0000.0000.0000.000
100A101VAL00.0510.02515.5380.0140.0140.0000.0000.0000.000
101A102LYS10.8600.91314.7440.0970.0970.0000.0000.0000.000
102A103LEU0-0.0050.00614.497-0.014-0.0140.0000.0000.0000.000
103A104CYS0-0.051-0.02511.2220.0610.0610.0000.0000.0000.000
104A105GLN0-0.011-0.01510.3530.0060.0060.0000.0000.0000.000
105A106ASP-1-0.807-0.87911.220-0.168-0.1680.0000.0000.0000.000
106A107LEU0-0.051-0.01610.0970.0220.0220.0000.0000.0000.000
107A108ASN0-0.003-0.0045.8880.1180.1180.0000.0000.0000.000
108A109PHE0-0.071-0.0435.7680.1380.1380.0000.0000.0000.000
109A110PRO00.0250.0205.5180.1000.1000.0000.0000.0000.000
110A111ILE00.014-0.0038.3170.2060.2060.0000.0000.0000.000
111A112THR0-0.010-0.00911.877-0.046-0.0460.0000.0000.0000.000
112A113PRO00.0240.02214.9000.0480.0480.0000.0000.0000.000
113A114GLY00.0050.02217.926-0.011-0.0110.0000.0000.0000.000
114A115VAL0-0.024-0.02921.408-0.003-0.0030.0000.0000.0000.000
115A116ASN0-0.007-0.01824.3420.0000.0000.0000.0000.0000.000
116A117ASN0-0.003-0.00127.844-0.003-0.0030.0000.0000.0000.000
117A118PRO00.0940.02928.401-0.004-0.0040.0000.0000.0000.000
118A119MET00.0350.03728.833-0.005-0.0050.0000.0000.0000.000
119A120ALA0-0.016-0.01425.434-0.005-0.0050.0000.0000.0000.000
120A121ILE00.0030.00324.356-0.009-0.0090.0000.0000.0000.000
121A122GLU-1-0.835-0.89324.291-0.084-0.0840.0000.0000.0000.000
122A123ILE0-0.016-0.00523.112-0.008-0.0080.0000.0000.0000.000
123A124ALA0-0.012-0.01620.275-0.009-0.0090.0000.0000.0000.000
124A125LEU0-0.020-0.01320.258-0.025-0.0250.0000.0000.0000.000
125A126GLU-1-0.912-0.93821.818-0.134-0.1340.0000.0000.0000.000
126A127MET0-0.118-0.04918.2770.0020.0020.0000.0000.0000.000
127A128GLY00.0240.01817.724-0.028-0.0280.0000.0000.0000.000
128A129ILE0-0.095-0.05115.241-0.048-0.0480.0000.0000.0000.000
129A130SER00.0440.02017.5570.0260.0260.0000.0000.0000.000
130A131ALA0-0.036-0.01915.2460.0200.0200.0000.0000.0000.000
131A132VAL00.0250.01016.585-0.002-0.0020.0000.0000.0000.000
132A133LYS10.8580.92616.260-0.039-0.0390.0000.0000.0000.000
133A134PHE0-0.021-0.00420.246-0.005-0.0050.0000.0000.0000.000
134A135PHE00.0070.00223.7890.0140.0140.0000.0000.0000.000
135A136PRO0-0.0200.00225.712-0.004-0.0040.0000.0000.0000.000
136A137ALA00.0430.00126.522-0.005-0.0050.0000.0000.0000.000
137A138GLU-1-0.762-0.85228.4540.0100.0100.0000.0000.0000.000
138A139ALA0-0.040-0.02031.931-0.003-0.0030.0000.0000.0000.000
139A140SER0-0.020-0.00530.234-0.002-0.0020.0000.0000.0000.000
140A141GLY00.001-0.00932.477-0.005-0.0050.0000.0000.0000.000
141A142GLY00.0170.01230.749-0.002-0.0020.0000.0000.0000.000
142A143VAL00.0310.00630.566-0.006-0.0060.0000.0000.0000.000
143A144LYS10.9390.97631.9250.0040.0040.0000.0000.0000.000
144A145MET0-0.0080.00631.176-0.006-0.0060.0000.0000.0000.000
145A146ILE00.0140.00926.466-0.005-0.0050.0000.0000.0000.000
146A147LYS10.9430.97129.9740.0130.0130.0000.0000.0000.000
147A148ALA0-0.0280.00032.440-0.004-0.0040.0000.0000.0000.000
148A149LEU0-0.005-0.01428.810-0.004-0.0040.0000.0000.0000.000
149A150LEU0-0.011-0.01426.217-0.007-0.0070.0000.0000.0000.000
150A151GLY0-0.0100.01229.957-0.004-0.0040.0000.0000.0000.000
151A152PRO0-0.048-0.01731.576-0.004-0.0040.0000.0000.0000.000
152A153TYR0-0.060-0.07326.769-0.005-0.0050.0000.0000.0000.000
153A154ALA00.0400.02526.727-0.007-0.0070.0000.0000.0000.000
154A155GLN0-0.023-0.01023.8510.0080.0080.0000.0000.0000.000
155A156LEU0-0.0090.00722.145-0.021-0.0210.0000.0000.0000.000
