FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: RY3N8

Calculation Name: 1V1H-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V1H

Chain ID: A

ChEMBL ID:

UniProt ID: P03275

Base Structure: X-ray

Registration Date: 2025-07-11

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 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 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -505112.685463
FMO2-HF: Nuclear repulsion 467657.696797
FMO2-HF: Total energy -37454.988666
FMO2-MP2: Total energy -37565.132328


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:319:VAL)


Summations of interaction energy for fragment #1(A:319:VAL)
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.
-1.0870.790.018-0.81-1.0850.004
Interaction energy analysis for fragmet #1(A:319:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.151 / q_NPA : 0.008
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].
4A320SER0-0.0740.0584.3850.0240.2220.000-0.101-0.0960.000
5A321ILE00.050-0.1143.766-1.257-0.022-0.012-0.608-0.6160.003
6A321ILE0-0.0600.1354.3170.0750.144-0.001-0.011-0.0570.000
7A322LYS00.153-0.0776.4320.5330.5330.0000.0000.0000.000
8A322LYS10.7841.02310.4150.5040.5040.0000.0000.0000.000
9A323LYS00.119-0.13010.122-0.026-0.0260.0000.0000.0000.000
10A323LYS10.9121.1088.5001.0851.0850.0000.0000.0000.000
11A324SER00.018-0.04111.9720.0500.0500.0000.0000.0000.000
12A324SER0-0.0500.07115.037-0.007-0.0070.0000.0000.0000.000
13A325SER0-0.124-0.12113.5470.1120.1120.0000.0000.0000.000
14A325SER0-0.0350.06213.1720.0340.0340.0000.0000.0000.000
15A326GLY00.115-0.05413.759-0.077-0.0770.0000.0000.0000.000
16A327LEU00.0950.01910.0720.1350.1350.0000.0000.0000.000
17A327LEU0-0.0430.1198.520-0.094-0.0940.0000.0000.0000.000
18A328ASN00.072-0.11110.3760.1070.1070.0000.0000.0000.000
19A328ASN0-0.0810.08811.291-0.051-0.0510.0000.0000.0000.000
20A329PHE00.083-0.0838.335-0.331-0.3310.0000.0000.0000.000
21A329PHE0-0.1230.0683.4960.2240.4860.002-0.079-0.1840.000
22A330ASP00.134-0.1039.2830.2590.2590.0000.0000.0000.000
23A330ASP-1-1.013-0.83712.716-0.847-0.8470.0000.0000.0000.000
24A331ASN00.098-0.04411.816-0.073-0.0730.0000.0000.0000.000
25A331ASN0-0.1460.01612.4520.0970.0970.0000.0000.0000.000
26A332THR00.013-0.0298.058-0.026-0.0260.0000.0000.0000.000
27A332THR0-0.0430.0207.7030.0500.0500.0000.0000.0000.000
28A333ALA00.146-0.1126.828-0.888-0.8880.0000.0000.0000.000
29A333ALA0-0.0620.1329.6540.0860.0860.0000.0000.0000.000
30A334ILE00.090-0.1276.8320.3030.3030.0000.0000.0000.000
31A334ILE0-0.1160.1073.549-0.334-0.2210.029-0.011-0.1320.001
32A335ALA00.089-0.1257.6880.1600.1600.0000.0000.0000.000
33A335ALA0-0.0290.16912.0980.0480.0480.0000.0000.0000.000
34A336ILE00.054-0.10611.297-0.158-0.1580.0000.0000.0000.000
35A336ILE0-0.0530.11013.4160.0190.0190.0000.0000.0000.000
36A337ASN00.111-0.05313.6740.0510.0510.0000.0000.0000.000
37A337ASN0-0.1760.02814.3560.0420.0420.0000.0000.0000.000
38A338ALA00.060-0.13315.6950.0240.0240.0000.0000.0000.000
39A338ALA0-0.0220.13819.0070.0050.0050.0000.0000.0000.000
40A339GLY0-0.011-0.08819.1110.0270.0270.0000.0000.0000.000
41A340LYS00.091-0.05422.0560.0020.0020.0000.0000.0000.000
42A340LYS10.8791.09326.1190.2640.2640.0000.0000.0000.000
43A341GLY00.001-0.07925.272-0.004-0.0040.0000.0000.0000.000
44A342LEU00.0360.03822.6090.0260.0260.0000.0000.0000.000
45A342LEU0-0.0480.07320.769-0.011-0.0110.0000.0000.0000.000
46A343GLU00.025-0.10722.705-0.001-0.0010.0000.0000.0000.000
47A343GLU-1-0.918-0.83924.605-0.319-0.3190.0000.0000.0000.000
48A344PHE00.124-0.08120.878-0.009-0.0090.0000.0000.0000.000
49A344PHE0-0.1350.07316.831-0.016-0.0160.0000.0000.0000.000
50A345ASP00.146-0.13121.9570.0250.0250.0000.0000.0000.000
51A345ASP-1-0.981-0.83024.458-0.331-0.3310.0000.0000.0000.000
52A346THR0-0.001-0.06124.120-0.023-0.0230.0000.0000.0000.000
53A346THR0-0.0750.04223.622-0.001-0.0010.0000.0000.0000.000
54A347ASN00.068-0.05125.5520.0090.0090.0000.0000.0000.000
55A347ASN0-0.1430.03929.6250.0060.0060.0000.0000.0000.000
56A348THR00.101-0.05726.2300.0280.0280.0000.0000.0000.000
57A348THR0-0.0630.02724.969-0.007-0.0070.0000.0000.0000.000
58A349SER00.044-0.07627.4900.0010.0010.0000.0000.0000.000
59A349SER0-0.0380.03327.5180.0030.0030.0000.0000.0000.000
60A350GLU00.102-0.02723.9450.0220.0220.0000.0000.0000.000
61A350GLU-1-1.025-0.86622.301-0.373-0.3730.0000.0000.0000.000
62A351SER00.000-0.09823.228-0.039-0.0390.0000.0000.0000.000
63A351SER0-0.0160.09323.7910.0090.0090.0000.0000.0000.000
64A352PRO0-0.053-0.12723.1240.0330.0330.0000.0000.0000.000
65A353ASP00.111-0.02020.282-0.038-0.0380.0000.0000.0000.000
66A353ASP-1-1.010-0.85320.198-0.430-0.4300.0000.0000.0000.000
67A354ILE00.024-0.11318.590-0.087-0.0870.0000.0000.0000.000
68A354ILE0-0.1140.08818.227-0.009-0.0090.0000.0000.0000.000
69A355ASN00.059-0.11018.9670.0540.0540.0000.0000.0000.000
70A355ASN0-0.0730.10619.9460.0370.0370.0000.0000.0000.000
71A356PRO00.011-0.05919.060-0.068-0.0680.0000.0000.0000.000
72A357ILE00.1190.03319.4200.0210.0210.0000.0000.0000.000
73A357ILE0-0.0930.05918.004-0.015-0.0150.0000.0000.0000.000
74A358LYS00.012-0.12620.5290.0110.0110.0000.0000.0000.000
75A358LYS10.8101.05224.5830.3220.3220.0000.0000.0000.000
76A359THR00.052-0.05824.006-0.026-0.0260.0000.0000.0000.000
77A359THR00.0030.04525.9830.0030.0030.0000.0000.0000.000
78A360LYS00.106-0.06426.3140.0040.0040.0000.0000.0000.000
79A360LYS10.8351.06626.7320.3040.3040.0000.0000.0000.000
80A361ILE0-0.061-0.14928.3360.0020.0020.0000.0000.0000.000
81A361ILE0-0.0250.12730.5180.0010.0010.0000.0000.0000.000
82A362GLY00.038-0.09231.9810.0000.0000.0000.0000.0000.000
83A363SER00.0540.01435.2510.0010.0010.0000.0000.0000.000
84A363SER0-0.0720.06139.3540.0000.0000.0000.0000.0000.000
85A364GLY00.029-0.08338.381-0.001-0.0010.0000.0000.0000.000
86A365ILE00.0820.01435.6810.0090.0090.0000.0000.0000.000
87A365ILE0-0.0820.09233.745-0.002-0.0020.0000.0000.0000.000
88A366ASP00.064-0.10436.080-0.004-0.0040.0000.0000.0000.000