156A157GLN0-0.0140.00016.4770.0160.0160.0000.0000.0000.000
157A158ILE00.0230.00719.631-0.001-0.0010.0000.0000.0000.000
158A159MET0-0.0040.00415.9040.0080.0080.0000.0000.0000.000
159A160PRO00.0130.01720.3510.0100.0100.0000.0000.0000.000
160A161THR00.0560.02121.0880.0090.0090.0000.0000.0000.000
161A162GLY00.0290.01324.020-0.004-0.0040.0000.0000.0000.000
162A163GLY00.009-0.00327.461-0.007-0.0070.0000.0000.0000.000
163A164ILE0-0.039-0.00525.100-0.003-0.0030.0000.0000.0000.000
164A165GLY00.035-0.00328.6700.0090.0090.0000.0000.0000.000
165A166LEU00.009-0.00129.787-0.005-0.0050.0000.0000.0000.000
166A167HIS0-0.0020.01131.620-0.001-0.0010.0000.0000.0000.000
167A168ASN00.012-0.00930.8970.0000.0000.0000.0000.0000.000
168A169ILE00.0050.00024.691-0.005-0.0050.0000.0000.0000.000
169A170ARG10.8840.92328.016-0.024-0.0240.0000.0000.0000.000
170A171ASP-1-0.900-0.94830.0840.0020.0020.0000.0000.0000.000
171A172TYR0-0.119-0.10326.527-0.008-0.0080.0000.0000.0000.000
172A173LEU0-0.006-0.01623.138-0.009-0.0090.0000.0000.0000.000
173A174ALA0-0.0140.01426.513-0.005-0.0050.0000.0000.0000.000
174A175ILE0-0.064-0.02527.252-0.006-0.0060.0000.0000.0000.000
175A176PRO00.0340.00825.583-0.002-0.0020.0000.0000.0000.000
176A177ASN0-0.042-0.02923.565-0.001-0.0010.0000.0000.0000.000
177A178ILE0-0.081-0.03322.269-0.010-0.0100.0000.0000.0000.000
178A179VAL0-0.036-0.00616.0170.0000.0000.0000.0000.0000.000
179A180ALA00.021-0.00617.6600.0150.0150.0000.0000.0000.000
180A181CYS0-0.057-0.00319.675-0.011-0.0110.0000.0000.0000.000
181A182GLY00.0430.02020.4530.0160.0160.0000.0000.0000.000
182A183GLY0-0.023-0.03221.300-0.013-0.0130.0000.0000.0000.000
183A184SER00.0250.01022.7380.0100.0100.0000.0000.0000.000
184A185TRP00.0190.01225.0740.0060.0060.0000.0000.0000.000
185A186PHE00.0550.01721.742-0.002-0.0020.0000.0000.0000.000
186A187VAL0-0.008-0.00421.9060.0090.0090.0000.0000.0000.000
187A188GLU-1-0.819-0.87825.2190.1060.1060.0000.0000.0000.000
188A189LYS10.8730.90727.255-0.131-0.1310.0000.0000.0000.000
189A190LYS10.8750.91628.281-0.085-0.0850.0000.0000.0000.000
190A191LEU0-0.0040.01529.311-0.002-0.0020.0000.0000.0000.000
191A192ILE00.0230.02324.1100.0030.0030.0000.0000.0000.000
192A193GLN0-0.0050.00428.0070.0010.0010.0000.0000.0000.000
193A194SER0-0.070-0.04430.699-0.004-0.0040.0000.0000.0000.000
194A195ASN0-0.024-0.03328.402-0.003-0.0030.0000.0000.0000.000
195A196ASN00.0030.01730.4910.0000.0000.0000.0000.0000.000
196A197TRP00.025-0.01224.9000.0030.0030.0000.0000.0000.000
197A198ASP-1-0.882-0.93728.3950.1160.1160.0000.0000.0000.000
198A199GLU-1-0.853-0.89830.9860.0820.0820.0000.0000.0000.000
199A200ILE0-0.017-0.00425.089-0.001-0.0010.0000.0000.0000.000
200A201GLY00.0290.00426.5630.0020.0020.0000.0000.0000.000
201A202ARG10.6780.79627.611-0.081-0.0810.0000.0000.0000.000
202A203LEU0-0.0160.00128.497-0.005-0.0050.0000.0000.0000.000
203A204VAL0-0.017-0.01423.114-0.003-0.0030.0000.0000.0000.000
204A205ARG10.9160.95325.865-0.111-0.1110.0000.0000.0000.000
205A206GLU-1-0.805-0.87427.9100.0630.0630.0000.0000.0000.000
206A207VAL0-0.015-0.01924.833-0.009-0.0090.0000.0000.0000.000
207A208ILE0-0.020-0.00822.796-0.008-0.0080.0000.0000.0000.000
208A209ASP-1-0.848-0.92025.9530.0610.0610.0000.0000.0000.000
209A210ILE0-0.038-0.00829.220-0.008-0.0080.0000.0000.0000.000
210A211ILE0-0.042-0.02624.084-0.008-0.0080.0000.0000.0000.000
211A212LYS10.8020.89823.725-0.074-0.0740.0000.0000.0000.000
212A213GLU-1-0.928-0.93128.7440.0150.0150.0000.0000.0000.000