89A366ASP-1-0.994-0.85436.969-0.175-0.1750.0000.0000.0000.000
90A367TYR00.087-0.12533.586-0.002-0.0020.0000.0000.0000.000
91A367TYR0-0.0700.07628.818-0.005-0.0050.0000.0000.0000.000
92A368ASN00.060-0.02634.6540.0080.0080.0000.0000.0000.000
93A368ASN0-0.0730.05035.184-0.009-0.0090.0000.0000.0000.000
94A369GLU00.027-0.14535.066-0.014-0.0140.0000.0000.0000.000
95A369GLU-1-0.871-0.81437.325-0.152-0.1520.0000.0000.0000.000
96A370ASN0-0.005-0.11233.687-0.004-0.0040.0000.0000.0000.000
97A370ASN0-0.1220.08133.4940.0000.0000.0000.0000.0000.000
98A371GLY00.032-0.09030.685-0.013-0.0130.0000.0000.0000.000
99A372ALA00.0610.01730.504-0.021-0.0210.0000.0000.0000.000
100A372ALA0-0.0370.07733.0400.0030.0030.0000.0000.0000.000
101A373MET00.074-0.10032.1510.0080.0080.0000.0000.0000.000
102A373MET0-0.1000.12929.192-0.006-0.0060.0000.0000.0000.000
103A374ILE0-0.016-0.12333.4900.0010.0010.0000.0000.0000.000
104A374ILE0-0.0280.12636.6520.0020.0020.0000.0000.0000.000
105A375THR00.123-0.10737.159-0.008-0.0080.0000.0000.0000.000
106A375THR0-0.0240.10438.6680.0020.0020.0000.0000.0000.000
107A376LYS00.068-0.07239.6060.0040.0040.0000.0000.0000.000
108A376LYS10.8321.05439.7010.1550.1550.0000.0000.0000.000
109A377LEU0-0.017-0.15241.5910.0000.0000.0000.0000.0000.000
110A377LEU0-0.0660.13143.9330.0010.0010.0000.0000.0000.000
111A378GLY00.023-0.08345.2830.0000.0000.0000.0000.0000.000
112A379ALA00.070-0.00748.2210.0010.0010.0000.0000.0000.000
113A379ALA0-0.0530.09252.7070.0010.0010.0000.0000.0000.000
114A380GLY0-0.013-0.10551.8660.0000.0000.0000.0000.0000.000
115A381LEU00.102-0.00748.6160.0040.0040.0000.0000.0000.000
116A381LEU0-0.0850.11146.857-0.001-0.0010.0000.0000.0000.000
117A382SER0-0.050-0.09048.515-0.002-0.0020.0000.0000.0000.000
118A382SER0-0.0010.07150.1340.0020.0020.0000.0000.0000.000
119A383PHE00.114-0.11545.9720.0000.0000.0000.0000.0000.000
120A383PHE0-0.0640.10541.933-0.001-0.0010.0000.0000.0000.000
121A384ASP00.076-0.03447.0800.0030.0030.0000.0000.0000.000
122A384ASP-1-0.881-0.81947.455-0.095-0.0950.0000.0000.0000.000
123A385ASN00.065-0.09447.340-0.004-0.0040.0000.0000.0000.000
124A385ASN0-0.0990.04649.2340.0010.0010.0000.0000.0000.000
125A386SER0-0.055-0.11745.577-0.001-0.0010.0000.0000.0000.000
126A386SER0-0.0610.05545.0070.0000.0000.0000.0000.0000.000
127A387GLY0-0.013-0.09242.709-0.005-0.0050.0000.0000.0000.000
128A388ALA00.071-0.02742.630-0.008-0.0080.0000.0000.0000.000
129A388ALA0-0.0520.13644.7970.0010.0010.0000.0000.0000.000
130A389ILE00.078-0.12344.5370.0030.0030.0000.0000.0000.000
131A389ILE0-0.0730.10341.845-0.001-0.0010.0000.0000.0000.000
132A390THR00.013-0.04445.8950.0010.0010.0000.0000.0000.000
133A390THR0-0.0290.05849.7390.0020.0020.0000.0000.0000.000
134A391ILE00.063-0.08949.666-0.003-0.0030.0000.0000.0000.000
135A391ILE0-0.0820.10350.8470.0000.0000.0000.0000.0000.000
136A392GLY0-0.060-0.10952.5320.0030.0030.0000.0000.0000.000
137A401GLY00.0480.00554.0530.0020.0020.0000.0000.0000.000
138A402SER00.055-0.00155.2610.0000.0000.0000.0000.0000.000
139A402SER0-0.0630.08254.9060.0000.0000.0000.0000.0000.000
140A457GLY0-0.029-0.11757.0590.0010.0010.0000.0000.0000.000
141A458TYR00.0460.00959.2880.0030.0030.0000.0000.0000.000
142A458TYR0-0.0530.09056.2710.0000.0000.0000.0000.0000.000
143A459ILE00.054-0.09560.524-0.001-0.0010.0000.0000.0000.000
144A459ILE0-0.1080.08964.1620.0000.0000.0000.0000.0000.000
145A460PRO00.022-0.09660.3770.0000.0000.0000.0000.0000.000
146A461GLU00.1520.00461.8350.0010.0010.0000.0000.0000.000
147A461GLU-1-1.024-0.86562.776-0.050-0.0500.0000.0000.0000.000
148A462ALA0-0.013-0.12963.934-0.001-0.0010.0000.0000.0000.000
149A462ALA0-0.0180.12068.5460.0000.0000.0000.0000.0000.000
150A463PRO0-0.028-0.12066.8450.0000.0000.0000.0000.0000.000
151A464ARG00.0730.03367.5570.0010.0010.0000.0000.0000.000
152A464ARG10.8401.04563.5200.0480.0480.0000.0000.0000.000
153A465ASP00.064-0.11468.8090.0000.0000.0000.0000.0000.000
154A465ASP-1-0.855-0.80571.260-0.038-0.0380.0000.0000.0000.000
155A466GLY0-0.021-0.11671.8510.0010.0010.0000.0000.0000.000
156A467GLN0-0.011-0.02574.2260.0010.0010.0000.0000.0000.000
157A467GLN0-0.0440.10075.2820.0000.0000.0000.0000.0000.000
158A468ALA00.143-0.06674.185-0.001-0.0010.0000.0000.0000.000
159A468ALA0-0.0810.10077.0360.0000.0000.0000.0000.0000.000
160A469TYR00.000-0.13872.6230.0010.0010.0000.0000.0000.000
161A469TYR0-0.0860.08872.026-0.001-0.0010.0000.0000.0000.000
162A470VAL00.064-0.08974.0060.0000.0000.0000.0000.0000.000
163A470VAL0-0.0680.09575.5930.0000.0000.0000.0000.0000.000
164A471ARG00.134-0.09971.0390.0000.0000.0000.0000.0000.000
165A471ARG10.8461.08764.8220.0510.0510.0000.0000.0000.000
166A472LYS00.049-0.08871.9560.0000.0000.0000.0000.0000.000
167A472LYS10.8481.04774.1040.0400.0400.0000.0000.0000.000
168A473ASP00.064-0.12171.2740.0000.0000.0000.0000.0000.000
169A473ASP-1-0.987-0.84771.277-0.043-0.0430.0000.0000.0000.000
170A474GLY00.011-0.11467.178-0.001-0.0010.0000.0000.0000.000
171A475GLU00.036-0.04666.476-0.002-0.0020.0000.0000.0000.000
172A475GLU-1-0.977-0.81566.801-0.048-0.0480.0000.0000.0000.000
173A476TRP00.052-0.12368.5650.0010.0010.0000.0000.0000.000
174A476TRP0-0.1210.10065.9360.0010.0010.0000.0000.0000.000
175A477VAL00.094-0.08970.1830.0000.0000.0000.0000.0000.000
176A477VAL0-0.0870.09272.9880.0000.0000.0000.0000.0000.000
177A478LEU00.129-0.08673.8150.0000.0000.0000.0000.0000.000
178A478LEU0-0.0730.11475.0120.0000.0000.0000.0000.0000.000
179A479LEU00.145-0.09576.2850.0000.0000.0000.0000.0000.000
180A479LEU0-0.0890.11078.1240.0000.0000.0000.0000.0000.000
181A480SER00.032-0.07878.9760.0010.0010.0000.0000.0000.000
182A480SER0-0.0290.05680.6020.0000.0000.0000.0000.0000.000
183A481THR0-0.062-0.05980.2280.0010.0010.0000.0000.0000.000
184A481THR0-0.0140.06079.2330.0000.0000.0000.0000.0000.000
185A482PHE00.056-0.09381.6330.0000.0000.0000.0000.0000.000
186A482PHE0-0.0880.07677.7260.0000.0000.0000.0000.0000.000
187A483LEU0-0.064-0.12283.1600.0010.0010.0000.0000.0000.000
188A483LEU00.0310.02983.0610.0000.0000.0000.0000.0000.000